WormBase-Caltech Weekly Calls

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Previous Years

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2015 Meetings

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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

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