From 26b93f9bf6a7ea4353f8ef102fdac520b89db7d2 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 11:14:06 -0500 Subject: [PATCH 1/6] fix: use direct liquid assign expressions and remove redundant bioportal browser links --- _layouts/ontology_detail.html | 28 +++++++++++++++++++++++++++- _plugins/bioportal_identifier.rb | 28 ---------------------------- ontology/bfo.md | 4 ---- ontology/fbbt.md | 3 --- ontology/kisao.md | 3 --- ontology/nbo.md | 4 ---- ontology/obi.md | 4 ---- ontology/occo.md | 4 ---- ontology/ontoneo.md | 4 ---- ontology/pato.md | 4 ---- ontology/pr.md | 3 --- ontology/slso.md | 4 ---- ontology/txpo.md | 3 --- 13 files changed, 27 insertions(+), 69 deletions(-) delete mode 100644 _plugins/bioportal_identifier.rb diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 8bdc6d2f3..b6a1f7f7b 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -70,7 +70,33 @@

OLS - + {% assign bioportal_id = page.id | upcase %} + {% if bioportal_id == 'FBBT' %} + {% assign bioportal_id = 'FB-BT' %} + {% elsif bioportal_id == 'ro' %} + {% assign bioportal_id = 'OBOREL' %} + {% elsif bioportal_id == 'apollo_sv' %} + {% assign bioportal_id = 'APOLLO-SV' %} + {% elsif bioportal_id == 'trans' %} + {% assign bioportal_id = 'PTRANS' %} + {% elsif bioportal_id == 'wbls' %} + {% assign bioportal_id = 'WB-LS' %} + {% elsif bioportal_id == 'fbdv' %} + {% assign bioportal_id = 'FB-DV' %} + {% elsif bioportal_id == 'wbbt' %} + {% assign bioportal_id = 'WB-BT' %} + {% elsif bioportal_id == 'wbphenotype' %} + {% assign bioportal_id = 'WB-PHENOTYPE' %} + {% elsif bioportal_id == 'to' %} + {% assign bioportal_id = 'PTO' %} + {% elsif bioportal_id == 'fbcv' %} + {% assign bioportal_id = 'FB-CV' %} + {% elsif bioportal_id == 'umod' %} + {% assign bioportal_id = 'PSIMOD' %} + {% elsif bioportal_id == 'pso' %} + {% assign bioportal_id = 'PLANTSO' %} + {% endif %} + BioPortal {% for b in page.browsers %} diff --git a/_plugins/bioportal_identifier.rb b/_plugins/bioportal_identifier.rb deleted file mode 100644 index 7c37d23e9..000000000 --- a/_plugins/bioportal_identifier.rb +++ /dev/null @@ -1,28 +0,0 @@ -module CustomFilter - def make_bioportal_id(obo_id) - return obo_id unless obo_id.is_a?(String) - - # ID requirements should be locked down moving forward, so additions to this table - # should be rare - special_cases = { - 'fbbt' => 'FB-BT', - 'ro' => 'OBOREL', - 'apollo_sv' => 'APOLLO-SV', - 'trans' => 'PTRANS', - 'wbls' => 'WB-LS', - 'fbdv' => 'FB-DV', - 'wbbt' => 'WB-BT', - 'wbphenotype' => 'WB-PHENOTYPE', - 'to' => 'PTO', - 'fbcv' => 'FB-CV', - 'mod' => 'PSIMOD', - 'pso' => 'PLANTSO' - } - - return special_cases[obo_id] if special_cases.key? obo_id - - obo_id == obo_id.downcase ? obo_id.upcase : obo_id - end -end - -Liquid::Template.register_filter(CustomFilter) diff --git a/ontology/bfo.md b/ontology/bfo.md index c7b91decc..b12eae316 100644 --- a/ontology/bfo.md +++ b/ontology/bfo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: bfo title: Basic Formal Ontology -browsers: -- title: BioPortal Browser - label: BioPortal - url: http://bioportal.bioontology.org/ontologies/BFO?p=classes contact: email: phismith@buffalo.edu github: phismith diff --git a/ontology/fbbt.md b/ontology/fbbt.md index edca1dd0d..b7b29fcac 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -9,9 +9,6 @@ browsers: - title: Virtual Fly Brain label: VFB url: http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401 -- title: BioPortal Browser - label: BioPortal - url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes build: checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git path: . diff --git a/ontology/kisao.md b/ontology/kisao.md index ada4f660f..ad8cf30e3 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -6,9 +6,6 @@ browsers: - title: Ontology Lookup Service label: OLS url: https://www.ebi.ac.uk/ols/ontologies/kisao -- title: BioPortal - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/KISAO - title: OntoBee label: OntoBee url: https://www.ontobee.org/ontology/KISAO diff --git a/ontology/nbo.md b/ontology/nbo.md index e1b5b337b..29bffeb17 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: nbo title: Neuro Behavior Ontology -browsers: -- title: BioPortal Ontology Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/NBO build: method: owl2obo source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl diff --git a/ontology/obi.md b/ontology/obi.md index 9fb6670e0..bc231225a 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -2,10 +2,6 @@ layout: ontology_detail id: obi title: Ontology for Biomedical Investigations -browsers: -- title: BioPortal Browser - label: BioPortal - url: http://bioportal.bioontology.org/ontologies/OBI?p=classes build: source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/ contact: diff --git a/ontology/occo.md b/ontology/occo.md index f39e6ea66..b9f21e07f 100644 --- a/ontology/occo.md +++ b/ontology/occo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: occo title: Occupation Ontology -browsers: -- title: BioPortal Ontology Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/OCCO?p=classes contact: email: zhengj2007@gmail.com github: zhengj2007 diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index ca25ceb76..16b23544b 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: ontoneo title: Obstetric and Neonatal Ontology -browsers: -- title: BioPortal Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/ONTONEO build: source_url: http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl contact: diff --git a/ontology/pato.md b/ontology/pato.md index f4e9ed12b..70b1e6f5a 100644 --- a/ontology/pato.md +++ b/ontology/pato.md @@ -2,10 +2,6 @@ layout: ontology_detail id: pato title: Phenotype And Trait Ontology -browsers: -- title: BioPortal Ontology Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/PATO contact: email: g.gkoutos@gmail.com github: gkoutos diff --git a/ontology/pr.md b/ontology/pr.md index ea1b08642..4233c216b 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -3,9 +3,6 @@ layout: ontology_detail id: pr title: PRotein Ontology (PRO) browsers: -- title: BioPortal Browser - label: BioPortal - url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001 - title: PRO Home label: PRO url: http://proconsortium.org diff --git a/ontology/slso.md b/ontology/slso.md index bc4e1d9fa..53936d903 100644 --- a/ontology/slso.md +++ b/ontology/slso.md @@ -2,10 +2,6 @@ layout: ontology_detail id: slso title: Space Life Sciences Ontology -browsers: -- title: BioPortal Ontology Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/SLSO contact: email: daniel.c.berrios@nasa.gov github: DanBerrios diff --git a/ontology/txpo.md b/ontology/txpo.md index 3f778e300..c1f4bdad1 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -3,9 +3,6 @@ layout: ontology_detail id: txpo title: Toxic Process Ontology browsers: -- title: BioPortal Browser - label: BioPortal - url: http://bioportal.bioontology.org/ontologies/TXPO?p=classes - title: TOXPILOT label: TOXPILOT url: https://toxpilot.nibiohn.go.jp/ From acfa350c366e3ab36e42b51a55ef1ecc8c6600cb Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 11:17:59 -0500 Subject: [PATCH 2/6] upcase checks --- _layouts/ontology_detail.html | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index b6a1f7f7b..2aed34065 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -73,27 +73,27 @@

{% assign bioportal_id = page.id | upcase %} {% if bioportal_id == 'FBBT' %} {% assign bioportal_id = 'FB-BT' %} - {% elsif bioportal_id == 'ro' %} + {% elsif bioportal_id == 'RO' %} {% assign bioportal_id = 'OBOREL' %} - {% elsif bioportal_id == 'apollo_sv' %} + {% elsif bioportal_id == 'APOLLO_SV' %} {% assign bioportal_id = 'APOLLO-SV' %} - {% elsif bioportal_id == 'trans' %} + {% elsif bioportal_id == 'TRANS' %} {% assign bioportal_id = 'PTRANS' %} - {% elsif bioportal_id == 'wbls' %} + {% elsif bioportal_id == 'WBLS' %} {% assign bioportal_id = 'WB-LS' %} - {% elsif bioportal_id == 'fbdv' %} + {% elsif bioportal_id == 'FBDV' %} {% assign bioportal_id = 'FB-DV' %} - {% elsif bioportal_id == 'wbbt' %} + {% elsif bioportal_id == 'WBBT' %} {% assign bioportal_id = 'WB-BT' %} - {% elsif bioportal_id == 'wbphenotype' %} + {% elsif bioportal_id == 'WBPHENOTYPE' %} {% assign bioportal_id = 'WB-PHENOTYPE' %} - {% elsif