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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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cavities and linings #86

Closed cmungall closed 9 years ago

cmungall commented 12 years ago

The FMA has the scheme:

E.g. pleural sac (showing constitutional part of hierarchy):

EHDAA2 has the scheme "cavity" = lining (e.g. mesothelium) + lumen. Note the "lumen" is equivalent to what FMA calls a cavity, whereas EHDAA2's "cavity" includes the lining as part. Compare the representation of the embryonic form of the same structure:

The PCL is equivalent to the mesothelium of pleura, but there isn't a clean map for what EHDAA2 calls the cavity.

Note that in MA, pleura (a type of cavity lining) is part_of the pleural cavity. This makes MA:pleura equivalent to PCL in EHDAA2

Uberon doesn't do a great job of generalizing over these consistent but different schemes. Awaiting advice from JB on development of these structures.

For a more complex example:

FMA also has "pericardial serosa" in a separate hierarchy

cmungall commented 12 years ago

See also: https://sourceforge.net/tracker/?func=detail&atid=1127722&aid=2995492&group_id=76834

cmungall commented 11 years ago

Note from JB: A quick glance at the web (http://en.wikipedia.org/wiki/Visceral_pleura) says that the pleura are actually the mesothelial linings of the lung or what EHDAA2 calls lung mesothelium, which is derived from lateral mesoderm. I think that this is a terminology rather than a biological problem