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| | [[WormBase-Caltech_Weekly_Calls_March_2012|March]] | | [[WormBase-Caltech_Weekly_Calls_March_2012|March]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_April_2012|April]] |
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| − | == April 12, 2012 ==
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| − | RNAi OA
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| − | *OA almost ready to go live
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| − | *Testing now with test curation
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| − | *Should go live next week for official curation
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| − | New Website
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| − | *Most problems are being fixed in a timely manner
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| − | *Curators can now edit links and add custom widgets
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| − | *Issues (tracked on GitHub) being dealt with quickly
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| − | BioCurator Meeting
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| − | *Good meeting, bigger than before
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| − | *Common themes: data standards, how to educate users of database materials and how to use it (and think critically)
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| − | *How can MODs work better with journals and PubMed to solve the 'triage' problem?
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| − | **Streamlining the paper acquisition/curation process
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| − | **MODs should ask NLM to take the burden of retrieving PDFs
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| − | **Get lawyers involved to make available?
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| − | **Publishers tend to be lax on text mining rules, maybe will evolve into an easier process
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| − | *Maybe write a grant for research project as a proof-of-principle that triage can be done in an effective/efficient manner
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| − | *May ask ISB (Int Society Biocurators) for help with this
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| − | *Sequence and protein curation: tools, databases (topic-specific; pathways, cancer, etc.)
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| − | *GeneWiki for human gene annotation
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| − | **One page for each gene; already have ~10,000 articles
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| − | **~Dozen editors, credibility of authors checked (?)
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| − | **Reasonably satisfied with coverage of human disease genes
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| − | *Whole-genome sequencing of individuals
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| − | **Newly identified genetic disorder
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| − | **VAST instead of BLAST
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| − | *Tool to identify primers from papers and map them to the genome automatically
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| − | *Intermine discussed
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| − | **Comparable to WormMart
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| − | **Object-oriented database
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| − | **Performs similar to WormBase
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| − | **Many pre-canned queries
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| − | **Advanced search Query-builder available
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| − | **MODs switched over to Intermine from BioMart
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| − | **WormMart - Will Spooner tried to provide queries that are more natural
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| − | **We can work to build an interface on top of Intermine, etc.
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| − | **Todd has made progress with getting Intermine for WormBase
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| − | *Lot's of specialized talks, reduced the productivity (compared to BioCreative meeting)
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| − | *Curators explaining their curation pipeline
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| − | *Textpresso still popular ;)
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| − | **Six out of seven MODs using Textpresso
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| − | **Discussed text mining in particular applications (eg. CCC)
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| − | **Textpresso only tool using full-text for mining
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| − | **Pete from FlyBase: SVM results are deteriorating (similar to WormBase)
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| − | ***Start training from scratch; hopefully get better recall/precision numbers
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| − | *Natural language processing on figure legends/captions
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| − | **Tries to find text in the body that relates to figure
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| − | **Possible collaboration with Texpresso
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| − | *NLP research group in Germany
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| − | **'Actor', 'agent' etc. and relationships (RDF triplets)
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| − | *Doug Howe (ZFIN), zebrafish corpus small enough, doesn't need Textpresso
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| − | *Julio Collado-Vides, Textpresso for E. coli fell apart, but trying to get back together
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| − | Paul will meet someone from Elsevier
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| − | *Image curation/ rights issues
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| − | Genetic Interaction ontology
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| − | *SGD on board with ontology so far; performing trial curation
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| − | *FlyBase interested in using as well; will meet with Chris and Rose in May to discuss
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| − | == April 19, 2012 ==
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| − | Interaction object displays on WormBase website
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| − | *Chris and Maher will sort out on GitHub
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| − | *Chris will map data from old tags to new tags and suggest display changes for new data types where necessary
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| − | *One issue to deal with is the complex objects with multiple Interaction_types (and intended to be separate objects)
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| − | Interaction model and intragenic suppression
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| − | *We need to make some modifications to the new Interaction model if we want to accommodate intragenic suppression (or other intragenic) events
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| − | *Proposed change is to:
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| − | #Make each allele a separate object
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| − | #Move the Variation (and Transgene) tag out of the Interactor_info hash and into the main Interaction model under the Interactor tag
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| − | #Add a Cis_intragenic_suppression and a Trans_intragenic_suppression tag under the Interaction_type tag (perhaps also intragenic_enhancement?)
