Definition request: ceratotrichium #129

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cmungall opened this Issue Oct 11, 2012 · 7 comments

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cmungall commented Oct 11, 2012

Can you review UBERON_4400001 in ext? I added this as a placeholder for the homology work

required:

  • definition needs improved
  • a more specific superclass is needed
  • part_of should be more specific?

nice to have:

  • rough taxonomic range (in comments or logical taxon constraints)
  • connected_to relationships (comments or axioms)
  • composed_primarily_of relationship (fishbase says elastin)

thanks!

pmabee commented Oct 11, 2012

  1. Please replace temp def with the below:
    Definition 'ceratotrichium': Elastoidin fin ray that is thickened, generally unbranched and found in the fins of Chondrichthyes.
    Dev_from mesenchyme (comment: possibly from neural crest, see Smith et al., 1994)
    Parent: 'bony fin ray'
    Taxon: Chondrichthyes
  2. Actinotrichium: please replace def in uberon with the below:
    Definition actinotrichium: Elastoidin fin ray that is slender, sometimes branched distally and present in the embryonic fin fold. Actinotrichia are translucent and exhibit birefringence.
    Dev_from epidermal tissue (not mesenchyme)
    Comment: Actinotrichia are required for lepidotrichium development. They are occasionally retained in adult fishes.
    Taxon: Actinopterygii and Sarcopterygii
    Further taxon comments from Witten & Huysseune (2007): "Actinotrichia are found in the embryonic fin fold, along the outer edge of the fin in Actinopterygii, and in the adipose fin in teleosts (Starck 1979; Géraudie and Meunier 1982; Becerra et al. 1983). Only in polypterids has their presence been reported in the joints between adjacent lepidotrichial elements (Géraudie 1988). In the sarcopterygian lineage, actinotrichia are present in coelacanths (Géraudie and Meunier 1980) and in young dipnoans (Arratia et al. 2001)."
  3. Parent of both actinotrichium and ceratotrichium is (new term suggestion) 'elastoidin fin ray'.
    Definition 'elastoidin fin ray': Fin ray that is composed of elastoidin, unmineralized, and unsegmented.
    Taxon: Present in Vertebrates (possibly Chordates)

Other comment: it used to be thought that actinotrichia and ceratotrichia were composed of a 'horny' substance. This is incorrect and misleading (see Witten & Huysseune (2007) in Mendeley e.g., for more info.

Note: Lepidotrichium is_a dermal bone; lepidotrichium is_a fin ray

  1. Add new term: 'camptotrichium'
    Def camptotrichium: Fin ray found in dipnoans that are composed of a superficial region of acellular fibrous bone, and a deep, mostly unmineralized, zone (Géraudie and Meunier 1982)."
    Taxon: dipnoans.
    Comment: From Witten & Huysseune (2007): "Two zones have been recognized in these camptotrichia: a superficial region of acellular fibrous bone, and a deep, mostly unmineralized, zone (Géraudie and Meunier 1982)."
  2. Need to add 'fin ray' as parent of 'elastoidin fin ray', 'lepidotrichium' and 'camptotrichium'
    def 'fin ray': rod-like entity that functions in support of fin folds and fins.
    parent: ....suggestions?

pmabee commented Oct 11, 2012

Done! And more -- one thing leads to another… Paula

On 10/10/12 10:14 PM, "Chris Mungall" <notifications@github.commailto:notifications@github.com> wrote:

Can you review UBERON_4400001 in ext? I added this as a placeholder for the homology work

required:

  • definition needs improved
  • a more specific superclass is needed
  • part_of should be more specific?

nice to have:

  • rough taxonomic range (in comments or logical taxon constraints)
  • connected_to relationships (comments or axioms)
  • composed_primarily_of relationship (fishbase says elastin)

thanks!


Reply to this email directly or view it on GitHubhttps://github.com/cmungall/uberon/issues/129.

Owner

cmungall commented Oct 12, 2012

I can take care of this later. A few extra quick questions.

we lifted lepidotrichia from http://purl.obolibrary.org/obo/VSAO_0000172 - no parthood axioms. Which of the above can we make all-some part_of relationships for?

Should we request elastoidin from GO? Currently:

  • GO:0044420 ! extracellular matrix part
  • GO:0005581 ! collagen ***
  • GO:0005582 ! collagen type XV
  • GO:0005583 ! fibrillar collagen
  • GO:0005584 ! collagen type I
  • GO:0005585 ! collagen type II
  • GO:0005586 ! collagen type III
  • GO:0005588 ! collagen type V
  • GO:0005592 ! collagen type XI
  • GO:0030934 ! anchoring collagen
  • GO:0005589 ! collagen type VI
  • GO:0005590 ! collagen type VII
  • GO:0005593 ! FACIT collagen
  • GO:0005594 ! collagen type IX
  • GO:0005595 ! collagen type XII
  • GO:0005596 ! collagen type XIV
  • GO:0005597 ! collagen type XVI
  • GO:0030938 ! collagen type XVIII
  • GO:0030935 ! sheet-forming collagen
  • GO:0005587 ! collagen type IV
  • GO:0005598 ! short-chain collagen
  • GO:0005591 ! collagen type VIII
  • GO:0005599 ! collagen type X
  • GO:0030936 ! transmembrane collagen
  • GO:0005600 ! collagen type XIII
  • GO:0030937 ! collagen type XVII

pmabee commented Oct 12, 2012

On 10/11/12 8:24 PM, "Chris Mungall" <notifications@github.commailto:notifications@github.com> wrote:

I can take care of this later. A few extra quick questions.

we lifted lepidotrichia from http://purl.obolibrary.org/obo/VSAO_0000172 - no parthood axioms. Which of the above can we make all-some part_of relationships for?

--not completely sure what you are asking (sorry). Might be easier to talk about on Friday call? Paula

Should we request elastoidin from GO? Currently:

--sent you an article referencing collagen composition of elastoidin. I don't know which type of collagen it is composed of.

  • GO:0044420 ! extracellular matrix part
  • GO:0005581 ! collagen ***
  • GO:0005582 ! collagen type XV
  • GO:0005583 ! fibrillar collagen
  • GO:0005584 ! collagen type I
  • GO:0005585 ! collagen type II
  • GO:0005586 ! collagen type III
  • GO:0005588 ! collagen type V
  • GO:0005592 ! collagen type XI
  • GO:0030934 ! anchoring collagen
  • GO:0005589 ! collagen type VI
  • GO:0005590 ! collagen type VII
  • GO:0005593 ! FACIT collagen
  • GO:0005594 ! collagen type IX
  • GO:0005595 ! collagen type XII
  • GO:0005596 ! collagen type XIV
  • GO:0005597 ! collagen type XVI
  • GO:0030938 ! collagen type XVIII
  • GO:0030935 ! sheet-forming collagen
  • GO:0005587 ! collagen type IV
  • GO:0005598 ! short-chain collagen
  • GO:0005591 ! collagen type VIII
  • GO:0005599 ! collagen type X
  • GO:0030936 ! transmembrane collagen
  • GO:0005600 ! collagen type XIII
  • GO:0030937 ! collagen type XVII


Reply to this email directly or view it on GitHubhttps://github.com/cmungall/uberon/issues/129#issuecomment-9364001.

Owner

cmungall commented Oct 12, 2012

Thanks for the comments Paula. We didn't have time today on the call. Let me clarify. Our current structure is identical to the one from VSAO:

  • CARO:0000003 ! anatomical structure
    • CARO:0000024 ! compound organ
      • VSAO:0000128 ! skeletal element [part_of: "skeleton"]
      • VSAO:0000057 ! bone element [SYNONYM: "bone" (related)] [SYNONYM: "bone organ" (exact)]
      • VSAO:0000023 ! membrane bone
      • VSAO:0000130 ! dermal bone [SYNONYM: "dermal element" (exact)] [SYNONYM: "membrane bone" (related)] [part_of: "dermal skeleton"]
        • VSAO:0000172 ! lepidotrichium *** [SYNONYM: "fin ray" (exact)]

Note that "fin ray" is an exact syn for "lepidotrichium".

The def is:

Dermal bone that is rod-like, formed and usually contained in a fin membrane, and jointed to or adjacent to distal radials. Lepidotrichia are formed from paired hemitrichia surrounding actinotrichia. There are usually two more lepidotrichia than distal radials

You said:

Note: Lepidotrichium is_a dermal bone; lepidotrichium is_a fin ray

and

    Need to add 'fin ray' as parent of 'elastoidin fin ray', 'lepidotrichium' and 'camptotrichium'
    def 'fin ray': rod-like entity that functions in support of fin folds and fins.
    parent: ....suggestions?

So it sounds like we should remove the exact syn and have something like:

  • fin ray
    • lepidotrichium
    • elastoidin fin ray
    • ceratotrichium
    • actinotrichium

Also, presumably fin rays are parts of fins. We don't have this at the moment, querying for fin parts will not return lepidotrichium

pmabee commented Oct 13, 2012

Hi Chris, comments below. Thanks for making the changes --Paula

On 10/12/12 6:06 PM, "Chris Mungall" <notifications@github.commailto:notifications@github.com> wrote:

So it sounds like we should remove the exact syn

yes - please remove fin ray as exact syn. It is frequently used a syn for all of those terms.

and have something like:

  • fin ray
  • lepidotrichium
  • camptotrichium
  • elastoidin fin ray
  • ceratotrichium
  • actinotrichium
  • Also, presumably fin rays are parts of fins. We don't have this at the moment, querying for fin parts will not return lepidotrichium

--yes! please add this! fin rays are parts of fins. They function to strengthen the fins and the fin fold (fins like dorsal, anal, and caudal develop from the fin fold (also finfold).

Owner

cmungall commented Oct 22, 2012

Fixed in revision 3671 to ext

Notes:

  • I made fin ray a skeletal element, and part of fin
    • lepidotrichium is both a fin ray and a dermal bone, as suggested above
  • actinotrichium in TAO was part_of median fin fold. This can't be universally true, as there are subclasses for non-median fins. I removed this. I will open a new item on fin fold and ask ZFA editors for comments.
  • we already had subclasses of actinotrichium for various fins and folds
    • will we want similar compositional classes for campto- and cerato-?
  • we already had named classes for the serial lepidotrichia 1-7 for various fins from TAO. Synonyms have not been checked to conform to new fin ray vs lepidotrichium distinction
  • added develops_from some epidermis for actinotrichium but this may need reviewed

cmungall closed this Oct 22, 2012

cmungall added the ext label Jun 9, 2015

cerivs referenced this issue in cerivs/zebrafish-anatomical-ontology Jul 30, 2015

Closed

actinotrichium #54

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