https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_January_2017&feed=atom&action=historyWormBase-Caltech Weekly Calls January 2017 - Revision history2024-03-28T19:19:54ZRevision history for this page on the wikiMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_January_2017&diff=30387&oldid=prevCgrove: Created page with "== January 5, 2017 == === BioCurator meeting === * Who from WormBase will go? ** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go ** Daniela maybe f..."2017-02-02T16:44:04Z<p>Created page with "== January 5, 2017 == === BioCurator meeting === * Who from WormBase will go? ** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go ** Daniela maybe f..."</p>
<p><b>New page</b></p><div>== January 5, 2017 ==<br />
<br />
=== BioCurator meeting ===<br />
* Who from WormBase will go?<br />
** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go<br />
** Daniela maybe for micropublication<br />
<br />
=== International C. elegans Meeting ===<br />
* June 2017<br />
* Whether all WB staff go depends on whether we have an all hands meeting before/after<br />
* Plenty of things to present; AGR stuff etc.<br />
<br />
=== Citace upload ===<br />
* Prepare files by 10am on Tuesday, Jan 10<br />
<br />
=== LEGO curation ===<br />
* Kimberly working on different C. elegans models<br />
* Working on several pathways simultaneously<br />
* Should be in production soon (this year), fully evidenced<br />
* Full benefit may not be apparent until AGR has LEGO fully integrated<br />
* Working out how inferred annotations propagate from Noctua/LEGO model to GAF<br />
* MGI creating many LEGO models<br />
* How are curators, that went to training, using LEGO?<br />
* Curation level view may not be amenable to general biologist/user viewing<br />
* What is the best existing pathway display? WikiPathways? Protege?<br />
* GO people (Seth, Chris M., Suzi etc.) are working on display, but have limited resources for this<br />
* Maybe we could work with WikiPathways team?<br />
* Pathway studio at RGD? Manually generated<br />
* Should WB have a LEGO call? Yes, probably<br />
* Curators may need access to Protein2GO for full curation/inference by sequence similarity<br />
* How do we/should we resolve parallel pipelines for curating cellular component data (Go versus Expression pattern)?<br />
* How do we accommodate specific versus general processes? E.g. specific versus general cell division<br />
* We would like a mechanism for a LEGO curator to pull relevant data from GAF<br />
* We would like curators to focus on pathway perspective of curation, where authors can submit experimental details with a potential automated or semi-automated mechanism to bridge the gap<br />
<br />
=== Expression widget ===<br />
* Daniela and Sibyl working on a more compact display of the expression data widget on gene pages<br />
* Should we keep subcellular localization in the expression widget? Yes<br />
<br />
=== SObA for Gene Ontology ===<br />
* Raymond and Juancarlos working on<br />
* First for WormBase, eventually want for AGR<br />
* For GO data, will have three different roots (for each branch of GO); One DAG for each<br />
* Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.<br />
* Would be great to have a comparative view mechanism<br />
<br />
== January 12, 2017 ==<br />
=== Caltech LEGO Call ===<br />
*Confirm time: Mondays, 11am PST (2pm EST/7pm GMT)<br />
*Start January 23rd<br />
*Format?<br />
**Start with curation of one paper together?<br />
***Possible paper: [https://www.ncbi.nlm.nih.gov/pubmed/27881675 The Intestinal Copper Exporter CUA-1 Is Required for Systemic Copper Homeostasis in Caenorhabditis elegans.]<br />
**Curators then select individual topics?<br />
<br />
=== Switching website to run off Datomic ===<br />
* Juancarlos joining biweekly call on Wednesdays with Adam, Matt, and Sibyl<br />
* Juancarlos working on Person page widgets currently<br />
** Intellectual lineage graph will need to be rewritten in Clojure<br />
* Web team is working out the file/directory structure to organize widget generation<br />
* Is the Datomic database denormalized? To what extent? No, not really<br />
** This affects how we might eventually write into Datomic from our curation database<br />
* May be best for Caltech to keep a Postgres curation database in parallel to Datomic (and eventually sync nightly)<br />
** This may also be best with AGR as well<br />
<br />
=== Biocuration meeting 2017 ===<br />
* Who's going? Ranjana, Chris, Raymond, Mary Ann, Daniela (if she gets a talk)<br />
* Ranjana - automated descriptions<br />
* Raymond - SObA graph<br />
* Chris - Genetic interactions<br />
* Mary Ann - Community curation<br />
* Daniela - Micropublications<br />
<br />
=== Community curation presentation on AGR curator call ===<br />
* Chris and Val Wood presented; minutes are here- [https://docs.google.com/document/d/1PdmdnTduxidxaljExTbalNA4ReyIRsZZmV6U-5ckXiI/edit AGR minutes]<br />
* WB community curation numbers<br />
** 321 papers solicited and community curated (Phenotype OA)<br />
** 417 papers community curated in total (Phenotype OA)<br />
** 313 unique community curators (Phen OA); average 8 annotations per curator<br />
** 64 papers solicited and community curated (RNAi OA)<br />
** 74 papers community curated in total (RNAi OA)<br />
** 61 unique community curators (RNAi OA); average 16 annotations per curator<br />
** 3324 annotations total; 2969 valid and confirmed<br />
** 2111 solicitations gone out; 16% response rate<br />
<br />
