2017-10-28 release: thagomizer

Improved alignment with NIFSTD, better representation of lymph sacs, and the addition of Thagomizer
2017-10-28 release: thagomizer image

Summary

New terms

  • thagomizer - contributed by balhoff
  • interoceptive system fixes 1385
  • piriform aperture. See https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2396

Obsoletions

  • Obsoleted Shreckstoff.
  • Obsoleted mitochondrial cloud. See https://github.com/obophenotype/uberon/issues/1360, Fixes https://github.com/obophenotype/uberon/issues/1365
  • obsoleting nematocyst; should be added to GO See 1360

Taxon Constraints

  • pGCI for seminiferous tubules, fixes 1381
  • weaked TC for gyrus, fixes 1378
  • Relaxing TC on placenta to include yolk-type placenta of marsupials, Fixes 1376
  • removing dev relationship between liver parenchyma and bile duct. Fixes 2614
  • Removed TC excluding stomach from platypus, fixes 1377

Neuro

Thanks to tgbugs

  • Fixed relationships to obsolete brain regional part for EG. https://github.com/obophenotype/uberon/issues/1360
  • dorsal longitudinal fasciculus subclasses->parts, 1362
  • medial lemniscus fixes 1362
  • Improved sourced def to cerebrocerebellum. Fixes 1368
  • NT: zona pectinata of basilar membrane of cochlea * Fixes 1357

lymph sacs

  • multiple improvements to representation of lymph sacs; see 1383

Other

  • remove references to go multi-organism signaling, fixes 1384
  • Fixed syn scope for multicellular organism. Fixes 1361. Added provenance for syns
  • NT: interdigital space. Tidies editor notes

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2017-09-09/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2017-10-28/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 11

New Class : zone of basilar membrane of cochlea

New Class : interdigital space

New Class : orifice of skull

New Class : piriform aperture

New Class : interoceptive system

New Class : iliac lymph sac

New Class : cardial lymph propulsor

New Class : embryonic cisterna chyli

New Class : accessory lymph sac

New Class : zona pectinata of basilar membrane of cochlea

New Class : thagomizer

Changed Class objects: 43

Changes for: eminentia granularis

Changes for: obsolete Schreckstoff

Changes for: round window of inner ear

Changes for: oval window

Changes for: posterior nasal aperture

Changes for: medial lemniscus of pons

Changes for: dorsal trigeminal tract

Changes for: dorsal longitudinal fasciculus of pons

Changes for: pleural effusion

Changes for: gyrus

Changes for: zona arcuata of basilar membrane of cochlea

Changes for: seminiferous tubule of testis

Changes for: lymph node

Changes for: sartorius muscle

  • Deleted
    • - sartorius muscle comment . We do NOT group this AAO class here at this stage until further evidence of shared attachments
  • Added

Changes for: dorsal longitudinal fasciculus of medulla

Changes for: medial lemniscus of midbrain

Changes for: cerebrocerebellum

  • Deleted
    • - cerebrocerebellum definition A phylogenetic subdivision of the cerenellum, the newest part, which is involved in planning movement and evaluating sensory information for action. It receives input exclusively from the cerebral cortex (especially the parietal lobe) via the pontine nuclei (forming cortico-ponto-cerebellar pathways), and sends fibres mainly to the ventrolateral thalamus (in turn connected to motor areas of the premotor cortex and primary motor area of the cerebral cortex) and to the red nucleus (in turn connected to the inferior olivary nucleus, which links back to the cerebellar hemispheres). { database cross reference=Phylogenetic and functional divisions }
  • Added

Changes for: medial lemniscus of medulla

Changes for: liver parenchyma

Changes for: placenta

  • Deleted
    • - placenta comment Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
  • Added
    • + placenta comment Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.

Changes for: bile

Changes for: multicellular organism

Changes for: nasal cavity

  • Deleted
    • - nasal cavity editor note defne the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
  • Added
    • + nasal cavity editor note define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.

Changes for: chin

Changes for: obsolete nematocyst

Changes for: pennate muscle

Changes for: sagulum nucleus

  • Deleted
  • Added

Changes for: jugular lymph sac

Changes for: lymph sac of lymph heart

Changes for: embryonic lymph sac

Changes for: retroperitoneal embryonic lymph sac

Changes for: interdigital region

Changes for: obsolete mitochondrial aggregate

Changes for: hepatic duct

Changes for: interoceptor

Changes for: upper part of cisterna chyli

Changes for: non-neural ectoderm

  • Deleted
    • - non-neural ectoderm comment Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). Editor note: todo - epidermis? todo - track down EHDAA2 class in new release
  • Added
    • + non-neural ectoderm comment Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
    • + non-neural ectoderm editor note todo - epidermis? todo - track down EHDAA2 class in new release

Changes for: periocular mesenchyme

Changes for: accessory circulatory organ

Changes for: lymph heart

  • Added
    • + lymph heart taxon notes Caecilians posses a lymph heart at every segment boundary thus having up to 200 in number.

Changes for: dorsal longitudinal fasciculus of hypothalamus

Changes for: dorsal longitudinal fasciculus of midbrain

Changes for: nervous system lemniscus

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

October 28, 2017 |

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