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obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
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cervical rib in mice? #116

Open cmungall opened 6 years ago

cmungall commented 6 years ago 
id: EMAPA:37825
name: cervical rib
namespace: anatomical_structure
is_a: EMAPA:18010  ! rib
relationship: ends_at TS28 ! TS28
relationship: starts_at TS28 ! TS28

if as the name suggests this extends from a cervical vertebra should this have a part_of neck?

We incorporated the new EMAPA mappings in a pre-release (https://github.com/obophenotype/uberon/issues/1445) but currently this gets flagged as an error as uberon says Theria lack a cervical rib. We don't have a publication for this assertion however.

Maybe it's the case that this is a variant but non-pathological structure?

cmungall commented 6 years ago

http://www.informatics.jax.org/cookbook/figures/figure19.shtml

is this a true rib?

tfhayamizu commented 6 years ago

The figure from the "The Anatomy of the Laboratory Mouse" (Margaret Cook, 1965) is likely the reference for this term. Clearly we consider this source reliable. Whether or not the cervical rib is a 'true' rib may be debatable. According to "The Anatomical Basis of Mouse Development" (Kaufman and Bard, 1999): (p. 51) "very occasionally, 'accessory' ribs may be found associated with the lowest of the cervical vertebra", and (p. 59) "Variations in the total number of ribs present may occasionally be encountered. The extra ribs are usually associated with the lowest of the cervical vertebra ..." (The Kaufman and Bard book was developed to provide an index for Matt Kaufman's "The Atlas of Mouse Development" (1994), which was the basis of the original EMAP ontology.)

tfhayamizu commented 6 years ago

A more recent reference (Pathology of the Developing Mouse: A Systematic Approach, 2015) reports "findings in outbred CD-1 mice ... rib irregularities ranging from 0% to 33% in the cervical region"