WormBase-Caltech Weekly Calls

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October 6, 2016

Citace upload

  • Tuesday, October 25th, 2016

Automated descriptions

  • Ranjana working with Juancarlos to run and update automated descriptions pipeline

Intellectual lineage

  • First draft up on WormBase development site


  • Raymond trying to annotate axioms for anatomy function
  • How to connect cell types in different organisms to those in C. elegans anatomy ontology?
  • Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
  • Raymond attempting to use Noctua to draw relationships between anatomy terms and function
  • There's a distinction between annotating to an instance vs. to a class
  • Raymond worked on modeling a statement on excretory cell function from WormAtlas
  • Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable

Expr_pattern model change

  • Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
  • Would be inline with "Reporter gene", "In situ", "Antibody", etc.
  • Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
  • Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
  • Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
  • Maybe we'll just stick with a "Genome_editing" tag

October 13, 2016

Strain requests

  • Ranjana sending strain requests to Mary Ann
  • Mary Ann processing published strains requested by Ranjana

GO meeting

  • Registration is now setup
  • Sarah (Torres) could register all WB CIT participants
  • Kimberly is helping organize

AGR Portal Use Case working group update

  • Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
  • Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
  • Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
  • We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
  • We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
  • Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
  • We'll eventually want to pull data directly from OMIM and GO

Extending SPELL virtual machine

  • Has a lot of data; may be contributing to SPELL downtime
  • Could possibly move to the cloud, but we would need a machine in the cloud
  • Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
  • Possibly SGD could run a worm instance on their machine(s)


  • Junacarlos finished parsing the transgenome data with Daniela
  • Checking parse output numbers with the Transgenome group
  • Will the expression data be dumped out in the expression GAF? Yes, should be
  • Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
  • Some Expr_pattern objects can be linked to WBPerson, if not a WBPaper
  • Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project
  • Raymond suspects issues with it; what if users cannot trace data back to source (by looking up the paper)?
  • Would be best to link directly to the respective Transgenome database page when displaying their data
  • Notes can be added to release notes that the Transgenome data has been added to the database


  • Trial with uploading Nemametrix data; hopefully finished by end of month
  • Added micropublication type in the ?Paper class
  • Micropublications will acquire WBPaper IDs
  • Previous micropublications were only ?Expr_pattern objects; now will be ?Paper objects
  • Ideally micropubs. will be indexed by PubMed and enter the WB pipeline through the normal paper route
  • Question: create WBPaper objects as soon as accepted? That is plan for now
  • Micropubs. will first be hosted by WormBase, but may move to an independent repository (Micropublication: biology)
  • Will we display images/figures from micropubs. only or for all papers? We'll need to wait and see
  • Could we accommodate any digital data to associate with the micropub.? E.g. data points, plasmid maps, etc.
  • Micropubs. text will be marked up as much as possible; what about making all sentences OWL statements?
  • Would this be changing the way that authors write papers? Maybe, but should be independent of core micropublication pipeline
  • Each micropublication/data/result could be combined as modules to create a larger, more comprehensive narrative
  • There is a notion of a "millipublication" that could be a larger narrative from collected micropublications
  • One original idea was that micropublications would capture data that people would not otherwise want to publish
  • Data submitted as micropublication will not be able to be submitted as another publication later but will be cited as data point
  • Micropubs. will be considered primary research article, not just an abstract (equivalent to meeting abstract)