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_dynamic_files.jinja2
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{#-
Jinja2 Template for multile dynamic files
See odk.py for how this is processed.
This is first expanded into a single text file;
Each entry starting with ^^^ denotes a single file
-#}
{#-
Ontology source file, e.g. src/ontology/foo-edit.owl
We seed this with basic info such as ontology IRI and
a fake root class (this can be customized).
Note that when running odk.py, you can pass in a --source
argument to substitute this with your own edit file
#}
^^^ src/ontology/{{ project.id }}-edit.{{ project.edit_format }}
{% if project.edit_format == "obo" %}
format-version: 1.2
{% if project.import_group is defined -%}
{% for imp in project.import_group.products %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/imports/{{ imp.id }}_import.owl
{% endfor %}
{% endif %}
{%- if project.use_dosdps %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/patterns/definitions.owl
{%- if project.import_pattern_ontology %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/patterns/pattern.owl
{% endif -%}
{% endif %}
ontology: {{project.id}}
property_value: http://purl.org/dc/terms/description "{{ project.description }}" xsd:string
property_value: http://purl.org/dc/terms/title "{{ project.title }}" xsd:string
property_value: http://purl.org/dc/terms/license {{ project.license }}
[Term]
id: {{ project.id | upper }}:0000000
name: root node
[Typedef]
id: http://purl.org/dc/terms/description
name: description
is_metadata_tag: true
[Typedef]
id: http://purl.org/dc/terms/title
name: title
is_metadata_tag: true
[Typedef]
id: http://purl.org/dc/terms/license
name: license
is_metadata_tag: true
{% else %}
Prefix(:=<http://purl.obolibrary.org/obo/{{ project.id }}.owl#>)
Prefix(dce:=<http://purl.org/dc/elements/1.1/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(dcterms:=<http://purl.org/dc/terms/>)
Ontology(<http://purl.obolibrary.org/obo/{{ project.id }}.owl>
{% if project.import_group is defined -%}
{% for imp in project.import_group.products %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/imports/{{ imp.id }}_import.owl>)
{% endfor %}
{% endif %}
{%- if project.use_dosdps %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/patterns/definitions.owl>)
{%- if project.import_pattern_ontology %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/patterns/pattern.owl>)
{% endif -%}
{% endif %}
Annotation(dcterms:description "{{ project.description }}")
Annotation(dcterms:license <{{ project.license }}>)
Annotation(dcterms:title "{{ project.title }}")
Declaration(Class(<http://purl.obolibrary.org/obo/{{ project.id | upper }}_0000000>))
Declaration(AnnotationProperty(dcterms:description))
Declaration(AnnotationProperty(dcterms:license))
Declaration(AnnotationProperty(dcterms:title))
############################
# Annotation Properties
############################
AnnotationAssertion(rdfs:label dcterms:description "description")
AnnotationAssertion(rdfs:label dcterms:license "license")
AnnotationAssertion(rdfs:label dcterms:title "title")
############################
# Classes
############################
# Class: <http://purl.obolibrary.org/obo/{{ project.id | upper }}_0000000> (root node)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/{{ project.id | upper }}_0000000> "root node"@en)
)
{% endif %}
{#-
ID ranges file
#}
^^^ src/ontology/{{ project.id }}-idranges.owl
## ID Ranges File
Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Prefix: idsfor: <http://purl.obolibrary.org/obo/IAO_0000598>
Prefix: dce: <http://purl.org/dc/elements/1.1/>
Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>
Prefix: allocatedto: <http://purl.obolibrary.org/obo/IAO_0000597>
Prefix: xml: <http://www.w3.org/XML/1998/namespace>
Prefix: idprefix: <http://purl.obolibrary.org/obo/IAO_0000599>
Prefix: iddigits: <http://purl.obolibrary.org/obo/IAO_0000596>
Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>
Prefix: idrange: <http://purl.obolibrary.org/obo/ro/idrange/>
Prefix: owl: <http://www.w3.org/2002/07/owl#>
Ontology: <http://purl.obolibrary.org/obo/{{ project.id }}/{{ project.id }}-idranges.owl>
Annotations:
idsfor: "{{ project.id | upper }}",
idprefix: "http://purl.obolibrary.org/obo/{{ project.id | upper }}_",
iddigits: 7
AnnotationProperty: idprefix:
AnnotationProperty: iddigits:
AnnotationProperty: idsfor:
AnnotationProperty: allocatedto:
Datatype: idrange:1
Annotations:
allocatedto: "ONTOLOGY-CREATOR"
EquivalentTo:
xsd:integer[>= 0 , <= 999999]
Datatype: idrange:2
Annotations:
allocatedto: "ADDITIONAL EDITOR"
EquivalentTo:
xsd:integer[>= 1000000 , <= 1999999]
Datatype: xsd:integer
Datatype: rdf:PlainLiteral
^^^ src/ontology/{{ project.id }}.Makefile
## Customize Makefile settings for {{project.id}}
##
## If you need to customize your Makefile, make
## changes here rather than in the main Makefile
{% if project.import_group is defined -%}
{%- if 'custom' == project.import_group.module_type %}
imports/%_import.owl: mirror/%.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in {{ project.id }}.Makefile!" && touch $@
{% endif %}
{%- endif %}
{#-
Imports files, one per import
#}
{% for imp in project.import_group.products %}
^^^ src/ontology/imports/{{ imp.id }}_import.owl
<?xml version="1.0"?>
<rdf:RDF
xml:base="http://purl.obolibrary.org/obo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
<owl:Ontology rdf:about="{{ project.uribase }}/{{ project.id }}/imports/{{ imp.id }}_import.owl"/>
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
{#-
Import Term files
We seed each of these with some random terms. This is a little unsatisfactory and fragile;
ROBOT extract will fail if it cannot find any of the terms. While this doesn't matter in the long term,
as the ontology maintainer will provide their own lists, but it is problematic for the initial seed.
TODO: Decide if we should either query ontobee for seed terms OR have the seed list provided in the project.yaml
#}
^^^ src/ontology/imports/{{ imp.id }}_terms.txt
{% endfor %}
{#-
Metadata files.
These are convenient for submission to OBO. Note that OBO maintains two files, a .md and a .yml
TODO: include a script that makes it easy for maintainers to do this.
#}
{%- if project.create_obo_metadata %}
^^^ src/metadata/README.md
Metadata files for the OBO Library
* [{{ project.id }}.yml]({{ project.id }}.yml)
* Determines how your purl.obolibrary.org/obo/{{ project.id }}/ redirects will be handled
* Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
* Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
* Paste in the contents of [{{ project.id }}.yml]({{ project.id }}.yml)
* Click "Commit new file"
* IMPORTANT: remember to make a pull request
* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
* [{{ project.id }}.md]({{ project.id }}.md)
* Determines how your metadata is shown on OBO Library, OLS and AberOWL
* Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
* Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
* Paste in the contents of [{{ project.id }}.md]({{ project.id }}.md)
* Click "Commit new file"
* IMPORTANT: remember to make a pull request
* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
For more background see:
* http://obofoundry.org/
* http://obofoundry.org/faq/how-do-i-edit-metadata.html
^^^ src/metadata/{{ project.id }}.md
---
layout: ontology_detail
id: {{ project.id }}
title: {{ project.title }}
jobs:
- id: https://travis-ci.org/{{ project.github_org }}/{{ project.repo }}
type: travis-ci
build:
checkout: git clone https://github.com/{{ project.github_org }}/{{ project.repo }}.git
system: git
path: "."
contact:
email: {{ project.contact.email }}
label: {{ project.contact.name }}
github: {{ project.contact.github }}
description: {{ project.title }} is an ontology...
domain: stuff
homepage: https://github.com/{{ project.github_org }}/{{ project.repo }}
products:
- id: {{ project.id }}.owl
name: "{{ project.title }} main release in OWL format"
- id: {{ project.id }}.obo
name: "{{ project.title }} additional release in OBO format"
- id: {{ project.id }}.json
name: "{{ project.title }} additional release in OBOJSon format"
- id: {{ project.id }}/{{ project.id }}-base.owl
name: "{{ project.title }} main release in OWL format"
- id: {{ project.id }}/{{ project.id }}-base.obo
name: "{{ project.title }} additional release in OBO format"
- id: {{ project.id }}/{{ project.id }}-base.json
name: "{{ project.title }} additional release in OBOJSon format"
dependencies:
{% for imp in project.import_group.products -%}
- id: {{ imp.id }}
{% endfor %}
tracker: https://github.com/{{ project.github_org }}/{{ project.repo }}/issues
license:
url: http://creativecommons.org/licenses/by/3.0/
label: CC-BY
activity_status: active
---
Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML.
You can also embed images too.
^^^ src/metadata/{{ project.id }}.yml
# PURL configuration for http://purl.obolibrary.org/obo/{{ project.id }}
idspace: {{ project.id|upper }}
base_url: /obo/{{ project.id }}
products:
- {{ project.id }}.owl: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/{{ project.id }}.owl
- {{ project.id }}.obo: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/{{ project.id }}.obo
term_browser: ontobee
example_terms:
- {{ project.id.upper() }}_0000000
entries:
- prefix: /releases/
replacement: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/v
- prefix: /tracker/
replacement: https://github.com/{{ project.github_org }}/{{ project.repo }}/issues
- prefix: /about/
replacement: http://www.ontobee.org/ontology/{{ project.id|upper }}?iri=http://purl.obolibrary.org/obo/
## generic fall-through, serve direct from github by default
- prefix: /
replacement: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/
{%- endif %}
{#-
Example pattern implementation TSV
#}
{%- if project.use_dosdps %}
^^^ src/patterns/definitions.owl
Prefix(:=<http://purl.obolibary.org/obo/{{ project.id }}/definitions.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(<http://purl.obolibary.org/obo/{{ project.id }}/definitions.owl>
)
^^^ src/patterns/pattern.owl
Prefix(:=<http://purl.obolibary.org/obo/{{ project.id }}/pattern.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(<http://purl.obolibary.org/obo/{{ project.id }}/pattern.owl>
)
^^^ src/patterns/README.md
# DOSDP patterns - editors docs
^^^ src/patterns/data/default/example.tsv
defined_class example
^^^ src/patterns/dosdp-patterns/example.yaml
pattern_name: example
pattern_iri: http://purl.obolibrary.org/obo/{{ project.id }}/example.yaml
description: "This is a minimal example pattern."
classes:
example: owl:Thing
relations:
part_of: BFO:0000050
vars:
example: "'example'"
name:
text: "Part of %s"
vars:
- example
equivalentTo:
text: "'part_of' some %s"
vars:
- example
^^^ src/patterns/dosdp-patterns/external.txt
^^^ src/patterns/data/default/README.md
Documentation of the Default DOSDP Pipeline
{%- if project.pattern_pipelines_group is defined %}
{%- for pipeline in project.pattern_pipelines_group.products %}
^^^ src/patterns/data/{{ pipeline.id }}/README.md
# Documentation of the {{ pipeline.id }} DOSDP Pipeline
{%- endfor %}
{%- endif %}
{%- endif %}
{#-
SPARQL QUERY to collect all terms that belong to an ontology
#}
^^^ src/sparql/{{ project.id }}_terms.sparql
SELECT DISTINCT ?term
WHERE {
{ ?s1 ?p1 ?term . }
UNION
{ ?term ?p2 ?o2 . }
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
}
{#-
SPARQL QUERY QC checks
#}
{%- if project.robot_report.custom_sparql_checks is not defined or 'owldef-self-reference' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/owldef-self-reference-violation.sparql
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term WHERE {
{ ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] }
UNION
{ ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] }
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'redundant-subClassOf' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/redundant-subClassOf-violation.sparql
PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term ?xl ?y ?yl ?z ?zl WHERE {
?term rdfs:subClassOf ?y ;
rdfs:label ?xl .
?y rdfs:subClassOf+ ?z ;
rdfs:label ?yl .
?term rdfs:subClassOf ?z .
?z rdfs:label ?zl .
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'taxon-range' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/taxon-range-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
SELECT ?term ?property ?taxon
WHERE {
VALUES ?property { never_in_taxon: present_in_taxon: }
?term ?property ?taxon .
FILTER (!isIRI(?taxon) || !STRSTARTS(STR(?taxon), "http://purl.obolibrary.org/obo/NCBITaxon_"))
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'iri-range' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/iri-range-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?term ?property ?value
WHERE {
VALUES ?property {
never_in_taxon:
present_in_taxon:
foaf:depicted_by
oboInOwl:inSubset
dcterms:contributor }
?term ?property ?value .
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
FILTER (!isIRI(?value))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'iri-range-advanced' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/iri-range-advanced-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?term ?property ?value
WHERE {
VALUES ?property {
never_in_taxon:
present_in_taxon:
rdfs:seeAlso
foaf:depicted_by
oboInOwl:inSubset
dcterms:contributor }
?term ?property ?value .
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
FILTER (!isIRI(?value))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'label-with-iri' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/label-with-iri-violation.sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term ?value
WHERE {
?term rdfs:label ?value .
FILTER (REGEX(?value, "http[s]?[:]"))
FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/{{ project.id.upper() }}_"){% if project.namespaces %}{% for ns in project.namespaces %} || STRSTARTS(str(?term), "{{ ns }}"){% endfor %}{% endif %}))
}
{% endif %}
{%- if project.components is defined %}
{%- for component in project.components.products %}
^^^ src/ontology/components/{{ component.filename }}
<?xml version="1.0"?>
<rdf:RDF
xml:base="http://purl.obolibrary.org/obo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
<owl:Ontology rdf:about="{{ project.uribase }}/{{ project.id }}/components/{{ component.filename }}"/>
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
{%- endfor %}
{%- endif %}
{%- if project.robot_report.custom_profile %}
^^^ src/ontology/profile.txt
WARN annotation_whitespace
ERROR deprecated_boolean_datatype
ERROR deprecated_class_reference
ERROR deprecated_property_reference
ERROR duplicate_definition
WARN duplicate_exact_synonym
WARN duplicate_label_synonym
ERROR duplicate_label
WARN duplicate_scoped_synonym
WARN equivalent_pair
WARN invalid_xref
ERROR label_formatting
ERROR label_whitespace
INFO lowercase_definition
WARN missing_definition
ERROR missing_label
WARN missing_obsolete_label
ERROR missing_ontology_description
ERROR missing_ontology_license
ERROR missing_ontology_title
INFO missing_superclass
ERROR misused_obsolete_label
ERROR multiple_definitions
ERROR multiple_equivalent_classes
ERROR multiple_labels
{%- endif %}
{%- if 'basic' in project.release_artefacts or project.primary_release == 'basic' %}
^^^ src/ontology/keeprelations.txt
BFO:0000050
{% endif -%}
{% if project.ci is defined -%}{% if 'travis' in project.ci %}
^^^ .travis.yml
## REMEMBER TO SET UP YOUR GIT REPO FOR TRAVIS
## Go to: https://travis-ci.org/{{ project.github_org }} for details
sudo: required
services:
- docker
before_install:
- docker pull obolibrary/odkfull
# command to run tests
script: cd src/ontology && sh run.sh make test
#after_success:
# coveralls
# whitelist
branches:
only:
- {{ project.git_main_branch }}
- test-travis
### Add your own lists here
### See https://github.com/INCATools/ontology-development-kit/issues/35
notifications:
email:
- obo-ci-reports-all@groups.io
{% endif -%}{% if 'github_actions' in project.ci %}
^^^ .github/workflows/qc.yml
# Basic ODK workflow
name: CI
# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the {{ project.git_main_branch }} branch
push:
branches: [ {{ project.git_main_branch }} ]
pull_request:
branches: [ {{ project.git_main_branch }} ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "ontology_qc"
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:{% if env is defined -%}{{env['ODK_VERSION'] or "v1.2.25" }}{%- else %}v1.2.25{% endif %}
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
- name: Run ontology QC checks
env:
DEFAULT_BRANCH: {{ project.git_main_branch }}
run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
{% endif -%}
{% endif -%}
{% if (('github_actions' in project.ci) and ('diff' in project.workflows)) %}
^^^ .github/workflows/diff.yml
name: 'Create ROBOT diffs on Pull requests'
on:
# Triggers the workflow on pull request events for the master branch
pull_request:
branches: [ master ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
edit_file:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "v1.2.32" }}{%- else %}v1.2.32{% endif %}
steps:
- uses: actions/checkout@v2
# Checks-out main branch under "main" directory
- uses: actions/checkout@v2
with:
ref: master
path: master
- name: Diff classification
run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/{{ project.id }}-edit.{{ project.edit_format }} --left-catalog master/src/ontology/catalog-v001.xml --right src/ontology/{{ project.id }}-edit.{{ project.edit_format }} --right-catalog src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
- name: Upload diff
uses: actions/upload-artifact@v2
with:
name: edit-diff.md
path: edit-diff.md
classify_branch:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "v1.2.32" }}{%- else %}v1.2.32{% endif %}
steps:
- uses: actions/checkout@v2
- name: Classify ontology
run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE {{ project.id }}.owl
- name: Upload PR {{ project.id }}.owl
uses: actions/upload-artifact@v2
with:
name: {{ project.id }}-pr.owl
path: src/ontology/{{ project.id }}.owl
retention-days: 1
classify_main:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "v1.2.32" }}{%- else %}v1.2.32{% endif %}
steps:
- uses: actions/checkout@v2
with:
ref: master
- name: Classify ontology
run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE {{ project.id }}.owl
- name: Upload master {{ project.id }}.owl
uses: actions/upload-artifact@v2
with:
name: {{ project.id }}-master.owl
path: src/ontology/{{ project.id }}.owl
retention-days: 1
diff_classification:
needs:
- classify_branch
- classify_main
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "v1.2.32" }}{%- else %}v1.2.32{% endif %}
steps:
- uses: actions/checkout@v2
- name: Download master classification
uses: actions/download-artifact@v2
with:
name: {{ project.id }}-master.owl
path: src/ontology/{{ project.id }}-master.owl
- name: Download PR classification
uses: actions/download-artifact@v2
with:
name: {{ project.id }}-pr.owl
path: src/ontology/{{ project.id }}-pr.owl
- name: Diff classification
run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left {{ project.id }}-master.owl/{{ project.id }}.owl --left-catalog catalog-v001.xml --right {{ project.id }}-pr.owl/{{ project.id }}.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
- name: Upload diff
uses: actions/upload-artifact@v2
with:
name: classification-diff.md
path: src/ontology/classification-diff.md
post_comment:
needs: [diff_classification, edit_file]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Download reasoned diff
uses: actions/download-artifact@v2
with:
name: classification-diff.md
path: classification-diff.md
- name: Prepare reasoned comment
run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
- name: Post reasoned comment
env:
GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
uses: NejcZdovc/comment-pr@v1.1.1
with:
file: "../../comment.md"
identifier: "REASONED"
- uses: actions/checkout@v2
- name: Download edit diff
uses: actions/download-artifact@v2
with:
name: edit-diff.md
path: edit-diff.md
- name: Prepare edit file comment
run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" >edit-comment.md; cat edit-diff.md/edit-diff.md >>edit-comment.md"
- name: Post comment
env:
GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
uses: NejcZdovc/comment-pr@v1.1.1
with:
file: "../../edit-comment.md"
identifier: "UNREASONED"
{% endif -%}
{% if project.use_custom_import_module %}
^^^ src/templates/external_import.tsv
ID Entity Type
ID TYPE
owl:Thing owl:Class
{% endif -%}
{% if project.documentation is not none %}
^^^ docs/index.md
# {{ project.id.upper() }} Ontology Documentation
[//]: # "This file is meant to be edited by the ontology maintainer."
Welcome to the {{ project.id.upper() }} documentation!
You can find descriptions of the standard ontology engineering workflows [here](odk-workflows/index.md).
^^^ docs/history.md
# A brief history of {{ project.id.upper() }}
The following page gives an overview of the history of {{ project.id.upper() }}.
^^^ docs/cite.md
# How to cite {{ project.id.upper() }}
^^^ docs/contributing.md
# How to contribute to {{ project.id.upper() }}
^^^ docs/odk-workflows/index.md
# Default ODK Workflows
- [Daily Editors Workflow](EditorsWorkflow.md)
- [Release Workflow](ReleaseWorkflow.md)
- [Manage your ODK Repository](RepoManagement.md)
- [Setting up Docker for ODK](SettingUpDockerForODK.md)
- [Imports management](UpdateImports.md)
- [Managing the documentation](ManageDocumentation.md)
^^^ docs/odk-workflows/ContinuousIntegration.md
# Introduction to Continuous Integration Workflows with ODK
Historically, most repos have been using Travis CI for continuous integration testing and building, but due to
runtime restrictions, we recently switched a lot of our repos to GitHub actions. You can set up your repo with CI by adding
this to your configuration file (src/ontology/{{ project.id }}-odk.yaml):
```
ci:
- github_actions
```
When [updateing your repo](RepoManagement.md), you will notice a new file being added: `.github/workflows/qc.yml`.
This file contains your CI logic, so if you need to change, or add anything, this is the place!
^^^ docs/odk-workflows/EditorsWorkflow.md
# Editors Workflow
The editors workflow is one of the formal [workflows](index.md) to ensure that the ontology is developed correctly according to ontology engineering principles. There are a few different editors workflows:
1. Local editing workflow: Editing the ontology in your local environment by hand, using tools such as Protégé, ROBOT templates or DOSDP patterns.
2. Completely automated data pipeline (GitHub Actions)
3. DROID workflow
This document only covers the first editing workflow, but more will be added in the future
### Local editing workflow
Workflow requirements:
- git
- github
- docker
- editing tool of choice, e.g. Protégé, your favourite text editor, etc
#### 1. _Create issue_
Ensure that there is a ticket on your issue tracker that describes the change you are about to make. While this seems optional, this is a very important part of the social contract of building an ontology - no change to the ontology should be performed without a good ticket, describing the motivation and nature of the intended change.
#### 2. _Update main branch_
In your local environment (e.g. your laptop), make sure you are on the `main` (prev. `master`) branch and ensure that you have all the upstream changes, for example:
```
git checkout {{ project.git_main_branch }}
git pull
```
#### 3. _Create feature branch_
Create a new branch. Per convention, we try to use meaningful branch names such as:
- issue23removeprocess (where issue 23 is the related issue on GitHub)
- issue26addcontributor
- release20210101 (for releases)
On your command line, this looks like this:
```
git checkout -b issue23removeprocess
```
#### 4. _Perform edit_
Using your editor of choice, perform the intended edit. For example:
_Protege_
1. Open `src/ontology/{{ project.id }}-edit.owl` in Protege
2. Make the change
3. Save the file
_TextEdit_
1. Open `src/ontology/{{ project.id }}-edit.owl` in TextEdit (or Sublime, Atom, Vim, Nano)
2. Make the change
3. Save the file
Consider the following when making the edit.
1. According to our development philosophy, the only places that should be manually edited are:
- `src/ontology/{{ project.id }}-edit.owl`
- Any ROBOT templates you chose to use (the TSV files only)
- Any DOSDP data tables you chose to use (the TSV files, and potentially the associated patterns)
- components (anything in `src/ontology/components`), see [here](RepositoryFileStructure.md).
2. Imports should not be edited (any edits will be flushed out with the next update). However, refreshing imports is a potentially breaking change - and is discussed [elsewhere](UpdateImports.md).
3. Changes should usually be small. Adding or changing 1 term is great. Adding or changing 10 related terms is ok. Adding or changing 100 or more terms at once should be considered very carefully.
#### 4. _Check the Git diff_
This step is very important. Rather than simply trusting your change had the intended effect, we should always use a git diff as a first pass for sanity checking.
In our experience, having a visual git client like [GitHub Desktop](https://desktop.github.com/) or [sourcetree](https://www.sourcetreeapp.com/) is really helpful for this part. In case you prefer the command line:
```
git status
git diff
```
#### 5. Quality control
Now its time to run your quality control checks. This can either happen locally ([5a](#Local-testing)) or through your continuous integration system ([7/5b](#continuous-integration-testing)).
#### 5a. Local testing
If you chose to run your test locally:
```
sh run.sh make IMP=false test
```
This will run the whole set of configured ODK tests on including your change. If you have a complex DOSDP pattern pipeline you may want to add `PAT=false` to skip the potentially lengthy process of rebuilding the patterns.
```
sh run.sh make IMP=false PAT=false test
```
#### 6. Pull request
When you are happy with the changes, you commit your changes to your feature branch, push them upstream (to GitHub) and create a pull request. For example:
```
git add NAMEOFCHANGEDFILES
git commit -m "Added biological process term #12"
git push -u origin issue23removeprocess
```
Then you go to your project on GitHub, and create a new pull request from the branch, for example: https://github.com/INCATools/ontology-development-kit/pulls
There is a lot of great advise on how to write pull requests, but at the very least you should:
- mention the tickets affected: `see #23` to link to a related ticket, or `fixes #23` if, by merging this pull request, the ticket is fixed. Tickets in the latter case will be closed automatically by Github when the pull request is merged.
- summarise the changes in a few sentences. Consider the reviewer: what would they want to know right away.
- If the diff is large, provide instructions on how to review the pull request best (sometimes, there are many changed files, but only one important change).
#### 7/5b. Continuous Integration Testing
If you didn't run and local quality control checks (see [5a](#Local-testing)), you should have Continuous Integration (CI) set up, for example:
- Travis
- GitHub Actions
More on how to set this up [here](ContinuousIntegration.md). Once the pull request is created, the CI will automatically trigger. If all is fine, it will show up green, otherwise red.
#### 8. Community review
Once all the automatic tests have passed, it is important to put a second set of eyes on the pull request. Ontologies are inherently social - as in that they represent some kind of community consensus on how a domain is organised conceptually. This seems high brow talk, but it is very important that as an ontology editor, you have your work validated by the community you are trying to serve (e.g. your colleagues, other contributors etc). In our experience, it is hard to get more than one review on a pull request - two is great. You can set up GitHub branch protection to actually require a review before a pull request can be merged! We recommend this.
This step seems daunting to some hopefully under-resourced ontologies, but we recommend to put this high up on your list of priorities - train a colleague, reach out!
#### 9. Merge and cleanup
When the QC is green and the reviews are in (approvals), it is time to merge the pull request. After the pull request is merged, remember to delete the branch as well (this option will show up as a big button right after you have merged the pull request). If you have not done so, close all the associated tickets fixed by the pull request.
#### 10. Changelog (Optional)
It is sometimes difficult to keep track of changes made to an ontology. Some ontology teams opt to document changes in a changelog (simply a text file in your repository) so that when release day comes, you know everything you have changed. This is advisable at least for major changes (such as a new release system, a new pattern or template etc).
^^^ docs/odk-workflows/ReleaseWorkflow.md
# The release workflow
The release workflow recommended by the ODK is based on GitHub releases and works as follows:
1. Run a release with the ODK
2. Review the release
3. Merge to main branch
4. Create a GitHub release
These steps are outlined in detail in the following.
## Run a release with the ODK
Preparation:
1. Ensure that all your pull requests are merged into your main (master) branch
2. Make sure that all changes to {{ project.git_main_branch }} are committed to Github (`git status` should say that there are no modified files)
3. Locally make sure you have the latest changes from {{ project.git_main_branch }} (`git pull`)
4. Checkout a new branch (e.g. `git checkout -b release-2021-01-01`)
5. You may or may not want to refresh your imports as part of your release strategy (see [here](UpdateImports.md))
6. Make sure you have the latest ODK installed by running `docker pull obolibrary/odkfull`
To actually run the release, you:
1. Open a command line terminal window and navigate to the src/ontology directory (`cd {{ project.id }}/src/ontology`)
2. Run release pipeline:`sh run.sh make prepare_release -B`. Note that for some ontologies, this process can take up to 90 minutes - especially if there are large ontologies you depend on, like PRO or CHEBI.
