releases/2014-03-13

Multiple new terms and improved aligned terms with MA and WBls
releases/2014-03-13 image

Release Highlight: Incorporation of stages from the worm life cycle ontology, see Issue 395

Changes:

  • Stages
  • olfactory system
    • fixed confusion w nasal cavity vs nasal chamber
    • using more generic labels
    • septal organs
      • NT: septal organ of Masera
      • fixes to grueneberg ganglion
  • muscles
    • fixed cranial/facial muscle fonfusion
  • ontology alignemt
    • multiple new terms, from unions of MA,ncita,fma
    • MA xrefs
    • NT: bifurcation of trachea
    • def of cranial NC from MP
    • fixed def ids to be the same as RO
    • Added xref tags [Paula]. Fixes issue #409
    • Added additional Ce embryonic stages. Addresses #395
  • synonyms
    • eyelid syn
    • iris plural

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-03-05/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-03-13/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 57

New Class : septal organ of Masera

New Class : septal olfactory organ

New Class : accessory olfactory bulb granule cell layer

New Class : digit skin

New Class : bifurcation of trachea

New Class : modified sebaceous gland

New Class : inferior olivary commissure

New Class : coat hair follicle

New Class : pancreas left lobe

New Class : pancreas right lobe

New Class : saphenous artery

New Class : respiratory system basement membrane

New Class : muscle layer in fatty layer of subcutaneous tissue

New Class : acinus of olfactory gland

New Class : duct of olfactory gland

New Class : upper respiratory conduit

New Class : respiratory segment of nasal mucosa

New Class : cranial or facial muscle

New Class : olfactory apparatus chamber

New Class : anal canal epithelium

New Class : smooth muscle tissue layer of ejaculatory duct

New Class : sagittal sinus

New Class : rostrum of corpus callosum

New Class : splenium of the corpus callosum

New Class : heterogeneous tissue

New Class : inferior tarsal muscle

New Class : transitional epithelium of prostatic urethra

New Class : epithelium of duct of salivary gland

New Class : dense regular elastic tissue

New Class : mixed stratified cuboidal and columnar epithelium

New Class : genu of corpus callosum

New Class : frontal gyrus

New Class : body of corpus callosum

New Class : left hepatic artery

New Class : right hepatic artery

New Class : skin of metapodial pad

New Class : proper hepatic artery

New Class : choledocho-duodenal junction

New Class : sural nerve

New Class : tracheobronchial lymph node

New Class : nose skin

New Class : axillary fat pad

New Class : axilla skin

New Class : scrotum skin

New Class : splenic lymph node

New Class : mediastinal fat pad

New Class : accessory hepatic vein

New Class : pancreatic fat pad

New Class : subcutaneous lymph node

New Class : anterior lingual gland duct

New Class : external elastic membrane

New Class : accessory olfactory bulb mitral cell layer

New Class : levator auris longus muscle

New Class : ureteral valve

New Class : hilar portion of hepatic duct

New Class : heart plus pericardium

New Class : urethra mesenchymal layer

Changed Class objects: 165

Changes for: metaphysis of tibia

Changes for: cardiac endomysium

Changes for: inferior colliculus

Changes for: elastic cartilage tissue

Changes for: olfactory epithelium

Changes for: inferior frontal gyrus

Changes for: tarsal gland

Changes for: paravertebral ganglion

Changes for: nasal-associated lymphoid tissue

Changes for: ovarian bursa

Changes for: perianal skin

Changes for: cauda equina

Changes for: holocrine gland

Changes for: dentate gyrus of hippocampal formation

Changes for: sebaceous gland

Changes for: nasal cavity mucosa

Changes for: cloacal lumen

  • Deleted
  • Added
    • + cloacal lumen comment the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/

