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]]
 
−
 
 
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[[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]]
+
=== 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)
  
−
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== 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)
  
−
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
+
=== Reference widget Textpresso linkouts ===
 +
* 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 7, 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
  
−
=== WS275 Citace upload ===
+
=== Noctua/GO-CAM ===
−
* Maybe Nov 22 upload to Hinxton
+
* New version of the Noctua form released next week
−
* CIT curators upload to Spica on Tues Nov 19
+
* 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
  
−
=== ?Genotype class ===
+
=== Variation curation ===
−
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* Have a backlog; Paul D is assigned but has been overwhelmed
−
* Several classes have a "Genotype" tag with text entry
+
* Have asserted this as a priority
−
** Strain
+
* We have the allele-sequence form; where does it go? Hinxton
−
** 2_point_data
+
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
−
** Pos_neg_data
+
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
−
** Multi_pt_data
 
−
** RNAi
 
−
** Phenotype_info
 
−
** Mass_spec_experiment (no data as of WS273)
 
−
** Condition
 
−
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
−
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
−
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
−
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
−
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
−
** 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)"
 
−
** 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)"
 
  
−
=== Gene comparison SObA ===
+
=== Topic meetings ===
−
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* 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
  
  
−
== November 14, 2019 ==
+
== January 16, 2020 ==
  
−
=== TAGC meeting ===
+
=== Variation names ===
−
* The Allied Genetics Conference next April (2020) in/near Washington DC
+
* 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
.
−
* Abstract deadline is Dec 5th
+
* Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
−
* Alliance has a shared booth (3 adjacent booths)
+
* Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
−
* Micropublications will have a booth (Karen and Daniela will attend)
+
* 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.
−
* Focus will be on highlighting the Alliance
+
* We will wait for Paul D/Tim response and act accordingly
−
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
+
* for now the CGI has been changed to allow 4 letters, we will revert if need be
  
−
=== Alliance all hands meeting ===
+
=== Webinars ===
−
* Lightning talk topics?
+
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
−
** Single cell RNA Seq (Eduardo)
+
* Is having a webinar series something WB is interested in doing?
−
** SimpleMine? (Wen)
+
** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
−
** 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
 
  
  
−
== November 21, 2019 ==
+
== January 23, 2020 ==
  
−
=== Textpresso: merging main docs and supps? ===
+
=== WS276 Citace upload ===
−
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
+
* Next Tuesday, Jan 28 10am Pacific
−
* This results in possibly getting many results for the same publication, each scored and displayed separately
 
−
* Do we want Texptpresso to search on a single, consolidated file containing the main document of a paper AND the supplementals?
 
−
* 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)
 
−
* This cannot be done completely manually; agreed, this would have to be largely (completely?) automated
 
−
* 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)
 
−
* 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
 
  
−
=== Europe PMC: biocuration landscape analysis ===
+
=== Extracellular/secreted proteins list ===
−
* 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
+
* Peter Roy looking for a list of C. elegans genes whose protein products are secreted
−
* Chris has asked for details but has so far not received anything specific
+
* Chris pointed him to BioMart search for SignalP and transmembrane proteins, and to the GO term page for "extracellular region" but Peter doesn't think that's exhaustive enough
−
* Should we attend? Yes, at least to listen. If complex questions come up, we can just tell them we'll look it up
+
* Does anyone have any other suggestions or know of an empirical data set?
−
* 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
+
* A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome: https://www.ncbi.nlm.nih.gov/pubmed/22823938
 +
* PF00188 Cysteine-rich secretory protein family Pfam
 +
** This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [PMID:12625841]

Revision as of 19:18, 23 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


January 23, 2020

WS276 Citace upload

  • Next Tuesday, Jan 28 10am Pacific

Extracellular/secreted proteins list

  • Peter Roy looking for a list of C. elegans genes whose protein products are secreted
  • Chris pointed him to BioMart search for SignalP and transmembrane proteins, and to the GO term page for "extracellular region" but Peter doesn't think that's exhaustive enough
  • Does anyone have any other suggestions or know of an empirical data set?
  • A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome: https://www.ncbi.nlm.nih.gov/pubmed/22823938
  • PF00188 Cysteine-rich secretory protein family Pfam
    • This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [PMID:12625841]
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