diff --git a/.dockerignore b/.dockerignore index c82a741..2558b11 100644 --- a/.dockerignore +++ b/.dockerignore @@ -11,3 +11,5 @@ solr-config/data *.xml *.md !oxo-web/target/oxo-web.war +__pycache__ +*.pyc diff --git a/.gitignore b/.gitignore index 2fbaee0..cca16b1 100644 --- a/.gitignore +++ b/.gitignore @@ -3,13 +3,11 @@ target/ *.DS_store .idea *~ -data properties -sorl-config/data -db application.properties -dataloading/venv/ -dataloading/oxo/config_localdev.ini *.pyc .mvn oxo-web/src/main/resources/templates/search-orig.html +oxo-web/src/main/asciidoc/generated-snippets +oxo-web/src/main/resources/static +.settings \ No newline at end of file diff --git a/.project b/.project new file mode 100644 index 0000000..f8ee3c5 --- /dev/null +++ b/.project @@ -0,0 +1,17 @@ + + + oxo + + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.m2e.core.maven2Nature + + diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index e3a6123..0000000 --- a/Dockerfile +++ /dev/null @@ -1,6 +0,0 @@ - -#use alpine base for minimal size -#includes OpenJDK 8 (and Maven 3) -FROM openjdk:8-jre-alpine - -COPY oxo-web/target/oxo-web.war /home/oxo.war \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..9adf78b --- /dev/null +++ b/README.md @@ -0,0 +1,64 @@ +OxO is a service for finding mappings (or cross-references) between terms from +ontologies, vocabularies and coding standards. OxO imports mappings from a +variety of sources including the [Ontology Lookup Service](https://www.ebi.ac.uk/ols/index) and a subset of +mappings provided by the [UMLS](https://www.nlm.nih.gov/research/umls/index.html). + +# OxO with Docker + +OxO is comprised of three components: + +* The loader scripts (oxo-loader/), which pull data about terms and mappings from the OLS, OBO xrefs, and UMLS and upload them to neo4j +* The indexer (oxo-indexer/), which indexes terms and mappings found in neo4j in solr +* The Web application (oxo-web/), which provides the user interface + +The OxO Web application, solr, and neo4j can be started using docker-compose: + + docker-compose up + +The docker-compose configuration, by default, stores all persistent data (the hsqldb, neo4j, and solr data files) in the data/ directory by mounting volumes. However, these datasets are empty until the loader and indexer have been executed. + +## Running the loader + +The loader requires neo4j to be running. If using docker-compose, neo4j can be +started on its own: + + docker-compose up neo4j + +The loader scripts can then be used as documented in the oxo-loader/ directory +to load data into neo4j. + +## Running the indexer + +The indexer requires neo4j and solr to be running. If using docker-compose: + + docker-compose up neo4j solr + +The indexer can be executed using Docker: + + docker build -f oxo-indexer/Dockerfile -t oxo-indexer + docker run oxo-indexer + + +# OxO without Docker + +Sometimes it is impractical to use Docker (e.g. for local development). To get +OxO up and running without Docker, first install: + +* neo4j community edition 3.1.1 +* solr 5.3.0 +* Java 1.8 +* Maven + +The instructions for the loader are not Docker-specific, and can be found in the +oxo-loader/ directory. For the indexer and Web application, first compile the +project using Maven: + + mvn clean package + +Then run the indexer: + + java -Xmx10g -jar oxo-indexer.jar + +The Web application is a standard WAR and can be deployed using e.g. Tomcat. + + diff --git a/data/hsqldb/.gitkeep b/data/hsqldb/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/data/neo4j/.gitkeep b/data/neo4j/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/data/neo4jimport/.gitkeep b/data/neo4jimport/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/db/solr/mapping/conf/_rest_managed.json b/data/solr/mapping/conf/_rest_managed.json similarity index 100% rename from db/solr/mapping/conf/_rest_managed.json rename to data/solr/mapping/conf/_rest_managed.json diff --git a/db/solr/mapping/conf/lang/stopwords_en.txt b/data/solr/mapping/conf/lang/stopwords_en.txt similarity index 100% rename from db/solr/mapping/conf/lang/stopwords_en.txt rename to data/solr/mapping/conf/lang/stopwords_en.txt diff --git a/db/solr/mapping/conf/protwords.txt b/data/solr/mapping/conf/protwords.txt similarity index 100% rename from db/solr/mapping/conf/protwords.txt rename to data/solr/mapping/conf/protwords.txt diff --git a/db/solr/mapping/conf/schema.xml b/data/solr/mapping/conf/schema.xml similarity index 100% rename from db/solr/mapping/conf/schema.xml rename to data/solr/mapping/conf/schema.xml diff --git a/db/solr/mapping/conf/solrconfig.xml b/data/solr/mapping/conf/solrconfig.xml similarity index 100% rename from db/solr/mapping/conf/solrconfig.xml rename to data/solr/mapping/conf/solrconfig.xml diff --git a/db/solr/mapping/conf/stopwords.txt b/data/solr/mapping/conf/stopwords.txt similarity index 100% rename from db/solr/mapping/conf/stopwords.txt rename to data/solr/mapping/conf/stopwords.txt diff --git a/db/solr/mapping/conf/synonyms.txt b/data/solr/mapping/conf/synonyms.txt similarity index 100% rename from db/solr/mapping/conf/synonyms.txt rename to data/solr/mapping/conf/synonyms.txt diff --git a/db/solr/mapping/core.properties b/data/solr/mapping/core.properties similarity index 100% rename from db/solr/mapping/core.properties rename to data/solr/mapping/core.properties diff --git a/db/solr/solr.xml b/data/solr/solr.xml similarity index 100% rename from db/solr/solr.xml rename to data/solr/solr.xml diff --git a/dataloading/oxo/.dockerignore b/dataloading/oxo/.dockerignore deleted file mode 100644 index 449876a..0000000 --- a/dataloading/oxo/.dockerignore +++ /dev/null @@ -1 +0,0 @@ -#config_localdev.ini \ No newline at end of file diff --git a/dataloading/oxo/Dockerfile b/dataloading/oxo/Dockerfile deleted file mode 100644 index 7b07098..0000000 --- a/dataloading/oxo/Dockerfile +++ /dev/null @@ -1,12 +0,0 @@ -FROM jfloff/alpine-python:2.7 -MAINTAINER Simon Jupp "jupp@ebi.ac.uk" - -RUN mkdir /app -WORKDIR /app -COPY *.py requirements.txt ./ - -RUN apk add --no-cache mariadb-dev build-base -#RUN apk --update add mysql mysql-client -RUN pip install -r requirements.txt - -CMD bash \ No newline at end of file diff --git a/dataloading/readme.md b/dataloading/readme.md deleted file mode 100755 index c11749a..0000000 --- a/dataloading/readme.md +++ /dev/null @@ -1,6 +0,0 @@ - -### Project structure - -- The *oxo folder* contains the scripts to load data into OxO. -- The *paxo folder* contains the scripts to generate predicted mappings. - - You can evaluate paxo using a gold standard set of mappings. The *standard folder* contains an example of how the gold standard mapppings needs to be formatted. diff --git a/docker-compose.common.yml b/docker-compose.common.yml new file mode 100644 index 0000000..b9f103c --- /dev/null +++ b/docker-compose.common.yml @@ -0,0 +1,25 @@ +version: '2' +services: + solr: + image: solr:5.5.3-alpine + environment: + - SOLR_HOME=/mnt/solr + ports: + - 8983:8983 + volumes: + - ./data/solr:/mnt/solr + command: ["solr", "-f"] + neo4j: + image: neo4j:3.1.1 + environment: + - NEO4J_HEAP_MEMORY=10g # configure the heap memory + - NEO4J_dbms_memory_heap_maxSize=8g + - NEO4J_AUTH=neo4j/dba + cap_add: + - SYS_RESOURCE + ports: + - 7474:7474 + - 7687:7687 + volumes: + - ./data/neo4jimport:/var/lib/neo4j/import + - ./data/neo4j:/data \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 7a3a521..abd60db 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,30 +1,15 @@ version: '2' services: solr: - image: solr:5.5.3-alpine - environment: - - SOLR_HOME=/home/mysolrhome - ports: - - 8983:8983 - volumes: - - ./solr-config:/home/mysolrhome - - ./solr-config/data:/home/mysolrhome/mapping/data - command: ["solr", "-f"] + extends: + file: docker-compose.common.yml + service: solr neo4j: - image: neo4j:3.1.1 - environment: - - NEO4J_HEAP_MEMORY=10g # configure the heap memory - - NEO4J_dbms_memory_heap_maxSize=8g - - NEO4J_AUTH=neo4j/dba - cap_add: - - SYS_RESOURCE - ports: - - 7474:7474 - - 7687:7687 - volumes: - - ./neo4jimport:/var/lib/neo4j/import + extends: + file: docker-compose.common.yml + service: neo4j oxo: - build: . + build: oxo-web depends_on: - neo4j - solr @@ -32,13 +17,11 @@ services: - neo4j - solr environment: - - spring.datasource.url=jdbc:hsqldb:file:/home/hsqldb + - spring.datasource.url=jdbc:hsqldb:file:/mnt/hsqldb - oxo.neo.driver=org.neo4j.ogm.drivers.http.driver.HttpDriver - oxo.neo.uri=http://neo4j:dba@neo4j:7474 - spring.data.solr.host=http://solr:8983/solr - command: - - java - - -jar - - /home/oxo.war + volumes: + - ./data/hsqldb:/mnt/hsqldb ports: - 8080:8080 diff --git a/oxo-indexer/.classpath b/oxo-indexer/.classpath new file mode 100644 index 0000000..f0257c5 --- /dev/null +++ b/oxo-indexer/.classpath @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-indexer/.factorypath b/oxo-indexer/.factorypath new file mode 100644 index 0000000..7c862f6 --- /dev/null +++ b/oxo-indexer/.factorypath @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-indexer/.project b/oxo-indexer/.project new file mode 100644 index 0000000..a762db6 --- /dev/null +++ b/oxo-indexer/.project @@ -0,0 +1,23 @@ + + + oxo-indexer + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/oxo-indexer/Dockerfile b/oxo-indexer/Dockerfile new file mode 100644 index 0000000..c7b0fdf --- /dev/null +++ b/oxo-indexer/Dockerfile @@ -0,0 +1,11 @@ + +FROM maven:3.5-jdk-8 AS build +COPY pom.xml /opt/OxO/pom.xml +COPY oxo-web /opt/OxO/ +COPY oxo-model /opt/OxO/ +COPY oxo-indexer /opt/OxO/ +RUN cd /opt/OxO && mvn clean package + +FROM openjdk:8-jre-alpine +COPY --from=build /opt/OxO/oxo-indexer/target/oxo-indexer.jar /opt/oxo-indexer.jar +RUN ["java", "-Xmx10g", "-jar", "/opt/oxo-indexer.jar"] diff --git a/oxo-loader/Dockerfile b/oxo-loader/Dockerfile new file mode 100644 index 0000000..fdec68c --- /dev/null +++ b/oxo-loader/Dockerfile @@ -0,0 +1,9 @@ +FROM python:3-alpine + +ADD oxo-loader /opt/ + +RUN apk add --no-cache mariadb-dev build-base +#RUN apk --update add mysql mysql-client +RUN cd /opt/oxo-loader && pip install -r requirements.txt + +CMD bash diff --git a/dataloading/oxo/MappingLoader.py b/oxo-loader/MappingLoader.py similarity index 100% rename from dataloading/oxo/MappingLoader.py rename to oxo-loader/MappingLoader.py diff --git a/dataloading/oxo/OlsDatasetLoader.py b/oxo-loader/OlsDatasetExtractor.py old mode 100644 new mode 100755 similarity index 56% rename from dataloading/oxo/OlsDatasetLoader.py rename to oxo-loader/OlsDatasetExtractor.py index fcd5e54..d131fef --- a/dataloading/oxo/OlsDatasetLoader.py +++ b/oxo-loader/OlsDatasetExtractor.py @@ -1,11 +1,22 @@ -import urllib +#!/usr/bin/env python +""" +This script pulls data about ontologies and databases registeted in EBI's OLS, identifiers.org and OBO xrefs. This creates a +CSV file of datasources that can be loaded into OxO using the OxoNeo4jLoader.py script. Datasources must be loaded into OxO +before any mappings can be loaded. +""" +__author__ = "jupp" +__license__ = "Apache 2.0" +__date__ = "03/03/2018" + + +import urllib.request, urllib.parse, urllib.error import json import xml.etree.ElementTree as ET import yaml -import OxoClient as OXO -import csv -from ConfigParser import SafeConfigParser -import sys +import OxoClient +from configparser import ConfigParser +from optparse import OptionParser + prefixToPreferred = {} idorgNamespace = {} @@ -14,34 +25,53 @@ termToIri = {} termToLabel = {} -#Parse the input parameters. A config file and a flag is expected -if len(sys.argv)!=2: - print "\nNot enough arguments! Please pass a (path) of a config file!" - raise Exception("Not enough arguments! Please pass in a config file!") -else: - config = SafeConfigParser() - config.read(sys.argv[1]) +parser = OptionParser() +parser.add_option("-d", "--datasources", help="datasources csv export file") +parser.add_option("-i", "--idorg", help="id.org config file") +parser.add_option("-c", "--config", help="config file", default="config.ini") + +(options, args) = parser.parse_args() + +config = ConfigParser() +config.read(options.config) +OXO = OxoClient.OXO() OXO.oxoUrl = config.get("Basics","oxoUrl") -OXO.apikey = config.get("Basics", "oxoAPIkey") oboDbxrefUrl= config.get("Basics", "oboDbxrefUrl") olsurl=config.get("Basics", "olsurl") olsurl=olsurl+"/ontologies?size=1000" idorgDataLocation = config.get("Paths", "idorgDataLocation") +if options.idorg: + idorgDataLocation = options.idorg + +exportFileDatasources=config.get("Paths","exportFileDatasources") +if options.datasources: + exportFileDatasources = options.datasources -reply = urllib.urlopen(olsurl) +reply = urllib.request.urlopen(olsurl) anwser = json.load(reply) ontologies = anwser["_embedded"]["ontologies"] +datasources = {} + for ontology in ontologies: namespace = ontology["config"]["namespace"] version = ontology["updated"] + altPrefixes = [namespace] if namespace == 'ordo': prefPrefix = 'Orphanet' + elif namespace == 'hp': + prefPrefix = 'HP' + altPrefixes = [namespace, "hpo"] + prefixToPreferred["HPO"] = prefPrefix + prefixToPreferred["hpo"] = prefPrefix + elif namespace == "ncit": + prefPrefix = "NCIT" + altPrefixes = [namespace, "NCI_Thesaurus", "NCI", "ncithesaurus", "NCI2009_04D"] else: prefPrefix = ontology["config"]["preferredPrefix"] @@ -50,7 +80,9 @@ prefixToPreferred[prefPrefix.lower()] = prefPrefix prefixToPreferred[namespace.lower()] = prefPrefix - OXO.saveDatasource(prefPrefix, None, title, desc, "ONTOLOGY", None, [namespace], "https://creativecommons.org/licenses/by/4.0/", "Last updated in the ontology lookup service on "+version ) + datasources[prefPrefix] = OxoClient.Datasource(prefPrefix, None, title, desc, "ONTOLOGY", None, altPrefixes, "https://creativecommons.org/licenses/by/4.0/", "Last updated in the ontology lookup service on "+version ) + +altPrefixes = [] # get namespaces from identifiers.org #urllib.urlopen('http://www.ebi.ac.uk/miriam/main/export/xml/') @@ -65,7 +97,6 @@ namespace = datatype.find('{http://www.biomodels.net/MIRIAM/}namespace').text prefPrefix = namespace - title = datatype.find('{http://www.biomodels.net/MIRIAM/}name').text desc = datatype.find('{http://www.biomodels.net/MIRIAM/}definition').text licence = None @@ -92,9 +123,9 @@ altPrefixes.append(altPrefixs.text) if prefPrefix.lower() in prefixToPreferred: - print "Ignoring "+namespace+" from idorg as it is already registered as a datasource" + print(("Ignoring "+namespace+" from idorg as it is already registered as a datasource")) elif namespace.lower() in prefixToPreferred: - print "Ignoring " + namespace + " from idorg as it is already registered as a datasource" + print(("Ignoring " + namespace + " from idorg as it is already registered as a datasource")) else: idorgNamespace[prefPrefix.lower()] = prefPrefix idorgNamespace[namespace.lower()] = prefPrefix @@ -102,12 +133,14 @@ prefixToPreferred[prefPrefix.lower()] = prefPrefix prefixToPreferred[namespace.lower()] = prefPrefix prefixToPreferred[title.lower()] = prefPrefix - OXO.saveDatasource(prefPrefix, namespace, title, desc, "DATABASE", None, altPrefixes, licence, versionInfo) + + if prefPrefix not in datasources: + datasources[prefPrefix] = OxoClient.Datasource (prefPrefix, namespace, title, desc, "DATABASE", None, altPrefixes, licence, versionInfo) #oboDbxrefUrl = 'https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml' # Read from OBO db-xrefs -yamlData = yaml.load(urllib.urlopen(oboDbxrefUrl)) +yamlData = yaml.load(urllib.request.urlopen(oboDbxrefUrl)) for database in yamlData: namespace= database["database"] @@ -116,7 +149,7 @@ altPrefixes = [namespace] if namespace.lower() in prefixToPreferred: - print "Ignoring " + namespace + " from OBO as it is already registered as a datasource" + print(("Ignoring " + namespace + " from OBO as it is already registered as a datasource")) else: urlSyntax = None if "entity_types" in database: @@ -124,11 +157,15 @@ urlSyntax = database["entity_types"][0]["url_syntax"].replace("[example_id]", "") prefixToPreferred[namespace.lower()] = prefPrefix - OXO.saveDatasource(prefPrefix, None, title, None, "DATABASE",urlSyntax, altPrefixes, None, None) + if prefPrefix not in datasources: + print("New datasource " + namespace + " from GO db-xrefs file") + + datasources[prefPrefix] = OxoClient.Datasource (prefPrefix, None, title, None, "DATABASE",urlSyntax, altPrefixes, None, None) + # Create Paxo as datasources -print "Save paxo as datasource" +print("Adding paxo as datasource") prefPrefix="paxo" namespace=None title="paxo" @@ -138,4 +175,10 @@ altPrefixes=["paxo"] licence=None versionInfo=1 -OXO.saveDatasource(prefPrefix, namespace, title, desc, sourceType, urlSyntax, altPrefixes, licence, versionInfo) +datasources[prefPrefix] = OxoClient.Datasource(prefPrefix, namespace, title, desc, sourceType, urlSyntax, altPrefixes, licence, versionInfo) + +# print OxO loading csv file +import OxoCsvBuilder + +buider = OxoCsvBuilder.Builder() +buider.exportDatasourceToCsv(exportFileDatasources, datasources) diff --git a/dataloading/oxo/OlsDatasetExtractor.py b/oxo-loader/OlsDatasetExtractor.py.bak similarity index 100% rename from dataloading/oxo/OlsDatasetExtractor.py rename to oxo-loader/OlsDatasetExtractor.py.bak diff --git a/dataloading/oxo/OlsMappingExtractor.py b/oxo-loader/OlsMappingExtractor.py similarity index 100% rename from dataloading/oxo/OlsMappingExtractor.py rename to oxo-loader/OlsMappingExtractor.py diff --git a/dataloading/oxo/OxoClient.py b/oxo-loader/OxoClient.py similarity index 100% rename from dataloading/oxo/OxoClient.py rename to oxo-loader/OxoClient.py diff --git a/dataloading/oxo/OxoCsvBuilder.py b/oxo-loader/OxoCsvBuilder.py similarity index 91% rename from dataloading/oxo/OxoCsvBuilder.py rename to oxo-loader/OxoCsvBuilder.py index bea3d15..09f9f07 100644 --- a/dataloading/oxo/OxoCsvBuilder.py +++ b/oxo-loader/OxoCsvBuilder.py @@ -33,10 +33,10 @@ def exportDatasourceToCsv(self, file, datasources): value.alternatePrefixes.append(key) alternatePrefixes = self.generateAllAltPrefixes(value.alternatePrefixes) - spamwriter.writerow([value.prefPrefix, value.idorgNamespace, str(value.title).encode("utf-8"), - str(value.description).encode("utf-8"), value.sourceType, value.baseUri, - ",".join(alternatePrefixes), str(value.licence).encode("utf-8"), - str(value.versionInfo).encode("utf-8")]) + spamwriter.writerow([value.prefPrefix, value.idorgNamespace, str(value.title), + str(value.description), value.sourceType, value.baseUri, + ",".join(alternatePrefixes), str(value.licence), + str(value.versionInfo)]) def exportTermsToCsv(self, file, terms): with open(file, 'w') as csvfile: diff --git a/dataloading/oxo/OxoNeo4jLoader.py b/oxo-loader/OxoNeo4jLoader.py similarity index 100% rename from dataloading/oxo/OxoNeo4jLoader.py rename to oxo-loader/OxoNeo4jLoader.py diff --git a/oxo-loader/README.md b/oxo-loader/README.md new file mode 100644 index 0000000..ec7f824 --- /dev/null +++ b/oxo-loader/README.md @@ -0,0 +1,75 @@ +These Python scripts are used to + +1. To dump a list of datasources to CSV from identifiers.org, OLS, and UMLS (`OlsDatasetExtractor.py`) +2. To load this list of datasources from the the CSV generated in 1. to the neo4j database used by OxO (`OxoNeo4jLoader.py`) +3. To pull terms mappings from OLS and UMLS and generate CSV files (`OlsMappingExtractor.py`, `UmlsMappingExtractor.py`) +2. To load these terms and mappings into the neo4j database used by OxO (`OxoNeo4jLoader.py`) + +They are configured by a config.ini file, an example of which is provided as +config.sample.ini. The path to the config is passed using to each script using +the `-c` option. + +# OlsDatasetExtractor + +The `OlsDatasetExtractor.py` script pulls metadata about ontologies and databases +registered in OLS, identifiers.org and OBO xrefs, and generates a CSV file. + +* OLS is accessed via its API, configurable in config.ini with the `olsurl` option + +* The identifiers.org data is loaded from the idorg.xml file, configurable in config.ini with the `idorgDataLocation` option. + This file is provided in the root of this repository. + +* OBO xrefs are loaded from a yaml file, configurable in config.ini with the `oboDbxrefUrl` option + +The CSV file is exported to the filename specified in the `exportFileDatasources` configuration option, or the -d command line option. +If specified, the command line option takes precedence over the config.ini option. + +Example command: + + python OlsDatasetExtractor.py -c config.ini -i idorg.xml -d datasources.csv + +The output CSV file has the form: + + "prefix","idorgNamespace","title","description","sourceType","baseUri","alternatePrefixes","licence","versionInfo" + +For example: + + "DrugBank","drugbank","DrugBank","The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.","DATABASE","","drugbank,DRUGBANK,DrugBank","None","None" + +This metadata can then be loaded into the OxO neo4j database using the `OxoNeo4jLoader.py` script: + + python OxoNeo4jLoader.py -c config.ini -W -d datasources.csv + +# OlsMappingExtractor + +After the metadata about datasets has been loaded into neo4j, the `OlsMappingExtractor.py` script is used to +pull mappings from OLS and generate two CSV files: one for terms, and one for mappings. + + python OlsMappingExtractor.py -c config.ini -t ols_terms.csv -m ols_mappings.csv + +These terms and mappings can then be loaded into neo4j using the `OxoNeo4jLoader.py` script: + + python OxoNeo4jLoader.py -c config.ini -t ols_terms.csv -m ols_mappings.csv + +# UmlsMappingExtractor + +Like the OlsMappingExtractor, the UmlsMappingExtractor is used to pull mappings from UMLS and generate +CSV files. + + python UmlsMappingExtractor.py -c config.ini -t umls_terms.csv -m umls_mappings.csv + +These terms and mappings can then be loaded into neo4j using the `OxoNeo4jLoader.py` script: + + python OxoNeo4jLoader.py -c config.ini -t umls_terms.csv -m umls_mappings.csv + +# Docker + +These scripts can also be executed using Docker for convenience. For example, +having prepared a host directory `mydir` with the config.ini and idorg.xml, the +OlsDatasetExtractor can be executed as follows: + + docker build -t oxo-loader . + + docker run -v ./mydir:/mnt -it oxo-loader python OlsDatasetExtractor.py + -c /mnt/config.ini -i /mnt/idorg.xml -d /mnt/datasources.csv + diff --git a/dataloading/oxo/UmlsMappingExtractor.py b/oxo-loader/UmlsMappingExtractor.py similarity index 100% rename from dataloading/oxo/UmlsMappingExtractor.py rename to oxo-loader/UmlsMappingExtractor.py diff --git a/dataloading/oxo/config/oxo_config.ini b/oxo-loader/config.ini similarity index 87% rename from dataloading/oxo/config/oxo_config.ini rename to oxo-loader/config.ini index 19cb9ec..37e7a10 100644 --- a/dataloading/oxo/config/oxo_config.ini +++ b/oxo-loader/config.ini @@ -4,10 +4,13 @@ oxoAPIkey=key solrBaseUrl=http://url/solr solrChunks=5000 neoURL=bolt://localhost:7687 +neoUser=neo4j +neoPass=neo4j olsurl=http://www.ebi.ac.uk/ols/api oboDbxrefUrl=https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml [Paths] +exportFileDatasources=datasources.csv exportFileTerms=/path/terms.csv exportFileMappings=/path/mappings.csv idorgDataLocation = /path/idorg.xml diff --git a/oxo-loader/config.sample.ini b/oxo-loader/config.sample.ini new file mode 100644 index 0000000..37e7a10 --- /dev/null +++ b/oxo-loader/config.sample.ini @@ -0,0 +1,23 @@ +[Basics] +oxoUrl=http://localhost:8080/oxo +oxoAPIkey=key +solrBaseUrl=http://url/solr +solrChunks=5000 +neoURL=bolt://localhost:7687 +neoUser=neo4j +neoPass=neo4j +olsurl=http://www.ebi.ac.uk/ols/api +oboDbxrefUrl=https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml + +[Paths] +exportFileDatasources=datasources.csv +exportFileTerms=/path/terms.csv +exportFileMappings=/path/mappings.csv +idorgDataLocation = /path/idorg.xml + +[SQLumls] +user=username +password=password +host=mysql-name +db=dbName +port=4570 diff --git a/oxo-loader/idorg.csv b/oxo-loader/idorg.csv new file mode 100644 index 0000000..f99fde0 --- /dev/null +++ b/oxo-loader/idorg.csv @@ -0,0 +1,1011 @@ +"prefix","idorgNamespace","title","description","sourceType","baseUri","alternatePrefixes","licence","versionInfo" +"AFO","","Allotrope Merged Ontology Suite","Allotrope Merged Ontology Suite","ONTOLOGY","","afo,AFO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:20.168+0000" +"APOLLO_SV","","Apollo Structured Vocabulary (Apollo-SV)","Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models","ONTOLOGY","","apollo_sv,APOLLO_SV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:19.249+0000" +"CLO","","CLO: Cell Line Ontology","The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.","ONTOLOGY","","clo,CLO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:51.828+0000" +"CO_323","","Barley ontology","ICARDA - TDv5 - Sept 2018","ONTOLOGY","","co_323,CO_323","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:00.159+0000" +"CO_325","","Banana ontology","Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019","ONTOLOGY","","co_325,CO_325","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:01.236+0000" +"CO_327","","Pearl millet ontology","Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016","ONTOLOGY","","co_327,CO_327","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:00.985+0000" +"CO_330","","Potato ontology","CIP - potato ontology - december 2018","ONTOLOGY","","co_330,CO_330","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:01.109+0000" +"CO_331","","Sweet Potato ontology","Sweet Potato Trait Dictionary in template v5 - CIP - November 2019","ONTOLOGY","","co_331,CO_331","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:21.076+0000" +"CO_333","","Beet Ontology ontology","This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRA, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Daphne Verdelet (Florimond Desprez) - Submitted in November 2017.","ONTOLOGY","","co_333,CO_333","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:23.317+0000" +"CO_339","","Lentil ontology","Lentil Trait Dictionary in template v5 - ICARDA - July 2015","ONTOLOGY","","co_339,CO_339","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:01.018+0000" +"CO_340","","Cowpea ontology","Cowpea Trait Dictionary in template v5 - IITA - August 2015","ONTOLOGY","","co_340,CO_340","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:01.208+0000" +"CO_341","","Pigeonpea ontology","Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015","ONTOLOGY","","co_341,CO_341","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.086+0000" +"CO_343","","Yam ontology","version 2019 - pvs","ONTOLOGY","","co_343,CO_343","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:06.454+0000" +"CO_345","","Brachiaria ontology","Brachiaria (forages) ontology TD v5 - Version Oct 2016","ONTOLOGY","","co_345,CO_345","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:22.114+0000" +"CO_346","","Mungbean ontology","oct 2016","ONTOLOGY","","co_346,CO_346","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.082+0000" +"CO_347","","Castor bean ontology","March 2017 version ","ONTOLOGY","","co_347,CO_347","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.083+0000" +"CO_348","","Brassica ontology","Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).","ONTOLOGY","","co_348,CO_348","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:01.467+0000" +"CO_350","","Oat ontology","Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo","ONTOLOGY","","co_350,CO_350","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.142+0000" +"CO_356","","Vitis ontology","Grape Ontology including OIV and bioversity descriptors. INRA July 2017","ONTOLOGY","","co_356,CO_356","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:43.964+0000" +"CO_357","","Woody Plant Ontology ontology","This ontology list all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRA) & Ines Chaves (IBET) - Version 1 submitted on August 2017 by INRA.","ONTOLOGY","","co_357,CO_357","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:11.237+0000" +"CO_358","","Cotton ontology","Cotton ontology from CottonGen database - June 2019","ONTOLOGY","","co_358,CO_358","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:20.198+0000" +"CO_359","","Sunflower ontology","December 2019","ONTOLOGY","","co_359,CO_359","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:49.531+0000" +"CO_360","","Sugar Kelp trait ontology","Sugar Kelp trait ontology","ONTOLOGY","","co_360,CO_360","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:48.782+0000" +"CO_365","","Fababean ontology","developed by ICARDA - Dec 2018","ONTOLOGY","","co_365,CO_365","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:18.979+0000" +"CO_366","","Bambara groundnut ontology","version Dec 2019","ONTOLOGY","","co_366,CO_366","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:41.978+0000" +"COB","","Core Ontology for Biology and Biomedicine","COB brings together key terms from a wide range of OBO projects to improve interoperability.","ONTOLOGY","","cob,COB","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:16.671+0000" +"CRO","","Contributor Role Ontology","A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.","ONTOLOGY","","cro,CRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.587+0000" +"CTENO","","Ctenophore Ontology","An anatomical and developmental ontology for ctenophores (Comb Jellies)","ONTOLOGY","","cteno,CTENO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:55.849+0000" +"DRON","","The Drug Ontology","An ontology to support comparative effectiveness researchers studying claims data.","ONTOLOGY","","dron,DRON","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.946+0000" +"FBcv","","Drosophila Phenotype Ontology (DPO)","An ontology for the description of Drosophila melanogaster phenotypes.","ONTOLOGY","","dpo,DPO,FBcv,fbcv,FBCV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:03.011+0000" +"HAO","","Hymenoptera Anatomy Ontology","A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)","ONTOLOGY","","hao,HAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:18.385+0000" +"HCAO","","Human Cell Atlas Ontology","Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.","ONTOLOGY","","hcao,HCAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:29.444+0000" +"HOM","","Homology Ontology","This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.","ONTOLOGY","","hom,HOM","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:10.122+0000" +"MMUSDV","","Mouse Developmental Stages","Life cycle stages for Mus Musculus","ONTOLOGY","","mmusdv,MMUSDV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.138+0000" +"MP","","The Mammalian Phenotype Ontology","The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/obophenotype/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330.","ONTOLOGY","","mp,MP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:45.775+0000" +"NCBITAXON","","NCBI organismal classification","An ontology representation of the NCBI organismal taxonomy","ONTOLOGY","","ncbitaxon,NCBITAXON","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:44:18.578+0000" +"PDUMDV","","Platynereis Developmental Stages","Life cycle stages for Platynereis dumerilii","ONTOLOGY","","pdumdv,PDUMDV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.146+0000" +"PECO","","Plant Experimental Conditions Ontology","A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.","ONTOLOGY","","peco,PECO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:16.720+0000" +"PHI","","PHI-base Ontology","Pathogen-Host Interaction database Ontology used by Ensembl","ONTOLOGY","","phi,PHI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:55.216+0000" +"PHIPO","","Pathogen Host Interactions Phenotype Ontology","Ontology of species-neutral phenotypes observed in pathogen-host interactions.","ONTOLOGY","","phipo,PHIPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:56.818+0000" +"PLANA","","planaria-ontology","planaria-ontology is an ontology for planarian anatomy and developmental stages of S.med","ONTOLOGY","","plana,PLANA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-05-06T02:30:34.361+0000" +"PO","","Plant Ontology","The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.","ONTOLOGY","","po,PO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:32.975+0000" +"SO","","Sequence types and features ontology","A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.","ONTOLOGY","","so,SO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:20.639+0000" +"SPD","","Spider Ontology","An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).","ONTOLOGY","","spd,SPD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:19.926+0000" +"SRAO","","FAIRsharing Subject Ontology (SRAO)","The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.","ONTOLOGY","","srao,SRAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:54.775+0000" +"STATO","","STATO: the statistical methods ontology","STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.","ONTOLOGY","","stato,STATO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:20.401+0000" +"SWO","","SWO (The Software Ontology)","The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.","ONTOLOGY","","swo,SWO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:52.049+0000" +"SYMP","","Symptom Ontology","The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.","ONTOLOGY","","symp,SYMP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:52.250+0000" +"TAXRANK","","Taxonomic rank vocabulary","A vocabulary of taxonomic ranks (species, family, phylum, etc)","ONTOLOGY","","taxrank,TAXRANK","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:19.924+0000" +"TEDDY","","Terminology for Description of Dynamics","TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology.","ONTOLOGY","","teddy,TEDDY","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:34.042+0000" +"TGMA","","Mosquito gross anatomy ontology","A structured controlled vocabulary of the anatomy of mosquitoes.","ONTOLOGY","","tgma,TGMA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:25.732+0000" +"UO","","Units of measurement ontology","Metrical units for use in conjunction with PATO","ONTOLOGY","","uo,UO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:20.871+0000" +"XL","","Cross-linker reagents ontology","A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.","ONTOLOGY","","xl,XL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:45.323+0000" +"XLMOD","","HUPO-PSI cross-linking and derivatization reagents controlled vocabulary","A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.","ONTOLOGY","","xlmod,XLMOD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:49.952+0000" +"XPO","","Xenopus Phenotype Ontology","The XPO represents phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.","ONTOLOGY","","xpo,XPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:49.899+0000" +"ZECO","","Zebrafish Experimental Conditions Ontology","None","ONTOLOGY","","zeco,ZECO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.829+0000" +"ZFA","","Zebrafish anatomy and development ontology","A structured controlled vocabulary of the anatomy and development of the Zebrafish","ONTOLOGY","","zfa,ZFA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:11.841+0000" +"ZFS","","Zebrafish developmental stages ontology","Developmental stages of the Zebrafish","ONTOLOGY","","zfs,ZFS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:24.468+0000" +"ZP","","Zebrafish Phenotype Ontology","The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.","ONTOLOGY","","zp,ZP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:45.130+0000" +"DUO","","The Data Use Ontology","DUO is an ontology which represent data use conditions.","ONTOLOGY","","duo,DUO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:53.056+0000" +"ECO","","Evidence & Conclusion Ontology (ECO)","The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.","ONTOLOGY","","eco,ECO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:03.602+0000" +"EFO","","Experimental Factor Ontology","The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org","ONTOLOGY","","efo,EFO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:32.855+0000" +"EMAP","","Mouse gross anatomy and development, timed","A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).","ONTOLOGY","","emap,EMAP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:09.995+0000" +"EMAPA","","Mouse Developmental Anatomy Ontology","An ontology for mouse anatomy covering embryonic development and postnatal stages.","ONTOLOGY","","emapa,EMAPA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.768+0000" +"ENVO","","Environment Ontology","Ontology of environmental features and habitats","ONTOLOGY","","envo,ENVO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:52.192+0000" +"EO","","Plant Environment Ontology","A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.","ONTOLOGY","","eo,EO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.945+0000" +"AERO","","Adverse Event Reporting Ontology","The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events","ONTOLOGY","","aero,AERO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:31.013+0000" +"EPO","","Epidemiology Ontology","An ontology designed to support the semantic annotation of epidemiology resources","ONTOLOGY","","epo,EPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:03.082+0000" +"ERO","","eagle-i resource ontology","An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.","ONTOLOGY","","ero,ERO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.234+0000" +"EXO","","Exposure ontology","Vocabularies for describing exposure data to inform understanding of environmental health.","ONTOLOGY","","exo,EXO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:57.557+0000" +"FAO","","Fungal gross anatomy","A structured controlled vocabulary for the anatomy of fungi.","ONTOLOGY","","fao,FAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:03.812+0000" +"FBdv","","FlyBase Developmental Ontology (FBdv)","An ontology of Drosophila melanogaster developmental stages.","ONTOLOGY","","fbdv,FBDV,FBdv","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.370+0000" +"GO","","Gene Ontology","The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.","ONTOLOGY","","go,GO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T16:42:43.222+0000" +"AGRO","","Agronomy Ontology","Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments","ONTOLOGY","","agro,AGRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:23.923+0000" +"HTN","","Hypertension Ontology For Clinical Data","An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines","ONTOLOGY","","htn,HTN","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:20.396+0000" +"AMPHX","","Amphioxus Development and Anatomy Ontology (AMPHX)","An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).","ONTOLOGY","","amphx,AMPHX","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:06.819+0000" +"IAO","","Information Artifact Ontology","An ontology of information entities.","ONTOLOGY","","iao,IAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:51.022+0000" +"APO","","Ascomycete phenotype ontology","A structured controlled vocabulary for the phenotypes of Ascomycete fungi","ONTOLOGY","","apo,APO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:03.791+0000" +"ICEO","","ICEO: Ontology of Integrative and Conjugative Elements","A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.","ONTOLOGY","","iceo,ICEO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:54.562+0000" +"CHEMINF","","chemical information ontology (cheminf) - information entities about chemical entities","Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.","ONTOLOGY","","cheminf,CHEMINF","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:46.797+0000" +"ICO","","Informed Consent Ontology","The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.","ONTOLOGY","","ico,ICO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:56.800+0000" +"MOD","","Protein modification","PSI-MOD is an ontology consisting of terms that describe protein chemical modifications","ONTOLOGY","","mod,MOD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:45.671+0000" +"CIO","","Confidence Information Ontology","An ontology to capture confidence information about annotations.","ONTOLOGY","","cio,CIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.638+0000" +"MPATH","","Mouse pathology ontology","A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes","ONTOLOGY","","mpath,MPATH","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:46.668+0000" +"CL","","Cell Ontology","The Cell Ontology is a structured controlled vocabulary for cell types in animals.","ONTOLOGY","","cl,CL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:35.331+0000" +"MPIO","","Minimum PDDI Information Ontology","An ontology of minimum information regarding potential drug-drug interaction information.","ONTOLOGY","","mpio,MPIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:22.267+0000" +"MRO","","MHC Restriction Ontology","The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.","ONTOLOGY","","mro,MRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.947+0000" +"CMO","","Clinical measurement ontology","Morphological and physiological measurement records generated from clinical and model organism research and health programs.","ONTOLOGY","","cmo,CMO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:56.493+0000" +"MS","","Mass spectrometry ontology","A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.","ONTOLOGY","","ms,MS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:58.903+0000" +"CMPO","","Cellular Microscopy Phenotype Ontology","CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.","ONTOLOGY","","cmpo,CMPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:35.100+0000" +"NCIT","","NCI Thesaurus OBO Edition","The NCIt OBO Edition project aims to increase integration of the NCIt with OBO Library ontologies. NCIt is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. NCIt OBO Edition releases should be considered experimental.","ONTOLOGY","","ncit,NCIT,NCI_Thesaurus,nci_thesaurus,NCI_THESAURUS,NCI,nci,ncithesaurus,NCITHESAURUS,NCI2009_04D,nci2009_04d","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:35.643+0000" +"OMRSE","","Ontology of Medically Related Social Entities","This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.","ONTOLOGY","","omrse,OMRSE","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:52.145+0000" +"CO_320","","Rice ontology","Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables","ONTOLOGY","","co_320,CO_320","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:53.918+0000" +"ONTONEO","","Obstetric and Neonatal Ontology","The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.","ONTOLOGY","","ontoneo,ONTONEO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:56.799+0000" +"CO_321","","Wheat ontology","July 2018","ONTOLOGY","","co_321,CO_321","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:41.713+0000" +"OOSTT","","Ontology of Organizational Structures of Trauma centers and Trauma Systems","An ontology built for representating the organizational components of trauma centers and trauma systems.","ONTOLOGY","","oostt,OOSTT","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:39.678+0000" +"CO_321:ROOT","","Wheat ontology","T3 Wheat traits","ONTOLOGY","","co_321:root,CO_321:ROOT","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:01.114+0000" +"OPL","","Ontology for Parasite Lifecycle","The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.","ONTOLOGY","","opl,OPL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.416+0000" +"CO_322","","Maize ontology","Maize Trait Dictionary in template 5 - CIMMYT- September 2016","ONTOLOGY","","co_322,CO_322","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:53.716+0000" +"CO_324","","Sorghum ontology","Sorghum TDv5 - Oct 2019","ONTOLOGY","","co_324,CO_324","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:58.175+0000" +"CO_334","","Cassava ontology","Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016","ONTOLOGY","","co_334,CO_334","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:41.041+0000" +"CO_335","","Common Bean ontology","CIAT Common bean trait dictionary - version August 2014","ONTOLOGY","","co_335,CO_335","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:05.813+0000" +"CO_336","","Soybean ontology","Soybean Trait Dictionary in template v5 - IITA - July 2015","ONTOLOGY","","co_336,CO_336","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:53.701+0000" +"OPMI","","OPMI: Ontology of Precision Medicine and Investigation","OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.","ONTOLOGY","","opmi,OPMI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:00.661+0000" +"CO_337","","Groundnut ontology","Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015","ONTOLOGY","","co_337,CO_337","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:05.789+0000" +"CO_338","","Chickpea ontology","Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015","ONTOLOGY","","co_338,CO_338","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:00.748+0000" +"Orphanet","","Orphanet Rare Disease Ontolog","The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10).","ONTOLOGY","","ordo,ORDO,Orphanet,orphanet,ORPHANET","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:44.946+0000" +"ECOCORE","","An ontology of core ecological entities","An ontology to provide core semantics for ecological entities.","ONTOLOGY","","ecocore,ECOCORE","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:06.429+0000" +"ECTO","","Environment Exposure Ontology","ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).","ONTOLOGY","","ecto,ECTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:16.980+0000" +"EDAM","","Bioinformatics operations, data types, formats, identifiers and topics","EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use.","ONTOLOGY","","edam,EDAM","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:50.120+0000" +"EHDAA2","","Human developmental anatomy, abstract","A structured controlled vocabulary of stage-specific anatomical structures of the developing human.","ONTOLOGY","","ehdaa2,EHDAA2","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:03.004+0000" +"ORNASEQ","","Ontology for RNA sequencing (ORNASEQ)","An application ontology designed to annotate next-generation sequencing experiments performed on RNA.","ONTOLOGY","","ornaseq,ORNASEQ","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.847+0000" +"ENM","","eNanoMapper Ontology","The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ","ONTOLOGY","","enm,ENM","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:50.044+0000" +"OVAE","","OVAE: Ontology of Vaccine Adverse Events","OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ","ONTOLOGY","","ovae,OVAE","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:19.834+0000" +"ENSGLOSS","","Ensembl Glossary","The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.","ONTOLOGY","","ensemblglossary,ENSEMBLGLOSSARY,ENSGLOSS,ensgloss","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:39.847+0000" +"PATO","","PATO - the Phenotype And Trait Ontology","An ontology of phenotypic qualities (properties, attributes or characteristics).","ONTOLOGY","","pato,PATO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:47.320+0000" +"EOL","","Environment Ontology for Livestock","L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage","ONTOLOGY","","eol,EOL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:30.272+0000" +"EUPATH","","VEuPathDB Ontology","The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.","ONTOLOGY","","eupath,EUPATH","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:37.913+0000" +"PCO","","Population and Community Ontology","An ontology about groups of interacting organisms such as populations and communities","ONTOLOGY","","pco,PCO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.258+0000" +"PDRO","","The Prescription of Drugs Ontology","An ontology to describe entities related to prescription of drugs","ONTOLOGY","","pdro,PDRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:22.192+0000" +"PLANP","","Planarian Phenotype Ontology (PLANP)","Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.","ONTOLOGY","","planp,PLANP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:06.814+0000" +"FBbi","","Biological Imaging Methods Ontology","A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.","ONTOLOGY","","fbbi,FBBI,FBbi","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.090+0000" +"PORO","","Porifera (sponge) ontology","An ontology describing the anatomical structures and characteristics of Porifera (sponges)","ONTOLOGY","","poro,PORO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.556+0000" +"FIX","","Physico-chemical methods and properties","An ontology of physico-chemical methods and properties.","ONTOLOGY","","fix,FIX","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.183+0000" +"HANCESTRO","","Human Ancestry Ontology","The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.","ONTOLOGY","","hancestro,HANCESTRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:44.736+0000" +"TADS","","Tick Anatomy Ontology","The anatomy of the Tick, Families: Ixodidae, Argassidae","ONTOLOGY","","tads,TADS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:20.250+0000" +"IDO","","Infectious Disease Ontology","A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.","ONTOLOGY","","ido,IDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:34.905+0000" +"TO","","Plant Trait Ontology","A controlled vocabulary of describe phenotypic traits in plants.","ONTOLOGY","","to,TO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:24.720+0000" +"IDOMAL","","Malaria Ontology","An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.","ONTOLOGY","","idomal,IDOMAL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.012+0000" +"TRANS","","Pathogen Transmission Ontology","The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.","ONTOLOGY","","trans,TRANS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:52.143+0000" +"UNIMOD","","Unimod protein modification database for mass spectrometry","Unimod