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| | [[WormBase-Caltech_Weekly_Calls_September_2012|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2012|September]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_October_2012|October]] |
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| − | == October 4, 2012 ==
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| − | FlyBase SAB topics
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| − | *Genome Space - can integrate data in different formats
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| − | **Cloud-based data integration
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| − | **File conversion done automatically - no need to write scripts
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| − | *FlyBase talking about joining [http://www.genomespace.org/ Genome Space]?
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| − | Protein-to-GO Tool
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| − | *Ranjana and Kimberly performing data checks for testing
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| − | *If file can get to Rachel and Tony, maybe can discuss this weekend (at GO meeting)
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| − | GO Annotator Tool
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| − | *Kimberly looking over
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| − | *James will make a couple slides to introduce tool and provide demo
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| − | **1-minute demo: can have file in XML/HTML format, can highlight, annotate a sentence, and save annotation as a link
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| − | ***Demo: simpler = better
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| − | ***Prepare for live feedback and discussion
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| − | Curation Status/Statistics Tool
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| − | *How many papers have given data types?
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| − | *How many papers have been curated, how many not?
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| − | *How many objects/connections do we have of a given type?
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| − | *How many objects per paper (average, distribution?)?
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| − | *Estimated number of objects/papers exist vs. how many we have curated?
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| − | *Do we care about types of flagging? Curator first pass, author first pass, etc? Yes
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| − | **All flagging types should be shown; combined and individual statistics would be useful
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| − | *Interactive form vs. static page showing curation/flagging statisitcs
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| − | *Tracking negatives (true vs false)
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| − | *Data types in OA vs not (microarray, Protein-to-GO output)
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| − | **Microarray data - Wen can write script to generate stats for microarray curation
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| − | *Curation stats per paper (Raymond): write comments in a remark field; traceable, transparent, available
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| − | Process pages
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| − | *GPML - may be able to automatically map Postgres data to GPML
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| − | *WikiPathways has color, formatting, labels, etc. so we can define types/views of different relationships (should follow standards)
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| − | *AWC-ON/AWC-OFF sample page: only single connection type; can be many different types, as we define it
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| − | *"Too many arrows" editorial?
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| − | Physical interaction curation
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| − | *On interaction OA (Tab2) physical interactions; 'Colocalizes', etc.
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| − | *Need to establish our data exchange with BioGRID; get BioGRID data in Postgres/OA (daily cronjob?)
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| − | *Interaction model was modeled to be compatible with BioGRID's data
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| − | *Revive curator first pass for physical interactions? To tag papers (in the meantime)
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| − | == October 11, 2012 ==
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| − | Molecules
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| − | *Changing to WBMolIDs
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| − | *OA dumpers need to be modified
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| − | GO Meeting
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| − | *How to make GO more expressive/inclusive
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| − | *How can GO represent more of the biology
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| − | *GO Extensions: LEGO
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| − | *Deeper annotations can help develop the "big picture"
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| − | *Phenotype-2-GO mapping: What is the purpose? How does it work?
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| − | **Broad vs specific term mapping; how good is the mapping?
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| − | CSHace merge with CITace?
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| − | *PCR_product info discrepancies
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| − | *CITace data was overwriting CSHace data, but changed
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| − | *8 classes of data in CSHace
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| − | *CSHace data had never been read into CITace minus
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| − | *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)
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| − | *Can we assume that all CITace data is better/newer/more-up-to-date than CSHace data?
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| − | Consensus Sequence tag in PWM model
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| − | *OK to add, but leave as 'Text' not '?Text'
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| − | *DNA_text field instead? Xiaodong will run by EBI
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| − | *This data is denormalized from a PWM if both are provided
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| − | *Should only be used if no PWM is provided
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| − | *Perhaps this should not be added
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| − |
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| − | == October 25, 2012 ==
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| − | Curation Stats Table
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| − | *Can be viewed (on sandbox) here: http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
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| − | *Click on the button "Curation Statistics Page"
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| − | *Will show overall statistics per data type as well as per flagging method
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| − | *Working out details/aesthetics of display
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| − | WS235 Upload next Thursday (Nov 1)
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| − | Microarrays
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| − | *24 new datasets
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| − | *Five new species
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| − | *We want to perform cluster analysis for end users (SPELL itself not capable)
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| − |
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| − | PWM/PFM data
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| − | *~5000 PFM/PWM data objects in .ace files from Stormo data set
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| − | *How the motif finder tool should work? (without using 1000s of GBrowse tracks?)
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| − | *Single GBrowse track that consolidates all PFMs/PWMs; one track with all 'binding sites' above threshold?
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| − | *Another tool to look for, for example, co-occurrence?
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| − | Disease info
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| − | *Adding 'Disease_relevant_info' tag in Gene model
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| − | *Human ortholog pulled from OMIM by Hinxton/EBI
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| − | Ranjana will do a blog item every Thursday
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| − | *Doing series heading, e.g. "Developments to GO"
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| − | **Updates could fall under same headings to organize blog posts
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| − | New RNAi clones from Ahringer lab
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| − | *Working with Kevin Howe as to how the new PCR_product and Oligo objects should be created and stored
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| − | *Ultimately would like (for all RNAi clones) to have a one-to-one mapping of best RNAi clones for a gene
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| − | *Gene pages could then display "THE" RNAi clone for a gene per library (e.g. Vidal or Ahringer), along with resource address/location
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| − | *If multiple clones per gene, indicate which clone is unique to that gene
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| − | Protein-2-GO Tool
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| − | *Gene-product-information file
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| − | *Working with other MODs
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| − | Transgenes up to date
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| − | Legacy phenotypes
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| − | *Still have ~800 legacy phenotypes to add through phenotype curation
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| − | Process pages
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| − | *Karen writing summaries for processes
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| − | *People can help cull the list and/or help write summaries
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| − | *Look at Processes in the Process OA by querying for "Karen" as a curator
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| − | *Connecting to relevant papers (reviews, research articles, WormBook chapters/abstracts)
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| − | *Linking to WikiPathways, Reactome?
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| − | *What should be editable by users/broader community?
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