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| | [[WormBase-Caltech_Weekly_Calls_July_2014|July]] | | [[WormBase-Caltech_Weekly_Calls_July_2014|July]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_August_2014|August]] |
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| − | == August 7, 2014 ==
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| − | * Topic Curation
| + | == September 4, 2014 == |
| − | ** Working out pipeline for curation
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| − | ** Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects for these?
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| − | *** Do we want to display these published diagrams on ?Paper pages and/or ?Topic pages
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| − | *** We need to determine copyrights/accessibility to images
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| − | ** Would be good to automate identification of Review articles (or "non-primary" in general) in the Topic OA
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| − | *** This could be done at the bulk import step
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| − | *** Would require a new (possibly read-only) field in the Topic OA to indicate "primary" or "non-primary"
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| − | ** Chris will look into whether "non-primary" articles are automatically excluded from the Curation Status Form
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| − | ** The "Curation Status Omit" toggle in the Topic OA may become obsolete once we have a field/column for primary/non-primary status
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| − | ** Current topic : Wnt signaling
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| − | ** We have a list of 282 papers from PubMed search using "Wnt" search term (not Mesh term) and C. elegans (Mesh term)
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| − | ** Finding all papers for a category/topic remains an ad hoc approach; different topics are harder or easier to find all papers for
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| − | ** We can create a Textpresso category for topics, like "Wnt signaling"
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| − | | + | * Topic 1 |
| − | * WormBase Ontology Browser
| + | * Topic 2 |
| − | ** Needs documenting
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| − | ** Once everything is clarified, will be pushed to the live site
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| − | | |
| − | == August 14, 2014 ==
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| − | | |
| − | * WormBase Ontology Browser (WOBr)
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| − | ** Should be ready but may need some additional testing before pushing to staging site
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| − | ** Juancarlos will push to staging during meeting
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| − | ** Curators should test this afternoon (on staging) and report any issues before 5pm
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| − | | |
| − | * DataBase call this morning (and every Thursday that doesn't have a site-wide call)
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| − | ** Thomas Down testing Datomic (costs money) and Neo4J (very slow)
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| − | ** May look again at DynamoDB
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| − | ** No DB has been officially chosen
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| − | ** Will have an Amazon AWS for collaboration.
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| − | ** Expand smallace into bigger mediumace.
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| − | ** Demo off one database for advisory board meeting.
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| − | | |
| − | * SAB
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| − | ** Paul Sternberg back next week; will settle travel plans then
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| − | ** What advisors are attending?
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| − | ** What feedback do we want to get from advisors?
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| − | ** How to show curation/DB progress? What stats/numbers to show?
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| − | ** We want big picture feedback from biologist advisors; what's useful to the community? What should we prioritize?
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| − | ** Karen: Perhaps a question to ask is "what are the main questions they are trying to answer when they go to the website?". When they explore a gene or protein function, what is it that they would want to see, and how? I don't think we are missing information so much as a lack of integration of the information at the model level, for example, variation phenotype affects linked to altered protein domain function
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| − | | |
| − | * Belated apologies from Mary Ann - clash of evening events.
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| − | | |
| − | == August 21, 2014 ==
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| − | | |
| − | * Generating a Site-Map for WormBase
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| − | ** Use a crawler to generate? Output would need to be made human-readable
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| − | ** We could use the legacy site as a site map
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| − | * Citace upload report modifications
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| − | ** wikipage here: [[Citace_upload_report]]
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| − | ** Goals of this report
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| − | *** Summary of the uploaded data classes/objects - this summary should be blind to requests from curators and should alert Caltech to missing data classes or severe changes in numbers of objects within preexisting data classes
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| − | *** Summary of curation work - this summary should be curator driven, in some cases the summary will require a more involved aceperl query to get at the actual annotation rather than a straight data class object number.
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| − | ** Can we get a comparison for those data that are curated through postgres? It would be very helpful to be able to compare the changes in postgres with the changes in the Citace upload.
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| − | ** Can we automate the generation of this report to make it easier to change and track?
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| − | ** Regardless of manual or automated report generation when there is a model change or data class addition/subtraction, the responsible curator needs to inform Wen of the need for compensatory modification in the report.
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| − | | |
| − | == August 28, 2014 ==
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| − | | |
| − | * Curation Statistics for SAB
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| − | ** Curators should send Chris all stats for their respective data types: total papers curated, total backlog, false positives
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| − | ** Can we ignore SVM results for certain data types?
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| − | ** Can we include Textpresso search results for relevant data types?
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| − | ** Curators that use a Textpresso pipeline: Karen, Ranjana, Xiaodong, (Daniela?), Mary Ann
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| − | ** Can we get detailed web usage statistics on particular datatypes?
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| − | ** We want to articulate our priorities to the SAB; get feedback
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| − | ** RNAi curation could get up to speed in 5 years if we have two FTEs on RNAi curation
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| − | ** Are there certain genes that have less phenotype coverage that we should prioritize?
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| − | | |
| − | * Database migration call
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| − | ** MongoDB, CouchDB, Neo4J, Datomic, OrientDB, postgreSQL, Cassandra candidates
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| − | ** Neo4J likely ruled out because of slow performance
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| − | ** Will compare performance of Datomic vs. Postgres and ACEDB, etc.
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| − | ** Datomic has good history tracking
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| − | ** Thomas Down has experience with Datomic
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| − | ** Probably won't go with a relational database
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| − | ** We should use the Gene page (webpage) as a demo/example of what we want to try to emulate
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| − | ** Adam (from Lincoln's group) working with OrientDB (graph database)
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| − | | |
| − | * Citace Upload Report
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| − | ** Classes/datatypes missing from Citace Upload Report
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| − | ** Karen started a Wiki page to capture this info: [[Citace_upload_report]]
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| − | ** Curators should take a look and make sure it is properly filled out for their data types | |
| − | ** Columns are present in the table to make requests for certain numbers in Citace Upload Report and/or the Build Report | |
| − | ** Wen will take requests for queries to Citace etc. to add data to report
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| − | | |
| − | * UniProt linking to and from WormBase
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| − | **UniProt would like us to add information about some specific curated datatypes to a file we already supply that maps paper and gene identifiers
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| − | **Kimberly and Juancarlos will work on this
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| − | **Need to clarify with UniProt how links back to WormBase can/will be implemented
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| − | | |
| − | * Paul S going to NIH for data science meeting next week
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| − | | |
| − | * FlyBase pushing human disease curation
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| − | | |
| − | * LEGO backend updates
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| − | ** Still need to get some backend logistics sorted out
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| − | ** Communication between Michael Muller and Chris Mungall
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| − | ** OA-like interface for Noctua?
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