Manager Call 2015-11-04

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Final progress report for this grant cycle

  • ACTION ITEM Several reports- One in a doc and then the more detailed one on the wiki. We will split things out later, but looking for content now. We need both the normal one and one for the for the last five years.

Identifiers used in Annotation Extensions

  • Follow-up from Annotation Conference Call of 2015-10-13
  • miRNA guidelines paper from Rachael nearly ready for submission to RNA, but issue of what DB identifiers to put in annotation extension field is not resolved. The current plan is to suggest using ENSEMBL gene IDs (and I believe MOD gene IDs, if applicable) but not transcript IDs. This doesn't allow for capturing targets that are isoforms, however.
    • What identifiers should we use, particularly for targets of regulation (column 16 values); ensembl identifiers or MOD identifiers? What about isoforms? ACTION ITEM------We will try to translate these to MOD identifiers. We have decided to go the route of a gene ID. What about isoforms? If the regulation is to a specific transcript isoform, how do we capture it? If you are not referring to a specific transcript, then use a MOD gene ID, a generic UniProtKB ID (human) or an ENSEMBL gene ID. If it is a specific transcript use the ENSEMBL transcript ID.

Items from Previous calls

Moved from Manager Call 2015-10-21

Annotation Extension

  • has_regulation_target can all annotation with this relation be updated to regulates_transcription_of? Yes. We have to figure out who will do it.
    • Can only be done for transcription terms.
  • Tony will send a list of annotations that have deprecated relations to all the groups.

Action item: groups will take time to rehouse the annotations (we will not delete/drop those annotations)

Reactome Annotations

  • contact a text miner to determine which papers (of the reactome set) correspond to which players (gene products) in the reactome annotations. Peter d’E will contact Jo McEntyre who may have already done this (cc-ing Claire).
    • Proposal is for now not to translate the data into EXP evidence codes. Using TAS makes sense to us because it is very similar to annotating from a review where you can trace to a source, but the origin is not the primary experimental data.

Tracing the Annotation source

  • We need to form a working group to figure this out.
    • Not sure what this means.

Chromatin Binding

  • In 2014 we decided to annotate ChiP experiments to chromatin (CC) and not chromatin binding (MF). We will continue with that practice. We should update documentation on this.
    • Can't find any documentation that we reached a consensus on this. Still need to discuss this. Need to present a concrete proposal.

Other topics

  1. Follow-up: collaboration with Trey Ideker's group on autophagy (David)
    • This would be really good to show community engagement. Status update, publication plans, etc.
  2. Moving tickets from Jira (EBI instance, NOT Jira helpdesk) to GitHub (David)
  3. Update on the GO survey from Paola
    • 470 responses so far. Would like to see 500. Only 2 responses from social media sources so far.