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 =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 +
 +
 +
 +
== May 7, 2020 ==
 +
 +
=== Alliance COVID Page ===
 +
* Available on stage
 +
* Textpresso for Coronavirus up for testing
 +
 +
=== SimpleMine at Alliance ===
 +
* Still some confusion about what it is
 +
* Will try to help clarify on PI meeting on Friday
  
= 2019 Meetings =
+
=== Development environment for Alliance work ===
 +
* Raymond and Juancarlos have been working on
 +
* Existing hardware is strained; set up virtual machine
 +
* Still some technical issues
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
=== Open Publishing Festival ===
 +
* Later this month
 +
* Micropublications involved
 +
* Organized by the Collaborative Knowledge Foundation
 +
* Will involve publishers of books, journals, etc.
 +
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 +
* Open to all
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== Genotype class ===
 +
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 +
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 +
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 +
* Would be good to be clear/transparent about which components were automatically inferred
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== WS277/278 ===
 +
* Pipelines are pushed back by about 14 days/2 weeks
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
==May 13, 2020==
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
=== SURF students ===
 +
* Welcome Fernando!
 +
* Will work on neuron function with respect to dauer formation
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
=== Progress Report ===
 +
* Review Google Doc from Paul to make sure you're latest updates are there
 +
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
===Genotype class===
 +
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
 +
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
 +
*Disease OA annotations now converted to the newly created genotypes where needed
 +
*Need to work on disease dumper changes next
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== What genes should be linked to genotypes? ===
 +
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
 +
* What should we consider a "relevant gene"?
 +
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
 +
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
 +
* For rearrangements, consider relevant any genes "inside" the rearrangement?
 +
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
 +
* In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
+
=== Volunteer Community Curators ===
 +
* Have had an additional 13 people volunteer
 +
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 +
* Chris will hold a tutorial today and tomorrow for everyone else
 +
* Have received many new community annotations from volunteers (and authors), validation still pending
  
 +
=== Open Publishing Festival ===
 +
* Ranjana will join as a panelist
 +
* Other MOD curators will also join
 +
* Festival calendar: https://openpublishingfest.org/calendar.html
  
== November 7, 2019 ==
+
=== Move to Chen building ===
 +
* Scheduled for late January 2021
  
=== WS275 Citace upload ===
+
=== First completely virtual GO meeting ===
* Maybe Nov 22 upload to Hinxton
+
* Kimberly: went really well
* CIT curators upload to Spica on Tues Nov 19
+
* Only met 4 hours per day, due to time zone differences
 +
* Had breakout sessions for focus groups
  
=== ?Genotype class ===
+
=== Alliance Literature Acquisition working group ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* Plan to come up with use cases for OntoMate and Textpresso
* Several classes have a "Genotype" tag with text entry
+
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
** Strain
 
** 2_point_data
 
** Pos_neg_data
 
** 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 ===
+
* Kimberly plans to draw up most common use cases for Textpresso
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
  
  
== November 14, 2019 ==
+
== May 21, 2020 ==
  
=== TAGC meeting ===
+
=== Volunteer curators ===
* The Allied Genetics Conference next April (2020) in/near Washington DC
+
* Received surge of annotations earlier this week
* Abstract deadline is Dec 5th
+
* All tutorials done for now; all but 3 recorded
* Alliance has a shared booth (3 adjacent booths)
+
* Each tutorial is ~1 hour in length
* Micropublications will have a booth (Karen and Daniela will attend)
 
* Focus will be on highlighting the Alliance
 
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
 
  
=== Alliance all hands meeting ===
+
=== AFP tutorial ===
* Lightning talk topics?
+
* AFP group working on tutorial/webinar
** Single cell RNA Seq (Eduardo)
+
* Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)
** SimpleMine? (Wen)
 
** SObA? (Raymond); still working on multi-species SObA
 
** Phenotype community curation?
 
** Micropublications?
 
** AFP?
 
  
=== Alliance general ===
+
=== Open Publishing Festival ===
* Alliance needs a curation database
+
* Had micropublication session yesterday, went well
** A curation working group was proposed
+
* Had ~50 participants
** What needs to happen to get this going?
+
* Saved Zoom chats? Can get public ones, maybe not private ones
** 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 ==
+
== May 28, 2020 ==
  
=== Textpresso: merging main docs and supps? ===
+
=== Wormicloud ===
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
+
* Introducing a new tool for a graphical summary of queried papers, Please take a look and leave any comments on it. (http://textpressocentral.org:5010/)
* 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 ===
+
=== Genes to Physical Map ===
* 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
+
* https://colab.research.google.com/drive/1e83jv94-eO_VQ7kKdJ36TgDDb4WRkFhM?usp=sharing
* Chris has asked for details but has so far not received anything specific
+
To run: Runtime->Run All. Change the list of gene names and run again.
* Should we attend? Yes, at least to listen. If complex questions come up, we can just tell them we'll look it up
 
* 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 18:15, 28 May 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 7, 2020

Alliance COVID Page

  • Available on stage
  • Textpresso for Coronavirus up for testing

SimpleMine at Alliance

  • Still some confusion about what it is
  • Will try to help clarify on PI meeting on Friday

Development environment for Alliance work

  • Raymond and Juancarlos have been working on
  • Existing hardware is strained; set up virtual machine
  • Still some technical issues

Open Publishing Festival

  • Later this month
  • Micropublications involved
  • Organized by the Collaborative Knowledge Foundation
  • Will involve publishers of books, journals, etc.
  • Will have a MOD-focused event, would be good to have WB curators participate/attend
  • Open to all

Genotype class

  • Ranjana finished populating the Genotype OA with genotypes needed for disease curation
  • Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
  • There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
  • Would be good to be clear/transparent about which components were automatically inferred

WS277/278

  • Pipelines are pushed back by about 14 days/2 weeks


May 13, 2020

SURF students

  • Welcome Fernando!
  • Will work on neuron function with respect to dauer formation

Progress Report

Genotype class

  • Have 27 genotypes in the genotype OA, dumper and test .ace file ready
  • Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
  • Disease OA annotations now converted to the newly created genotypes where needed
  • Need to work on disease dumper changes next

What genes should be linked to genotypes?

  • We have a "Gene" tag in the ?Genotype model for capturing relevant genes
  • What should we consider a "relevant gene"?
  • We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
  • For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
  • For rearrangements, consider relevant any genes "inside" the rearrangement?
  • For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
  • In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype

Volunteer Community Curators

  • Have had an additional 13 people volunteer
  • Single one-on-one tutorial for someone in Hong Kong this past Monday
  • Chris will hold a tutorial today and tomorrow for everyone else
  • Have received many new community annotations from volunteers (and authors), validation still pending

Open Publishing Festival

Move to Chen building

  • Scheduled for late January 2021

First completely virtual GO meeting

  • Kimberly: went really well
  • Only met 4 hours per day, due to time zone differences
  • Had breakout sessions for focus groups

Alliance Literature Acquisition working group


May 21, 2020

Volunteer curators

  • Received surge of annotations earlier this week
  • All tutorials done for now; all but 3 recorded
  • Each tutorial is ~1 hour in length

AFP tutorial

  • AFP group working on tutorial/webinar
  • Had someone on phenotype curation tutorial specifically asking about it (Kimberly responded)

Open Publishing Festival

  • Had micropublication session yesterday, went well
  • Had ~50 participants
  • Saved Zoom chats? Can get public ones, maybe not private ones


May 28, 2020

Wormicloud

Genes to Physical Map

To run: Runtime->Run All. Change the list of gene names and run again.