From c00c6191f58d432ff7becdddf4dd479736d5f99d Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 8 Feb 2025 00:33:54 +0200 Subject: [PATCH 1/5] Add VT URI pattern for OBA to obo.yml --- config/obo.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/config/obo.yml b/config/obo.yml index 391a047b..01f1eadf 100644 --- a/config/obo.yml +++ b/config/obo.yml @@ -148,6 +148,17 @@ entries: - from: /DOID_0014667 to: https://disease-ontology.org/?id=DOID:0014667 +# Term redirects for OBA +# Some OBA IDs start with VT_, because they were originally sourced from VT +- regex: ^/obo/OBA_([VT]?[VT]?\d+)$ + replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_$1 + status: see other + tests: + - from: /OBA_0000001 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_0000001 + - from: /OBA_VT0000002 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_VT0000002 + ### OBO Format Specification - exact: /oboformat/ replacement: http://owlcollab.github.io/oboformat/doc/obo-syntax.html From 66fb19285d0caeb733f498ee8cc05d6d5a30959c Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 8 Feb 2025 00:41:23 +0200 Subject: [PATCH 2/5] Update oba.yml to use OLS as term browser --- config/oba.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/oba.yml b/config/oba.yml index 24255943..c40e557a 100644 --- a/config/oba.yml +++ b/config/oba.yml @@ -44,6 +44,6 @@ entries: - prefix: / replacement: https://github.com/obophenotype/bio-attribute-ontology/releases/latest/download/ -term_browser: ontobee +term_browser: ols example_terms: - OBA_0000001 From 925d7a4e63fa897c9c18f008f60c5be8e05289ed Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 8 Feb 2025 00:45:16 +0200 Subject: [PATCH 3/5] Update obo.yml --- config/obo.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config/obo.yml b/config/obo.yml index 01f1eadf..5654ded8 100644 --- a/config/obo.yml +++ b/config/obo.yml @@ -151,13 +151,13 @@ entries: # Term redirects for OBA # Some OBA IDs start with VT_, because they were originally sourced from VT - regex: ^/obo/OBA_([VT]?[VT]?\d+)$ - replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_$1 + replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_$1 status: see other tests: - from: /OBA_0000001 - to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_0000001 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_0000001 - from: /OBA_VT0000002 - to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/?iri=http://purl.obolibrary.org/obo/OBA_VT0000002 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000002 ### OBO Format Specification - exact: /oboformat/ From 89070e42a9f031f9b389d6867fcbe3ddc7274f24 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 8 Feb 2025 00:54:32 +0200 Subject: [PATCH 4/5] Update OBA URL redirect pattern in obo.yml --- config/obo.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config/obo.yml b/config/obo.yml index 5654ded8..73d45014 100644 --- a/config/obo.yml +++ b/config/obo.yml @@ -151,13 +151,13 @@ entries: # Term redirects for OBA # Some OBA IDs start with VT_, because they were originally sourced from VT - regex: ^/obo/OBA_([VT]?[VT]?\d+)$ - replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_$1 + replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http://purl.obolibrary.org/obo/OBA_$1 status: see other tests: - from: /OBA_0000001 - to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_0000001 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http://purl.obolibrary.org/obo/OBA_0000001 - from: /OBA_VT0000002 - to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000002 + to: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http://purl.obolibrary.org/obo/OBA_VT0000002 ### OBO Format Specification - exact: /oboformat/ From fafe49dcf7161b66ad4b8e49c3870a7a160be423 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Mon, 10 Feb 2025 12:06:58 -0500 Subject: [PATCH 5/5] Fixes for OBA VT ID changes --- config/oba.yml | 10 +++++----- config/obo.yml | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/config/oba.yml b/config/oba.yml index c40e557a..05e6fecf 100644 --- a/config/oba.yml +++ b/config/oba.yml @@ -8,6 +8,10 @@ products: - oba.obo: https://github.com/obophenotype/bio-attribute-ontology/releases/latest/download/oba.obo - oba.json: https://github.com/obophenotype/bio-attribute-ontology/releases/latest/download/oba.json +term_browser: custom +example_terms: +- OBA_0000001 + entries: - exact: /subsets/oba-basic.owl replacement: https://github.com/obophenotype/bio-attribute-ontology/releases/latest/download/oba-basic.owl @@ -40,10 +44,6 @@ entries: - prefix: /imports/ replacement: https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/imports/ - prefix: /about/ - replacement: http://www.ontobee.org/ontology/OBA?iri=http://purl.obolibrary.org/obo/ + replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http://purl.obolibrary.org/obo/ - prefix: / replacement: https://github.com/obophenotype/bio-attribute-ontology/releases/latest/download/ - -term_browser: ols -example_terms: -- OBA_0000001 diff --git a/config/obo.yml b/config/obo.yml index 73d45014..755605b9 100644 --- a/config/obo.yml +++ b/config/obo.yml @@ -149,8 +149,8 @@ entries: to: https://disease-ontology.org/?id=DOID:0014667 # Term redirects for OBA -# Some OBA IDs start with VT_, because they were originally sourced from VT -- regex: ^/obo/OBA_([VT]?[VT]?\d+)$ +# Some OBA IDs start with VT, because they were originally sourced from VT +- regex: ^/obo/OBA_((VT)?\d+)$ replacement: https://www.ebi.ac.uk/ols4/ontologies/oba/entities/http://purl.obolibrary.org/obo/OBA_$1 status: see other tests: