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Use EBI OLS and syncronize schema copies

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bussec committed Dec 16, 2019
1 parent b6560d5 commit 8ffead47097c1810a2a5f3363c4eae4e30abf784
Showing with 21 additions and 24 deletions.
  1. +7 −8 lang/R/inst/extdata/airr-schema.yaml
  2. +7 −8 lang/python/airr/specs/airr-schema.yaml
  3. +7 −8 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
@@ -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
@@ -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

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