Ontology meeting 2014-03-27: Difference between revisions

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The cell cycle ones may be a special case, I'll need to confer with Val. But what about the development ones? Is the transcription regulation really part of the process or is it really upstream?
The cell cycle ones may be a special case, I'll need to confer with Val. But what about the development ones? Is the transcription regulation really part of the process or is it really upstream?


=== happens_during ===
There has been some confusion amongst annotators about the use of happens_during in c16. For example:
Human miR-29b: GO:0035195 gene silencing by miRNA IDA C16: has_ regulation_target human COL1A1 [and COL3A1] happens_during GO:0071560 cellular response to transforming growth factor beta stimulus.
In this case the gene silencing by miRNA is actually '''part_of''' the response to TGF beta, but the temptation that if you're not sure whether one process is part of another to use happens_during but this doesn't imply causality.
Are we happy restricting the use of happens_during to being between bps and phases as we discussed? ATM in protein2go the only restriction for happens_during is biological process.
[[Category:Meeting]]
[[Category:Meeting]]
[[Category:Ontology]]
[[Category:Ontology]]

Revision as of 07:54, 25 March 2014

Attendees:

Minutes:

gene expression/transcription 'involved in' terms

Following a discussion with Ruth and Rachael, it seems that using the TG 'involved in' template for gene expression/transcription may have been wrong e.g. 'regulation of gene expression involved in extracellular matrix organization'. Here the regulation of gene expression shouldn't be part of the process extracellular matrix organization, I think instead it should be 'causally_upstream_of'.

Here is the full list of terms:

GO:0060807	regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification
GO:2000976	regulation of transcription from RNA polymerase II promoter involved in detection of glucose
GO:1900094	regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
GO:0003258	regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation
GO:0021882	regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment
GO:1901213	regulation of transcription from RNA polymerase II promoter involved in heart development
GO:0060994	regulation of transcription from RNA polymerase II promoter involved in kidney development
GO:0060500	regulation of transcription from RNA polymerase II promoter involved in lung bud formation
GO:0060597	regulation of transcription from RNA polymerase II promoter involved in mammary gland formation
GO:0061216	regulation of transcription from RNA polymerase II promoter involved in mesonephros development
GO:0072212	regulation of transcription from RNA polymerase II promoter involved in metanephros development
GO:0003256	regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
GO:0021918	regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment
GO:0090236	regulation of transcription from RNA polymerase II promoter involved in somitogenesis
GO:1902064	regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
GO:0021909	regulation of transcription from RNA polymerase II promoter involved in spinal cord anterior-posterior patterning
GO:0021920	regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification
GO:0021912	regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification
GO:0021913	regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification
GO:0090019	regulation of transcription involved in anterior neural plate formation
GO:0044324	regulation of transcription involved in anterior/posterior axis specification
GO:0060850	regulation of transcription involved in cell fate commitment
GO:0060899	regulation of transcription involved in eye field cell fate commitment of camera-type eye
GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0000117	regulation of transcription involved in G2/M transition of mitotic cell cycle
GO:0060849	regulation of transcription involved in lymphatic endothelial cell fate commitment
GO:0090020	regulation of transcription involved in posterior neural plate formation
GO:0060796	regulation of transcription involved in primary germ layer cell fate commitment
GO:0060852	regulation of transcription involved in venous endothelial cell fate commitment
GO:1901311    regulation of gene expression involved in extracellular matrix organization

The cell cycle ones may be a special case, I'll need to confer with Val. But what about the development ones? Is the transcription regulation really part of the process or is it really upstream?

happens_during

There has been some confusion amongst annotators about the use of happens_during in c16. For example:

Human miR-29b: GO:0035195 gene silencing by miRNA IDA C16: has_ regulation_target human COL1A1 [and COL3A1] happens_during GO:0071560 cellular response to transforming growth factor beta stimulus.

In this case the gene silencing by miRNA is actually part_of the response to TGF beta, but the temptation that if you're not sure whether one process is part of another to use happens_during but this doesn't imply causality.

Are we happy restricting the use of happens_during to being between bps and phases as we discussed? ATM in protein2go the only restriction for happens_during is biological process.