Difference between revisions of "WormBase-Caltech Weekly Calls"
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== September 1, 2016 == | == September 1, 2016 == | ||
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=== Working group discussions === | === Working group discussions === |
Revision as of 17:09, 1 September 2016
Contents
Previous Years
2016 Meetings
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
Citace local upload August 30
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
September 1, 2016
Working group discussions
- More clear about issues surrounding orthology sets
- ZFIN has protein curation that may be becoming a bit out of date
Single-cell RNA profiling
- We've been curating some data, but not clear how to display the data
- Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
- Genes that are detected at convincing levels (present call) in cell/tissue
- Should we display expression data that we do not (or cannot) update differently from other data
- Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
- Could capture quantitative assessments; transcripts per million, etc.
- Should we provide an analysis of raw data to users to perform their own comparative analyses
- Bob Goldstein's group prepared software tools in their paper; could we make use of them?
- Big question: how do we handle divergent (expression) data?
- David (Angeles) working on an expression data analysis pipeline
- Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
- There's difficulty in reconciling small and large datasets (or different data types)
- Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
- In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage