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Merge pull request #54 from INCATools/registry
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| db/phenio.owl: STAMP | ||
| curl -L -s https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/bero.owl: STAMP | ||
| curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/aio.owl: STAMP | ||
| curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/reacto.owl: STAMP | ||
| curl -L -s http://purl.obolibrary.org/obo/go/extensions/reacto.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/go-lego.owl: STAMP | ||
| curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-lego.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/bao.owl: STAMP | ||
| robot merge -I http://www.bioassayontology.org/bao/bao_complete.owl -o $@ | ||
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| db/biolink.owl: STAMP | ||
| robot merge -I https://w3id.org/biolink/biolink-model.owl.ttl -o $@ | ||
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| db/biopax.owl: STAMP | ||
| curl -L -s http://www.biopax.org/release/biopax-level3.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/enanomapper.owl: STAMP | ||
| robot merge -I http://enanomapper.github.io/ontologies/enanomapper.owl -o $@ | ||
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| db/efo.owl: STAMP | ||
| robot merge -I http://www.ebi.ac.uk/efo/efo.owl -o $@ | ||
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| db/edam.owl: STAMP | ||
| curl -L -s http://edamontology.org/EDAM.owl > $@.tmp && mv $@.tmp $@ | ||
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| db/sweetAll.owl: STAMP | ||
| robot merge -I http://sweetontology.net/sweetAll -o $@ | ||
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| db/lov.owl: STAMP | ||
| robot merge -I https://lov.linkeddata.es/lov.n3.gz -o $@ | ||
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| db/schema-dot-org.owl: STAMP | ||
| curl -L -s https://schema.org/version/latest/schemaorg-current-https.rdf > $@.tmp && mv $@.tmp $@ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,9 +7,12 @@ | |
| from typing import Optional | ||
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| import requests | ||
| from linkml_runtime.loaders import yaml_loader | ||
| from sqlalchemy import create_engine | ||
| from sqlalchemy.orm import sessionmaker | ||
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| from semsql.builder.registry import registry_schema | ||
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| this_path = Path(__file__).parent | ||
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@@ -103,3 +106,27 @@ def connect(owl_file: str): | |
| Session = sessionmaker(bind=engine) | ||
| session = Session() | ||
| return session | ||
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| def compile_registry(registry_path: str) -> str: | ||
| """ | ||
| Generate makefile content from registry | ||
| :param registry_path: | ||
| :return: | ||
| """ | ||
| registry: registry_schema.Registry | ||
| registry = yaml_loader.load(registry_path, target_class=registry_schema.Registry) | ||
| mkfile = "" | ||
| onts = [] | ||
| for ont in registry.ontologies.values(): | ||
| target = f"db/{ont.id}.owl" | ||
| dependencies = ["STAMP"] | ||
| if ont.has_imports or (ont.format and ont.format != 'rdfxml'): | ||
| command = f"robot merge -I {ont.url} -o $@" | ||
| else: | ||
| command = f"curl -L -s {ont.url} > [email protected] && mv [email protected] $@" | ||
| dependencies_str = " ".join(dependencies) | ||
| mkfile += f"{target}: {dependencies_str}\n\t{command}\n\n" | ||
| onts.append(ont.id) | ||
| mkfile += f"EXTRA_ONTOLOGIES = {' '.join(onts)}" | ||
| return mkfile | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| id: semantic-sql-registry | ||
| description: Registry overlap for Semantic-SQL designed to supplement OBO vocabularies | ||
| license: CC0 | ||
| ontologies: | ||
| phenio: | ||
| description: Monarch Phenomics Integrated Ontology | ||
| url: https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl | ||
| bero: | ||
| url: https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl | ||
| aio: | ||
| url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl | ||
| reacto: | ||
| url: http://purl.obolibrary.org/obo/go/extensions/reacto.owl | ||
| go-lego: | ||
| url: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl | ||
| bao: | ||
| url: http://www.bioassayontology.org/bao/bao_complete.owl | ||
| has_imports: true | ||
| biolink: | ||
| url: https://w3id.org/biolink/biolink-model.owl.ttl | ||
| jsonld_context: https://biolink.github.io/biolink-model/context.jsonld | ||
| format: turtle | ||
| # | ||
| biopax: | ||
| url: http://www.biopax.org/release/biopax-level3.owl | ||
| enanomapper: | ||
| url: http://enanomapper.github.io/ontologies/enanomapper.owl | ||
| has_imports: true | ||
| prefixmap: | ||
| evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# | ||
| fix: http://purl.org/obo/owl/FIX# | ||
| efo: | ||
| url: http://www.ebi.ac.uk/efo/efo.owl | ||
| has_imports: true | ||
| edam: | ||
| url: http://edamontology.org/EDAM.owl | ||
| sweetAll: | ||
| url: http://sweetontology.net/sweetAll | ||
| has_imports: true | ||
| named_prefixmaps: | ||
| - sweet | ||
| - prefixcc | ||
| lov: | ||
| url: https://lov.linkeddata.es/lov.n3.gz | ||
| format: n3 | ||
| compression: gzip | ||
| schema-dot-org: | ||
| url: https://schema.org/version/latest/schemaorg-current-https.rdf |
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