WormBase-Caltech Weekly Calls

From WormBaseWiki
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings


2016 Meetings

January

February

March

April

May

June

July

August

September


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

Noctua

  • 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)

Transgenome

  • 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

Micropublications

  • Trial with uploading Nemametrix data; aiming in putting data for the next upload (2-4 micro)
  • 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)


October 20, 2016

AGR search prototype

  • URL: http://search.alliancegenome.org/
  • Searching "WNT4", then choosing category "Gene Ontology" provides facets for species
  • Question is: how are these species associated to the GO terms?
  • Associated genes could have a species prefix or indicator

AGR gene page

  • There was resistance to creating AGR gene pages
  • Some see it as redundant with what is already available elsewhere
  • Although we may want to build a foundation gene page and develop from there
  • Maybe MODs could develop their respective gene pages to look more like an AGR standard
  • One main reason to create AGR is to have a consolidated, consistent, standard view for data, including genes
  • Would be good to assemble a user group (or intended audience) to receive feedback from
  • Use Case working group has put together some ideas for a gene comparison page, keyed off of orthology group:

Citace upload

  • Next Tuesday, October 25th 10am

Curator call next week

  • Topic: curation styles
  • Curation by paper, by topic, etc.
  • Curation inter-dependencies
  • Daniela will present for WormBase
  • Send ideas to Daniela for her to cover
  • Send older slides with relevant information to Daniela


October 27, 2016

AGR Portal Use Case working group

  • Working group had call yesterday with Paul Thomas and Judy Blake
  • Decision was made to abandon the idea of displaying "orthology groups"/"homology groups"
  • Instead we will display a gene-centric page with comparisons of focus gene data with data from all orthologs and paralogs
  • Paul Thomas' group had built a prototype for pulling out orthologs with GO info: http://umodtest.usc.edu/
  • This prototype returns closest orthologs of a focus/query gene and then displays a table of all GO annotations for all genes
  • We would want to display orthologs for a focus gene as well as paralogs
  • This display is very similar to the gene comparison page mockup the use case working group had been envisioning, except now the focus will be a single gene, not a PANTHER subfamily

Disease-Strain curation

  • Ranjana working on disease-strain associations for WormBase
  • Disease group working on the DAF (disease association file) format
  • Ranjana will discuss the strain curation pipeline with Mary Ann and Karen
  • Will want a unique ID for each strain, especially for when we merge strain data with other MODs
    • One solution is to just prefix the strain name with "WBStrain:" to indicate it came from WormBase

Kimberly visiting CA

  • Kimberly will be at CIT next Wednesday
  • Noctua developers will be around to discuss integration with Textpresso
  • Kimberly can send around schedule for the GO meeting
  • Would be good for curators to setup a Noctua account before the Noctua workshop (on Nov 7)
  • Kimberly will also be at CIT on Tuesday Nov 8th

Paper editor CGI

  • Michael had some issues with the paper editor
  • Seems to be working now

November 3, 2016

Micropublication update

  • First Nemametrix micro in for WS257
  • Two lined up for WS258
  • Karen and Daniela in touch with e-publishing platforms (HighWire [1], Collaborative knowledge foundation[2]), to set up collaborations for the Micropublication: biology e-journal [3]
  • Discussing putting worm breeder's gazette articles into micropublications
  • Collaborative knowledge foundation is a non-profit publisher, some former member of Highwire
  • Would be good to have a faster way to display micropublications (standard WB pipeline needs at least 4 months)
    • Could use content management systems (CMSs)
  • Maybe will propose a workshop for the 2017 international C. elegans meeting

Intellectual (Person) Lineage

Tim Schedl visiting WB tomorrow

  • Will come to WB CIT around 11:30am