Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Expression patterns? | *Expression patterns? | ||
*Tables/templates of suggested data/types that authors could/should submit for a paper | *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 | ||
+ | *[www.openbadges.org Open Badges] for micro-attribution |
Revision as of 16:57, 1 November 2012
2012 Meetings
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
- 1-minute demo: can have file in XML/HTML format, can highlight, annotate a sentence, and save annotation as a link
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
- [www.openbadges.org Open Badges] for micro-attribution