LEGO July 11, 2016

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Bluejeans URL


UK Training Session

  • Doodle poll for dates from late-August through late-October
  • Please fill out so we can find a time to meet

Software Updates

NEO Overview and GPI Files

  • Chris to provide an overview of what NEO is and how it's constructed
  • GPI files - examples on Google spreadsheet
  • Questions, issues still to be sorted out?
    • What IDs should each group enter in Col. 1?
    • What is the purpose of the db_xref column and how will it be used wrt NEO and Noctua?
  • 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


On call: Dan, David H., Giulia, Helen, Jim, Kimberly, Melanie, Paul T., Ruth, Sabrina, Seth, Stacia

UK Training Session

  • Doodle poll created for dates from late-August through late-October
  • A number of groups would like to attend, e.g. UniProt, FlyBase, PomBase, UCL, Synapse project curators, but finding a mutually agreeable time is getting difficult
  • Tack on a day or two to the USC meeting in November?
  • Could be useful, but would likely not be as big a group as could attend in the UK, so may have to do both anyway

Training Materials

  • Videos - no new videos yet; Stacia needed to put on hold
  • Seth - can do some quick videos using Vimeo if given a good outline
  • Volunteers for writing outlines?
  • Can use simple examples from previous workshops to start
  • Also need feedback from new users on Google doc

Software Updates

  • No new updates here
  • Textpresso link out is on a development machine at Berkeley
  • Seth will move to production site so more real-world use/testing can happen
  • Current Textpresso corpus in PMCOA - a start, but not everything, although users will be able to upload their own papers
  • Ruth mentioned that UK granting agencies are setting aside funds to allow immediate open access for publications
  • Host a Textpresso instance in the UK?

NEO Overview and GPI Files

  • Chris was at a retreat today; Seth gave a brief explanation but we punted on some questions until Chris is back and can comment
  • GPI files - examples on Google spreadsheet
    • Melanie asked why an ontology is created for entities instead of just using the gpi file format
      • Seth explained that the autocomplete mechanism in Noctua relies on use of ontologies to create input and output that uses human readable labels; basically making use of existing mechanism to populate entities for curation
    • Outstanding questions
      • db_xref entries: will these be available for annotation?
      • Mapping entities to GCRP accessions - can all IDs used be mapped back to the GCRP? If a curator needs to annotate to a TrEMBL ID, can it be mapped somehow to the GCRP?
  • We had additional discussion, though, about IDs and a few questions came up:
    • Helen asked about ID synchronization and keeping IDs up-to-date when there are changes at the host databases
      • For example, gene merges, splits
      • A separate process would be needed to handle ID udpates
      • Curators will need to document use cases - merges are generally simpler than splits, as with a gene split curators need to manually review the annotations to make sure they migrate to the correct entity
      • Wait until Noctua switches over to the new system to sort out this issue?