is a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, an d site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).","ONTOLOGY","","unimod,UNIMOD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:57.143+0000" +"INO","","INO: Interaction Network Ontology","he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.","ONTOLOGY","","ino,INO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:48.760+0000" +"UPA","","Unipathway","A manually curated resource for the representation and annotation of metabolic pathways","ONTOLOGY","","upa,UPA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:45.449+0000" +"LABO","","clinical LABoratory Ontology","LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.","ONTOLOGY","","labo,LABO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:46.045+0000" +"MA","","Mouse adult gross anatomy","A structured controlled vocabulary of the adult anatomy of the mouse (Mus).","ONTOLOGY","","ma,MA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:18.320+0000" +"XCO","","Experimental condition ontology","Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.","ONTOLOGY","","xco,XCO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:24.485+0000" +"MCO","","Microbial Conditions Ontology","Microbial Conditions Ontology is an ontology...","ONTOLOGY","","mco,MCO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:19.137+0000" +"MFMO","","Mammalian Feeding Muscle Ontology","The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.","ONTOLOGY","","mfmo,MFMO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:19.185+0000" +"MI","","Molecular Interactions Controlled Vocabulary","A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.","ONTOLOGY","","mi,MI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:34.673+0000" +"MICRO","","Ontology of Prokaryotic Phenotypic and Metabolic Characters","An ontology of prokaryotic phenotypic and metabolic characters","ONTOLOGY","","micro,MICRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:39.542+0000" +"MMO","","Measurement method ontology","A representation of the variety of methods used to make clinical and phenotype measurements. ","ONTOLOGY","","mmo,MMO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:27.901+0000" +"MOP","","MOP","MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.","ONTOLOGY","","mop,MOP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:34.849+0000" +"NBO","","Neuro Behavior Ontology","An ontology of human and animal behaviours and behavioural phenotypes","ONTOLOGY","","nbo,NBO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:50.658+0000" +"NMR","","nuclear magnetic resonance CV","This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.","ONTOLOGY","","nmrcv,NMRCV,NMR,nmr","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:22.890+0000" +"AEO","","Anatomical Entity Ontology","AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology","ONTOLOGY","","aeo,AEO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:03.670+0000" +"NOMEN","","NOMEN - A nomenclatural ontology for biological names","NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.","ONTOLOGY","","nomen,NOMEN","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:15.210+0000" +"ARO","","Antibiotic Resistance Ontology","Antibiotic resistance genes and mutations","ONTOLOGY","","aro,ARO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:55.796+0000" +"OAE","","OAE: Ontology of Adverse Events","The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.","ONTOLOGY","","oae,OAE","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:16.779+0000" +"ATOL","","Animal Trait Ontology for Livestock","ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.","ONTOLOGY","","atol,ATOL","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:29.668+0000" +"OARCS","","Ontology of Arthropod Circulatory Systems","OArCS is an ontology describing the Arthropod ciruclatory system.","ONTOLOGY","","oarcs,OARCS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:56.798+0000" +"BAO","","BioAssay Ontology","The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.","ONTOLOGY","","bao,BAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:46.599+0000" +"OBA","","Ontology of Biological Attributes","A collection of biological attributes (traits) covering all kingdoms of life.","ONTOLOGY","","oba,OBA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:35.075+0000" +"OBCS","","Ontology of Biological and Clinical Statistics","OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ","ONTOLOGY","","obcs,OBCS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:05.910+0000" +"BCGO","","Beta Cell Genomics Ontology","An application ontology built for beta cell genomics studies.","ONTOLOGY","","bcgo,BCGO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:47.128+0000" +"OBI","","Ontology for Biomedical Investigations","The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.","ONTOLOGY","","obi,OBI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:58.857+0000" +"BCO","","Biological Collections Ontology","An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.","ONTOLOGY","","bco,BCO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:46.450+0000" +"OBIB","","Ontology for BIoBanking (OBIB)","An ontology built for annotation and modeling of biobank repository and biobanking administration","ONTOLOGY","","obib,OBIB","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:06.286+0000" +"BFO","","Basic Formal Ontology","The upper level ontology upon which OBO Foundry ontologies are built.","ONTOLOGY","","bfo,BFO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:35.472+0000" +"OGG","","OGG: Ontology of Genes and Genomes","OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ","ONTOLOGY","","ogg,OGG","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:10.248+0000" +"BSPO","","Biological Spatial Ontology","An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces","ONTOLOGY","","bspo,BSPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:30.570+0000" +"OGI","","Ontology for genetic interval","OGI formalized the genomic element by defining an upper class 'genetic interval'. + +The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" + +Related paper: + +1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) +Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf) +Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF) + + +","ONTOLOGY","","ogi,OGI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:05.860+0000" +"BTO","","The BRENDA Tissue Ontology (BTO)","A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.","ONTOLOGY","","bto,BTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.630+0000" +"OGMS","","Ontology for General Medical Science","An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities","ONTOLOGY","","ogms,OGMS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:05.806+0000" +"OGSF","","Ontology of Genetic Susceptibility Factor","An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.","ONTOLOGY","","ogsf,OGSF","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:06.571+0000" +"CARO","","Common Anatomy Reference Ontology","An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species","ONTOLOGY","","caro,CARO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.060+0000" +"OHD","","The Oral Health and Disease Ontology","The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records.","ONTOLOGY","","ohd,OHD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:52.632+0000" +"CCO","","Cell Cycle Ontology","The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.","ONTOLOGY","","cco,CCO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:00.848+0000" +"OHMI","","OHMI: Ontology of Host-Microbiome Interactions","OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.","ONTOLOGY","","ohmi,OHMI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:41.013+0000" +"OHPI","","OHPI: Ontology of Host-Pathogen Interactions","OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).","ONTOLOGY","","ohpi,OHPI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:46.065+0000" +"CDAO","","Comparative Data Analysis Ontology","The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.","ONTOLOGY","","cdao,CDAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:24.571+0000" +"OLATDV","","Medaka Developmental Stages","Life cycle stages for Medaka","ONTOLOGY","","olatdv,OLATDV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:06.526+0000" +"OMIABIS","","Ontologized MIABIS","An ontological version of MIABIS (Minimum Information About BIobank data Sharing)","ONTOLOGY","","omiabis,OMIABIS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.406+0000" +"CEPH","","Cephalopod Ontology","An anatomical and developmental ontology for cephalopods","ONTOLOGY","","ceph,CEPH","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:47.073+0000" +"OMIT","","Ontology for MIRNA Target","Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain","ONTOLOGY","","omit,OMIT","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:25.381+0000" +"CHEBI","","Chemical Entities of Biological Interest","A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.","ONTOLOGY","","chebi,CHEBI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:11.842+0000" +"OMP","","Ontology of Microbial Phenotypes","An ontology of phenotypes covering microbes","ONTOLOGY","","omp,OMP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:12.194+0000" +"CHIRO","","CHEBI Integrated Role Ontology","CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.","ONTOLOGY","","chiro,CHIRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:50.375+0000" +"PR","","PRotein Ontology (PRO)","An ontological representation of protein-related entities","ONTOLOGY","","pr,PR","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T23:02:53.508+0000" +"CHMO","","Chemical Methods Ontology","CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).","ONTOLOGY","","chmo,CHMO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:02.921+0000" +"PRIDE","","PRIDE Controlled Vocabulary","The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.","ONTOLOGY","","pride,PRIDE","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-29T16:47:24.449+0000" +"CIDO","","CIDO: Ontology of Coronavirus Infectious Disease","The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.","ONTOLOGY","","cido,CIDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:06.506+0000" +"CLYH","","Clytia hemisphaerica Development and Anatomy Ontology (CLYH)","Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.","ONTOLOGY","","clyh,CLYH","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:41:16.295+0000" +"PROBONTO","","Probability Distribution Ontology","ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas.","ONTOLOGY","","probonto,PROBONTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.482+0000" +"CVDO","","Cardiovascular Disease Ontology","An ontology to describe entities related to cardiovascular diseases","ONTOLOGY","","cvdo,CVDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.274+0000" +"PSDO","","Performance Summary Display Ontology","Ontology to reproducibly study visualizations of clinical performance","ONTOLOGY","","psdo,PSDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:19.926+0000" +"DDANAT","","Dictyostelium discoideum anatomy","A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum","ONTOLOGY","","ddanat,DDANAT","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.227+0000" +"DDPHENO","","Dictyostelium discoideum phenotype ontology","A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.","ONTOLOGY","","ddpheno,DDPHENO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:05.112+0000" +"PW","","Pathway ontology","A controlled vocabulary for annotating gene products to pathways.","ONTOLOGY","","pw,PW","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:51.664+0000" +"ReTO","","Regulation of Transcription Ontology","Regulation of Transcription","ONTOLOGY","","reto,RETO,ReTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:53.160+0000" +"DICOM","","DICOM Controlled Terminology","DICOM Controlled Terminology","ONTOLOGY","","dicom,DICOM","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:48.790+0000" +"REX","","Physico-chemical process","An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.","ONTOLOGY","","rex,REX","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:52.501+0000" +"ReXO","","Regulation of Gene Expression Ontology","Regulation of Gene Expression","ONTOLOGY","","rexo,REXO,ReXO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:57.865+0000" +"RNAO","","The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data","Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.","ONTOLOGY","","rnao,RNAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:35.421+0000" +"RO","","OBO Relations Ontology","The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.","ONTOLOGY","","ro,RO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.382+0000" +"DIDEO","","Drug-drug Interaction and Drug-drug Interaction Evidence Ontology","The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology","ONTOLOGY","","dideo,DIDEO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:56.479+0000" +"RS","","Rat Strain Ontology","Ontology of rat strains","ONTOLOGY","","rs,RS","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:12.019+0000" +"RXNO","","RXNO","RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.","ONTOLOGY","","rxno,RXNO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:20.755+0000" +"SBO","","Systems Biology Ontology","Terms commonly used in Systems Biology, and in particular in computational modeling.","ONTOLOGY","","sbo,SBO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-28T00:30:08.459+0000" +"DINTO","","The Drug-Drug Interactions Ontology","A formal represention for drug-drug interactions knowledge.","ONTOLOGY","","dinto,DINTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:45.043+0000" +"SCDO","","Sickle Cell Disease Ontology","The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.","ONTOLOGY","","scdo,SCDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:41.359+0000" +"DOID","","Human Disease Ontology","The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.","ONTOLOGY","","doid,DOID","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:10.204+0000" +"FBbt","","Drosophila Anatomy Ontology (DAO)","An ontology of Drosophila melanogaster anatomy.","ONTOLOGY","","fbbt,FBBT,FBbt","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:00.690+0000" +"SDGIO","","Sustainable Development Goals Interface Ontology","An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.","ONTOLOGY","","sdgio,SDGIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:44.176+0000" +"FLOPO","","Flora Phenotype Ontology","Traits and phenotypes of flowering plants occurring in digitized Floras","ONTOLOGY","","flopo,FLOPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:54.443+0000" +"SEP","","Sample processing and separation techniques","A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.","ONTOLOGY","","sep,SEP","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:11.773+0000" +"FLU","","Influenza ontology","The influenza ontology is an application ontology that covers the natural, experimental and clinical realms related to influenza virus life cycle, infection and disease. It is an extension of the infectious disease ontology (IDO).","ONTOLOGY","","flu,FLU","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:34.578+0000" +"SEPIO","","Scientific Evidence and Provenance Information Ontology","An ontology for representing the provenance of scientific claims and the evidence that supports them.","ONTOLOGY","","sepio,SEPIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:49.615+0000" +"FMA","","Foundational Model of Anatomy Ontology (subset)","This is currently a slimmed down version of FMA","ONTOLOGY","","fma,FMA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:33.819+0000" +"SIBO","","Social Insect Behavior Ontology","Social Behavior in insects","ONTOLOGY","","sibo,SIBO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:19.877+0000" +"FOBI","","FOBI","FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data","ONTOLOGY","","fobi,FOBI","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:55.890+0000" +"SIO","","Semanticscience Integrated Ontology","The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.","ONTOLOGY","","sio,SIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:46.339+0000" +"FOODON","","Food Ontology","FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world.","ONTOLOGY","","foodon,FOODON","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:45.332+0000" +"FYPO","","Fission Yeast Phenotype Ontology (FYPO)","A formal ontology of phenotypes observed in fission yeast.","ONTOLOGY","","fypo,FYPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:39.651+0000" +"VT","","Vertebrate trait ontology","An ontology of traits covering vertebrates","ONTOLOGY","","vt,VT","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:50.245+0000" +"GAZ","","Gazetteer","A gazetteer constructed on ontological principles","ONTOLOGY","","gaz,GAZ","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:33.963+0000" +"WBbt","","C. elegans Gross Anatomy Ontology","Ontology about the gross anatomy of the C. elegans","ONTOLOGY","","wbbt,WBBT,WBbt","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:25.772+0000" +"WBls","","C. elegans Development Ontology","Ontology about the development and life stages of the C. elegans","ONTOLOGY","","wbls,WBLS,WBls","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:12.540+0000" +"WBPhenotype","","C elegans Phenotype Ontology","Ontology about C. elegans and other nematode phenotypes","ONTOLOGY","","wbphenotype,WBPHENOTYPE,WBPhenotype","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:50.695+0000" +"XAO","","Xenopus Anatomy Ontology","XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.","ONTOLOGY","","xao,XAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:34:47.381+0000" +"GENEPIO","","Genomic Epidemiology Ontology","The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.","ONTOLOGY","","genepio,GENEPIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:30.471+0000" +"GENO","","GENO ontology","GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. + +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013","ONTOLOGY","","geno,GENO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:34.848+0000" +"GEO","","Geographical Entity Ontology","An ontology of geographical entities","ONTOLOGY","","geo,GEO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:09.728+0000" +"GeXO","","Gene Expression Ontology","Gene Expression Ontology","ONTOLOGY","","gexo,GEXO,GeXO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:39.047+0000" +"GNO","","Glycan Naming Ontology","An ontology for glycans based on GlyTouCan, but organized by subsumption.","ONTOLOGY","","gno,GNO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:29.817+0000" +"HP","","Human Phenotype Ontology","The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.","ONTOLOGY","","hp,HP,hpo,HPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:38:29.541+0000" +"MC","","Histopathology Ontology","An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.","ONTOLOGY","","hpath,HPATH,MC,mc","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:40:24.056+0000" +"HSAPDV","","Human Developmental Stages","Life cycle stages for Human","ONTOLOGY","","hsapdv,HSAPDV","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:18.302+0000" +"KISAO","","Kinetic Simulation Algorithm Ontology","A classification of algorithms available for the simulation of models in biology.","ONTOLOGY","","kisao,KISAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:18.283+0000" +"LBO","","Livestock Breed Ontology","A vocabulary for cattle, chicken, horse, pig, and sheep breeds.","ONTOLOGY","","lbo,LBO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:35.310+0000" +"MAMO","","Mathematical Modelling Ontology","The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.","ONTOLOGY","","mamo,MAMO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:27.902+0000" +"MAXO","","Medical Action Ontology","An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.","ONTOLOGY","","maxo,MAXO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-29T12:32:16.923+0000" +"MF","","Mental Functioning Ontology","The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.","ONTOLOGY","","mf,MF","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T18:08:51.049+0000" +"MFOEM","","Emotion Ontology","An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.","ONTOLOGY","","mfoem,MFOEM","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T19:36:25.780+0000" +"MFOMD","","Mental Disease Ontology","The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).","ONTOLOGY","","mfomd,MFOMD","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T21:04:35.397+0000" +"MIAPA","","Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology","The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. + +This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.","ONTOLOGY","","miapa,MIAPA","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:19.128+0000" +"MIRNAO","","microRNA Ontology","An application ontology for use with miRNA databases.","ONTOLOGY","","mirnao,MIRNAO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:19.060+0000" +"MIRO","","Mosquito insecticide resistance","Application ontology for entities related to insecticide resistance in mosquitos","ONTOLOGY","","miro,MIRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:34.951+0000" +"MONDO","","Mondo Disease Ontology","An ontology that harmonizes multiple disease resources.","ONTOLOGY","","mondo,MONDO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:06.575+0000" +"MSIO","","Metabolomics Standards Initiative Ontology (MSIO)","an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.","ONTOLOGY","","msio,MSIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:54.989+0000" +"NCRO","","Non-Coding RNA Ontology","An ontology for non-coding RNA, both of biological origin, and engineered.","ONTOLOGY","","ncro,NCRO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:28.986+0000" +"PPO","","Plant Phenology Ontology","An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.","ONTOLOGY","","ppo,PPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:35:35.092+0000" +"TTO","","Teleost taxonomy ontology","An ontology covering the taxonomy of teleosts (bony fish)","ONTOLOGY","","tto,TTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:40.401+0000" +"TXPO","","TOXic Process Ontology (TXPO)","Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. + +The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. + +In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp","ONTOLOGY","","txpo,TXPO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-30T10:39:37.657+0000" +"UBERON","","Uber-anatomy ontology","Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.","ONTOLOGY","","uberon,UBERON","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:08.873+0000" +"UPHENO","","Unified phenotype ontology (uPheno)","The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.","ONTOLOGY","","upheno,UPHENO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:39:22.264+0000" +"VARIO","","Variation Ontology","Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.","ONTOLOGY","","vario,VARIO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:21.011+0000" +"VO","","Vaccine Ontology","The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.","ONTOLOGY","","vo,VO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:36:25.777+0000" +"VTO","","Vertebrate Taxonomy Ontology","Comprehensive hierarchy of extinct and extant vertebrate taxa.","ONTOLOGY","","vto,VTO","https://creativecommons.org/licenses/by/4.0/","Last updated in the ontology lookup service on 2020-04-27T14:37:46.479+0000" +"BIND","bind","BIND","BIND is a database of protein-protein interactions. This data-resource is not open-access.","DATABASE","","bind,BIND","None","None" +"Ensembl","ensembl","Ensembl","Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.","DATABASE","","ensembl,ENSEMBL,Ensembl","None","None" +"ec-code","ec-code","Enzyme Nomenclature","The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.","DATABASE","","ec-code,EC-CODE","None","None" +"uniprot","uniprot","UniProt Knowledgebase","The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.","DATABASE","","uniprot,UNIPROT","None","None" +"Taxonomy","taxonomy","Taxonomy","The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.","DATABASE","","taxonomy,TAXONOMY,Taxonomy","None","None" +"biomodels.db","biomodels.db","BioModels Database","BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.","DATABASE","","biomodels.db,BIOMODELS.DB","None","None" +"miriam.collection","miriam.collection","MIRIAM Registry