3. If everything went well, you should see the following output on your machine: `Release files are now in ../.. - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab`.
This will create all the specified release targets (OBO, OWL, JSON, and the variants, ont-full and ont-base) and copy them into your release directory (the top level of your repo).
## Review the release
1. (Optional) Rough check. This step is frequently skipped, but for the more paranoid among us (like the author of this doc), this is a 3 minute additional effort for some peace of mind. Open the main release ({{ project.id }}.owl) in you favourite development environment (i.e. Protege) and eyeball the hierarchy. We recommend two simple checks:
1. Does the very top level of the hierarchy look ok? This means that all new terms have been imported/updated correctly.
2. Does at least one change that you know should be in this release appear? For example, a new class. This means that the release was actually based on the recent edit file.
2. Commit your changes to the branch and make a pull request
3. In your GitHub pull request, review the following three files in detail (based on our experience):
1. `{{ project.id }}.obo` - this reflects a useful subset of the whole ontology (everything that can be covered by OBO format). OBO format has that speaking for it: it is very easy to review!
2. `{{ project.id }}-base.owl` - this reflects the asserted axioms in your ontology that you have actually edited.
3. Ideally also take a look at `{{ project.id }}-full.owl`, which may reveal interesting new inferences you did not know about. Note that the diff of this file is sometimes quite large.
4. Like with every pull request, we recommend to always employ a second set of eyes when reviewing a PR!
## Merge the main branch
Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews are completed, you can now merge the branch into your main branch (don't forget to delete the branch afterwards - a big button will appear after the merge is finished).
## Create a GitHub release
1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/{{ project.github_org }}/{{ project.repo }}/releases. Then click "Draft new release"
1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `{{ project.id }}.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`.
1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions.
1. Click "Publish release". Done.
## Debugging typical ontology release problems
### Problems with memory
When you are dealing with large ontologies, you need a lot of memory. When you see error messages relating to large ontologies such as CHEBI, PRO, NCBITAXON, or Uberon, you should think of memory first, see [here](https://github.com/INCATools/ontology-development-kit/blob/master/docs/DealWithLargeOntologies.md).
### Problems when using OBO format based tools
Sometimes you will get cryptic error messages when using legacy tools using OBO format, such as the ontology release tool (OORT), which is also available as part of the ODK docker container. In these cases, you need to track down what axiom or annotation actually caused the breakdown. In our experience (in about 60% of the cases) the problem lies with duplicate annotations (`def`, `comment`) which are illegal in OBO. Here is an example recipe of how to deal with such a problem:
1. If you get a message like `make: *** [cl.Makefile:84: oort] Error 255` you might have a OORT error.
2. To debug this, in your terminal enter `sh run.sh make IMP=false PAT=false oort -B` (assuming you are already in the ontology folder in your directory)
3. This should show you where the error is in the log (eg multiple different definitions)
WARNING: THE FIX BELOW IS NOT IDEAL, YOU SHOULD ALWAYS TRY TO FIX UPSTREAM IF POSSIBLE
4. Open `{{ project.id }}-edit.owl` in Protege and find the offending term and delete all offending issue (e.g. delete ALL definition, if the problem was "multiple def tags not allowed") and save.
*While this is not idea, as it will remove all definitions from that term, it will be added back again when the term is fixed in the ontology it was imported from and added back in.
5. Rerun `sh run.sh make IMP=false PAT=false oort -B` and if it all passes, commit your changes to a branch and make a pull request as usual.
^^^ docs/odk-workflows/RepoManagement.md
# Managing your ODK repository
## Updating your ODK repository
Your ODK repositories configuration is managed in `src/ontology/{{ project.id }}-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
```