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* Made groove a feature of a tissue (anatomical structure). Created …
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…separate class for groove qua line (not clear if this is useful). Addressses #314
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@cmungall
cmungall committed Jul 24, 2013
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Showing 1 changed file with 37 additions and 23 deletions.
60 changes: 37 additions & 23 deletions uberon_edit.obo
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -67382,15 +67384,15 @@ 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]
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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down

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