Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2012|February]]
  
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[[WormBase-Caltech_Weekly_Calls_March_2012|March]]
  
  
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== March 1, 2012 ==
 
  
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GO Meeting
 
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*Focused on annotation pipelines; improving efficiency/effectiveness
 
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*How to make GO annotations more 'expressive'
 
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*GO would like to move towards more expressive statements
 
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*Example: If a gene is involved in a function or process, where in the cell does this take place
 
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*Common Annotation Framework
 
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*Current/future members of the GO network can annotate using the same version of GO, same tools and standards
 
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*Quality controls checks: e.g. do you have all the fields necessary to make an annotation
 
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*GO hopes to centralize all of the data handling, formatting
 
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*LEGO - Logical Extensions of GO
 
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*We should pilot how we want to handle this; similar to how concise descriptions are constructed
 
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*WormBase curates phenotypes, pathways, etc.
 
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*Defining useful relationships to curate/annotate: Cross-products with defined relations
 
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*Pilot: Take subdomains, pathways, try extended version of curation on these
 
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*How do we capture that fly eye development is relevant to human biology?
 
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**Humans don't have compound eyes - not the point
 
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**The pathways are the same or similar; EGF signaling
 
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*WormBase Process curation could really benefit from GO's adoption of this strategy
 
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*Need to consider what the "right" way to approach this issue; need good pilot
 
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*Where is the value? How do we focus on this?
 
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*Another annotation pipeline: Phylogenetic Annotation and INference Tool (PAINT)
 
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**How best to make these inferences?
 
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**What kind of inferences can you make about organismal- or organ-specific processes?
 
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***Uberon has framework for interspecies anatomical comparisons
 
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**PAINT tool for nematodes?
 
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Upload for WS231
 
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*Interaction file upload took several hours
 
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*Check if virtual memory is being used
 
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*Likely culprit is the extra data and XREFs in the Interactor_info hash
 
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*Can objectify the Interactor_info to be a tag in the main ?Interaction model
 
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*We should warn EBI/Hinxton about this
 
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WormBase Curator Interview next Thursday
 
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Migration of Reporter_gene object annotations from Expr_pattern OA to Transgene OA
 
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*Everything seems OK
 
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SPELL
 
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*Papers with less than three experiments, statistics calculations cause slow-down, memory limitations
 
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*Now can bypass this problem
 
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*We are now operating SPELL on our local machines
 
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*Do Amazon instances function/behave differently than local server?
 
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**Need to compare; find benefits & drawbacks
 
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*Use Amazon server as a dynamic name server
 
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*Users shouldn't notice a difference
 
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*We won't need to ask Todd for anything; we can fix it ourselves
 
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GO Meeting breakout session
 
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*Software architecture for upcoming GO expansion (CAT - Common Annotation Tool)
 
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*How does Textpresso integrate?
 
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*What kind of annotation would GO expect Textpresso to do?
 
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*User will be able to do guided text mining operations
 
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**Example: regular expressions, then HMM, then export to CAT
 
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*No forseeable roadblocks
 
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*Maybe standardize all of the text mining types and methods behind them
 
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*Develop paper-viewer? Apart from CAT, text mining flow? Separate module
 
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== March 15, 2012 ==
 
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RNAi clone mappings
 
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*Can we submit PCR primers to Hinxton for genome mapping?
 
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**They say so, we'll have to test
 
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**Usually we deal with PCR_product objects like sjj_* or mv_*
 
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Transgene sequences
 
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*Authors explain PCR construction of transgenes; provide explicit sequence?
 
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Should we make a standard submission format for authors?
 
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*Maybe, authors should have to submit explicit sequences for RNAi probes, transgenes, etc.
 
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*Enforce standards at what level? Editors, reviewers, journal, user community, etc...
 
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*Submit PCR primers?
 
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*We will draft a letter to community/editors to request explicit sequences for RNAi experiments
 
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Should we perform sequencing of Ahringer (and other) clones ourselves?
 
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*Write grant, perform sequencing?
 
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New website release
 
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*We will draft an e-mail/blog post about official release of new website at end of March
 
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SVM Precision/Recall
 
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*Standardize methods of calculating precision and recall on SVM results?
 
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*True Positive = a positive identified by SVM that is actually positive
 
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*False Positive = a positive identified by SVM that is actually negative
 
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*True Negative = a negative identified by SVM that is actually negative
 
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*False Negative = a negative identified by SVM that is actually positive
 
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*Precision Rate (Positive Predictive Value) - how many SVM-identified positives are true positives? = True Positives/(True Positives + False Positives)
 
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*Recall Rate (Sensitivity) = True Positives/(True Positives + False Negatives)
 
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*Specificity = True Negatives/(True Negatives + False Positives)
 
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*NPV (Negative Predictive Value) = True Negatives/(True Negatives + False Negatives)
 
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Curator Candidates
 
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== March 22, 2012 ==
 
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New website release
 
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*Sending around mass e-mail to WormBase community (9960 e-mail addresses) announcing release
 
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*Will notify that old site will still be available (at legacy.wormbase.org?)
 
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*Provide link to old website on new website homepage?
 
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Browsable worm model
 
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*Implemented by Open Worm project team
 
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SPELL
 
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*Monitoring to see if it is up and running
 
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*Had a few shutdowns that we weren't aware of
 
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*Would like to be ahead of the users so we can restart it
 
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*Trying to figure out how to be made aware of any shutdowns
 
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*Yeast SPELL has set it up such that a user could paste in a URL to get results
 
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**Worm SPELL cannot do this; not setup in the same way
 
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**Wen will contact yeast SPELL team; already contacted Michael Cherry
 
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*http://imperio.princeton.edu - has nice functionality
 
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*Kimberly will ask around
 
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RNAi OA
 
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*Working on the new RNAi OA
 
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*Will take advantage of Igor's RNAi processing script for dumping from the OA
 
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*Would be good if we had a working tool (locally) to map primer sets and clones to DNA text
 
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Interaction and Gene Regulation OAs
 
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*Need to be updated (OA and dumping script) to accommodate the new ?Interaction model
 
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== March 29, 2012 ==
 
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BioCurator Meeting
 
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*QC Fast poster looks good
 
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*Wen presenting poster on SPELL
 
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*Kimberly has multiple presentations
 
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**WormBase workflow
 
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**CCC for Dictybase
 
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**Another presentation
 
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*Michael and Yuling going; will meet with collaborators
 
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*Text-linking groups (Reflect)
 
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*Keep an eye out for PDF(paper) viewers/editors/annotators
 
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SPELL upgrade
 
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*Upgraded to newer version of software
 
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*Automatically keep track of whether or not it is functioning
 
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**Regular test query every 30 min to 1 hr
 
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*Still using Amazon server as a forwarding service
 
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OA edits
 
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*Interaction and Gene_regulation OAs under modification for new ?Interaction model
 
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*RNAi OA, generating OA and dumping
 
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*Configuring OAs so that single objects exist on a single row in the OA
 
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**Is it necessary to map interaction objects (Transgene, Antibody, etc.) to a core interaction entity (Gene, Protein, etc.)
 
  
  

Revision as of 20:58, 12 April 2012

2009 Meetings

2011 Meetings


2012 Meetings

January

February

March



April 12, 2012

RNAi OA

  • OA almost ready to go live
  • Testing now with test curation
  • Should go live next week for official curation


New Website

  • Most problems are being fixed in a timely manner
  • Curators can now edit links and add custom widgets
  • Issues (tracked on GitHub) being dealt with quickly


BioCurator Meeting

  • Good meeting, bigger than before
  • Common themes: data standards, how to educate users of database materials and how to use it (and think critically)
  • How can MODs work better with journals and PubMed to solve the 'triage' problem?
    • Streamlining the paper acquisition/curation process
    • MODs should ask NLM to take the burden of retrieving PDFs
    • Get lawyers involved to make available?
    • Publishers tend to be lax on text mining rules, maybe will evolve into an easier process
  • Maybe write a grant for research project as a proof-of-principle that triage can be done in an effective/efficient manner
  • May ask ISB (Int Society Biocurators) for help with this
  • Sequence and protein curation: tools, databases (topic-specific; pathways, cancer, etc.)
  • GeneWiki for human gene annotation
    • One page for each gene; already have ~10,000 articles
    • ~Dozen editors, credibility of authors checked (?)
    • Reasonably satisfied with coverage of human disease genes
  • Whole-genome sequencing of individuals
    • Newly identified genetic disorder
    • VAST instead of BLAST
  • Tool to identify primers from papers and map them to the genome automatically
  • Intermine discussed
    • Comparable to WormMart
    • Object-oriented database
    • Performs similar to WormBase
    • Many pre-canned queries
    • Advanced search Query-builder available
    • MODs switched over to Intermine from BioMart
    • WormMart - Will Spooner tried to provide queries that are more natural
    • We can work to build an interface on top of Intermine, etc.
    • Todd has made progress with getting Intermine for WormBase
  • Lot's of specialized talks, reduced the productivity (compared to BioCreative meeting)
  • Curators explaining their curation pipeline
  • Textpresso still popular ;)
    • Six out of seven MODs using Textpresso
    • Discussed text mining in particular applications (eg. CCC)
    • Textpresso only tool using full-text for mining
    • Pete from FlyBase: SVM results are deteriorating (similar to WormBase)
      • Start training from scratch; hopefully get better recall/precision numbers
  • Natural language processing on figure legends/captions
    • Tries to find text in the body that relates to figure
    • Possible collaboration with Texpresso
  • NLP research group in Germany
    • 'Actor', 'agent' etc. and relationships (RDF triplets)
  • Doug Howe (ZFIN), zebrafish corpus small enough, doesn't need Textpresso
  • Julio Collado-Vides, Textpresso for E. coli fell apart, but trying to get back together


Paul will meet someone from Elsevier

  • Image curation/ rights issues


Genetic Interaction ontology

  • SGD on board with ontology so far; performing trial curation
  • FlyBase interested in using as well; will meet with Chris and Rose in May to discuss
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