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data update: OT 21.02, intact, ensembl
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data update: OT 21.02, intact, ensembl
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Daniel Suveges authored Feb 15, 2021
2 parents 96e2f06 + 2336a75 commit 956d632
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18 changes: 9 additions & 9 deletions Makefile
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Expand Up @@ -13,25 +13,25 @@ UNIPROTCOVIDQUERY="https://www.ebi.ac.uk/uniprot/api/covid-19/uniprotkb/stream?f
UNIPROTIDMAPPINGURL=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz

# OT files
OTTRACTABILITYBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/input/annotation-files/tractability_buckets-2020-08-14.tsv
OTKNOWNTARGETSAFETYBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/input/annotation-files/known_target_safety-2020-09-02.json
OTEXPERIMENTALTOXICITYBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/input/annotation-files/experimental-toxicity-2020-04-07.tsv
OTBASELINEBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/input/annotation-files/baseline_expression_counts-2020-05-07.tsv
OTTRACTABILITYBUCKET="https://storage.googleapis.com/open-targets-data-releases/21.02/input/annotation-files/tractability_buckets-2021-01-12.tsv"
OTKNOWNTARGETSAFETYBUCKET=https://storage.googleapis.com/open-targets-data-releases/21.02/input/annotation-files/known_target_safety-2021-02-09.json
OTEXPERIMENTALTOXICITYBUCKET=https://storage.googleapis.com/open-targets-data-releases/21.02/input/annotation-files/experimental-toxicity-2020-04-07.tsv
OTBASELINEBUCKET=https://storage.googleapis.com/open-targets-data-releases/21.02/input/annotation-files/baseline_expression_counts-2020-05-07.tsv
OTBASELINETISSUEMAPGITHUB=https://raw.githubusercontent.com/opentargets/expression_hierarchy/master/process/map_with_efos.json
OTEVIDENCEBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/output/20.09_evidence_data.json.gz
OTTARGETLISTBUCKET=https://storage.googleapis.com/open-targets-data-releases/20.09/output/20.09_target_list.csv.gz
OTEVIDENCEBUCKET=https://storage.googleapis.com/open-targets-data-releases/21.02/output/21.02_evidence_data.json.gz
OTTARGETLISTBUCKET=https://storage.googleapis.com/open-targets-data-releases/21.02/output/21.02_target_list.csv.gz

# Ensembl json
ENSEMBLURL = ftp://ftp.ensembl.org/pub/release-100/json/homo_sapiens/homo_sapiens.json
ENSEMBLURL = ftp://ftp.ensembl.org/pub/release-102/json/homo_sapiens/homo_sapiens.json

# COVID complex file:
COVIDCOMPLEXURL=http://ftp.ebi.ac.uk/pub/databases/IntAct/complex/2020-09-25/complextab/sars-cov-2.tsv
COVIDCOMPLEXURL=http://ftp.ebi.ac.uk/pub/databases/IntAct/complex/2020-11-05/complextab/sars-cov-2.tsv

# IntAct COVID related interaction query:
INTACTCOVIDURL="https://www.ebi.ac.uk/intact/export?format=mitab_27&query=annot%3A%22dataset%3ACoronavirus%22&negative=false&spoke=false&ontology=false&sort=intact-miscore&asc=false"

# Full human intact data:
INTACTHUMANURL='ftp://ftp.ebi.ac.uk/pub/databases/intact/various/ot_graphdb/2020-10-05/data/interactor_pair_interactions.json'
INTACTHUMANURL='ftp://ftp.ebi.ac.uk/pub/databases/intact/various/ot_graphdb/2021-01-18/data/interactor_pair_interactions.json'

# HPA
HPAURL=https://www.proteinatlas.org/download/proteinatlas.json.gz
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64 changes: 32 additions & 32 deletions docs/metrics.md
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@@ -1,6 +1,6 @@
COVID data integration report
================
09 October, 2020
15 February, 2021

# Data available

Expand All @@ -22,38 +22,38 @@ df %>%
## Warning: Unknown levels in `f`: ensembl_id, drugs_in_covid_trials

