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Zfin import models #184

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Jul 22, 2021
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aea07dc
add ZFIN models
sierra-moxon May 6, 2021
474c681
add ZFIN models
sierra-moxon May 6, 2021
a5dddb3
add ZFIN models
sierra-moxon May 6, 2021
7eb00c5
add ZFIN models
sierra-moxon May 6, 2021
4c3ade0
add ZFIN models
sierra-moxon May 6, 2021
4f0547a
add ZFIN models
sierra-moxon May 6, 2021
876cb61
add ZFIN models
sierra-moxon May 6, 2021
8ebcdd7
add ZFIN models
sierra-moxon May 6, 2021
bf7340d
add ZFIN models
sierra-moxon May 6, 2021
c8ecc7b
add ZFIN models
sierra-moxon May 6, 2021
62222c9
add ZFIN models
sierra-moxon May 6, 2021
07b9f78
add ZFIN models
sierra-moxon May 6, 2021
1dcd537
add ZFIN models
sierra-moxon May 6, 2021
e52e17e
add ZFIN models
sierra-moxon May 6, 2021
a8069c6
add ZFIN models
sierra-moxon May 6, 2021
e1889ed
add ZFIN models
sierra-moxon May 6, 2021
c250216
add ZFIN models
sierra-moxon May 6, 2021
0c602d0
add ZFIN models
sierra-moxon May 6, 2021
d6cf08b
add ZFIN-GENEP
sierra-moxon May 6, 2021
87ac9c7
fixing travis
sierra-moxon May 6, 2021
f0ed5ff
convert travis to github actions
sierra-moxon May 6, 2021
d0dbc9d
adding providedBy tag to namedIndividuals
sierra-moxon May 13, 2021
e98d3ae
change to production models
sierra-moxon May 13, 2021
1a71393
add models with IPI evidence-with value
sierra-moxon May 26, 2021
ce431bd
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
48ac1d2
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
49b156c
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
9cb760b
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
5a750df
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
c505207
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
5394af1
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
ebf3b84
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
36e3de9
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
7d7a8b1
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
53c4c84
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
ee1ff23
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
f0c282a
regenerate models with only one pub instead of ZDB-PUB and PMID
sierra-moxon Jun 3, 2021
0a80cb7
Merge branch 'master' into zfin_import_models
sierra-moxon Jun 23, 2021
7ddb136
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
9f83bdc
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
93b4856
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
f200c4c
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
5b6430a
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
2c3f624
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
5d383a8
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
7cda123
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
ffeac24
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
3e595f7
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
f32dc16
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
49c7ba8
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
cf8fc7d
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
d7afc5e
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
bbb0d6e
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
71c369a
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
05ef8dd
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
482b585
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
956fa45
updated zfin models with corrected title
sierra-moxon Jun 23, 2021
0f56453
updated to merged gene id
sierra-moxon Jul 12, 2021
966d5c3
migrating gene to merged gene id
sierra-moxon Jul 12, 2021
e16ec02
merging in master
sierra-moxon Jul 12, 2021
22be256
Merge branch 'master' into zfin_import_models
sierra-moxon Jul 22, 2021
15fd422
Merge branch 'master' into zfin_import_models
sierra-moxon Jul 22, 2021
2ef1ce1
Merge branch 'master' into zfin_import_models
sierra-moxon Jul 22, 2021
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17 changes: 17 additions & 0 deletions .github/workflows/run-tests.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
name: run-owltools-test
on: [push]

jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2

- name: Run tests
run: |
mkdir -p bin
export PATH=$PATH:$PWD/bin
wget https://github.com/owlcollab/owltools/releases/download/2020-04-06/owltools -O bin/owltools
wget https://github.com/owlcollab/owltools/releases/download/2020-04-06/owltools-oort-all.jar -O bin/owltools-runner-all.jar
chmod +x bin/*
make travis-test
13 changes: 8 additions & 5 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,12 +1,15 @@
language: java
jdk:
- oraclejdk8
dist: xenial

before_install:
- sudo apt-get update
- sudo apt-get install -y wget

before_script:
- mkdir -p bin
- export PATH=$PATH:$PWD/bin
- wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools
- wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar
- wget https://github.com/owlcollab/owltools/releases/download/2020-04-06/owltools -O bin/owltools
- wget https://github.com/owlcollab/owltools/releases/download/2020-04-06/owltools-oort-all.jar -O bin/owltools-runner-all.jar
- chmod +x bin/*

# command to run tests
Expand All @@ -22,5 +25,5 @@ branches:

notifications:
email:
- cjmungall@lbl.gov
- sjcarbon@lbl.gov

14 changes: 7 additions & 7 deletions models/593423e000000023.ttl
Original file line number Diff line number Diff line change
Expand Up @@ -138,14 +138,14 @@ owl:versionInfo rdf:type owl:AnnotationProperty .
# Classes
#################################################################

### http://identifiers.org/zfin/ZDB-GENE-090929-156
<http://identifiers.org/zfin/ZDB-GENE-090929-156> rdf:type owl:Class ;
<http://www.geneontology.org/formats/oboInOwl#id> "ZFIN:ZDB-GENE-090929-156"^^xsd:string .
### http://identifiers.org/zfin/ZDB-MIRNAG-090929-156
<http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> rdf:type owl:Class ;
<http://www.geneontology.org/formats/oboInOwl#id> "ZFIN:ZDB-MIRNAG-090929-156"^^xsd:string .

[ rdf:type owl:Axiom ;
owl:annotatedSource <http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
owl:annotatedSource <http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
owl:annotatedProperty <http://www.geneontology.org/formats/oboInOwl#id> ;
owl:annotatedTarget "ZFIN:ZDB-GENE-090929-156"^^xsd:string ;
owl:annotatedTarget "ZFIN:ZDB-MIRNAG-090929-156"^^xsd:string ;
<http://geneontology.org/lego/derived> "true"^^xsd:string
] .

Expand All @@ -172,7 +172,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty .

### http://model.geneontology.org/593423e000000023/593423e000000752
<http://model.geneontology.org/593423e000000023/593423e000000752> rdf:type owl:NamedIndividual ,
<http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
<http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-1009-339X"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2017-06-04"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .
Expand Down Expand Up @@ -232,7 +232,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty .

### http://model.geneontology.org/593423e000000023/593423e000000761
<http://model.geneontology.org/593423e000000023/593423e000000761> rdf:type owl:NamedIndividual ,
<http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
<http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-1009-339X"^^xsd:string ;
<http://purl.org/dc/elements/1.1/date> "2017-06-04"^^xsd:string ;
<http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .
Expand Down
8 changes: 4 additions & 4 deletions models/5966411600000170.ttl
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@

<http://identifiers.org/zfin/ZDB-GENE-070912-124> a <http://www.w3.org/2002/07/owl#Class> .

<http://identifiers.org/zfin/ZDB-GENE-090929-156> a <http://www.w3.org/2002/07/owl#Class> .
<http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> a <http://www.w3.org/2002/07/owl#Class> .

<http://identifiers.org/zfin/ZDB-GENE-091027-1> a <http://www.w3.org/2002/07/owl#Class> .

Expand Down Expand Up @@ -167,7 +167,7 @@
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2021-02-02"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://model.geneontology.org/5966411600000170/5966411600000198> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
<http://model.geneontology.org/5966411600000170/5966411600000198> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2017-07-12"^^<http://www.w3.org/2001/XMLSchema#string> .

Expand Down Expand Up @@ -259,7 +259,7 @@
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2021-02-02"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://model.geneontology.org/5966411600000170/596a6e0600000057> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
<http://model.geneontology.org/5966411600000170/596a6e0600000057> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2017-07-17"^^<http://www.w3.org/2001/XMLSchema#string> .

Expand All @@ -274,7 +274,7 @@
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2021-02-02"^^<http://www.w3.org/2001/XMLSchema#string> .

<http://model.geneontology.org/5966411600000170/596a6e0600000060> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-GENE-090929-156> ;
<http://model.geneontology.org/5966411600000170/596a6e0600000060> a <http://www.w3.org/2002/07/owl#NamedIndividual> , <http://identifiers.org/zfin/ZDB-MIRNAG-090929-156> ;
<http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0002-4142-7153"^^<http://www.w3.org/2001/XMLSchema#string> ;
<http://purl.org/dc/elements/1.1/date> "2017-07-17"^^<http://www.w3.org/2001/XMLSchema#string> .

Expand Down
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