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cavities and linings #86

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cmungall opened this Issue Sep 19, 2012 · 2 comments

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cmungall commented Sep 19, 2012

The FMA has the scheme:

  • Serous sac = serous membrane + serous cavity
  • serous membrane = mesothelium + connective tissue

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

  • FMA:9690 - Pleural sac (isa "Serous sac")
    • FMA:9583 - Pleura (isa "Viscus serous membrane")
    • FMA:18148 - Mesothelium of pleura (isa "Mesothelium", *isa" "Epithelium")
    • FMA:20061 - Connective tissue of pleura (isa "Connective tissue of serous membrane")
    • FMA:9740 - Pleural cavity (isa "Cavity of serous sac")

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:

  • EHDAA2:0004737 - pleural cavity (isa "multi-tissue structure")
    • (located_in) EHDAA2:0001475 - pleural cavity lumen (isa "open cavity")
    • EHDAA2:0001476 - pleural cavity lining (isa "mesothelium")

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:9869 - Pericardium (isa "Organ cluster")
    • FMA:9586 - Fibrous pericardium (isa "Membrane organ")
    • FMA:223155 - Fibroelastic connective tissue of fibrous pericardium (isa "Fibroelastic connective tissue")
    • FMA:84052 - Fibrocollagenous connective tissue of fibrous pericardium (isa "Fibrocollagenous connective tissue")
    • FMA:9868 - Pericardial sac (isa "Serous sac")
    • FMA:11350 - Pericardial cavity (isa "Cavity of serous sac")
    • FMA:9582 - Serous pericardium (isa "Viscus serous membrane")
    • FMA:18149 - Mesothelium of serous pericardium (isa "Mesothelium")
    • FMA:20062 - Connective tissue of serous pericardium (isa "Connective tissue of serous membrane")

FMA also has "pericardial serosa" in a separate hierarchy

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cmungall Jan 9, 2013

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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

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cmungall commented Jan 9, 2013

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

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