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first proposed new GO terms from Wormbase
Erich Schwarz
emsch at its.caltech.edu
Wed Jul 25 18:40:24 PDT 2001
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.
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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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