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| | [[WormBase-Caltech_Weekly_Calls_April_2011|April]] | | [[WormBase-Caltech_Weekly_Calls_April_2011|April]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_May_2011|May]] |
| − | == May 5, 2011 ==
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| − | | |
| − | Citace upload
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| − | *Using current citace release (WS226) for Progress Report
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| − | | |
| − | | |
| − | Pictures
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| − | *Daniela did not actually curate ~7000 pictures this month ;)
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| − | *Script to fetch pictures automatically
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| − | | |
| − | | |
| − | Snehal starts next week
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| − | *working on phenotype curation
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| − | **90 genes >= 10 publications
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| − | **Of these 90, 54 with no annotated phenotype
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| − | **20,000 genes with RNAi data
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| − | *Concise Descriptions? May be appropriate
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| − | **Prioritize by genes that currently have no description but have new papers
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| − | *Picture curation?
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| − | *Learning an ontology may be difficult, but she can stick to familiar material
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| − | | |
| − | | |
| − | Aldrin
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| − | *Karen, Raymond, Chris will talk to Todd
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| − | *Lineage browser for ontologies?
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| − | *Cell lineage browser? Capture multi-parentage issues
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| − | | |
| − | | |
| − | Ranjana - Preplanning WormBase side meetings at IWM?
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| − | | |
| − | | |
| − | Periodically sending someone to different sites
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| − | *E.g. Someone from Caltech goes to Hinxton, etc.
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| − | | |
| − | | |
| − | Practice Talks before International Worm Meeting
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| − | *on Monday before meeting
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| − | | |
| − | == May 12, 2011 ==
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| − | | |
| − | | |
| − | Example of Bandana for International Worm Meeting
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| − | *Looks good!
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| − | | |
| − | | |
| − | GO Consortium meeting next week
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| − | *Paul, Michael, Ranjana, and Kimberly going
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| − | *Discussion about tools (Juancarlos?)
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| − | *Section in meeting agenda to discuss curation
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| − | **Textpresso-based curation
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| − | **Ontology Annotator
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| − | **Demo by Kimberly or Ranjana?
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| − | **Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos)
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| − | **Discuss what's been proposed in the grant
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| − | **What does the consortium want? Brainstorming/Fantasizing
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| − | **People are likely partial to their own tools
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| − | **Make use of the best parts of everyone's tools
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| − | **Are others using flat/text files or web-based/java-based tools? Mostly web-based
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| − | **Phenote? Funding? Bio-Portal e-mail?
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| − | **PAINT tool (Phylogenetic Annotation and INference Tool) (http://wiki.geneontology.org/index.php/PAINT)
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| − | | |
| − | | |
| − | Progress Report
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| − | *Paul has received some reports, but not all, yet
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| − | | |
| − | | |
| − | Picture curation
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| − | *Started receiving permission from Elsevier!!
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| − | *Blanket-permission for 11 journals
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| − | *Publicly display list of cooperating journals online
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| − | | |
| − | | |
| − | Talks at the Int Worm Meeting
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| − | *Paul S listed for a Plenary talk during Workshop
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| − | *Two Wormbase Plenary talks
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| − | | |
| − | | |
| − | Snehal
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| − | *Concise descriptions
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| − | *Kimberly helping
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| − | *Will get into phenotypes soon
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| − | | |
| − | | |
| − | Juancarlos waiting to hear back from some people about OA
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| − | *People need more time to test
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| − | *Karen has encountered some issues; needs to reproduce
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| − | *Ranjana - loads slowly?
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| − | *Mangolassi issues?
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| − | | |
| − | | |
| − | Genetic Interactions
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| − | *Group met on Tuesday
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| − | *Made headway on genetic interaction organization
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| − | *Add "Additive" type term and "No Apparent Interaction", etc.
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| − | | |
| − | | |
| − | Paper pipeline
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| − | *Kimberly & Juancarlos working on
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| − | *Documented on Wiki
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| − | *CGI's still being used?
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| − | *Remove outdated or unused CGI's?
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| − | | |
| − | | |
| − | Rewriting script from Jack Chen
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| − | *Neuron connection search
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| − | *Inroad to working on more web-interface topics
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| − | | |
| − | | |
| − | Adding interaction datasets into WormMart (Xiaodong and Ruihua)
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| − | | |
| − | | |
| − | Gene interaction dumping script (Raymond/Todd)
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| − | | |
| − | | |
| − | Strain Display
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| − | *Karen doing queries at CGC
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| − | *How many genes represented in CGC strain list?
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| − | *Protein-coding genes with alleles in strains?
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| − | *12,000 genes that are NOT represented in CGC
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| − | *Discrepancy wrt alleles; negative in AQL query, but present on site
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| − | *Strains with LOTS of alleles; how to handle?
