https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_March_2015&feed=atom&action=historyWormBase-Caltech Weekly Calls March 2015 - Revision history2024-03-29T00:19:39ZRevision history for this page on the wikiMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_March_2015&diff=26563&oldid=prevCgrove: Created page with "= March 2015 = == March 5, 2015 == === New curation topic for WS249 === * We will do Lipid Metabolism for WS249 === Paper ID converter tool === * Juancarlos built a simple..."2015-04-02T15:32:30Z<p>Created page with "= March 2015 = == March 5, 2015 == === New curation topic for WS249 === * We will do Lipid Metabolism for WS249 === Paper ID converter tool === * Juancarlos built a simple..."</p>
<p><b>New page</b></p><div>= March 2015 =<br />
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== March 5, 2015 ==<br />
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=== New curation topic for WS249 ===<br />
* We will do Lipid Metabolism for WS249<br />
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=== Paper ID converter tool ===<br />
* Juancarlos built a simple CGI to convert a list of PubMed IDs to WBPaper IDs<br />
* http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=PapIdToWBPaper<br />
* Would other curators use this or a more comprehensive tool?<br />
* What ID types would curators want to convert between?<br />
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=== GO data model change ===<br />
* Change for WS248<br />
* More detail with each annotation<br />
* Pipeline for data incorporation into the build has changed; path goes through Caltech/Postgres for QC<br />
* Changes to gene association file has implications for automated descriptions<br />
* Do we want to include PAINT annotations for automated descriptions?<br />
** Based on phylogenetic evidence codes<br />
** Yes, could be a great benefit to the automated descriptions<br />
** New GO annotations include a Panther tree node<br />
** 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<br />
* Clickable (linkable) evidence throughout the description?<br />
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=== International meeting give-aways ===<br />
* Worm pick holders (pencil grips) with WormBase logos; can they be printed on?<br />
* T-shirts and/or hats/caps; personalized for curators<br />
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=== Topic & Regional meeting abstracts ===<br />
* Usually we receive the data for these meeting abstracts in a non-standardized format; makes it difficult/time-consuming to parse<br />
* Would be good to request submissions in standard format<br />
* Good to maybe go through GSA pipeline?<br />
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=== NIH request for info on sustaining bio-databases ===<br />
* NIH requesting info on:<br />
** best practices<br />
** collaborations/partnerships<br />
** efficiency<br />
** alternative funding sources<br />
*** requiring a DB funding allocation in individual grant applications?<br />
** medical application<br />
* What benefit do databases provide? <br />
** Differential usefulness: transient DBs versus maintained, broader impact DBs<br />
* Should MODs merge?<br />
* So much has changed in terms of database and web technology since online bio DBs began<br />
* Value distinction of manually curated annotations<br />
* How much redundancy is there between DB effort?<br />
* How do we assess the value of WormBase (or any DB) for academia and industry?<br />
* We should assess the scientific value to determine monetary value<br />
** Promote the benefit of transparency and reproducibility<br />
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=== Micropublication ===<br />
* We can introduce the idea at the international meeting<br />
* May be nice to group all micropublications into a single official publication<br />
* Maybe use "Gene Expression" journal for gene expression data as a pilot<br />
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== March 12, 2015 ==<br />
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=== Historical_gene tag ===<br />
* Issues came up with layered hash references in ACEDB when converting to Datomic <br />
* Changing line from "Historical_gene ?Gene #Evidence" to "Historical_gene ?Gene Text"<br />
* Affects ?Interaction, ?Expr_pattern, ?Antibody, ?Construct, and ?WBProcess<br />
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=== WormBook Chapters ===<br />
* Do we want/need a separate chapter/section on the new WormBase Ontology Browser?<br />
** Maybe only need a few small paragraphs in other relevant chapters, should be sufficient<br />
* Gene Function & Interaction chapter almost complete<br />
** Need to finish intro for phenotypes<br />
** Need to add predicted & regulatory interaction descriptions<br />
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=== Topic OA reminder ===<br />
* The 'primary'/'nonprimary' paper status is updated automatically every night by a cron job<br />
* 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)<br />
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=== Cloud bio-data storage ===<br />
* Cloud has potential advantage of distributed colocation; robust for queries, performance etc.<br />
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=== Modeling user-submitted data ===<br />
* How should we distinguish user-submitted data from curator-submitted data?<br />
* Should we distinguish at the data model level, with a new tag for example? Probably only need to apply WBPerson evidence, etc.<br />
* This issue came up with user-submitted/user-edited concise descriptions<br />
* The distinction can be made explicit exclusively at the display (web page) level<br />
* There could be a toggle in the OA to indicate user-submitted data<br />
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== March 19, 2015 ==<br />
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=== WormBook Chapters ===<br />
* Most chapters mostly complete as a draft<br />
* Paul S. working on introduction<br />
* Process chapter may not fill a chapter; also pending some website updates<br />
* Person/author section can be added to nomenclature section<br />
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=== Mapping Bio-Annotations to Process ===<br />
* Can we achieve automated mapping of annotations to processes?<br />
* e.g. phenotype-to-process mapping, site-of-action (cells and genes) mapping to process<br />
* Some phenotypes are indicative of a process, but some cannot be unambiguously mapped<br />
* Some processes can be mapped to based on sequence homology (e.g. Wnt signaling) rather than phenotype<br />
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=== GO Physical interactions into WormBase ===<br />
* Several (~400) papers in curation status form are considered "curated" for physical interactions via the GO pipeline<br />
* We would like to import these annotations into WormBase<br />
* Directionality information has been lost in the GO annotations<br />
* We want to re-curate the interactions to capture detection method and directionality<br />
* We could import all interactions in bulk without detection method or directionality with flag indicating a need to re-curate with additional information<br />
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=== Topic curation ===<br />
* Reminder for curators to check their lipid metabolism papers<br />
* Daniela working with web team to create a Pictures widget on Topic pages to display pathway/topic images (with permission)<br />
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=== Interaction-based phenotypes ===<br />
* On staging, Sibyl has added an "Interaction-based Phenotypes" table in the Gene page Phenotypes widget<br />
* This phenotype data is taken exclusively from genetic interaction objects to associate the gene with the phenotype<br />
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== March 26, 2015 ==<br />
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=== Community submission forms ===<br />
* Micropublication<br />
** People may submit expression data directly, with future citation (e.g. DOI)<br />
** Data submissions will need to adhere to some criteria providing evidence and reviewed by Paul, Daniela, and some other reviewer<br />
** Form could be recycled for published data submission<br />
** Forms remember user e-mails from IP used; makes easier to fill out subsequent submissions<br />
** Daniela will talk to Daniel about assigning DOIs<br />
** Can these be indexed by PubMed, etc.? Daniela discussing with Caltech librarians<br />
* We should focus on promoting/pushing one data type submission so as not to overwhelm the community; focus on others later<br />
* Concise description forms<br />
** Want to send automated descriptions (or existing manual descriptions) to users to quality check based on their expert (published) knowledge<br />
** User will use form to submit edits to descriptions<br />
** Do we want/need users to stick to automated description format/guidelines?<br />
** We could have direct links to forms from the Overview widget on gene pages<br />
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=== Funding Supplement Dedicated to Interoperability between MODs ===<br />
* Textpresso can be used to create common text mining pipelines across databases<br />
* Combining concise descriptions or taking advantage of other MOD data<br />
* Supplement funding application due in April (soon)<br />
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=== Database migration ===<br />
* Hope to have a pilot of new databases (Datomic?) done by mid-Fall<br />
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=== Global correlation of RNAseq gene expression data ===<br />
* All pairs of genes could have a correlation calculation performed (based on RNAseq) and displayed on WormBase<br />
* Significant correlations could be a type of interaction/association</div>Cgrove