diff --git a/external-dev/aopo-slim.owl b/external-dev/aopo-slim.owl
index c4fe50d3..977970b6 100644
--- a/external-dev/aopo-slim.owl
+++ b/external-dev/aopo-slim.owl
@@ -43,8 +43,8 @@
https://raw.githubusercontent.com/jmillanacosta/aop-ontology/patch-1/aopo.owl
Slimmer
- 2023-12-01 01:36:46
- 27:10:2023 19:30
+ 07:12:2023 17:27
+ 2024-01-01 01:36:43
chebi_ontology
human_phenotype
1.2
diff --git a/external-dev/bao-slim.owl b/external-dev/bao-slim.owl
index c964249d..3b40c78f 100644
--- a/external-dev/bao-slim.owl
+++ b/external-dev/bao-slim.owl
@@ -24,7 +24,7 @@
http://bioassayontology.org/bao/bao_complete_merged.owl
Slimmer
- 2023-12-01 01:36:53
+ 2024-01-01 01:36:51
Contact:
Stephan Schurer
stephan dot schurer at gmail dot com
diff --git a/external-dev/bfo-slim.owl b/external-dev/bfo-slim.owl
index 48aedf7c..96beac3b 100644
--- a/external-dev/bfo-slim.owl
+++ b/external-dev/bfo-slim.owl
@@ -45,7 +45,7 @@
http://purl.obolibrary.org/obo/bfo/classes-only.owl
Slimmer
- 2023-12-01 01:36:56
+ 2024-01-01 01:36:53
The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl.
If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies.
diff --git a/external-dev/bto-slim.owl b/external-dev/bto-slim.owl
index 354401e2..fa54b399 100644
--- a/external-dev/bto-slim.owl
+++ b/external-dev/bto-slim.owl
@@ -20,7 +20,7 @@
http://purl.obolibrary.org/obo/bto.owl
OBO-Edit 2.3.1
Slimmer
- 2023-12-01 01:37:02
+ 2024-01-01 01:36:59
23:10:2021 16:56
BrendaTissueOBO
1.2
diff --git a/external-dev/ccont-slim.owl b/external-dev/ccont-slim.owl
index f5a678e6..5d43717e 100644
--- a/external-dev/ccont-slim.owl
+++ b/external-dev/ccont-slim.owl
@@ -15,7 +15,7 @@
https://raw.githubusercontent.com/enanomapper/ontologies/master/internal/ccont-ext.owl
Matthias Ganzinger, matthias.ganzinger@med.uni-heidelberg.de
Slimmer
- 2023-12-01 01:37:03
+ 2024-01-01 01:37:00
cell culture ontology (CCONT)
1.1
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/chebi-slim.owl b/external-dev/chebi-slim.owl
index b85c404f..faefb615 100644
--- a/external-dev/chebi-slim.owl
+++ b/external-dev/chebi-slim.owl
@@ -17,8 +17,8 @@
http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi_lite.obo
Slimmer
- 2023-12-01 01:39:05
- 27:10:2023 19:30
+ 07:12:2023 17:27
+ 2024-01-01 01:39:17
chebi_ontology
1.2
chebi
@@ -1145,6 +1145,20 @@
+
+
+
+
+
+ Any herbicide composed of urea or substituted urea substructure.
+ chebi_ontology
+ CHEBI:188147
+
+ urea herbicide
+
+
+
+
@@ -1272,6 +1286,34 @@
+
+
+
+
+
+ Any agent that inhibits nociception.
+ chebi_ontology
+ CHEBI:228138
+
+ antinociceptive agent
+
+
+
+
+
+
+
+
+
+ A sigma receptor modulator that activates the sigma-1 receptor.
+ chebi_ontology
+ CHEBI:228237
+
+ sigma-1 receptor agonist
+
+
+
+
diff --git a/external-dev/cheminf-slim.owl b/external-dev/cheminf-slim.owl
index c4646fe1..216db7bf 100644
--- a/external-dev/cheminf-slim.owl
+++ b/external-dev/cheminf-slim.owl
@@ -79,7 +79,7 @@
http://creativecommons.org/publicdomain/zero/1.0/
http://semanticchemistry.github.io/semanticchemistry/ontology/cheminf.owl
Slimmer
- 2023-12-01 01:37:07
+ 2024-01-01 01:37:05
An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
Document containing upporting external terms
IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
diff --git a/external-dev/chmo-slim.owl b/external-dev/chmo-slim.owl
index c049e53b..df92e584 100644
--- a/external-dev/chmo-slim.owl
+++ b/external-dev/chmo-slim.owl
@@ -19,7 +19,7 @@
http://purl.obolibrary.org/obo/chmo.owl
Slimmer
- 2023-12-01 01:39:11
+ 2024-01-01 01:39:23
1.2
batchelorc
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/clo-slim.owl b/external-dev/clo-slim.owl
index 2a8428fa..3b65c87f 100644
--- a/external-dev/clo-slim.owl
+++ b/external-dev/clo-slim.owl
@@ -44,9 +44,9 @@
http://purl.obolibrary.org/obo/cl.owl
Slimmer
- 2023-12-01 01:39:23
+ 2024-01-01 01:39:35
See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.
- 2023-10-19
+ 2023-12-05
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
@@ -337,6 +337,7 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (
2023-03-03
abbreviation
+
@@ -351,6 +352,7 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (
2023-03-03
plural form
+
@@ -793,6 +795,18 @@ WHERE {
+
+
+
+
+ 2023-11-22T11:18:57Z
+ a subset of general classes related to specific cell types in the kidney
+ kidney_upper_slim
+
+
+
+
+
@@ -1154,15 +1168,6 @@ WHERE {
-
-
-
-
-
-
-
-
-
@@ -1254,15 +1259,6 @@ WHERE {
-
-
-
-
-
-
-
-
-
@@ -1606,6 +1602,13 @@ WHERE {
+
+
+
+
+
+
+
@@ -1692,14 +1695,18 @@ WHERE {
-
+
+ created by
+
-
+
+ creation date
+
@@ -1724,13 +1731,6 @@ WHERE {
-
-
-
-
-
-
-
@@ -1889,7 +1889,9 @@ WHERE {
-
+
+ id
+
@@ -2021,13 +2023,6 @@ WHERE {
-
-
-
-
-
-
-
@@ -2093,13 +2088,6 @@ WHERE {
-
-
-
-
-
-
-
@@ -2156,17 +2144,17 @@ WHERE {
-
-
-
-
-
-
-
-
+
+ http://xmlns.com/foaf/0.1/depiction
+ uberon
+ depiction
+ true
+ depiction
+ depiction
+
diff --git a/external-dev/efo-slim.owl b/external-dev/efo-slim.owl
index 6e1a0941..655814ec 100644
--- a/external-dev/efo-slim.owl
+++ b/external-dev/efo-slim.owl
@@ -29,10 +29,23 @@
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
1.4
+ Catherine Leroy
+ Dani Welter
+ Drashtti Vasant
+ Ele Holloway
+ Eleanor Williams
+ Emma Kate Hastings
Gautier Koscielny
+ Helen Parkinson
+ James Malone
+ Jon Ison
Laura Huerta Martinez
+ Natalja Kurbatova
Olamidipupo Ajigboye
Paola Roncaglia
+ Simon Jupp
+ Sirarat Sarntivijai
+ Tomasz Adamusiak
Trish Whetzel
Zoe May Pendlington
Copyright [2014] EMBL - European Bioinformatics Institute
@@ -40,23 +53,10 @@ Licensed under the Apache License, Version 2.0 (the "License"); you ma
License.
www.apache.org/licenses/LICENSE-2.0
http://www.ebi.ac.uk/efo/efo.owl
- Catherine Leroy
- Dani Welter
- Drashtti Vasant
- Ele Holloway
- Eleanor Williams
- Emma Kate Hastings
- Helen Parkinson
- James Malone
- Jon Ison
- Natalja Kurbatova
- Simon Jupp
- Sirarat Sarntivijai
- Tomasz Adamusiak
Slimmer
- 2023-12-01 01:40:55
- 2023-11-15
- 3.60.0
+ 2024-01-01 01:40:41
+ 2023-12-18
+ 3.61.0
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
@@ -943,7 +943,13 @@ This annotation property may be replaced with an annotation property from an ext
-
+
+ http://purl.org/dc/elements/1.1/creator
+ 3.61.0
+ Duplication
+ obsolete_creator
+ true
+
@@ -951,7 +957,7 @@ This annotation property may be replaced with an annotation property from an ext
- definition
+ obsolete_definition
true
@@ -8445,6 +8451,46 @@ Established melanoma cell line from the Skin Cancer Unit at the German Cancer Re
+
+
+
+
+
+ The mass density of a breast.
+ https://orcid.org/0000-0001-6757-4744
+ PMID:37345113
+ breast tissue density
+ mass density of breast
+ breast density
+
+
+
+
+ The mass density of a breast.
+ AUTO:patterns/patterns/entity_attribute
+
+
+
+
+ mass density of breast
+ AUTO:patterns/patterns/entity_attribute
+
+
+
+
+
+
+
+
+
+ The age at which pancreatic ductal adenocarcinoma manifestations first appear.
+ age at onset of pancreatic ductal adenocarcinoma
+ age pancreatic ductal adenocarcinoma symptoms begin
+ age of onset of pancreatic ductal adenocarcinoma
+
+
+
+
@@ -61874,7 +61920,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The determination of the amount of jasmonic acid present in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
PMID:34503513
jasmonic acid measurement
@@ -61887,7 +61933,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The determination of the amount of octadecanoids present in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
octadecanoids measurement
@@ -61901,7 +61947,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The determination of the amount of eicosanoids present in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
ecosanoids measurement
@@ -61927,7 +61973,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of phosphatidylcholine 18:1 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
PMID:34503513
phosphatidylcholine 18:1 measurement
@@ -61940,7 +61986,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of phosphatidate levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
phosphatidate measurement
@@ -61954,7 +62000,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of lysophosphatidylserine levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
lysophosphatidylserine measurement
@@ -61968,7 +62014,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of phosphatidylserines levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
phosphatidylserines measurement
@@ -61982,7 +62028,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 30:1 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
bile acid measurement
@@ -61996,7 +62042,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 30:0 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 30:1 measurement
@@ -62010,7 +62056,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 30:1 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 30:0 measurement
@@ -62024,7 +62070,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 28:0 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
PMID:34503513
diacylglycerol 28:0 measurement
@@ -62037,7 +62083,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 32:0 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 32:0 measurement
@@ -62051,7 +62097,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 32:2 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 32.2 measurement
@@ -62065,7 +62111,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 33:1 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 33:1 measurement
@@ -62079,7 +62125,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 33:3 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 33:3 measurement
@@ -62093,7 +62139,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 34:0 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 34:0 measurement
@@ -62107,7 +62153,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 34:3 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 34:3 measurement
@@ -62121,7 +62167,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 36:3 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 36:3 measurement
@@ -62135,7 +62181,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 36:4 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 36:4 measurement
@@ -62149,7 +62195,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 36:5 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 36:5 measurement
@@ -62163,7 +62209,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 38:3 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 38:3 measurement
@@ -62177,7 +62223,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 38:4 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 38:4 measurement
@@ -62191,7 +62237,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 38:5 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 38:5 measurement
@@ -62205,7 +62251,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 42:7 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 42:7 measurement
@@ -62219,7 +62265,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 44:7 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 44:7 measurement
@@ -62233,7 +62279,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
The quantification of diacylglycerol 44:6 levels in a sample, typically blood
- Annalisa Buniello
+ Annalisa Buniello
true
PMID:34503513
diacylglycerol 44:6 measurement
@@ -80752,7 +80798,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 15:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 15:0 measurement
@@ -80766,7 +80812,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 16:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 16:2 measurement
@@ -80780,7 +80826,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 17:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 17:0 measurement
@@ -80794,7 +80840,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 17:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 17:1 measurement
@@ -80808,7 +80854,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 20:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 20:0 measurement
@@ -80822,7 +80868,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 20:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 20:1 measurement
@@ -80836,7 +80882,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 20:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 20:2 measurement
@@ -80850,7 +80896,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 22:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 22:0 measurement
@@ -80864,7 +80910,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 22:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 22:1 measurement
@@ -80878,7 +80924,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 22:4 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 22:4 measurement
@@ -80892,7 +80938,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 22:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 22:5 measurement
@@ -80906,7 +80952,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 24:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 24:0 measurement
@@ -80920,7 +80966,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 24:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 24:1 measurement
@@ -80934,7 +80980,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 24:4 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 24:4 measurement
@@ -80948,7 +80994,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 24:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 24:5 measurement
@@ -80962,7 +81008,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of cholesteryl ester 24:6 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
cholesteryl ester 24:6 measurement
@@ -80976,7 +81022,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of GM1 ganglioside in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
GM1 ganglioside measurement
@@ -80990,7 +81036,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of GM3 ganglioside in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
GM3 ganglioside measurement
@@ -81004,7 +81050,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 17:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 17:0 measurement
@@ -81018,7 +81064,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 17:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 17:1 measurement
@@ -81032,7 +81078,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 18:3 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 18:3 measurement
@@ -81046,7 +81092,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 19:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 19:0 measurement
@@ -81060,7 +81106,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 20:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 20:0 measurement
@@ -81074,7 +81120,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 20:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 20:1 measurement
@@ -81088,7 +81134,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 20:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 20:2 measurement
@@ -81102,7 +81148,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 22:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 22:0 measurement
@@ -81116,7 +81162,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 22:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 22:1 measurement
@@ -81130,7 +81176,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 22:4 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 22:4 measurement
@@ -81144,7 +81190,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 22:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 22:5 measurement
@@ -81158,7 +81204,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 24:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 24:0 measurement
@@ -81172,7 +81218,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylcholine 26:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylcholine 26:0 measurement
@@ -81186,7 +81232,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of lysophosphatidylethanolamine 17:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
lysophosphatidylethanolamine 17:0 measurement
@@ -81200,7 +81246,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 28:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 28:0 measurement
@@ -81214,7 +81260,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 31:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 31:0 measurement
@@ -81228,7 +81274,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 33:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 33:0 measurement
@@ -81242,7 +81288,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 33:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 33:1 measurement
@@ -81256,7 +81302,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 33:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 33:2 measurement
@@ -81270,7 +81316,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 34:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 34:5 measurement
@@ -81284,7 +81330,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 35:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 35:5 measurement
@@ -81298,7 +81344,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 36:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 36:0 measurement
@@ -81312,7 +81358,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 36:6 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 36:6 measurement
@@ -81326,7 +81372,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 38:7 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 38:7 measurement
@@ -81340,7 +81386,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 39:5 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 39:5 measurement
@@ -81354,7 +81400,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 40:7 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 40:7 measurement
@@ -81368,7 +81414,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of phosphatidylcholine 40:8 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
phosphatidylcholine 40:8 measurement
@@ -81382,7 +81428,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 49:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 49:1 measurement
@@ -81396,7 +81442,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 50:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 50:0 measurement
@@ -81410,7 +81456,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 51:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 51:0 measurement
@@ -81424,7 +81470,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 51:1 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 51:1 measurement
@@ -81438,7 +81484,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 51:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 51:2 measurement
@@ -81452,7 +81498,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 53:2 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 53:2 measurement
@@ -81466,7 +81512,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of triacylglycerol 54:0 in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
triacylglycerol 54:0 measurement
@@ -81480,7 +81526,7 @@ of diseased coronary vessels at the time of a catheterization procedure. The var
Quantification of ubiquinone in a sample.