collection","MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.","DATABASE","","miriam.collection,MIRIAM.COLLECTION","None","None" +"ICD10CM","icd10","ICD-10","The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.","DATABASE","","icd10,ICD10,ICD-10,icd-10,ICD-10CM,icd-10cm,ICD-10-CM,icd-10-cm,ICD10CM,icd10cm","https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf","2016AB" +"ICD9CM","icd9","ICD-9","The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.","DATABASE","","icd9,ICD9,ICD-9,icd-9,ICD-9CM,icd-9cm,ICD-9-CM,icd-9-cm,ICD9CM,icd9cm","https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf","2016AB" +"IntAct","intact","IntAct","IntAct provides a freely available, open source database system and analysis tools for protein interaction data.","DATABASE","","intact,INTACT,IntAct","None","None" +"InterPro","interpro","InterPro","InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.","DATABASE","","interpro,INTERPRO,InterPro","None","None" +"kegg.pathway","kegg.pathway","KEGG Pathway","KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.","DATABASE","","kegg.pathway,KEGG.PATHWAY","None","None" +"KEGG_COMPOUND","kegg.compound","KEGG Compound","KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.","DATABASE","","kegg.compound,KEGG.COMPOUND,KEGG COMPOUND,kegg compound,KEGG_COMPOUND,kegg_compound","None","None" +"kegg.reaction","kegg.reaction","KEGG Reaction","KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.","DATABASE","","kegg.reaction,KEGG.REACTION","None","None" +"PubMed","pubmed","PubMed","PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.","DATABASE","","pubmed,PUBMED,PubMed","None","None" +"OMIM","omim","OMIM","Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.","DATABASE","","omim,OMIM","None","None" +"PIRSF","pirsf","PIRSF","The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.","DATABASE","","pirsf,PIRSF","None","None" +"Reactome","reactome","Reactome","The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.","DATABASE","","reactome,REACTOME,Reactome","None","None" +"DOI","doi","DOI","The Digital Object Identifier System is for identifying content objects in the digital environment.","DATABASE","","doi,DOI","None","None" +"pdb","pdb","Protein Data Bank","The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.","DATABASE","","pdb,PDB","None","None" +"CluSTr","clustr","CluSTr","The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons (Smith-Waterman) between protein sequences.","DATABASE","","clustr,CLUSTR,CluSTr","None","None" +"SGD","sgd","SGD","The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.","DATABASE","","sgd,SGD","None","None" +"biomodels.sbo","biomodels.sbo","Systems Biology Ontology","The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.","DATABASE","","biomodels.sbo,BIOMODELS.SBO","None","None" +"KEGG_DRUG","kegg.drug","KEGG Drug","KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.","DATABASE","","kegg.drug,KEGG.DRUG,KEGG DRUG,kegg drug,KEGG_DRUG,kegg_drug","None","None" +"kegg.glycan","kegg.glycan","KEGG Glycan","KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.","DATABASE","","kegg.glycan,KEGG.GLYCAN","None","None" +"WormBase","wormbase","WormBase","WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes.","DATABASE","","wormbase,WORMBASE,WormBase","None","None" +"Pfam","pfam","Pfam","The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.","DATABASE","","pfam,PFAM,Pfam","None","None" +"insdc","insdc","Nucleotide Sequence Database","The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.","DATABASE","","insdc,INSDC","None","None" +"FlyBase","flybase","FlyBase","FlyBase is the database of the Drosophila Genome Projects and of associated literature.","DATABASE","","flybase,FLYBASE,FlyBase","None","None" +"Wormpep","wormpep","Wormpep","Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.","DATABASE","","wormpep,WORMPEP,Wormpep","None","None" +"PROSITE","prosite","PROSITE","PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.","DATABASE","","prosite,PROSITE","None","None" +"PubChem-substance","pubchem.substance","PubChem-substance","PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.","DATABASE","","pubchem.substance,PUBCHEM.SUBSTANCE,PubChem-substance,pubchem-substance,PUBCHEM-SUBSTANCE","None","None" +"PubChem-compound","pubchem.compound","PubChem-compound","PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.","DATABASE","","pubchem.compound,PUBCHEM.COMPOUND,PubChem-compound,pubchem-compound,PUBCHEM-COMPOUND","None","None" +"arXiv","arxiv","arXiv","arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.","DATABASE","","arxiv,ARXIV,arXiv","None","None" +"ArrayExpress","arrayexpress","ArrayExpress","ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.","DATABASE","","arrayexpress,ARRAYEXPRESS,ArrayExpress","None","None" +"mgd","mgd","Mouse Genome Database","The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.","DATABASE","","mgd,MGD","None","None" +"sabiork.reaction","sabiork.reaction","SABIO-RK Reaction","SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.","DATABASE","","sabiork.reaction,SABIORK.REACTION","None","None" +"RefSeq","refseq","RefSeq","The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.","DATABASE","","refseq,REFSEQ,RefSeq","None","None" +"tcdb","tcdb","Transport Classification Database","The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.","DATABASE","","tcdb,TCDB","None","None" +"UniParc","uniparc","UniParc","The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.","DATABASE","","uniparc,UNIPARC,UniParc","None","None" +"MINT","mint","MINT","The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.","DATABASE","","mint,MINT","None","None" +"IPI","ipi","IPI","The International Protein Index (IPI) provides complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases","DATABASE","","ipi,IPI","None","None" +"dip","dip","Database of Interacting Proteins","The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions","DATABASE","","dip,DIP","None","None" +"signaling-gateway","signaling-gateway","Signaling Gateway","The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.","DATABASE","","signaling-gateway,SIGNALING-GATEWAY","None","None" +"RESID","resid","RESID","The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.","DATABASE","","resid,RESID","None","None" +"rgd","rgd","Rat Genome Database","Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.","DATABASE","","rgd,RGD","None","None" +"tair.protein","tair.protein","TAIR Protein","The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept","DATABASE","","tair.protein,TAIR.PROTEIN","None","None" +"tair.gene","tair.gene","TAIR Gene","The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.","DATABASE","","tair.gene,TAIR.GENE","None","None" +"tair.locus","tair.locus","TAIR Locus","The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.","DATABASE","","tair.locus,TAIR.LOCUS","None","None" +"HMDB","hmdb","HMDB","The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.","DATABASE","","hmdb,HMDB","None","None" +"LIPID_MAPS","lipidmaps","LIPID MAPS","The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.","DATABASE","","lipidmaps,LIPIDMAPS,LIPID MAPS,lipid maps,LIPID_MAPS,lipid_maps","None","None" +"PeptideAtlas","peptideatlas","PeptideAtlas","The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.","DATABASE","","peptideatlas,PEPTIDEATLAS,PeptideAtlas","None","None" +"psimod","psimod","Protein Modification Ontology","The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.","DATABASE","","psimod,PSIMOD","None","None" +"sgd.pathways","sgd.pathways","Saccharomyces genome database pathways","Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).","DATABASE","","sgd.pathways,SGD.PATHWAYS","None","None" +"BioGRID","biogrid","BioGRID","BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.","DATABASE","","biogrid,BIOGRID,BioGRID","None","None" +"MEROPS","merops","MEROPS","The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.","DATABASE","","merops,MEROPS","None","None" +"panther.family","panther.family","PANTHER Family","The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.","DATABASE","","panther.family,PANTHER.FAMILY","None","None" +"PRINTS","sprint","PRINTS","PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.","DATABASE","","sprint,SPRINT,PRINTS,prints","None","None" +"ligandexpo","ligandexpo","Ligand Expo","Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.","DATABASE","","ligandexpo,LIGANDEXPO","None","None" +"Aclame","aclame","Aclame","ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.","DATABASE","","aclame,ACLAME,Aclame","None","None" +"ISBN","isbn","ISBN","The International Standard Book Number (ISBN) is for identifying printed books.","DATABASE","","isbn,ISBN","None","None" +"3DMET","3dmet","3DMET","3DMET is a database collecting three-dimensional structures of natural metabolites.","DATABASE","","3dmet,3DMET","None","None" +"MatrixDB","matrixdb.association","MatrixDB","MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.","DATABASE","","matrixdb.association,MATRIXDB.ASSOCIATION,MatrixDB,matrixdb,MATRIXDB","None","None" +"ncbigene","ncbigene","NCBI Gene","Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.","DATABASE","","ncbigene,NCBIGENE","None","None" +"kegg.genes","kegg.genes","KEGG Genes","KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.","DATABASE","","kegg.genes,KEGG.GENES","None","None" +"BRENDA","brenda","BRENDA","BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.","DATABASE","","brenda,BRENDA","None","None" +"PubChem-bioassay","pubchem.bioassay","PubChem-bioassay","PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.","DATABASE","","pubchem.bioassay,PUBCHEM.BIOASSAY,PubChem-bioassay,pubchem-bioassay,PUBCHEM-BIOASSAY","None","None" +"pathwaycommons","pathwaycommons","Pathway Commons","Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.","DATABASE","","pathwaycommons,PATHWAYCOMMONS","None","None" +"HOVERGEN","hovergen","HOVERGEN","HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.","DATABASE","","hovergen,HOVERGEN","None","None" +"biomaps","biomaps","Melanoma Molecular Map Project Biomaps","A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.","DATABASE","","biomaps,BIOMAPS","None","None" +"WikiPathways","wikipathways","WikiPathways","WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. +All content is under the Creative Commons Attribution 3.0 Unported license.","DATABASE","","wikipathways,WIKIPATHWAYS,WikiPathways","None","None" +"MACiE","macie","MACiE","MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.","DATABASE","","macie,MACIE,MACiE","None","None" +"mirbase","mirbase","miRBase Sequence","The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).","DATABASE","","mirbase,MIRBASE","None","None" +"zfin","zfin","ZFIN Gene","ZFIN serves as the zebrafish model organism database. This collection references gene information.","DATABASE","","zfin,ZFIN","None","None" +"HGNC","hgnc","HGNC","The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC ids refer to records in the HGNC symbol database.","DATABASE","","hgnc,HGNC","None","None" +"Rhea","rhea","Rhea","Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed \"spontaneous\".","DATABASE","","rhea,RHEA,Rhea","None","None" +"Unipathway","unipathway","Unipathway","UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.","DATABASE","","unipathway,UNIPATHWAY,Unipathway","None","None" +"chembl.compound","chembl.compound","ChEMBL compound","ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.","DATABASE","","chembl.compound,CHEMBL.COMPOUND","None","None" +"chembl.target","chembl.target","ChEMBL target","ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.","DATABASE","","chembl.target,CHEMBL.TARGET","None","None" +"sabiork.kineticrecord","sabiork.kineticrecord","SABIO-RK Kinetic Record","SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.","DATABASE","","sabiork.kineticrecord,SABIORK.KINETICRECORD","None","None" +"lgic","lgic","Ligand-Gated Ion Channel database","The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.","DATABASE","","lgic,LGIC","None","None" +"atc","atc","Anatomical Therapeutic Chemical","The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.","DATABASE","","atc,ATC","None","None" +"pharmgkb.pathways","pharmgkb.pathways","PharmGKB Pathways","The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. +PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.","DATABASE","","pharmgkb.pathways,PHARMGKB.PATHWAYS","None","None" +"pharmgkb.disease","pharmgkb.disease","PharmGKB Disease","The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.","DATABASE","","pharmgkb.disease,PHARMGKB.DISEASE","None","None" +"pharmgkb.drug","pharmgkb.drug","PharmGKB Drug","The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.","DATABASE","","pharmgkb.drug,PHARMGKB.DRUG","None","None" +"ttd.drug","ttd.drug","TTD Drug","The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.","DATABASE","","ttd.drug,TTD.DRUG","None","None" +"ttd.target","ttd.target","TTD Target","The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.","DATABASE","","ttd.target,TTD.TARGET","None","None" +"NeuronDB","neurondb","NeuronDB","NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.","DATABASE","","neurondb,NEURONDB,NeuronDB","None","None" +"NeuroMorpho","neuromorpho","NeuroMorpho","NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.","DATABASE","","neuromorpho,NEUROMORPHO,NeuroMorpho","None","None" +"ChemIDplus","chemidplus","ChemIDplus","ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.","DATABASE","","chemidplus,CHEMIDPLUS,ChemIDplus","None","None" +"BioSystems","biosystems","BioSystems","The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.","DATABASE","","biosystems,BIOSYSTEMS,BioSystems","None","None" +"ctd.chemical","ctd.chemical","CTD Chemical","The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.","DATABASE","","ctd.chemical,CTD.CHEMICAL","None","None" +"ctd.disease","ctd.disease","CTD Disease","The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.","DATABASE","","ctd.disease,CTD.DISEASE","None","None" +"ctd.gene","ctd.gene","CTD Gene","The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.","DATABASE","","ctd.gene,CTD.GENE","None","None" +"BioNumbers","bionumbers","BioNumbers","BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. +","DATABASE","","bionumbers,BIONUMBERS,BioNumbers","None","None" +"DrugBank","drugbank","DrugBank","The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.","DATABASE","","drugbank,DRUGBANK,DrugBank","None","None" +"T3DB","t3db","T3DB","Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.","DATABASE","","t3db,T3DB","None","None" +"smpdb","smpdb","Small Molecule Pathway Database","The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.","DATABASE","","smpdb,SMPDB","None","None" +"phosphosite.protein","phosphosite.protein","PhosphoSite Protein","PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.","DATABASE","","phosphosite.protein,PHOSPHOSITE.PROTEIN","None","None" +"GeneDB","genedb","GeneDB","GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.","DATABASE","","genedb,GENEDB,GeneDB","None","None" +"psimi","psimi","Molecular Interactions Ontology","The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.","DATABASE","","psimi,PSIMI","None","None" +"pdb-ccd","pdb-ccd","Chemical Component Dictionary","The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.","DATABASE","","pdb-ccd,PDB-CCD","None","None" +"GlycomeDB","glycomedb","GlycomeDB","GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.","DATABASE","","glycomedb,GLYCOMEDB,GlycomeDB","None","None" +"LipidBank","lipidbank","LipidBank","LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.","DATABASE","","lipidbank,LIPIDBANK,LipidBank","None","None" +"kegg.orthology","kegg.orthology","KEGG Orthology","KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.","DATABASE","","kegg.orthology,KEGG.ORTHOLOGY","None","None" +"ProDom","prodom","ProDom","ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.","DATABASE","","prodom,PRODOM,ProDom","None","None" +"SMART","smart","SMART","The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.","DATABASE","","smart,SMART","None","None" +"cdd","cdd","Conserved Domain Database","The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.","DATABASE","","cdd,CDD","None","None" +"mmdb","mmdb","Molecular Modeling Database","The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.","DATABASE","","mmdb,MMDB","None","None" +"IMEx","imex","IMEx","The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.","DATABASE","","imex,IMEX,IMEx","None","None" +"iRefWeb","irefweb","iRefWeb","iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.","DATABASE","","irefweb,IREFWEB,iRefWeb","None","None" +"mpid","mpid","Microbial Protein Interaction Database","The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.","DATABASE","","mpid,MPID","None","None" +"phosphosite.residue","phosphosite.residue","PhosphoSite Residue","PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.","DATABASE","","phosphosite.residue,PHOSPHOSITE.RESIDUE","None","None" +"NeuroLex","neurolex","NeuroLex","The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).","DATABASE","","neurolex,NEUROLEX,NeuroLex","None","None" +"sabiork.ec","sabiork.ec","SABIO-RK EC Record","SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.","DATABASE","","sabiork.ec,SABIORK.EC","None","None" +"opb","opb","Ontology of Physics for Biology","The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.","DATABASE","","opb,OPB","None","None" +"jws","jws","JWS Online","JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.","DATABASE","","jws,JWS","None","None" +"ModelDB","modeldb","ModelDB","ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.","DATABASE","","modeldb,MODELDB,ModelDB","None","None" +"SubtiWiki","subtiwiki","SubtiWiki","SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. +Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.","DATABASE","","subtiwiki,SUBTIWIKI,SubtiWiki","None","None" +"pid.pathway","pid.pathway","NCI Pathway Interaction Database: Pathway","The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.","DATABASE","","pid.pathway,PID.PATHWAY","None","None" +"doqcs.model","doqcs.model","Database of Quantitative Cellular Signaling: Model","The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.","DATABASE","","doqcs.model,DOQCS.MODEL","None","None" +"doqcs.pathway","doqcs.pathway","Database of Quantitative Cellular Signaling: Pathway","The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.","DATABASE","","doqcs.pathway,DOQCS.PATHWAY","None","None" +"unit","unit","Unit Ontology","Ontology of standardized units","DATABASE","","unit,UNIT","None","None" +"ClinicalTrials.gov","clinicaltrials","ClinicalTrials.gov","ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries","DATABASE","","clinicaltrials,CLINICALTRIALS,ClinicalTrials.gov,clinicaltrials.gov,CLINICALTRIALS.GOV","None","None" +"ChemSpider","chemspider","ChemSpider","ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.","DATABASE","","chemspider,CHEMSPIDER,ChemSpider","None","None" +"BioCatalogue","biocatalogue.service","BioCatalogue","The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.","DATABASE","","biocatalogue.service,BIOCATALOGUE.SERVICE,BioCatalogue,biocatalogue,BIOCATALOGUE","None","None" +"OMIA","omia","OMIA","Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).","DATABASE","","omia,OMIA","None","None" +"ChemBank","chembank","ChemBank","ChemBank stores small molecule information, as well as measurements derived from cells and other biological assay systems treated with small molecules.","DATABASE","","chembank,CHEMBANK,ChemBank","None","None" +"CSA","csa","CSA","The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.","DATABASE","","csa,CSA","None","None" +"cgd","cgd","Candida Genome Database","The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.","DATABASE","","cgd,CGD","None","None" +"AntWeb","antweb","AntWeb","AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.","DATABASE","","antweb,ANTWEB,AntWeb","None","None" +"pmc","pmc","PMC International","PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.","DATABASE","","pmc,PMC","None","None" +"AmoebaDB","amoebadb","AmoebaDB","AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","amoebadb,AMOEBADB,AmoebaDB","None","None" +"CryptoDB","cryptodb","CryptoDB","CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","cryptodb,CRYPTODB,CryptoDB","None","None" +"PlasmoDB","plasmodb","PlasmoDB","AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","plasmodb,PLASMODB,PlasmoDB","None","None" +"GiardiaDB","giardiadb","GiardiaDB","GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","giardiadb,GIARDIADB,GiardiaDB","None","None" +"MicrosporidiaDB","microsporidia","MicrosporidiaDB","MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","microsporidia,MICROSPORIDIA,MicrosporidiaDB,microsporidiadb,MICROSPORIDIADB","None","None" +"ToxoDB","toxoplasma","ToxoDB","ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","toxoplasma,TOXOPLASMA,ToxoDB,toxodb,TOXODB","None","None" +"TrichDB","trichdb","TrichDB","TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","trichdb,TRICHDB,TrichDB","None","None" +"TriTrypDB","tritrypdb","TriTrypDB","TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","tritrypdb,TRITRYPDB,TriTrypDB","None","None" +"bdgp.insertion","bdgp.insertion","BDGP insertion DB","BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.","DATABASE","","bdgp.insertion,BDGP.INSERTION","None","None" +"BeetleBase","beetlebase","BeetleBase","BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.","DATABASE","","beetlebase,BEETLEBASE,BeetleBase","None","None" +"bold.taxonomy","bold.taxonomy","BOLD Taxonomy","The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.","DATABASE","","bold.taxonomy,BOLD.TAXONOMY","None","None" +"dbEST","dbest","dbEST","The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.","DATABASE","","dbest,DBEST,dbEST","None","None" +"dbProbe","dbprobe","dbProbe","The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.","DATABASE","","dbprobe,DBPROBE,dbProbe","None","None" +"dbSNP","dbsnp","dbSNP","The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.","DATABASE","","dbsnp,DBSNP,dbSNP","None","None" +"UniSTS","unists","UniSTS","UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.","DATABASE","","unists,UNISTS,UniSTS","None","None" +"EcoGene","ecogene","EcoGene","The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.","DATABASE","","ecogene,ECOGENE,EcoGene","None","None" +"GABI","gabi","GABI","GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.","DATABASE","","gabi,GABI","None","None" +"GreenGenes","greengenes","GreenGenes","A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.","DATABASE","","greengenes,GREENGENES,GreenGenes","None","None" +"grin.taxonomy","grin.taxonomy","GRIN Plant Taxonomy","GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.","DATABASE","","grin.taxonomy,GRIN.TAXONOMY","None","None" +"hinv.locus","hinv.locus","H-InvDb Locus","H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.","DATABASE","","hinv.locus,HINV.LOCUS","None","None" +"hinv.transcript","hinv.transcript","H-InvDb Transcript","H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.","DATABASE","","hinv.transcript,HINV.TRANSCRIPT","None","None" +"hinv.protein","hinv.protein","H-InvDb Protein","H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.","DATABASE","","hinv.protein,HINV.PROTEIN","None","None" +"homd.seq","homd.seq","HOMD Sequence Metainformation","The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.","DATABASE","","homd.seq,HOMD.SEQ","None","None" +"homd.taxon","homd.taxon","HOMD Taxonomy","The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.","DATABASE","","homd.taxon,HOMD.TAXON","None","None" +"ird.segment","ird.segment","IRD Segment Sequence","Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).","DATABASE","","ird.segment,IRD.SEGMENT","None","None" +"ISFinder","isfinder","ISFinder","ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.","DATABASE","","isfinder,ISFINDER,ISFinder","None","None" +"jcm","jcm","Japan Collection of Microorganisms","The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.","DATABASE","","jcm,JCM","None","None" +"img.taxon","img.taxon","Integrated Microbial Genomes Taxon","The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.","DATABASE","","img.taxon,IMG.TAXON","None","None" +"img.gene","img.gene","Integrated Microbial Genomes Gene","The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.","DATABASE","","img.gene,IMG.GENE","None","None" +"maizegdb.locus","maizegdb.locus","MaizeGDB Locus","MaizeGDB is the maize research community's central repository for genetics and genomics information.","DATABASE","","maizegdb.locus,MAIZEGDB.LOCUS","None","None" +"MycoBank","mycobank","MycoBank","MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.","DATABASE","","mycobank,MYCOBANK,MycoBank","None","None" +"nbrc","nbrc","NITE Biological Research Center Catalogue","NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.","DATABASE","","nbrc,NBRC","None","None" +"pseudomonas","pseudomonas","Pseudomonas Genome Database","The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.","DATABASE","","pseudomonas,PSEUDOMONAS","None","None" +"gramene.protein","gramene.protein","Gramene protein","Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.","DATABASE","","gramene.protein,GRAMENE.PROTEIN","None","None" +"gramene.gene","gramene.gene","Gramene genes","Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.","DATABASE","","gramene.gene,GRAMENE.GENE","None","None" +"gramene.taxonomy","gramene.taxonomy","Gramene Taxonomy","Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.","DATABASE","","gramene.taxonomy,GRAMENE.TAXONOMY","None","None" +"gramene.qtl","gramene.qtl","Gramene QTL","Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.","DATABASE","","gramene.qtl,GRAMENE.QTL","None","None" +"sgn","sgn","Sol Genomics Network","The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.","DATABASE","","sgn,SGN","None","None" +"Xenbase","xenbase","Xenbase","Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.","DATABASE","","xenbase,XENBASE,Xenbase","None","None" +"BioPortal","bioportal","BioPortal","BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.","DATABASE","","bioportal,BIOPORTAL,BioPortal","None","None" +"miriam.resource","miriam.resource","MIRIAM Registry resource","MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.","DATABASE","","miriam.resource,MIRIAM.RESOURCE","None","None" +"pmdb","pmdb","Protein Model Database","The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.","DATABASE","","pmdb,PMDB","None","None" +"2d-page.protein","2d-page.protein","2D-PAGE protein","2DBase of Escherichia coli stores 2D polyacrylamide gel electrophoresis and mass spectrometry proteome data for E. coli. This collection references a subset of Uniprot, and contains general information about the protein record.","DATABASE","","2d-page.protein,2D-PAGE.PROTEIN","None","None" +"AGD","agd","AGD","AGD 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from the fungi Ashbya gossypii and Saccharomyces cerevisiae.","DATABASE","","agd,AGD","None","None" +"ArachnoServer","arachnoserver","ArachnoServer","ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.","DATABASE","","arachnoserver,ARACHNOSERVER,ArachnoServer","None","None" +"BioCyc","biocyc","BioCyc","BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.","DATABASE","","biocyc,BIOCYC,BioCyc","None","None" +"CAZy","cazy","CAZy","The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.","DATABASE","","cazy,CAZY,CAZy","None","None" +"GOA","goa","GOA","The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.","DATABASE","","goa,GOA","None","None" +"PaleoDB","paleodb","PaleoDB","The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.","DATABASE","","paleodb,PALEODB,PaleoDB","None","None" +"Compulyeast","compulyeast","Compulyeast","Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.","DATABASE","","compulyeast,COMPULYEAST,Compulyeast","None","None" +"DisProt","disprot","DisProt","The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.","DATABASE","","disprot,DISPROT,DisProt","None","None" +"EchoBASE","echobase","EchoBASE","EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.","DATABASE","","echobase,ECHOBASE,EchoBASE","None","None" +"eggNOG","eggnog","eggNOG","eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).","DATABASE","","eggnog,EGGNOG,eggNOG","None","None" +"ensembl.bacteria","ensembl.bacteria","Ensembl Bacteria","Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.","DATABASE","","ensembl.bacteria,ENSEMBL.BACTERIA","None","None" +"ensembl.protist","ensembl.protist","Ensembl Protists","Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.","DATABASE","","ensembl.protist,ENSEMBL.PROTIST","None","None" +"ensembl.metazoa","ensembl.metazoa","Ensembl Metazoa","Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.","DATABASE","","ensembl.metazoa,ENSEMBL.METAZOA","None","None" +"ensembl.plant","ensembl.plant","Ensembl Plants","Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.","DATABASE","","ensembl.plant,ENSEMBL.PLANT","None","None" +"ensembl.fungi","ensembl.fungi","Ensembl Fungi","Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.","DATABASE","","ensembl.fungi,ENSEMBL.FUNGI","None","None" +"HCVDB","hcvdb","HCVDB","the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.","DATABASE","","hcvdb,HCVDB","None","None" +"Genatlas","genatlas","Genatlas","GenAtlas is a database containing information on human genes, markers and phenotypes.","DATABASE","","genatlas,GENATLAS,Genatlas","None","None" +"cath.superfamily","cath.superfamily","CATH superfamily","The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.","DATABASE","","cath.superfamily,CATH.SUPERFAMILY","None","None" +"cath.domain","cath.domain","CATH domain","The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.","DATABASE","","cath.domain,CATH.DOMAIN","None","None" +"GeneFarm","genefarm","GeneFarm","GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.","DATABASE","","genefarm,GENEFARM,GeneFarm","None","None" +"GPCRDB","gpcrdb","GPCRDB","The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.","DATABASE","","gpcrdb,GPCRDB","None","None" +"HOGENOM","hogenom","HOGENOM","HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.","DATABASE","","hogenom,HOGENOM","None","None" +"GeneTree","genetree","GeneTree","Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.","DATABASE","","genetree,GENETREE,GeneTree","None","None" +"HSSP","hssp","HSSP","HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.","DATABASE","","hssp,HSSP","None","None" +"myco.tuber","myco.tuber","MycoBrowser tuberculosis","Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.","DATABASE","","myco.tuber,MYCO.TUBER","None","None" +"myco.lepra","myco.lepra","MycoBrowser leprae","Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.","DATABASE","","myco.lepra,MYCO.LEPRA","None","None" +"myco.marinum","myco.marinum","MycoBrowser marinum","Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.","DATABASE","","myco.marinum,MYCO.MARINUM","None","None" +"myco.smeg","myco.smeg","MycoBrowser smegmatis","Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.","DATABASE","","myco.smeg,MYCO.SMEG","None","None" +"OrthoDB","orthodb","OrthoDB","OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups","DATABASE","","orthodb,ORTHODB,OrthoDB","None","None" +"Peroxibase","peroxibase","Peroxibase","Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.","DATABASE","","peroxibase,PEROXIBASE,Peroxibase","None","None" +"PhylomeDB","phylomedb","PhylomeDB","PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.","DATABASE","","phylomedb,PHYLOMEDB,PhylomeDB","None","None" +"SubstrateDB","pmap.substratedb","SubstrateDB","The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.","DATABASE","","pmap.substratedb,PMAP.SUBSTRATEDB,SubstrateDB,substratedb,SUBSTRATEDB","None","None" +"CutDB","pmap.cutdb","CutDB","The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).","DATABASE","","pmap.cutdb,PMAP.CUTDB,CutDB,cutdb,CUTDB","None","None" +"ProtClustDB","protclustdb","ProtClustDB","ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.","DATABASE","","protclustdb,PROTCLUSTDB,ProtClustDB","None","None" +"PMP","pmp","PMP","The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt ids.","DATABASE","","pmp,PMP","None","None" +"protonet.proteincard","protonet.proteincard","ProtoNet ProteinCard","ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.","DATABASE","","protonet.proteincard,PROTONET.PROTEINCARD","None","None" +"protonet.cluster","protonet.cluster","ProtoNet Cluster","ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.","DATABASE","","protonet.cluster,PROTONET.CLUSTER","None","None" +"REBASE","rebase","REBASE","REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.","DATABASE","","rebase,REBASE","None","None" +"SWISS-MODEL","swiss-model","SWISS-MODEL","The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT.","DATABASE","","swiss-model,SWISS-MODEL","None","None" +"VectorBase","vectorbase","VectorBase","VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.","DATABASE","","vectorbase,VECTORBASE,VectorBase","None","None" +"mirbase.mature","mirbase.mature","miRBase mature sequence","The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.","DATABASE","","mirbase.mature,MIRBASE.MATURE","None","None" +"nextProt","nextprot","nextProt","neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.","DATABASE","","nextprot,NEXTPROT,nextProt","None","None" +"CAS","cas","CAS","CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.","DATABASE","","cas,CAS","None","None" +"kegg.genome","kegg.genome","KEGG Genome","KEGG Genome is a collection of organisms whose genomes have been completely sequenced.","DATABASE","","kegg.genome,KEGG.GENOME","None","None" +"kegg.metagenome","kegg.metagenome","KEGG Metagenome","The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.","DATABASE","","kegg.metagenome,KEGG.METAGENOME","None","None" +"NARCIS","narcis","NARCIS","NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.","DATABASE","","narcis,NARCIS","None","None" +"jcsd","jcsd","Japan Chemical Substance Dictionary","The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).","DATABASE","","jcsd,JCSD","None","None" +"insdc.sra","insdc.sra","Sequence Read Archive","The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.","DATABASE","","insdc.sra,INSDC.SRA","None","None" +"ScerTF","scretf","ScerTF","ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.","DATABASE","","scretf,SCRETF,ScerTF,scertf,SCERTF","None","None" +"pharmgkb.gene","pharmgkb.gene","PharmGKB Gene","The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.","DATABASE","","pharmgkb.gene,PHARMGKB.GENE","None","None" +"miRNEST","mirnest","miRNEST","miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.","DATABASE","","mirnest,MIRNEST,miRNEST","None","None" +"NAPP","napp","NAPP","NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.","DATABASE","","napp,NAPP","None","None" +"noncodev3","noncodev3","NONCODE v3","NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.","DATABASE","","noncodev3,NONCODEV3","None","None" +"VIRsiRNA","virsirna","VIRsiRNA","The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.","DATABASE","","virsirna,VIRSIRNA,VIRsiRNA","None","None" +"ELM","elm","ELM","Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.","DATABASE","","elm,ELM","None","None" +"MimoDB","mimodb","MimoDB","MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.","DATABASE","","mimodb,MIMODB,MimoDB","None","None" +"SitEx","sitex","SitEx","SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.","DATABASE","","sitex,SITEX,SitEx","None","None" +"BYKdb","bykdb","BYKdb","The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.","DATABASE","","bykdb,BYKDB,BYKdb","None","None" +"Conoserver","conoserver","Conoserver","ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.","DATABASE","","conoserver,CONOSERVER,Conoserver","None","None" +"TopFind","topfind","TopFind","TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.","DATABASE","","topfind,TOPFIND,TopFind","None","None" +"MIPModDB","mipmod","MIPModDB","MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.","DATABASE","","mipmod,MIPMOD,MIPModDB,mipmoddb,MIPMODDB","None","None" +"cellimage","cellimage","Cell Image Library","The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.","DATABASE","","cellimage,CELLIMAGE","None","None" +"combine.specifications","combine.specifications","COMBINE specifications","The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.","DATABASE","","combine.specifications,COMBINE.SPECIFICATIONS","None","None" +"zfin.phenotype","zfin.phenotype","ZFIN Phenotype","ZFIN serves as the zebrafish model organism database. This collection references the phenotypes observed for any given genotype.","DATABASE","","zfin.phenotype,ZFIN.PHENOTYPE","None","None" +"zfin.expression","zfin.expression","ZFIN Expression","ZFIN serves as the zebrafish model organism database. This collection references the set of expressed genes for any given genotype.","DATABASE","","zfin.expression,ZFIN.EXPRESSION","None","None" +"CABRI","cabri","CABRI","CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.","DATABASE","","cabri,CABRI","None","None" +"CYGD","cygd","CYGD","The MIPS Comprehensive Yeast Genome Database (CYGD) provides information on the molecular structure and functional network of the entirely sequenced the budding yeast, Saccharomyces cerevisiae, as well as on related yeasts which are used for comparative analysis.","DATABASE","","cygd,CYGD","None","None" +"HUGE","huge","HUGE","The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.","DATABASE","","huge,HUGE","None","None" +"BindingDB","bindingDB","BindingDB","BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.","DATABASE","","bindingDB,bindingdb,BINDINGDB,BindingDB","None","None" +"STRING","string","STRING","STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. +The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.","DATABASE","","string,STRING","None","None" +"STITCH","stitch","STITCH","STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.","DATABASE","","stitch,STITCH","None","None" +"atcvet","atcvet","Anatomical Therapeutic Chemical Vetinary","The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.","DATABASE","","atcvet,ATCVET","None","None" +"Phenol-Explorer","phenolexplorer","Phenol-Explorer","Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.","DATABASE","","phenolexplorer,PHENOLEXPLORER,Phenol-Explorer,phenol-explorer,PHENOL-EXPLORER","None","None" +"SNOMEDCT","snomedct","SNOMED CT","SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.","DATABASE","","snomedct,SNOMEDCT,SNOMED,snomed,SNOMED-CT,snomed-ct,SNOMED-CT-US,snomed-ct-us,SNOMED-CT_US,snomed-ct_us,SNOMEDCT_US,snomedct_us,SNOMEDCT_US_2015_03_01,snomedct_us_2015_03_01,SNOMEDCT_US_2016_03_01,snomedct_us_2016_03_01,SNOMEDCT_2010_1_31,snomedct_2010_1_31","http://www.snomed.org/snomed-ct/get-snomed-ct","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO). All rights reserved. SNOMED CT®, was originally created by The College of American Pathologists. \"SNOMED\" and \"SNOMED CT\" are registered trademarks of the IHTSDO." +"mesh.2012","mesh.2012","MeSH 2012","MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.","DATABASE","","mesh.2012,MESH.2012","None","None" +"KNApSAcK","knapsack","KnapSack","Knapsack provides information on metabolites and the taxonomic class with which they are associated.","DATABASE","","knapsack,KNAPSACK,KnapSack,KNApSAcK","None","None" +"cdpd","cdpd","Canadian Drug Product Database","The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).","DATABASE","","cdpd,CDPD","None","None" +"MassBank","massbank","MassBank","MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).","DATABASE","","massbank,MASSBANK,MassBank","None","None" +"gmd","gmd","Golm Metabolome Database","Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.","DATABASE","","gmd,GMD","None","None" +"HomoloGene","homologene","HomoloGene","HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.","DATABASE","","homologene,HOMOLOGENE,HomoloGene","None","None" +"umbbd.compound","umbbd.compound","UM-BBD Compound","The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.","DATABASE","","umbbd.compound,UMBBD.COMPOUND","None","None" +"ABS","abs","ABS","The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.","DATABASE","","abs,ABS","None","None" +"APD","apd","APD","The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.","DATABASE","","apd,APD","None","None" +"ChemDB","chemdb","ChemDB","ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.","DATABASE","","chemdb,CHEMDB,ChemDB","None","None" +"DPV","dpv","DPV","Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.","DATABASE","","dpv,DPV","None","None" +"iuphar.receptor","iuphar.receptor","IUPHAR receptor","The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.","DATABASE","","iuphar.receptor,IUPHAR.RECEPTOR","None","None" +"aceview.worm","aceview.worm","Aceview Worm","AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.","DATABASE","","aceview.worm,ACEVIEW.WORM","None","None" +"ASAP","asap","ASAP","ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.","DATABASE","","asap,ASAP","None","None" +"ATCC","atcc","ATCC","The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.","DATABASE","","atcc,ATCC","None","None" +"bdgp.est","bdgp.est","BDGP EST","The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).","DATABASE","","bdgp.est,BDGP.EST","None","None" +"dictybase.gene","dictybase.gene","Dictybase Gene","The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.","DATABASE","","dictybase.gene,DICTYBASE.GENE","None","None" +"imgt.ligm","imgt.ligm","IMGT LIGM","IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.","DATABASE","","imgt.ligm,IMGT.LIGM","None","None" +"Worfdb","worfdb","Worfdb","WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).","DATABASE","","worfdb,WORFDB,Worfdb","None","None" +"NEXTDB","nextdb","NEXTDB","NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.","DATABASE","","nextdb,NEXTDB","None","None" +"pgn","pgn","Plant Genome Network","The Plant Genome Network (PGN) is a resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. All data are directly derived from chromatograms with original and intermediate data stored in the database.","DATABASE","","pgn,PGN","None","None" +"SoyBase","soybase","SoyBase","SoyBase is a repository for curated genetics, genomics and related data resources for soybean.","DATABASE","","soybase,SOYBASE,SoyBase","None","None" +"HAMAP","hamap","HAMAP","HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.","DATABASE","","hamap,HAMAP","None","None" +"Rouge","rouge","Rouge","The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.","DATABASE","","rouge,ROUGE,Rouge","None","None" +"arrayexpress.platform","arrayexpress.platform","ArrayExpress Platform","ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.","DATABASE","","arrayexpress.platform,ARRAYEXPRESS.PLATFORM","None","None" +"cgsc","cgsc","CGSC Strain","The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.","DATABASE","","cgsc,CGSC","None","None" +"COGs","cogs","COGs","Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.","DATABASE","","cogs,COGS,COGs","None","None" +"dragondb.dna","dragondb.dna","DragonDB DNA","DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.","DATABASE","","dragondb.dna,DRAGONDB.DNA","None","None" +"dragondb.protein","dragondb.protein","DragonDB Protein","DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.","DATABASE","","dragondb.protein,DRAGONDB.PROTEIN","None","None" +"dragondb.locus","dragondb.locus","DragonDB Locus","DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.","DATABASE","","dragondb.locus,DRAGONDB.LOCUS","None","None" +"dragondb.allele","dragondb.allele","DragonDB Allele","DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.","DATABASE","","dragondb.allele,DRAGONDB.ALLELE","None","None" +"ISSN","issn","ISSN","The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.","DATABASE","","issn,ISSN","None","None" +"merops.family","merops.family","MEROPS Family","The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.","DATABASE","","merops.family,MEROPS.FAMILY","None","None" +"mo","mo","MGED Ontology","The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.","DATABASE","","mo,MO","None","None" +"nasc","nasc","NASC code","The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.","DATABASE","","nasc,NASC","None","None" +"NIAEST","niaest","NIAEST","A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.","DATABASE","","niaest,NIAEST","None","None" +"pazar","pazar","Pazar Transcription Factor","The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.","DATABASE","","pazar,PAZAR","None","None" +"rnamods","rnamods","RNA Modification Database","The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.","DATABASE","","rnamods,RNAMODS","None","None" +"sciencesignaling.pic","sciencesignaling.pic","Science Signaling Pathway-Independent Component","The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway independent component information.","DATABASE","","sciencesignaling.pic,SCIENCESIGNALING.PIC","None","None" +"sciencesignaling.pdc","sciencesignaling.pdc","Science Signaling Pathway-Dependent Component","The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway-dependent component information.","DATABASE","","sciencesignaling.pdc,SCIENCESIGNALING.PDC","None","None" +"sciencesignaling.path","sciencesignaling.path","Science Signaling Pathway","The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway information.","DATABASE","","sciencesignaling.path,SCIENCESIGNALING.PATH","None","None" +"TreeBASE","treebase","TreeBASE","TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.","DATABASE","","treebase,TREEBASE,TreeBASE","None","None" +"tgd","tgd","Tetrahymena Genome Database","The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.","DATABASE","","tgd,TGD","None","None" +"cmr.gene","cmr.gene","CMR Gene","The Comprehensive Microbial Resource (CMR) contains annotation for all complete microbial genomes and allows for a wide variety of data retrievals. This collection refers to the Gene Page which provides information pertaining to a specific gene such as the Locus Name, Gene Symbol, Coordinates, DNA Molecule Name, and Gene Length.","DATABASE","","cmr.gene,CMR.GENE","None","None" +"TIGRFAMS","tigrfam","TIGRFAMS","TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.","DATABASE","","tigrfam,TIGRFAM,TIGRFAMS,tigrfams","None","None" +"atfdb.family","atfdb.family","Animal TFDB Family","The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.","DATABASE","","atfdb.family,ATFDB.FAMILY","None","None" +"iuphar.family","iuphar.family","IUPHAR family","The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.","DATABASE","","iuphar.family,IUPHAR.FAMILY","None","None" +"dbg2introns","dbg2introns","DBG2 Introns","The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.","DATABASE","","dbg2introns,DBG2INTRONS","None","None" +"sdbs","sdbs","Spectral Database for Organic Compounds","The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.","DATABASE","","sdbs,SDBS","None","None" +"Vbase2","vbase2","Vbase2","The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.","DATABASE","","vbase2,VBASE2,Vbase2","None","None" +"spike.map","spike.map","SPIKE Map","SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.","DATABASE","","spike.map,SPIKE.MAP","None","None" +"METLIN","metlin","METLIN","The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.","DATABASE","","metlin,METLIN","None","None" +"GeneCards","genecards","GeneCards","The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.","DATABASE","","genecards,GENECARDS,GeneCards","None","None" +"MMRRC","mmrrc","MMRRC","The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.","DATABASE","","mmrrc,MMRRC","None","None" +"umbbd.reaction","umbbd.reaction","UM-BBD Reaction","The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.","DATABASE","","umbbd.reaction,UMBBD.REACTION","None","None" +"umbbd.enzyme","umbbd.enzyme","UM-BBD Enzyme","The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.","DATABASE","","umbbd.enzyme,UMBBD.ENZYME","None","None" +"umbbd.pathway","umbbd.pathway","UM-BBD Pathway","The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.","DATABASE","","umbbd.pathway,UMBBD.PATHWAY","None","None" +"umbbd.rule","umbbd.rule","UM-BBD Biotransformation Rule","The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.","DATABASE","","umbbd.rule,UMBBD.RULE","None","None" +"mirEX","mirex","mirEX","mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.","DATABASE","","mirex,MIREX,mirEX","None","None" +"dictybase.est","dictybase.est","Dictybase EST","The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.","DATABASE","","dictybase.est,DICTYBASE.EST","None","None" +"imgt.hla","imgt.hla","IMGT HLA","IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.","DATABASE","","imgt.hla,IMGT.HLA","None","None" +"Flystock","flystock","Flystock","The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.","DATABASE","","flystock,FLYSTOCK,Flystock","None","None" +"OPM","opm","OPM","The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.","DATABASE","","opm,OPM","None","None" +"Allergome","allergome","Allergome","Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.","DATABASE","","allergome,ALLERGOME,Allergome","None","None" +"PomBase","pombase","PomBase","PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.","DATABASE","","pombase,POMBASE,PomBase","None","None" +"HPA","hpa","HPA","The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene ids.","DATABASE","","hpa,HPA","None","None" +"jaxmice","jaxmice","JAX Mice","JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.","DATABASE","","jaxmice,JAXMICE","None","None" +"ubio.namebank","ubio.namebank","uBio NameBank","NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.","DATABASE","","ubio.namebank,UBIO.NAMEBANK","None","None" +"YeTFasCo","yetfasco","YeTFasCo","The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.","DATABASE","","yetfasco,YETFASCO,YeTFasCo","None","None" +"TarBase","tarbase","TarBase","TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.","DATABASE","","tarbase,TARBASE,TarBase","None","None" +"CharProt","charprot","CharProt","CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.","DATABASE","","charprot,CHARPROT,CharProt","None","None" +"oma.protein","oma.protein","OMA Protein","OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.","DATABASE","","oma.protein,OMA.PROTEIN","None","None" +"oma.grp","oma.grp","OMA Group","OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.","DATABASE","","oma.grp,OMA.GRP","None","None" +"ncbiprotein","ncbiprotein","NCBI Protein","The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.","DATABASE","","ncbiprotein,NCBIPROTEIN","None","None" +"GenPept","genpept","GenPept","The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.","DATABASE","","genpept,GENPEPT,GenPept","None","None" +"UniGene","unigene","UniGene","A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.","DATABASE","","unigene,UNIGENE,UniGene","None","None" +"bitterdb.rec","bitterdb.rec","BitterDB Receptor","BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.","DATABASE","","bitterdb.rec,BITTERDB.REC","None","None" +"bitterdb.cpd","bitterdb.cpd","BitterDB Compound","BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.","DATABASE","","bitterdb.cpd,BITTERDB.CPD","None","None" +"BioProject","bioproject","BioProject","BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.","DATABASE","","bioproject,BIOPROJECT,BioProject","None","None" +"BioSample","biosample","BioSample","The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.","DATABASE","","biosample,BIOSAMPLE,BioSample","None","None" +"PiroplasmaDB","piroplasma","PiroplasmaDB","PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","DATABASE","","piroplasma,PIROPLASMA,PiroplasmaDB,piroplasmadb,PIROPLASMADB","None","None" +"Unite","unite","Unite","UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.","DATABASE","","unite,UNITE,Unite","None","None" +"NCIm","ncim","NCIm","NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.","DATABASE","","ncim,NCIM,NCIm","None","None" +"ProGlycProt","proglyc","ProGlycProt","ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.","DATABASE","","proglyc,PROGLYC,ProGlycProt,proglycprot,PROGLYCPROT","None","None" +"PolBase","polbase","PolBase","Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.","DATABASE","","polbase,POLBASE,PolBase","None","None" +"NucleaRDB","nuclearbd","NucleaRDB","NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.","DATABASE","","nuclearbd,NUCLEARBD,NucleaRDB,nucleardb,NUCLEARDB","None","None" +"SUPFAM","supfam","SUPFAM","SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.","DATABASE","","supfam,SUPFAM","None","None" +"ricegap","ricegap","Rice Genome Annotation Project","The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.","DATABASE","","ricegap,RICEGAP","None","None" +"PINA","pina","PINA","Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.","DATABASE","","pina,PINA","None","None" +"tissuelist","tissuelist","Tissue List","The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.","DATABASE","","tissuelist,TISSUELIST","None","None" +"bacmap.biog","bacmap.biog","BacMap Biography","BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.","DATABASE","","bacmap.biog,BACMAP.BIOG","None","None" +"hgnc.symbol","hgnc.symbol","HGNC Symbol","The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.","DATABASE","","hgnc.symbol,HGNC.SYMBOL","None","None" +"panther.pathway","panther.pathway","PANTHER Pathway","The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.","DATABASE","","panther.pathway,PANTHER.PATHWAY","None","None" +"BioSharing","biosharing","BioSharing","The web-based BioSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.","DATABASE","","biosharing,BIOSHARING,BioSharing","None","None" +"FungiDB","fungidb","FungiDB","FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.","DATABASE","","fungidb,FUNGIDB,FungiDB","None","None" +"DARC","darc","DARC","DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.","DATABASE","","darc,DARC","None","None" +"DRSC","drsc","DRSC","The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, ids, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.","DATABASE","","drsc,DRSC","None","None" +"oridb.schizo","oridb.schizo","OriDB Schizosaccharomyces","OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.","DATABASE","","oridb.schizo,ORIDB.SCHIZO","None","None" +"oridb.sacch","oridb.sacch","OriDB Saccharomyces","OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.","DATABASE","","oridb.sacch,ORIDB.SACCH","None","None" +"PSCDB","pscdb","PSCDB","The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.","DATABASE","","pscdb,PSCDB","None","None" +"SCOP","scop","SCOP","The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes.","DATABASE","","scop,SCOP","None","None" +"ENA","ena.embl","ENA","The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank ids.","DATABASE","","ena.embl,ENA.EMBL,ENA,ena","None","None" +"DOMMINO","dommino","DOMMINO","DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.","DATABASE","","dommino,DOMMINO","None","None" +"panther.node","panther.node","PANTHER Node","The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.","DATABASE","","panther.node,PANTHER.NODE","None","None" +"ccds","ccds","Consensus CDS","The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.","DATABASE","","ccds,CCDS","None","None" +"lrg","lrg","Locus Reference Genomic","Locus Reference Genomic (LRG) provides ids to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI).","DATABASE","","lrg,LRG","None","None" +"HPRD","hprd","HPRD","The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.","DATABASE","","hprd,HPRD","None","None" +"gxa.gene","gxa.gene","GXA Gene","The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.","DATABASE","","gxa.gene,GXA.GENE","None","None" +"gxa.expt","gxa.expt","GXA Expt","The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.","DATABASE","","gxa.expt,GXA.EXPT","None","None" +"MetaboLights","metabolights","MetaboLights","MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.","DATABASE","","metabolights,METABOLIGHTS,MetaboLights","None","None" +"nbn","nbn","National Bibliography Number","The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.","DATABASE","","nbn,NBN","None","None" +"ORCID","orcid","ORCID","ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique ids for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.","DATABASE","","orcid,ORCID","None","None" +"InChI","inchi","InChI","The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.","DATABASE","","inchi,INCHI,InChI","None","None" +"wikipedia.en","wikipedia.en","Wikipedia (En)","Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.","DATABASE","","wikipedia.en,WIKIPEDIA.EN","None","None" +"phosphopoint.kinase","phosphopoint.kinase","PhosphoPoint Kinase","PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.","DATABASE","","phosphopoint.kinase,PHOSPHOPOINT.KINASE","None","None" +"phosphopoint.protein","phosphopoint.protein","PhosphoPoint Phosphoprotein","PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.","DATABASE","","phosphopoint.protein,PHOSPHOPOINT.PROTEIN","None","None" +"InChIKey","inchikey","InChIKey","The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.","DATABASE","","inchikey,INCHIKEY,InChIKey","None","None" +"uniprot.isoform","uniprot.isoform","UniProt Isoform","The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.","DATABASE","","uniprot.isoform,UNIPROT.ISOFORM","None","None" +"kegg.environ","kegg.environ","KEGG Environ","KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.","DATABASE","","kegg.environ,KEGG.ENVIRON","None","None" +"CLDB","cldb","CLDB","The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.","DATABASE","","cldb,CLDB","None","None" +"HGMD","hgmd","HGMD","The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.","DATABASE","","hgmd,HGMD","None","None" +"aphidbase.transcript","aphidbase.transcript","AphidBase Transcript","AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.","DATABASE","","aphidbase.transcript,APHIDBASE.TRANSCRIPT","None","None" +"affy.probeset","affy.probeset","Affymetrix Probeset","An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.","DATABASE","","affy.probeset,AFFY.PROBESET","None","None" +"TreeFam","treefam","TreeFam","TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.","DATABASE","","treefam,TREEFAM,TreeFam","None","None" +"CAPS-DB","caps","CAPS-DB","CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.","DATABASE","","caps,CAPS,CAPS-DB,caps-db","None","None" +"cubedb","cubedb","Cube db","Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.","DATABASE","","cubedb,CUBEDB","None","None" +"IDEAL","ideal","IDEAL","IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.","DATABASE","","ideal,IDEAL","None","None" +"STAP","stap","STAP","STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).","DATABASE","","stap,STAP","None","None" +"Pocketome","pocketome","Pocketome","Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.","DATABASE","","pocketome,POCKETOME,Pocketome","None","None" +"gold.genome","gold.genome","GOLD genome","The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.","DATABASE","","gold.genome,GOLD.GENOME","None","None" +"gold.meta","gold.meta","GOLD metadata","The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.","DATABASE","","gold.meta,GOLD.META","None","None" +"bugbase.protocol","bugbase.protocol","BugBase Protocol","BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.","DATABASE","","bugbase.protocol,BUGBASE.PROTOCOL","None","None" +"bugbase.expt","bugbase.expt","BugBase Expt","BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.","DATABASE","","bugbase.expt,BUGBASE.EXPT","None","None" +"tol","tol","Tree of Life","The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). + +Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.","DATABASE","","tol,TOL","None","None" +"vipr","vipr","ViPR Strain","The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.","DATABASE","","vipr,VIPR","None","None" +"EPD","epd","EPD","The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.","DATABASE","","epd,EPD","None","None" +"RFAM","rfam","RFAM","The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.","DATABASE","","rfam,RFAM","None","None" +"fbol","fbol","Fungal Barcode","DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.","DATABASE","","fbol,FBOL","None","None" +"AFTOL","aftol.taxonomy","AFTOL","The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.","DATABASE","","aftol.taxonomy,AFTOL.TAXONOMY,AFTOL,aftol","None","None" +"aspgd.locus","aspgd.locus","AspGD Locus","The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.","DATABASE","","aspgd.locus,ASPGD.LOCUS","None","None" +"aspgd.protein","aspgd.protein","AspGD Protein","The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.","DATABASE","","aspgd.protein,ASPGD.PROTEIN","None","None" +"drugbank.target","drugbank.target","DrugBank Target v3","The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 3 of the database.","DATABASE","","drugbank.target,DRUGBANK.TARGET","None","None" +"AutDB","autdb","AutDB","AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.","DATABASE","","autdb,AUTDB,AutDB","None","None" +"bacmap.map","bacmap.map","BacMap Map","BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.","DATABASE","","bacmap.map,BACMAP.MAP","None","None" +"bgee.family","bgee.family","Bgee family","Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.","DATABASE","","bgee.family,BGEE.FAMILY","None","None" +"bgee.gene","bgee.gene","Bgee gene","Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression within anatomical structures within a species.","DATABASE","","bgee.gene,BGEE.GENE","None","None" +"bgee.stage","bgee.stage","Bgee stage","Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.","DATABASE","","bgee.stage,BGEE.STAGE","None","None" +"bgee.organ","bgee.organ","Bgee organ","Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.","DATABASE","","bgee.organ,BGEE.ORGAN","None","None" +"biocarta.pathway","biocarta.pathway","BioCarta Pathway","BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.","DATABASE","","biocarta.pathway,BIOCARTA.PATHWAY","None","None" +"panther.pthcmp","panther.pthcmp","PANTHER Pathway Component","The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway +components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.","DATABASE","","panther.pthcmp,PANTHER.PTHCMP","None","None" +"gmd.profile","gmd.profile","Golm Metabolome Database Profile","Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.","DATABASE","","gmd.profile,GMD.PROFILE","None","None" +"gmd.gcms","gmd.gcms","Golm Metabolome Database GC-MS spectra","Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.","DATABASE","","gmd.gcms,GMD.GCMS","None","None" +"gmd.ref","gmd.ref","Golm Metabolome Database Reference Substance","Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.","DATABASE","","gmd.ref,GMD.REF","None","None" +"gmd.analyte","gmd.analyte","Golm Metabolome Database Analyte","Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.","DATABASE","","gmd.analyte,GMD.ANALYTE","None","None" +"intact.molecule","intact.molecule","IntAct Molecule","IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.","DATABASE","","intact.molecule,INTACT.MOLECULE","None","None" +"DEPOD","depod","DEPOD","The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.","DATABASE","","depod,DEPOD","None","None" +"cst","cst","Cell Signaling Technology Pathways","Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.","DATABASE","","cst,CST","None","None" +"cst.ab","cst.ab","Cell Signaling Technology Antibody","Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.","DATABASE","","cst.ab,CST.AB","None","None" +"ndc","ndc","National Drug Code","The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.","DATABASE","","ndc,NDC","None","None" +"phytozome.locus","phytozome.locus","Phytozome Locus","Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.","DATABASE","","phytozome.locus,PHYTOZOME.LOCUS","None","None" +"SubtiList","subtilist","SubtiList","SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. +SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.","DATABASE","","subtilist,SUBTILIST,SubtiList","None","None" +"DailyMed","dailymed","DailyMed","DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.","DATABASE","","dailymed,DAILYMED,DailyMed","None","None" +"sider.drug","sider.drug","SIDER Drug","SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.","DATABASE","","sider.drug,SIDER.DRUG","None","None" +"sider.effect","sider.effect","SIDER Side Effect","SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.","DATABASE","","sider.effect,SIDER.EFFECT","None","None" +"WikiGenes","wikigenes","WikiGenes","WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.","DATABASE","","wikigenes,WIKIGENES,WikiGenes","None","None" +"broad","broad","Broad Fungal Genome Initiative","Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.","DATABASE","","broad,BROAD","None","None" +"coriell","coriell","Coriell Cell Repositories","The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.","DATABASE","","coriell,CORIELL","None","None" +"CORUM","corum","CORUM","The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.","DATABASE","","corum,CORUM","None","None" +"cogs.function","cogs.function","COGs Function","Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. This collection references functional groups.","DATABASE","","cogs.function,COGS.FUNCTION","None","None" +"EcoliWiki","ecoliwiki","EcoliWiki","EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.","DATABASE","","ecoliwiki,ECOLIWIKI,EcoliWiki","None","None" +"genprop","genprop","Genome Properties","The Genome Properties system captures key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties, expressed using controlled vocabulary, reflect gene content, phenotype, phylogeny and computational analyses. Additional properties are derived from curation, published reports and other forms of evidence.","DATABASE","","genprop,GENPROP","None","None" +"JSTOR","jstor","JSTOR","JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.","DATABASE","","jstor,JSTOR","None","None" +"VBRC","vbrc","VBRC","The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.","DATABASE","","vbrc,VBRC","None","None" +"ViralZone","viralzone","ViralZone","ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.","DATABASE","","viralzone,VIRALZONE,ViralZone","None","None" +"go.ref","go.ref","Gene Ontology Reference","The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.","DATABASE","","go.ref,GO.REF","None","None" +"rgd.qtl","rgd.qtl","Rat Genome Database qTL","Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.","DATABASE","","rgd.qtl,RGD.QTL","None","None" +"rgd.strain","rgd.strain","Rat Genome Database strain","Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.","DATABASE","","rgd.strain,RGD.STRAIN","None","None" +"DOOR","door","DOOR","DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.","DATABASE","","door,DOOR","None","None" +"degradome","degradome","Degradome Database","The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.","DATABASE","","degradome,DEGRADOME","None","None" +"DBD","dbd","DBD","The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.","DATABASE","","dbd,DBD","None","None" +"DATF","datf","DATF","DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.","DATABASE","","datf,DATF","None","None" +"iuphar.ligand","iuphar.ligand","IUPHAR ligand","The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.","DATABASE","","iuphar.ligand,IUPHAR.LIGAND","None","None" +"Molbase","molbase","Molbase","Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.","DATABASE","","molbase,MOLBASE,Molbase","None","None" +"yrcpdr","yrcpdr","YRC PDR","The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.","DATABASE","","yrcpdr,YRCPDR","None","None" +"yid","yid","Yeast Intron Database v3","The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].","DATABASE","","yid,YID","None","None" +"funcbase.fly","funcbase.fly","FuncBase Fly","Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.","DATABASE","","funcbase.fly,FUNCBASE.FLY","None","None" +"funcbase.human","funcbase.human","FuncBase Human","Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.","DATABASE","","funcbase.human,FUNCBASE.HUMAN","None","None" +"funcbase.mouse","funcbase.mouse","FuncBase Mouse","Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.","DATABASE","","funcbase.mouse,FUNCBASE.MOUSE","None","None" +"funcbase.yeast","funcbase.yeast","FuncBase Yeast","Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.","DATABASE","","funcbase.yeast,FUNCBASE.YEAST","None","None" +"YDPM","ydpm","YDPM","The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.","DATABASE","","ydpm,YDPM","None","None" +"wormbase.rnai","wormbase.rnai","WormBase RNAi","WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.","DATABASE","","wormbase.rnai,WORMBASE.RNAI","None","None" +"FunCat","funcat","FunCat","The Functional Catalogue (FunCat) is a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. It has been applied for the manual annotation of prokaryotes, fungi, plants and animals.","DATABASE","","funcat,FUNCAT,FunCat","None","None" +"PASS2","pass2","PASS2","The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.","DATABASE","","pass2,PASS2","None","None" +"iceberg.element","iceberg.element","ICEberg element","ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.","DATABASE","","iceberg.element,ICEBERG.ELEMENT","None","None" +"iceberg.family","iceberg.family","ICEberg family","ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.","DATABASE","","iceberg.family,ICEBERG.FAMILY","None","None" +"vfdb.genus","vfdb.genus","VFDB Genus","VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.","DATABASE","","vfdb.genus,VFDB.GENUS","None","None" +"vfdb.gene","vfdb.gene","VFDB Gene","VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.","DATABASE","","vfdb.gene,VFDB.GENE","None","None" +"mesh.2013","mesh.2013","MeSH 2013","MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.","DATABASE","","mesh.2013,MESH.2013","None","None" +"kegg.module","kegg.module","KEGG Module","KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.","DATABASE","","kegg.module,KEGG.MODULE","None","None" +"kegg.disease","kegg.disease","KEGG Disease","The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.","DATABASE","","kegg.disease,KEGG.DISEASE","None","None" +"MedlinePlus","medlineplus","MedlinePlus","MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.","DATABASE","","medlineplus,MEDLINEPLUS,MedlinePlus","None","None" +"LigandBox","ligandbox","LigandBox","LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.","DATABASE","","ligandbox,LIGANDBOX,LigandBox","None","None" +"GlycoEpitope","glycoepitope","GlycoEpitope","GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.","DATABASE","","glycoepitope,GLYCOEPITOPE,GlycoEpitope","None","None" +"JCGGDB","jcggdb","JCGGDB","JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.","DATABASE","","jcggdb,JCGGDB","None","None" +"noncodev4.gene","noncodev4.gene","NONCODE v4 Gene","NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.","DATABASE","","noncodev4.gene,NONCODEV4.GENE","None","None" +"noncodev4.rna","noncodev4.rna","NONCODE v4 Transcript","NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.","DATABASE","","noncodev4.rna,NONCODEV4.RNA","None","None" +"oryzabase.gene","oryzabase.gene","Oryzabase Gene","Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.","DATABASE","","oryzabase.gene,ORYZABASE.GENE","None","None" +"oryzabase.mutant","oryzabase.mutant","Oryzabase Mutant","Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.","DATABASE","","oryzabase.mutant,ORYZABASE.MUTANT","None","None" +"oryzabase.strain","oryzabase.strain","Oryzabase Strain","Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.","DATABASE","","oryzabase.strain,ORYZABASE.STRAIN","None","None" +"oryzabase.stage","oryzabase.stage","Oryzabase Stage","Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.","DATABASE","","oryzabase.stage,ORYZABASE.STAGE","None","None" +"otl","otl","Oryza Tag Line","Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.","DATABASE","","otl,OTL","None","None" +"genewiki","genewiki","Gene Wiki","The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene ids from NCBI.","DATABASE","","genewiki,GENEWIKI","None","None" +"paxdb.organism","paxdb.organism","PaxDb Organism","PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.","DATABASE","","paxdb.organism,PAXDB.ORGANISM","None","None" +"paxdb.protein","paxdb.protein","PaxDb Protein","PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.","DATABASE","","paxdb.protein,PAXDB.PROTEIN","None","None" +"pdb.ligand","pdb.ligand","Protein Data Bank Ligand","The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.","DATABASE","","pdb.ligand,PDB.LIGAND","None","None" +"merops.inhibitor","merops.inhibitor","MEROPS Inhibitor","The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.","DATABASE","","merops.inhibitor,MEROPS.INHIBITOR","None","None" +"adw","adw","Animal Diversity Web","Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.","DATABASE","","adw,ADW","None","None" +"glida.gpcr","glida.gpcr","GLIDA GPCR","The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.","DATABASE","","glida.gpcr,GLIDA.GPCR","None","None" +"glida.ligand","glida.ligand","GLIDA Ligand","The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.","DATABASE","","glida.ligand,GLIDA.LIGAND","None","None" +"GRSDB","grsdb","GRSDB","GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.","DATABASE","","grsdb,GRSDB","None","None" +"F-SNP","fsnp","F-SNP","The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.","DATABASE","","fsnp,FSNP,F-SNP,f-snp","None","None" +"hdr","hdr","Homeodomain Research","The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.","DATABASE","","hdr,HDR","None","None" +"NORINE","norine","NORINE","Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.","DATABASE","","norine,NORINE","None","None" +"ordb","ordb","Olfactory Receptor Database","The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).","DATABASE","","ordb,ORDB","None","None" +"odor","odor","Odor Molecules DataBase","OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors","DATABASE","","odor,ODOR","None","None" +"p3db.protein","p3db.protein","P3DB Protein","Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.","DATABASE","","p3db.protein,P3DB.PROTEIN","None","None" +"p3db.site","p3db.site","P3DB Site","Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.","DATABASE","","p3db.site,P3DB.SITE","None","None" +"TOPDB","topdb","TOPDB","The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.","DATABASE","","topdb,TOPDB","None","None" +"cattleqtldb","cattleqtldb","Animal Genome Cattle QTL","The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.","DATABASE","","cattleqtldb,CATTLEQTLDB","None","None" +"chickenqtldb","chickenqtldb","Animal Genome Chicken QTL","The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.","DATABASE","","chickenqtldb,CHICKENQTLDB","None","None" +"pigqtldb","pigqtldb","Animal