WormBase-Caltech Weekly Calls

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2012 Meetings

January

February

March 1, 2012

GO Meeting

• Focused on annotation pipelines; improving efficiency/effectiveness
• How to make GO annotations more 'expressive'
• GO would like to move towards more expressive statements
• Example: If a gene is involved in a function or process, where in the cell does this take place
• Common Annotation Framework
• Current/future members of the GO network can annotate using the same version of GO, same tools and standards
• Quality controls checks: e.g. do you have all the fields necessary to make an annotation
• GO hopes to centralize all of the data handling, formatting
• LEGO - Logical Extensions of GO
• We should pilot how we want to handle this; similar to how concise descriptions are constructed
• WormBase curates phenotypes, pathways, etc.
• Defining useful relationships to curate/annotate: Cross-products with defined relations
• Pilot: Take subdomains, pathways, try extended version of curation on these
• How do we capture that fly eye development is relevant to human biology?
  • Humans don't have compound eyes - not the point
  • The pathways are the same or similar; EGF signaling
• WormBase Process curation could really benefit from GO's adoption of this strategy
• Need to consider what the "right" way to approach this issue; need good pilot
• Where is the value? How do we focus on this?
• Another annotation pipeline: Phylogenetic Annotation and INference Tool (PAINT)
  • How best to make these inferences?
  • What kind of inferences can you make about organismal- or organ-specific processes?
    • Uberon has framework for interspecies anatomical comparisons
  • PAINT tool for nematodes?

Upload for WS231

• Interaction file upload took several hours
• Check if virtual memory is being used
• Likely culprit is the extra data and XREFs in the Interactor_info hash
• Can objectify the Interactor_info to be a tag in the main ?Interaction model
• We should warn EBI/Hinxton about this

WormBase Curator Interview next Thursday

Migration of Reporter_gene object annotations from Expr_pattern OA to Transgene OA

• Everything seems OK

SPELL

• Papers with less than three experiments, statistics calculations cause slow-down, memory limitations
• Now can bypass this problem
• We are now operating SPELL on our local machines
• Do Amazon instances function/behave differently than local server?
  • Need to compare; find benefits & drawbacks
• Use Amazon server as a dynamic name server
• Users shouldn't notice a difference
• We won't need to ask Todd for anything; we can fix it ourselves

GO Meeting breakout session

• Software architecture for upcoming GO expansion (CAT - Common Annotation Tool)
• How does Textpresso integrate?
• What kind of annotation would GO expect Textpresso to do?
• User will be able to do guided text mining operations
  • Example: regular expressions, then HMM, then export to CAT
• No forseeable roadblocks
• Maybe standardize all of the text mining types and methods behind them
• Develop paper-viewer? Apart from CAT, text mining flow? Separate module

March 15, 2012

RNAi clone mappings

• Can we submit PCR primers to Hinxton for genome mapping?
  • They say so, we'll have to test
  • Usually we deal with PCR_product objects like sjj_* or mv_*

Transgene sequences

• Authors explain PCR construction of transgenes; provide explicit sequence?

Should we make a standard submission format for authors?

• Maybe, authors should have to submit explicit sequences for RNAi probes, transgenes, etc.
• Enforce standards at what level? Editors, reviewers, journal, user community, etc...
• Submit PCR primers?
• We will draft a letter to community/editors to request explicit sequences for RNAi experiments

Should we perform sequencing of Ahringer (and other) clones ourselves?

• Write grant, perform sequencing?

New website release

• We will draft an e-mail/blog post about official release of new website at end of March

SVM Precision/Recall

• Standardize methods of calculating precision and recall on SVM results?
• True Positive = a positive identified by SVM that is actually positive
• False Positive = a positive identified by SVM that is actually negative
• True Negative = a negative identified by SVM that is actually negative
• False Negative = a negative identified by SVM that is actually positive
• Precision Rate (Positive Predictive Value) - how many SVM-identified positives are true positives? = True Positives/(True Positives + False Positives)
• Recall Rate (Sensitivity) = True Positives/(True Positives + False Negatives)
• Specificity = True Negatives/(True Negatives + False Positives)
• NPV (Negative Predictive Value) = True Negatives/(True Negatives + False Negatives)

Curator Candidates

March 22, 2012

New website release

• Sending around mass e-mail to WormBase community (9960 e-mail addresses) announcing release
• Will notify that old site will still be available (at legacy.wormbase.org?)
• Provide link to old website on new website homepage?

Browsable worm model

• Implemented by Open Worm project team

SPELL

• Monitoring to see if it is up and running
• Had a few shutdowns that we weren't aware of
• Would like to be ahead of the users so we can restart it
• Trying to figure out how to be made aware of any shutdowns
• Yeast SPELL has set it up such that a user could paste in a URL to get results
  • Worm SPELL cannot do this; not setup in the same way
  • Wen will contact yeast SPELL team; already contacted Michael Cherry
• http://imperio.princeton.edu - has nice functionality
• Kimberly will ask around

RNAi OA

• Working on the new RNAi OA
• Will take advantage of Igor's RNAi processing script for dumping from the OA
• Would be good if we had a working tool (locally) to map primer sets and clones to DNA text

Interaction and Gene Regulation OAs

• Need to be updated (OA and dumping script) to accommodate the new ?Interaction model

March 29, 2012

BioCurator Meeting

• QC Fast poster looks good
• Wen presenting poster on SPELL
• Kimberly has multiple presentations
  • WormBase workflow
  • CCC for Dictybase
  • Another presentation
• Michael and Yuling going; will meet with collaborators
• Text-linking groups (Reflect)
• Keep an eye out for PDF(paper) viewers/editors/annotators

SPELL upgrade

• Upgraded to newer version of software
• Automatically keep track of whether or not it is functioning
  • Regular test query every 30 min to 1 hr
• Still using Amazon server as a forwarding service

OA edits

• Interaction and Gene_regulation OAs under modification for new ?Interaction model
• RNAi OA, generating OA and dumping
• Configuring OAs so that single objects exist on a single row in the OA
  • Is it necessary to map interaction objects (Transgene, Antibody, etc.) to a core interaction entity (Gene, Protein, etc.)

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 (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