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| | [[WormBase-Caltech_Weekly_Calls_February_2015|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2015|February]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_March_2015|March]] |
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| | ** Does anyone want Species information for any of the other files | | ** Does anyone want Species information for any of the other files |
| | ** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/ | | ** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/ |
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| − | = March 2015 =
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| − |
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| − | == March 5, 2015 ==
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| − |
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| − | === New curation topic for WS249 ===
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| − | * We will do Lipid Metabolism for WS249
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| − |
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| − | === Paper ID converter tool ===
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| − | * Juancarlos built a simple CGI to convert a list of PubMed IDs to WBPaper IDs
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| − | * http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=PapIdToWBPaper
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| − | * Would other curators use this or a more comprehensive tool?
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| − | * What ID types would curators want to convert between?
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| − |
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| − | === GO data model change ===
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| − | * Change for WS248
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| − | * More detail with each annotation
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| − | * Pipeline for data incorporation into the build has changed; path goes through Caltech/Postgres for QC
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| − | * Changes to gene association file has implications for automated descriptions
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| − | * Do we want to include PAINT annotations for automated descriptions?
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| − | ** Based on phylogenetic evidence codes
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| − | ** Yes, could be a great benefit to the automated descriptions
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| − | ** New GO annotations include a Panther tree node
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| − | ** Should we include both manually annotated data AND PAINT data in automated descriptions equally? Should look at examples and check how we want to handle
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| − | * Clickable (linkable) evidence throughout the description?
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| − |
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| − | === International meeting give-aways ===
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| − | * Worm pick holders (pencil grips) with WormBase logos; can they be printed on?
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| − | * T-shirts and/or hats/caps; personalized for curators
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| − |
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| − | === Topic & Regional meeting abstracts ===
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| − | * Usually we receive the data for these meeting abstracts in a non-standardized format; makes it difficult/time-consuming to parse
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| − | * Would be good to request submissions in standard format
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| − | * Good to maybe go through GSA pipeline?
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| − |
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| − | === NIH request for info on sustaining bio-databases ===
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| − | * NIH requesting info on:
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| − | ** best practices
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| − | ** collaborations/partnerships
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| − | ** efficiency
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| − | ** alternative funding sources
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| − | *** requiring a DB funding allocation in individual grant applications?
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| − | ** medical application
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| − | * What benefit do databases provide?
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| − | ** Differential usefulness: transient DBs versus maintained, broader impact DBs
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| − | * Should MODs merge?
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| − | * So much has changed in terms of database and web technology since online bio DBs began
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| − | * Value distinction of manually curated annotations
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| − | * How much redundancy is there between DB effort?
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| − | * How do we assess the value of WormBase (or any DB) for academia and industry?
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| − | * We should assess the scientific value to determine monetary value
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| − | ** Promote the benefit of transparency and reproducibility
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| − |
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| − | === Micropublication ===
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| − | * We can introduce the idea at the international meeting
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| − | * May be nice to group all micropublications into a single official publication
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| − | * Maybe use "Gene Expression" journal for gene expression data as a pilot
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| − |
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| − |
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| − | == March 12, 2015 ==
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| − |
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| − | === Historical_gene tag ===
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| − | * Issues came up with layered hash references in ACEDB when converting to Datomic
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| − | * Changing line from "Historical_gene ?Gene #Evidence" to "Historical_gene ?Gene Text"
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| − | * Affects ?Interaction, ?Expr_pattern, ?Antibody, ?Construct, and ?WBProcess
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| − |
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| − | === WormBook Chapters ===
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| − | * Do we want/need a separate chapter/section on the new WormBase Ontology Browser?
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| − | ** Maybe only need a few small paragraphs in other relevant chapters, should be sufficient
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| − | * Gene Function & Interaction chapter almost complete
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| − | ** Need to finish intro for phenotypes
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| − | ** Need to add predicted & regulatory interaction descriptions
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| − |
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| − | === Topic OA reminder ===
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| − | * The 'primary'/'nonprimary' paper status is updated automatically every night by a cron job
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| − | * The "Curation Status Omit" toggle button on TAB 3 was intended to flag nonprimary papers, but is no longer needed for that; only for rare noncuratable, primary, relevant articles (e.g. Methods papers)
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| − |
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| − | === Cloud bio-data storage ===
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| − | * Cloud has potential advantage of distributed colocation; robust for queries, performance etc.
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| − |
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| − | === Modeling user-submitted data ===
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| − | * How should we distinguish user-submitted data from curator-submitted data?
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| − | * Should we distinguish at the data model level, with a new tag for example? Probably only need to apply WBPerson evidence, etc.
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| − | * This issue came up with user-submitted/user-edited concise descriptions
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| − | * The distinction can be made explicit exclusively at the display (web page) level
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| − | * There could be a toggle in the OA to indicate user-submitted data
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| − |
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| − |
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| − |
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| − | == March 19, 2015 ==
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| − |
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| − | === WormBook Chapters ===
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| − | * Most chapters mostly complete as a draft
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| − | * Paul S. working on introduction
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| − | * Process chapter may not fill a chapter; also pending some website updates
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| − | * Person/author section can be added to nomenclature section
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| − |
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| − | === Mapping Bio-Annotations to Process ===
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| − | * Can we achieve automated mapping of annotations to processes?
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| − | * e.g. phenotype-to-process mapping, site-of-action (cells and genes) mapping to process
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| − | * Some phenotypes are indicative of a process, but some cannot be unambiguously mapped
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| − | * Some processes can be mapped to based on sequence homology (e.g. Wnt signaling) rather than phenotype
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| − |
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| − | === GO Physical interactions into WormBase ===
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| − | * Several (~400) papers in curation status form are considered "curated" for physical interactions via the GO pipeline
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| − | * We would like to import these annotations into WormBase
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| − | * Directionality information has been lost in the GO annotations
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| − | * We want to re-curate the interactions to capture detection method and directionality
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| − | * We could import all interactions in bulk without detection method or directionality with flag indicating a need to re-curate with additional information
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| − |
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| − | === Topic curation ===
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| − | * Reminder for curators to check their lipid metabolism papers
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| − | * Daniela working with web team to create a Pictures widget on Topic pages to display pathway/topic images (with permission)
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| − |
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| − | === Interaction-based phenotypes ===
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| − | * On staging, Sibyl has added an "Interaction-based Phenotypes" table in the Gene page Phenotypes widget
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| − | * This phenotype data is taken exclusively from genetic interaction objects to associate the gene with the phenotype
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| − |
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| − |
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| − |
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| − | == March 26, 2015 ==
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| − |
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| − | === Community submission forms ===
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| − | * Micropublication
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| − | ** People may submit expression data directly, with future citation (e.g. DOI)
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| − | ** Data submissions will need to adhere to some criteria providing evidence and reviewed by Paul, Daniela, and some other reviewer
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| − | ** Form could be recycled for published data submission
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| − | ** Forms remember user e-mails from IP used; makes easier to fill out subsequent submissions
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| − | ** Daniela will talk to Daniel about assigning DOIs
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| − | ** Can these be indexed by PubMed, etc.? Daniela discussing with Caltech librarians
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| − | * We should focus on promoting/pushing one data type submission so as not to overwhelm the community; focus on others later
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| − | * Concise description forms
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| − | ** Want to send automated descriptions (or existing manual descriptions) to users to quality check based on their expert (published) knowledge
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| − | ** User will use form to submit edits to descriptions
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| − | ** Do we want/need users to stick to automated description format/guidelines?
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| − | ** We could have direct links to forms from the Overview widget on gene pages
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| − |
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| − | === Funding Supplement Dedicated to Interoperability between MODs ===
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| − | * Textpresso can be used to create common text mining pipelines across databases
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| − | * Combining concise descriptions or taking advantage of other MOD data
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| − | * Supplement funding application due in April (soon)
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| − |
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| − | === Database migration ===
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| − | * Hope to have a pilot of new databases (Datomic?) done by mid-Fall
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| − |
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| − | === Global correlation of RNAseq gene expression data ===
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| − | * All pairs of genes could have a correlation calculation performed (based on RNAseq) and displayed on WormBase
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| − | * Significant correlations could be a type of interaction/association
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