LEGO August 22, 2016

From GO Wiki
Revision as of 15:40, 24 August 2016 by Vanaukenk (talk | contribs)
Jump to navigation Jump to search

Bluejeans URL - NOTE NEW MEETING TIME: 8:00am PST

https://bluejeans.com/969313231

Agenda

Training and Documentation

UK Training Session

USC Training Session

  • Looks like the best day is 2016-11-07, the Monday after the consortium meeting
  • Paul T. looking into arranging a room at USC.

Documentation

  • Some comments and edits made to the Quick Start guide
  • Any more comments on Quick Start Guide?

Noctua-Minerva Mailing List

  • Review to make sure everyone who attends these meetings is on the list

Software Updates

NEO Overview and GPI Files

  • Questions, issues still to be sorted out?
    • We have entries for:
      • Genes
      • Proteins
      • Transcripts
      • ncRNAs
      • Protein Complexes
    • Convening on specs for Noctua
      • MODs should include UniProtKB GCRP accession as the db_xref for their gene-level entries
      • Protein, transcript, ncRNAs can include UniProtKB isoform accessions, PRO accessions, ENSEMBL IDs, RNACentral IDs in db_xref field
      • Acessions and IDs in db_xref field will be used for purposes of searching (in Noctua, and possibly also in AmiGO), but annotations in the models will be associated with the primary ID entered in each group's gpi file
      • Human gene products will use UniProtKB accessions as primary IDs
      • Also include HGNC gene IDs in human gpi
    • If groups don't have parent transcript or protein IDs, what ID should be used in Noctua and with what relation?
      • For example, if a curator needs to specify any mRNA transcript of a gene to add context to an MF annotation, should they use:
        • has_input(WB:WBGene00004804) OR has_input_some_product_of (WB:WBGene00004804) OR has_input_some_mRNA_transcript_of (WB:WBGene00004804)
    • How should protein complexes be represented?
  • Next steps - documentation of contents, communication of pipeline to other groups

MGI Meeting Follow Up

  • Review the list of software and annotation issues that were discussed at the MGI training session, June 15th-16th.
  • See the Google doc
  • Some specific follow-up:
    • GAF/GPAD output is probably highest priority
      • Remaining issues:
        • How to handle causal chains
        • Multiple evidence = multiple lines in the GAF
    • Using a limited set of relations in Noctua to make it easier for curators to find what they need github ticket 165
    • What should we use for internal refs that are not in PubMed; GO_REF, MGI:MGI:, J:?
    • We still need to figure out attribution. Right now everything coming in from Noctua has the group attribute GO_Noctua. That means that different groups making annotations to mouse genes cannot be distinguished.

LEGO Relations

  • Some specific issues have come up wrt LEGO relations that need clarification
  • The first concerns what to use to express the relationship between two activities, the acetylcholine transporter and the acetylcholinesterase, to the acetylcholine receptor in the Drosophila memory model
    • The transport and acetylcholinesterase are proposed to regulate the receptor activity by removing acetylcholine from the synaptic cleft, so there is a clear hypothesis about their mechanism of action
    • Currently, we have 'directly inhibits' to express the relation, but curators don't feel this accurately reflects the biology as there isn't a direct physical interaction between the gene products
    • However, use of 'negatively regulates' doesn't quite say enough, as there is a proposed molecular mechanism for the regulation
    • The RO has the relation 'directly provides input for' but does it have one for 'removes input for' (or 'directly removes iput for')? If so, would this be the correct relation to use?
  • The second issue concerns whether we should create additional relations for the 'causally upstream of or within' and 'causally upstream of' to indicate directionality, i.e. positive or negative
    • If we are going to stipulate that some understanding of mechanism is required to select a 'regulates' relationship, then having the directionality in the less granular parent relations would allow curators to still capture the effect of a gene product's activity on a process, even if the mechanism is not yet known.
    • These types of relations will probably be used widely to describe gene product effects based on mutant phenotypes

Minutes

  • On call: Chris, David H., David OS, Giulia, Jim, Judy, Kimberly, Midori, Moni, Paul T., Ruth, Seth, Stacia

Training and Documentation

UK Training Session

  • Reviewed agenda; okay for now, but fluid so we can make changes, if needed
  • Paul, Judy, David, Chris, Kimberly, Moni, Seth will plan to meet for a working dinner on Tuesday night; can meet earlier, too, if everyone has arrived in Hinxton
  • AI: email Claire to confirm schedule and who will be attending from UniProt - DONE

USC Training Session

  • Planning for a one-day training session the Monday (11/7) after the consortium meeting
  • With only one day, this will be a condensed session
  • We may have a number of curators (SGD, WB, etc.) who are completely new to LEGO, so need to think about how best to use our time
  • Sign up is on the meeting logistics page - so far, we have 13 attendees

Quick Start Guide

  • AI:Seth will absorb the Google doc into the github repo
  • This will enable the doc to always be publicly available, while still being editable in git

Noctua-Minerva Mailing List

  • Seth added a few more names to the mailing list
  • Reminder - if you attend the calls, and are not on the mailing list, please get in touch with Seth so he can add your email