LEGO July 11, 2016
Bluejeans URL
https://bluejeans.com/969313231
Agenda
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
Minutes
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?
- Melanie asked why an ontology is created for entities instead of just using the gpi file format
- 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?
- Helen asked about ID synchronization and keeping IDs up-to-date when there are changes at the host databases