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]] | ||
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− | == | + | == November 7, 2019 == |
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− | === | + | === WS275 Citace upload === |
− | * | + | * Maybe Nov 22 upload to Hinxton |
− | + | * CIT curators upload to Spica on Tues Nov 19 | |
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− | * | ||
− | === | + | === ?Genotype class === |
− | * | + | * [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing 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 === | ||
+ | * http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph | ||
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− | == | + | == November 14, 2019 == |
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− | === | + | === 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 |
Revision as of 19:58, 14 November 2019
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
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