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| | [[WormBase-Caltech_Weekly_Calls_July_2017|July]] | | [[WormBase-Caltech_Weekly_Calls_July_2017|July]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_August_2017|August]] |
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| − | == August 3, 2017 ==
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| − | === WB grant === | + | == September 14, 2017 == |
| − | * Progress (maintenance stuff) can be written as of last grant cycle
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| − | * Current projects and report the steady state
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| − | | |
| − | === CRISPR alleles ===
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| − | * Some authors not reporting CRISPR alleles with standard nomenclature
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| − | * Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
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| − | * Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
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| − | ** RNAi mapping pipeline not setup to handle this
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| − | ** Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
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| − | ** Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene
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| − | | |
| − | === Ontology Browser ===
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| − | * Has been less stable lately; Raymond has needed to restart machine
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| − | * Being served from Dell server (in Braun building)
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| − | | |
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| − | == August 10, 2017 ==
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| − | | |
| − | === WormBase grant ===
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| − | * Neuronal wiring with Scott Emmons? Maybe not for this round
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| − | * Transcription regulatory networks? Is a priority
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| − | * Paul will assemble existing parts and send around for review
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| − | | |
| − | === Entity markup ===
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| − | * InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
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| − | * There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
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| − | * Could Cecilia check links?
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| − | * New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
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| − | * Eventually markup should be job of authors during the process of writing. Need an authoring tool - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not
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| − | | |
| − | === Sequence features ===
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| − | * Should we have a standard human readable names for sequence features?
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| − | * Should we consolidate several features associated with the same gene when displaying in network views?
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| − | * Is there an automated way to give them public names?
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| − | * Maybe name automatically, but then allow manual overwriting
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| − | * Use gene name when experimentally demonstrated connection
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| − | * Needs to be automated, rule-based
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| − | * Could name based on neighboring gene(s)
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| − | | |
| − | === Person lineage graph ===
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| − | * Progress made in development, direct lineage running off of Datomic. All of it will need to be completed before it can go into production.
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| − | | |
| − | === Docker container system ===
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| − | * Potentially very useful for WB web services
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| − | | |
| − | === Consider content for NAR paper ===
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| − | * Send ideas to Raymond
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| − | | |
| − | === Micropublications ===
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| − | * Input for the WB grant?
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| − | * Could discuss microreviews
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| − | | |
| − | === Concise descriptions ===
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| − | * Automated descriptions good for genes with little info
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| − | * Human-written descriptions good for genes with lots of info; don't change too frequently
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| − | * Some have suggested including protein domain info
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| − | | |
| − | | |
| − | == August 17, 2017 ==
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| − | | |
| − | === Citace Upload ===
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| − | * Citace upload August 29th (most likely)
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| − | | |
| − | === AGR 1.0 Disease data ===
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| − | * Discussion of cutting back scope to only gene-disease associations versus pushing back deadline
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| − | * Problems stem from the fact that gene objects have already been instantiated as objects with human-readable names, synonyms, etc.
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| − | * Objects like strains, genotypes, fish, etc. still need to be instantiated with symbols, synonyms etc. and so will be difficult to get set up for human-readable display and linking to MOD pages
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| − | * We've already pushed back the deadline twice before, so we probably don't want to do that again
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| − | * We can put up disclaimers or notifications that we are only showing gene-disease associations for now, but other associations (to genotypes, strains, etc.) will come soon
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| − | | |
| − | === NAR paper community curation? ===
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| − | * Not much has changed about community curation fundamentally since last NAR paper
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| − | * Chris will write up update with specific numbers (response rates, annotation numbers, etc.) for NAR paper
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| − | | |
| − | === Community curation submission requests ===
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| − | * Chris & Juancarlos updated request pipeline
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| − | * Now focusing just on first authors; allows more emails to go out each month
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| − | * Have sent 333 emails since beginning of August, have received annotations for 20 papers so far (6% response, but still early; average tends to be 16%)
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| − | * Sending out more emails should result in more responses in absolute number
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| − | | |
| − | === Author First Pass (AFP) pipeline ===
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| − | * Karen brought up that the wrong author was emailed for AFP (Author First Pass)
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| − | * Probably an issue that last author happened to not be the corresponding author, may have thrown off automated detection of corresponding author
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| − | * To what extent do we and community benefit from the AFP pipeline?
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| − | * There may be cases where AFP flags a paper for a data type that was missed/false negative by SVM
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| − | * We can optimize/update the AFP form, leave it as is, or possibly abandon it
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| − | * Maybe Chris can take over over-seeing emails sent to authors for various requests
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| − | | |
| − | === WB Grant ===
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| − | * Would like more specifics on future plans
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| − | * Chris will send Paul some details on future plans for community annotation
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| − | | |
| − | == August 31, 2017 ==
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| − | === micropublications ===
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| − | * Mitani has submitted some for allele-phenotype and sequence change; we will not store the raw data for the sequence reads
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| − | === author first pass ===
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| − | *we will keep for now, but re-evaluate more thoroughly in the coming weeks, particularly wrt possible links to the micropublication platform
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| − | === the grant ===
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| − | * Paul will send around a version soon and will contact specific people if he needs more info on a certain section
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| − | === topic lists for SPELL and SpellMine ===
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| − | * we should take advantage of GO ontology structure for browsing topic lists
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| − | === new cuator ===
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| − | *Jae will start at WB on the 1st of September
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| − | *he'll work on PPI and possibly phenotype curation first, will add GO curation a bit later
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