XP:biological process xp cellular component

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Revision as of 09:34, 18 November 2008 by Midori (talk | contribs) (Curator Notes)

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XPs defining biological processes in terms of cellular components; example:

[Term]
id: GO:0010020 ! chloroplast fission
intersection_of: GO:0048285  ! organelle fission
intersection_of: OBO_REL:results_in_division_of GO:0009507 ! chloroplast

[Term]
id: GO:0043572 ! plastid fission
intersection_of: GO:0048285  ! organelle fission
intersection_of: OBO_REL:results_in_division_of GO:0009536 ! plastid

i.e.

This allows a reasoner to compute the is_a relation between the two BP terms (based on the definition and the is_a relation between the CCs)

Availability

See the go/scratch/xps directory

This xp file has been registered in the OBO xps metadata so it is available here:

Methods

An initial parse was made using Obol. The results were then manually vetted by cjm, and new xp defs manually added

mitochondrial X

Terms of the form "mitochondrial X" are typically defined as

* An X that unfolds_in a mitochondrion

Here unfolds_in is a relation between a process and the location of the participants throughout the process

E.g.

[Term]
id: GO:0000963 ! mitochondrial RNA processing
intersection_of: GO:0006396 ! RNA processing
intersection_of: OBO_REL:unfolds_in GO:0005739 ! mitochondrion

See this sf item for clarification on RNA processing terms

Cellular X

Cellular X means X is executed at the level of the cell.

See sf item for clarification

For now we define cellular X using the has_level relation, but this is difficult to define

biogenesis, organization etc

Awaiting clarification. See: Cellular_component_processes

Existing xp defs may be changed once this is resolved

The current plan is to get replace "organization and biogenesis" with "organization". See above page for details.

export terms

Examples:

[Term]
id: GO:0000056 ! ribosomal small subunit export from nucleus
intersection_of: GO:0051168 ! nuclear export
intersection_of: OBO_REL:results_in_transport_of GO:0015935 ! small ribosomal subunit

[Term]
id: GO:0006608 ! snRNP protein import into nucleus
intersection_of: GO:0006606 ! protein import into nucleus
intersection_of: OBO_REL:results_in_transport_of GO:0030532 ! small nuclear ribonucleoprotein complex

[Term]
id: GO:0006626 ! protein targeting to mitochondrion
intersection_of: GO:0006605 ! protein targeting
intersection_of: OBO_REL:results_in_transport_to GO:0005739 ! mitochondrion

Examples

GO:0016043-cellular component organization GO:0022411-cellular component disassembly GO:0022607-cellular component assembly GO:0031555-transcriptional attenuation GO:0051168-nuclear export
GO:0005840-ribosome GO:0042254-ribosome biogenesisresults_in_organization_of GO:0032790-ribosome disassemblyOBO_REL:results_in_breakdown_of GO:0042255-ribosome assemblyOBO_REL:results_in_formation_of GO:0031556-transcriptional attenuation by ribosomeOBO_REL:mediated_by GO:0000054-ribosome export from nucleusOBO_REL:results_in_transport_of GO:0005840-ribosome
GO:0015934-large ribosomal subunit GO:0042273-ribosomal large subunit biogenesisresults_in_organization_of GO:0000055-ribosomal large subunit export from nucleusOBO_REL:results_in_transport_of GO:0015934-large ribosomal subunit
GO:0015935-small ribosomal subunit GO:0042274-ribosomal small subunit biogenesisresults_in_organization_of GO:0000056-ribosomal small subunit export from nucleusOBO_REL:results_in_transport_of GO:0015935-small ribosomal subunit
GO:0033279-ribosomal subunit GO:0042257-ribosomal subunit assemblyOBO_REL:results_in_formation_of GO:0033279-ribosomal subunit
GO:0016043-cellular component organization GO:0022411-cellular component disassembly GO:0022607-cellular component assembly GO:0031555-transcriptional attenuation GO:0051168-nuclear export

Results

Missing Parentage Reports


Curator Notes

2008-11-13

Committed some updates today:

  • updated alt_ids to ids:
    • 18994 -> 43186
    • 32842 -> 42575
  • updated GO term names
  • started adding comments on individual xps

Matters and questions arising

I'm checking to make sure it's OK to change results_in_organization_of to results_in_structural_organization_of; the latter is in ro_test.obo. It does seem to be OK in general in that the definition of the parent 'cellular component organization' is consistent with the relation def, but I'll also look at each xp that uses this relation.

Q: The xps also use has_level (see 'cellular x' above), which isn't in ro.obo or ro_test.obo, and I'm not as sure what to do about it.

Q: I've put in a bug report about how OBO-Edit 1 and 2 handle unrecognized relations (differently annoyingly) -- OBO-Edit 1.101 failed to load the file, reporting "unrecognized type results_in_organization_of", whereas OBO-Edit 2beta50 loads everything and automagically converts the results_in_organization_of relation to is_a in the cross-product panel. This worries me ... is it really the desired behavior?

update (18 Nov; relevant to 2 Qs above): emailed Chris to ask about relations without typedef stanzas in general, because it affects various things in OE (including the Graphviz viewer, as in this bug report)

Q: Is it correct to use unfolds_in for terms such as mitochondrial ornithine transport, when the transport def is "into, out of or within" the CC?

update (18 Nov): emailed Chris thusly:

The bp-xp-cc file has several entries for '[some organelle] transport' terms, e.g.

[Term]
id: GO:0000066 ! mitochondrial ornithine transport
intersection_of: GO:0015822 ! ornithine transport
intersection_of: OBO_REL:unfolds_in GO:0005739 ! mitochondrion

The def of GO:0000066, however, is "The directed movement of ornithine, 2,5-diaminopentanoic
acid, into, out of or within a mitochondrion."

It seems incorrect to use unfolds_in when the transport def is "into, out of or within" the CC
-- the unfolds_in def says "the execution of P is spatially contained by C", and that doesn't
seem to cover the "into" or "out of" bits. I guess the actual differentiae would be (unfolds_in
GO:0005739 OR results_in_transport_to GO:0005739 OR results_in_transport_from 
GO:0005739) ... but is that possible/allowable/desirable?

Less pressing matters:

RO and ro_test.obo aren't consistent w.r.t. derives_from, which makes OBO-Edit throw a warning. I've ignored it for now, since derives_from is in RO, but would like to know which to use when these xps go live.

Even smaller thing: the inverse_of tags on the obsolete relations has_improper_part and improper_part_of cause an OE warning. Ignored.

(Midori)

2008-11-13

Might want to add a term for 'plasma membrane transport' (maybe 'transport across plasma membrane'as name or synonym) -- at present plasma membrane pyruvate transport GO:0006849, plasma membrane acetate transport GO:0006847, etc. don't have a common parent.

Uncovered a general problem with transport terms -- the xp-generating rules seem to make two kinds of mistakes with transport process terms that mention some organelle.

  • One is the problem noted above, where [organelle] [substrate X] transport is taken to mean transport of X that occurs within the organelle
  • Another is [organelle X] transport, taken to mean transport OF the organelle instead of transport into, out of, or within the organelle.

Maybe this is something that can be addressed by structured synonyms?

MAH to do:

  • check definition and come up with a better name for GO:0016182 (endosome to synaptic vesicle budding)
  • cherk GO:0006998 - name is nuclear membrane organization, but the term dates back to before we properly distinguished the nuclear envelope from nuclear membrane(s)
  • similar to above, for mitochondrial membrane org, GO:0007006
  • check defs, and make names consistent betweer BP and CC for focal adhesion/hemi-adherens junction (GO:0005925 & GO:0007045)

(midori)