WormBase-Caltech Weekly Calls

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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, AMIGO ontology browser, etc.
• Annotation on tablets, other mobile devices? Read only?
• Web app versus native app
• Open Badges for micro-attribution, incentives
• ORCID for unique person IDs
• Possible Ontology Annotator version for community?
• Templates/forms would need to be very straight-forward and simple to use
• Maybe display a form alongside web display to inform users of how the two relate
• Training users: tutorials, workshops (2013 IWM?)
• Daily updates to website could be more satisfying for users

November 8, 2012

Construction

• Burning smell frequently
• Now cigarette smoke smell (maybe completely unrelated to construction, of course)

Curation Status Form

• http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
• Curators cannot indicate both positive and negative for a data type per paper; conflict must be resolved by curators
• One free text comment field (and one "pre-canned" comment field) per paper per data type
• To what extent would a curator like to see all data for several papers at once? Likely only need to see one paper and one data type at a time
• The form provides a (unique) way for curators to "validate" a paper as "negative" for a data type
• It is important to decouple validation from curation, so we can capture both
• Ideal if each paper could be independently categorized according to flagging status, validation status, and curation status
• Papers can be identified as "Not Validated", "Validated Negative", "Validate Positive - Not Curated", or "Validate Positive - Curated"
• We will make adjustments to form to accomodate

Dead Genes

• How do we/should we handle objects (e.g. interactions) that now refer to dead genes?
• Would be best if we could keep the original gene reference with a downstream automated process (at dump, ACE build, webdisplay???) to convert to new IDs (if there are merges) or a remark indicating a dead gene
• Will discuss more next week

November 15, 2012

Scripts from Mary Ann

• Mary Ann sent to James and Raymond
• Updating strain and allele designations

AQL/WQL Queries

• HTML vs plain text output
• HTML output takes much longer than plain text and often times out
• Not optimal to give users AQL queries; will be better once Intermine is up and running
• User data requests are use-cases for Intermine

Curation Statistics Tool

• Do curators want to see unions or intersections of specific flagging methods? Yes
• Will need to develop a visualization aside from the summary table
• Chris and Juancarlos will discuss offline

Human Disease tags for ?Gene model

• Using common vocabulary
• Human_disease_info tag with subset tags : OMIM_ortholog, Potential_model_for, Experimental_model_for, and Human_disease_relevance

?Gene
     Human_disease_info        OMIM_ortholog             ?Accession_number      #Evidence
                               Potential_model_for       ?DO_term      XREF  Gene    #Evidence
                               Experimental_model_for    ?DO_term      XREF  Gene    #Evidence
                               Human_disease_relevance   ?Text       #Evidence