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Source ontology files for the Gene Ontology
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new term suggestions, mostly C. elegans specific #1346

Closed gocentral closed 9 years ago

gocentral commented 20 years ago

1) term: pharyngeal pumping (sensu Nematoda) goid: GO:new definition: The contraction and relaxation movements of the pharyngeal muscle that mediate feeding in nematodes. definition_reference: WB:cab definition_reference: PMID:2181052

synonyms: pumping behavior

which would be a child-instance term of:

term: eating behavior goid: GO:0042755 definition: The specific actions or reactions of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.

2) term: regulation of pharyngeal pumping (sensu Nematoda) goid: GO:new definition: Control of the contraction and relaxation movements of the pharyngeal muscle that mediate feeding in nematodes. definition_reference: WB:cab definition_reference: PMID:2181052

which would be a child-part term of:

term: pharyngeal pumping (sensu Nematoda) goid: GO:new definition: The contraction and relaxation movements of the pharyngeal muscle that mediate feeding in nematodes. definition_reference: WB:cab definition_reference: PMID:2181052

3) term: thermotaxis goid: GO:new definition: The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards a higher temperature or a lower temperature. definition_reference: WB:cab definition_reference: WB:cgc467

which would be a child-instance term of:

term: taxis goid: GO:0042330 definition: The directed movement of a cell or organism in response to an external stimulus. definition_reference: ISBN:0192801023 definition_reference: GO:jl

4) term: dauer entry (sensu Nematoda) goid: GO:new definition: Entry of a nematode into the facultative diapause of the dauer ('enduring') larval stage. definition_reference: WB:cab definition_reference: PMID:10077613

which would be a child-part term of:

term: dauer larval development (sensu Nematoda) goid: GO:0040024 definition: Development of a nematode through the facultative diapause of the dauer ('enduring') larval stage, with specialized traits adapted for dispersal and long-term survival, with elevated stress resistance and without feeding. definition_reference: WB:ems definition_reference: ISBN:087969307X

5) term: dauer exit (sensu Nematoda) goid: GO:new definition: Exit of a nematode from the facultative diapause of the dauer ('enduring') larval stage. definition_reference: WB:cab definition_reference: PMID:12620986

which would be a child-part term of GO:0040024.

6) term: maintenance of dauer (sensu Nematoda) goid: GO:new definition: Maintenence of a nematode during the facultative diapause of the dauer ('enduring') larval stage. definition_reference: WB:cab definition_reference: WB:wm2003ab740

which would be a child-part term of GO:0040024.

7) term: forward locomotion goid: GO:new definition: Anterior movement of an organism, e.g., following the direction of the head in a fly or nematode. definition_reference: WB:cab definition_reference: WB:ems

which would be a child-part term of:

term: locomotion goid: GO:0040011 definition: Performing basic movements of any kind. definition_reference: WB:ems

8) term: regulation of forward locomotion goid: GO:new definition: Control of the speed, mechanical force, or rhythm of the anterior movement of an organism. definition_reference: WB:cab definition_reference: WB:ems

which would be a child-part of:

term: forward locomotion goid: GO:new definition: Anterior movement of an organism, e.g., following the direction of the head in a fly or nematode. definition_reference: WB:cab definition_reference: WB:ems

9) term: backward locomotion goid: GO:new definition: Posterior movement of an organism, e.g., following the direction of the tail in a fly or nematode. definition_reference: WB:cab definition_reference: WB:ems

which would be a child-part term of GO:0040011.

10) term: regulation of backward locomotion goid: GO:new definition: Control of the speed, mechanical force, or rhythm of the posterior movement of an organism. definition_reference: WB:cab definition_reference: WB:ems

which would be a child-part of:

term: backward locomotion goid: GO:new definition: Posterior movement of an organism, e.g., following the direction of the tail in a fly or nematode. definition_reference: WB:cab definition_reference: WB:ems

11) term: meiotic metaphase I plate congression goid: GO:new definition: The alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the meiotic spindle, during meiosis I. definition_reference: WB:cab definition_reference: PMID:10809666

which would be a child-part term of:

term: meiotic metaphase I goid: GO:0007132 definition: Metaphase of meiosis I; analogous to mitotic metaphase. definition_reference: SGD:mah

in analogy to the relationship of mitotic metaphase plate congression (GO:0007080) to mitotic metaphase (GO:0000089).

12) term: meiotic metaphase II plate congression goid: GO:new definition: The alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the meiotic spindle, during meiosis II. definition_reference: WB:cab definition_reference: PMID:10809666

which would be a child-part term of:

term: meiotic metaphase II goid: GO:0007137 definition: Metaphase of meiosis II; analogous to mitotic metaphase. definition_reference: SGD:mah

in analogy to the relationship of mitotic metaphase plate congression (GO:0007080) to mitotic metaphase (GO:0000089).

Reported by: carolbas

Original Ticket: "geneontology/ontology-requests/1349":https://sourceforge.net/p/geneontology/ontology-requests/1349

gocentral commented 20 years ago

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Most of these look fine, and we'll add the mas soon as we can. I have two comments on 'forward locomotion' and 'backward locomotion':

- It would be best to make the definitions more obviously generic, so I would rather say 'e.g., following the direction of the [head|tail] in an animal' than 'in a fly or nematode'.

- They should be is-a children of locomotion, not part-of.

Original comment by: mah11

gocentral commented 20 years ago

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Do you want to create a different dbxref for your internal paper base ids? You suggested 'definition_reference: WB:cgc467' for one of your terms, maybe for papers you could use something different to indicate that this is a paper e.g. at SGD they use SGD_REF:xxx

Just let me know and I can add to the GO.xref_abbs file.

Original comment by: jl242

gocentral commented 20 years ago

Original comment by: jl242

gocentral commented 20 years ago

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Response to jl242:

Yes, we will need a different dbxref for our internal paper base ids! Thank you for pointing this out.

cgc467 does not appear to have an associated PMID reference number that I can find. In addition to published papers that have a "cgc" prefix, abstracts from worm meetings, and articles from our Worm Breeder's Gazette are presently included in our internal paper base ids. Worm meeting abstracts will have the following prefixes: "euwm", "wcwm," "wm," "jwm," "ecwm," "mwwm." Worm Breeder's Gazette articles have the prefix, "wbg."

RIght now in WormBase, we are simply using the desination as I had it: "WB:cgc467," but we could alter it to WB_REF:xxx (where xxx would have any of the prefixes indicated above) if that would be better.

** I see that in addition to cgc467, I also used wm2003ab740 as a GO term reference.

Response to gomidori:

I agree with all of the changes that Midori recommends.

Original comment by: carolbas

gocentral commented 20 years ago

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Okay, I've given your internal paper references the dbxref WB_REF:xxx and I've added this to the xref_abbs file. Also added all the terms you wanted (ids below). Few minor modifications to definitions, and removed 'sensu Nematoda' from the pharyngeal pumping terms, as this process is only described for nematodes anyway.

GO:0043050 JL pharyngeal pumping GO:0043051 JL regulation of pharyngeal pumping GO:0043052 JL thermotaxis GO:0043053 JL dauer entry (sensu Nematoda) GO:0043054 JL dauer exit (sensu Nematoda) GO:0043055 JL maintenance of dauer (sensu Nematoda) GO:0043056 JL forward locomotion GO:0043057 JL backward locomotion GO:0043058 JL regulation of backward locomotion GO:0043059 JL regulation of forward locomotion GO:0043060 JL meiotic metaphase I plate congression GO:0043061 JL meiotic metaphase II plate congression

Original comment by: jl242

gocentral commented 20 years ago

Original comment by: jl242