first proposed new GO terms from Wormbase

[Erich Schwarz]

Hello everybody,

    As Raymond Lee and I discussed at the GO meeting, we are working
here at Caltech to map RNAi phenotypes onto GO.  This has induced me
to consider over a dozen possible new terms.  I list them below for
your consideration and criticism; I will be grateful for any
improvements you can suggest (even if the improvement is "don't use
that term at all").


--Erich


*****************************************************************

Proposed new GO terms, 7/25/01, Erich Schwarz, Wormbase.

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Components of each proposal:

A. a term string (descriptive term name)
B. a small definition of the term (desirable but not required)
C. a brief mention of where the new term would fit within
         the ontology (desirable but not required)

In cases where the parent or child terms have no definition themselves
(many), I tried to come up with one for the parent/child terms as well.

Reference: I have derived many definitions from _The American Heritage
Dictionary of the English Language, 3rd. ed._, Houghton Mifflin Company,
Boston.  Other terms have been derived from the _McGraw-Hill Dictionary
of Bioscience_, McGraw-Hill, New York.

-----------------------------------------------------------------

1. "fertility (sensu Nematoda)"

Definition: The capacity of an adult nematode to generate offspring.

Location:

This would have the following child-subset terms:

    GOid:       0007276
    GO_def:     gametogenesis
    Definition: The formation or production of gametes.

    GOid:       0007320
    GO_def:     insemination
    Definition: Introducing or injecting semen into the reproductive
                    tract of a female or hermaphrodite.

    GOid:       0007338
    GO_def:     fertilization
    Definition: The union of male and female gametes to form a zygote.

and would itself be a child-example term of:

    GOid:       0007582
    GO_def:     physiological processes
    Definition: Biological processes specifically aimed at the
                    maintenance and function of an organism in
                    homeostasis.


2. "positive regulation of growth rate"

Definition: Directing the growth of an organism so that
                it occurs at its usual speed rather than at
                an abnormally low speed.

Location:

    This could be a child-subset term of

    GOid:       0007275
    GO_def:     developmental processes
    Definition: Biological processes specifically aimed at the
                    progression of an organism from an initial
                    simple condition (typically a zygote) to a
                    generally more elaborate final condition
                    (typically an adult).


3. "larval survival"

Definition: Remaining alive through one or more larval life stages.

Location:

    This could be a child-subset term of:

    GOid:       0002119
    GO_def:     larval development (sensu Nematoda)
    Definition: Development of a nematode through one or more
                    larval life stages.


4. "positive regulation of body size"

Definition: Directing the growth of an organism so that
                it reaches its usual body size rather than
                an abnormally low body size.

Location:

    Child-subset of:

    GOid:       0007275
    GO_def:     developmental processes
    Definition: see above.


5. "vulval development (sensu Nematoda)"

Definition: Development of a nematode vulva during through one or more
                    larval life stages.

Location:

    A child-subset term of

    GOid:       0002119
    GO_def:     larval development (sensu Nematoda)
    Definition: see above.


6. "osmoregulation"

Definition: Control of the osmotic activity of the fluid
                in a cell, tissue, organ, or organism.

Location:

    A child-subset term of:

    GOid:       0006873
    GO_def:     ion homeostasis
    Definition: Control of the ionic concentrations of the fluid
                    in a cell, tissue, organ, or organism.


7. "moulting (sensu Nematoda)"

[N.B. is the British spelling "moulting" supposed to still be
    in use?  Or should it be "molting" by now?]

Definition: Periodically shedding part or all of a nematode cuticle,
                which is then replaced by a new cuticle.

Location:

    A child-subset term of

    GOid:       0007582
    GO_def:     physiological processes
    Definition: see above.

This would be an exact parallel to:

    GOid:       0007591
    GO_def:     moulting (sensu Insecta)
                [n.b.: British spelling? still in use?]


8. "egg-laying"

Definition: Depositing eggs upon a surface.

Location:

    A child-example term of:

    "adult behavior (sensu Nematoda)"
    Definition: The specific patterns of directed activity
                    characteristic of adult nematodes.

    which must also be invented, as a child-example of

    GOid:       0007610
    GO_def:     behavior
    Definition: Specific patterns of directed activity.

in analogy to:

    GOid:       0008044
    GO_def:     adult behavior (sensu Insecta)
    Definition: The specific patterns of directed activity
                    characteristic of adult insects.


9. "general mobility"

Definition: The ability to perform basic, rudimentary movements, as
                opposed to performing fully normal movements.

Location:

    A child-subset term of:

    GOid:       0007626
    GO_def:     locomotory behavior
    Definition: All abilities associated with normal movement, including
                   both general motion and specifically coordinated
                   patterns of activity.


10. "cuticular attachment to epithelium"

Definition: Attaching of a cuticle to the epithelium underlying it.

Location:

    A child-subset of yet another new term:

    GO_def:     cuticle biogenesis
    Definition: Synthesis and deposition of a noncellular, hardened,
                    or membranous secretion from an epithelial sheet.

    which itself might be a child-subset of:

    GOid:       0007398
    GO_def:     ectodermal development
    Definition: Growth and differentiation of an ectoderm.

    or perhaps of

    GOid:       0008544
    GO_def:     epidermal differentiation
    Definition: Acquisition of a terminally differentiated state by
                    an epidermis in a developing organism.


11. "negative regulation of body size"

Definition: Directing the growth of an organism so that
                it reaches its usual body size rather than
                an abnormally large body size.

Location:

    This could be a child-example term of

    GOid:       0007275
    GO_def:     developmental processes
    Definition: see above.


12. "adult survival"

Definition: Remaining alive through the normal adult life span.

Location:

    This could be a child-subset term of:

    GOid:       0007275
    GO_def:     developmental processes

in analogy to:

    GOid:       0007568
    GO_def:     aging


13. "somatic sex-determination"

Definition:

which doesn't yet exist by itself, so it must be invented -- namely as
child of:

    GOid:       0007530
    GO_def:     sex determination
    Definition: Determination of sex in an organism.

and a parent of both these two terms:

    GOid:       0007539
    GO_def:     primary sex determination -- soma
    Definition: Transmitting information about sexual status
                    from the initial, general determination to
                    signals specific to the soma.

    GOid:       0007546
    GO_def:     soma downstream of sex determination signal
    Definition: Events determining the somatic sexual phenotype
                    after the initial transmission of that
                    phenotype to soma-specific information pathways.


14. "germline sex-determination"

Definition:

Location:

    A child term of:

    GOid:       0007530
    GO_def:     sex determination
    Definition: see above

and a parent of both these two terms:

    GOid:       0007542
    GO_def:     primary sex determination -- germ-line
    Definition: Transmitting information about sexual status
                    from the initial, general determination to
                    signals specific to the germ-line.

    GOid:       0007547
    GO_def:     germ-line downstream of sex determination signal
    Definition: Events determining the somatic sexual phenotype
                    after the initial transmission of that
                    phenotype to germ-line-specific information pathways.


15. "negative regulation of locomotion"

Definition: Controlling the locomotion of an organism so that
                it occurs at normal intensity and frequency rather
                than at an abnormally large intensity or frequency.

Location:

    A child-subset term of

    GOid:       0007626
    GO_def:     locomotory behavior
    Definition: see above.


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