SourceForge meeting 2015-02-11

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#11449 query about nuclease relationships to DNA catabolic process

A bit like the ATP<->ADP problem?

Not currently an inference issue - manually maintained part relationships. Perhaps comb through individual cases?

#11413 cellular response to nutrient/ cellular response to nutrient levels

Why do we have both?

mitophagy and response to depolarized mitochondria

Three related tickets from Paul on this.

* #11291 NTR: depolarised mitochondrion
* #11348 NTR - response to depolarised mitochondrion
* PINK1-PARKIN dependent mitophagy pathway

The consensus on the first two tickets seems to be that they should not be added as the structure and process are non-physiological. References on the third ticket suggest that this is not the case - that depolarised mitochondria happen naturally and that there is process dedicated to clearing them, just as there is for dealing with naturally occuring DNA damage. I'm inclined to add terms for all three requests.

https://sourceforge.net/p/geneontology/ontology-requests/11459 # 11459 Transcription from intergenic noncoding regions

Request from Rama based on this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806484/

Intergenic is a poor name. If function is found, we'll call these genes. non-coding = non protein coding.

The transcription in question may actually be non-functional noise associated with normal gene transcription.

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000371