Val presented some information on how complete contributors were:<br />
*''1990s were getting 10 annotations/paper, in most recent years are now getting 50 annots/paper (years are publication years)''<br />
*''Curation quality - users often omit a data type, but for what they do curate, they are generally very accurate, and often request more specific terms''<br />
<br />
Chris suspects ~20% authors are complete in their phenotype curation of their paper.<br />
<br />
=== Pulling WB data into LEGO models ===<br />
* Phenotype data requires a mapping step to map alleles and RNAi to genes<br />
* How might we crowd source or get low cost curators to curate bulk data? Followed by expert curation for LEGO models<br />
* May be best for curators to take on specific topics of biology<br />
<br />
<br />
== January 19, 2017 ==<br />
<br />
=== SObA graph for Gene Ontology ===<br />
* Juancarlos and Raymond asking for feedback on GO SObA graph<br />
* Kimberly: Can we create graphs for subsets of annotations (manual vs. automated)?<br />
** Raymond: It's doable as a standalone graph, but may be difficult to make an option embedded within the core display<br />
** May be a way to display IEA annotations separately from non-IEA annotations<br />
** Raymond: Can develop a personal view for Kimberly to visualize manual vs. automated annotations<br />
* Three root terms for GO, displayed side-by-side in the same graph; root nodes are different sizes and not necessarily displayed aligned<br />
* May be able to force the root nodes to be the same size<br />
* May want to show/hide individual roots; doable although unclear how difficult to implement<br />
* GO function and component are likely to be smaller networks than process<br />
* Pulling data from GAF into Solr<br />
* Can this be adopted for the AGR portal? Yes<br />
<br />
=== WormBase workshop at 2017 IWM ===<br />
* Ranjana organizing<br />
* Discuss ideas with Ranjana<br />
* Have 1.5 - 2 hours<br />
* Will want to discuss micropublications and community annotations<br />
* We haven't had mirrors in a long time: discuss Datomic for people who want to query? Yes, brief announcement<br />
<br />
=== User Survey ===<br />
* We may want user surveys to prepare for grant writing, progress report<br />
* Could send out to users by May? <br />
* What to focus on: performance, data types, usability<br />
* Could have multiple short surveys<br />
* What one question would we want answers to help with design decisions?<br />
* Do we want (eventually for AGR) a professional surveyor?<br />
* Are our services meeting user needs?<br />
* We can take a closer look at user logs; see what data, widgets, tools used most frequently (least frequently)<br />
* We could create focus groups to get feedback from users on specific topics (30 minute sessions during poster sessions, for example); maybe at booth? during meal time?<br />
** Would want to post a schedule with dedicated locations<br />
* Could have WormBase hats, brightly colored ;), to indicate to people that we're WormBase staff<br />
<br />
=== Disease data display on AGR portal gene page ===<br />
* Working out a way to drill down from a summary view down to detailed table view<br />
* Need to make sure it is intuitive and non-jargony for end users<br />
* Yvonne Bradford drew up some mockups that represent a ribbon or heatmap display of annotations to disease categories for experimental models, etc.<br />
* We do want a SObA graph; could possibly create a SObA graph that represents annotations to a gene AND all of its orthologs<br />
<br />
=== First LEGO call ===<br />
* This Monday (Jan 23) 11am Pacific<br />
<br />
<br />
== January 26, 2017 ==<br />
<br />
=== GO-CC annotations to paper term info in OA ===<br />
* Daniela working on with Juancarlos<br />
<br />
=== Disease working group ===<br />
* Working to finalize the DAF (disease association file)<br />
* Having extra meeting tomorrow<br />
* Will then hand over DAF format to Kevin Howe (WB Data Quartermaster)<br />
* In general, Kevin would prefer AGR files to be generated from the WB build process<br />
<br />
=== Expression data working group? ===<br />
* Daniela asking about an expression working group<br />
* We don't have one currently, but one could be generated, although it may not make it into AGR portal 0.3, 0.6 or 1.0<br />
<br />
=== Coherence, Consistency, and Continuity working group ===<br />
* Working on a standard for table display in AGR portal<br />
* Asking for standard functionality<br />
** Table filtering, by column<br />
** Table sorting, including sort order<br />
** Paginated, choosing number of results per page<br />
** Download options, tab-delimited and other formats<br />
** Link to Intermine, to view, save and manipulate table and lists<br />
* Currently WormBase has insufficient means to download some lists of results, for example downloading list of RNAi's that cause a lethal phenotype on the "lethal" phenotype page<br />
** WB points users to FTP site, without specifying a file or how to parse<br />
<br />
=== WormMine vs AGR Intermine ===<br />
* Is Paulo working on shared/AGR Intermine or just WormMine? We think just WormMine<br />
* There was an issue with making orthology calls which may have interfered with integrating worm data into common Intermine</div>Cgrove