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| | [[WormBase-Caltech_Weekly_Calls_October_2012|October]] | | [[WormBase-Caltech_Weekly_Calls_October_2012|October]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_November_2012|November]] |
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| − | == November 1, 2012 ==
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| − | | + | == December 6, 2012 == |
| − | SPELL data
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| − | *Including new RNA-seq datasets
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| − | *Comparing different RNA-seq datasets
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| − | Dedicated ~2 weeks for issues
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| − | *Dedicated time during release cycle to fix bugs and address GitHub issues
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| − | | |
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| − | Intermine
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| − | *JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine
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| − | *Developed FlyBase Intermine instance
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| − | *Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)
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| − | **E.g. Display meta information for a gene; "How many genes show this phenotype?"
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| − | *We have resources provisioned for building and hosting
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| − | *Low hanging fruit: access to ontologies, gene models, phenotypes, homology, orthology (things already made for Intermine)
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| − | *Focus first on central dogma stuff
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| − | SAB Meeting
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| − | *January 28th, 29th, 2013
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| − | *At Caltech
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| − | Concise description template
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| − | *Curator version versus a community (simpler) version
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| − | *1) Transfer info from elegans to other species
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| − | *2) Updates
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| − | *Easier to script when there is little information; harder when lots of info
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| − | Pathways
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| − | *Karen spoke to Alex Pico
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| − | *There could be tagged for "WormBase-approved" pathways
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| − | *Would be good to have worm community also contribute; "Community Pathways" widget
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| − | *Conflict resolution? There could be many contributions to the same pathway
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| − | *Is there a way to pull up conflicting versions of a pathway?
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| − | *Open system: any registered user can modify any pathway
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| − | Community Annotation
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| − | *Possibilities?
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| − | *Concise descriptions, pathways, what else?
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| − | *Expression patterns?
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| − | *Tables/templates of suggested data/types that authors could/should submit for a paper
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| − | *Annotation Apps? iPhone, Android, etc.
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| − | **Controlled vocabulary, virtual worm, AMIGO ontology browser, etc.
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| − | *Annotation on tablets, other mobile devices? Read only?
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| − | *Web app versus native app
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| − | *[http://www.openbadges.org Open Badges] for micro-attribution, incentives
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| − | *[http://about.orcid.org/ ORCID] for unique person IDs
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| − | *Possible Ontology Annotator version for community?
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| − | *Templates/forms would need to be very straight-forward and simple to use
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| − | *Maybe display a form alongside web display to inform users of how the two relate
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| − | *Training users: tutorials, workshops (2013 IWM?)
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| − | *Daily updates to website could be more satisfying for users
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| − | == November 8, 2012 == | |
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| − | Construction
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| − | *Burning smell frequently
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| − | *Now cigarette smoke smell (maybe completely unrelated to construction, of course)
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| − | Curation Status Form
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| − | *http://mangolassi.caltech.edu/~postgres/cgi-bin/curation_status.cgi
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| − | *Curators cannot indicate both positive and negative for a data type per paper; conflict must be resolved by curators
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| − | *One free text comment field (and one "pre-canned" comment field) per paper per data type
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| − | *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
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| − | *The form provides a (unique) way for curators to "validate" a paper as "negative" for a data type
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| − | *It is important to decouple validation from curation, so we can capture both
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| − | *Ideal if each paper could be independently categorized according to flagging status, validation status, and curation status
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| − | *Papers can be identified as "Not Validated", "Validated Negative", "Validate Positive - Not Curated", or "Validate Positive - Curated"
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| − | *We will make adjustments to form to accomodate
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| − | Dead Genes
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| − | *How do we/should we handle objects (e.g. interactions) that now refer to dead genes?