bioportal_id == 'to' %} + {% elsif bioportal_id == 'TO' %} {% assign bioportal_id = 'PTO' %} - {% elsif bioportal_id == 'fbcv' %} + {% elsif bioportal_id == 'FBCV' %} {% assign bioportal_id = 'FB-CV' %} - {% elsif bioportal_id == 'umod' %} + {% elsif bioportal_id == 'MOD' %} {% assign bioportal_id = 'PSIMOD' %} - {% elsif bioportal_id == 'pso' %} + {% elsif bioportal_id == 'PSO' %} {% assign bioportal_id = 'PLANTSO' %} {% endif %} From 870c6fb7f24baf70ff42bc9732665a6aab335ef5 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 13:06:31 -0500 Subject: [PATCH 3/6] revert ontology metadata changes --- ontology/bfo.md | 4 ++++ ontology/fbbt.md | 3 +++ ontology/kisao.md | 3 +++ ontology/nbo.md | 4 ++++ ontology/obi.md | 4 ++++ ontology/occo.md | 4 ++++ ontology/ontoneo.md | 4 ++++ ontology/pato.md | 4 ++++ ontology/pr.md | 3 +++ ontology/slso.md | 4 ++++ ontology/txpo.md | 3 +++ 11 files changed, 40 insertions(+) diff --git a/ontology/bfo.md b/ontology/bfo.md index b12eae316..c7b91decc 100644 --- a/ontology/bfo.md +++ b/ontology/bfo.md @@ -2,6 +2,10 @@ layout: ontology_detail id: bfo title: Basic Formal Ontology +browsers: +- title: BioPortal Browser + label: BioPortal + url: http://bioportal.bioontology.org/ontologies/BFO?p=classes contact: email: phismith@buffalo.edu github: phismith diff --git a/ontology/fbbt.md b/ontology/fbbt.md index b7b29fcac..edca1dd0d 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -9,6 +9,9 @@ browsers: - title: Virtual Fly Brain label: VFB url: http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401 +- title: BioPortal Browser + label: BioPortal + url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes build: checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git path: . diff --git a/ontology/kisao.md b/ontology/kisao.md index ad8cf30e3..ada4f660f 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -6,6 +6,9 @@ browsers: - title: Ontology Lookup Service label: OLS url: https://www.ebi.ac.uk/ols/ontologies/kisao +- title: BioPortal + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/KISAO - title: OntoBee label: OntoBee url: https://www.ontobee.org/ontology/KISAO diff --git a/ontology/nbo.md b/ontology/nbo.md index 29bffeb17..e1b5b337b 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -2,6 +2,10 @@ layout: ontology_detail id: nbo title: Neuro Behavior Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/NBO build: method: owl2obo source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl diff --git a/ontology/obi.md b/ontology/obi.md index bc231225a..9fb6670e0 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -2,6 +2,10 @@ layout: ontology_detail id: obi title: Ontology for Biomedical Investigations +browsers: +- title: BioPortal Browser + label: BioPortal + url: http://bioportal.bioontology.org/ontologies/OBI?p=classes build: source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/ contact: diff --git a/ontology/occo.md b/ontology/occo.md index b9f21e07f..f39e6ea66 100644 --- a/ontology/occo.md +++ b/ontology/occo.md @@ -2,6 +2,10 @@ layout: ontology_detail id: occo title: Occupation Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/OCCO?p=classes contact: email: zhengj2007@gmail.com github: zhengj2007 diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index 16b23544b..ca25ceb76 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -2,6 +2,10 @@ layout: ontology_detail id: ontoneo title: Obstetric and Neonatal Ontology +browsers: +- title: BioPortal Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/ONTONEO build: source_url: http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl contact: diff --git a/ontology/pato.md b/ontology/pato.md index 70b1e6f5a..f4e9ed12b 100644 --- a/ontology/pato.md +++ b/ontology/pato.md @@ -2,6 +2,10 @@ layout: ontology_detail id: pato title: Phenotype And Trait Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/PATO contact: email: g.gkoutos@gmail.com github: gkoutos diff --git a/ontology/pr.md b/ontology/pr.md index 4233c216b..ea1b08642 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -3,6 +3,9 @@ layout: ontology_detail id: pr title: PRotein Ontology (PRO) browsers: +- title: BioPortal Browser + label: BioPortal + url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001 - title: PRO Home label: PRO url: http://proconsortium.org diff --git a/ontology/slso.md b/ontology/slso.md index 53936d903..bc4e1d9fa 100644 --- a/ontology/slso.md +++ b/ontology/slso.md @@ -2,6 +2,10 @@ layout: ontology_detail id: slso title: Space Life Sciences Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/SLSO contact: email: daniel.c.berrios@nasa.gov github: DanBerrios diff --git a/ontology/txpo.md b/ontology/txpo.md index c1f4bdad1..3f778e300 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -3,6 +3,9 @@ layout: ontology_detail id: txpo title: Toxic Process Ontology browsers: +- title: BioPortal Browser + label: BioPortal + url: http://bioportal.bioontology.org/ontologies/TXPO?p=classes - title: TOXPILOT label: TOXPILOT url: https://toxpilot.nibiohn.go.jp/ From c6e650d3012c8cbc0baca2a49ba7e9299f88ff4c Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 13:11:12 -0500 Subject: [PATCH 4/6] don't edit metadata, skip if available --- _layouts/ontology_detail.html | 43 +++++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 2aed34065..dc00f9666 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -70,35 +70,44 @@

OLS - {% assign bioportal_id = page.id | upcase %} - {% if bioportal_id == 'FBBT' %} + {% assign skip_bioportal = false %} + {% for browser in page.browsers %} + {% if browser.label == "BioPortal" %} + {% assign skip_bioportal = true %} + {% endif %} + {% endfor %} + + {% unless skip_bioportal %} + {% assign bioportal_id = page.id | upcase %} + {% if bioportal_id == 'FBBT' %} {% assign bioportal_id = 'FB-BT' %} - {% elsif bioportal_id == 'RO' %} + {% elsif bioportal_id == 'RO' %} {% assign bioportal_id = 'OBOREL' %} - {% elsif bioportal_id == 'APOLLO_SV' %} + {% elsif bioportal_id == 'APOLLO_SV' %} {% assign bioportal_id = 'APOLLO-SV' %} - {% elsif bioportal_id == 'TRANS' %} + {% elsif bioportal_id == 'TRANS' %} {% assign bioportal_id = 'PTRANS' %} - {% elsif bioportal_id == 'WBLS' %} + {% elsif bioportal_id == 'WBLS' %} {% assign bioportal_id = 'WB-LS' %} - {% elsif bioportal_id == 'FBDV' %} + {% elsif bioportal_id == 'FBDV' %} {% assign bioportal_id = 'FB-DV' %} - {% elsif bioportal_id == 'WBBT' %} + {% elsif bioportal_id == 'WBBT' %} {% assign bioportal_id = 'WB-BT' %} - {% elsif bioportal_id == 'WBPHENOTYPE' %} + {% elsif bioportal_id == 'WBPHENOTYPE' %} {% assign bioportal_id = 'WB-PHENOTYPE' %} - {% elsif bioportal_id == 'TO' %} + {% elsif bioportal_id == 'TO' %} {% assign bioportal_id = 'PTO' %} - {% elsif bioportal_id == 'FBCV' %} + {% elsif bioportal_id == 'FBCV' %} {% assign bioportal_id = 'FB-CV' %} - {% elsif bioportal_id == 'MOD' %} + {% elsif bioportal_id == 'MOD' %} {% assign bioportal_id = 'PSIMOD' %} - {% elsif bioportal_id == 'PSO' %} + {% elsif bioportal_id == 'PSO' %} {% assign bioportal_id = 'PLANTSO' %} - {% endif %} - - BioPortal - + {% endif %} + + BioPortal + + {% endunless %} {% for b in page.browsers %} {{b.label}} From e623db6f61d10cbc99ba367c88459c1a8c53f0e9 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 13:13:05 -0500 Subject: [PATCH 5/6] case neutral --- _layouts/ontology_detail.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index dc00f9666..3811f70f5 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -72,7 +72,7 @@

{% assign skip_bioportal = false %} {% for browser in page.browsers %} - {% if browser.label == "BioPortal" %} + {% if browser.label.upcase == "BIOPORTAL" %} {% assign skip_bioportal = true %} {% endif %} {% endfor %} From ad13307001830e67d4dd31fc6076eef7b800a569 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 25 Nov 2024 13:17:42 -0500 Subject: [PATCH 6/6] that doesn't work --- _layouts/ontology_detail.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 3811f70f5..dc00f9666 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -72,7 +72,7 @@

{% assign skip_bioportal = false %} {% for browser in page.browsers %} - {% if browser.label.upcase == "BIOPORTAL" %} + {% if browser.label == "BioPortal" %} {% assign skip_bioportal = true %} {% endif %} {% endfor %}