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#8818 forelimb and hindlimb

closed-fixed
RFoulger
4
2012-09-11
2011-09-23
Chris Mungall
No

.....is_a GO:0035108 ! limb morphogenesis
......is_a GO:0035136 ! forelimb morphogenesis
.......is_a GO:0035138 ! pectoral fin morphogenesis ***
......is_a GO:0035137 ! hindlimb morphogenesis
.......is_a GO:0035139 ! pelvic fin morphogenesis ***

This is wrong - fins are not limbs. Consider renaming structures - e.g. "forelimb/pectoral fin" or "forelimb/homolog"

Also whilst on limbs:

.......is_a GO:0035136 ! forelimb morphogenesis [DEF: "The process in which the anatomical structures of the forelimb are generated and organized."]
........is_a GO:0035140 ! arm morphogenesis *** [DEF: "The process in which the anatomical structures of the arm are generated and organized. In humans, the arms are the two upper limbs of the body from the shoulder to the hand."]

this should be part_of, as the forelmb zeugopod+stylopod are part_of the forelimb. They aren't types of forelimb, as the def indicates. How about:

"The process in which the anatomical structures of the arm are generated and organized. An arm is the part of the forelimb that extends from the shoulder to the autopod."?

the corresponding leg term is problematic, I'll make a separate request.

Discussion

  • Doug Howe
    Doug Howe
    2011-09-23

    HI Chris,
    WRT the fin aspect of this request, the genetics of fin development follow very closely the genetics of traditional limb development. It is common for fish researchers to consider fins as types of limbs for that reason. Where does one draw the distinction between a limb and a fin? Is a wing a type of forelimb for example? These were originally structured this way to support the view that fins share a lot of developmental aspects with more traditional limb development...they are different forms of the same thing. I suppose a renaming of the "limb" terms to indicate that those terms are intended to include traditional limbs as well as homologous structures that share similar genetics of their development would suffice?

     
  • Chris Mungall
    Chris Mungall
    2011-09-23

    I agree it's a fuzzy dividing line.

    Uberon has:

    + limb/fin *
    ++ forelimb/pectoral fin *
    +++ forelimb
    ++++ forelimb wing
    +++ pectoral fin *

    but there is no need for GO to name all these. I have marked with (*) the cases where development terms are materialized in GO. But what is confusing is that the structure that is clearly the union of the homologous structures is named according to the tetrapod structure. So a simple renaming as you say will work.

    In fact there's not really a strong use case for GO naming the fins. GO could just use the generic "forelimb/pec fin" and "hindlimb/pelv fin". The important thing is to have the names indicate the content

     
    • assigned_to: nobody --> rfoulger
     
  • RFoulger
    RFoulger
    2011-10-05

    The definition of:
    limb morphogenesis ; GO:0035108 includes some fins:
    The process in which the anatomical structures of a limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.

    Instead of renaming the forelimb and hindlimb terms, how about adding in synonyms?

    forelimb morphogenesis ; GO:0035136
    exact synonym: forelimb or pectoral fin morphogenesis

    hindlimb morphogenesis ; GO:0035137
    exact synonym: hindlimb or pelvic fin morphogenesis

     
  • RFoulger
    RFoulger
    2011-10-05

    • labels: --> UBERON/anatomy
     
  • Chris Mungall
    Chris Mungall
    2011-10-05

    I think synonyms are better than the current situation. But I still think it is wrong to label a developmental process in a teleost as being limb development.

    Alan Ruttenberg has been pushing the idea of community specific synonyms - there is no designated primary term for a class. However, we need a name field in obo format.

    My preferred solution would be to have the name field be completely neutral (e.g. limb/fin), and to have exact synonyms for tetrapods and fish. We would introduce new synonymtypedef TELEOST_COMMUNITY and TETRAPOD_COMMUNITY. Applications would have the option of making this the primary display label.

    However, I appreciate that this makes GO a teensy bit more opaque to use just to satisfy the fishy minority, so I'm happy to put this up for a vote.

     
  • RFoulger
    RFoulger
    2011-10-06

    Doug's comment below sounds like the fish community think of fins as limbs- is this all fins Doug, or just the pectoral and pelvic ones?

     
  • Chris Mungall
    Chris Mungall
    2011-10-06

    I doubt the dorsal fin would ever be considered a limb :-)

    I've asked some teleost evolutionary biologists about the terminology for pelvic/pectoral.

    However, I note that neither ZFA nor TAO includes any limb terms as synonyms for any of the fins.

    (TAO doesn't generalize beyond teleosts - once we start including transitional species then the terminology of course becomes murkier).

     
  • David Hill
    David Hill
    2011-12-21

    At a meeting post-GOC several years ago, Doug, Susan?, someone from rat? and me all talked about limbs for quite some time. I agree with Becky and Doug. At least pectoral and pelvic fins share developmental mechanisms with other limbs. I am also 99% sure that the fly community would consider the legs limbs.

    I'll have a look at the mouse annotations. Sounds to me like the first one is not morphogenesis, but the second one is. I think most developmental biologists would consider limb outgrowth (length) morphogenesis.

     
  • Chris Mungall
    Chris Mungall
    2011-12-21

    Of course pectoral and pelvic fins share developmental mechanisms with forelimbs and hindlimbs - they're homologous.

    It does not follow from this that pelvic fins are hindlimbs. The people on the phenoscape project are with me on this one. I would like to see GO used more in evo-devo contexts and we prohibit this by saying fins are limbs.

    By your same argument, forelimb development is a hindlimb development, because they share developmental mechanisms (they're serial homologs).

    See also this thread:
    https://sourceforge.net/tracker/index.php?func=detail&aid=3463209&group_id=36855&atid=440764

    There are plenty of other ways to represent the shared developmental mechanisms. We can have a grouping class like "limb or homolog development" and place pectoral and pelvic fin development under here. But I think it's simpler to just have a grouping class that doesn't mention homology.

    David, when you say "I'll have a look at the mouse annotations" - I think you mean in the other thread? I'll answer back there...

     
  • Chris Mungall
    Chris Mungall
    2011-12-21

    Re: fly limbs.

    I'm sure that some the fly community might sometimes use the term "limb", but they're not homologs. The structure of GO shouldn't reflect nomenculature, it should have biologically justified groupings. The drosophila anatomy should be taken as the authority here, they don't have any labels or synonyms "limb". They have:

    id: FBbt:00004640
    name: leg
    def: "The walking appendages of each segment of the ventral adult external thorax." [FBC:gg]
    is_a: FBbt:00007000 ! appendage
    relationship: part_of FBbt:00003019 ! adult thoracic segment
    relationship: part_of FBbt:00004551 ! adult external thorax

    (of course, this isn't a tetrapod leg, we've established that!)

    I think "appendage development" might be a more evolutionarily and developmentally justified grouping class for GO here. Although we have to be careful we're not substituting one vagueness for another. We might want to be more specific to state we're excluding feathers, hairs.

    I also think it would be useful to have a grouping class specifically for limb/fin-bud derived structures, but this isn't really necessary now it's getting easier to query using external homology and anatomy resources.

     
  • RFoulger
    RFoulger
    2012-01-23

    Hi Chris,

    I've lost track a bit of where we're up to with this one: what restriction are you suggesting for the current limb terms in GO?

    Also, I checked with David O-S on the lack of a 'limb' term in FB anatomy, and he says:

    Based on dictionary definitions it looks like fly legs and wings could be considered limbs.

    e.g.
    http://en.wiktionary.org/wiki/limb
    # A major appendage of human or animal, used for locomotion (such as an arm, leg or wing)

    But in my experience, limb is not a term commonly used by insect biologists so I've never really seen the need to add it.

    ... does this help ?

    - David

     
  • Chris Mungall
    Chris Mungall
    2012-08-11

    Here is where we stand:

    GO should reflect the structure in Uberon that has been agreed on by multiple evolutionary & devlopmental biologists:

    .is_a UBERON:0000026 ! appendage
    ..is_a UBERON:0004708 ! limb/fin
    ...is_a UBERON:0002101 ! limb
    ....is_a UBERON:0002102 ! forelimb ***
    ....is_a UBERON:0002103 ! hindlimb ***
    ...is_a UBERON:0002534 ! paired fin
    ....is_a UBERON:0000151 ! pectoral fin ***
    ....is_a UBERON:0000152 ! pelvic fin ***
    ...is_a UBERON:0004709 ! pelvic appendage
    ....is_a UBERON:0000152 ! pelvic fin ***
    ....is_a UBERON:0002103 ! hindlimb ***
    ...is_a UBERON:0004710 ! pectoral appendage
    ....is_a UBERON:0000151 ! pectoral fin ***
    ....is_a UBERON:0002102 ! forelimb ***

    The terminology is still under discussion (e.g. "paired appendage" may be preferred to limb/fin, "pectoral limb" may be preferred to "forelimb"). Also GO doesn't have to instantiate all intermediate or leaf classes. The important thing is consistency with the structure. fins are not limbs, GO is currently wrong.

    There is a design document outlining some of the decisions here, ask me if you want write/comment permissions:
    https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit

     
  • RFoulger
    RFoulger
    2012-08-15

    1/ FINS
    Moved the pectoral and pelvic fin morphogenesis terms out from under 'limb morphogenesis' so all of the fin development terms are now under 'appendage development' and none are under 'limb development', in agreement with Uberon. Won't create any of the other intermediate terms as not neccessary for now (limb/fin, paired fin, pelvic appendage, pectoral appendage).

    Still to do:

    2/ DROSOPHILA LEGS
    i) Will move the imaginal-disc derived leg terms out from under 'limb development' and put them directly under 'appendage development'.
    ii) will propose obsoletion of the term: imaginal disc-derived limb morphogenesis ; GO:0035109. It only has 1 direct annotation, which I've emailed Susan about rehousing.

    3/ ARMS
    Sure this has come up before, but while we're against mechano-functional grouping,
    MERGE:
    arm morphogenesis ; GO:0035140 into forelimb morphogenesis ; GO:0035136
    embryonic arm morphogenesis ; GO:0035117 into embryonic forelimb morphogenesis ; GO:0035115

     
  • RFoulger
    RFoulger
    2012-09-11

    Obsoleted: imaginal disc-derived limb morphogenesis ; GO:0035109.

    Just the arm/forelimb merge to do on this SF item.

     
  • RFoulger
    RFoulger
    2012-09-11

    Merged:
    arm morphogenesis ; GO:0035140
    into
    forelimb morphogenesis ; GO:0035136

    Merged:
    embryonic arm morphogenesis ; GO:0035117
    into
    embryonic forelimb morphogenesis ; GO:0035115

     
  • RFoulger
    RFoulger
    2012-09-11

    • status: open --> closed-fixed