diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index be734adf5..98b8cb731 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -85,9 +85,8 @@ Attributes: url: type: string description: > - Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) - Foundry set of ontologies, the OBO URL link should be used (e.g., - http://www.ontobee.org/ontology/ncbitaxon). + Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of + ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon). top_node: type: object description: Term to use as top node for ontology @@ -144,7 +143,7 @@ Study: ontology: draft: true name: NCIT - url: https://ncit.nci.nih.gov/ncitbrowser/ + url: https://www.ebi.ac.uk/ols/ontologies/ncit top_node: id: C63536 value: Study @@ -294,7 +293,7 @@ Subject: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata @@ -361,7 +360,7 @@ Subject: ontology: draft: true name: Units of measurement ontology - url: http://www.ontobee.org/ontology/UO + url: https://www.ebi.ac.uk/ols/ontologies/UO top_node: id: UO_0000003 value: time unit @@ -672,7 +671,7 @@ CellProcessing: ontology: draft: true name: CL - url: http://www.ontobee.org/ontology/cl + url: https://www.ebi.ac.uk/ols/ontologies/cl top_node: id: CL_0000542 value: lymphocyte @@ -705,7 +704,7 @@ CellProcessing: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index be734adf5..98b8cb731 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -85,9 +85,8 @@ Attributes: url: type: string description: > - Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) - Foundry set of ontologies, the OBO URL link should be used (e.g., - http://www.ontobee.org/ontology/ncbitaxon). + Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of + ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon). top_node: type: object description: Term to use as top node for ontology @@ -144,7 +143,7 @@ Study: ontology: draft: true name: NCIT - url: https://ncit.nci.nih.gov/ncitbrowser/ + url: https://www.ebi.ac.uk/ols/ontologies/ncit top_node: id: C63536 value: Study @@ -294,7 +293,7 @@ Subject: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata @@ -361,7 +360,7 @@ Subject: ontology: draft: true name: Units of measurement ontology - url: http://www.ontobee.org/ontology/UO + url: https://www.ebi.ac.uk/ols/ontologies/UO top_node: id: UO_0000003 value: time unit @@ -672,7 +671,7 @@ CellProcessing: ontology: draft: true name: CL - url: http://www.ontobee.org/ontology/cl + url: https://www.ebi.ac.uk/ols/ontologies/cl top_node: id: CL_0000542 value: lymphocyte @@ -705,7 +704,7 @@ CellProcessing: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index 4ea9fa455..98b8cb731 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -85,9 +85,8 @@ Attributes: url: type: string description: > - Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) - Foundry set of ontologies, the OBO URL link should be used (e.g., - http://www.ontobee.org/ontology/ncbitaxon). + Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of + ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon). top_node: type: object description: Term to use as top node for ontology @@ -144,7 +143,7 @@ Study: ontology: draft: true name: NCIT - url: http://www.ontobee.org/ontology/ncit + url: https://www.ebi.ac.uk/ols/ontologies/ncit top_node: id: C63536 value: Study @@ -294,7 +293,7 @@ Subject: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata @@ -361,7 +360,7 @@ Subject: ontology: draft: true name: Units of measurement ontology - url: http://www.ontobee.org/ontology/UO + url: https://www.ebi.ac.uk/ols/ontologies/UO top_node: id: UO_0000003 value: time unit @@ -672,7 +671,7 @@ CellProcessing: ontology: draft: true name: CL - url: http://www.ontobee.org/ontology/cl + url: https://www.ebi.ac.uk/ols/ontologies/cl top_node: id: CL_0000542 value: lymphocyte @@ -705,7 +704,7 @@ CellProcessing: ontology: draft: false name: NCBITAXON - url: http://www.ontobee.org/ontology/ncbitaxon + url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon top_node: id: 7776 value: Gnathostomata