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
  
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= 2020 Meetings =
  
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= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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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 ==
 
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=== WS275 Citace upload ===
 
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* Maybe Nov 22 upload to Hinxton
 
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* CIT curators upload to Spica on Tues Nov 19
 
−
 
 
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=== ?Genotype class ===
 
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* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
 
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* Several classes have a "Genotype" tag with text entry
 
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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."
 
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** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
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** 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"
 
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** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
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** 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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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
  
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
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== November 14, 2019 ==
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
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=== TAGC meeting ===
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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* The Allied Genetics Conference next April (2020) in/near Washington DC
 
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* Abstract deadline is Dec 5th
 
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* Alliance has a shared booth (3 adjacent booths)
 
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* Micropublications will have a booth (Karen and Daniela will attend)
 
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* Focus will be on highlighting the Alliance
 
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* 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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* Lightning talk topics?
 
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** Single cell RNA Seq (Eduardo)
 
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** SimpleMine? (Wen)
 
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** SObA? (Raymond); still working on multi-species SObA
 
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** Phenotype community curation?
 
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** Micropublications?
 
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** AFP?
 
  
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=== Alliance general ===
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== June 4, 2020 ==
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* Alliance needs a curation database
 
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** A curation working group was proposed
 
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** What needs to happen to get this going?
 
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** 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
 
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* Micropubs pushing data submission forms; might as well house them within the Alliance
 
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* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
 
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** Maybe MOD curators can manage configuration files to indicate what is relevant for their species
 
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** First priority is to focus on automatically recognizable entities/features from papers
 
  
 +
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
−
== November 21, 2019 ==
+
=== Caltech reopening ===
 +
* Paul looking to get plan approved
 +
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
−
=== Textpresso: merging main docs and supps? ===
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=== Nameserver ===
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* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
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* Nameserver was down
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* This results in possibly getting many results for the same publication, each scored and displayed separately
+
* CIT curators would still like to have a single form to interact with
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* Do we want Texptpresso to search on a single, consolidated file containing the main document of a paper AND the supplementals?
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
−
* 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)
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
−
* This cannot be done completely manually; agreed, this would have to be largely (completely?) automated
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
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* 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)
+
* Hinxton is pulling in CGC strains, how often?
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* Detecting duplicated sentences would be useful, but may be quite a thorny issue (need to research)
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* Caltech could possibly get a block of IDs
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* 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 ===
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=== Alliance SimpleMine ===
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* 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
+
* Any updates? 3.1 feature freeze is tomorrow
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* Chris has asked for details but has so far not received anything specific
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
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* Should we attend? Yes, at least to listen. If complex questions come up, we can just tell them we'll look it up
 
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* 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 00:09, 5 June 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

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
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