Merge pull request #3218 from obophenotype/misc-obsoletions-2

Obsolete and merge a handful of redundant terms

src/ontology/uberon-edit.obo

@@ -91900,7 +91900,7 @@ def: "A gland that is part of an anal canal [Automatically generated definition]
 subset: organ_slim
 synonym: "anal gland" RELATED []
 synonym: "anal sac" RELATED SENSU [Wikipedia:Anal_gland]
-synonym: "gland of anal canal" EXACT [OBOL:automatic]
+synonym: "gland of anal sac" RELATED []
 synonym: "gland of anus" RELATED []
 synonym: "rectal gland" RELATED []
 xref: EMAPA:27221
@@ -98109,14 +98109,11 @@ property_value: structure_notes "The fibroblasts in the interstitium provide the
 
 [Term]
 id: UBERON:0005216
-name: optic eminence surface ectoderm
-def: "An external ectoderm that is part of a optic eminence [Automatically generated definition]." [OBOL:automatic]
-xref: EMAPA:16539
-xref: RETIRED_EHDAA2:0001311
-xref: VHOG:0000520
-intersection_of: UBERON:0000076 ! external ectoderm
-intersection_of: part_of UBERON:0004348 ! optic eminence
-relationship: part_of UBERON:0005234 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! optic eminence ectoderm
+name: obsolete optic eminence surface ectoderm
+comment: Obsoleted because it is redundant with 'optic eminence ectoderm'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3156" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0005234
 
 [Term]
 id: UBERON:0005217
@@ -102546,6 +102543,7 @@ name: thymus lobe
 def: "Either of the two lateral lobes that constitute the thymus." [http://orcid.org/0000-0002-6601-2165]
 synonym: "lateral lobe of thymus" EXACT [http://orcid.org/0000-0002-6601-2165]
 synonym: "lobe of thymus" EXACT [FMA:71193]
+synonym: "thymus subunit" EXACT []
 xref: FMA:71193
 xref: RETIRED_EHDAA2:0002021
 intersection_of: UBERON:0009912 ! anatomical lobe
@@ -111261,6 +111259,7 @@ property_value: external_definition "Ventral part of the cloacal membrane separa
 id: UBERON:0006309
 name: venous vitelline plexus
 subset: emapa_ehdaa2
+synonym: "vitelline venous plexus" EXACT []
 xref: EHDAA:1945
 xref: EMAPA:17020
 xref: RETIRED_EHDAA2:0002172
@@ -111270,14 +111269,11 @@ relationship: part_of UBERON:0004582 ! venous system
 
 [Term]
 id: UBERON:0006310
-name: vitelline venous plexus
-subset: emapa_ehdaa2
-xref: EHDAA2:0002210
-xref: EHDAA:1945
-xref: EMAPA:17020
-is_a: UBERON:0002050 ! embryonic structure
-relationship: part_of UBERON:0004581 ! systemic venous system
-relationship: part_of UBERON:0004582 ! venous system
+name: obsolete vitelline venous plexus
+comment: Obsoleted as it is redundant with 'venous vitelline plexus'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3157" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0006309
 
 [Term]
 id: UBERON:0006311
@@ -145131,18 +145127,11 @@ property_value: external_definition "Exocrine glands in animals which secrete sc
 
 [Term]
 id: UBERON:0011253
-name: gland of anal sac
-synonym: "anal gland" RELATED []
-synonym: "anal sac gland" EXACT []
-synonym: "castor sac" NARROW SENSU [NCBITaxon:29132]
-synonym: "musk gland" RELATED []
-xref: NCIT:C32068
-xref: SCTID:91610001
-xref: UMLS:C0162322 {source="ncithesaurus:Anal_Gland"}
-xref: Wikipedia:Anal_gland
-is_a: UBERON:0011252 ! scent gland
-intersection_of: UBERON:0002365 ! exocrine gland
-intersection_of: part_of UBERON:0008978 ! anal sac
+name: obsolete gland of anal sac
+comment: Obsoleted as it seems to refer to the same concept as 'gland of anal canal'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3159" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0004760
 
 [Term]
 id: UBERON:0011255
@@ -155012,7 +155001,7 @@ synonym: "hyena butter" RELATED SENSU [Wikipedia:Hyena_butter]
 synonym: "musk" RELATED [NCBITaxon:30533]
 synonym: "odorous sac" RELATED []
 intersection_of: UBERON:0000456 ! secretion of exocrine gland
-intersection_of: produced_by UBERON:0011253 ! gland of anal sac
+intersection_of: produced_by UBERON:0004760 ! gland of anal canal
 relationship: present_in_taxon NCBITaxon:119825 ! Mephitidae
 relationship: present_in_taxon NCBITaxon:30533 ! Moschidae
 relationship: present_in_taxon NCBITaxon:9673 ! Viverridae
@@ -182342,11 +182331,11 @@ intersection_of: part_of UBERON:0000382 ! apocrine sweat gland
 
 [Term]
 id: UBERON:0035075
-name: thymus subunit
-synonym: "lobe or lobule of thymus" RELATED []
-xref: FMA:71193
-intersection_of: UBERON:0000063 ! organ subunit
-intersection_of: part_of UBERON:0002046 ! thyroid gland
+name: obsolete thymus subunit
+comment: Obsoleted as it is redundant with 'thymus lobe'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3158" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0005483
 
 [Term]
 id: UBERON:0035076
@@ -192959,11 +192948,11 @@ property_value: provenance_notes "This class was sourced from an external ontolo
 
 [Term]
 id: UBERON:2000597
-name: telencephalic tracts
-xref: ZFA:0000597
-is_a: UBERON:0002316 ! white matter
-relationship: part_of UBERON:0001893 ! telencephalon
-property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"}
+name: obsolete telencephalic tracts
+comment: Obsoleted as it is redundant with 'white matter of telencephalon'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3160" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0011299
 
 [Term]
 id: UBERON:2000599
@@ -194154,7 +194143,7 @@ replaced_by: CL:0005000
 id: UBERON:2000779
 name: lateral forebrain bundle telencephalon
 xref: ZFA:0000779
-is_a: UBERON:2000597 ! telencephalic tracts
+is_a: UBERON:0011299 ! white matter of telencephalon
 relationship: part_of UBERON:2007012 ! lateral forebrain bundle
 property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"}
 
@@ -195002,7 +194991,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo
 id: UBERON:2000910
 name: medial forebrain bundle telencephalon
 xref: ZFA:0000910
-is_a: UBERON:2000597 ! telencephalic tracts
+is_a: UBERON:0011299 ! white matter of telencephalon
 relationship: part_of UBERON:0001910 ! medial forebrain bundle
 property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"}
 
@@ -205744,11 +205733,11 @@ property_value: provenance_notes "This class was sourced from an external ontolo
 
 [Term]
 id: UBERON:2005411
-name: common crus
-xref: ZFA:0005411
-is_a: UBERON:0000058 ! duct
-relationship: part_of UBERON:2005409 ! pars superior ear
-property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"}
+name: obsolete common crus
+comment: Obsoleted as it is redundant with 'common crus of semircular duct'.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3161" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:0013764
 
 [Term]
 id: UBERON:2005412