From 8228655b1c7a78cfbd9c07bd38e10bd3c830e984 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Wed, 24 Jul 2013 10:05:21 -0700 Subject: [PATCH] * Made groove a feature of a tissue (anatomical structure). Created separate class for groove qua line (not clear if this is useful). Addressses #314 --- uberon_edit.obo | 60 ++++++++++++++++++++++++++++++------------------- 1 file changed, 37 insertions(+), 23 deletions(-) diff --git a/uberon_edit.obo b/uberon_edit.obo index 8d4e41ded2..1768b393ab 100644 --- a/uberon_edit.obo +++ b/uberon_edit.obo @@ -1338,11 +1338,13 @@ is_a: UBERON:0000466 ! immaterial anatomical entity [Term] id: UBERON:0007651 ! anatomical junction name: anatomical junction -def: "Anatomical structure in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts. Examples: gastroesophageal junction, line alba, knee joint.[FMA]" [FMA:5898] +def: "Anatomical structure in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts. Examples: gastroesophageal junction, line alba, knee joint.[FMA]" [FMA:5898, http://code.google.com/p/caro2/issues/detail?id=15] subset: upper_level +synonym: "junction" BROAD [] +synonym: "anatomical junction" EXACT [] xref: FMA:5898 ! anatomical junction xref: SCTID:91833003 ! Anatomical junction -is_a: UBERON:0000477 ! anatomical cluster +is_a: UBERON:0000061 {source="FMA"} ! anatomical structure [Term] id: UBERON:0006800 @@ -52264,7 +52266,7 @@ xref: EHDAA:9280 ! philtrum xref: EMAPA:17926 ! philtrum xref: VHOG:0000862 ! philtrum is_a: UBERON:0003102 ! surface structure -is_a: UBERON:0006846 {source="EHDAA2"} ! groove +is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: part_of UBERON:0001834 {source="EMAPA"} ! upper lip relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: develops_from UBERON:0004068 {source="Wikipedia"} ! medial nasal prominence @@ -64254,7 +64256,7 @@ comment: The formation of the esophageal groove is controlled by neural stimulat synonym: "esophageal groove" BROAD SENSU [] synonym: "reticular groove" BROAD SENSU [] synonym: "ruminant reticular groove" EXACT [] -is_a: UBERON:0006846 ! groove +is_a: UBERON:0006846 ! surface groove relationship: develops_from UBERON:0007361 ! ruminant reticulum relationship: channel_for UBERON:0001913 ! milk relationship: channels_from UBERON:0001043 ! esophagus @@ -67057,7 +67059,7 @@ xref: EMAPA:17166 ! fissure xref: SCTID:361508004 ! Choroidal fissure xref: EHDAA2:0001319 ! optic stalk fissure xref: http://upload.wikimedia.org/wikipedia/commons/9/98/Gray865.png -is_a: UBERON:0006846 {source="ZFA"} ! groove +is_a: UBERON:0006846 {source="ZFA"} ! surface groove relationship: part_of UBERON:0003072 {source="ZFA"} ! optic cup relationship: located_in UBERON:0003098 {source="EHDAA2"} ! optic stalk property_value: external_definition "A break in the continuity of the optic cup where the two sides of the cup meet.[AAO]" xsd:string {ontology="AAO", external_class="AAO:0011026", date_retrieved="2012-06-20", source="ISBN:0815318960"} @@ -67382,7 +67384,7 @@ id: UBERON:0009957 ! ciliated pit name: ciliated pit synonym: "pre-oral pit" RELATED [] comment: Development: joins with Hatschek’s diverticulum to form Hatschek’s pit in the adult. Location: anterior to the mouth. -is_a: UBERON:0006846 ! groove +is_a: UBERON:0006846 ! surface groove relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma [Term] @@ -67390,7 +67392,7 @@ id: UBERON:0009865 name: Hatschek's pit def: "a deep ciliated fossa on the dorsal midline of the buccal cavity (the region of the gut behind the mouth). Among other things, it secrets mucus which entraps food particles from the water[WP]." [Wikipedia:Hatschek's_pit] xref: Wikipedia:Hatschek's_pit -is_a: UBERON:0006846 ! groove +is_a: UBERON:0006846 ! surface groove relationship: only_in_taxon NCBITaxon:7737 {source="Wikipedia"} ! Branchiostoma relationship: capable_of GO:0070254 ! mucus secretion relationship: homologous_to UBERON:0002196 {source="PMID:9636084"} ! adenohypophysis @@ -90469,10 +90471,10 @@ xref: XAO:0000016 ! midbrain-hindbrain boundary xref: ZFA:0000042 ! midbrain hindbrain boundary xref: EHDAA2:0004395 ! isthmus xref: EHDAA:5789 ! isthmus -is_a: UBERON:0006800 {source="ZFA"} ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: adjacent_to UBERON:0001891 ! midbrain -intersection_of: adjacent_to UBERON:0002028 ! hindbrain +is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction +intersection_of: UBERON:0007651 ! anatomical junction +intersection_of: overlaps UBERON:0001891 ! midbrain +intersection_of: overlaps UBERON:0002028 ! hindbrain relationship: develops_from UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0000955 {source="ZFA"} ! brain disjoint_from: UBERON:0001609 ! isthmus of thyroid gland @@ -109595,7 +109597,7 @@ name: sulcus limitans of neural tube def: "A longitudinal groove in the neural tube wall of the embryo; stretches from the mesencephalon caudad[TMD]." [http://medical-dictionary.thefreedictionary.com/Sulcus+limitans] synonym: "neural tube lateral wall sulcus limitans" EXACT [EHDAA2:0001265] synonym: "sulcus limitans" BROAD [] -is_a: UBERON:0006846 ! groove +is_a: UBERON:0006846 ! surface groove relationship: part_of UBERON:0005496 {source="EHDAA2"} ! neural tube lateral wall [Term] @@ -115619,7 +115621,7 @@ synonym: "pharyngeal groove" EXACT [Wikipedia:Pharyngeal_groove] synonym: "pharyngeal groove ectoderm" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "sulcus pharyngei" RELATED LATIN [Wikipedia:Pharyngeal_groove] is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium -is_a: UBERON:0006846 {source="EHDAA2"} ! groove +is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000922 ! embryo relationship: overlaps UBERON:0002539 ! pharyngeal arch @@ -129219,7 +129221,7 @@ xref: VHOG:0000790 ! interventricular groove xref: EHDAA:1918 ! interventricular groove xref: EMAPA:17336 ! interventricular groove is_a: UBERON:0004111 ! anatomical conduit -is_a: UBERON:0006846 {source="EHDAA2"} ! groove +is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: part_of UBERON:0002082 ! cardiac ventricle xref: SCTID:277708006 ! Interventricular groove relationship: homologous_in NCBITaxon:7742 {source="VHOG:0000790"} ! Vertebrata @@ -135556,7 +135558,7 @@ synonym: "laryngotracheal endoderm" RELATED [] synonym: "sulcus laryngotrachealis" EXACT LATIN [Wikipedia:Laryngotracheal_groove] xref: EMAPA:16739 ! laryngo-tracheal groove xref: RETIRED_EHDAA2:0000909 ! laryngo-tracheal groove -is_a: UBERON:0006846 {source="EHDAA2"} ! groove +is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: part_of UBERON:0001041 {source="EHDAA2"} ! foregut relationship: part_of UBERON:0001558 {source="EHDAA2"} ! lower respiratory tract relationship: part_of UBERON:0000922 ! embryo @@ -141040,16 +141042,28 @@ property_value: external_definition "A muscle that moves a body part away from t property_value: axiom_lost_from_external_ontology "relationship loss: subclass cranial muscle (TAO:0001953)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0002135", date_retrieved="2012-08-14"} [Term] -id: UBERON:0006846 ! groove -name: groove -def: "Anatomical line that delineates a furrow or depression in an organ or tissue." [ZFA:0001690] +id: UBERON:0006846 ! surface groove +name: surface groove +def: "A furrow or an incomplete tube." [AEO:0000161, AEO:JB, https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/4] +synonym: "groove" RELATED [AEO:0000161] subset: grouping_class -xref: ZFA:0001690 ! groove -xref: FMA:75037 ! Groove -xref: EHDAA2:0003161 ! groove +xref: EHDAA2_RETIRED:0003161 ! groove xref: AEO:0000161 ! groove -is_a: UBERON:0006800 ! anatomical line +is_a: UBERON:0000061 ! anatomical structure +relationship: part_of UBERON:0000479 ! tissue + +[Term] +id: UBERON:0014764 +name: anatomical line along groove +def: "Anatomical line that delineates a furrow or depression in an organ or tissue." [ZFA:0001690, https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/4] +is_a: UBERON:0006800 {source="ZFA", source="FMA"} ! anatomical line +relationship: part_of UBERON:0006846 ! surface groove +synonym: "groove" RELATED [ZFA:0001690] +synonym: "line delineating groove" EXACT [] xref: AAO:0010276 ! groove +xref: HAO:0001525 ! groove +xref: FMA:75037 ! Groove +xref: ZFA:0001690 ! groove xref: TAO:0001838 ! groove [Term] @@ -141245,7 +141259,7 @@ synonym: "hypopharyngeal groove" RELATED [BTO:0003173] property_value: has_relational_adjective "endostylar" xsd:string xref: BTO:0003173 ! endostyle xref: ANISEED:1235299 ! Endostyle -is_a: UBERON:0006846 ! groove +is_a: UBERON:0006846 ! surface groove relationship: part_of UBERON:0006562 ! pharynx relationship: only_in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata relationship: part_of UBERON:0000949 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} ! endocrine system