- Santhi Ramachandran
+ Santhi Ramachandran
true
PMID:35668104
ubiquinone measurement
diff --git a/external-dev/envo-slim.owl b/external-dev/envo-slim.owl
index f933b050..85be8e73 100644
--- a/external-dev/envo-slim.owl
+++ b/external-dev/envo-slim.owl
@@ -35,7 +35,7 @@
https://github.com/EnvironmentOntology/envo/
https://github.com/EnvironmentOntology/envo/issues/
Slimmer
- 2023-12-01 01:41:02
+ 2024-01-01 01:40:48
ENVO
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 679 Logical Axioms: 119]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 206 Logical Axioms: 34]
diff --git a/external-dev/fabio-slim.owl b/external-dev/fabio-slim.owl
index 732c1d51..33d499cd 100644
--- a/external-dev/fabio-slim.owl
+++ b/external-dev/fabio-slim.owl
@@ -33,7 +33,7 @@ FaBiO classes are structured according to the FRBR schema of Works, Expressions,
fabio
http://purl.org/spar/fabio/
Slimmer
- 2023-12-01 01:41:07
+ 2024-01-01 01:40:52
FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies. Other SPAR ontologies are described at http://purl.org/spar/.
This ontology is available at http://purl.org/spar/fabio, and uses the namespace prefix fabio.
diff --git a/external-dev/go-slim.owl b/external-dev/go-slim.owl
index 5edf4ac8..27707391 100644
--- a/external-dev/go-slim.owl
+++ b/external-dev/go-slim.owl
@@ -24,7 +24,7 @@
http://purl.obolibrary.org/obo/go.owl
Slimmer
- 2023-12-01 01:41:28
+ 2024-01-01 01:41:14
gene_ontology
1.2
2023-11-15
diff --git a/external-dev/iao-slim.owl b/external-dev/iao-slim.owl
index 2cdda605..b819e0b0 100644
--- a/external-dev/iao-slim.owl
+++ b/external-dev/iao-slim.owl
@@ -57,7 +57,7 @@
http://purl.obolibrary.org/obo/iao.owl
Slimmer
- 2023-12-01 01:41:31
+ 2024-01-01 01:41:17
An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
diff --git a/external-dev/msio-slim.owl b/external-dev/msio-slim.owl
index 4b049e81..93809e4a 100644
--- a/external-dev/msio-slim.owl
+++ b/external-dev/msio-slim.owl
@@ -181,7 +181,7 @@ http://www.cosmos-fp7.eu/WP2
Slimmer
Daniel Schober
2017-10-19T10:11:26Z
- 2023-12-01 01:44:39
+ 2024-01-01 01:44:28
Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
The BSD license on the BFO project site refers to code used to build BFO.
This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges.
diff --git a/external-dev/ncit-slim.owl b/external-dev/ncit-slim.owl
index c043e3b9..989564c5 100644
--- a/external-dev/ncit-slim.owl
+++ b/external-dev/ncit-slim.owl
@@ -21,7 +21,7 @@
NCI Thesaurus OBO Edition
http://purl.obolibrary.org/obo/ncit.owl
Slimmer
- 2023-12-01 01:43:42
+ 2024-01-01 01:43:29
NCI Thesaurus, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A.
23.09d
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/npo-slim.owl b/external-dev/npo-slim.owl
index 03d346d0..b2062840 100644
--- a/external-dev/npo-slim.owl
+++ b/external-dev/npo-slim.owl
@@ -17,7 +17,7 @@
http://purl.bioontology.org/ontology/npo
https://raw.githubusercontent.com/enanomapper/npo/master/npo-inferred.owl
Slimmer
- 2023-12-01 01:43:46
+ 2024-01-01 01:43:33
Inferred version created with Pellet reasoner in Protege editor (v. 4.1)
The NPO was primarily developed by Dennis G. Thomas in collaboration with Nathan A. Baker and Rohit V. Pappu. This development was supported by the NIH through grants U54 CA119342 and U54 HG004028.
2013-05-31 (yyyy-mm-dd)
diff --git a/external-dev/oae-slim.owl b/external-dev/oae-slim.owl
index 2e49e708..29b419ef 100644
--- a/external-dev/oae-slim.owl
+++ b/external-dev/oae-slim.owl
@@ -58,7 +58,7 @@
OAE: Ontology of Adverse Events
http://purl.obolibrary.org/obo/oae.owl
Slimmer
- 2023-12-01 01:43:53
+ 2024-01-01 01:43:40
1.2.47
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/obcs-slim.owl b/external-dev/obcs-slim.owl
index 9e7e5235..2d14313f 100644
--- a/external-dev/obcs-slim.owl
+++ b/external-dev/obcs-slim.owl
@@ -9,26 +9,36 @@
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
+ xmlns:pato="http://purl.obolibrary.org/obo/pato#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#"
xmlns:terms="http://purl.org/dc/terms/"
- xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
+ Alfred Hero
+ Anna Maria Masci
+ Chris Stoeckert
Barry Smith
Huan Li
Jean-François Ethier
Jie Zheng
+ Jinjing Guo
Marcy Harris
Qingzhi Liu
Yongqun "Oliver" He
Yu Lin
Adrien Barton
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.
+ OWL-DL
+ A formal ontology in the domain of biological and clinical statistics
+ OBCS: Ontology of Biological and Clinical Statistics
http://purl.obolibrary.org/obo/obcs.owl
Slimmer
- 2023-12-01 01:43:57
- 101
+ 2024-01-01 01:43:44
+ 2023-12-08
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
@@ -46,11 +56,17 @@
+
+
+
+
+
+
+
- BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
@@ -63,7 +79,6 @@
- BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
@@ -77,15 +92,13 @@
- editor preferred label
+ editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- editor preferred label
editor preferred term
- editor preferred term
@@ -96,7 +109,7 @@
example of usage
- A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
+ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
@@ -105,6 +118,19 @@
+
+
+
+
+ in branch
+ An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
+ GROUP:OBI
+ OBI_0000277
+ in branch
+
+
+
+
@@ -113,7 +139,6 @@
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
- OBI_0000281
has curation status
@@ -123,9 +148,8 @@
- definition
+ definition
- The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
@@ -146,13 +170,31 @@ We don't have definitions of 'meaning' or 'expression'
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
+We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
+ 2012-04-05:
+Barry Smith
+
+The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
+
+Can you fix to something like:
+
+A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
+
+Alan Ruttenberg
+
+Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
+
+On the specifics of the proposed definition:
+
+We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
+
+Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
+
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
- definition
- textual definition
@@ -165,7 +207,7 @@ We also have the outstanding issue of how to aim different definitions to differ
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
+ GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
editor note
@@ -179,7 +221,7 @@ We also have the outstanding issue of how to aim different definitions to differ
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
- 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
+ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
@@ -192,13 +234,15 @@ We also have the outstanding issue of how to aim different definitions to differ
- alternative term
+ alternative label
- An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
+ A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
PERSON:Daniel Schober
+ OBO Operations committee
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
+ Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
- alternative term
+ alternative label
@@ -209,16 +253,29 @@ We also have the outstanding issue of how to aim different definitions to differ
definition source
- formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
+ Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
+ Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source
+
+
+
+
+ has obsolescence reason
+ Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
+ PERSON:Alan Ruttenberg
+ PERSON:Melanie Courtot
+ has obsolescence reason
+
+
+
+
@@ -233,6 +290,50 @@ We also have the outstanding issue of how to aim different definitions to differ
+
+
+
+
+ term tracker item
+ the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
+
+ An IRI or similar locator for a request or discussion of an ontology term.
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
+ The 'tracker item' can associate a tracker with a specific ontology term.
+ term tracker item
+
+
+
+
+
+
+
+
+ ontology term requester
+
+ The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
+ The 'term requester' can credit the person, organization or project who request the ontology term.
+ ontology term requester
+
+
+
+
+
+
+
+
+ is denotator type
+ Relates an class defined in an ontology, to the type of it's denotator
+ In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
+ Alan Ruttenberg
+ is denotator type
+
+
+
+
@@ -249,6 +350,151 @@ We also have the outstanding issue of how to aim different definitions to differ
+
+
+
+
+ expand expression to
+ ObjectProperty: RO_0002104
+Label: has plasma membrane part
+Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
+
+ A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
+ Chris Mungall
+ expand expression to
+
+
+
+
+
+
+
+
+ expand assertion to
+ ObjectProperty: RO???
+Label: spatially disjoint from
+Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
+
+ A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
+ Chris Mungall
+ expand assertion to
+
+
+
+
+
+
+
+
+ first order logic expression
+ PERSON:Alan Ruttenberg
+ first order logic expression
+
+
+
+
+
+
+
+
+ antisymmetric property
+ part_of antisymmetric property xsd:true
+ Use boolean value xsd:true to indicate that the property is an antisymmetric property
+ Alan Ruttenberg
+ antisymmetric property
+
+
+
+
+
+
+
+
+
+ OBO foundry unique label
+
+ An alternative name for a class or property which is unique across the OBO Foundry.
+ The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
+ PERSON:Alan Ruttenberg
+ PERSON:Bjoern Peters
+ PERSON:Chris Mungall
+ PERSON:Melanie Courtot
+ GROUP:OBO Foundry <http://obofoundry.org/>
+ OBO foundry unique label
+
+
+
+
+
+
+
+
+ has ID digit count
+ Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"
+ Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
+ Person:Alan Ruttenberg
+ has ID digit count
+
+
+
+
+
+
+
+
+ has ID range allocated
+ Datatype: idrange:1
+Annotations: 'has ID range allocated to': "Chris Mungall"
+EquivalentTo: xsd:integer[> 2151 , <= 2300]
+
+ Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
+ Person:Alan Ruttenberg
+ has ID range allocated to
+
+
+
+
+
+
+
+
+ has ID policy for
+ Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"
+ Relating an ontology used to record id policy to the ontology namespace whose policy it manages
+ Person:Alan Ruttenberg
+ has ID policy for
+
+
+
+
+
+
+
+
+ has ID prefix
+ Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"
+ Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
+ Person:Alan Ruttenberg
+ has ID prefix
+
+
+
+
@@ -291,13 +537,98 @@ We also have the outstanding issue of how to aim different definitions to differ
+
+
+
+
+ is allocated id range
+ Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
+ PERSON:Alan Ruttenberg
+ Add as annotation triples in the granting ontology
+ is allocated id range
+
+
+
+
+
+
+
+
+ has ontology root term
+ Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
+ Nicolas Matentzoglu
+ has ontology root term
+
+
+
+
+
+
+
+
+ may be identical to
+ A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
+ David Osumi-Sutherland
+ #40
+ VFB
+ Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
+ may be identical to
+
+
+
+
+
+
+
+
+ scheduled for obsoletion on or after
+ Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
+ Chris Mungall, Jie Zheng
+ https://github.com/geneontology/go-ontology/issues/15532
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/32
+ GO ontology
+ scheduled for obsoletion on or after
+
+
+
+
+
+
+
+
+
+ has axiom id
+ Person:Alan Ruttenberg
+ Person:Alan Ruttenberg
+ A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
+
+ has axiom label
+
+
+
+
+
+
+
+
+ term replaced by
+
+ Use on obsolete terms, relating the term to another term that can be used as a substitute
+ Person:Alan Ruttenberg
+ Person:Alan Ruttenberg
+ Add as annotation triples in the granting ontology
+ term replaced by
+
+
+
+
A normal distribution probability density function has a formula of:
f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2))
- an annotation property that represents a mathematical formula.
+ An annotation property that represents a mathematical formula.
Asiyah Yu Lin, Jie Zheng, Yongqun He
mathematical formula
@@ -317,7 +648,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
-
@@ -332,7 +662,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term
-
@@ -347,7 +676,241 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
-
+
+
+
+
+
+
+
+
+ This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
+ OBO Operations call
+
+ logical characteristic of object property
+
+
+
+
+
+
+
+
+ 'part disjoint with' 'defined by construct' """
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX : <http://example.org/
+ CONSTRUCT {
+ [
+ a owl:Restriction ;
+ owl:onProperty :part_of ;
+ owl:someValuesFrom ?a ;
+ owl:disjointWith [
+ a owl:Restriction ;
+ owl:onProperty :part_of ;
+ owl:someValuesFrom ?b
+ ]
+ ]
+ }
+ WHERE {
+ ?a :part_disjoint_with ?b .
+ }
+ Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
+
+
+
+ defined by construct
+
+
+
+
+
+
+
+
+ CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
+ A synonym type for describing abbreviations or initalisms
+
+
+ 2023-03-03
+ abbreviation
+
+
+
+
+
+
+
+
+
+ A synonym type for describing ambiguous synonyms
+
+
+ 2023-03-03
+ ambiguous synonym
+
+
+
+
+
+
+
+
+
+ A synonym type for describing dubious synonyms
+
+
+ 2023-03-03
+ dubious synonym
+
+
+
+
+
+
+
+
+
+ EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
+ A synonym type for describing layperson or colloquial synonyms
+
+
+ 2023-03-03
+ layperson synonym
+
+
+
+
+
+
+
+
+
+ CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
+ A synonym type for describing pluralization synonyms
+
+
+ 2023-03-03
+ plural form
+
+
+
+
+
+
+
+
+
+ CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
+ A synonym type for describing UK spelling variants
+
+
+ 2023-03-03
+ UK spelling synonym
+
+
+
+
+
+
+
+
+
+ A synonym type for common misspellings
+
+
+ 2023-03-03
+ misspelling
+
+
+
+
+
+
+
+
+
+ A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
+
+
+ 2023-03-03
+ misnomer
+
+
+
+
+
+
+
+
+
+ MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
+ A synonym type for names that have been used as primary labels in the past.
+
+
+ 2023-07-25
+ previous name
+
+
+
+
+
+
+
+
+
+ The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
+ A synonym type for the legal entity name
+
+
+ 2023-07-27
+ legal name
+
+
+
+
+
+
+
+
+
+ CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
+ The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
+
+
+ 2023-09-30
+ INN
+ International Nonproprietary Name
+
+
+
+
+
+
+
+
+
+ nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
+ A synonym type for describing Latin term synonyms.
+
+
+ 2023-10-12
+ latin term
+
+
+
+
+
+
+
+
+
+ NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
+ A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
+
+
+ 2023-11-01
+ acronym
+
@@ -356,13 +919,204 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
- temporal interpretation
- temporal interpretation
- https://code.google.com/p/obo-relations/wiki/ROAndTime
+ An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
+ temporal interpretation
+
+
+
+
+
+
+
+
+
+ tooth SubClassOf 'never in taxon' value 'Aves'
+ x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
+
+
+
+ Class: ?X DisjointWith: RO_0002162 some ?Y
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
+PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
+CONSTRUCT {
+ in_taxon: a owl:ObjectProperty .
+ a owl:Restriction ;
+ owl:onProperty in_taxon: ;
+ owl:someValuesFrom ?taxon
+ ] .
+ ?x rdfs:subClassOf [
+ a owl:Restriction ;
+ owl:onProperty in_taxon: ;
+ owl:someValuesFrom [
+ a owl:Class ;
+ owl:complementOf ?taxon
+ ]
+ ] .
+}
+WHERE {
+ ?x never_in_taxon: ?taxon .
+}
+ never in taxon
+
+
+
+
+
+
+
+
+
+ A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
+ non-overlapping with
+ shares no parts with
+
+ Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
+PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171>
+CONSTRUCT {
+ part_of: a owl:ObjectProperty .
+ [
+ a owl:Restriction ;
+ owl:onProperty part_of: ;
+ owl:someValuesFrom ?x ;
+ a owl:Restriction ;
+ owl:onProperty part_of: ;
+ owl:someValuesFrom ?y
+ ]
+ ]
+}
+WHERE {
+ ?x mutually_spatially_disjoint_with: ?y .
+}
+ mutually spatially disjoint with
+
+ https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
+
+
+
+
+
+
+
+
+ An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
+ taxonomic class assertion
+
+
+
+
+
+
+
+
+
+ S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
+
+
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
+PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
+CONSTRUCT {
+ in_taxon: a owl:ObjectProperty .
+ ?witness rdfs:label ?label .
+ ?witness rdfs:subClassOf ?x .
+ ?witness rdfs:subClassOf [
+ a owl:Restriction ;
+ owl:onProperty in_taxon: ;
+ owl:someValuesFrom ?taxon
+ ] .
+}
+WHERE {
+ ?x present_in_taxon: ?taxon .
+ BIND(IRI(CONCAT(
+ "http://purl.obolibrary.org/obo/RO_0002175#",
+ MD5(STR(?x)),
+ "-",
+ MD5(STR(?taxon))
+ )) as ?witness)
+ BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label)
+}
+ The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
+ present in taxon
+
+
+
+
+
+ An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
+ logical macro assertion
+ http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/
+
+
+
+
+
+
+
+
+ A logical macro assertion whose domain is an IRI for a class
+ The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
+ logical macro assertion on a class
+
+
+
+
+
+
+
+
+ A logical macro assertion whose domain is an IRI for a property
+ logical macro assertion on a property
+
+
+
+
+
+
+
+
+ Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
+ logical macro assertion on an object property
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -370,6 +1124,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
@@ -377,20 +1138,94 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
- The present resource may be derived from the Source resource
- in whole or in part. Recommended best practice is to reference
- the resource by means of a string or number conforming to a
- formal identification system.
- A reference to a resource from which the present resource
- is derived.
-
- Source
- Source
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -401,6 +1236,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
@@ -408,6 +1250,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
@@ -415,6 +1264,20 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -422,6 +1285,27 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
+
+
+
+
+
+
+
+
+
+
+ An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/18
+ has broad synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/18
+
+
+
+
+
@@ -431,52 +1315,113 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
-
+
-
- label
+
+ An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/20
+ has exact synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/20
+
-
+
-
+
+ An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/19
+ has narrow synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/19
+
+
-
+
+
-
+
-
+
+ An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/21
+ has related synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/21
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
-
-
+
-
+
@@ -499,7 +1444,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
- a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
+ An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
@@ -515,6 +1460,7 @@ JAR: A data item is an approximately justified approximately true approximate be
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
+
data item
@@ -529,7 +1475,7 @@ JAR: A data item is an approximately justified approximately true approximate be
Yongqun He
Fisher-Snedecor distribution
WEB: http://stattrek.com/probability-distributions/f-distribution.aspx
- STATO_0000204
+ STATO:0000204
F distribution
@@ -543,7 +1489,7 @@ JAR: A data item is an approximately justified approximately true approximate be
A continuous probability distribution that is a two-parameter family of continuous probability distributions.
Yongqun He
WEB: http://en.wikipedia.org/wiki/Gamma_distribution
- STATO_0000268
+ STATO:0000268
gamma distribution
@@ -558,7 +1504,7 @@ JAR: A data item is an approximately justified approximately true approximate be
Yongqun He
Gaussian distribution
WEB: http://en.wikipedia.org/wiki/Normal_distribution
- STATO_0000227
+ STATO:0000227
normal distribution
@@ -573,7 +1519,7 @@ JAR: A data item is an approximately justified approximately true approximate be
Yongqun He
t-distribution
WEB: http://stattrek.com/probability-distributions/t-distribution.aspx
- STATO_0000059
+ STATO:0000059
Student's t distribution
@@ -761,7 +1707,7 @@ JAR: A data item is an approximately justified approximately true approximate be
A probability distribution that with k degrees of freedom is the distribution of a sum of the squares of k independent standard normal random variables.
Yongqun He
WEB: http://en.wikipedia.org/wiki/Chi-square_distribution
- STATO_0000229
+ STATO:0000229
chi-square distribution
@@ -775,7 +1721,7 @@ JAR: A data item is an approximately justified approximately true approximate be
A continuous probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate.
Yongqun He
WEB: http://en.wikipedia.org/wiki/Exponential_distribution
- STATO_0000160
+ STATO:0000160
exponential distribution
@@ -949,9 +1895,7 @@ The variance is p*q
- negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur.
-
-The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.
+ negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur. The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.
negative binomial distribution
@@ -986,7 +1930,7 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
- Person:Alan Ruttenberg
+ Person:Alan Ruttenberg
failed exploratory term
@@ -1008,8 +1952,7 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
organizational term
- term created to ease viewing/sort terms for development purpose, and will not be included in a release
- PERSON:Alan Ruttenberg
+ Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
@@ -1063,11 +2006,12 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
- core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
- core
+
+ obsolete_core
+ true
@@ -1119,11 +2063,11 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
- universal
- Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
- Alan Ruttenberg
- A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
- universal
+ universal
+ Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
+ Alan Ruttenberg
+ A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
+ universal
@@ -1132,11 +2076,11 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
- defined class
- A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
- "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
- Alan Ruttenberg
- defined class
+ defined class
+ A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
+ "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
+ Alan Ruttenberg
+ defined class
@@ -1145,11 +2089,11 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
- named class expression
- A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
- named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
- Alan Ruttenberg
- named class expression
+ named class expression
+ A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
+ named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
+ Alan Ruttenberg
+ named class expression
@@ -1184,7 +2128,7 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
- An confidence interval with 95 percent probability that the true population value can be found.
+ An confidence interval with 95 percent probability that the true population value can be found.
Jie Zheng
95% confidence interval
@@ -1224,87 +2168,64 @@ The negative binomial distribution, also known as the Pascal distribution or Pó
-
+
-
- Edingburgh handedness inventory
-
- The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
- PERSON:Alan Ruttenberg
- PERSON:Jessica Turner
- PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
- WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
- Edingburgh handedness inventory
+
+ The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
+ This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/77
+ https://orcid.org/0000-0001-5208-3432
+ out of scope
-
-
+
-
- axiom holds for all times
-
-## Elucidation
-
-This is used when the statement/axiom is assumed to hold true 'eternally'
-
-## How to interpret (informal)
-
-First the "atemporal" FOL is derived from the OWL using the standard
-interpretation. This axiom is temporalized by embedding the axiom
-within a for-all-times quantified sentence. The t argument is added to
-all instantiation predicates and predicates that use this relation.
-
-## Example
-
- Class: nucleus
- SubClassOf: part_of some cell
-
- forall t :
- forall n :
- instance_of(n,Nucleus,t)
- implies
- exists c :
- instance_of(c,Cell,t)
- part_of(n,c,t)
-
-## Notes
-
-This interpretation is *not* the same as an at-all-times relation
-
-
- axiom holds for all times
+
+ The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
+ This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/136
+ https://orcid.org/0000-0002-4142-7153
+ domain entity does not exist
-
-
-
-
-
-
-
-
- Description may include but is not limited to: an abstract,
- table of contents, reference to a graphical representation
- of content or a free-text account of the content.
- An account of the content of the resource.
-
- Description
- Description
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/external-dev/obi-slim.owl b/external-dev/obi-slim.owl
index 11d000e8..44cee41a 100644
--- a/external-dev/obi-slim.owl
+++ b/external-dev/obi-slim.owl
@@ -82,7 +82,7 @@
Ontology for Biomedical Investigations
http://purl.obolibrary.org/obo/obi.owl
Slimmer
- 2023-12-01 01:44:02
+ 2024-01-01 01:43:50
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
2023-09-20
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/pato-slim.owl b/external-dev/pato-slim.owl
index d4e3f885..7a9c8d8c 100644
--- a/external-dev/pato-slim.owl
+++ b/external-dev/pato-slim.owl
@@ -39,7 +39,7 @@
http://purl.obolibrary.org/obo/pato.owl
Slimmer
- 2023-12-01 01:44:12
+ 2024-01-01 01:44:00
quality
1.2
2023-05-18
diff --git a/external-dev/sio-slim.owl b/external-dev/sio-slim.owl
index f4ede258..6d8459a2 100644
--- a/external-dev/sio-slim.owl
+++ b/external-dev/sio-slim.owl
@@ -80,7 +80,7 @@ mailing list: http://groups.google.com/group/sio-ontology
role chains:
'has capability' o 'is realized in' -> 'is participant in'
Slimmer
- 2023-12-01 01:44:15
+ 2024-01-01 01:44:03
http://sio.semanticscience.org
1.59
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
diff --git a/external-dev/uberon-slim.owl b/external-dev/uberon-slim.owl
index 96ffa011..7319c36c 100644
--- a/external-dev/uberon-slim.owl
+++ b/external-dev/uberon-slim.owl
@@ -158,14 +158,13 @@
https://github.com/obophenotype/uberon/issues/
https://lists.sourceforge.net/lists/listinfo/obo-anatomy
Slimmer
- 2023-12-01 01:44:33
+ 2024-01-01 01:44:22
uberon
1.2
AEO
BILA
BSPO
CARO
- EFO
GO
OG
VSAO
@@ -174,17 +173,18 @@
NCIT
OGES
SCTID
+ BFO
VHOG
AAO part_of NCBITaxon:8292
DHBA part_of NCBITaxon:9606
EHDAA2 part_of NCBITaxon:9606
EMAPA part_of NCBITaxon:10090
- FBbt part_of NCBITaxon:7227
FBdv part_of NCBITaxon:7227
FMA part_of NCBITaxon:9606
HAO part_of NCBITaxon:7399
HBA part_of NCBITaxon:9606
HsapDv part_of NCBITaxon:9606
+ KUPO part_of NCBITaxon:9606
MA part_of NCBITaxon:10090
MFO part_of NCBITaxon:8089
MmusDv part_of NCBITaxon:10090
@@ -3705,6 +3705,7 @@ WHERE {
AAO:0010841
AEO:0000000
+ BFO:0000004
BILA:0000000
BIRNLEX:6
CARO:0000000
diff --git a/external-dev/uo-slim.owl b/external-dev/uo-slim.owl
index 61522151..5e3b8e15 100644
--- a/external-dev/uo-slim.owl
+++ b/external-dev/uo-slim.owl
@@ -12,7 +12,7 @@
http://purl.obolibrary.org/obo/uo.owl
Slimmer
- 2023-12-01 01:44:36
+ 2024-01-01 01:44:24
2023-05-25
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.