Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Xiaodong is writing up an abstract, will send around before submission
 
* Xiaodong is writing up an abstract, will send around before submission
 
* Xiaodong will run a curation tutorial for Chinese speakers
 
* Xiaodong will run a curation tutorial for Chinese speakers
 +
 +
 +
==Jan 22==
 +
=== ad hoc curation of tier III species (Mary Ann)===
 +
WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis?
 +
http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf
 +
 +
=== Complex Gene Loci (Mary Ann) ===
 +
e.g. lin-15A/lin-15B
 +
 +
unc-17/cha-1
 +
 +
We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g.  lin-15A lin-15B complex loci.
 +
 +
nb. Maybe hard to discuss w/o Paul Davies.
 +
 +
===micropublication===
 +
*Daniela starting to work on author submission forms
 +
*Requirements?  Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene

Revision as of 19:43, 22 January 2015

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings


2015 Meetings

January 2015

January 8, 2015

Community annotation

  • author participation
    • Cecilia: still lots of work, need to manually process data submitted by authors
    • old data kept for history and for comparison
    • people mess up institution names - institution field on submission form being changed to a controlled vocabulary
    • campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc.,
    • add example address
    • ~10 author submissions a week
    • most curation involves extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but information still needs to be parsed
    • can we mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- (1) easy- people associated with a laboratory, (2) difficult- people not in a registered lab

Cross-product development

Raymond

  • embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
  • wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL
  • Uberon has elegans anatomy

Gary

  • starting to work with Chris and Karen on developing cross-products, still in exploration phase
  • not looking at OWL yet
  • will get relationships from Raymond

Sequence feature curation

Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready, Mary Ann/Gary will start curating

Rose alleles

  • 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
  • phenotypes were only reported for a small fraction

CGC strains

Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques

WB WBook chapters

Main outline here- note this document cannot be edited, people can create their own shared docs for their respective papers

  • Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)

here

  • Pathways and Processes (Karen) here
  • Expression (Daniela)

Micropublication

  • Hobert- micropublication for expression = small facts, which are data that will never be published (Daniela working with Hobert on these)
  • Community annotation not linked to a publication
  • a couple models for WB dealing with the micropubs
    • WB captures all submissions blind and posts them
    • WB reviews submission - curators decide which micropubs have value
  • need to establish microattributions to increase the value of submissions
  • involve semi-peer review through automated fact review requests to scientists who've worked on the gene, cell, entity, etc.
  • need to set up a pilot, to get a feel for the amount of participation/work this tool will be

Picture curation

  • for topic curation
    • want to annotate figures with genes - involves model change
    • want dynamic display with slide show, different highlighted figures - need to work with webteam
  • community voting - crowdsourcing - need to work with webteam
  • WB-blessed image represented through wikipathways

Kimberly

Continuing work on the new GO model

Juancarlos

  • management of automated descriptions with Ranjana
  • phenotype requests through RNAi and allele phenotype done in december

Automated descriptions

  • playing with pulling out useful data to add to description automation (James and Ranjana)


January 15, 2015

New expression objects and pictures

  • Cross-species comparison of developmental gene expression
  • Have life stage annotation
  • Microarray experiments
  • Do we have data on significant differences from C. elegans? Can we get the analysis or algorithm?

Neuro anatomy

  • 3 ways to access neuro-connectivity data
  • ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity browser
  • We would like to adopt Nikhil's browser (for neural connectivity AND the cell lineage browser); we need to act before it disappears

FPKM RNA-Seq data display

  • Should we suggest splitting the data display by tissue, life stage, treatment, etc.?
  • Gary Williams is responsible; need to talk to him

Heavy metal toxicity/response

  • New topic, all papers have been checked
  • Need to send list of relevant genes to Hinxton
  • Curators can now flag figures relevant as topic diagrams

Phenotype picture curation

  • We will begin to collect pictures for phenotypes
  • Will require model changes

Phenotype OA Strain fields

  • "Parental strain" autocomplete field added to TAB 2 of Phenotype OA
  • Plan is to put parental strains in the Phenotype_info hash
  • Natural isolate strains can be directly annotated with phenotype?

BioCuration meeting in April

  • Xiaodong is writing up an abstract, will send around before submission
  • Xiaodong will run a curation tutorial for Chinese speakers


Jan 22

ad hoc curation of tier III species (Mary Ann)

WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis? http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf

Complex Gene Loci (Mary Ann)

e.g. lin-15A/lin-15B

unc-17/cha-1

We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci.

nb. Maybe hard to discuss w/o Paul Davies.

micropublication

  • Daniela starting to work on author submission forms
  • Requirements? Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene