Annotations to GO:0006917 'induction of apoptosis'

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As part of the apoptosis project, we looked at the term GO:0006917 'induction of apoptosis' (def: "A process that directly activates any of the steps required for cell death by apoptosis.").

This term is a child of GO:0043065 'positive regulation of apoptotic process'. However, upon checking some of the papers curated to this term in the light of our recent work on apoptosis, Pablo and I felt that 'induction of apoptosis' had sometimes been used ambiguously in the past. David confirmed this impression while recurating some MGI annotations:

"Rereading the papers, I think that this term was used in a variety of ways and was not necessarily restricted to processes that positively regulate apoptosis. In some cases the genes were involved in either the apoptotic signaling pathway or the apoptotic execution phase. In some cases the genes regulated either the signaling or the execution phases. In many papers the annotation was made because the experiment showed that apoptosis was triggered when the gene was expressed in a given cell type. The wording used in the paper stated that the gene induced apoptosis because when it was expressed, the cells underwent apoptosis. Some of those cases showed a mechanism and some did not.".

When a mechanism is described, it should now be possible to rehouse annotations to 'induction of apoptosis' to more precise terms, taking advantage of the newly revised apoptosis ontology node, where dozens of new terms have been added and many more have been edited. We feel that this re-housing is particularly important because, in enrichment analyses, 'induction of apoptosis' shows up often - when we expect that a significant percentage of its annotations should be placed elsewhere. If a paper fails to detail mechanisms at all, but occurrence of apoptosis is clearly shown by experimental evidence, then annotations should be made to GO:0006915 'apoptotic process'.

We considered various options and we think that, if no manual inspection is performed on annotations to 'induction of apoptosis', we should merge this term with GO:0006915 'apoptotic process'. However this would involve a loss of granularity. Therefore, we'd kindly ask you to review annotations to 'induction of apoptosis' and place them elsewhere, as discussed above. I'd like to propose a deadline of August 30th, following which 'induction of apoptosis' will be merged with 'apoptotic process'. To aid re-curation, we've provided a detailed apoptosis curation manual, including some annotation examples, at http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual.

Here's the breakdown of all manual annotations to 'induction of apoptosis' per database as of July 16th:

AgBase 6 BHF-UCL 4 FlyBase 53 HGNC 14 MGI 42 PINC 42 RefGenome 40 RGD 60 UniProtKB 146 WormBase 2 ZFIN 5

MGI have already re-assigned their annotations, though this may take some time to show up in GO browsers.

We hope you'll be available to help. If not, please let us know. The curation manual should be able to answer any doubts, but if not, please email both Pablo and myself (paola@ebi.ac.uk and pporras@ebi.ac.uk). If one of us is on summer leave, the other will pick up your message.

Thanks in advance for your help. Paola

Reported by: paolaroncaglia

Original Ticket: geneontology/annotation-issues/1057

[gocentral]

Update: Ruth took care of BHF-UCL and HGNC annotations; Kimberly will look at WormBase's; Fiona will look at AgBase's.

Original comment by: paolaroncaglia

[gocentral]

Update: Kimberly fixed WormBase annotations.

Original comment by: paolaroncaglia

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All the Drosophila melanogaster ones have now been updated. The changes will be visible in the next FlyBase release (FB2013_05) due out on Sept 6th.

Original comment by: stweedie

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Hi Paula,

Thanks for pointing this out. I have contacted our annotation team and we'll try to have a look at those ASAP.

Pascale

Original comment by: pgaudet

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Fiona has updated the AgBase annotations.

Original comment by: paolaroncaglia

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Doug will look into the ZFIN annotations.

Original comment by: paolaroncaglia

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Stan writes that RGD will recurate their manual annotations by the end of the month.

Original comment by: paolaroncaglia

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All the annotations from ZFIN curators have been adjusted. Other annotations that come from third parties (PAINT and GOA primarily) will be updated in ZFIN when those groups update the annotation on their end.

Original comment by: doughowe

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Stan writes: "All of the manual RGD annotations for 'induction of apoptosis' (GO:0006917) have been recurated to different terms or otherwise edited. We are set for the term merge."

Original comment by: paolaroncaglia

[gocentral]

Merged 'induction of apoptosis' with 'apoptotic process'.

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed

Original comment by: paolaroncaglia