WormBase-Caltech Weekly Calls
From WormBaseWiki
2012 Meetings
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
