2015-11-19 release

Improvements to representations of serous membranes and associated structures
2015-11-19 release image

Ontology Diff Report

  • Overhaul of body cavities and linings
    • Obsoleting dubious concept of cavity-lining in favor of serous membrane.
    • Obsoleting dubious concept of body-cavity-or-lining in favor of serous sac.
    • Using luminal_space_of pattern for cavities
    • Refactoring cavities and linings to conform to a standard design pattern, and clearing up many confusions. Fixes 86
    • fixed pericardial fat syn clash; diaphragm, muscle and future brain fixes
    • peritoneum xrefs for mouse, issue 86.
    • obsoleting: body membrane (NIFSTD)
    • NT: serous cavity
    • NT: visceral fat
    • NT: pericardial fat
    • Fixing unsatisfiable classes due to peritoneum vs peritoneal sac issues. Related to 86
    • Pericardium re-classified as multi-tissue. Fixes 1186
    • Ventral body cavity: now JEPD pattern for thoracic/abdominopelvic
    • Coelem fixes
    • Improved pleural cavities
  • neuro
    • added Area X and robust nucleus (songbirds). Fixes 12142
    • BA9 part of DLPFC. Fixes 1163
    • BA24 part of ACC. Fixes 1161
    • Removing inconsistent axioms for EW nucleus. 1160 and 1159
    • VT nucleus not part of VT area. See 1159
    • Additional work on hippocampus layers
    • made S1 part_of parietal cortex (more specific than lobe). Issue 1147
  • musculoskeletal
    • 1165 updated label on circulus and removed period from label on humeral facet on the ulna
    • added sharpey’s fiber, procurrent spur, pectoral splint
    • added gill membrane, pelvic intercleithral cartilage, nasal accessory organ
    • classifying multiple muscle organs as skeletal. 1154
    • merging hamstring and posterior compartment thihg muscle. Adding classification to skeletal muscle 1154
    • made rib skeletal system part of postcranial skeletal system, Fixes 1167
    • Bone of reproductive structure –> Bone of reproductive organ. Fixes 1158
    • added explicit skeletal muscle classification. 1154
    • made all quadriceps femoris (including vastus lateralis) skeletal, Fixes 1152
    • classifying transversus
  • reasoning
    • Various resolutions to incoherencies revealed by reflexive part-of
    • Added taxon notes and taxon axioms for sallet and TM
    • urinary bladder never in Aves. Fixes 454
  • dev
    • Some refactoring of early mouth: split into ectodermal and non-ectodermal components
    • thymoids are in branchial basket region, but not part of. See 1159
  • misc
    • NT: caval sphincter (Phocidae)
    • vanes are connected to rachis, not part of. See 1159
    • Adding stroma syn to mammary connective tissue. Fixes 1151
    • merging adrenal into suprarenal. https://github.com/obophenotype/mouse-anatomy-ontology/issues/110
    • Adding syns for outer limiting membrane pending https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2109#issuecomment-141523542
    • Fixing incorrect syn from FMA. 1176
    • NT: lower esophagus mucosa layer. Fixes 1177
    • NT: lower esophagus muscularis layer. Fixes 1176
    • tweak def of ab ex obl
    • NTs: L/R adrenal cortex/medulla. Fixes 1170
    • NT: Hensen stripe. https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2122
    • Modified relationships for sallet
    • NT: muscle layer of sigmoid colon. Fixes 1162
    • gastroepiploic arteries
    • NTs for apical zones of ventricles. Fixes 1169
  • xrefs and metadata
    • xref fixes from CatherineLeroy. Fixes 1150
    • Adding missing NCIt xrefs. Switch to using meaning-free numeric NCIT IDs. Confirmed with Gilberto that this is correct. Fixes 1149
    • latest EMAPA xrefs
    • IAO xref fixed for example
    • Corrected wrongly encoded accented characters. Addresses 1173

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-09-27/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-11-19/uberon.owl

Report for classes

Class objects lost from source: 1

Class objects new in target: 30

New Class : procurrent spur

New Class : pectoral splint

New Class : accessory nasal sac

New Class : Sharpey’s fiber

New Class : gill membrane

New Class : pelvic intercleithral cartilage

New Class : muscle layer of sigmoid colon

New Class : Hensen stripe

New Class : future mouth

New Class : serous cavity

New Class : area X of basal ganglion

New Class : robust nucleus of arcopallium

New Class : pericardial fat

New Class : paracardial fat

New Class : visceral fat

New Class : abdominopelvic cavity

New Class : peritoneal sac

New Class : right gastroepiploic artery

New Class : left adrenal gland medulla

New Class : left adrenal gland cortex

New Class : right adrenal gland medulla

New Class : right adrenal gland cortex

New Class : left gastroepiploic artery

New Class : costal diaphragm

New Class : apical region of left ventricle

New Class : lower esophagus mucosa

New Class : lower esophagus muscularis layer

New Class : caval sphincter

New Class : apical region of heart ventricle

New Class : apical region of right ventricle

Changed Class objects: 411

Changes for: metaphysis of humerus

Changes for: rostral linear nucleus

Changes for: paranigral nucleus

Changes for: parabrachial pigmental nucleus

Changes for: labial region

Changes for: posterolingual region

Changes for: lingual region

Changes for: chondroglossus muscle

Changes for: abductor pollicis muscle

Changes for: dulla

Changes for: parietal serous membrane

Changes for: jaw region

Changes for: flexor caudalis muscle

Changes for: great vessel of heart

Changes for: skin of sole of pes

Changes for: oral epithelium from ectoderm

Changes for: pineal recess of third ventricle

Changes for: cavity of feather shaft

Changes for: m. flexor indicis superficialis proprius

Changes for: cavity of feather follicle

Changes for: acinus of salivary gland

Changes for: body of tongue

Changes for: fold of peritoneum

Changes for: flexor hallucis brevis muscle

Changes for: brachioradialis

Changes for: flexor pollicis brevis muscle

Changes for: angle of oral opening

Changes for: muscle of Aristotle’s lantern

Changes for: rectum smooth muscle tissue

Changes for: lip taste bud

Changes for: lobule of mammary gland

Changes for: milk

Changes for: iliopsoas

Changes for: lacrimal

Changes for: odontoids

Changes for: retromolar triangle

Changes for: posterior segment of eyeball

Changes for: sensory ganglion

Changes for: anterior segment of eyeball

Changes for: obsolete body membrane

Changes for: perianal skin

Changes for: diencephalon

Changes for: midbrain

  • Deleted
    • - midbrain definition Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. { database cross reference=http://en.wikipedia.org/wiki/Midbrain , database cross reference=FMA:61993 , database cross reference=GO:0030901 , database cross reference=ZFIN:curator }
  • Added
    • + midbrain definition The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. { database cross reference=GO:0030901 }

Changes for: endolymph

Changes for: perilymph

Changes for: lip

Changes for: saliva

Changes for: sublingual duct

Changes for: duct of salivary gland

Changes for: sublingua

Changes for: bony labyrinth

Changes for: secretion of lacrimal gland

Changes for: outer limiting layer of retina

Changes for: jaw mesenchyme

Changes for: lamprey sucker

Changes for: sallet

Changes for: inner limiting layer of retina

Changes for: gas excreted from digestive tract

Changes for: pterygomandibular raphe

Changes for: lower jaw region

Changes for: papilla of tongue

Changes for: tongue

Changes for: anterior cerebral vein

Changes for: palatine bone

Changes for: obsolete caudal fin

Changes for: intrinsic muscle of tongue

Changes for: geniohyoid muscle

Changes for: intrinsic muscle of pes

Changes for: intrinsic muscle of manus

Changes for: depressor labii inferioris

Changes for: urethra muscle tissue

Changes for: mouth mucosa

Changes for: mediastinum

  • Deleted
    • - mediastinum SubClassOf thoracic cavity
    • - mediastinum definition A central thoracic cavity surrounded by loose connective tissue that contains (where present) the heart, the great vessels of the heart, esophagus, trachea, phrenic nerve, cardiac nerve, thoracic duct, thymus, and lymph nodes of the central chest. { database cross reference=http://en.wikipedia.org/wiki/Mediastinum }
    • - mediastinum taxon notes In humans, the mediastinum lies between the right and left pleura in and near the median sagittal plane of the chest. It extends from the sternum in front to the vertebral column behind, and contains all the thoracic viscera except the lungs. It may be divided for purposes of description into two parts:an upper portion, above the upper level of the pericardium, which is named the superior mediastinum with its superior limit at the superior thoracic opening and its inferior limit at the plane from the sternal angle to the disc of T4-T5 (Plane of Ludwig at Angle of Louis); and a lower portion, below the upper level of the pericardium. This lower portion is again subdivided into three parts, viz. that in front of the pericardium, the anterior mediastinum; that containing the pericardium and its contents, the middle mediastinum; and that behind the pericardium, the posterior mediastinum. It is surrounded by the chest wall anteriorly, the lungs laterally and the spine posteriorly. It is continuous with the loose connective tissue of the neck, and extends inferiorly onto the diaphragm { source=WP }
  • Added

Changes for: lower beak

Changes for: oral gland

Changes for: pancreaticoduodenal artery

Changes for: alveolar artery

Changes for: mental artery

Changes for: anterior part of tongue

Changes for: posterior part of tongue

Changes for: copula linguae

Changes for: sublingual artery

Changes for: lingual artery

Changes for: right coronary artery

Changes for: left coronary artery

Changes for: posterior communicating artery

Changes for: future tongue

Changes for: hypopharyngeal eminence

Changes for: hypoglossal cord

Changes for: future diaphragm

Changes for: submental vein

Changes for: orbital cavity

Changes for: baleen plate bristle

Changes for: baleen plate

Changes for: nephron tubule epithelium

Changes for: nose tip

Changes for: lacrimal gland epithelium

Changes for: ventral mesentery

Changes for: urethra skeletal muscle tissue

Changes for: lip skeletal muscle

Changes for: esophagus skeletal muscle

Changes for: corticospinal tract

Changes for: salivary gland epithelium

Changes for: anatomical cavity

Changes for: mediastinal lymph node

Changes for: intramembranous bone

Changes for: rib skeletal system

Changes for: gustatory epithelium of palate

Changes for: tongue taste bud

Changes for: sesamoid bone

Changes for: pleural sac

Changes for: prostate gland secretion

Changes for: mouth floor

Changes for: inner renal medulla vasa recta

Changes for: outer renal medulla vasa recta

Changes for: limb joint

Changes for: mesopodium bone

Changes for: gastrointestinal system mucosa

Changes for: abdominal cavity

Changes for: supraoccipital bone

Changes for: hippocampal sulcus

Changes for: cavity of left ventricle

Changes for: cavity of left atrium

Changes for: semimembranosus muscle

Changes for: cavity of right atrium

Changes for: cornual diverticulum

Changes for: lesser sac

  • Deleted
    • - lesser sac SubClassOf body cavity or lining
    • - lesser sac SubClassOf part of some peritoneum
    • - lesser sac definition The lesser sac, also known as the omental bursa, is the cavity in the abdomen that is formed by the lesser and greater omentum. Usually found in mammals, it is connected with the greater sac via the epiploic foramen (also known as the Foramen of Winslow). In mammals, it is not uncommon for the lesser sac to contain considerable amounts of fat. In human anatomy, the wall of the stomach, pancreas and splenic artery are a part of the wall of the lesser sac. If these structures rupture they may leak into the lesser sac. For the stomach, which lies anterior to the omental bursa, the rupture must be on the posterior side; if it were anteriorly located, the leak would collect in the greater sac. The lesser sac is embryologically formed from an infolding of the greater omentum. The open end of the infolding, known as the epiploic foramen, is usually proximal to the stomach. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Lesser_sac }
  • Added

Changes for: biceps femoris

Changes for: semitendinosus

Changes for: parietal peritoneum

Changes for: tibial nerve

Changes for: rib endochondral element

Changes for: tail skin

Changes for: left lung terminal bronchiole

Changes for: right lung respiratory bronchiole

Changes for: right lung terminal bronchiole

Changes for: left lung respiratory bronchiole

Changes for: zona limitans intrathalamica

Changes for: retina blood vessel

Changes for: corneal blood vessel

Changes for: leg blood vessel

Changes for: limb blood vessel

Changes for: upper lip protuberances

Changes for: dermis connective tissue

Changes for: bile canaliculus

Changes for: lunge feeding organ

Changes for: lunge feeding vibrissa

Changes for: lunge feeding organ papilla

Changes for: gastroepiploic artery

Changes for: transversus abdominis muscle

Changes for: duodenal gland

Changes for: epicardial fat

Changes for: serosa of stomach

Changes for: uterine spiral artery

Changes for: mesenchyme of sublingual gland

Changes for: abdominal fat pad

Changes for: mesenchyme of tongue

Changes for: myocoele

Changes for: thymoid

Changes for: abdominal mammary gland

Changes for: head blood vessel

Changes for: trunk bone

Changes for: trabecula carnea cardiac muscle tissue

Changes for: costochondral joint

Changes for: diaphragm

Changes for: scale circulus

Changes for: tectorial membrane of cochlea

  • Added
    • + tectorial membrane of cochlea taxon notes in some squamate lineages, the tectorial membrane may not cover the whole cochlear duct/papilla. In some lineages, the tectorial membrane is divided into units called sallets[ISBN:9780387714691]

Changes for: corpora quadrigemina

Changes for: anterior limb of parapophysis 4

Changes for: crus of diaphragm

Changes for: cartilaginous joint

Changes for: spiral organ of cochlea

Changes for: rib

Changes for: intraorbital lacrimal gland

Changes for: exorbital lacrimal gland

Changes for: thoracic cavity

Changes for: visceral peritoneum

Changes for: peritoneal cavity

Changes for: inferior recess of lesser sac

Changes for: strand of pelage hair

Changes for: superior recess of lesser sac

Changes for: lingual septum

Changes for: strand of awl hair

Changes for: strand of auchene hair

Changes for: strand of zigzag hair

Changes for: strand of guard hair

Changes for: arrector muscle

Changes for: buccal papilla

Changes for: intermediolateral nucleus

Changes for: substantia gelatinosa

Changes for: nucleus prepositus

Changes for: habenulo-interpeduncular tract

Changes for: parvocellular oculomotor nucleus

Changes for: nerve fasciculus

Changes for: musculotendinous bundle

Changes for: chin

Changes for: humeral facet on the ulna

Changes for: urine

Changes for: parotid main excretory duct

Changes for: pericardial cavity

Changes for: bony vertebral centrum

Changes for: feather vane

Changes for: Aristotle’s lantern

Changes for: pterygoid bone

Changes for: pelvic cavity

Changes for: cranial cavity

Changes for: saphenous nerve

Changes for: mandibular process mesenchyme from head mesenchyme

Changes for: prostate duct

Changes for: cochlear labyrinth

Changes for: obsolete median fin

Changes for: arch of centrum of vertebra

Changes for: dermal layer of tongue

Changes for: pyramidal layer of CA2

Changes for: parietal pleura

Changes for: visceral pleura

Changes for: pleural cavity

Changes for: parietal serous pericardium

Changes for: pericardium

Changes for: pericardial sac

Changes for: oral epithelium

Changes for: visceral serous pericardium

Changes for: ventral tegmental nucleus

Changes for: anterior abdominal wall muscle

Changes for: muscle of posterior compartment of hindlimb stylopod

Changes for: zygomatic arch

Changes for: dorsum of tongue

Changes for: umbilical blood vessel

Changes for: perineal muscle

Changes for: Brodmann (1909) area 9

Changes for: fibrous pericardium

Changes for: perineum

Changes for: serous pericardium

Changes for: peritoneum

Changes for: otocyst lumen

Changes for: choroid plexus epithelium

Changes for: caudalipuboischiotibialis

Changes for: nasal mucus

Changes for: nucleus K of ventral tegmentum

Changes for: nucleus H of ventral tegmentum

Changes for: epicardium

Changes for: coelemic cavity lumen

Changes for: median lingual swelling epithelium

Changes for: mesenchyme of sublingual gland primordium

Changes for: lateral lingual swelling epithelium

Changes for: intraembryonic coelom

Changes for: future coelemic cavity lumen

Changes for: extraembryonic coelomic cavity

Changes for: coat of hair

Changes for: abductor hallucis muscle

Changes for: abductor pollicis brevis muscle

Changes for: sputum

Changes for: ceratoglossus

Changes for: flexor pollicis longus muscle

Changes for: future diencephalon

Changes for: longitudinal hypochordal

Changes for: infraorbital 1

Changes for: lateral ethmoid bone

Changes for: lingual swellings

Changes for: infracarinalis

Changes for: supracarinalis

Changes for: superficial lateralis (teleost)

Changes for: rib pre-cartilage condensation

Changes for: rib cartilage element

Changes for: epicentral bone

Changes for: lingual tonsil

Changes for: Brodmann (1909) area 24

Changes for: epaxialis

Changes for: hair follicle placode

Changes for: hypaxialis

Changes for: gill raker

Changes for: epipleural

Changes for: baroreceptor

Changes for: serosa of infundibulum of uterine tube

Changes for: branchiostegal ray

Changes for: superficial pelvic abductor

Changes for: postcleithrum

Changes for: proepicardium

Changes for: dorsal arrector

Changes for: coracoradialis

Changes for: urethra smooth muscle layer

Changes for: mentalis muscle

Changes for: skin of body

Changes for: viscus

Changes for: hair shaft

Changes for: interradialis

Changes for: intermuscular bone

Changes for: chin ventral margin

Changes for: labial commissure

Changes for: tongue intermolar eminence

Changes for: supracleithrum

Changes for: communicating artery

Changes for: ventral ectodermal ridge

Changes for: pelvic abductor profundus

Changes for: nipple

Changes for: outflow tract pericardium

Changes for: joint of rib

Changes for: mammary gland alveolus

Changes for: epithelium of lower jaw

Changes for: vitelline blood vessel

Changes for: serous fluid

Changes for: zygote stage

Changes for: oral opening

Changes for: mouth

Changes for: bone of reproductive organ

Changes for: anal canal epithelium

Changes for: muscle tissue of terminal part of digestive tract

Changes for: mesentery of heart

Changes for: hemal spine

Changes for: mesentery of stomach

Changes for: presphenoid bone

Changes for: duct of epididymis

Changes for: pulmonary surfactant

Changes for: epithelium of duct of salivary gland

Changes for: epithelium of tongue

Changes for: mesenchyme of lower jaw

Changes for: musculature of perineum

Changes for: obsolete body cavity or lining

Changes for: obsolete cavity lining

Changes for: tibial artery

Changes for: synovial cavity of joint

Changes for: right kidney

Changes for: left kidney

Changes for: stria medullaris

Changes for: actinotrichium

  • Deleted
    • - actinotrichium comment Actinotrichia are required for lepidotrichium development. They are occasionally retained in adult fishes. Further taxon comments from Witten & Huysseune (2007): ‘Actinotrichia are found in the embryonic fin fold, along the outer edge of the fin in Actinopterygii, and in the adipose fin in teleosts (Starck 1979; G�raudie and Meunier 1982; Becerra et al. 1983). Only in polypterids has their presence been reported in the joints between adjacent lepidotrichial elements (G�raudie 1988). In the sarcopterygian lineage, actinotrichia are present in coelacanths (G�raudie and Meunier 1980) and in young dipnoans (Arratia et al. 2001).’
  • Added
    • + actinotrichium comment Actinotrichia are required for lepidotrichium development. They are occasionally retained in adult fishes. Further taxon comments from Witten & Huysseune (2007): ‘Actinotrichia are found in the embryonic fin fold, along the outer edge of the fin in Actinopterygii, and in the adipose fin in teleosts (Starck 1979; Géraudie and Meunier 1982; Becerra et al. 1983). Only in polypterids has their presence been reported in the joints between adjacent lepidotrichial elements (Géraudie 1988). In the sarcopterygian lineage, actinotrichia are present in coelacanths (Géraudie and Meunier 1980) and in young dipnoans (Arratia et al. 2001).’

Changes for: pre-Botzinger complex

Changes for: obsolete anal fin

Changes for: ventral intermandibularis anterior

Changes for: Peyer’s patch epithelium

Changes for: bulbourethral gland secretion

Changes for: venous system smooth muscle

Changes for: arterial system smooth muscle

Changes for: mandible condylar process

Changes for: serous membrane

Changes for: ventral intermandibularis posterior

Changes for: levator auris longus muscle

Changes for: macula lutea

Changes for: vena cava sinus

Changes for: insect labrum

Changes for: serous sac

Changes for: nerve innervating pinna

Changes for: fibular nerve

Changes for: ala of nose

Changes for: mandibular process mesenchyme

Changes for: lip epithelium

Changes for: coelomic epithelium

Changes for: gonad germinal epithelium

Changes for: camptotrichium

Changes for: tongue muscle

Changes for: ulnar sesamoid bone

Changes for: dermal papilla

Changes for: caudal fin

Changes for: median fin

Changes for: anal fin

Changes for: peritoneal mesentery

Changes for: bodily secretion

Changes for: ventral mesogastrium

Changes for: secondary palatal shelf epithelium

Changes for: primary palate epithelium

Changes for: peritoneal cavity mesothelium

Changes for: foramen cecum of tongue

Changes for: dorsal pelvic arrector

Changes for: epural

Changes for: superficial abductor

Changes for: sublingual caruncle

Changes for: mandibular symphysis

Changes for: alveolar canal

Changes for: abductor profundus

Changes for: jaw epithelium

Changes for: abdominal oblique muscle

Changes for: lower back

Changes for: otolymph

Changes for: ventral arrector

Changes for: interosseous muscle of autopod

Changes for: ventral pelvic arrector

Changes for: gingival epithelial attachment

Changes for: male reproductive system fluid/secretion

Changes for: respiratory system fluid/secretion

Changes for: seminal fluid

Changes for: mammary gland fluid/secretion

Changes for: aortic sac

Changes for: greater sac cavity

Changes for: abdominal internal oblique muscle

Changes for: intrinsic muscle

Changes for: greater sac

Changes for: abdominal external oblique muscle

Changes for: perirenal fat

Changes for: philtrum

Changes for: ventral striatum

Changes for: dorsal striatum

Changes for: diaphysis proper

Changes for: abductor muscle

Changes for: oral lamina propria

Changes for: pilosebaceous unit

Changes for: bulbus cordis myocardium

Changes for: vibrissa outer root sheath

Changes for: vibrissa inner root sheath

Changes for: stomatodeum gland

Changes for: peritubular capillary

Changes for: costotransverse joint

Changes for: coelom

Changes for: anterior communicating artery

Changes for: stomodeum

Changes for: alisphenoid bone

Changes for: endoderm

Changes for: hypural musculature

Changes for: pleura

Changes for: choroid plexus stroma

Changes for: mammalian vulva

Changes for: thoracic mammary gland

Changes for: trachea gland

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

November 19, 2015 |

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