Changes for: mammary duct

Changes for: bulbospongiosus muscle

Changes for: eyelid

Changes for: nasal cavity

Changes for: duodenal papilla

Changes for: ventral tegmental area

Changes for: superior frontal gyrus

Changes for: gracile fasciculus of medulla

Changes for: facial nerve muscle

Changes for: lateral process of malleus

Changes for: mouth mucosa

Changes for: mediastinum

Changes for: bronchus basement membrane

Changes for: trachea basement membrane

Changes for: posterior part of tongue

Changes for: entorhinal area

Changes for: cervical spinal cord

Changes for: medial dorsal nucleus of thalamus

Changes for: intralaminar nuclear group

Changes for: lung hilus

Changes for: oronasal membrane

Changes for: nasal fin

Changes for: middle frontal gyrus

Changes for: precentral gyrus

Changes for: intermediate hypothalamic region

Changes for: iliac crest

Changes for: gland

Changes for: subcutaneous abdominal adipose tissue

Changes for: visceral abdominal adipose tissue

Changes for: sinus of Valsalva

Changes for: ventral posterior nucleus

Changes for: gland of nasal mucosa

Changes for: forestomach-glandular stomach junction

Changes for: heart elastic tissue

Changes for: skeletal tissue

Changes for: tuber cinereum

Changes for: abdominal cavity

Changes for: masticatory muscle

Changes for: neuropil

Changes for: secondary olfactory cortex

Changes for: manual digit skin

Changes for: pedal digit skin

Changes for: ventral posteroinferior nucleus

Changes for: ventral posterolateral nucleus

Changes for: superior temporal gyrus

Changes for: marginal zone of spleen

Changes for: epicardial fat

Changes for: retrotrapezoid nucleus

Changes for: post-embryonic organism

Changes for: gland of tongue

Changes for: heart blood vessel

Changes for: Grueneberg ganglion

Changes for: metanephros induced blastemal cells

Changes for: olfactory gland

  • Deleted
    • - olfactory gland SubClassOf part of some olfactory epithelium
    • - olfactory gland definition Bowman’s glands (aka olfactory glands, glands of Bowman) are situated in the olfactory mucosa, beneath the olfactory epithelium, in the lamina propria, a connective tissue also containing fibroblasts, blood vessels, and bundles of fine axons from the olfactory neurons. The structure of the Bowman’s glands consists of an acinus in the lamina propria and a secretory duct going out through the olfactory epithelium. Electron microscopy studies show that Bowman’s glands contain cells with large secretory vesicles.[2] Bowman’s glands might secrete proteins such as Lysozyme, amylase and IgA similarly to serous glands. The exact composition of the secretions from Bowman’s glands is unclear, but there is evidence that Bowman’s glands do not produce odorant binding protein[WP]. { database cross reference=Wikipedia:Olfactory_glands }
  • Added
    • + olfactory gland SubClassOf part of some lamina propria
    • + olfactory gland SubClassOf part of some olfactory segment of nasal mucosa
    • + olfactory gland definition Bowman’s glands (aka olfactory glands, glands of Bowman) are situated in the olfactory mucosa, beneath the olfactory epithelium, in the lamina propria, a connective tissue also containing fibroblasts, blood vessels, and bundles of fine axons from the olfactory neurons. The structure of the Bowman’s glands consists of an acinus in the lamina propria and a secretory duct going out through the olfactory epithelium. Electron microscopy studies show that Bowman’s glands contain cells with large secretory vesicles. Bowman’s glands might secrete proteins such as Lysozyme, amylase and IgA similarly to serous glands. The exact composition of the secretions from Bowman’s glands is unclear, but there is evidence that Bowman’s glands do not produce odorant binding protein[WP]. { database cross reference=Wikipedia:Olfactory_glands }
    • + olfactory gland has related synonym gland of Bowman

Changes for: corpora quadrigemina

Changes for: main olfactory organ

Changes for: diaphysis of tibia

Changes for: synovial joint

Changes for: hepatic artery

Changes for: pennate muscle

Changes for: periungual skin

Changes for: superior tarsal muscle

Changes for: pelvic cavity

Changes for: cranial cavity

Changes for: parietal serous pericardium

Changes for: pericardium

Changes for: pericardial sac

Changes for: pituitary stalk

Changes for: prevertebral ganglion

Changes for: hyoid apparatus

Changes for: merocrine gland

Changes for: bone marrow

Changes for: rete testis

Changes for: fibrous pericardium

Changes for: serous pericardium

Changes for: nasal mucus

Changes for: intertarsal joint

Changes for: aortico-pulmonary spiral septum

Changes for: endolymphatic appendage

Changes for: plantar part of pes

Changes for: ectomesenchyme

  • Added
    • + ectomesenchyme external definition Portion of tissue that develops from the cranial neural crest and which cells populate a series of pharyngeal arches from which develops the support skeleton of the jaw and gills[ZFA:0005771]. { source=ZFA:0005771 }

Changes for: baroreceptor

Changes for: mucosa of nasal septum

Changes for: auricular vein

Changes for: orbital gyrus

Changes for: cardiac vein

Changes for: skin of snout

Changes for: Zymbal’s gland

Changes for: anterior lingual gland

Changes for: endocardial cushion

Changes for: cardiac skeleton

Changes for: outflow tract pericardium

Changes for: epiphysis of femur

Changes for: epiphysis of tibia

Changes for: gastrula stage

Changes for: blastula stage

Changes for: lobe of lung

Changes for: cheek pouch

Changes for: metapodial pad

Changes for: epithelium of vomeronasal organ

Changes for: mesoderm blood island

Changes for: facial neural crest

Changes for: accessory olfactory bulb glomerular layer

Changes for: thoracic spinal cord

Changes for: digit 1

Changes for: digit 2

Changes for: digit 5

Changes for: digit 3

Changes for: digit 4

Changes for: fibrous ring of heart

Changes for: cranial neural crest

  • Deleted
  • Added
    • + cranial neural crest definition neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. { database cross reference=MGI:anna }
    • + cranial neural crest has exact synonym cranial NCC population
    • + cranial neural crest has exact synonym head NCC population

Changes for: anal sac

Changes for: apocrine gland

Changes for: lamina propria

  • Deleted
    • - lamina propria comment Editor notes: need to implement rules such that “lamina propria of X” is classified as part of some “mucosa of X”

Changes for: embryo stage

Changes for: reticulum trabeculare

Changes for: conotruncal ridge

Changes for: spinal cord segment

Changes for: caudal segment of spinal cord

Changes for: sacral spinal cord

Changes for: preputial gland

Changes for: eccrine sweat gland

Changes for: portion of organism substance

Changes for: multi-cellular organism

Changes for: epithelium

Changes for: spinal vein

Changes for: meningeal cluster

Changes for: platysma

Changes for: superior mesenteric ganglion

Changes for: hyoid muscle

  • Deleted
    • - hyoid muscle comment Editor notes: PMID:19531159 states that facial muscles are hyoid muscles

Changes for: common hepatic artery

Changes for: inferior mesenteric ganglion

Changes for: olfactory bulb granule cell layer

Changes for: olfactory segment of nasal mucosa

Changes for: nasal cavity respiratory epithelium

Changes for: nasal cavity epithelium

Changes for: brain arachnoid mater

Changes for: carotid artery segment

Changes for: metaphysis of femur

Changes for: diaphysis of femur

Changes for: remnant of left anterior vena cava

Changes for: female preputial gland

Changes for: middle hepatic vein

Changes for: right hepatic vein

Changes for: left hepatic vein

Changes for: dorsal skin of digit

Changes for: head of femur

Changes for: heart

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 11

Changes for: anteriorly connected to

Changes for: transitively proximally connected to

Changes for: distally connected to

Changes for: transitively anteriorly connected to

Changes for: proximally connected to

Changes for: ends

Changes for: transitively distally connected to

Changes for: capable_of_part_of

Changes for: connected to

  • Deleted
  • Added
    • + connected to definition Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. { database cross reference=http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern }

Changes for: connects

  • Deleted
    • - connects definition Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. { database cross reference=UBERONREF:0000004 }
  • Added
    • + connects definition Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. { database cross reference=http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern }

Changes for: posteriorly connected to

March 13, 2014 |

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