From b6dca8fae7ae66fd826632886911a6aa50c8d1e0 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 28 Nov 2023 14:07:22 -0600 Subject: [PATCH 1/3] Obsoleting OBI's CD8 receptor class in favor of PR term --- src/ontology/modules/obsolete.owl | 20 ++++++++++++++++++++ src/ontology/obi-edit.owl | 3 +-- src/ontology/templates/obsolete.tsv | 1 + 3 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index a9d381f0..d1a15197 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -76,6 +76,12 @@ + + + + + + @@ -1140,6 +1146,20 @@ + + + + + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. + CD8 + https://github.com/obi-ontology/obi/issues/353 + + obsolete CD8 receptor + true + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 509f0623..6b70d264 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31871,7 +31871,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - CD8 receptor A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. @@ -33496,5 +33495,5 @@ realizes some 'host of immune response role' - + diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 200ddb54..3cb52b68 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -67,5 +67,6 @@ OBI:0600003 obsolete performing a clinical assessment metadata complete clinica OBI:0600065 obsolete_defined processes organizational term Place holder class, see editor note OBI branch derived PlanAndPlannedProcess Branch subclass Obsolete Class true IAO:0000226 OBI:1110002 obsolete_occurrence of disease metadata incomplete An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB subclass Obsolete Class true IAO:0000228 OBI:1110055 obsolete_disease organizational term placeholder to be imported from disease ontology IEDB IEDB subclass Obsolete Class true IAO:0000228 OGMS:0000031 +OBI:1110132 obsolete CD8 receptor CD8 A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. https://github.com/obi-ontology/obi/issues/353 subclass Obsolete Class true PR:000025402 REO:0000171 obsolete molecular label role ready for release molecular tracer role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002743 REO:0000280 obsolete molecular label ready for release molecular tracer A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002744 From 05330c02c5f3e81082b461b6cce6e6ebe0f32886 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 30 Nov 2023 12:16:40 -0600 Subject: [PATCH 2/3] removing cd8 receptor obsoleted term from obi-edit --- src/ontology/obi-edit.owl | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 6b70d264..5ada1e03 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31868,20 +31868,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - CD8 receptor - - A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. - This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. - CD8 - WEB: http://en.wikipedia.org/wiki/CD8 - CD8 receptor - - - - From 524212a43137263858404afd5ec8f7c50617553f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 30 Nov 2023 12:21:38 -0600 Subject: [PATCH 3/3] removing uses of cd8 receptor obsolete term --- src/ontology/obi-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 5ada1e03..aac49a88 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -31134,7 +31134,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31173,7 +31173,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31181,7 +31181,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - +