Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== NAR paper community curation? === | === NAR paper community curation? === | ||
− | * Chris will write up update with numbers | + | * Not much has changed about community curation fundamentally since last NAR paper |
+ | * Chris will write up update with specific numbers (response rates, annotation numbers, etc.) for NAR paper | ||
+ | |||
+ | === Community curation submission requests === | ||
+ | * Chris & Juancarlos updated request pipeline | ||
+ | * Now focusing just on first authors; allows more emails to go out each month | ||
+ | * 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%) | ||
+ | * Sending out more emails should result in more responses in absolute number | ||
+ | |||
+ | === Corresponding author AFP issue === | ||
+ | * Karen brought up that the wrong author was emailed for AFP | ||
+ | * Probably an issue that last author happened to not be the corresponding author, may have thrown off automated detection of corresponding author |
Revision as of 16:28, 17 August 2017
Contents
Previous Years
2017 Meetings
August 3, 2017
WB grant
- Progress (maintenance stuff) can be written as of last grant cycle
- Current projects and report the steady state
CRISPR alleles
- Some authors not reporting CRISPR alleles with standard nomenclature
- Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
- Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
- RNAi mapping pipeline not setup to handle this
- Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
- Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene
Ontology Browser
- Has been less stable lately; Raymond has needed to restart machine
- Being served from Dell server (in Braun building)
August 10, 2017
WormBase grant
- Neuronal wiring with Scott Emmons? Maybe not for this round
- Transcription regulatory networks? Is a priority
- Paul will assemble existing parts and send around for review
Entity markup
- 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
- 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
- Could Cecilia check links?
- New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
- 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
Sequence features
- Should we have a standard human readable names for sequence features?
- Should we consolidate several features associated with the same gene when displaying in network views?
- Is there an automated way to give them public names?
- Maybe name automatically, but then allow manual overwriting
- Use gene name when experimentally demonstrated connection
- Needs to be automated, rule-based
- Could name based on neighboring gene(s)
Person lineage graph
- Progress made in development, direct lineage running off of Datomic. All of it will need to be completed before it can go into production.
Docker container system
- Potentially very useful for WB web services
Consider content for NAR paper
- Send ideas to Raymond
Micropublications
- Input for the WB grant?
- Could discuss microreviews
Concise descriptions
- Automated descriptions good for genes with little info
- Human-written descriptions good for genes with lots of info; don't change too frequently
- Some have suggested including protein domain info
August 17, 2017
Citace Upload
- Citace upload August 29th (most likely)
AGR 1.0 Disease data
- Discussion of cutting back scope to only gene-disease associations versus pushing back deadline
- Problems stem from the fact that gene objects have already been instantiated as objects with human-readable names, synonyms, etc.
- Objects like strains, genotypes, fish, etc. still need to be instantiated with symbols, synonyms
NAR paper community curation?
- Not much has changed about community curation fundamentally since last NAR paper
- Chris will write up update with specific numbers (response rates, annotation numbers, etc.) for NAR paper
Community curation submission requests
- Chris & Juancarlos updated request pipeline
- Now focusing just on first authors; allows more emails to go out each month
- 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%)
- Sending out more emails should result in more responses in absolute number
Corresponding author AFP issue
- Karen brought up that the wrong author was emailed for AFP
- Probably an issue that last author happened to not be the corresponding author, may have thrown off automated detection of corresponding author