Genome Pig QTL","The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.","DATABASE","","pigqtldb,PIGQTLDB","None","None" +"sheepqtldb","sheepqtldb","Animal Genome Sheep QTL","The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.","DATABASE","","sheepqtldb,SHEEPQTLDB","None","None" +"gramene.growthstage","gramene.growthstage","Gramene Growth Stage Ontology","Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.","DATABASE","","gramene.growthstage,GRAMENE.GROWTHSTAGE","None","None" +"ncbigi","ncbigi","NCBI GI","The NCBI GI (or \"gi\") identifier is the original form of identifier for sequence records processed by the NCBI. This 'GenInfo' identifier system was used to access GenBank and related databases, and was assigned to both protein and nucleotide sequences.","DATABASE","","ncbigi,NCBIGI","None","None" +"ebimetagenomics.samp","ebimetagenomics.samp","EBI Metagenomics Sample","The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.","DATABASE","","ebimetagenomics.samp,EBIMETAGENOMICS.SAMP","None","None" +"ega.study","ega.study","European Genome-phenome Archive Study","The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.","DATABASE","","ega.study,EGA.STUDY","None","None" +"ega.dataset","ega.dataset","European Genome-phenome Archive Dataset","The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.","DATABASE","","ega.dataset,EGA.DATASET","None","None" +"ProteomeXchange","proteomexchange","ProteomeXchange","The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.","DATABASE","","proteomexchange,PROTEOMEXCHANGE,ProteomeXchange","None","None" +"biomodels.vocabulary","biomodels.vocabulary","SBML RDF Vocabulary","Vocabulary used in the RDF representation of SBML models.","DATABASE","","biomodels.vocabulary,BIOMODELS.VOCABULARY","None","None" +"pride.project","pride.project","PRIDE Project","The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.","DATABASE","","pride.project,PRIDE.PROJECT","None","None" +"antibodyregistry","antibodyregistry","Antibody Registry","The Antibody Registry provides ids for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.","DATABASE","","antibodyregistry,ANTIBODYREGISTRY","None","None" +"peo","peo","Plant Environment Ontology","The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.","DATABASE","","peo,PEO","None","None" +"idot","idot","Identifiers.org Terms","Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.","DATABASE","","idot,IDOT","None","None" +"hgnc.family","hgnc.family","HGNC Family","The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol.","DATABASE","","hgnc.family,HGNC.FAMILY","None","None" +"yeastintron","yeastintron","Yeast Intron Database v4.3","The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].","DATABASE","","yeastintron,YEASTINTRON","None","None" +"ardb","ardb","Antibiotic Resistance Genes Database","The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.","DATABASE","","ardb,ARDB","None","None" +"Pathema","pathema","Pathema","The over-arching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica — involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics.","DATABASE","","pathema,PATHEMA,Pathema","None","None" +"proteomicsdb.protein","proteomicsdb.protein","ProteomicsDB Protein","ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.","DATABASE","","proteomicsdb.protein,PROTEOMICSDB.PROTEIN","None","None" +"proteomicsdb.peptide","proteomicsdb.peptide","ProteomicsDB Peptide","ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.","DATABASE","","proteomicsdb.peptide,PROTEOMICSDB.PEPTIDE","None","None" +"hpm.protein","hpm.protein","Human Proteome Map Protein","The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.","DATABASE","","hpm.protein,HPM.PROTEIN","None","None" +"hpm.peptide","hpm.peptide","Human Proteome Map Peptide","The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.","DATABASE","","hpm.peptide,HPM.PEPTIDE","None","None" +"drugbankv4.target","drugbankv4.target","DrugBank Target v4","The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.","DATABASE","","drugbankv4.target,DRUGBANKV4.TARGET","None","None" +"ZINC","zinc","ZINC","ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.","DATABASE","","zinc,ZINC","None","None" +"foodb.compound","foodb.compound","FooDB Compound","FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.","DATABASE","","foodb.compound,FOODB.COMPOUND","None","None" +"UNII","unii","UNII","The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient ids (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.","DATABASE","","unii,UNII","None","None" +"orphanet.ordo","orphanet.ordo","Orphanet Rare Disease Ontology","The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. +It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).","DATABASE","","orphanet.ordo,ORPHANET.ORDO","None","None" +"psipar","psipar","Protein Affinity Reagents","Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.","DATABASE","","psipar,PSIPAR","None","None" +"clinvar.record","clinvar.record","ClinVar Record","ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.","DATABASE","","clinvar.record,CLINVAR.RECORD","None","None" +"ebimetagenomics.proj","ebimetagenomics.proj","EBI Metagenomics Project","The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references projects.","DATABASE","","ebimetagenomics.proj,EBIMETAGENOMICS.PROJ","None","None" +"euclinicaltrials","euclinicaltrials","EU Clinical Trials","The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. +It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.","DATABASE","","euclinicaltrials,EUCLINICALTRIALS","None","None" +"google.patent","google.patent","Google Patents","Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.","DATABASE","","google.patent,GOOGLE.PATENT","None","None" +"USPTO","uspto","USPTO","The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.","DATABASE","","uspto,USPTO","None","None" +"cpc","cpc","Cooperative Patent Classification","The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.","DATABASE","","cpc,CPC","None","None" +"gwascentral.study","gwascentral.study","GWAS Central Study","GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.","DATABASE","","gwascentral.study,GWASCENTRAL.STUDY","None","None" +"exac.variant","exac.variant","ExAC Variant","The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.","DATABASE","","exac.variant,EXAC.VARIANT","None","None" +"gwascentral.marker","gwascentral.marker","GWAS Central Marker","GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.","DATABASE","","gwascentral.marker,GWASCENTRAL.MARKER","None","None" +"gwascentral.phenotype","gwascentral.phenotype","GWAS Central Phenotype","GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.","DATABASE","","gwascentral.phenotype,GWASCENTRAL.PHENOTYPE","None","None" +"lincs.cell","lincs.cell","LINCS Cell","The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references cell lines.","DATABASE","","lincs.cell,LINCS.CELL","None","None" +"lincs.protein","lincs.protein","LINCS Protein","The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.","DATABASE","","lincs.protein,LINCS.PROTEIN","None","None" +"lincs.molecule","lincs.molecule","LINCS Molecule","The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references small molecules.","DATABASE","","lincs.molecule,LINCS.MOLECULE","None","None" +"exac.transcript","exac.transcript","ExAC Transcript","The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.","DATABASE","","exac.transcript,EXAC.TRANSCRIPT","None","None" +"exac.gene","exac.gene","ExAC Gene","The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.","DATABASE","","exac.gene,EXAC.GENE","None","None" +"Wikidata","wikidata","Wikidata","Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.","DATABASE","","wikidata,WIKIDATA,Wikidata","None","None" +"SwissLipids","swisslipid","SwissLipids","SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.","DATABASE","","swisslipid,SWISSLIPID,SwissLipids,swisslipids,SWISSLIPIDS","None","None" +"unipathway.compound","unipathway.compound","UniPathway Compound","UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.","DATABASE","","unipathway.compound,UNIPATHWAY.COMPOUND","None","None" +"seed","seed","SEED Subsystem","This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.","DATABASE","","seed,SEED","None","None" +"seed.compound","seed.compound","SEED Compound","This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.","DATABASE","","seed.compound,SEED.COMPOUND","None","None" +"bigg.model","bigg.model","BiGG Model","BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized ids called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.","DATABASE","","bigg.model,BIGG.MODEL","None","None" +"bigg.compartment","bigg.compartment","BiGG Compartment","BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized ids called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.","DATABASE","","bigg.compartment,BIGG.COMPARTMENT","None","None" +"bigg.metabolite","bigg.metabolite","BiGG Metabolite","BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized ids called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.","DATABASE","","bigg.metabolite,BIGG.METABOLITE","None","None" +"bigg.reaction","bigg.reaction","BiGG Reaction","BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized ids called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.","DATABASE","","bigg.reaction,BIGG.REACTION","None","None" +"RRID","rrid","RRID","The Research Resource Identification Initiative provides RRIDs to 3 main classes of resources: Antibodies, Model Organisms, and Databases / Software tools. +The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.","DATABASE","","rrid,RRID","None","None" +"UMLS","umls","UMLS","The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.","DATABASE","","umls,UMLS,UMLS_CUI,umls_cui","https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf","2016AB" +"MeSH","mesh","MeSH","MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.","DATABASE","","mesh,MESH,MeSH,MSH,msh","https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf","2016AB" +"emdb","emdb","Electron Microscopy Data Bank","The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.","DATABASE","","emdb,EMDB","None","None" +"miRTarBase","mirtarbase","miRTarBase","miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.","DATABASE","","mirtarbase,MIRTARBASE,miRTarBase","None","None" +"MedDRA","meddra","MedDRA","The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).","DATABASE","","meddra,MEDDRA,MedDRA,MDR,mdr,MeDRA,medra,MEDRA","https://uts.nlm.nih.gov/help/license/LicenseAgreement.pdf","2016AB" +"DASHR","dashr","DASHR","DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.","DATABASE","","dashr,DASHR","None","None" +"dashr.expression","dashr.expression","DASHR expression","DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.","DATABASE","","dashr.expression,DASHR.EXPRESSION","None","None" +"SPLASH","splash","SPLASH","The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.","DATABASE","","splash,SPLASH","None","None" +"metanetx.chemical","metanetx.chemical","MetaNetX chemical","MetaNetx integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.","DATABASE","","metanetx.chemical,METANETX.CHEMICAL","None","None" +"metanetx.reaction","metanetx.reaction","MetaNetX reaction","MetaNetx integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.","DATABASE","","metanetx.reaction,METANETX.REACTION","None","None" +"metanetx.compartment","metanetx.compartment","MetaNetX compartment","MetaNetx integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.","DATABASE","","metanetx.compartment,METANETX.COMPARTMENT","None","None" +"unipathway.reaction","unipathway.reaction","UniPathway Reaction","UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.","DATABASE","","unipathway.reaction,UNIPATHWAY.REACTION","None","None" +"SASBDB","sasbdb","SASBDB","Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.","DATABASE","","sasbdb,SASBDB","None","None" +"hgnc.genefamily","hgnc.genefamily","HGNC gene family","The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.","DATABASE","","hgnc.genefamily,HGNC.GENEFAMILY","None","None" +"MDM","mdm","MDM","The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.","DATABASE","","mdm,MDM","None","None" +"apid.interactions","apid.interactions","APID Interactomes","APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.","DATABASE","","apid.interactions,APID.INTERACTIONS","None","None" +"AgBase","","AgBase resource for functional analysis of agricultural plant and animal gene products","None","DATABASE","https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=","AgBase,agbase,AGBASE","None","None" +"AGI_LocusCode","","Arabidopsis Genome Initiative","None","DATABASE","http://arabidopsis.org/servlets/TairObject?type=locus&name=","AGI_LocusCode,agi_locuscode,AGI_LOCUSCODE","None","None" +"AGRICOLA_ID","","AGRICultural OnLine Access","None","DATABASE","","AGRICOLA_ID,agricola_id","None","None" +"AGRICOLA_IND","","AGRICultural OnLine Access","None","DATABASE","","AGRICOLA_IND,agricola_ind","None","None" +"Alzheimers_University_of_Toronto","","Alzheimers Project at University of Toronto","None","DATABASE","","Alzheimers_University_of_Toronto,alzheimers_university_of_toronto,ALZHEIMERS_UNIVERSITY_OF_TORONTO","None","None" +"ApiDB_PlasmoDB","","PlasmoDB Plasmodium Genome Resource","None","DATABASE","http://www.plasmodb.org/gene/","ApiDB_PlasmoDB,apidb_plasmodb,APIDB_PLASMODB","None","None" +"APweb","","Angiosperm Phylogeny Website","None","DATABASE","http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html","APweb,apweb,APWEB","None","None" +"ARUK-UCL","","Alzheimers Research Gene Ontology Initiative","None","DATABASE","","ARUK-UCL,aruk-ucl","None","None" +"AspGD","","Aspergillus Genome Database","None","DATABASE","http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=","AspGD,aspgd,ASPGD","None","None" +"AspGD_LOCUS","","Aspergillus Genome Database","None","DATABASE","http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=","AspGD_LOCUS,aspgd_locus,ASPGD_LOCUS","None","None" +"AspGD_REF","","Aspergillus Genome Database","None","DATABASE","http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=","AspGD_REF,aspgd_ref,ASPGD_REF","None","None" +"BHF-UCL","","Cardiovascular Gene Ontology Annotation Initiative","None","DATABASE","","BHF-UCL,bhf-ucl","None","None" +"BIOMD","","BioModels Database","None","DATABASE","https://www.ebi.ac.uk/biomodels/","BIOMD,biomd","None","None" +"bioRxiv","","bioRxiv","None","DATABASE","https://www.biorxiv.org/content/","bioRxiv,biorxiv,BIORXIV","None","None" +"CACAO","","Community Assessment of Community Annotation with Ontologies","None","DATABASE","https://gowiki.tamu.edu/wiki/index.php/","CACAO,cacao","None","None" +"CAFA","","Critical Assessment of Protein Function Annotation","None","DATABASE","","CAFA,cafa","None","None" +"CASGEN","","Catalog of Fishes genus database","None","DATABASE","http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=","CASGEN,casgen","None","None" +"CASREF","","Catalog of Fishes publications database","None","DATABASE","http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=","CASREF,casref","None","None" +"CASSPC","","Catalog of Fishes species database","None","DATABASE","http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=","CASSPC,casspc","None","None" +"DTU","","DTU Health Tech Services","None","DATABASE","","DTU,dtu","None","None" +"CGD_LOCUS","","Candida Genome Database","None","DATABASE","http://www.candidagenome.org/cgi-bin/locus.pl?locus=","CGD_LOCUS,cgd_locus","None","None" +"CGD_REF","","Candida Genome Database","None","DATABASE","http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=","CGD_REF,cgd_ref","None","None" +"CO_125","","Crop Ontology CGIAR Musa Anatomy","None","DATABASE","","CO_125,co_125","None","None" +"COG","","NCBI Clusters of Orthologous Groups","None","DATABASE","","COG,cog","None","None" +"COG_Cluster","","NCBI COG cluster","None","DATABASE","http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=","COG_Cluster,cog_cluster,COG_CLUSTER","None","None" +"COG_Function","","NCBI COG function","None","DATABASE","http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=","COG_Function,cog_function,COG_FUNCTION","None","None" +"COG_Pathway","","NCBI COG pathway","None","DATABASE","http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=","COG_Pathway,cog_pathway,COG_PATHWAY","None","None" +"CollecTF","","Database of transcription factor binding sites (TFBS) in the Bacteria domain","None","DATABASE","","CollecTF,collectf,COLLECTF","None","None" +"ComplexPortal","","Complex Portal database of macromolecular complexes","None","DATABASE","https://www.ebi.ac.uk/complexportal/complex/","ComplexPortal,complexportal,COMPLEXPORTAL","None","None" +"cribi_vitis","","Vitis CRIBI database","None","DATABASE","http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=&release=v1","cribi_vitis,CRIBI_VITIS","None","None" +"DDBJ","","DNA Databank of Japan","None","DATABASE","http://getentry.ddbj.nig.ac.jp/getentry/na/","DDBJ,ddbj","None","None" +"dictyBase","","dictyBase","None","DATABASE","http://dictybase.org/gene/","dictyBase,dictybase,DICTYBASE","None","None" +"dictyBase_gene_name","","dictyBase","None","DATABASE","http://dictybase.org/gene/","dictyBase_gene_name,dictybase_gene_name,DICTYBASE_GENE_NAME","None","None" +"dictyBase_REF","","dictyBase literature references","None","DATABASE","http://dictybase.org/publication/","dictyBase_REF,dictybase_ref,DICTYBASE_REF","None","None" +"EC","","Enzyme Commission","None","DATABASE","https://enzyme.expasy.org/EC/","EC,ec","None","None" +"EcoCyc","","Encyclopedia of E. coli metabolism","None","DATABASE","http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=","EcoCyc,ecocyc,ECOCYC","None","None" +"EcoCyc_REF","","Encyclopedia of E. coli metabolism","None","DATABASE","http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=","EcoCyc_REF,ecocyc_ref,ECOCYC_REF","None","None" +"EMBL","","EMBL Nucleotide Sequence Database","None","DATABASE","http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=","EMBL,embl","None","None" +"ENSEMBL_GeneID","","Ensembl database of automatically annotated genomic data","None","DATABASE","http://www.ensembl.org/id/","ENSEMBL_GeneID,ensembl_geneid,ENSEMBL_GENEID","None","None" +"ENSEMBL_ProteinID","","Ensembl database of automatically annotated genomic data","None","DATABASE","http://www.ensembl.org/id/","ENSEMBL_ProteinID,ensembl_proteinid,ENSEMBL_PROTEINID","None","None" +"ENSEMBL_TranscriptID","","Ensembl database of automatically annotated genomic data","None","DATABASE","http://www.ensembl.org/id/","ENSEMBL_TranscriptID,ensembl_transcriptid,ENSEMBL_TRANSCRIPTID","None","None" +"EnsemblFungi","","Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.","None","DATABASE","http://www.ensemblgenomes.org/id/","EnsemblFungi,ensemblfungi,ENSEMBLFUNGI","None","None" +"EnsemblMetazoa","","Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.","None","DATABASE","http://www.ensemblgenomes.org/id/","EnsemblMetazoa,ensemblmetazoa,ENSEMBLMETAZOA","None","None" +"EnsemblPlants","","Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.","None","DATABASE","http://www.ensemblgenomes.org/id/","EnsemblPlants,ensemblplants,ENSEMBLPLANTS","None","None" +"EnsemblProtists","","Ensembl Protists, the Ensembl database for accessing genome-scale data from protists.","None","DATABASE","http://www.ensemblgenomes.org/id/","EnsemblProtists,ensemblprotists,ENSEMBLPROTISTS","None","None" +"ENZYME","","Swiss Institute of Bioinformatics enzyme database","None","DATABASE","https://enzyme.expasy.org/EC/","ENZYME,enzyme","None","None" +"EO_GIT","","GitHub Issue Tracker for EO","None","DATABASE","https://github.com/Planteome/plant-environment-ontology/issues/","EO_GIT,eo_git","None","None" +"EuPathDB","","The Eukaryotic Pathogen Database","None","DATABASE","http://eupathdb.org/gene/","EuPathDB,eupathdb,EUPATHDB","None","None" +"Eurofung","","Eurofungbase community annotation","None","DATABASE","","Eurofung,eurofung,EUROFUNG","None","None" +"FB","","FlyBase","None","DATABASE","http://flybase.org/reports/.html","FB,fb","None","None" +"GenBank","","GenBank","None","DATABASE","http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=","GenBank,genbank,GENBANK","None","None" +"Gene3D","","Domain Architecture Classification","None","DATABASE","http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=","Gene3D,gene3d,GENE3D","None","None" +"Genesys-pgr","","Gene DB, Genesys","None","DATABASE","https://www.genesys-pgr.org/acn/search?q=","Genesys-pgr,genesys-pgr,GENESYS-PGR","None","None" +"GO_Central","","GO Central","None","DATABASE","","GO_Central,go_central,GO_CENTRAL","None","None" +"GO_Noctua","","GO Noctua","None","DATABASE","","GO_Noctua,go_noctua,GO_NOCTUA","None","None" +"GO_REF","","Gene Ontology Database references","None","DATABASE","http://purl.obolibrary.org/obo/go/references/","GO_REF,go_ref","None","None" +"gomodel","","Gene Ontology Causal Activity Model Database","None","DATABASE","http://www.geneontology.org/gocam/","gomodel,GOMODEL","None","None" +"GOC","","Gene Ontology Consortium","None","DATABASE","","GOC,goc","None","None" +"GOC-OWL","","Gene Ontology Consortium - Logical inferences","None","DATABASE","","GOC-OWL,goc-owl","None","None" +"GONUTS","","Gene Ontology Normal Usage Tracking System (GONUTS)","None","DATABASE","https://gowiki.tamu.edu/wiki/index.php/","GONUTS,gonuts","None","None" +"GOREL","","GO Extensions to OBO Relation Ontology Ontology","None","DATABASE","","GOREL,gorel","None","None" +"GR","","Gramene","None","DATABASE","http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=","GR,gr","None","None" +"GR_GENE","","Gramene","None","DATABASE","http://www.gramene.org/db/genes/search_gene?acc=","GR_GENE,gr_gene","None","None" +"GR_MUT","","A Comparative Mapping Resource for Grains","None","DATABASE","http://www.gramene.org/db/genes/search_gene?acc=","GR_MUT,gr_mut","None","None" +"GR_PROTEIN","","Gramene","None","DATABASE","http://www.gramene.org/db/protein/protein_search?acc=","GR_PROTEIN,gr_protein","None","None" +"GR_QTL","","Gramene","None","DATABASE","http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=","GR_QTL,gr_qtl","None","None" +"GR_REF","","Gramene","None","DATABASE","http://www.gramene.org/db/literature/pub_search?ref_id=","GR_REF,gr_ref","None","None" +"GRIN","","Germplasm Resources Information Network","None","DATABASE","https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=","GRIN,grin","None","None" +"GRINDesc","","Germplasm Resources Information Network","None","DATABASE","https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=","GRINDesc,grindesc,GRINDESC","None","None" +"H-invDB","","H-invitational Database","None","DATABASE","","H-invDB,h-invdb,H-INVDB","None","None" +"H-invDB_cDNA","","H-invitational Database","None","DATABASE","http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=","H-invDB_cDNA,h-invdb_cdna,H-INVDB_CDNA","None","None" +"H-invDB_locus","","H-invitational Database","None","DATABASE","http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=","H-invDB_locus,h-invdb_locus,H-INVDB_LOCUS","None","None" +"HPA_antibody","","Human Protein Atlas antibody information","None","DATABASE","http://www.proteinatlas.org/antibody_info.php?antibody_id=","HPA_antibody,hpa_antibody,HPA_ANTIBODY","None","None" +"HUGO","","Human Genome Organisation","None","DATABASE","","HUGO,hugo","None","None" +"IMG","","Integrated Microbial Genomes; JGI web site for genome annotation","None","DATABASE","http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=","IMG,img","None","None" +"IMGT_HLA","","IMGT/HLA human major histocompatibility complex sequence database","None","DATABASE","","IMGT_HLA,imgt_hla","None","None" +"IMGT_LIGM","","ImMunoGeneTics database covering immunoglobulins and T-cell receptors","None","DATABASE","","IMGT_LIGM,imgt_ligm","None","None" +"iPTMnet","","iPTMnet protein post-translational modification database","None","DATABASE","https://research.bioinformatics.udel.edu/iptmnet/entry//","iPTMnet,iptmnet,IPTMNET","None","None" +"IRIC","","International Rice Research Institute","None","DATABASE","https://oryzasnp.org/_variety.zul?irisid=","IRIC,iric","None","None" +"IRGC","","International Rice Genebank Collection","None","DATABASE","https://www.genesys-pgr.org/acn/search?q=IRGC+","IRGC,irgc","None","None" +"IUPHAR/BPS","","IUPHAR/BPS Guide to Pharmacology","None","DATABASE","","IUPHAR/BPS,iuphar/bps","None","None" +"IUPHAR_GPCR","","International Union of Pharmacology","None","DATABASE","https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=","IUPHAR_GPCR,iuphar_gpcr","None","None" +"IUPHAR_RECEPTOR","","International Union of Pharmacology","None","DATABASE","https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=","IUPHAR_RECEPTOR,iuphar_receptor","None","None" +"Jaiswal_Lab","","Jaiswal_Lab","None","DATABASE","http://wiki.plantontology.org/index.php/PO_REF:00008","Jaiswal_Lab,jaiswal_lab,JAISWAL_LAB","None","None" +"KEGG","","Kyoto Encyclopedia of Genes and Genomes","None","DATABASE","","KEGG,kegg","None","None" +"KEGG_ENZYME","","KEGG