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| − | *Polymorphisms vs. alleles
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| − | | |
| − | | |
| − | Aldrin Montana working over the summer
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| − | *We invited him to visit
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| − | *We'll come up with projects
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| − | *Web team fully involved in web site
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| − | *Help with minor GO issues (Ranjana)
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| − | **Requires knowledge of Perl
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| − | **Non-C.elegans species
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| − | **InterPro-to-GO mapping
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| − | **Export pipelines for other species?
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| − | **Maybe small project; requires more communication than coding?
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| − | *Raymond could help provide projects
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| − | *Would be nice to use PAINT across the nematodes for annotation
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| − | | |
| − | | |
| − | New Web site (Todd)
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| − | *Web team wrapping up various projects
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| − | *Polishing user interface
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| − | *Abby working on user interface
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| − | *Todd working on production environment
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| − | *Norie working on code that interfaces with database
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| − | *Release beta version at International Worm Meeting
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| − | *Working with Kevin Howe to standardize formats of files used during build
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| − | *Can now host new data for new species
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| − | | |
| − | | |
| − | | |
| − | == May 19, 2011 ==
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| − | | |
| − | | |
| − | Login System for people to submit and modify (WBPerson) personal information
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| − | *How to validate that someone registering for the site is the actual person?
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| − | **Use e-mail address, although some people don't have e-mail addresses; snail mail?
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| − | | |
| − | | |
| − | Poster Session Help Desk for International Worm Meeting
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| − | *Wen- yes, all set
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| − | *People will bring their own laptops
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| − | *Wen will make a Wiki page for people to sign up for sessions
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| − | | |
| − | | |
| − | Aldrin visiting
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| − | *June 16th/17th OK for people
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| − | *We could start making a list of possible topics for Aldrin to work on
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| − | | |
| − | | |
| − | Clone Model Update
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| − | *Working with current clone model to test adding plasmid objects
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| − | **Works OK, but will probably want a couple of new tags
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| − | **One idea is to have a tag that links nematode-specific sequence in the plasmid to genomic regions and GBrowse viewer
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| − | *Test plasmid objects and ideas for genome alignment sent to Paul Davis, waiting to hear back
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| − | | |
| − | | |
| − | Inter-Release Patch files?
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| − | *Still need to work out, but should wait until the new website has stabilized
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| − | | |
| − | | |
| − | | |
| − | == May 26, 2011 ==
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| − | | |
| − | | |
| − | Genetic Interactions (Interactions Group)
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| − | *Made headway on genetic interactions organization and nomenclature
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| − | *We have talked about (previously) separating physical, genetic, predicted, and regulatory interactions into different models
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| − | **This will need more time and work
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| − | *We can immediately add the new genetic interaction type tags to the interaction model
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| − | *New types include: Enhancement/Suppression, Complex, No Apparent Interaction/Additive, Asynthetic
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| − | *BioGRID will use their own curation strategy and pipeline, but may eventually incorporate our curation approach
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| − | | |
| − | | |
| − | Concise Descriptions (Snehal)
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| − | *Avergaing 9 genes/week
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| − | *Prioritized on new publications
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| − | *Also working on FlyBase GSA markup (e.g. false negatives)
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| − | | |
| − | | |
| − | Picture Curation (Daniela)
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| − | *Have authorization from ~50% of Elsevier journals
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| − | *Still need Developmental Biology access (many C. elegans papers)
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| − | | |
| − | | |
| − | Textpresso for Cell Function (Raymond)
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| − | *Have scheme for decent precision (still accumulating numbers)
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| − | *Recall?
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| − | *Review papers are, by default, tagged as primary literature and can affect the numbers
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| − | *Textpresso needs to add a review tagging step (earlier in the pipeline)
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| − | *Search done with keywords like "mosaic", anatomy terms, site of action, etc.
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| − | *Many anatomy terms are not very specific (e.g. E, AB, MS, etc.)
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| − | *Can give Michael new category list criteria for Textpresso (cleaner than current from postgres table pap_primary_data)
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| − | **Can have inclusion & exclusion criteria
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| − | | |
| − | | |
| − | User Interface Query Tool (Raymond)
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| − | | |
| − | | |
| − | Human Disease Curation (Ranjana)
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| − | *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?
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| − | *Right now, everything is simply writing to a text file that Arun has setup
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| − | *Connect Arun's script to Curation Status form?
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| − | *OMIM tags
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| − | *Accession/evidence tags?
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| − | *Apoptosis working group - identify apoptosis genes in various model organisms
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| − | | |
| − | | |
| − | KOG data
| |
| − | *What should we do about it?
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| − | *EggNOG?
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| − | *Michael Paulini will change the data model for homology groups
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| − | *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?
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| − | *Any new data coming from Caltech? No
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| − | *Transfer data to Hinxton
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| − | | |
| − | | |
| − | 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?
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| − | *Karen will coordinate a clean up process
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| − | *Group needs to participate in evaluating the automation pipeline
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| − | | |
| − | | |
| − | 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
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| − | | |
| − | | |
| − | International Worm Meeting WormBase Bandanas
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| − | *Which to choose?
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