releases/2014-02-04

Chris Mungall

releases/2014-02-04

Stable URL: http://purl.obolibrary.org/obo/uberon/releases/2014-02-04/uberon.owl

Release notes

syns for branches of ocm nerve
additional metadata relations (function, structure notes).
Added terms from invert neuroanat paper. See issue 393
various additions relating to harerian gland, see 392
added xrefs to AAO for extra-ocular, see issue 394
NTs for branches of arteries around the eye
NT conjunctival space
NTs grouping for glands, based on PMID:7559104
NT: infundibulum of gallbladder
Fixed name of term brought in from MP
New hair types by body location, for MP
Added taxon metadata for Harderian gland. Fixes issue 392
Making blood and analogs a subtype of bodily fluid. Addresses http://code.google.com/p/phenotype-ontologies/issues/detail?id=7
NTs for defining CL classes

Ontology Diff Report

Original Ontology

IRI: http://purl.obolibrary.org/obo/uberon.owl
VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-01-23/uberon.owl

New Ontology

IRI: http://purl.obolibrary.org/obo/uberon.owl
VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-02-04/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 41

New Class : nauplius eye

nauplius eye id UBERON:0015170
nauplius eye has_narrow_synonym three-partite eye { database_cross_reference=PMID:21062451 }
nauplius eye SubClassOf has_part some median eye
nauplius eye has_narrow_synonym four-partite eye { database_cross_reference=PMID:21062451 }
nauplius eye has_obo_namespace uberon
nauplius eye label nauplius eye
nauplius eye SubClassOf eye
nauplius eye definition An eye that consists of a cluster of three or four ➞median eyes that form a single structural unit but are separated from one another by pigment layers { database_cross_reference=PMID:21062451 }

New Class : superior branch of oculomotor nerve

superior branch of oculomotor nerve has_obo_namespace uberon
superior branch of oculomotor nerve SubClassOf supplies some levator palpebrae superioris
superior branch of oculomotor nerve has_exact_synonym oculomotor nerve superior division { database_cross_reference=FMA:52572 }
superior branch of oculomotor nerve id UBERON:0015162
superior branch of oculomotor nerve has_exact_synonym superior ramus of oculomotor nerve { database_cross_reference=FMA:52572 }
superior branch of oculomotor nerve database_cross_reference AAO:0010628
superior branch of oculomotor nerve has_related_synonym dorsal ramus of oculomotor nerve { database_cross_reference=AAO:0010628 }
superior branch of oculomotor nerve SubClassOf nerve
superior branch of oculomotor nerve SubClassOf branching_part_of some oculomotor nerve
superior branch of oculomotor nerve EquivalentTo nerve and supplies some superior rectus extraocular muscle and branching_part_of some oculomotor nerve
superior branch of oculomotor nerve SubClassOf supplies some superior rectus extraocular muscle
superior branch of oculomotor nerve has_exact_synonym ramus superior (nervus oculomotorius [III]) { database_cross_reference=FMA:52572 }
superior branch of oculomotor nerve has_related_synonym dorsal ramus of occulomotor nerve { database_cross_reference=AAO:0010628 }
superior branch of oculomotor nerve label superior branch of oculomotor nerve
superior branch of oculomotor nerve database_cross_reference Wikipedia:Superior_branch_of_oculomotor_nerve
superior branch of oculomotor nerve definition The superior branch of the oculomotor nerve or the superior division, the smaller, passes medialward over the optic nerve. It supplies the Superior rectus and Levator palpebrae superioris. { database_cross_reference=Wikipedia:Superior_branch_of_oculomotor_nerve }
superior branch of oculomotor nerve SubClassOf structure with developmental contribution from neural crest
superior branch of oculomotor nerve database_cross_reference SCTID:280205004
superior branch of oculomotor nerve has_exact_synonym ramus superior nervi oculomotorii { database_cross_reference=Wikipedia:Superior_branch_of_oculomotor_nerve has_synonym_type=latin term }
superior branch of oculomotor nerve SubClassOf ectoderm-derived structure
superior branch of oculomotor nerve database_cross_reference FMA:52572

New Class : multi-unit eye

multi-unit eye EquivalentTo eye and composed_primarily_of some sense organ
multi-unit eye SubClassOf composed_primarily_of some sense organ
multi-unit eye has_obo_namespace uberon
multi-unit eye present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_6544 { notes=present on mantle edge in arcacean Bivalvia source=PMID:21062451 }
multi-unit eye definition An eye consisting of multiple light-sensing organs { database_cross_reference=PMID:21062451 database_cross_reference=UBERON:cjm }
multi-unit eye present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_6340 { notes=present on tentacular crown source=PMID:21062451 }
multi-unit eye SubClassOf eye
multi-unit eye label multi-unit eye
multi-unit eye id UBERON:0015165
multi-unit eye present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_7588 { notes=The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species source=PMID:21062451 }

New Class : supraorbital artery

supraorbital artery SubClassOf structure with developmental contribution from neural crest
supraorbital artery SubClassOf supplies some levator palpebrae superioris
supraorbital artery has_exact_synonym supra-orbital artery { database_cross_reference=FMA:49973 }
supraorbital artery database_cross_reference Wikipedia:Supraorbital_artery
supraorbital artery database_cross_reference SCTID:369330002
supraorbital artery SubClassOf systemic artery
supraorbital artery SubClassOf mixed endoderm/mesoderm-derived structure
supraorbital artery has_exact_synonym supraorbital artery { database_cross_reference=FMA:49973 }
supraorbital artery database_cross_reference FMA:49973
supraorbital artery SubClassOf supplies some frontal sinus
supraorbital artery label supraorbital artery
supraorbital artery has_obo_namespace uberon
supraorbital artery SubClassOf branching_part_of some ophthalmic artery
supraorbital artery has_related_synonym supraorbital branch of external ophthalmic artery
supraorbital artery has_exact_synonym arteria supraorbitalis { database_cross_reference=Wikipedia:Supraorbital_artery has_synonym_type=latin term }
supraorbital artery definition The supraorbital artery is an artery of the head. It springs from the ophthalmic artery as that vessel is crossing over to the medial side of the optic nerve. { database_cross_reference=Wikipedia:Supraorbital_artery }
supraorbital artery id UBERON:0015160

New Class : inferior branch of oculomotor nerve

inferior branch of oculomotor nerve SubClassOf supplies some inferior rectus extraocular muscle
inferior branch of oculomotor nerve SubClassOf branching_part_of some oculomotor nerve
inferior branch of oculomotor nerve database_cross_reference SCTID:280206003
inferior branch of oculomotor nerve has_related_synonym ventral ramus of occulomotor nerve { database_cross_reference=AAO:0010632 }
inferior branch of oculomotor nerve definition The inferior branch of the oculomotor nerve or the inferior division, the larger, divides into three branches. One passes beneath the optic nerve to the medial rectus. Another, to the inferior rectus. The third and longest runs forward between the inferior recti and lateralis to the inferior oblique. From the last a short thick branch is given off to the lower part of the ciliary ganglion, and forms its short root. All these branches enter the muscles on their ocular surfaces, with the exception of the nerve to the inferior oblique, which enters the muscle at its posterior border. { database_cross_reference=Wikipedia:Inferior_branch_of_oculomotor_nerve }
inferior branch of oculomotor nerve id UBERON:0015161
inferior branch of oculomotor nerve has_obo_namespace uberon
inferior branch of oculomotor nerve has_related_synonym ventral ramus of oculomotor nerve { database_cross_reference=AAO:0010632 }
inferior branch of oculomotor nerve SubClassOf nerve
inferior branch of oculomotor nerve database_cross_reference FMA:52573
inferior branch of oculomotor nerve EquivalentTo nerve and supplies some inferior rectus extraocular muscle and branching_part_of some oculomotor nerve
inferior branch of oculomotor nerve SubClassOf ectoderm-derived structure
inferior branch of oculomotor nerve has_exact_synonym ramus inferior nervi oculomotorii { database_cross_reference=Wikipedia:Inferior_branch_of_oculomotor_nerve has_synonym_type=latin term }
inferior branch of oculomotor nerve label inferior branch of oculomotor nerve
inferior branch of oculomotor nerve has_exact_synonym inferior ramus of oculomotor nerve { database_cross_reference=FMA:52573 }
inferior branch of oculomotor nerve SubClassOf supplies some medial rectus extraocular muscle
inferior branch of oculomotor nerve database_cross_reference Wikipedia:Inferior_branch_of_oculomotor_nerve
inferior branch of oculomotor nerve has_exact_synonym ramus inferior (nervus oculomotorius [III]) { database_cross_reference=FMA:52573 }
inferior branch of oculomotor nerve database_cross_reference AAO:0010632
inferior branch of oculomotor nerve has_exact_synonym oculomotor nerve inferior division { database_cross_reference=FMA:52573 }
inferior branch of oculomotor nerve SubClassOf structure with developmental contribution from neural crest

New Class : tapetum

tapetum has_relational_adjective tapetal
tapetum database_cross_reference SPD:0000343
tapetum has_obo_namespace uberon
tapetum label tapetum
tapetum id UBERON:0015169
tapetum present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_72037
tapetum definition Light reflecting layer found in a variety of different types of eye. { database_cross_reference=UBERON:cjm }
tapetum SubClassOf part_of some eye
tapetum SubClassOf tissue
tapetum has_exact_synonym tapetal layer
tapetum has_exact_synonym tapetum layer

New Class : dorsal hair

dorsal hair has_obo_namespace uberon
dorsal hair id UBERON:0015150
dorsal hair EquivalentTo strand of hair and part_of some dorsum
dorsal hair label dorsal hair
dorsal hair SubClassOf part_of some dorsum
dorsal hair has_related_synonym dorsal coat hair
dorsal hair SubClassOf strand of hair
dorsal hair has_related_synonym back hair

New Class : medial gland of orbital region

medial gland of orbital region SubClassOf intersects_midsagittal_plane_of some orbital region
medial gland of orbital region id UBERON:0015153
medial gland of orbital region SubClassOf part_of some orbital region
medial gland of orbital region EquivalentTo gland and part_of some orbital region and intersects_midsagittal_plane_of some orbital region
medial gland of orbital region label medial gland of orbital region
medial gland of orbital region has_obo_namespace uberon
medial gland of orbital region SubClassOf gland of orbital region

New Class : lateral gland of orbital region

lateral gland of orbital region id UBERON:0015154
lateral gland of orbital region EquivalentTo gland and part_of some orbital region and in_lateral_side_of some orbital region
lateral gland of orbital region SubClassOf in_lateral_side_of some orbital region
lateral gland of orbital region SubClassOf gland of orbital region
lateral gland of orbital region SubClassOf part_of some orbital region
lateral gland of orbital region has_obo_namespace uberon
lateral gland of orbital region label lateral gland of orbital region

New Class : Harderian gland duct

Harderian gland duct SubClassOf neural crest-derived structure
Harderian gland duct has_exact_synonym duct of Harder’s gland
Harderian gland duct EquivalentTo duct and part_of some Harderian gland
Harderian gland duct has_obo_namespace uberon
Harderian gland duct comment The duct of the gland opens into the conjunctival sac at the base of the nictitating membrane.
Harderian gland duct SubClassOf duct
Harderian gland duct label Harderian gland duct
Harderian gland duct has_related_synonym Harderian duct
Harderian gland duct SubClassOf part_of some Harderian gland
Harderian gland duct id UBERON:0015151
Harderian gland duct has_exact_synonym duct of Harderian gland

New Class : gland of orbital region

gland of orbital region has_obo_namespace uberon
gland of orbital region id UBERON:0015152
gland of orbital region label gland of orbital region
gland of orbital region SubClassOf gland
gland of orbital region SubClassOf part_of some orbital region
gland of orbital region SubClassOf neural crest-derived structure
gland of orbital region EquivalentTo gland and part_of some orbital region

New Class : zygomatico-orbital artery

zygomatico-orbital artery definition The middle temporal artery occasionally gives off a zygomatico-orbital branch, which runs along the upper border of the zygomatic arch, between the two layers of the temporal fascia, to the lateral angle of the orbit. This branch, which may arise directly from the superficial temporal artery, supplies the Orbicularis oculi, and anastomoses with the lacrimal and palpebral branches of the ophthalmic artery. { database_cross_reference=Wikipedia:Zygomatico-orbital_artery }
zygomatico-orbital artery database_cross_reference FMA:49663
zygomatico-orbital artery has_related_synonym zygomaticoorbital branch { database_cross_reference=Wikipedia:Zygomatico-orbital_artery }
zygomatico-orbital artery database_cross_reference Wikipedia:Zygomatico-orbital_artery
zygomatico-orbital artery label zygomatico-orbital artery
zygomatico-orbital artery has_related_synonym zygomaticooerbital branch { database_cross_reference=Wikipedia:Zygomatico-orbital_artery }
zygomatico-orbital artery database_cross_reference SCTID:146753008
zygomatico-orbital artery SubClassOf branching_part_of some superficial temporal artery
zygomatico-orbital artery SubClassOf artery
zygomatico-orbital artery SubClassOf head blood vessel
zygomatico-orbital artery has_obo_namespace uberon
zygomatico-orbital artery id UBERON:0015157

New Class : ophthalmotemporal branch of external ophthalmic artery

ophthalmotemporal branch of external ophthalmic artery label ophthalmotemporal branch of external ophthalmic artery
ophthalmotemporal branch of external ophthalmic artery id UBERON:0015158
ophthalmotemporal branch of external ophthalmic artery has_obo_namespace uberon
ophthalmotemporal branch of external ophthalmic artery SubClassOf lacrimal artery
ophthalmotemporal branch of external ophthalmic artery SubClassOf supplies some Harderian gland
ophthalmotemporal branch of external ophthalmic artery comment The blood supply to the (Harderian) gland has been reported in greatest detail in the sparrow Passer domesticus (Slonaker, 1918), where it is derived through the ophthalmotemporal branch of the external ophthalmic artery PMID:7559104
ophthalmotemporal branch of external ophthalmic artery has_related_synonym ophthalmotemporal artery
ophthalmotemporal branch of external ophthalmic artery SubClassOf branching_part_of some ophthalmic artery

New Class : conjunctival space

conjunctival space EquivalentTo anatomical space and enclosed_by some conjunctiva
conjunctival space id UBERON:0015155
conjunctival space has_narrow_synonym subbrillar space { database_cross_reference=NCBITaxon:8570 database_cross_reference=PMID:7559104 }
conjunctival space SubClassOf anatomical space
conjunctival space label conjunctival space
conjunctival space SubClassOf part_of some conjunctival sac
conjunctival space has_exact_synonym conjunctival sac cavity { database_cross_reference=FMA:59083 }
conjunctival space database_cross_reference SCTID:280957009
conjunctival space has_obo_namespace uberon
conjunctival space database_cross_reference FMA:59083
conjunctival space has_exact_synonym subconjunctival space
conjunctival space SubClassOf enclosed_by some conjunctiva
conjunctival space has_exact_synonym cavity of conjunctival sac { database_cross_reference=FMA:59083 }

New Class : terminal branch of ophthalmic artery

terminal branch of ophthalmic artery definition The two terminal branches of the ophthalmic artery in humans are the dorsal nasal artery and the supratrochlear artery { database_cross_reference=Wikipedia:Dorsal_nasal_artery database_cross_reference=Wikipedia:Supratrochlear_artery }
terminal branch of ophthalmic artery SubClassOf structure with developmental contribution from neural crest
terminal branch of ophthalmic artery id UBERON:0015156
terminal branch of ophthalmic artery label terminal branch of ophthalmic artery
terminal branch of ophthalmic artery has_obo_namespace uberon
terminal branch of ophthalmic artery database_cross_reference FMA:51956
terminal branch of ophthalmic artery SubClassOf systemic artery
terminal branch of ophthalmic artery SubClassOf mixed endoderm/mesoderm-derived structure
terminal branch of ophthalmic artery SubClassOf branching_part_of some ophthalmic artery

New Class : falciform fat

falciform fat has_related_synonym falciform fat depot
falciform fat SubClassOf mesenteric fat pad
falciform fat has_obo_namespace uberon
falciform fat SubClassOf part_of some falciform ligament
falciform fat has_related_synonym falciform ligament fat pad
falciform fat SubClassOf abdominal fat pad
falciform fat SubClassOf embryonic tissue
falciform fat label falciform fat
falciform fat SubClassOf mixed endoderm/mesoderm-derived structure
falciform fat id UBERON:0015142
falciform fat EquivalentTo fat pad and part_of some falciform ligament
falciform fat definition A large fat pad that is located at the base of the abdominal wall, in the falciform ligament of the liver. { database_cross_reference=MURDOCH:768 }

New Class : mesenteric fat pad

mesenteric fat pad has_exact_synonym mesenteric fat depot { database_cross_reference=MP:0008903 }
mesenteric fat pad label mesenteric fat pad
mesenteric fat pad EquivalentTo fat pad and part_of some mesentery
mesenteric fat pad definition Encapsulated adipose tissue associated with the mesentery { database_cross_reference=MP:0008903 }
mesenteric fat pad SubClassOf part_of some mesentery
mesenteric fat pad SubClassOf fat pad
mesenteric fat pad SubClassOf mesoderm-derived structure
mesenteric fat pad has_obo_namespace uberon
mesenteric fat pad id UBERON:0015143

New Class : autopod hair

autopod hair has_exact_synonym hand/foot hair
autopod hair has_obo_namespace uberon
autopod hair id UBERON:0015144
autopod hair has_narrow_synonym paw hair
autopod hair label autopod hair
autopod hair SubClassOf part_of some autopod region
autopod hair SubClassOf strand of hair
autopod hair EquivalentTo strand of hair and part_of some autopod region
autopod hair has_exact_synonym hair of hand/foot

New Class : pes hair

pes hair id UBERON:0015145
pes hair has_exact_synonym hind foot hair
pes hair SubClassOf part_of some pes
pes hair EquivalentTo strand of hair and part_of some pes
pes hair SubClassOf autopod hair
pes hair has_exact_synonym hair of foot
pes hair label pes hair
pes hair has_obo_namespace uberon
pes hair has_narrow_synonym hind paw hair
pes hair has_exact_synonym foot hair

New Class : manus hair

manus hair EquivalentTo strand of hair and part_of some manus
manus hair has_exact_synonym hand hair
manus hair has_narrow_synonym front paw hair
manus hair SubClassOf part_of some manus
manus hair id UBERON:0015146
manus hair has_obo_namespace uberon
manus hair SubClassOf autopod hair
manus hair label manus hair
manus hair has_exact_synonym hair of hand

New Class : pinna hair

pinna hair label pinna hair
pinna hair SubClassOf strand of hair
pinna hair has_related_synonym ear hair
pinna hair id UBERON:0015147
pinna hair has_obo_namespace uberon
pinna hair EquivalentTo strand of hair and part_of some pinna
pinna hair SubClassOf part_of some pinna

New Class : tail hair

tail hair label tail hair
tail hair SubClassOf strand of hair
tail hair id UBERON:0015148
tail hair SubClassOf part_of some tail
tail hair has_obo_namespace uberon
tail hair EquivalentTo strand of hair and part_of some tail

New Class : ventral hair

ventral hair id UBERON:0015149
ventral hair EquivalentTo strand of hair and part_of some ventrum
ventral hair SubClassOf part_of some ventrum
ventral hair has_related_synonym ventral coat hair
ventral hair has_obo_namespace uberon
ventral hair SubClassOf strand of hair
ventral hair label ventral hair

Changed Class objects: 52

Changes for: notochordal canal

Added
- + notochordal canal EquivalentTo anatomical conduit and part_of some notochordal process

Changes for: obsolete ventral ramus of occulomotor nerve

Deleted
- - ventral ramus of occulomotor nerve SubClassOf ectoderm-derived structure
- - ventral ramus of occulomotor nerve SubClassOf innervated some musculus obliquus inferior
- - ventral ramus of occulomotor nerve SubClassOf innervated some musculus rectus inferior
- - ventral ramus of occulomotor nerve SubClassOf innervated some musculus rectus medialis
- - ventral ramus of occulomotor nerve SubClassOf nerve
- - ventral ramus of occulomotor nerve SubClassOf part_of some oculomotor nerve
- - ventral ramus of occulomotor nerve SubClassOf structure with developmental contribution from neural crest
- - ventral ramus of occulomotor nerve label ventral ramus of occulomotor nerve
Added
- + obsolete ventral ramus of occulomotor nerve deprecated true
- + obsolete ventral ramus of occulomotor nerve label obsolete ventral ramus of occulomotor nerve
- + obsolete ventral ramus of occulomotor nerve term replaced by UBERON:0015161

Changes for: strand of pubic hair

Added
- + strand of pubic hair definition A hair in the frontal genital area of adolescent and adult humans, located on and around the sex organs, the crotch, and sometimes at the top of the inside of the thighs, in the pubic region around the pubis bone. { database_cross_reference=Wikipedia:Pubic_hair }

Changes for: anatomical line between inner canthi

Deleted
- - anatomical line between inner canthi definition An anatomical line of the face that connects the two inner (medial) canthi of the eye { database_cross_reference=UBERON:cjm }
Added
- + anatomical line between inner canthi definition An anatomical line of the face that connects the two inner (medial) canthi of the eye. The length of this line is known as the inter canthal distance. { database_cross_reference=UBERON:cjm }

Changes for: obsolete dorsal ramus of occulomotor nerve

Deleted
- - dorsal ramus of occulomotor nerve SubClassOf ectoderm-derived structure
- - dorsal ramus of occulomotor nerve SubClassOf innervates some musculus rectus superior
- - dorsal ramus of occulomotor nerve SubClassOf part_of some oculomotor nerve
- - dorsal ramus of occulomotor nerve SubClassOf structure with developmental contribution from neural crest
- - dorsal ramus of occulomotor nerve SubClassOf tissue
- - dorsal ramus of occulomotor nerve label dorsal ramus of occulomotor nerve
Added
- + obsolete dorsal ramus of occulomotor nerve deprecated true
- + obsolete dorsal ramus of occulomotor nerve label obsolete dorsal ramus of occulomotor nerve
- + obsolete dorsal ramus of occulomotor nerve term replaced by UBERON:0015162

Changes for: nerve cord

Deleted
- - nerve cord in_subset dubious_grouping
Added
- + nerve cord definition A cluster of ➞neurons that is the most prominent longitudinally extending condensed part of a ➞nervous system. { database_cross_reference=PMID:21062451 }

