WormBase-Caltech Weekly Calls

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October 4, 2012

FlyBase SAB topics

• Genome Space - can integrate data in different formats
  • Cloud-based data integration
  • File conversion done automatically - no need to write scripts
• FlyBase talking about joining Genome Space?

Protein-to-GO Tool

• Ranjana and Kimberly performing data checks for testing
• If file can get to Rachel and Tony, maybe can discuss this weekend (at GO meeting)

GO Annotator Tool

• Kimberly looking over
• James will make a couple slides to introduce tool and provide demo
  • 1-minute demo: can have file in XML/HTML format, can highlight, annotate a sentence, and save annotation as a link
    • Demo: simpler = better
    • Prepare for live feedback and discussion

Curation Status/Statistics Tool

• How many papers have given data types?
• How many papers have been curated, how many not?
• How many objects/connections do we have of a given type?
• How many objects per paper (average, distribution?)?
• Estimated number of objects/papers exist vs. how many we have curated?
• Do we care about types of flagging? Curator first pass, author first pass, etc? Yes
  • All flagging types should be shown; combined and individual statistics would be useful
• Interactive form vs. static page showing curation/flagging statisitcs
• Tracking negatives (true vs false)
• Data types in OA vs not (microarray, Protein-to-GO output)
  • Microarray data - Wen can write script to generate stats for microarray curation
• Curation stats per paper (Raymond): write comments in a remark field; traceable, transparent, available

Process pages

• GPML - may be able to automatically map Postgres data to GPML
• WikiPathways has color, formatting, labels, etc. so we can define types/views of different relationships (should follow standards)
• AWC-ON/AWC-OFF sample page: only single connection type; can be many different types, as we define it
• "Too many arrows" editorial?

Physical interaction curation

• On interaction OA (Tab2) physical interactions; 'Colocalizes', etc.
• Need to establish our data exchange with BioGRID; get BioGRID data in Postgres/OA (daily cronjob?)
• Interaction model was modeled to be compatible with BioGRID's data
• Revive curator first pass for physical interactions? To tag papers (in the meantime)

October 11, 2012

Molecules

• Changing to WBMolIDs
• OA dumpers need to be modified

GO Meeting

• How to make GO more expressive/inclusive
• How can GO represent more of the biology
• GO Extensions: LEGO
• Deeper annotations can help develop the "big picture"
• Phenotype-2-GO mapping: What is the purpose? How does it work?
  • Broad vs specific term mapping; how good is the mapping?

CSHace merge with CITace?

• PCR_product info discrepancies
• CITace data was overwriting CSHace data, but changed
• 8 classes of data in CSHace
• CSHace data had never been read into CITace minus
• Proposal: read CSHace data into ACEDB and then read in CITace minus data (which would overwrite CSHace data with CITace data where there is a conflict)
• Can we assume that all CITace data is better/newer/more-up-to-date than CSHace data?

Consensus Sequence tag in PWM model

• OK to add, but leave as 'Text' not '?Text'
• DNA_text field instead? Xiaodong will run by EBI
• This data is denormalized from a PWM if both are provided
• Should only be used if no PWM is provided
• Perhaps this should not be added

October 25, 2012

Curation Stats Table

• Can be viewed (on sandbox) here: http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
• Click on the button "Curation Statistics Page"
• Will show overall statistics per data type as well as per flagging method
• Working out details/aesthetics of display

WS235 Upload next Thursday (Nov 1)

Microarrays

• 24 new datasets
• Five new species
• We want to perform cluster analysis for end users (SPELL itself not capable)

PWM/PFM data

• ~5000 PFM/PWM data objects in .ace files from Stormo data set
• How the motif finder tool should work? (without using 1000s of GBrowse tracks?)
• Single GBrowse track that consolidates all PFMs/PWMs; one track with all 'binding sites' above threshold?
• Another tool to look for, for example, co-occurrence?

Disease info

• Adding 'Disease_relevant_info' tag in Gene model
• Human ortholog pulled from OMIM by Hinxton/EBI

Ranjana will do a blog item every Thursday

• Doing series heading, e.g. "Developments to GO"
  • Updates could fall under same headings to organize blog posts

New RNAi clones from Ahringer lab

• Working with Kevin Howe as to how the new PCR_product and Oligo objects should be created and stored
• Ultimately would like (for all RNAi clones) to have a one-to-one mapping of best RNAi clones for a gene
• Gene pages could then display "THE" RNAi clone for a gene per library (e.g. Vidal or Ahringer), along with resource address/location
• If multiple clones per gene, indicate which clone is unique to that gene

Protein-2-GO Tool

• Gene-product-information file
• Working with other MODs

Transgenes up to date

Legacy phenotypes

• Still have ~800 legacy phenotypes to add through phenotype curation

Process pages

• Karen writing summaries for processes
• People can help cull the list and/or help write summaries
• Look at Processes in the Process OA by querying for "Karen" as a curator
• Connecting to relevant papers (reviews, research articles, WormBook chapters/abstracts)
• Linking to WikiPathways, Reactome?
• What should be editable by users/broader community?

November 1, 2012

SPELL data

• Including new RNA-seq datasets
• Comparing different RNA-seq datasets

Dedicated ~2 weeks for issues

• Dedicated time during release cycle to fix bugs and address GitHub issues

Intermine

• JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine
• Developed FlyBase Intermine instance
• Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)
  • E.g. Display meta information for a gene; "How many genes show this phenotype?"
• We have resources provisioned for building and hosting
• Low hanging fruit: access to ontologies, gene models, phenotypes, homology, orthology (things already made for Intermine)
• Focus first on central dogma stuff

SAB Meeting

• January 28th, 29th, 2013
• At Caltech

Concise description template

• Curator version versus a community (simpler) version
• 1) Transfer info from elegans to other species
• 2) Updates
• Easier to script when there is little information; harder when lots of info

Pathways

• Karen spoke to Alex Pico
• There could be tagged for "WormBase-approved" pathways
• Would be good to have worm community also contribute; "Community Pathways" widget
• Conflict resolution? There could be many contributions to the same pathway
• Is there a way to pull up conflicting versions of a pathway?
• Open system: any registered user can modify any pathway

Community Annotation

• Possibilities?
• Concise descriptions, pathways, what else?
• Expression patterns?
• Tables/templates of suggested data/types that authors could/should submit for a paper
• Annotation Apps? iPhone, Android, etc.
  • Controlled vocabulary, virtual worm, etc.
• Annotation on tablets, other mobile devices? Read only?
• Web app versus native app
• Open-Badges for micro-attribution