Difference between revisions of "WormBase-Caltech Weekly Calls"
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Revision as of 17:07, 19 January 2017
Contents
Previous Years
2017 Meetings
January 5, 2017
BioCurator meeting
- Who from WormBase will go?
- Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go
- Daniela maybe for micropublication
International C. elegans Meeting
- June 2017
- Whether all WB staff go depends on whether we have an all hands meeting before/after
- Plenty of things to present; AGR stuff etc.
Citace upload
- Prepare files by 10am on Tuesday, Jan 10
LEGO curation
- Kimberly working on different C. elegans models
- Working on several pathways simultaneously
- Should be in production soon (this year), fully evidenced
- Full benefit may not be apparent until AGR has LEGO fully integrated
- Working out how inferred annotations propagate from Noctua/LEGO model to GAF
- MGI creating many LEGO models
- How are curators, that went to training, using LEGO?
- Curation level view may not be amenable to general biologist/user viewing
- What is the best existing pathway display? WikiPathways? Protege?
- GO people (Seth, Chris M., Suzi etc.) are working on display, but have limited resources for this
- Maybe we could work with WikiPathways team?
- Pathway studio at RGD? Manually generated
- Should WB have a LEGO call? Yes, probably
- Curators may need access to Protein2GO for full curation/inference by sequence similarity
- How do we/should we resolve parallel pipelines for curating cellular component data (Go versus Expression pattern)?
- How do we accommodate specific versus general processes? E.g. specific versus general cell division
- We would like a mechanism for a LEGO curator to pull relevant data from GAF
- We would like curators to focus on pathway perspective of curation, where authors can submit experimental details with a potential automated or semi-automated mechanism to bridge the gap
Expression widget
- Daniela and Sibyl working on a more compact display of the expression data widget on gene pages
- Should we keep subcellular localization in the expression widget? Yes
SObA for Gene Ontology
- Raymond and Juancarlos working on
- First for WormBase, eventually want for AGR
- For GO data, will have three different roots (for each branch of GO); One DAG for each
- Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.
- Would be great to have a comparative view mechanism
January 12, 2017
Caltech LEGO Call
- Confirm time: Mondays, 11am PST (2pm EST/7pm GMT)
- Start January 23rd
- Format?
- Start with curation of one paper together?
- Curators then select individual topics?
Switching website to run off Datomic
- Juancarlos joining biweekly call on Wednesdays with Adam, Matt, and Sibyl
- Juancarlos working on Person page widgets currently
- Intellectual lineage graph will need to be rewritten in Clojure
- Web team is working out the file/directory structure to organize widget generation
- Is the Datomic database denormalized? To what extent? No, not really
- This affects how we might eventually write into Datomic from our curation database
- May be best for Caltech to keep a Postgres curation database in parallel to Datomic (and eventually sync nightly)
- This may also be best with AGR as well
Biocuration meeting 2017
- Who's going? Ranjana, Chris, Raymond, Mary Ann, Daniela (if she gets a talk)
- Ranjana - automated descriptions
- Raymond - SObA graph
- Chris - Genetic interactions
- Mary Ann - Community curation
- Daniela - Micropublications
Community curation presentation on AGR curator call
- Chris and Val Wood presented; minutes are here- AGR minutes
- WB community curation numbers
- 321 papers solicited and community curated (Phenotype OA)
- 417 papers community curated in total (Phenotype OA)
- 313 unique community curators (Phen OA); average 8 annotations per curator
- 64 papers solicited and community curated (RNAi OA)
- 74 papers community curated in total (RNAi OA)
- 61 unique community curators (RNAi OA); average 16 annotations per curator
- 3324 annotations total; 2969 valid and confirmed
- 2111 solicitations gone out; 16% response rate
Val presented some information on how complete contributors were:
- 1990s were getting 10 annotations/paper, in most recent years are now getting 50 annots/paper (years are publication years)
- Curation quality - users often omit a data type, but for what they do curate, they are generally very accurate, and often request more specific terms
Chris suspects ~20% authors are complete in their phenotype curation of their paper.
Pulling WB data into LEGO models
- Phenotype data requires a mapping step to map alleles and RNAi to genes
- How might we crowd source or get low cost curators to curate bulk data? Followed by expert curation for LEGO models
- May be best for curators to take on specific topics of biology
January 19, 2017
SObA graph for Gene Ontology
- Juancarlos and Raymond asking for feedback on graph