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Merge pull request #94 from INCATools/new-entries-and-uri-resolution
Adding new entries for kbase
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -243,6 +243,11 @@ ontologies: | |
| url: https://w3id.org/orcidio/orcidio.owl | ||
| prefixmap: | ||
| orcid: https://orcid.org/ | ||
| ror: | ||
| url: https://w3id.org/biopragmatics/resources/ror/ror.owl.gz | ||
| compression: gzip | ||
| prefixmap: | ||
| ror: https://ror.org/ | ||
| cpont: | ||
| url: https://w3id.org/cpont/cpont.owl | ||
| biolink: | ||
|
|
@@ -307,6 +312,7 @@ ontologies: | |
| zip_extract_file: Mus_musculus.owl | ||
| post_processing_steps: | ||
| - "sqlite3 {db} < views/reactome.sql" | ||
|
|
||
| efo: | ||
| url: http://www.ebi.ac.uk/efo/efo.owl | ||
| has_imports: true | ||
|
|
@@ -426,6 +432,11 @@ ontologies: | |
| format: obo | ||
| prefixmap: | ||
| InterPro: http://purl.obolibrary.org/obo/InterPro_ | ||
| pfam: | ||
| url: https://w3id.org/biopragmatics/resources/pfam/pfam.owl | ||
| prefixmap: | ||
| PFAM: https://www.ebi.ac.uk/interpro/entry/pfam/ | ||
| PFAM.CLAN: https://www.ebi.ac.uk/interpro/set/pfam/ | ||
| hgnc.genegroup: | ||
| url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz | ||
| compression: gzip | ||
|
|
@@ -441,29 +452,40 @@ ontologies: | |
| url: https://w3id.org/biopragmatics/resources/sgd/sgd.obo | ||
| format: obo | ||
| prefixmap: | ||
| SGD: http://purl.obolibrary.org/obo/sgd_ | ||
| dictybase: | ||
| url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/dictybase/dictybase.owl.gz | ||
| compression: gzip | ||
| SGD: https://www.yeastgenome.org/locus/ | ||
| gtdb: | ||
| url: https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl | ||
| prefixmap: | ||
| hgnc.genegroup: http://purl.obolibrary.org/obo/dictybase_ | ||
| gtdb: https://gtdb.ecogenomic.org/tree?r= | ||
| eccode: | ||
| url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz | ||
| compression: gzip | ||
| prefixmap: | ||
| EC: http://purl.obolibrary.org/obo/eccode_ | ||
| uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ | ||
| EC: "https://bioregistry.io/eccode:" | ||
| UniProtKB: "https://bioregistry.io/uniprot:" | ||
| uniprot: | ||
| url: https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz | ||
| url: https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz | ||
| compression: gzip | ||
| prefixmap: | ||
| uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ | ||
| UniProtKB: "https://bioregistry.io/uniprot:" | ||
| uniprot.ptm: | ||
| url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.owl | ||
| prefixmap: | ||
| RESID: https://proteininformationresource.org/cgi-bin/resid?id= | ||
| UNIMOD: http://www.unimod.org/modifications_view.php?editid1= | ||
| uniprot.ptm: https://biopragmatics.github.io/providers/uniprot.ptm/ | ||
| credit: | ||
| url: https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/credit/credit.owl | ||
| prefixmap: | ||
| credit: https://credit.niso.org/contributor-roles/ | ||
| rhea: | ||
| url: https://w3id.org/biopragmatics/resources/rhea/rhea.obo | ||
| build_command: "robot merge -i $< -o $@" | ||
| url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz | ||
| # https://github.com/biopragmatics/obo-db-ingest/issues/15 | ||
| build_command: "perl -npe 's@https://www.ebi.ac.uk/.*ec=@https://bioregistry.io/eccode:@g' $< > [email protected] && robot convert -i [email protected] -o $@" | ||
| compression: gzip | ||
| # build_command: "robot merge -i $< -o $@" | ||
| prefixmap: | ||
| RHEA: http://purl.obolibrary.org/obo/rhea_ | ||
| uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ | ||
| RHEA: https://www.rhea-db.org/rhea/ | ||
| swisslipid: | ||
| url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/swisslipid/2023-02-03/swisslipid.obo.gz | ||
| format: obo | ||
|
|
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