https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_November_2019&feed=atom&action=historyWormBase-Caltech Weekly Calls November 2019 - Revision history2024-03-29T12:13:54ZRevision history for this page on the wikiMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_November_2019&diff=34621&oldid=prevCgrove: Created page with "== November 7, 2019 == === WS275 Citace upload === * Maybe Nov 22 upload to Hinxton * CIT curators upload to Spica on Tues Nov 19 === ?Genotype class === * [https://docs.goo..."2019-12-05T16:31:39Z<p>Created page with "== November 7, 2019 == === WS275 Citace upload === * Maybe Nov 22 upload to Hinxton * CIT curators upload to Spica on Tues Nov 19 === ?Genotype class === * [https://docs.goo..."</p>
<p><b>New page</b></p><div>== November 7, 2019 ==<br />
<br />
=== WS275 Citace upload ===<br />
* Maybe Nov 22 upload to Hinxton<br />
* CIT curators upload to Spica on Tues Nov 19<br />
<br />
=== ?Genotype class ===<br />
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]<br />
* Several classes have a "Genotype" tag with text entry<br />
** Strain<br />
** 2_point_data<br />
** Pos_neg_data<br />
** Multi_pt_data<br />
** RNAi<br />
** Phenotype_info<br />
** Mass_spec_experiment (no data as of WS273)<br />
** Condition<br />
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:<br />
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"<br />
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"<br />
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"<br />
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"<br />
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."<br />
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"<br />
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"<br />
** Reference to parent strain, like "Parent strain is AG359"<br />
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"<br />
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"<br />
<br />
=== Gene comparison SObA ===<br />
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph<br />
<br />
<br />
== November 14, 2019 ==<br />
<br />
=== TAGC meeting ===<br />
* The Allied Genetics Conference next April (2020) in/near Washington DC<br />
* Abstract deadline is Dec 5th<br />
* Alliance has a shared booth (3 adjacent booths)<br />
* Micropublications will have a booth (Karen and Daniela will attend)<br />
* Focus will be on highlighting the Alliance<br />
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)<br />
<br />
=== Alliance all hands meeting ===<br />
* Lightning talk topics?<br />
** Single cell RNA Seq (Eduardo)<br />
** SimpleMine? (Wen)<br />
** SObA? (Raymond); still working on multi-species SObA<br />
** Phenotype community curation?<br />
** Micropublications?<br />
** AFP?<br />
<br />
=== Alliance general ===<br />
* Alliance needs a curation database<br />
** A curation working group was proposed<br />
** What needs to happen to get this going?<br />
** Would include text mining tools/resources<br />
** Would be good to have something like the curation status form<br />
** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features<br />
** Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type<br />
* Micropubs pushing data submission forms; might as well house them within the Alliance<br />
* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members<br />
** Maybe MOD curators can manage configuration files to indicate what is relevant for their species<br />
** First priority is to focus on automatically recognizable entities/features from papers<br />
<br />
<br />
== November 21, 2019 ==<br />
<br />
=== Textpresso: merging main docs and supps? ===<br />
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately<br />
* This results in possibly getting many results for the same publication, each scored and displayed separately<br />
* Do we want Texptpresso to search on a single, consolidated file containing the main document of a paper AND the supplementals?<br />
* Currently, the scoring algorithm is often scoring supplemental documents higher than main papers, presumably due to a weighting of documents in which there is a higher percentage of sentences with matches to the keyword(s)<br />
* This cannot be done completely manually; agreed, this would have to be largely (completely?) automated<br />
* Would be good to check how PMC/Europe PMC handles articles in which main docs and supps are consolidated into a single PDF already (in addition to individual files)<br />
* Detecting duplicated sentences would be useful, but may be quite a thorny issue (need to research)<br />
* Chris will update GitHub ticket to ask Sibyl to NOT search on C. elegans supplementals, for now, and only search on main documents<br />
<br />
=== Europe PMC: biocuration landscape analysis ===<br />
* Dayane Araújo has asked that a curator (Chris currently) attend a conference call (next Monday, Nov 25) hosted by Europe PMC about assessing biocuration across databases<br />
* Chris has asked for details but has so far not received anything specific<br />
* Should we attend? Yes, at least to listen. If complex questions come up, we can just tell them we'll look it up<br />
* Would be great if there were aggregated references for particular datasets so that users of data and analyses could be given all references to properly cite in their own article</div>Cgrove