Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
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= 2019 Meetings =
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== January 9, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
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[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
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[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
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[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
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[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
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[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
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[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
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[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
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== November 7, 2019 ==
 
  
−
=== WS275 Citace upload ===
+
=== Phenotype Curation Requests ===
−
* Maybe Nov 22 upload to Hinxton
+
* 1,229 emails sent Dec 3-6, 2019
−
* CIT curators upload to Spica on Tues Nov 19
+
* Received 194 annotations from 40 papers and from 37 distinct community curators
 +
** 37 papers requested, 3 additional papers annotated
 +
** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
 +
** 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
 +
* 43 bounced emails
 +
** 2 resent to new addresses
 +
** 5 have backup email addresses (also sent)
  
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=== ?Genotype class ===
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=== Worm Area Meetings ===
−
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
−
* Several classes have a "Genotype" tag with text entry
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* Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
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** Strain
 
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** 2_point_data
 
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** Pos_neg_data
 
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** Multi_pt_data
 
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** RNAi
 
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** Phenotype_info
 
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** Mass_spec_experiment (no data as of WS273)
 
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** Condition
 
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* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
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** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
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** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
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** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
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** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
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** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
−
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
−
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
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** Reference to parent strain, like "Parent strain is AG359"
 
−
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
−
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
 
  
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=== Gene comparison SObA ===
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=== Reference widget Textpresso linkouts ===
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* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
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* Now live on WormBase, WS274
 +
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
 +
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
 +
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
 +
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
 +
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
 +
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
 +
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
 +
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
 +
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
 +
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
 +
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
 +
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
 +
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
 +
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
 +
* Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
 +
* Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
 +
* Process examples:
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10
 +
* Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
  
 +
=== WS276 Citace upload ===
 +
* Hinxton upload Jan 31, 2020
 +
* Citace upload on Tuesday, Jan 28, 2020
  
−
== November 14, 2019 ==
+
=== Author First Pass paper ===
 +
* AFP resent to Database
 +
* Automated descriptions about to be sent
 +
* SObA, write for micropub? One micropub on SObA and another on comparative SObA
  
−
=== TAGC meeting ===
+
=== Noctua/GO-CAM ===
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* The Allied Genetics Conference next April (2020) in/near Washington DC
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* New version of the Noctua form released next week
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* Abstract deadline is Dec 5th
+
* Imports from WormBase?
−
* Alliance has a shared booth (3 adjacent booths)
+
** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
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* Micropublications will have a booth (Karen and Daniela will attend)
+
** Need to work on annotation history on back end
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* Focus will be on highlighting the Alliance
+
** May have face-to-face meeting in Pasadena
−
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
 
  
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=== Alliance all hands meeting ===
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=== Variation curation ===
−
* Lightning talk topics?
+
* Have a backlog; Paul D is assigned but has been overwhelmed
−
** Single cell RNA Seq (Eduardo)
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* Have asserted this as a priority
−
** SimpleMine? (Wen)
+
* We have the allele-sequence form; where does it go? Hinxton
−
** SObA? (Raymond); still working on multi-species SObA
+
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
−
** Phenotype community curation?
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* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
−
** Micropublications?
 
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** AFP?
 
  
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=== Alliance general ===
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=== Topic meetings ===
−
* Alliance needs a curation database
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* Asia (Taipei) meeting, Paul S going
−
** A curation working group was proposed
+
* Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
−
** What needs to happen to get this going?
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* TAGC in April, Chris going
−
** Would include text mining tools/resources
 
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** Would be good to have something like the curation status form
 
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** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
 
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** Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type
 
−
* Micropubs pushing data submission forms; might as well house them within the Alliance
 
−
* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
 
−
** Maybe MOD curators can manage configuration files to indicate what is relevant for their species
 
−
** First priority is to focus on automatically recognizable entities/features from papers
 
  
  
−
== November 21, 2019 ==
+
== January 16, 2020 ==
  
−
=== Textpresso: merging main docs and supps? ===
+
=== Variation names ===
−
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
+
* Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
.
−
* This results in possibly getting many results for the same publication, each scored and displayed separately
+
* Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
−
* Do we want Texptpresso to search on a single, consolidated file containing the main document of a paper AND the supplementals?
+
* Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
−
* 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)
+
* From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII.
−
* This cannot be done completely manually; agreed, this would have to be largely (completely?) automated
+
* We will wait for Paul D/Tim response and act accordingly
−
* 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)
+
* for now the CGI has been changed to allow 4 letters, we will revert if need be
−
* Detecting duplicated sentences would be useful, but may be quite a thorny issue (need to research)
 
−
* Chris will update GitHub ticket to ask Sibyl to NOT search on C. elegans supplementals, for now, and only search on main documents
 
  
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=== Europe PMC: biocuration landscape analysis ===
+
=== Webinars ===
−
* 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
+
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
−
* Chris has asked for details but has so far not received anything specific
+
* Is having a webinar series something WB is interested in doing?
−
* Should we attend? Yes, at least to listen. If complex questions come up, we can just tell them we'll look it up
+
** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
−
* 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
 

Revision as of 20:05, 16 January 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January 9, 2020

Phenotype Curation Requests

  • 1,229 emails sent Dec 3-6, 2019
  • Received 194 annotations from 40 papers and from 37 distinct community curators
    • 37 papers requested, 3 additional papers annotated
    • 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
    • 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
  • 43 bounced emails
    • 2 resent to new addresses
    • 5 have backup email addresses (also sent)

Worm Area Meetings

  • Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
  • Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)

Reference widget Textpresso linkouts

WS276 Citace upload

  • Hinxton upload Jan 31, 2020
  • Citace upload on Tuesday, Jan 28, 2020

Author First Pass paper

  • AFP resent to Database
  • Automated descriptions about to be sent
  • SObA, write for micropub? One micropub on SObA and another on comparative SObA

Noctua/GO-CAM

  • New version of the Noctua form released next week
  • Imports from WormBase?
    • Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
    • Need to work on annotation history on back end
    • May have face-to-face meeting in Pasadena

Variation curation

  • Have a backlog; Paul D is assigned but has been overwhelmed
  • Have asserted this as a priority
  • We have the allele-sequence form; where does it go? Hinxton
  • Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
  • Need to integrate curation with the Variant Effect Predictor (VEP) pipeline

Topic meetings

  • Asia (Taipei) meeting, Paul S going
  • Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
  • TAGC in April, Chris going


January 16, 2020

Variation names

  • Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
.
  • Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
  • Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
  • From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII.
  • We will wait for Paul D/Tim response and act accordingly
  • for now the CGI has been changed to allow 4 letters, we will revert if need be

Webinars

  • During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
  • Is having a webinar series something WB is interested in doing?
    • we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
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