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Use EBI OLS and syncronize schema copies
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@bussec
bussec committed Jan 4, 2020
1 parent b6560d5 commit 8ffead4
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Showing 3 changed files with 21 additions and 24 deletions.
15 changes: 7 additions & 8 deletions lang/R/inst/extdata/airr-schema.yaml
View file
Expand Up @@ -85,9 +85,8 @@ Attributes:
url: url:
type: string type: string
description: > description: >
Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of
Foundry set of ontologies, the OBO URL link should be used (e.g., ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon).
http://www.ontobee.org/ontology/ncbitaxon).
top_node: top_node:
type: object type: object
description: Term to use as top node for ontology description: Term to use as top node for ontology
Expand Down Expand Up @@ -144,7 +143,7 @@ Study:
ontology: ontology:
draft: true draft: true
name: NCIT name: NCIT
url: https://ncit.nci.nih.gov/ncitbrowser/ url: https://www.ebi.ac.uk/ols/ontologies/ncit
top_node: top_node:
id: C63536 id: C63536
value: Study value: Study
Expand Down Expand Up @@ -294,7 +293,7 @@ Subject:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down Expand Up @@ -361,7 +360,7 @@ Subject:
ontology: ontology:
draft: true draft: true
name: Units of measurement ontology name: Units of measurement ontology
url: http://www.ontobee.org/ontology/UO url: https://www.ebi.ac.uk/ols/ontologies/UO
top_node: top_node:
id: UO_0000003 id: UO_0000003
value: time unit value: time unit
Expand Down Expand Up @@ -672,7 +671,7 @@ CellProcessing:
ontology: ontology:
draft: true draft: true
name: CL name: CL
url: http://www.ontobee.org/ontology/cl url: https://www.ebi.ac.uk/ols/ontologies/cl
top_node: top_node:
id: CL_0000542 id: CL_0000542
value: lymphocyte value: lymphocyte
Expand Down Expand Up @@ -705,7 +704,7 @@ CellProcessing:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down
15 changes: 7 additions & 8 deletions lang/python/airr/specs/airr-schema.yaml
View file
Expand Up @@ -85,9 +85,8 @@ Attributes:
url: url:
type: string type: string
description: > description: >
Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of
Foundry set of ontologies, the OBO URL link should be used (e.g., ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon).
http://www.ontobee.org/ontology/ncbitaxon).
top_node: top_node:
type: object type: object
description: Term to use as top node for ontology description: Term to use as top node for ontology
Expand Down Expand Up @@ -144,7 +143,7 @@ Study:
ontology: ontology:
draft: true draft: true
name: NCIT name: NCIT
url: https://ncit.nci.nih.gov/ncitbrowser/ url: https://www.ebi.ac.uk/ols/ontologies/ncit
top_node: top_node:
id: C63536 id: C63536
value: Study value: Study
Expand Down Expand Up @@ -294,7 +293,7 @@ Subject:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down Expand Up @@ -361,7 +360,7 @@ Subject:
ontology: ontology:
draft: true draft: true
name: Units of measurement ontology name: Units of measurement ontology
url: http://www.ontobee.org/ontology/UO url: https://www.ebi.ac.uk/ols/ontologies/UO
top_node: top_node:
id: UO_0000003 id: UO_0000003
value: time unit value: time unit
Expand Down Expand Up @@ -672,7 +671,7 @@ CellProcessing:
ontology: ontology:
draft: true draft: true
name: CL name: CL
url: http://www.ontobee.org/ontology/cl url: https://www.ebi.ac.uk/ols/ontologies/cl
top_node: top_node:
id: CL_0000542 id: CL_0000542
value: lymphocyte value: lymphocyte
Expand Down Expand Up @@ -705,7 +704,7 @@ CellProcessing:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down
15 changes: 7 additions & 8 deletions specs/airr-schema.yaml
View file
Expand Up @@ -85,9 +85,8 @@ Attributes:
url: url:
type: string type: string
description: > description: >
Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of
Foundry set of ontologies, the OBO URL link should be used (e.g., ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon).
http://www.ontobee.org/ontology/ncbitaxon).
top_node: top_node:
type: object type: object
description: Term to use as top node for ontology description: Term to use as top node for ontology
Expand Down Expand Up @@ -144,7 +143,7 @@ Study:
ontology: ontology:
draft: true draft: true
name: NCIT name: NCIT
url: http://www.ontobee.org/ontology/ncit url: https://www.ebi.ac.uk/ols/ontologies/ncit
top_node: top_node:
id: C63536 id: C63536
value: Study value: Study
Expand Down Expand Up @@ -294,7 +293,7 @@ Subject:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down Expand Up @@ -361,7 +360,7 @@ Subject:
ontology: ontology:
draft: true draft: true
name: Units of measurement ontology name: Units of measurement ontology
url: http://www.ontobee.org/ontology/UO url: https://www.ebi.ac.uk/ols/ontologies/UO
top_node: top_node:
id: UO_0000003 id: UO_0000003
value: time unit value: time unit
Expand Down Expand Up @@ -672,7 +671,7 @@ CellProcessing:
ontology: ontology:
draft: true draft: true
name: CL name: CL
url: http://www.ontobee.org/ontology/cl url: https://www.ebi.ac.uk/ols/ontologies/cl
top_node: top_node:
id: CL_0000542 id: CL_0000542
value: lymphocyte value: lymphocyte
Expand Down Expand Up @@ -705,7 +704,7 @@ CellProcessing:
ontology: ontology:
draft: false draft: false
name: NCBITAXON name: NCBITAXON
url: http://www.ontobee.org/ontology/ncbitaxon url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node: top_node:
id: 7776 id: 7776
value: Gnathostomata value: Gnathostomata
Expand Down

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