Serialisation protégé 5.6.3

Serialisation protégé 5.6.3

src/ontology/uberon-edit.obo

@@ -927,7 +927,7 @@ intersection_of: UBERON:0000026 ! appendage
 intersection_of: has_quality PATO:0002236 ! aliform
 relationship: capable_of_part_of GO:0060361 ! flight
 relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha
-relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} ! Otomorpha
+relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha
 relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires
 relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} ! Nematoda
 relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} ! Dipnomorpha
@@ -7752,7 +7752,7 @@ xref: ENVO:02000026
 xref: FMA:62961
 xref: Wikipedia:Chyme
 is_a: UBERON:0006314 {source="WP"} ! bodily fluid
-is_a: UBERON:0012112 {editor_note="consider changing to derivation relationship", source="FMA"} ! ingested food
+is_a: UBERON:0012112 {IAO:0000116="consider changing to derivation relationship", source="FMA"} ! ingested food
 disjoint_from: UBERON:0012113 ! bolus of food
 relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! acidic
 relationship: located_in UBERON:0004908 ! upper digestive tract
@@ -15949,7 +15949,7 @@ xref: Wikipedia:Peyer's_patch
 is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue
 relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} ! Testudines
 relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota
-relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria
+relationship: part_of UBERON:0000030 {IAO:0000116="check this"} ! lamina propria
 relationship: part_of UBERON:0001242 ! intestinal mucosa
 property_value: external_ontology_notes "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"}
 property_value: external_ontology_notes "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"}
@@ -22423,7 +22423,7 @@ relationship: preaxialmost_part_of UBERON:0002398 ! manus
 property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg" xsd:anyURI
 property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/2/2c/Thumbs_up.jpg" xsd:anyURI
 property_value: taxon_notes "Not present in Anurans (Phenotype RCN Oct 2012)" xsd:string
-property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012260", source="PMID:10220427", source="PhenoscapeRCN"}
+property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"}
 
 [Term]
 id: UBERON:0001464
@@ -28121,7 +28121,7 @@ relationship: part_of UBERON:0010272 ! hyoid apparatus
 property_value: axiom_lost_from_external_ontology "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO"}
 property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI
 property_value: external_definition "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO", source="AAO:LAP"}
-property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/548", source="WP"}
+property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"}
 
 [Term]
 id: UBERON:0001686
@@ -34095,7 +34095,7 @@ xref: VHOG:0001625
 xref: Wikipedia:Olfactory_tubercle
 is_a: UBERON:0000125 {source="EHDAA2"} ! neural nucleus
 relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex
-relationship: dubious_for_taxon NCBITaxon:9443 {editor_note="check EHDAA2", source="MP"} ! Primates
+relationship: dubious_for_taxon NCBITaxon:9443 {IAO:0000116="check EHDAA2", source="MP"} ! Primates
 relationship: mutually_spatially_disjoint_with UBERON:0001882 {source="ABA"} ! nucleus accumbens
 relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex
 relationship: part_of UBERON:0005401 {source="BTO"} ! cerebral hemisphere gray matter
@@ -35074,7 +35074,7 @@ xref: Wikipedia:Pineal_gland
 xref: XAO:0000160
 xref: ZFA:0000019
 is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ
-relationship: capable_of GO:0030187 {editor_note="add secretion"} ! melatonin biosynthetic process
+relationship: capable_of GO:0030187 {IAO:0000116="add secretion"} ! melatonin biosynthetic process
 relationship: contributes_to_morphology_of UBERON:0001899 ! epithalamus
 relationship: has_part CL:0000652 ! pinealocyte
 relationship: has_part CL:0002220 ! interstitial cell of pineal gland
@@ -38619,7 +38619,7 @@ xref: Wikipedia:Spinal_accessory_nerve
 xref: XAO:0004214
 intersection_of: UBERON:0001021 ! nerve
 intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus
-relationship: dubious_for_taxon NCBITaxon:8292 {seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7", source="VHOG", source="Wikipedia"} ! Amphibia
+relationship: dubious_for_taxon NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia
 relationship: innervates UBERON:0001737 ! larynx
 relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris
 relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda
@@ -44580,7 +44580,7 @@ xref: Wikipedia:Nerve_root
 is_a: UBERON:0000122 ! neuron projection bundle
 relationship: extends_fibers_into UBERON:0001017 ! central nervous system
 relationship: extends_fibers_into UBERON:0001021 ! nerve
-relationship: part_of UBERON:0001016 {editor_note="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system
+relationship: part_of UBERON:0001016 {IAO:0000116="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system
 property_value: editor_note "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string
 property_value: external_definition "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." xsd:string {source="FBbt:00007602, FBC:DOS"}
 property_value: external_ontology_notes "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" xsd:string {external_ontology="FMA"}
@@ -74713,7 +74713,7 @@ relationship: part_of UBERON:5003622 ! manual digit 2 plus metapodial segment
 property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/d/d5/Index_finger.JPG" xsd:anyURI
 property_value: has_relational_adjective "indicis" xsd:string
 property_value: taxon_notes "Anurans lack manual digit 1, so manual digit 2 is the digit after the prepollex (Phenotype RCN Oct 2012)" xsd:string
-property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012261", source="PMID:10220427", source="PhenoscapeRCN"}
+property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"}
 
 [Term]
 id: UBERON:0003623
@@ -74750,7 +74750,7 @@ relationship: ambiguous_for_taxon NCBITaxon:8782 ! Aves
 relationship: part_of UBERON:0012141 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! manual digitopodium region
 relationship: part_of UBERON:5003623 ! manual digit 3 plus metapodial segment
 property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/f/fd/Middle_finger.jpg" xsd:anyURI
-property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012262", source="PMID:10220427", source="PhenoscapeRCN"}
+property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"}
 
 [Term]
 id: UBERON:0003624
@@ -76083,7 +76083,7 @@ xref: Wikipedia:Canine_tooth
 intersection_of: UBERON:0001091 ! calcareous tooth
 intersection_of: has_quality PATO:0005021 ! unicuspidate
 disjoint_from: UBERON:0007120 ! premolar tooth
-relationship: has_part UBERON:0006844 {count="1", editor_note="cardinality not allowed with transitivity in OWL"} ! cusp of tooth
+relationship: has_part UBERON:0006844 {IAO:0000116="cardinality not allowed with transitivity in OWL", count="1"} ! cusp of tooth
 relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea
 relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia
 property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/5/57/Azawakh_K9.jpg" xsd:anyURI
@@ -113227,7 +113227,7 @@ name: seminal fluid
 def: "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended." [http://orcid.org/0000-0002-6601-2165]
 synonym: "male genital fluid" RELATED []
 synonym: "male genital secretion" RELATED []
-synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {http://purl.obolibrary.org/obo/IAO_0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."}
+synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {IAO:0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."}
 synonym: "seminal fluid" RELATED [BTO:0001232]
 synonym: "seminal plasma" EXACT [BTO:0001232]
 xref: BTO:0001232
@@ -118699,7 +118699,7 @@ xref: SCTID:304572005
 xref: UMLS:C1704302 {source="ncithesaurus:Bicuspid_Tooth"}
 xref: Wikipedia:Premolar
 is_a: UBERON:0013164 ! molariform tooth
-relationship: has_part UBERON:0006844 {editor_note="cardinality not allowed with transitivity in OWL", min_count="2", taxon_notes="some premolars may have 3 cusps"} ! cusp of tooth
+relationship: has_part UBERON:0006844 {IAO:0000116="cardinality not allowed with transitivity in OWL", UBPROP:0000008="some premolars may have 3 cusps", min_count="2"} ! cusp of tooth
 relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea
 property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1003.png" xsd:anyURI
 property_value: taxon_notes "In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4" xsd:string
@@ -139085,7 +139085,7 @@ name: spleen marginal sinus
 def: "The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood." [MP:MP]
 subset: pheno_slim
 synonym: "splenic marginal sinus" EXACT [MP:0002363]
-xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"}
+xref: EMAPA:37964 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"}
 xref: MA:0000754
 xref: NCIT:C49776
 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"}
@@ -142048,7 +142048,7 @@ synonym: "ventral nasal capsule" EXACT [PMID:21270050]
 xref: AAO:0000303
 is_a: UBERON:0010363 {source="TAO"} ! endochondral element
 relationship: develops_from UBERON:0005945 {source="TAO"} ! neurocranial trabecula
-relationship: dubious_for_taxon NCBITaxon:8292 {editor_note="check AAO"} ! Amphibia
+relationship: dubious_for_taxon NCBITaxon:8292 {IAO:0000116="check AAO"} ! Amphibia
 relationship: never_in_taxon NCBITaxon:8782 ! Aves
 relationship: overlaps UBERON:0001703 {source="TAO"} ! neurocranium
 relationship: part_of UBERON:0002241 {source="TAO"} ! chondrocranium
@@ -151883,7 +151883,7 @@ xref: SCTID:361795009
 xref: Wikipedia:Malleolus
 is_a: UBERON:0005913 ! zone of bone organ
 relationship: part_of UBERON:0004410 ! distal epiphysis of fibula
-property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", seeAlso="UBERON:0004410", source="UBERON:skansa"}
+property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", source="UBERON:skansa", seeAlso="UBERON:0004410"}
 
 [Term]
 id: UBERON:0012292
@@ -181505,7 +181505,7 @@ id: UBERON:0034930
 name: auricular feather
 intersection_of: UBERON:0000022 ! feather
 intersection_of: surrounds UBERON:0001691 ! external ear
-relationship: has_quality PATO:0001297 {editor_note="request more specific terms from PATO"} ! reflectivity
+relationship: has_quality PATO:0001297 {IAO:0000116="request more specific terms from PATO"} ! reflectivity
 property_value: function_notes "the auricular feathers play a role in hearing by reflecting and funneling sound into the external acoustic meatus" xsd:string
 
 [Term]
@@ -223934,7 +223934,7 @@ property_value: dcterms-date "2022-10-31T07:56:47Z" xsd:dateTime
 id: UBERON:8480041
 name: testicular sheath
 def: "Bilayer sheath that covers both the insect male mature gonad and a portion of genital disc-derived structures. It is composed of an outer pigment cell layer, an inner muscle cell layer, and their respective basal laminae." [PMID:9553045]
-synonym: "testis sheath" EXACT [] {http://purl.obolibrary.org/obo/IAO_0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"}
+synonym: "testis sheath" EXACT [] {IAO:0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"}
 is_a: UBERON:0004923 ! organ component layer
 relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli
 relationship: in_taxon NCBITaxon:50557 ! Insecta