WormBase-Caltech Weekly Calls August 2016

August 4, 2016

Parasite Paper Pipeline and Curation Status Tracking

• ~4% of Journal articles (roughly, but not precisely, translates to curatable papers) mention both Caenorhabditis species and parasite species
• We discussed last week the options for accurately tracking data type flagging and curation status for these papers
• SVM does not flag data at the species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton
• One option would be to have separate status tables
  • Lump Caltech and Hinxton species together or distinguish each species separately?
• Other options?

Intellectual lineage graph

• Raymond - are we ready to implement as a widget on person page?
• Can toggle to show only direct relationships
• Will eventually be able to toggle by relationship type
• These will simplify complex graphs

SVM for MGI

• Yuling is tying up loose ends for MGI SVM before he leaves

AGR Timeline meeting

• Timeline still pretty high-level but making progress

Complex genotype to phenotype annotation

• Chris - still planning to work out details over models mailing list
• We can go ahead with the creation of phenotype report objects to encapsulate complex genotypes
• Another approach to consider is whether or not to create "set" objects that contain sets of, for example, alleles, genes, etc.
• We could potentially reuse sets as they come up again in different contexts, or in replicate experiments

Teleconference line

• New AT&T conference call is OK, not great
• BlueJeans is too expensive for our purposes

August 11, 2016

Micropublications

• Would like to make more prominent on homepage
• Expanding micropublications to phenotype
  • Would we require images, photographs of mutant worms
  • Can clone phenotype form, but remove requirement for publication; also add funding sources
  • Would negative data require controls?

August 18, 2016

Tazendra

• Raymond installing new network card
• Recent network crashes, unclear why
• Raymond sent a help desk ticket to IMSS; no response so far
• Michael and Ranjana have gotten network errors as well (when trying to deal with automated descriptions)

Models updating

• Wen has GitHub page bookmarked to retrieve latest models.wrm file
• Older CVS system had used explicit release ID in name of file; not same now with GitHub
• With GitHub, it could be easy to script retrieval of latest models.wrm file

Anatomy ontology, from OBO to OWL

• Major reason to do it: make direct connections to terms in other ontologies
• Can take advantage of other anatomy ontologies
• Should the WBbt "cell" be synonymous with generic "cell" or be referred to as "C. elegans cell"?
• Import versus cross-reference approach to linking ontologies

Noctua, LEGO curation

• Weekly meetings, Monday mornings
• Nearly ready to release Noctua for use
• Ongoing discussion about use of relations from the relations ontology; maybe need some new terms
• Idea is to make Noctua the main GO annotation tool, for simple or complex annotations
• People still using legacy GAF file, need to transition to OWL format
• Training session at end of month (next week)
• GO meeting at USC in November; will dedicate the following week to Noctua/LEGO training workshop (Monday Nov 7th?)
• While curating need to consider whether a molecular function regulates a process or is part of a process; requires explicit positioning
• Need to deal with annotations to a generic gene product versus a specific gene product (one or all isoforms, for example)
• Would want a "enabled by product of" relation for genes
• Chris M concerned with having too many relations for curators to know/keep track of
• Training material should be available from the Noctua homepage

Community Phenotype annotation

• Still sending out emails, reached stopping point, for now (emailed most authors within last month)
• Still getting consistent responses from authors
• Working on homepage widget to display top contributors

Micropublications

• Daniela had sent out solicitations for expression data; some people expressed interest, but haven't heard back
• We could take the phenotype form and modify for micropublication