WormBase-Caltech Weekly Calls

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Feb 4th, 2021

How the "duplicate" function works in OAs with respect to object IDs (Ranjana and Juancarlos)

  • A word of caution: when you duplicate a row, for those OAs with Object IDs (eg., WBGenotype00000014) note that the object ID gets duplicated as well and does not advance to the next ID like the PGID does
  • If you do use the "duplicate" function, remember to manually change the Object ID
  • We can implement checks to make sure distinct annotations/objects don't share the same ID

GAF Wiki and headers

Missing references in expression GAFs

  • ~300 missing from anatomy association file and ~45 missing from development association file
  • Daniela looking into missing refs; many are personal communications or very old papers
  • Will change ?Expr_pattern model to possibly remove ?Author reference and add in a ?Person reference instead
    • 399 objects in WS279 reference an author; Daniela will take a look
  • Would be good to have some reference for those objects in the GAF file on the FTP site; could use WBPerson when ready

Feb 11th, 2021

Alliance Literature Paper Tags

  • What do we definitely want to transfer to the Alliance?
  • Alliance literature group spreadsheet
  • Current flags vs legacy flags
  • Can we map everything to the proposed hierarchy or do we need to add some more classes?
  • Kimberly will review existing tags/flags to sort out what we know we need and what is questionable

Personal communications in Expr_pattern

  • 27 objects missing reference (personal communications)
    • Even if we capture the WBPerson in the Person tag, how are we submitting these to Alliance? The evidence required by the expression JSON spec https://github.com/alliance-genome/agr_schemas/blob/master/ingest/expression/wildtypeExpressionModelAnnotation.json (and other specs) must be a publication, as defined by the publicationRef.json https://github.com/alliance-genome/agr_schemas/blob/master/ingest/publicationRef.json. If there's no PMID for a publication listed as evidence, a MOD ID will suffice for the "publicationId" but we have no WBPaperID created for such objects.
    • One way to solve this: Daniela can go over the list and see if the initial personal communication resulted in a publication later on. One example is Expr181 (expression of cpl-1 in hypodermis and pharynx), communicated via email by Sarwar Hashmi in 2000, Expr450 (expression of cpl-1 in hypodermis, intestine) communicated by Britton in 2001. The pattern was published in 2002 by Hashmi and Britton in 2002 (WBPaper00005099). Daniela can then associate WBPaper00005099 to Expr181 and Expr450.
    • The solution above still does not work for all: An example is lad-2 personal communication from Oliver Hobert, 2002. Later published by Lishia Chen (2008). Removing Oliver’s personal communication will remove evidence of data provenance from the Hobert’s lab. Unless Oliver published this in a paper that was eluded from our flagging system (e.g. flagged SVM negative).
    • Daniela can go over the entire list and contact the authors for such cases.
    • Are personal communications used in other classes?
    • Action item: Daniela will add Persons in the person tag for such communications. Will request a model change to Hinxton. Will ask Magda to populate column 6 of the GAF file with Author data. Will add a request for the DQMs to allow Persons in the 'Evidence' in the JSON in addition to Papers

Author data in Expr_pattern

  • 399 Expression objects have the author tag populated. Most of them were submitted even prior Wen started working on Expr_pattern.
    • out of 399 objects, we have 32 for which the authors partially match. One example is Expr60, which has Bauer as extra author in the .ace file. Bauer is not listed as author in the paper.
    • should we keep the author info and store it in the Person tag? Even if we do, how are we submitting these to Alliance? And should we at all? This is legacy data
    • Decision: we can remove the authors and add in the remarks the historic info

Date tag in Expr_pattern

  • The date tag seems to be populated for objects that have authors (above) to probably capture when the submission occurred.
  • In addition, Date is populated for a large scale submission from Ian hope (2006-03), later published.
  • We can still keep this info as is for WB (currently stored in citace minus) but what are we going to do for the Alliance submission? The tag was used last time in 2006 for the Hope study but prior to this was used in the ‘90s (1990, 1998).
    • We can get rid of date, too. And pull the fo for the ones for which authors do not match

Proposed WormBase metrics page

Feb 18th, 2021

CenGen data

  • How can we incorporate the CenGen data into WormBase pages? i.e. provide users info:
    • Per gene: what cells express this gene?
    • Per cell: what genes are expressed in this cell?
    • May be derived from Eduardo's data processing
  • CenGen has a weekly call: have invited Wen, Daniela, and Raymond
    • Too much for all three to join?
  • Good to establish healthy boundaries for responsibilities
  • Do they want to collaborate or no?
  • We can link to the main CenGen page; once gene-level data is available we can consume and make available
  • Eduardo's tool is one WormBase tool for processing and providing CenGen data; will make them aware
  • Ultimately this data (and its presentation) will need to get into the Alliance; may remain a WB-specific/portal feature for the near future
  • Alaska? Probably won't be maintained

Cleaning up bounced emails to outreach@wormbase.org

  • Many unread messages (~140) in inbox
  • Many of those are bounced emails from AFP pipeline and webinar announcements
  • If relevant people could review those bounced emails and, as appropriate, add people or email addresses to the Omit list using the Omit Form CGI (http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi) that would be appreciated.

Feb 25th, 2021

Expr_pattern clean up

  • Seldom populated tags. Can we move the associated info into remarks and get rid of the tag? This is in view of the Alliance import
    • Protein_description 33 objects
Example: Expr_pattern : "Expr450"
	Gene	 "WBGene00000776"
	Protein_description	 "CPL-1"

	Expr_pattern : "Expr552"
	Gene	 "WBGene00006528"
	Protein_description	 "Tubulin alpha"
    • Sequence 12 objects
Example: Expr_pattern : "Expr12"
		      Gene	 "WBGene00003976"
		      Sequence	 "Z28377|Z28375|Z28376"
    • Laboratory 23 objects -> can infer via publication
Example: Expr_pattern : "Expr87"
	Laboratory	 "ML"
	Gene	 "WBGene00003012"

  • Empty tags. Can remove tags from WB Expression model?
    • Cell -> 0 objects
    • Expressed_in -> 0 objects
    • Protein -> 0 objects
    • Pseudogene -> 0 objects
  • Microarray, Tiling Array, RNAseq associations
    • Microarray, Microarray_results
example: Expr1050000 -Yanai study
Currently accessible via the schema

    • Tiling_array
Example: Expr1040545 - Miller study
Currently accessible via the schema

    • RNASeq
	Expr_pattern : "Expr1142792" - Yanai study
	Gene	 "WBGene00007063"
	RNASeq	 "RNASeq_Study.SRP029448"
Currently accessible  via the  schema
  • Others
    • Historical_gene -> 51 objects. How are historical gene tags treated for other classes in Alliance?
    • EPIC -> Ad hoc Tag for Murray, no correspondence with method ontology terms
    • Species -> what are we doing with non elegans annotations?
    • MovieURL -> 32 - Mohler -> move to movies