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| − | *With these changes:
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| − | **Each variation (and transgene) can be listed as an interactor with Interactor_info indicating Affected, Effector, or Non_directional
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| − | **Genes associated with intragenic, interacting variations will display (in Cytoscape view) as interacting with themselves via a Genetic Interaction
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| − | **Mary Ann can then indicate/curate the flanking sequences for each allele
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| − | Life_stage objects still dump as names, not IDs
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| − | *This is because ACEDB only handles names, not IDs
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| − | *Daniela is in charge of this class; we can discuss with her when she's back
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| − | *We likely want to change to a system where we use only IDs in .ACE objects
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| − | URL Constructors for GSA markup
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| − | *Todd has taken care of much of the issue of URL construction for GSA marked-up papers
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| − | *Karen will send Todd examples of Anatomy_term/Anatomy_name links that need to be checked
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| − | *GSA papers will need to be rechecked to ensure that all links are working
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| − | Network outages
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| − | *Various office network ports are non-functional as of yesterday
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| − | *IMSS/Network admins aware of issue and working on it
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| − | Interaction and Gene_regulation objects for next upload
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| − | *Conversion scripts will need to be run again to convert objects to new model format
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| − | *Chris will look into whether or not the mapping files (needed to update Gene_regulation objects) will need to be updated for the newest data
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| − | *Xiaodong will dump Gene_regulation objects out of the OA using the old dumping script
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| − | == April 26, 2012 ==
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| − | Meeting with Elsevier rep
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| − | *Elsevier getting more open to text-mining
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| − | *People build apps and then put them on the Science-Direct site (e.g. TAIR app)
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| − | *Wanted a couple sentences on what we want from text-mining
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| − | *GO consortium would like text-mining for triage of new papers
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| − | *'Climate is better now'
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| − | Yeast-two-hybrid data issues
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| − | *Lots of redundancies, bogus objects, many objects per bait/target (Sequences, CDSs, genes, etc.)
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| − | *Provenance of data isn't clear
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| − | *Should mv PCR products be mapped each build to genes?
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| − | *May want to start from scratch and collect YH data from Vidal and Walhout labs
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| − | *Check if BioGrid is curating this data already
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| − | Next WormBase grant due in 6 months
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| − | *30 pages
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| − | *Need to figure out what we want to do in next 5 years; how we want to organize
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| − | *Combine SAB meeting and grant writing?
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| − | *New page types lagged behind due to updating of web site: e.g. Process pages
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| − | *What is reasonable/realistic for what new content can get online?
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| − | Curation wish-list on Wiki (Ranjana)
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| − | *Many papers on new topics coming out
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| − | *Drug-screening, drug interaction
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| − | *Infection, parasitism
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| − | Anatomy links from Worm Atlas broken
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| − | *Links need to be fixed/cleaned up
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| − | *Going forward, may need some sort of DOI system (stable links indefinitely)
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| − | *An issue of GSA markup as well
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| − | *Published links will never change; will need to accommodate
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| − | Ontology searches
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| − | *Trying to adapt AMIGO to use our .OBO files
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| − | *National Center for Biomedical Ontologies uses Protege instead of OBO Edit
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| − | *Consider adopting Protege/OWL files? Conversion could be trivial
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| − | *Parent-child relationships file for C. elegans cell lineage; need to accommodate indeterminacy
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| − | *Use synonym assignment to handle different possible outcomes/identities?
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| − | Elbrus has reached capacity limit
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| − | *Broke RNAi curation pipeline
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| − | *Useful bits of code on elbrus
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| − | **Data submission forms (RNAi data)
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| − | **Microarray query tool (broken/toss)
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| − | *Should put (working) code on GitHub repository
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| − | User datamining demands
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| − | *We need to accommodate users requests for data
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| − | *Fix WormMart/incorporate Intermine
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| − | *Bring back Batch Gene query
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| − | *Custom query building (by curators) based on user requests?
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| − | *Look at help desk e-mails and determine what users want
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| − | *Pre-canned queries?
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| − | *AcePerl scripts could perform batch gene queries
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