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]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
= 2019 Meetings =
+
== January 9, 2020 ==
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
 
 
  
== November 7, 2019 ==
+
=== 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)
  
=== WS275 Citace upload ===
+
=== Worm Area Meetings ===
* Maybe Nov 22 upload to Hinxton
+
* Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
* CIT curators upload to Spica on Tues Nov 19
+
* Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
  
=== ?Genotype class ===
+
=== Reference widget Textpresso linkouts ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* Now live on WormBase, WS274
* Several classes have a "Genotype" tag with text entry
+
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
** Strain
+
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
** 2_point_data
+
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
** Pos_neg_data
+
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
** Multi_pt_data
+
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
** RNAi
+
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
** Phenotype_info
+
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
** Mass_spec_experiment (no data as of WS273)
+
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
** Condition
+
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
+
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
+
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
+
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
+
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
+
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
+
* Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
+
* Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
+
* Process examples:
** Reference to parent strain, like "Parent strain is AG359"
+
** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
+
** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
+
* Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
  
=== Gene comparison SObA ===
+
=== WS276 Citace upload ===
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* 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
  
== November 14, 2019 ==
+
=== 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
  
=== TAGC meeting ===
+
=== Variation curation ===
* The Allied Genetics Conference next April (2020) in/near Washington DC
+
* Have a backlog; Paul D is assigned but has been overwhelmed
* Abstract deadline is Dec 5th
+
* Have asserted this as a priority
* Alliance has a shared booth (3 adjacent booths)
+
* We have the allele-sequence form; where does it go? Hinxton
* Micropublications will have a booth (Karen and Daniela will attend)
+
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
* Focus will be on highlighting the Alliance
+
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
 
  
=== Alliance all hands meeting ===
+
=== Topic meetings ===
* Lightning talk topics?
+
* Asia (Taipei) meeting, Paul S going
** Single cell RNA Seq (Eduardo)
+
* Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
** SimpleMine? (Wen)
+
* TAGC in April, Chris going
** SObA? (Raymond); still working on multi-species SObA
 
** Phenotype community curation?
 
** Micropublications?
 
** AFP?
 
  
=== Alliance general ===
 
* Alliance needs a curation database
 
** A curation working group was proposed
 
** What needs to happen to get this going?
 
** Would include text mining tools/resources
 
** Would be good to have something like the curation status form
 
** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
 
** 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
 
  
 +
== January 16, 2020 ==
  
== November 21, 2019 ==
+
=== 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
  
=== Textpresso: merging main docs and supps? ===
+
=== Webinars ===
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
+
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
* Do we want Texptpresso to search on a single, consolidated file containing the main document of a paper AND the supplementals?
+
* 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

Latest 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