Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
  
 +
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
  
== November 7, 2019 ==
 
  
=== WS275 Citace upload ===
+
== December 5, 2019 ==
* Maybe Nov 22 upload to Hinxton
 
* CIT curators upload to Spica on Tues Nov 19
 
  
=== ?Genotype class ===
+
=== New interaction Venn diagram tool ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
* Several classes have a "Genotype" tag with text entry
+
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
** Strain
+
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
** 2_point_data
+
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
** Pos_neg_data
+
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
** Multi_pt_data
+
* Request: could there be a toggle to include/exclude high-throughput interactions?
** RNAi
+
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
** Phenotype_info
+
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
** Mass_spec_experiment (no data as of WS273)
+
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
** 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 ===
+
=== New round of phenotype requests ===
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* GMail really throttling email sending
 +
* Chris will reach out to Google/GMail to see if we can:
 +
** A) get a clear explanation about what their restrictions are and how they work and
 +
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
  
 +
=== Aligning interaction data with GO and GO-CAM ===
 +
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
 +
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
 +
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 +
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 +
* Chris and Kimberly will meet to discuss further
  
== November 14, 2019 ==
+
=== Short SObA talk at Alliance meeting ===
 +
* Raymond prepared to give short talk on SObA to the Alliance group
  
=== TAGC meeting ===
+
=== Single cell data visualization tool ===
* The Allied Genetics Conference next April (2020) in/near Washington DC
+
* Eduardo will present to Paul's lab meeting tomorrow
* Abstract deadline is Dec 5th
+
* Will discuss at Alliance expression working group pre-meeting
* 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
 
 
 
 
 
== November 21, 2019 ==
 
 
 
=== Textpresso: merging main docs and supps? ===
 
* Currently, Textpresso searches in paper main documents and all individual supplemental documents separately
 
* 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)
 

Latest revision as of 21:08, 5 December 2019

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2019 Meetings

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December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting