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.