WormBase-Caltech Weekly Calls May 2011

May 5, 2011

Citace upload

• Using current citace release (WS226) for Progress Report

Pictures

• Daniela did not actually curate ~7000 pictures this month ;)
• Script to fetch pictures automatically

Snehal starts next week

• working on phenotype curation
  • 90 genes >= 10 publications
  • Of these 90, 54 with no annotated phenotype
  • 20,000 genes with RNAi data
• Concise Descriptions? May be appropriate
  • Prioritize by genes that currently have no description but have new papers
• Picture curation?
• Learning an ontology may be difficult, but she can stick to familiar material

Aldrin

• Karen, Raymond, Chris will talk to Todd
• Lineage browser for ontologies?
• Cell lineage browser? Capture multi-parentage issues

Ranjana - Preplanning WormBase side meetings at IWM?

Periodically sending someone to different sites

• E.g. Someone from Caltech goes to Hinxton, etc.

Practice Talks before International Worm Meeting

• on Monday before meeting

May 12, 2011

Example of Bandana for International Worm Meeting

• Looks good!

GO Consortium meeting next week

• Paul, Michael, Ranjana, and Kimberly going
• Discussion about tools (Juancarlos?)
• Section in meeting agenda to discuss curation
  • Textpresso-based curation
  • Ontology Annotator
  • Demo by Kimberly or Ranjana?
  • Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos)
  • Discuss what's been proposed in the grant
  • What does the consortium want? Brainstorming/Fantasizing
  • People are likely partial to their own tools
  • Make use of the best parts of everyone's tools
  • Are others using flat/text files or web-based/java-based tools? Mostly web-based
  • Phenote? Funding? Bio-Portal e-mail?
  • PAINT tool (Phylogenetic Annotation and INference Tool) (http://wiki.geneontology.org/index.php/PAINT)

Progress Report

• Paul has received some reports, but not all, yet

Picture curation

• Started receiving permission from Elsevier!!
• Blanket-permission for 11 journals
• Publicly display list of cooperating journals online

Talks at the Int Worm Meeting

• Paul S listed for a Plenary talk during Workshop
• Two Wormbase Plenary talks

Snehal

• Concise descriptions
• Kimberly helping
• Will get into phenotypes soon

Juancarlos waiting to hear back from some people about OA

• People need more time to test
• Karen has encountered some issues; needs to reproduce
• Ranjana - loads slowly?
• Mangolassi issues?

Genetic Interactions

• Group met on Tuesday
• Made headway on genetic interaction organization
• Add "Additive" type term and "No Apparent Interaction", etc.

Paper pipeline

• Kimberly & Juancarlos working on
• Documented on Wiki
• CGI's still being used?
• Remove outdated or unused CGI's?

Rewriting script from Jack Chen

• Neuron connection search
• Inroad to working on more web-interface topics

Adding interaction datasets into WormMart (Xiaodong and Ruihua)

Gene interaction dumping script (Raymond/Todd)

Strain Display

• Karen doing queries at CGC
• How many genes represented in CGC strain list?
• Protein-coding genes with alleles in strains?
• 12,000 genes that are NOT represented in CGC
• Discrepancy wrt alleles; negative in AQL query, but present on site
• Strains with LOTS of alleles; how to handle?
• Polymorphisms vs. alleles

Aldrin Montana working over the summer

• We invited him to visit
• We'll come up with projects
• Web team fully involved in web site
• Help with minor GO issues (Ranjana)
  • Requires knowledge of Perl
  • Non-C.elegans species
  • InterPro-to-GO mapping
  • Export pipelines for other species?
  • Maybe small project; requires more communication than coding?
• Raymond could help provide projects
• Would be nice to use PAINT across the nematodes for annotation

New Web site (Todd)

• Web team wrapping up various projects
• Polishing user interface
• Abby working on user interface
• Todd working on production environment
• Norie working on code that interfaces with database
• Release beta version at International Worm Meeting
• Working with Kevin Howe to standardize formats of files used during build
• Can now host new data for new species

May 19, 2011

Login System for people to submit and modify (WBPerson) personal information

• How to validate that someone registering for the site is the actual person?
  • Use e-mail address, although some people don't have e-mail addresses; snail mail?

Poster Session Help Desk for International Worm Meeting

• Wen- yes, all set
• People will bring their own laptops
• Wen will make a Wiki page for people to sign up for sessions

Aldrin visiting

• June 16th/17th OK for people
• We could start making a list of possible topics for Aldrin to work on

Clone Model Update

• Working with current clone model to test adding plasmid objects
  • Works OK, but will probably want a couple of new tags
  • One idea is to have a tag that links nematode-specific sequence in the plasmid to genomic regions and GBrowse viewer
• Test plasmid objects and ideas for genome alignment sent to Paul Davis, waiting to hear back

Inter-Release Patch files?

• Still need to work out, but should wait until the new website has stabilized

May 26, 2011

Genetic Interactions (Interactions Group)

• Made headway on genetic interactions organization and nomenclature
• We have talked about (previously) separating physical, genetic, predicted, and regulatory interactions into different models
  • This will need more time and work
• We can immediately add the new genetic interaction type tags to the interaction model
• New types include: Enhancement/Suppression, Complex, No Apparent Interaction/Additive, Asynthetic
• BioGRID will use their own curation strategy and pipeline, but may eventually incorporate our curation approach

Concise Descriptions (Snehal)

• Avergaing 9 genes/week
• Prioritized on new publications
• Also working on FlyBase GSA markup (e.g. false negatives)

Picture Curation (Daniela)

• Have authorization from ~50% of Elsevier journals
• Still need Developmental Biology access (many C. elegans papers)

Textpresso for Cell Function (Raymond)

• Have scheme for decent precision (still accumulating numbers)
• Recall?
• Review papers are, by default, tagged as primary literature and can affect the numbers
• Textpresso needs to add a review tagging step (earlier in the pipeline)
• Search done with keywords like "mosaic", anatomy terms, site of action, etc.
• Many anatomy terms are not very specific (e.g. E, AB, MS, etc.)
• Can give Michael new category list criteria for Textpresso (cleaner than current from postgres table pap_primary_data)
  • Can have inclusion & exclusion criteria

User Interface Query Tool (Raymond)

Human Disease Curation (Ranjana)

• C. elegans as a model for human disease
• Textpresso script identifies C. elegans papers with relevance to human disease
• Where should this information go? Curation status form?
• Right now, everything is simply writing to a text file that Arun has setup
• Connect Arun's script to Curation Status form?
• OMIM tags
• Accession/evidence tags?
• Apoptosis working group - identify apoptosis genes in various model organisms

KOG data

• What should we do about it?
• EggNOG?
• Michael Paulini will change the data model for homology groups
• Old data comes from citace; we need to reformat the data if we want to keep
• Remove old KOG data entirely and replace with EggNOG data?
• Any new data coming from Caltech? No
• Transfer data to Hinxton

Author Flag (First-Pass) Forms

• Who is taking care of/in charge of this (curators)?
• Do curators look at them? Yes
• Gary prioritizes RNAi papers based on them, Xiaodong uses it, Daniela uses it
• Should we remove outdated/unused data types?
• We get the author form results before we have the PDF
  • Check is in place now so author is not e-mailed until we have the PDF
  • Have authors send us the flags and the PDF?
• Karen will coordinate a clean up process
• Group needs to participate in evaluating the automation pipeline

SVM performance

• Retraining SVM
• SVM performs most poorly on Expression Patterns and Gene Regulation
• RNAi SVM performs best
• Subtract papers that are already curated from the paper pool
• Let Ruihua know if there are any thoughts as to how to better train the SVM
• First-pass forms identify some papers that are missed by SVM (maybe help?)
• BioGRID interest? Can we use SVM on abstract only? Mostly use entire paper; could try abstracts
  • Hard to get access to full text for all papers
  • Good to encourage all databases/groups to get access to full text
  • Abstract SVM depends on what is acceptable Recall/Precision values

GSA for FlyBase (Karen/Snehal)

• GSA markup from FlyBase is not as good as it could be
• Snehal may focus more on GSA for the time being

International Worm Meeting WormBase Bandanas

• Which to choose?