Changes for: Harderian gland

Deleted
- - Harderian gland definition The Harderian gland is an anterior orbital structure usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species[GO]. An accessory lacrimal gland on the inner side of the orbit in reptiles and birds but usually degenerate in mammals[BTO]. { database_cross_reference=GO:0070384 database_cross_reference=Wikipedia:Harderian_gland }
Added
- + Harderian gland SubClassOf innervated_by some inferior branch of oculomotor nerve
- + Harderian gland SubClassOf intersects_midsagittal_plane_of some orbital region
- + Harderian gland SubClassOf medial gland of orbital region
- + Harderian gland definition The Harderian gland is an anterior orbital structure usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species[GO]. { database_cross_reference=GO:0070384 database_cross_reference=Wikipedia:Harderian_gland }
- + Harderian gland function_notes The functions attributed to the gland are many and diverse. Amongst these, it has been held to be a site of immune responses, a source of thermoregulatory lipids, a source of pheromones, a photoprotective organ and part of a retinal-pineal axis. It is arguably the last remaining large organ of widespread dis- tribution among the vertebrates to which we cannot confidently ascribe a confirmed function. { source=PMID:7559104 }
- + Harderian gland has_related_synonym deep gland of the nictitating membrane { database_cross_reference=PMID:7559104 }
- + Harderian gland has_related_synonym glandula palpebra tertia profundus { database_cross_reference=PMID:7559104 has_synonym_type=latin term }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_8293 { source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_8342 { source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_9263 { source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_9397 { source=PMID:20665821 source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_9608 { source=PMID:14803383 source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_9681 { source=PMID:6997222 source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland present_in_taxon http://purl.obolibrary.org/obo/NCBITaxon_9845 { source=PMID:12969024 source=https://sourceforge.net/p/geneontology/ontology-requests/10639 }
- + Harderian gland structure_notes The harderian gland may be compound tubular (MacLeod, 1880; Paule, 1957) or compound tubuloacinar/tubuloalveolar (Aureli, 1957; Hoffman, 1971). { source=PMID:7559104 }

Changes for: prostate gland stroma

Deleted
- - prostate gland stroma SubClassOf male anatomical structure
- - prostate gland stroma SubClassOf reproductive structure
Added
- + prostate gland stroma SubClassOf connective tissue of prostate

Changes for: inferior oblique extraocular muscle

Added
- + inferior oblique extraocular muscle database_cross_reference AAO:0010117
- + inferior oblique extraocular muscle has_exact_synonym m. obliquus inferior
- + inferior oblique extraocular muscle has_exact_synonym musculus obliquus inferior { database_cross_reference=AAO:0010117 }

Changes for: superior rectus extraocular muscle

Added
- + superior rectus extraocular muscle database_cross_reference AAO:0010099
- + superior rectus extraocular muscle has_exact_synonym m. rectus superior
- + superior rectus extraocular muscle has_exact_synonym musculus rectus superior { database_cross_reference=AAO:0010099 }

Changes for: inferior rectus extraocular muscle

Added
- + inferior rectus extraocular muscle database_cross_reference AAO:0010101
- + inferior rectus extraocular muscle has_exact_synonym m, rectus inferior
- + inferior rectus extraocular muscle has_exact_synonym musculus rectus inferior { database_cross_reference=AAO:0010101 }

Changes for: acinus of lacrimal gland

Deleted
- - acinus of lacrimal gland SubClassOf ectoderm-derived structure
Added
- + acinus of lacrimal gland SubClassOf neural crest-derived structure

Changes for: vasculature

Added
- + vasculature has_relational_adjective vascular

Changes for: median eye

Deleted
- - median ocellus SubClassOf dorsal ocellus
- - median ocellus definition The ocellus that is is located medially on the cranium[HAO]. The number, form, and function of the dorsal ocelli varies markedly throughout insect orders. They tend to be larger and more strongly expressed in flying insects (particularly bees, wasps, dragonflies and locusts), where they are typically found as a triplet. Two lateral ocelli are directed to the left and right of the head respectively, while a central (median) ocellus is directed frontally. In some terrestrial insects (e.g. some ants and cockroaches), only two lateral ocelli are present: the median ocellus is absent. Note that the unfortunately labelled ‘lateral ocelli’ here refers to the sideways facing position of the ocelli, which are of the dorsal type. They should not be confused with the lateral ocelli of some insect larvae (see stemmata)[Wikipedia]. { database_cross_reference=HAO:0000526 database_cross_reference=Ocelli }
- - median ocellus label median ocellus
Added
- + median eye SubClassOf eye
- + median eye definition A median eye is an ➞eye that is connected to a paired or unpaired median anterior ➞neuropil of the ➞syncerebrum by one or several median eye nerves. { database_cross_reference=PMID:21062451 }
- + median eye has_exact_synonym medial ocellus { database_cross_reference=FBbt:00004507 }
- + median eye has_exact_synonym median ocellus { database_cross_reference=HAO:0000526 }
- + median eye has_related_synonym frontal ocellus { database_cross_reference=PMID:21062451 }
- + median eye label median eye

Changes for: haemolymphatic fluid

Deleted
- - haemolymphatic fluid SubClassOf portion of organism substance
Added
- + haemolymphatic fluid SubClassOf bodily fluid

Changes for: cerebral artery

Added
- + cerebral artery EquivalentTo artery and supplies some telencephalon
- + cerebral artery SubClassOf supplies some telencephalon

Changes for: obsolete musculus obliquus inferior

Deleted
- - musculus obliquus inferior SubClassOf extra-ocular muscle
- - musculus obliquus inferior has_obo_namespace uberon/phenoscape-anatomy
- - musculus obliquus inferior label musculus obliquus inferior
- - musculus obliquus inferior provenance_notes This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Added
- + obsolete musculus obliquus inferior deprecated true
- + obsolete musculus obliquus inferior label obsolete musculus obliquus inferior
- + obsolete musculus obliquus inferior term replaced by UBERON:0006320

Changes for: obsolete musculus rectus medialis

Deleted
- - musculus rectus medialis SubClassOf extra-ocular muscle
- - musculus rectus medialis has_obo_namespace uberon/phenoscape-anatomy
- - musculus rectus medialis label musculus rectus medialis
- - musculus rectus medialis provenance_notes This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Added
- + obsolete musculus rectus medialis deprecated true
- + obsolete musculus rectus medialis label obsolete musculus rectus medialis
- + obsolete musculus rectus medialis term replaced by UBERON:0001602

Changes for: obsolete musculus rectus inferior

Deleted
- - musculus rectus inferior SubClassOf extra-ocular muscle
- - musculus rectus inferior label musculus rectus inferior
- - musculus rectus inferior provenance_notes This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Added
- + obsolete musculus rectus inferior deprecated true
- + obsolete musculus rectus inferior label obsolete musculus rectus inferior
- + obsolete musculus rectus inferior term replaced by UBERON:0006322

Changes for: lacrimal gland

Deleted
- - lacrimal gland SubClassOf ectoderm-derived structure
Added
- + lacrimal gland EquivalentTo gland and part_of some lacrimal apparatus and in_lateral_side_of some orbital region
- + lacrimal gland SubClassOf in_lateral_side_of some orbital region
- + lacrimal gland SubClassOf lateral gland of orbital region

Changes for: nerve plexus

Added
- + nerve plexus has_broad_synonym plexus

Changes for: Harderian gland epithelium

Deleted
- - harderian gland epithelium label harderian gland epithelium
Added
- + Harderian gland epithelium has_exact_synonym epithelium of harderian gland
- + Harderian gland epithelium has_exact_synonym harderian gland epithelium { database_cross_reference=MA:0001248 }
- + Harderian gland epithelium label Harderian gland epithelium

Changes for: glossopharyngeal ganglion

Deleted
- - glossopharyngeal ganglion comment This class was created automatically from a combination of ontologies

Changes for: compound eye

Deleted
- - compound eye SubClassOf eye
- - compound eye SubClassOf has_part some ommatidium
Added
- + compound eye EquivalentTo eye and composed_primarily_of some ommatidium
- + compound eye SubClassOf composed_primarily_of some ommatidium
- + compound eye SubClassOf multi-unit eye
- + compound eye has_related_synonym faceted eye
- + compound eye taxon_notes The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures { source=PMID:21062451 }

Changes for: gastropod cerebral ganglion

Added
- + gastropod cerebral ganglion comment Editors note: consider merging into brain

Changes for: medial rectus extraocular muscle

Added
- + medial rectus extraocular muscle database_cross_reference AAO:0010113
- + medial rectus extraocular muscle has_exact_synonym m. rectus medialis
- + medial rectus extraocular muscle has_exact_synonym musculus rectus medialis { database_cross_reference=AAO:0010113 }

Changes for: frontal artery

Deleted
- - frontal artery SubClassOf branching_part_of some ophthalmic artery
- - frontal artery SubClassOf mixed endoderm/mesoderm-derived structure
- - frontal artery SubClassOf structure with developmental contribution from neural crest
- - frontal artery SubClassOf systemic artery
Added
- + frontal artery SubClassOf terminal branch of ophthalmic artery

Changes for: dorsal nasal artery

Deleted
- - dorsal nasal artery SubClassOf artery
- - dorsal nasal artery comment This class was created automatically from a combination of ontologies
- - dorsal nasal artery has_exact_synonym dorsal nasal branch of ophthalmic artery
- - dorsal nasal artery has_exact_synonym external nasal artery
Added
- + dorsal nasal artery SubClassOf terminal branch of ophthalmic artery
- + dorsal nasal artery has_exact_synonym dorsal nasal branch of ophthalmic artery { database_cross_reference=FMA:50000 }
- + dorsal nasal artery has_exact_synonym external nasal artery { database_cross_reference=FMA:50000 }

Changes for: lacrimal artery

Deleted
- - lacrimal artery SubClassOf artery
- - lacrimal artery comment This class was created automatically from a combination of ontologies
Added
- + lacrimal artery EquivalentTo artery and supplies some lacrimal gland
- + lacrimal artery SubClassOf branching_part_of some ophthalmic artery
- + lacrimal artery SubClassOf mixed endoderm/mesoderm-derived structure
- + lacrimal artery SubClassOf structure with developmental contribution from neural crest
- + lacrimal artery SubClassOf supplies some lacrimal gland
- + lacrimal artery SubClassOf systemic artery

Changes for: oculomotor nerve

Deleted
- - oculomotor nerve definition Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles. // Cranial nerve that runs to the eye muscles. { database_cross_reference=ISBN:0471209627 database_cross_reference=Wikipedia:Oculomotor_nerve }
Added
- + oculomotor nerve definition Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles. { database_cross_reference=ISBN:0471209627 database_cross_reference=Wikipedia:Oculomotor_nerve }

Changes for: tapetum lucidum of camera-type eye

Deleted
- - tapetum lucidum SubClassOf tissue
- - tapetum lucidum label tapetum lucidum
Added
- + tapetum lucidum of camera-type eye SubClassOf tapetum
- + tapetum lucidum of camera-type eye has_exact_synonym tapetum lucidum
- + tapetum lucidum of camera-type eye label tapetum lucidum of camera-type eye

Changes for: outflow part of right ventricle

Deleted
- - outflow part of right ventricle definition Outflow part of ventricle which is continuous with the pulmonary trunk[FNA]. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery[WP]. { database_cross_reference=FMA:7216 }
- - outflow part of right ventricle has_exact_synonym RVOT
- - outflow part of right ventricle has_exact_synonym right ventricular outflow tract
Added
- + outflow part of right ventricle definition anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_exact_synonym RVOT { database_cross_reference=MP:0010428 has_synonym_type=abbreviation }
- + outflow part of right ventricle has_exact_synonym infundibulum of right ventricle { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_exact_synonym right ventricle pulmonary outflow tract { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_exact_synonym right ventricular outflow tract { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_related_synonym arterial cone { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_related_synonym conus arteriosus { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_related_synonym pulmonary cone { database_cross_reference=MP:0010428 }
- + outflow part of right ventricle has_related_synonym pulmonary conus { database_cross_reference=MP:0010428 }

Changes for: outflow part of left ventricle

Deleted
- - outflow part of left ventricle definition Outflow part of ventricle which is continuous with the aorta[FMA]. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. { database_cross_reference=FMA:9473 }
- - outflow part of left ventricle has_exact_synonym LVOT
Added
- + outflow part of left ventricle definition anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. { database_cross_reference=MP:0010429 }
- + outflow part of left ventricle has_exact_synonym LVOT { database_cross_reference=MP:0010429 has_synonym_type=abbreviation }
- + outflow part of left ventricle has_exact_synonym Sibson vestibule { database_cross_reference=MP:0010429 }
- + outflow part of left ventricle has_exact_synonym aortic vestibule { database_cross_reference=MP:0010429 }
- + outflow part of left ventricle has_exact_synonym heart left ventricle outflow tract { database_cross_reference=MP:0010429 }

Changes for: lacrimal gland epithelium

Added
- + lacrimal gland epithelium SubClassOf neural crest-derived structure

Changes for: femoral fat pad

Deleted
- - abnormal femoral fat pad morphology label abnormal femoral fat pad morphology
Added
- + femoral fat pad label femoral fat pad

Changes for: segmental subdivision of nervous system

Deleted
- - segmental subdivision of nervous system comment Editor note: revisit this after CARO is revised and/or we have defined metameric segment
Added
- + segmental subdivision of nervous system comment Editor note: revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)

Changes for: neuropil

Deleted
- - neuropil definition A dense intricate feltwork of interwoven fine glial processes, fibrils, synaptic terminals, axons, and dendrites interspersed among the nerve cells of the central nervous system[MESH] { database_cross_reference=MESH:A08.637.500 database_cross_reference=Wikipedia:Neuropil }
Added
- + neuropil definition A cluster of ➞neurites that is part of a ➞nervous system and forms a network of dendrites and axons where ➞synapses are present and in which neuronal somata do not occur. { database_cross_reference=PMID:21062451 }

Changes for: ascidian cerebral ganglion

Deleted
- - ascidian cerebral ganglion comment the CG appears to be a diencephalic brain. It originates mainly from the posterior sensory vesicle (Takamura 2002; Dufour et al. 2006) and shows endocrine activity. For examples, ascidian genes orthologous to GnRH and OT/VP, which are secreted from the hypothalamus and the NH, respectively, in vertebrates, are expressed in the cortex of the CG, suggesting that the NC is not distinctly compartmentalized as are vertebrate brains (Tsutsui et al. 1998; Kavanaugh et al. 2005; Kawada et al. 2008; Ukena et al. 2008; Kawada et al. 2009). Moreover, PC2 expression in the cortex of the CG supports possible endocrine activity (Sekiguchi et al. 2007).
Added
- + ascidian cerebral ganglion comment the CG appears to be a diencephalic brain. It originates mainly from the posterior sensory vesicle (Takamura 2002; Dufour et al. 2006) and shows endocrine activity. For examples, ascidian genes orthologous to GnRH and OT/VP, which are secreted from the hypothalamus and the NH, respectively, in vertebrates, are expressed in the cortex of the CG, suggesting that the NC is not distinctly compartmentalized as are vertebrate brains (Tsutsui et al. 1998; Kavanaugh et al. 2005; Kawada et al. 2008; Ukena et al. 2008; Kawada et al. 2009). Moreover, PC2 expression in the cortex of the CG supports possible endocrine activity (Sekiguchi et al. 2007). // Editor notes: consider merging into brain, based on PMID:21062451 “We suggest using the term ➞brain not only for the ‘dorsal ganglia’ of adult Tunicata and Pterobranchia, but also for the larval ‘cerebral ganglion’ of tunicates.”

Changes for: obsolete musculus rectus superior

Deleted
- - musculus rectus superior SubClassOf extra-ocular muscle
- - musculus rectus superior has_obo_namespace uberon/phenoscape-anatomy
- - musculus rectus superior label musculus rectus superior
- - musculus rectus superior provenance_notes This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Added
- + obsolete musculus rectus superior deprecated true
- + obsolete musculus rectus superior label obsolete musculus rectus superior
- + obsolete musculus rectus superior term replaced by UBERON:0006323

Changes for: gland of nictitating membrane

Deleted
- - gland of nictitating membrane comment Consider merging with Harderian
Added
- + gland of nictitating membrane SubClassOf intersects_midsagittal_plane_of some orbital region
- + gland of nictitating membrane SubClassOf medial gland of orbital region
- + gland of nictitating membrane comment This gland is distinct from the other medial ocular gland, the Harderian gland, and is typified by clusters of glandular tissue within the nictitating membrane
- + gland of nictitating membrane has_related_synonym glandula palpebra tertia superficialis { database_cross_reference=PMID:7559104 has_synonym_type=latin term }
- + gland of nictitating membrane has_related_synonym superficial gland of the nictitating membrane { database_cross_reference=PMID:7559104 }

Changes for: lateral palpebral artery

Added
- + lateral palpebral artery SubClassOf mixed endoderm/mesoderm-derived structure
- + lateral palpebral artery SubClassOf structure with developmental contribution from neural crest
- + lateral palpebral artery SubClassOf systemic artery

Changes for: brille

Deleted
- - brille comment Taxon notes: In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a “glassy-eyed” blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids.
- - brille definition layer of transparent, immovable disc-shaped skin or scale covering the eyes of some animals for protection, especially in animals without eyelids. The brille has evolved from a fusion of the upper and lower eyelids. { database_cross_reference=Wikipedia:Brille }
Added
- + brille SubClassOf has_fused_element some lower eyelid
- + brille SubClassOf has_fused_element some upper eyelid
- + brille comment Taxon notes: In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a “glassy-eyed” blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids. // there are transitional stages between total lid loss and full brille formation (Bellairs & Boyd, 1947).
- + brille definition A layer of transparent, immovable disc-shaped skin or scale covering the eyes of some animals for protection, especially in animals without eyelids. The brille has evolved from a fusion of the upper and lower eyelids. { database_cross_reference=Wikipedia:Brille }

Changes for: parametrial fat pad

Deleted
- - parametrial fat pad SubClassOf fat pad
- - parametrial fat pad SubClassOf mesoderm-derived structure
Added
- + parametrial fat pad SubClassOf mesenteric fat pad

Changes for: central nervous system

Deleted
- - central nervous system external_definition The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina. { source=GO:1 }

Changes for: mushroom body

Deleted
- - mushroom body has_exact_synonym corpora pedunculata { database_cross_reference=FBbt:00005801 }
Added
- + mushroom body has_related_synonym corpora pedunculata { database_cross_reference=FBbt:00005801 database_cross_reference=PMID:21062451 }
- + mushroom body has_related_synonym corps pédonculés@fr { database_cross_reference=PMID:21062451 }

Changes for: region of conjunctiva

Added
- + region of conjunctiva database_cross_reference SCTID:29445007

Changes for: nictitating membrane

Added
- + nictitating membrane has_exact_synonym palperbra tertia { database_cross_reference=PMID:7559104 has_synonym_type=latin term }

Changes for: brain

Added
- + brain SubClassOf in_anterior_side_of some multi-cellular organism

Changes for: canthus

Added
- + canthus SubClassOf part_of some face

Changes for: eye

Deleted
- - eye has_broad_synonym photoreceptor

Changes for: ommatidium

Deleted
- - ommatidium definition One of the small facets of the compound eye. { database_cross_reference=ISBN:3110148986 database_cross_reference=Wikipedia:Ommatidium }
Added
- + ommatidium SubClassOf eye
- + ommatidium definition The smallest morphological and functional unit of the ➞compound eye that consists of a usually limited and often constant number of rhabdomeric ➞photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells. { database_cross_reference=PMID:21062451 }
- + ommatidium has_related_synonym omatidia { has_synonym_type=plural term }

releases/2014-02-04

Release notes

Ontology Diff Report

Original Ontology

New Ontology

Report for classes

Class objects lost from source: 0

Class objects new in target: 41

New Class : anterior internodal tract

New Class : anatomical line between outer canthi

New Class : epicardial fat

New Class : subepicardial layer of epicardium

New Class : posterior internodal tract

New Class : middle internodal tract

New Class : left outer canthus

New Class : right outer canthus

New Class : main lactiferous duct

New Class : terminal lactiferous duct

New Class : secondary lactiferous duct

New Class : primary lactiferous duct

New Class : quarternary lactiferous duct

New Class : tertiary lactiferous duct

New Class : infundibulum of gallbladder

New Class : connective tissue of prostate

New Class : extralobar lactiferous duct

New Class : subepithelial connective tissue of prostatic gland

New Class : nauplius eye

New Class : superior branch of oculomotor nerve

New Class : multi-unit eye

New Class : supraorbital artery

New Class : inferior branch of oculomotor nerve

New Class : tapetum

New Class : dorsal hair

New Class : medial gland of orbital region

New Class : lateral gland of orbital region

New Class : Harderian gland duct

New Class : gland of orbital region

New Class : zygomatico-orbital artery

New Class : ophthalmotemporal branch of external ophthalmic artery

New Class : conjunctival space

New Class : terminal branch of ophthalmic artery

New Class : falciform fat

New Class : mesenteric fat pad

New Class : autopod hair

New Class : pes hair

New Class : manus hair

New Class : pinna hair

New Class : tail hair

New Class : ventral hair

Changed Class objects: 52

Changes for: notochordal canal

Changes for: obsolete ventral ramus of occulomotor nerve

Changes for: strand of pubic hair

Changes for: anatomical line between inner canthi

Changes for: obsolete dorsal ramus of occulomotor nerve

Changes for: nerve cord

Changes for: Harderian gland

Changes for: prostate gland stroma

Changes for: inferior oblique extraocular muscle

Changes for: superior rectus extraocular muscle

Changes for: inferior rectus extraocular muscle

Changes for: acinus of lacrimal gland

Changes for: vasculature

Changes for: median eye

Changes for: haemolymphatic fluid

Changes for: cerebral artery

Changes for: obsolete musculus obliquus inferior

Changes for: obsolete musculus rectus medialis

Changes for: obsolete musculus rectus inferior

Changes for: lacrimal gland

Changes for: nerve plexus

Changes for: Harderian gland epithelium

Changes for: glossopharyngeal ganglion

Changes for: compound eye

Changes for: gastropod cerebral ganglion

Changes for: medial rectus extraocular muscle

Changes for: frontal artery

Changes for: dorsal nasal artery

Changes for: lacrimal artery

Changes for: oculomotor nerve