| variable | Category | targets |
| :------------------------------------------- | :------------------------------- | ------: |
| scientificName | TARGET INFO | 27639 |
| name | TARGET INFO | 27610 |
| biotype | TARGET INFO | 27610 |
| description | TARGET INFO | 27418 |
| uniprot\_ids | TARGET INFO | 19872 |
| COVID-19 UniprotKB | TARGET INFO | 57 |
| FILTER\_network | FILTERS | 7639 |
| FILTER\_network+drug | FILTERS | 395 |
| FILTER\_network+covid\_tests | FILTERS | 7961 |
| Covid\_direct\_interactions | PROTEIN INTERACTIONS | 1653 |
| Covid\_indirect\_interactions | PROTEIN INTERACTIONS | 6781 |
| Implicated\_in\_viral\_infection | PROTEIN INTERACTIONS | 1904 |
| max\_phase | DRUGS FOR TARGET | 1191 |
| drugs\_in\_clinic | DRUGS FOR TARGET | 1191 |
| has\_invitro\_covid\_activity | DRUGS FOR TARGET | 522 |
| invitro\_covid\_activity | DRUGS FOR TARGET | 522 |
|:---------------------------------------------|:---------------------------------|--------:|
| scientificName | TARGET INFO | 27682 |
| name | TARGET INFO | 27650 |
| biotype | TARGET INFO | 27650 |
| description | TARGET INFO | 27628 |
| uniprot\_ids | TARGET INFO | 19882 |
| COVID-19 UniprotKB | TARGET INFO | 92 |
| FILTER\_network | FILTERS | 8573 |
| FILTER\_network+drug | FILTERS | 439 |
| FILTER\_network+covid\_tests | FILTERS | 8874 |
| Covid\_direct\_interactions | PROTEIN INTERACTIONS | 2009 |
| Covid\_indirect\_interactions | PROTEIN INTERACTIONS | 7566 |
| Implicated\_in\_viral\_infection | PROTEIN INTERACTIONS | 2387 |
| max\_phase | DRUGS FOR TARGET | 1202 |
| drugs\_in\_clinic | DRUGS FOR TARGET | 1202 |
| has\_invitro\_covid\_activity | DRUGS FOR TARGET | 520 |
| invitro\_covid\_activity | DRUGS FOR TARGET | 520 |
| has\_drug\_in\_covid\_trials | DRUGS FOR TARGET | 99 |
| hpa\_subcellular\_location | BASELINE GENE EXPRESSION | 12297 |
| hpa\_rna\_tissue\_distribution | BASELINE GENE EXPRESSION | 19347 |
| hpa\_rna\_tissue\_specificity | BASELINE GENE EXPRESSION | 19347 |
| hpa\_rna\_specific\_tissues | BASELINE GENE EXPRESSION | 10838 |
| respiratory\_system\_is\_expressed | BASELINE GENE EXPRESSION | 20124 |
| respiratory\_system\_expressed\_tissue\_list | BASELINE GENE EXPRESSION | 26021 |
| immune\_system\_is\_expressed | BASELINE GENE EXPRESSION | 22765 |
| immune\_system\_expressed\_tissue\_list | BASELINE GENE EXPRESSION | 26021 |
| is\_abundance\_reg\_on\_covid | COVID-19 HOST PROTEIN REGULATION | 1147 |
| abundance\_reg\_on\_covid | COVID-19 HOST PROTEIN REGULATION | 1147 |
| Tractability\_Top\_bucket\_(sm) | TARGET TRACTABILITY | 5035 |
| Tractability\_Top\_bucket\_(ab) | TARGET TRACTABILITY | 9882 |
| Tractability\_Top\_bucket\_(other) | TARGET TRACTABILITY | 215 |
| hpa\_subcellular\_location | BASELINE GENE EXPRESSION | 12709 |
| hpa\_rna\_tissue\_distribution | BASELINE GENE EXPRESSION | 19364 |
| hpa\_rna\_tissue\_specificity | BASELINE GENE EXPRESSION | 19364 |
| hpa\_rna\_specific\_tissues | BASELINE GENE EXPRESSION | 10848 |
| respiratory\_system\_is\_expressed | BASELINE GENE EXPRESSION | 20132 |
| respiratory\_system\_expressed\_tissue\_list | BASELINE GENE EXPRESSION | 26039 |
| immune\_system\_is\_expressed | BASELINE GENE EXPRESSION | 22778 |
| immune\_system\_expressed\_tissue\_list | BASELINE GENE EXPRESSION | 26039 |
| is\_abundance\_reg\_on\_covid | COVID-19 HOST PROTEIN REGULATION | 1145 |
| abundance\_reg\_on\_covid | COVID-19 HOST PROTEIN REGULATION | 1145 |
| Tractability\_Top\_bucket\_(sm) | TARGET TRACTABILITY | 5030 |
| Tractability\_Top\_bucket\_(ab) | TARGET TRACTABILITY | 9890 |
| Tractability\_Top\_bucket\_(other) | TARGET TRACTABILITY | 222 |
| has\_safety\_risk | TARGET SAFETY | 439 |
| safety\_info\_source | TARGET SAFETY | 439 |
| safety\_organs\_systems\_affected | TARGET SAFETY | 193 |
| covid\_literature | LITERATURE | 264 |
| covid\_literature | LITERATURE | 1096 |

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