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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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tair process terms #564

Closed gocentral closed 9 years ago

gocentral commented 22 years ago
  1. epidermal cell fate specification ISA cell fate specification
  2. root gravitropism ISA gravitropism
  3. shoot gravitropism ISA gravitropism
  4. seed endosperm development isa development/morphogenesis/organogenesis?
  5. response to 1-Aminocyclopropane-1-carboxylic Acid isa response to hormone stimulus
  6. negative regulation of flavonoid biosynthesis isa need regulation of flavonoid biosynthesis, -/+ regulation of flavonoid biosynthesis as children of GO:0009813
  7. leaf morphogenesis isa morphogenesis
  8. negative regulation of signal transduction isa signal transduction isa regulator of signal transduction
  9. positive control of trichome initiation [isa] determination of epidermal cell identity. [part of] trichome development
  10. xyloglucan biosynthesis isa GO:0009250 glucan biosynthesis
  11. response to dehydration isa GO:0009415 (response to water)
  12. response to sulfate starvation isa response to starvation GO:0009267
  13. male meiotic spindle assembly (sensu Viridiplantae) isa GO:0000212 meiotic spindle assembly partof GO:0007140 male meiosis
  14. early endosome fusion [part of]endosome transport (GO:0016197) or endocytosis
  15. cytidine deamination isa GO:0046087 : cytidine metabolism and GO:0046133 : pyrimidine ribonucleoside catabolism

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/564":https://sourceforge.net/p/geneontology/ontology-requests/564

gocentral commented 21 years ago

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Hi Suparna,

A couple of comments:

8) negative regulation of signal transduction: the structure should be

signal transduction [P] regulation of signal transduction ---[I] negative regulation of signal transduction ---[I] positive regulation of signal transduction

The structure would be the same for no. 6, negative regulation of flavonoid biosynth.

15) cytidine deamination could go directly under cytidine catabolism. Check that it is different from GO:0004126 first, though.

Original comment by: girlwithglasses

gocentral commented 21 years ago

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  1. root gravitropism ISA gravitropism

Should be anatomy independent. Call it "positive gravitropism"

  1. shoot gravitropism ISA gravitropism

Should be anatomy independent. Call it "negative gravitropism"

  1. seed endosperm development isa

Endosperm development is enough. seed endosperm is a relationship between two anatomical term. Does endosperm exists in any other place other than seed ?

All the terms, including the ones I suggested for gravitropism as above, containing "negative" and "positive" should actually become obsolete/modified. As Michael, GO members and others who attended the Phenotype Ontology meeting held at TIGR, 7-8 Dec., agreed that these (negative/positive) are the values of attributes (response/action) of the GO process/function. In GO the terms should cover the concept mainly and not the attributes associated to it (barring some cases where its considered as an event in a biological process and is unavoidable to constrian the NO_USE of such attributes)

It's something like this

GO_term has an attribute. Each attribute has a value and a qualifier. The qualifier can be measured/observed in a relative or an absolute scale.

So in this case the GO product should be annotated for its association to GO_Process "Gravtropism". Whereas the response observed in presence of Gravity(an environment factor) is either negative/positive.

Original comment by: jaiswalp

gocentral commented 21 years ago

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Pankaj,

I will use positive and negative gravitropisms instead of shoot and root gravitropism as well as endosperm development in place of seed endosperm development. I will be adding these terms to GO today. Thanx for the input.

Suparna

Original comment by: smundodi

gocentral commented 21 years ago

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Amelia,

GO:0004126 is a function term cytidine deaminase. We need a process term cytidine deaminase toassign the process the gene is involved in. I will make it a direct child of cytidine catabolism.

Thanx for pointing out the relationship descrepancy in regulation of signal transduction term.

Suparna

Original comment by: smundodi

gocentral commented 21 years ago

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That's fine. -pankaj

Original comment by: jaiswalp

gocentral commented 21 years ago

Original comment by: smundodi