Enzyme Database","None","DATABASE","http://www.genome.jp/dbget-bin/www_bget?ec:","KEGG_ENZYME,kegg_enzyme","None","None" +"KEGG_LIGAND","","KEGG LIGAND Database","None","DATABASE","http://www.genome.jp/dbget-bin/www_bget?cpd:","KEGG_LIGAND,kegg_ligand","None","None" +"KEGG_PATHWAY","","KEGG Pathways Database","None","DATABASE","http://www.genome.jp/dbget-bin/www_bget?path:","KEGG_PATHWAY,kegg_pathway","None","None" +"KEGG_REACTION","","KEGG Reaction Database","None","DATABASE","http://www.genome.jp/dbget-bin/www_bget?rn:","KEGG_REACTION,kegg_reaction","None","None" +"LIFEdb","","LifeDB","None","DATABASE","https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=","LIFEdb,lifedb,LIFEDB","None","None" +"MACSC_REF","","Maize Genetics and Genomics Database","None","DATABASE","http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=","MACSC_REF,macsc_ref","None","None" +"MaizeGDB","","MaizeGDB","None","DATABASE","https://maizegdb.org/gene_center/gene/","MaizeGDB,maizegdb,MAIZEGDB","None","None" +"MaizeGDB_Locus","","MaizeGDB","None","DATABASE","https://www.maizegdb.org/gene_center/gene/","MaizeGDB_Locus,maizegdb_locus,MAIZEGDB_LOCUS","None","None" +"MaizeGDB_QTL","","Maize Genetics and Genomics Database","None","DATABASE","https://www.maizegdb.org/data_center/trait?id=","MaizeGDB_QTL,maizegdb_qtl,MAIZEGDB_QTL","None","None" +"MaizeGDB_REF","","Maize Genetics and Genomics Database","None","DATABASE","http://maizegdb.org/data_center/reference?id=","MaizeGDB_REF,maizegdb_ref,MAIZEGDB_REF","None","None" +"MaizeGDB_stock","","Maize Genetics and Genomics Database","None","DATABASE","https://maizegdb.org/data_center/stock?id=","MaizeGDB_stock,maizegdb_stock,MAIZEGDB_STOCK","None","None" +"MEDLINE","","Medline literature database","None","DATABASE","","MEDLINE,medline","None","None" +"MEROPS_fam","","MEROPS peptidase database","None","DATABASE","http://merops.sanger.ac.uk/cgi-bin/famsum?family=","MEROPS_fam,merops_fam,MEROPS_FAM","None","None" +"MetaCyc","","Metabolic Encyclopedia of metabolic and other pathways","None","DATABASE","http://biocyc.org/META/NEW-IMAGE?type=NIL&object=","MetaCyc,metacyc,METACYC","None","None" +"MGCSC_GENETIC_STOCKS","","Maize Genetics and Genomics Database","None","DATABASE","http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=","MGCSC_GENETIC_STOCKS,mgcsc_genetic_stocks","None","None" +"MGI","","Mouse Genome Informatics","None","DATABASE","http://www.informatics.jax.org/accession/","MGI,mgi","None","None" +"MIPS_funcat","","MIPS Functional Catalogue","None","DATABASE","http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=","MIPS_funcat,mips_funcat,MIPS_FUNCAT","None","None" +"MITRE","","The MITRE Corporation","None","DATABASE","","MITRE,mitre","None","None" +"ModBase","","ModBase comprehensive Database of Comparative Protein Structure Models","None","DATABASE","http://salilab.org/modbase/searchbyid?databaseID=","ModBase,modbase,MODBASE","None","None" +"NASC_code","","Nottingham Arabidopsis Stock Centre Seeds Database","None","DATABASE","http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=","NASC_code,nasc_code,NASC_CODE","None","None" +"NC-IUBMB","","Nomenclature Committee of the International Union of Biochemistry and Molecular Biology","None","DATABASE","","NC-IUBMB,nc-iubmb","None","None" +"NCBI","","National Center for Biotechnology Information","None","DATABASE","","NCBI,ncbi","None","None" +"NCBI_gi","","NCBI databases","None","DATABASE","http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=","NCBI_gi,ncbi_gi,NCBI_GI","None","None" +"NCBI_GP","","NCBI GenPept","None","DATABASE","https://www.ncbi.nlm.nih.gov/protein/","NCBI_GP,ncbi_gp","None","None" +"NCBI_locus_tag","","NCBI locus tag","None","DATABASE","","NCBI_locus_tag,ncbi_locus_tag,NCBI_LOCUS_TAG","None","None" +"NCBI_NP","","NCBI Protein","None","DATABASE","","NCBI_NP,ncbi_np","None","None" +"NIF_Subcellular","","Neuroscience Information Framework standard ontology, subcellular hierarchy","None","DATABASE","http://www.neurolex.org/wiki/","NIF_Subcellular,nif_subcellular,NIF_SUBCELLULAR","None","None" +"NTNU_SB","","Norwegian University of Science and Technology, Systems Biology team","None","DATABASE","","NTNU_SB,ntnu_sb","None","None" +"OBO_SF_PO","","Source Forge OBO Plant Ontology (PO) term request tracker","None","DATABASE","https://sourceforge.net/tracker/index.php?func=detail&aid=&group_id=76834&atid=835555","OBO_SF_PO,obo_sf_po","None","None" +"OBO_SF2_PO","","Source Forge OBO Plant Ontology (PO) term request tracker","None","DATABASE","http://sourceforge.net/p/obo/plant-ontology-po-term-requests/","OBO_SF2_PO,obo_sf2_po","None","None" +"OBO_SF2_PECO","","Source Forge OBO plant-experimental-conditions-ontology (PECO) term request tracker","None","DATABASE","https://sourceforge.net/p/obo/plant-environment-ontology-eo/","OBO_SF2_PECO,obo_sf2_peco","None","None" +"OMSSA","","Open Mass Spectrometry Search Algorithm","None","DATABASE","","OMSSA,omssa","None","None" +"PANTHER","","Protein ANalysis THrough Evolutionary Relationships Classification System","None","DATABASE","http://www.pantherdb.org/panther/lookupId.jsp?id=","PANTHER,panther","None","None" +"ParkinsonsUK-UCL","","Parkinsons Disease Gene Ontology Initiative","None","DATABASE","","ParkinsonsUK-UCL,parkinsonsuk-ucl,PARKINSONSUK-UCL","None","None" +"PATRIC","","PathoSystems Resource Integration Center","None","DATABASE","https://www.patricbrc.org/view/Feature/","PATRIC,patric","None","None" +"PECO_GIT","","GitHub Issue Tracker for PECO","None","DATABASE","https://github.com/Planteome/plant-environment-ontology/issues/","PECO_GIT,peco_git","None","None" +"PharmGKB","","Pharmacogenetics and Pharmacogenomics Knowledge Base","None","DATABASE","https://www.pharmgkb.org/do/serve?objId=","PharmGKB,pharmgkb,PHARMGKB","None","None" +"PhenoScape","","PhenoScape Knowledgebase","None","DATABASE","","PhenoScape,phenoscape,PHENOSCAPE","None","None" +"PIR","","Protein Information Resource","None","DATABASE","https://proteininformationresource.org/cgi-bin/nbrfget?uid=","PIR,pir","None","None" +"PlantSystematics_image_archive","","PlantSystematics.org","None","DATABASE","http://www.plantsystematics.org/imagebyid_.html","PlantSystematics_image_archive,plantsystematics_image_archive,PLANTSYSTEMATICS_IMAGE_ARCHIVE","None","None" +"PMCID","","Pubmed Central","None","DATABASE","https://www.ncbi.nlm.nih.gov/pmc/articles/","PMCID,pmcid","None","None" +"PMID","","PubMed","None","DATABASE","http://www.ncbi.nlm.nih.gov/pubmed/","PMID,pmid","None","None" +"PO_GIT","","GitHub Issue Tracker for PO","None","DATABASE","https://github.com/Planteome/plant-ontology/issues/","PO_GIT,po_git","None","None" +"PO_REF","","Plant Ontology custom references","None","DATABASE","http://planteome.org/po_ref/","PO_REF,po_ref","None","None" +"POC","","Plant Ontology Consortium","None","DATABASE","","POC,poc","None","None" +"Pompep","","Schizosaccharomyces pombe protein data","None","DATABASE","","Pompep,pompep,POMPEP","None","None" +"PPI","","Pseudomonas syringae community annotation project","None","DATABASE","","PPI,ppi","None","None" +"protein_id","","DDBJ / ENA / GenBank","None","DATABASE","","protein_id,PROTEIN_ID","None","None" +"PseudoCAP","","Pseudomonas Genome Project","None","DATABASE","http://www.pseudomonas.com/feature/show?locus_tag=","PseudoCAP,pseudocap,PSEUDOCAP","None","None" +"PSO_GIT","","GitHub Issue Tracker for PSO","None","DATABASE","https://github.com/Planteome/plant-stress-ontology/issues/","PSO_GIT,pso_git","None","None" +"PSI-MI","","Proteomic Standard Initiative for Molecular Interaction","None","DATABASE","http://purl.obolibrary.org/obo/","PSI-MI,psi-mi","None","None" +"PSI-MOD","","Proteomics Standards Initiative protein modification ontology","None","DATABASE","http://purl.obolibrary.org/obo/","PSI-MOD,psi-mod","None","None" +"PSORT","","PSORT protein subcellular localization databases and prediction tools for bacteria","None","DATABASE","","PSORT,psort","None","None" +"PubChem_BioAssay","","NCBI PubChem database of bioassay records","None","DATABASE","https://pubchem.ncbi.nlm.nih.gov/bioassay/","PubChem_BioAssay,pubchem_bioassay,PUBCHEM_BIOASSAY","None","None" +"PubChem_Compound","","NCBI PubChem database of chemical structures","None","DATABASE","https://pubchem.ncbi.nlm.nih.gov/compound/","PubChem_Compound,pubchem_compound,PUBCHEM_COMPOUND","None","None" +"PubChem_Substance","","NCBI PubChem database of chemical substances","None","DATABASE","https://pubchem.ncbi.nlm.nih.gov/substance/","PubChem_Substance,pubchem_substance,PUBCHEM_SUBSTANCE","None","None" +"RAP-DB","","Rice annotation Project database","None","DATABASE","https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=","RAP-DB,rap-db","None","None" +"RefGenome","","GO Reference Genomes","None","DATABASE","","RefGenome,refgenome,REFGENOME","None","None" +"RiceSES","","Rice Knowledge Bank","None","DATABASE","http://www.knowledgebank.irri.org/extension/crop-damage-diseases/.html","RiceSES,riceses,RICESES","None","None" +"RNAcentral","","RNAcentral","None","DATABASE","https://rnacentral.org/rna/","RNAcentral,rnacentral,RNACENTRAL","None","None" +"SABIO-RK","","SABIO Reaction Kinetics","None","DATABASE","http://sabio.villa-bosch.de/reacdetails.jsp?reactid=","SABIO-RK,sabio-rk","None","None" +"Sanger","","Wellcome Trust Sanger Institute","None","DATABASE","","Sanger,sanger,SANGER","None","None" +"SGD_LOCUS","","Saccharomyces Genome Database","None","DATABASE","http://www.yeastgenome.org/locus//overview","SGD_LOCUS,sgd_locus","None","None" +"SGD_REF","","Saccharomyces Genome Database","None","DATABASE","http://www.yeastgenome.org/reference//overview","SGD_REF,sgd_ref","None","None" +"SGN_ref","","Sol Genomics Network","None","DATABASE","https://sgn.cornell.edu/chado/publication.pl?pub_id=","SGN_ref,sgn_ref,SGN_REF","None","None" +"SGN_germplasm","","Sol Genomics Network","None","DATABASE","http://solgenomics.net/stock//view/","SGN_germplasm,sgn_germplasm,SGN_GERMPLASM","None","None" +"Soy_gene","","SoyBase","None","DATABASE","https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=","Soy_gene,soy_gene,SOY_GENE","None","None" +"SOY_QTL","","SoyBase","None","DATABASE","https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=","SOY_QTL,soy_qtl","None","None" +"SOY_ref","","SoyBase","None","DATABASE","https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=","SOY_ref,soy_ref,SOY_REF","None","None" +"SUPERFAMILY","","SUPERFAMILY protein annotation database","None","DATABASE","http://supfam.org/scop/","SUPERFAMILY,superfamily","None","None" +"SynGO","","The Synapse Gene Ontology and Annotation Initiative","None","DATABASE","","SynGO,syngo,SYNGO","None","None" +"SynGO-UCL","","The Synapse Gene Ontology and Annotation Initiative at UCL","None","DATABASE","","SynGO-UCL,syngo-ucl,SYNGO-UCL","None","None" +"SYSCILIA_CCNET","","Syscilia","None","DATABASE","","SYSCILIA_CCNET,syscilia_ccnet","None","None" +"TAIR","","The Arabidopsis Information Resource","None","DATABASE","http://arabidopsis.org/servlets/TairObject?accession=","TAIR,tair","None","None" +"taxon","","NCBI Taxonomy","None","DATABASE","http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=","taxon,TAXON","None","None" +"TC","","Transport Protein Database","None","DATABASE","http://www.tcdb.org/tcdb/index.php?tc=","TC,tc","None","None" +"TGD_LOCUS","","Tetrahymena Genome Database","None","DATABASE","http://db.ciliate.org/cgi-bin/locus.pl?locus=","TGD_LOCUS,tgd_locus","None","None" +"TGD_REF","","Tetrahymena Genome Database","None","DATABASE","http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=","TGD_REF,tgd_ref","None","None" +"TO_GIT","","GitHub Issue Tracker for TO","None","DATABASE","https://github.com/Planteome/plant-trait-ontology/issues/","TO_GIT,to_git","None","None" +"TRANSFAC","","TRANSFAC database of eukaryotic transcription factors","None","DATABASE","","TRANSFAC,transfac","None","None" +"TreeGenes","","Forest Tree Genome Database","None","DATABASE","http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=","TreeGenes,treegenes,TREEGENES","None","None" +"UM-BBD","","EAWAG Biocatalysis/Biodegradation Database","None","DATABASE","","UM-BBD,um-bbd","None","None" +"UM-BBD_enzymeID","","EAWAG Biocatalysis/Biodegradation Database","None","DATABASE","http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=","UM-BBD_enzymeID,um-bbd_enzymeid,UM-BBD_ENZYMEID","None","None" +"UM-BBD_pathwayID","","EAWAG Biocatalysis/Biodegradation Database","None","DATABASE","http://eawag-bbd.ethz.ch//_map.html","UM-BBD_pathwayID,um-bbd_pathwayid,UM-BBD_PATHWAYID","None","None" +"UM-BBD_reactionID","","EAWAG Biocatalysis/Biodegradation Database","None","DATABASE","http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=","UM-BBD_reactionID,um-bbd_reactionid,UM-BBD_REACTIONID","None","None" +"UM-BBD_ruleID","","EAWAG Biocatalysis/Biodegradation Database","None","DATABASE","http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=","UM-BBD_ruleID,um-bbd_ruleid,UM-BBD_RULEID","None","None" +"UniProtKB","","Universal Protein Knowledgebase","None","DATABASE","https://www.uniprot.org/uniprot/","UniProtKB,uniprotkb,UNIPROTKB","None","None" +"UniProtKB-KW","","UniProt Knowledgebase keywords","None","DATABASE","https://www.uniprot.org/keywords/","UniProtKB-KW,uniprotkb-kw,UNIPROTKB-KW","None","None" +"UniProtKB-SubCell","","UniProt Knowledgebase Subcellular Location vocabulary","None","DATABASE","http://www.uniprot.org/locations/","UniProtKB-SubCell,uniprotkb-subcell,UNIPROTKB-SUBCELL","None","None" +"UniRule","","Manually curated rules for automatic annotation of UniProtKB unreviewed entries","None","DATABASE","https://www.uniprot.org/unirule/","UniRule,unirule,UNIRULE","None","None" +"VZ","","ViralZone","None","DATABASE","http://viralzone.expasy.org/all_by_protein/.html","VZ,vz","None","None" +"WB","","WormBase database of nematode biology","None","DATABASE","http://www.wormbase.org/get?name=","WB,wb","None","None" +"WB_REF","","WormBase database of nematode biology","None","DATABASE","http://www.wormbase.org/get?name=","WB_REF,wb_ref","None","None" +"Wikipedia","","Wikipedia","None","DATABASE","http://en.wikipedia.org/wiki/","Wikipedia,wikipedia,WIKIPEDIA","None","None" +"YeastFunc","","Yeast Function","None","DATABASE","","YeastFunc,yeastfunc,YEASTFUNC","None","None" +"YuBioLab","","CITGeneDB","None","DATABASE","","YuBioLab,yubiolab,YUBIOLAB","None","None" +"TFClass","","TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains","None","DATABASE","http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=","TFClass,tfclass,TFCLASS","None","None" +"HGNC-UCL","","UCL-based HGNC","None","DATABASE","","HGNC-UCL,hgnc-ucl","None","None" +"paxo","","paxo","None","DATABASE","","paxo,PAXO","None","1" diff --git a/oxo-loader/load_all.sh b/oxo-loader/load_all.sh new file mode 100644 index 0000000..d4f9370 --- /dev/null +++ b/oxo-loader/load_all.sh @@ -0,0 +1,8 @@ +python /app/OlsDatasetExtractor.py -c /app/config/config.ini -i /app/config/idorg.xml -d /app/data/datasources.csv +python /app/OxoNeo4jLoader.py -W -d datasources.csv -c /app/config/config.ini + +python /app/OlsMappingExtractor.py -c /app/config/config.ini -t /app/data/ols_terms.csv -m /app/data/ols_mappings.csv +python /app/OxoNeo4jLoader.py -c /app/config/config.ini -t ols_terms.csv -m ols_mappings.csv + +python /app/UmlsMappingExtractor.py -c /app/config/config.ini -t /app/data/umls_terms.csv -m /app/data/umls_mappings.csv +python /app/OxoNeo4jLoader.py -c /app/config/config.ini -t umls_terms.csv -m umls_mappings.csv diff --git a/dataloading/oxo/requirements.txt b/oxo-loader/requirements.txt similarity index 100% rename from dataloading/oxo/requirements.txt rename to oxo-loader/requirements.txt diff --git a/oxo-model/.classpath b/oxo-model/.classpath new file mode 100644 index 0000000..39abf1c --- /dev/null +++ b/oxo-model/.classpath @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-model/.factorypath b/oxo-model/.factorypath new file mode 100644 index 0000000..1011126 --- /dev/null +++ b/oxo-model/.factorypath @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-model/.project b/oxo-model/.project new file mode 100644 index 0000000..926cf9f --- /dev/null +++ b/oxo-model/.project @@ -0,0 +1,23 @@ + + + oxo-model + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/oxo-web/.classpath b/oxo-web/.classpath new file mode 100644 index 0000000..39abf1c --- /dev/null +++ b/oxo-web/.classpath @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-web/.factorypath b/oxo-web/.factorypath new file mode 100644 index 0000000..1c53937 --- /dev/null +++ b/oxo-web/.factorypath @@ -0,0 +1,159 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/oxo-web/.project b/oxo-web/.project new file mode 100644 index 0000000..546bc93 --- /dev/null +++ b/oxo-web/.project @@ -0,0 +1,23 @@ + + + oxo-web + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/oxo-web/Dockerfile b/oxo-web/Dockerfile new file mode 100644 index 0000000..859e38d --- /dev/null +++ b/oxo-web/Dockerfile @@ -0,0 +1,12 @@ + +FROM maven:3.5-jdk-8 AS build +COPY pom.xml /opt/OxO/pom.xml +COPY oxo-web /opt/OxO/ +COPY oxo-model /opt/OxO/ +COPY oxo-indexer /opt/OxO/ +RUN cd /opt/OxO && mvn clean package + +FROM openjdk:8-jre-alpine +COPY --from=build /opt/OxO/oxo-web/target/oxo-web.war /opt/oxo-web.war +EXPOSE 8080 +ENTRYPOINT ["java", "-jar", "/opt/oxo-web.war"] \ No newline at end of file diff --git a/dataloading/paxo/config/listprocessing_dummy_config.ini b/paxo-loader/config/listprocessing_dummy_config.ini similarity index 100% rename from dataloading/paxo/config/listprocessing_dummy_config.ini rename to paxo-loader/config/listprocessing_dummy_config.ini diff --git a/dataloading/paxo/config/paxo_dummy_config.ini b/paxo-loader/config/paxo_dummy_config.ini similarity index 100% rename from dataloading/paxo/config/paxo_dummy_config.ini rename to paxo-loader/config/paxo_dummy_config.ini diff --git a/dataloading/paxo/listprocessing.py b/paxo-loader/listprocessing.py similarity index 100% rename from dataloading/paxo/listprocessing.py rename to paxo-loader/listprocessing.py diff --git a/dataloading/paxo/listprocessing_config.ini b/paxo-loader/listprocessing_config.ini similarity index 100% rename from dataloading/paxo/listprocessing_config.ini rename to paxo-loader/listprocessing_config.ini diff --git a/dataloading/paxo/neoExporter.py b/paxo-loader/neoExporter.py similarity index 100% rename from dataloading/paxo/neoExporter.py rename to paxo-loader/neoExporter.py diff --git a/dataloading/paxo/paxo.py b/paxo-loader/paxo.py similarity index 100% rename from dataloading/paxo/paxo.py rename to paxo-loader/paxo.py diff --git a/dataloading/paxo/paxo_config.ini b/paxo-loader/paxo_config.ini similarity index 100% rename from dataloading/paxo/paxo_config.ini rename to paxo-loader/paxo_config.ini diff --git a/dataloading/paxo/paxo_internals.py b/paxo-loader/paxo_internals.py similarity index 100% rename from dataloading/paxo/paxo_internals.py rename to paxo-loader/paxo_internals.py diff --git a/dataloading/paxo/readme.md b/paxo-loader/readme.md similarity index 95% rename from dataloading/paxo/readme.md rename to paxo-loader/readme.md index 62522e5..4b25137 100644 --- a/dataloading/paxo/readme.md +++ b/paxo-loader/readme.md @@ -1,3 +1,7 @@ + +scripts to generate predicted mappings. +You can evaluate paxo using a gold standard set of mappings. The *standard folder* contains an example of how the gold standard mapppings needs to be formatted. + ### Prerequisite - In order to install dependencies, first ensure that you have Python 2.7 and a corresponding version of pip. diff --git a/dataloading/paxo/requirements.txt b/paxo-loader/requirements.txt similarity index 100% rename from dataloading/paxo/requirements.txt rename to paxo-loader/requirements.txt diff --git a/dataloading/standard/dummy-standard.csv b/paxo-loader/standard/dummy-standard.csv similarity index 100% rename from dataloading/standard/dummy-standard.csv rename to paxo-loader/standard/dummy-standard.csv diff --git a/dataloading/paxo/validation.py b/paxo-loader/validation.py similarity index 100% rename from dataloading/paxo/validation.py rename to paxo-loader/validation.py diff --git a/solr-config/mapping/conf/_rest_managed.json b/solr-config/mapping/conf/_rest_managed.json deleted file mode 100644 index 6a4aec3..0000000 --- a/solr-config/mapping/conf/_rest_managed.json +++ /dev/null @@ -1 +0,0 @@ -{"initArgs":{},"managedList":[]} diff --git a/solr-config/mapping/conf/lang/stopwords_en.txt b/solr-config/mapping/conf/lang/stopwords_en.txt deleted file mode 100644 index 2c164c0..0000000 --- a/solr-config/mapping/conf/lang/stopwords_en.txt +++ /dev/null @@ -1,54 +0,0 @@ -# Licensed to the Apache Software Foundation (ASF) under one or more -# contributor license agreements. See the NOTICE file distributed with -# this work for additional information regarding copyright ownership. -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -# a couple of test stopwords to test that the words are really being -# configured from this file: -stopworda -stopwordb - -# Standard english stop words taken from Lucene's StopAnalyzer -a -an -and -are -as -at -be -but -by -for -if -in -into -is -it -no -not -of -on -or -such -that -the -their -then -there -these -they -this -to -was -will -with diff --git a/solr-config/mapping/conf/protwords.txt b/solr-config/mapping/conf/protwords.txt deleted file mode 100644 index 1dfc0ab..0000000 --- a/solr-config/mapping/conf/protwords.txt +++ /dev/null @@ -1,21 +0,0 @@ -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -#----------------------------------------------------------------------- -# Use a protected word file to protect against the stemmer reducing two -# unrelated words to the same base word. - -# Some non-words that normally won't be encountered, -# just to test that they won't be stemmed. -dontstems -zwhacky - diff --git a/solr-config/mapping/conf/schema.xml b/solr-config/mapping/conf/schema.xml deleted file mode 100644 index fa799e7..0000000 --- a/solr-config/mapping/conf/schema.xml +++ /dev/null @@ -1,496 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - id - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/solr-config/mapping/conf/solrconfig.xml b/solr-config/mapping/conf/solrconfig.xml deleted file mode 100644 index 7d30fea..0000000 --- a/solr-config/mapping/conf/solrconfig.xml +++ /dev/null @@ -1,583 +0,0 @@ - - - - - - - - - 5.2.1 - - - ${solr.data.dir:} - - - - - - - - - - - - - - - - ${solr.lock.type:native} - - - true - - - - - - - - - - - - - - - - ${solr.ulog.dir:} - ${solr.ulog.numVersionBuckets:65536} - - - - - ${solr.autoCommit.maxTime:15000} - false - - - - - ${solr.autoSoftCommit.maxTime:-1} - - - - - - - - 1024 - - - - - - - - - - - - - - - - - - true - - - 20 - - - 200 - - - false - - - 2 - - - - - - - - - - - - - - - - - - - - explicit - 10 - - - - - - - - explicit - json - true - text - - - - - - - {!xport} - xsort - false - - - - query - - - - - - - text - - - - - - - - - - - - - - explicit - true - - - - - - - - - - - - - - true - false - - - terms - - - - - - *:* - - - diff --git a/solr-config/mapping/conf/stopwords.txt b/solr-config/mapping/conf/stopwords.txt deleted file mode 100644 index ae1e83e..0000000 --- a/solr-config/mapping/conf/stopwords.txt +++ /dev/null @@ -1,14 +0,0 @@ -# Licensed to the Apache Software Foundation (ASF) under one or more -# contributor license agreements. See the NOTICE file distributed with -# this work for additional information regarding copyright ownership. -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. diff --git a/solr-config/mapping/conf/synonyms.txt b/solr-config/mapping/conf/synonyms.txt deleted file mode 100644 index 7f72128..0000000 --- a/solr-config/mapping/conf/synonyms.txt +++ /dev/null @@ -1,29 +0,0 @@ -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -#----------------------------------------------------------------------- -#some test synonym mappings unlikely to appear in real input text -aaafoo => aaabar -bbbfoo => bbbfoo bbbbar -cccfoo => cccbar cccbaz -fooaaa,baraaa,bazaaa - -# Some synonym groups specific to this example -GB,gib,gigabyte,gigabytes -MB,mib,megabyte,megabytes -Television, Televisions, TV, TVs -#notice we use "gib" instead of "GiB" so any WordDelimiterFilter coming -#after us won't split it into two words. - -# Synonym mappings can be used for spelling correction too -pixima => pixma - diff --git a/solr-config/mapping/core.properties b/solr-config/mapping/core.properties deleted file mode 100644 index 1c4c381..0000000 --- a/solr-config/mapping/core.properties +++ /dev/null @@ -1,3 +0,0 @@ -#Written by CorePropertiesLocator -#Tue Oct 14 12:47:52 BST 2014 -name=mapping diff --git a/solr-config/solr.xml b/solr-config/solr.xml deleted file mode 100644 index bb8e629..0000000 --- a/solr-config/solr.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - ${host:} - ${jetty.port:8983} - ${hostContext:solr} - - ${genericCoreNodeNames:true} - - ${zkClientTimeout:30000} - ${distribUpdateSoTimeout:600000} - ${distribUpdateConnTimeout:60000} - - - - - ${socketTimeout:600000} - ${connTimeout:60000} - - -