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| − | *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
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| − | *Will discuss more next week
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| − | | |
| − | == November 15, 2012 ==
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| − | Scripts from Mary Ann
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| − | *Script for recognizing alleles for Textpresso
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| − | *Mary Ann sent to James and Raymond
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| − | *James has been working on it
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| − | AQL/WQL Queries
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| − | *HTML vs plain text output
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| − | *HTML output takes much longer than plain text and often times out
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| − | *Not optimal to give users AQL queries; will be better once Intermine is up and running
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| − | *User data requests are use-cases for Intermine
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| − | *Problem with web browsers timing out before AQL query can finish: this is a browser issue
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| − | | |
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| − | Curation Statistics Tool
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| − | *Do curators want to see unions or intersections of specific flagging methods? Yes
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| − | *Will need to develop a visualization aside from the summary table
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| − | *Chris and Juancarlos will discuss offline
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| − | | |
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| − | Human Disease tags for ?Gene model
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| − | *Using common vocabulary
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| − | *Human_disease_info tag with subset tags : OMIM_ortholog, Potential_model_for, Experimental_model_for, and Human_disease_relevance
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| − | | |
| − | <pre>
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| − | ?Gene
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| − | Human_disease_info OMIM_ortholog ?Accession_number #Evidence
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| − | Potential_model_for ?DO_term XREF Gene #Evidence
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| − | Experimental_model_for ?DO_term XREF Gene #Evidence
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| − | Human_disease_relevance ?Text #Evidence
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| − | </pre>
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| − | | |
| − | *Change "?Accession_number" above to full database reference "?Database, ?Database_field, ?Accession_number"
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| − | *And add tags to #Evidence hash?
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| − | | |
| − | <pre>
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| − | ?Evidence
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| − | Inferred_from_sequence_orthology ?Accession_number
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| − | Inferred_from_mutant_phenotype ?Variation
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| − | Inferred_from_genetic_interaction ?Accession_number
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| − | </pre>
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| − | | |
| − | *Evidence_code tag instead of using #Evidence hash?
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| − | | |
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| − | Automated, template-based draft concise descriptions
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| − | *Kimberly and Ranjana had been working on a form before grant writing
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| − | *Idea is to use prompts to guide curators/community to write concise description sentences
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| − | *Have tested on some complex examples
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| − | *Once form is developed will send out to community
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| − | *If easy enough to use, we could make a student assignment for credit? - Gary S
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| − | == November 30, 2012 ==
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| − | | |
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| − | Curation Status Form
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| − | *Should we stick with "concatenated" SVM or "document" SVM?
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| − | **General trend is that "concatenated" SVM performs better
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| − | **We will go with "concatendated" SVM
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| − | *Once we clean up the code and document, we can move to Tazendra
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| − | *Curators can start tracking curation and flagging in earnest once we've switched to Tazendra
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| − | *Textpresso pipelines for curation and flagging?
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| − | *We can integrate other pipelines later
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| − | *Need to think about how to incorporate Mary Ann's curation pipeline
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| − | | |
| − | | |
| − | Anatomy Data Types in Author/Curation First Pass Forms
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| − | *Adapt to handle anatomy data types that Raymond actually curates
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| − | *Best to get rid of (or hide?) original 4 anatomy data types and replace with (5?) new ones
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| − | *Not needed to add new types to the Curation Status Form
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| − | | |
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| − | Next data upload will be December 20th
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| − | | |
| − | | |
| − | Model Changes for Parasites
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| − | *Mary Ann speaking with parasite nematode labs
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| − | *Need to capture drug resistance/susceptibility in Strains or Phenotypes
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| − | *How to change data models to accommodate
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| − | *Put everything in the Remark field (of #Phenotype_info of Phenotype wrt Strain)?
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| − | *What are the use cases for this data? Are we to act as basic/core repository for this info?
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| − | *What info should be indexed/modeled in tags? What would be queried, filtered, sorted?
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| − | *Phenotypes may/will need to account for host-parasite interactions; capture experimental model host? Natural/isolation host?
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| − | *One-time-use strains, or propagate-able?
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| − | | |
| − | | |
| − | AMIGO 2 Ontology Browser
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| − | *Raymond has AMIGO 2 running on our machines
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| − | *Not currently running off of our (worm) database/ontologies
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| − | *Currently troubleshooting installation/database problems
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| − | *AMIGO 2 reads OWL files; Need convert OBO to OWL? Not necessary
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| − | *Is the problem with the structure of the ontology(ies)? Test with phenotype ontology?
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| − | *Apache SOLR used for AMIGO; need to understand SOLR; then, may not need AMIGO
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