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| | [[WormBase-Caltech_Weekly_Calls_May_2018|May]] | | [[WormBase-Caltech_Weekly_Calls_May_2018|May]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_June_2018|June]] |
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| − | == June 7, 2018 ==
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| − | === Alliance literature pipeline working group === | + | == July 5, 2018 == |
| − | * Has anyone gotten back to Carol Bult about WB/Textpresso membership in the group? Not yet
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| − | * Paul & Kimberly can join; Kimberly will sit in on group meetings
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| | | | |
| − | === SPELL migration === | + | === Community Curation Mass Email update === |
| − | * SGD put SPELL into the cloud; will give us code to set up WB SPELL in cloud
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| − | * Want to have common interface but two instances (yeast & worm)
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| − | * Worm data in SPELL may be more complicated than the yeast data (different species, platforms, meta data, etc.)
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| − | * Mike Cherry proposed to use GTEx to replace SPELL. (www.gtexportal.org)
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| − | * Trying to get GTEX to have same functionality as SPELL
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| − | | |
| − | === Progress report ===
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| − | * Wen can generate numbers of changes since last year
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| − | * 5-year progress report coming up (for funding agencies)
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| − | * Want a progress report-like document to give to SAB in July
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| − | * WS259 - WS265
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| − | | |
| − | === Paper author name ===
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| − | * Jonathan Ewbank wrote in about an incorrect author name
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| − | * Issue for WBPaper00048704: https://wormbase.org/resources/paper/WBPaper00048704#0--10
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| − | * First author is "Li, C" as in PubMed (correct name) in WormBase as "Chun, L"
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| − | * Will make a GitHub ticket; web team may need to look at
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| − | | |
| − | === Lab class ===
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| − | * Lab data is not clean/consistent; has gotten messy
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| − | * Cecilia trying to clean it up
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| − | * There is conflicting data from lab class, author class, and person class
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| − | * Currently there is a ~redundant curation pipeline; considering pulling person info into lab class
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| − | * When looking at lab page, if there is a problem with a person's info, changes would be made (requested) in the person class, not the lab class
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| − | * Cecilia will contact labs to ask about correctness of information
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| − | * Can have a discussion with Ann and Aric at CGC
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| − | | |
| − | === How many C. elegans genes have "good" knockouts? ===
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| − | * Paul giving talk next week, wants to report
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| − | * Chris will look into
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| − | * Mitani did 1,000 deletions in last year
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| − | | |
| − | === Server logs ===
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| − | * SimpleMine logs are all coming from Amazon; will need to ask Todd about SimpleMine usage (from AWS stats?)
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| − | | |
| − | === Migration of lab data ===
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| − | * Data for labs was coming from Name Server (in Hinxton) - <font color= red>Comment:</font>[PD] Not coming from the Nameserver, geneace was the only source of Lab data prior to handover.
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| − | * Now Paul D has stopped curating lab info - <font color= red>Comment:</font>[PD] Build config has been updated to take the majority of lab data from citace rather than geneace
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| − | Database File Class remove/format
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| − | ----------------------------------------------------------------------------------------------------------------
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| − | db=geneace file=geneace_Laboratory.ace class=Laboratory format="Alleles WBVar\d{8}" delete=Representative delete=Registered_lab_members delete=Past_lab_members delete=Allele_designation delete=Strain_designation delete=Address
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| − | db=citace file=caltech_Laboratory.ace class=Laboratory delete=Alleles format="Representative WBPerson\d{1,5}" format="Registered_lab_members WBPerson\d{1,5}" format="Past_lab_members WBPerson\d{1,5}"
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| − | | |
| − | * Now that Cecilia is curating, will pull lab info from Postgres
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| − | | |
| − | | |
| − | == June 21, 2018 ==
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| − | | |
| − | === SAB ===
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| − | * Lightning talks at project meeting; everyone should consider what they want to present (5 minutes with 5 minutes for questions)
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| − | * 45 minutes curation talk to SAB; Chris volunteered; anyone else interested?
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| − | * What data types are being incorporated with the Alliance? What have we gained from those conversations?
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| − | * How have Alliance interactions benefited us?
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| − | * How does the Datomic migration affect our curation and data models?
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| − | * Alliance data models should be union of existing MOD data models, but does not require curation of all attributes at each MOD
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| − | * Do WB and our users benefit from creating a ?Genotype class?
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| − | | |
| − | === Phenotype & Disease Face-to-Face ===
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| − | * Reviewed phenotype curation practices at each MOD
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| − | * Discussed strain and genotype classes
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| − | * Generally it's felt that genotypes should only represent full genotypes of actual individuals or strains
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| − | * For phenotype annotations WB will still need a mechanism to attribute the specific genotypic components that are responsible for the observed phenotype along with a way to capture the complete or background genotype for context
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| − | * MGI considers strains to be part of a genotype (i.e. background inbred strain into which alleles are introduced)
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| − | * WB and SGD consider genotype to be part of strain
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| − | * WB will still consider moving ahead with instantiating a ?Genotype class for capturing genotypes (e.g. for disease models) that don't have an explicitly reported strain name; also for capturing transient genotypes like heterozygosity as well as paternal and maternal contributions/genotypes
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| − | | |
| − | | |
| − | | |
| − | == June 28, 2018 ==
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| − | | |
| − | === Bulk emailing community for phenotypes ===
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| − | * Chris & Juancarlos have now setup a pipeline to send requests in bulk
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| − | * Can send 75 emails at a time; GMail may limit to 500 per day (was hoping for 3,000 at a time)
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| − | * Sent out 338 emails in past week; already received annotations for 18 papers, ~50 annotations
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| − | * Papers go back to 1987, earliest paper received curation from in last week 2008
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| − | * Have sent about 25 papers from 2018, got annotations for 5 of them
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| − | * Ask SAB about email frequency
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| − | * Would be good to link to a Textpresso search
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| − | * Maybe make a link people can click on to indicate there is no phenotype data
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| − | * Can a submitter chat with a curator? Maybe integrate Olark chat? Would be good to make available, indicate how to chat
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| − | | |
| − | === SAB ===
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| − | * Chris & Paul will present (curation & intro respectively)
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| − | * Tools? Raymond can bring up enrichment analysis
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| − | * Project meeting
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| − | ** Everyone should sign up for a topic if they haven't already
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| − | | |
| − | === Phenotype Ontology ===
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| − | * Is the Phenotype ontology growing? Very slowly
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| − | * Received several suggested phenotypes from community in last batch
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| − | * Want to focus on logical definitions
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| − | * Mammalian Phenotype ontology - precomposed terms with logical definitions
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| − | * Raymond trying to use the SObA approach to display logically defined phenotype terms; needs to figure out how to effectively model it
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| − | * Should get useful feedback at the ICBO meeting in August
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| − | ** Would be good to establish ahead of time what we want to get from the meeting
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| − | * Want feedback on:
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| − | ** Pre-composed vs. post-composed
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| − | ** Granularity
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| − | ** Logical definitions
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| − | * Looking up phenotypes: want to make more user friendly
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| − | ** We could map phenotype terms to processes to allow community to find relevant terms
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| − | ** Want to find "male hook" phenotypes; correct term is "male copulatory structure variant"; the term "hook" should find "male copulatory structure"
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| − | * What is the best use of a user's time? curator's time?
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| − | * How are ontology logical definitions being used now?
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| − | ** Kimberly: To calculate/reason the inferences based on ontology parentage
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| − | ** Logical definitions are not very visible on relevant pages (like Amigo); should we make it more visible to users?
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| − | | |
| − | === Protein interactions ===
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| − | * Now up to date; how should we publish this info?
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| − | * Can make a blog post and/or micropublication and put in next NAR paper
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| − | | |
| − | === Marie-Claire arriving next week ===
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| − | * What's the plan?
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| − | * Phenotype curation? GO curation?
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| − | * Daniela wants help with Picture curation; could explain over Skype
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| − | ** Mega-sync system could help (Daniela will discuss with Valerio)
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| − | ** Images stored on canopus machine; can canopus be bypassed in sync process?
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| − | ** Mega has data limits (50GB+ requires a paid account)
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| − | ** Could setup a custom sync pipeline locally
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| − | | |
| − | === GO vs. Phenotype ===
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| − | * Lots of GO QC/review going on now; Marie-Claire could start there
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| − | * Would it be easier to start out with GO or phenotype? Just different
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| − | * Kimberly could walk her through next week
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| − | * Paul will try to get Marie-Claire to Toronto for the SAB
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| − | | |
| − | === Alliance U24 grant ===
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| − | * ~30-pager due September (using familiar format)
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| − | * Databases, knowledge-bases and tools will all be considered separately
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| − | * Format changes after September
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| − | * Scope could be focused on web portal and infrastructure (not curation, for example)
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