WormBase-Caltech Weekly Calls January 2017

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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

January 19, 2017

SObA graph for Gene Ontology

  • Juancarlos and Raymond asking for feedback on GO SObA graph
  • Kimberly: Can we create graphs for subsets of annotations (manual vs. automated)?
    • Raymond: It's doable as a standalone graph, but may be difficult to make an option embedded within the core display
    • May be a way to display IEA annotations separately from non-IEA annotations
    • Raymond: Can develop a personal view for Kimberly to visualize manual vs. automated annotations
  • Three root terms for GO, displayed side-by-side in the same graph; root nodes are different sizes and not necessarily displayed aligned
  • May be able to force the root nodes to be the same size
  • May want to show/hide individual roots; doable although unclear how difficult to implement
  • GO function and component are likely to be smaller networks than process
  • Pulling data from GAF into Solr
  • Can this be adopted for the AGR portal? Yes

WormBase workshop at 2017 IWM

  • Ranjana organizing
  • Discuss ideas with Ranjana
  • Have 1.5 - 2 hours
  • Will want to discuss micropublications and community annotations
  • We haven't had mirrors in a long time: discuss Datomic for people who want to query? Yes, brief announcement

User Survey

  • We may want user surveys to prepare for grant writing, progress report
  • Could send out to users by May?
  • What to focus on: performance, data types, usability
  • Could have multiple short surveys
  • What one question would we want answers to help with design decisions?
  • Do we want (eventually for AGR) a professional surveyor?
  • Are our services meeting user needs?
  • We can take a closer look at user logs; see what data, widgets, tools used most frequently (least frequently)
  • We could create focus groups to get feedback from users on specific topics (30 minute sessions during poster sessions, for example); maybe at booth? during meal time?
    • Would want to post a schedule with dedicated locations
  • Could have WormBase hats, brightly colored ;), to indicate to people that we're WormBase staff

Disease data display on AGR portal gene page

  • Working out a way to drill down from a summary view down to detailed table view
  • Need to make sure it is intuitive and non-jargony for end users
  • Yvonne Bradford drew up some mockups that represent a ribbon or heatmap display of annotations to disease categories for experimental models, etc.
  • We do want a SObA graph; could possibly create a SObA graph that represents annotations to a gene AND all of its orthologs

First LEGO call

  • This Monday (Jan 23) 11am Pacific

January 26, 2017

GO-CC annotations to paper term info in OA

  • Daniela working on with Juancarlos

Disease working group

  • Working to finalize the DAF (disease association file)
  • Having extra meeting tomorrow
  • Will then hand over DAF format to Kevin Howe (WB Data Quartermaster)
  • In general, Kevin would prefer AGR files to be generated from the WB build process

Expression data working group?

  • Daniela asking about an expression working group
  • We don't have one currently, but one could be generated, although it may not make it into AGR portal 0.3, 0.6 or 1.0

Coherence, Consistency, and Continuity working group

  • Working on a standard for table display in AGR portal
  • Asking for standard functionality
    • Table filtering, by column
    • Table sorting, including sort order
    • Paginated, choosing number of results per page
    • Download options, tab-delimited and other formats
    • Link to Intermine, to view, save and manipulate table and lists
  • Currently WormBase has insufficient means to download some lists of results, for example downloading list of RNAi's that cause a lethal phenotype on the "lethal" phenotype page
    • WB points users to FTP site, without specifying a file or how to parse

WormMine vs AGR Intermine

  • Is Paulo working on shared/AGR Intermine or just WormMine? We think just WormMine
  • There was an issue with making orthology calls which may have interfered with integrating worm data into common Intermine