WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2019 Meetings










October 3, 2019

SObA comparison graphs

  1. What terms (nodes) are annotated to gene 1 and what terms to gene 2
  2. For a given term, what is the relative number of annotations between gene 1 and gene 2.
  3. For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
  • # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
  • Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
  • In either case users need a good legend and/or documentation
  • Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes

Germ line discussion

  • Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
  • Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
  • Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)

Script to remove blank entries from Postgres

  • Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
  • Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
  • Does anyone object to removing these entries throughout Postgres?
  • Juancarlos will remove all the empty fields identified by his script

October 10, 2019

Biocuration 2020

  • Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
  • Dates: Sunday May 17th to Wednesday May 20th, 2020
  • Will have 3rd POTATO workshop
  • Meeting website
  • Key Dates
    • October 31, 2019 - Paper Submission Deadline
    • January 24, 2020 - Abstract and Workshop Submission Deadline
    • March 6, 2020 - Notification of Acceptance
    • April 6, 2020 - Early Bird Registration Ends
    • May 8, 2020 - Registration Deadline
  • Academic ISB Member, early bird registration fee is $250
  • Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference

ICBO 2020

  • International Conference on Biomedical Ontologies
  • Meeting website
  • Held in Bozen-Bolzano, Italy
  • 16 - 19 September 2020

SObA comparison tool

Textpresso derived paper connections

  • For example for strains and constructs, maybe anatomy terms?
  • May want to flag Textpresso predictions (as opposed to manually connected)
  • Couple of options:
    • 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
    • 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
      • A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
      • Do a diff so that Textpresso pulls up only additional papers (not already associated)?
    • 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
  • Transgene pipeline:
    • Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
    • Another script, captures Ex transgenes as well, automatically connects to construct objects
    • WB only displays verified papers; unverified (predicted) associations are not dumped
  • Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
  • Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
  • Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
  • Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities

October 17, 2019

Alliance All Hands Face-to-Face

  • Flights: has everyone already booked? No, not yet
  • Any coordination of flights from Pasadena/LA?
    • Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings

SObA Comparison Tool

  • http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
  • Prototype discussed last week, updated with feedback from prior discussions
  • Would this be a stand-alone tool discoverable under the Tools menu?
    • Possibly; could be a gene page widget, but may be out of place
    • Stand-alone tool probably makes more sense
  • Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)


  • Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
  • For example, share GO SObA graph for other species
  • Will need to be dependent on a SOLR server with all species data
    • Raymond has run into problems trying to setup his own SOLR server
    • Raymond asked Seth Carbon if we could us GO server, but he prefers not
    • Appear to be software versioning issues, possible memory issues

GO meeting

  • Kimberly can give update on recent updates to GO from the recent GO meeting
  • Slides are shared online

"all stages Ce" life stage

  • Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
  • "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
  • Should we:
    • 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
      • Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
    • 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
  • Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
  • Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
  • Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually

Gene class missing description

  • The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
  • Jae or Ranjana will create a ticket and assign it to someone at Hinxton

October 24, 2019

Textpresso links from WB page References widgets

  • Discussed with Sibyl and Adam on last week's Textpresso call
  • Sibyl working on mockups for including Textpresso derived paper associations in the References widget
  • Had originally considered for the following classes
    • Strain
    • Gene
    • Variation
    • Transgene
    • Construct
    • Anatomy_term
  • Sibyl asks: could we put this link in all References widgets in WB?
    • Classes with References widgets include:
      • Antibody
      • Clone
      • Construct
      • Expression cluster
      • Expression pattern
      • Gene
      • Interaction
      • Life stage
      • Rearrangement
      • RNAi
      • Strain
      • Transgene
      • Variation
      • Analysis
      • Molecule
      • Process
    • Any Textpresso search on internal WB identifiers, like WBInteraction000###### or WBRNAi00######, or on long complicated names is certainly meaningless, so the following classes are probably ruled out:
      • Antibody
      • Expression cluster
      • Expression pattern
      • Interaction
      • RNAi
      • Analysis
    • Otherwise it could probably be beneficial to include the additional classes, searching on public name:
      • Clone
      • Life stage
      • Rearrangement
      • Molecule
      • Process
  • Created Google Doc summary here
  • So the current list of candidate classes is:
    • Strain
    • Gene
    • Variation
    • Transgene
    • Construct
    • Anatomy_term (no References widget currently)
    • Clone
    • Life stage
    • Rearrangement
    • Molecule
    • Process
  • Eventually, we may want to incorporate papers found by Textpresso directly into the References widget
    • We would want predicted associations to be made explicitly so
    • We could populate the database, but there are reservations about doing this

Updates from GOC Meeting, Berkeley

  • Status of MOD Imports into Noctua
    • Starting with WormBase and MGI GO annotations into GO-CAM
    • GPAD/GPI is standard import format
  • GO-CAM Specifications and Validation
  • Noctua Form
  • Pathways2GO
  • Priorities for next 6 months:
    • Create gene-centric Noctua views
    • Create pathway-centric Noctua views

October 31, 2019

Alliance 2.3 release

  • Are variants listed on gene pages? Yes, in Alleles and Variants table
  • Should we be listing strains as models if they don't have phenotype or disease data?

New SObA tools

  • Gene comparison tool
    • Select a data/ontology type, type in two genes, and graph will be generated/displayed
    • Nodes colored red and blue respective to annotations from each gene
      • Absolute count slices - shows percentage of annotations to that node coming from each gene
      • Relative count slices - shows percentage of annotations to that node compared to all annotations for that gene
      • Percentage slices rendered after binning/rounding; will update to not round (be more precise) so that 80% doesn't fill the node portion
    • Amigo/Solr now using MD5 Checksums instead of text strings; loss of data, may request rollback or some feature that can restore data; SObA now "frozen" at an older release of Amigo because of this
    • Clicking on a node gives a total count of annotations to that node (direct and inferred); can we make an easy way for users to see all those annotations? Maybe provide a pop-up table that can be viewed and downloaded/exported?
    • Node pop-ups for "Relative count slices" view says, for example, "75% of gene total". This is confusing; might be better to say "75% of total annotations to gene" or something.
    • User interface updates
      • Right now, graph is automatically rendered after entering second gene; genes with no data do not show up in autocomplete
      • Will implement a "Submit" button so that user can make selections in various orders and then confirm
      • Problematic to allow a lookup on all possible genes because the tool is indexing the Solr database; if no data for a gene (for a data type) the gene does not appear to exist; Will change lookup to look at Postgres on Tazendra (or some other complete source)
      • We eventually want a gene name lookup service/API for the Alliance to provide all gene names for all species
      • It would be better to either:
        • (A) provide clear text that explains that a gene will not appear in the autocomplete if it has no data for the selected data type
        • OR (B) allow a user to type in their gene, but if it doesn't have data indicate so in the autocomplete (will need to consider when genes are entered but then user switches data type; will it then perform another lookup and indicate presence of data or not?)
  • Enriched term list tool

November 7, 2019

?Genotype class

  • Working data model document
  • Several classes have a "Genotype" tag with text entry
    • Strain
    • 2_point_data
    • Pos_neg_data
    • Multi_pt_data
    • RNAi
    • Phenotype_info
    • Mass_spec_experiment (no data as of WS273)
    • Condition
  • Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
    • Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
    • Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
    • Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
    • Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
    • Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
    • Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
    • Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
    • Reference to parent strain, like "Parent strain is AG359"
    • Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
    • Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"