PomBase Curator Meetings

PreviousCurationMeetings

Next Items, in rough order of priority

Curation issues biology

• Issues related to branching and T-shaped phenotype

• representing core stress response genes and "response to stress", specifically i) stress signalling ii) antioxidants etc (thread 'Annotation extension paper' this came up in AE pper egs)

Ontology questions

• Discuss the item about capturing phenotypic observations vs. Phenotypes thread PMID:19033384

Annotation issues, syntax, procedures, extensions etc

• Is this regulation, or 'indirect' ​https://sourceforge.net/p/pombase/curation-tasks/375/

• transcript IDs in extensions ​https://www.ebi.ac.uk/panda/jira/browse/PB-1554#comment-91446 (see work in progress on wiki)

• Go through curation tracker, assign people, priorities

• discuss Rama's question about "response to extensions
  • also discuss what is being regulated here .....I don't think it is -ve reg of the transition (this acts through cdc2 and not through trancription)

• Follow up output_of etc, this ticket ​https://sourceforge.net/p/pombase/fission-yeast-phenotype/1501/

Documentation

• Canto documentation required
  • From Scott: provide even one paper and walk the user through entering the paper, the genes and a sample entry. Then you could also walk through an administrative approval and saving the data to Chado (Kim suggested we start with just a list of bullet points)
  • and ​https://sourceforge.net/p/pombase/curation-tasks/365/
• Tidy wiki, move obsolete pages

Outreach

• plan roadshow dates/places
  • Val will get UK lab list (done)
  • Midori will draft e-mail (done)
  • after BYGa and Toronto, will begin to pin down dates. Antonia will try to set up some whilst at BYG

PomBase website

• from planning meeting next curator meeting links to GO terms from gene pages, genes annotated to, genes in extensions, genes expressed duritn

also CDRE motif ​http://stage.pombase.org/spombe/result/SPBC106.10#fission_yeast_phenotype

• Phenotypes for double mutants
  • Jira tickets for display changes: ​PB-1836 and sub-tasks
  • querying/enrichment etc (postponed, discuss in context of querying alleles, conditions etc plan for 2 days, 2nd day with Mark)
• GO display
• Gene page changes to do through with Mark in person
  • compact GO & FYPO displays as in Jira tickets above
  • column sorting (click header etc.)
  • clever ways to group ontology terms by some sort of similarity measure
  • redundancy filtering, esp. for GO
  • user configuration
    • page section order
    • compact vs. expanded view (where relevant)
    • show/hide page sections

Community curation paper

• Community curation spreadsheet: Community Curation errors spreadsheet replace
• Talk about spreadsheets. We should be able to use Canto to report differences between curator and community now all annotations have recorded person. The only thing we won't be able to capture is when a curation is wrong an d is deleted and replaces so we will need to continue to monitor this?
• Discuss paper outline (contents)

Lower priority

• collection of phenotype images

• Low penetracne check (I think this is about population phenotype-> fully penetrant?)

• Idea for accessing completed curation sessions add review links to paper section for community curated papers

• Future Pombelist posts
  • physical interaction Biogrid vs GO
  • phenotypes vs. processes
  • Did you know's
  • Adding gene names
  • preparing HTP datasets
  • community curation demo etc
  • alignments Draw attention too specifically, Update re improved alignments and Schizos new 'did you knows'
  • ​https://sourceforge.net/apps/trac/pombase/wiki/CommunityAlerts etc

• gene name descriptions to phenotypes, add to phenotype ontology for searching?
• Val- Go through curation tracker high priority items (some are duplicated below)
• Val- update on phenotype mapping, where it is, what to do with removed annotations
• Antonia- Summarize community curation session quality/ ommissions
• Val- viability exercise results (query intersection)
• PHAF/GPAD/GPI files for export/import etc.

• Genetic interactions ontology

• Discuss regulation of G1/S in relation to 6ff4c9edff12167b (look at annotation in context of all genes in this session)

• discuss response to "cellular response to drug" ​http://www.pombase.org/spombe/result/SPAC31G5.13

• discuss establishment of cell polarity and the signalling network (MOR) (see e-mail Created new session 31b82829d0c47e4d from PMID:23649273 )

• transcription related Sushils thesis and e-mail "2 MF transcription terms, sound the same"

• regulation of histone modifications., GO or phenotype? /curs/97535c919f7436fe thread

• advanced search, better to have just query management ?

• no entry into meiosis and cell cycle phenotype ​https://sourceforge.net/p/pombase/fission-yeast-phenotype/709/

Later/ In progress

• penetrance high/medium/low
  • see e-mail "extending penetrance extensions"

• Curating alternative transcripts
  • ​https://sourceforge.net/p/pombase/curation-tasks/31/
  • related - ​uvi15 UTRs

• remapping DNA replication
  • currently 25 genes mapped to "nuclear DNA replication"
  • eventually all genes should be mapped to "nuclear" or "mitochondrial" and then, when the terms are implemented to "mitotic"
  • anything further waiting on completion of ​https://sourceforge.net/p/geneontology/ontology-requests/10620/

• remapping cytokinesis
  • ​https://sourceforge.net/p/pombase/curation-tasks/269/ (i.e nothing to do here, waiting for new, more specific terms)
  • terms exist ​https://sourceforge.net/p/geneontology/ontology-requests/10310/

• Do not annotate subset. On hold until reports generated ​https://sourceforge.net/p/pombase/curation-tasks/214/

• check Biogrid data alignment progress with Antonia

​https://sourceforge.net/p/pombase/curation-tasks/258/

• how to represent the reintegration assays ? (see for example Alper/Partridege? and Shanker/PArtridge
  • decided for now just to represent the deletion phenotype , and then do a GO process for the 'reestablishment etc.