Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
 +
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
  
== October 3, 2019 ==
 
  
=== SObA comparison graphs ===
+
== November 7, 2019 ==
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
 +
=== WS275 Citace upload ===
 +
* Maybe Nov 22 upload to Hinxton
 +
* CIT curators upload to Spica on Tues Nov 19
  
=== Germ line discussion ===
+
=== ?Genotype class ===
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
+
* Several classes have a "Genotype" tag with text entry
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
+
** Strain
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
+
** 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)"
  
=== Script to remove blank entries from Postgres ===
+
=== Gene comparison SObA ===
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
+
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
+
 
* Does anyone object to removing these entries throughout Postgres?
+
 
* Juancarlos will remove all the empty fields identified by his script
+
== November 14, 2019 ==
 +
 
 +
=== TAGC meeting ===
 +
* The Allied Genetics Conference next April (2020) in/near Washington DC
 +
* Abstract deadline is Dec 5th
 +
* Alliance has a shared booth (3 adjacent booths)
 +
* 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 ===
 +
* Lightning talk topics?
 +
** Single cell RNA Seq (Eduardo)
 +
** SimpleMine? (Wen)
 +
** 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

Latest revision as of 19:58, 14 November 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


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


2019 Meetings

January

February

March

April

May

June

July

August

September

October


November 7, 2019

WS275 Citace upload

  • Maybe Nov 22 upload to Hinxton
  • CIT curators upload to Spica on Tues Nov 19

?Genotype class

  • Working data model document
  • Several classes have a "Genotype" tag with text entry
    • 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


November 14, 2019

TAGC meeting

  • The Allied Genetics Conference next April (2020) in/near Washington DC
  • Abstract deadline is Dec 5th
  • Alliance has a shared booth (3 adjacent booths)
  • 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

  • Lightning talk topics?
    • Single cell RNA Seq (Eduardo)
    • SimpleMine? (Wen)
    • 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