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| | [[WormBase-Caltech_Weekly_Calls_February_2017|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2017|February]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_March_2017|March]] |
| − | == March 2, 2017 ==
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| − | | |
| − | === Expression Cluster SVM ===
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| − | * Started curating expression clusters in 2007
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| − | * Had been using text pattern match to identify expression cluster papers
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| − | * Now with more papers for positive and negative training set, shifting to SVM identification
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| − | * 540 positive papers, 900 negative papers for training
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| − | * Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
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| − | * Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)
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| − | | |
| − | === Karen's SBIR grant ===
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| − | * Looks like it will get funded
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| − | * Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
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| − | * Paul put in a request for posting another curator position
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| − | ** If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
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| − | * Will need to consider re-allocation of curation responsibilities
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| − | * Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
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| − | ** Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
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| − | ** Do other AGR members curate molecules? In some cases yes; don't capture metabolites
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| − | * Transgene curation could be distributed
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| − | ** Karen will be working on more automated curation of transgenes from papers; maybe also for molecules
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| − | | |
| − | === Metabolomics ===
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| − | * What would we like to see in WB for metabolomics?
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| − | * Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
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| − | * WB enzyme gene pages link out to respective gene pages on WormFlux
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| − | * How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?
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| − | | |
| − | === Pathway representation ===
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| − | * What are the best ways to capture empirical evidence as support for pathway models?
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| − | * Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
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| − | * How can micropublications be used to fill in the gaps?
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| − | | |
| − | === SObA GO on human data ===
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| − | * What would be a good set of genes to test?
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| − | * If we omit IEAs (most from mouse), are we left with substantial data for human genes?
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| − | | |
| − | | |
| − | == March 9, 2017 ==
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| − | | |
| − | === Expression widget via Datomic ===
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| − | * Sibyl is working on delivering the Expression widget from Datomic
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| − | * Issue with gene expression "mountain" data
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| − | * AcePerl script/query underlying the data, may be incorrect and needs an update
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| − | | |
| − | === Human GO SObA graph ===
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| − | * Working SObA graph for human gene ontology data:
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| − | ** http://131.215.12.204/~raymond/cgi-bin/soba_go_hs.cgi?action=annotSummaryCytoscape&focusTermId=UniProtKB:O94905
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| − | * Running off GOLR server for now
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| − | * Would be great to have a SObA widget on AGR portal
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| − | * Will need to get widgets working on AGR portal
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| − | * Will be good to have, for now, a stand alone version
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| − | | |
| − | === AGR update ===
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| − | * SAB meeting on Tuesday (two days ago)
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| − | * Positive feedback
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| − | | |
| − | === AGR database ===
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| − | * Although official database has not been chosen, most portal processes are running just on memory, need to start storing things in a database
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| − | * The database used may be the stepping stone for eventual database migration for AGR
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| − | | |
| − | === AGR Curator calls ===
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| − | * Karen asking about purpose of curator calls going forward
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| − | * Have covered a good number of topics, a few still yet to be covered: synteny browser, person curation
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| − | * Possibly have discussions about the functions of different (and possibly new) working groups
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| − | * Can revisit curation procedures
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| − | * Should curator calls happen independently of AGR to share thoughts and methods about curation
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| − | | |
| − | === Methods in Molecular Biology chapter update ===
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| − | * Have received drafts for most sections
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| − | * Working on making them consistent and making figures legible
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| − | | |
| − | | |
| − | == March 16, 2017 ==
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| − | | |
| − | === Funding opportunities ===
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| − | * Could we focus on curation for disease genes and work with other groups?
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| − | * Maybe work with GO
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| − | * What diseases would rely more on worm research than others?
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| − | * Lots of disease models on neurodegeneration diseases testing herbal treatments and compounds to treat
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| − | * Parasitic nematode research? May not work out
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| − | * Really want to focus on what worm research informs about human disease
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| − | * What are the studies that focus on orthology to human disease genes?
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| − | * If some funding is cut, there will likely be refunding in a targeted manner (e.g. Alzheimer's research)
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| − | * Can we do Textpresso search for funding agencies?
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| − | * Much more funding is going to military research; could look at what could apply (Tropical diseases, responses to pathogen, etc.)
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| − | | |
| − | === IWM swag ===
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| − | * Still have tattoos from last years TAGC meeting
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| − | * WormBase piggy bank?
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| − | | |
| − | === Human GO SObA ===
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| − | * Server that Raymond used originally is not appropriate
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| − | * Will require some reworking of the backend code
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| − | * Might be ready after the Biocuration meeting
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| − | * Could use in AGR disease pages, showing enriched GO terms (from genes implicated in the disease)
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| − | * Could have (instead of enriched terms) a graph of all gene annotations merged
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| − | * What is a reasonably sized list of items to manage in the human mind? 7 +/- 3? 20?
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| − | ** Can define a cutoff at which point using SObA is helpful
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| − | | |
| − | === Micropublications ===
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| − | * Deadline for grant rebuttal?
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| − | * Organization name at IWM will be: Micropublication biology
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| − | * Each micropublication is intended as a curatable unit
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| − | * Shohei Mitani wants, for example, to submit 100 knockout phenotypes; should be 100 micropublications
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| − | ** Tim concerned that 100 micropubs is too much, but that is probably OK
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| − | * Want to generate a "narrative" from multiple individual micropubs
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| − | * Can DOI's be part of another DOI? Are relationships between DOI's allowed?
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| − | | |
| − | === AGR communication and data pipeline ===
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| − | * Discussion about number of calls and modes of communication
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| − | * There was concern about data pipeline demands becoming overwhelming, e.g. loading data for Intermine as well as AGR portal
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| − | * There are questions about which database will be used as an interim database, which could possibly become the standard database
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| − | * AGR members like the Datomic techonology, but are concerned about the non-open-source aspect
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| − | * Should we have an all-hands call once a month (or every two weeks) where working groups could present and discuss issues? Yes, Kimberly will email Stacia about this idea
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| − | * AGR PI's were in favor of having a technical meeting face-to-face; disease working group face-to-face meeting worked well
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| − | * There may be AGR working group meetings at Biocuration meeting
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| − | | |
| − | | |
| − | == March 23, 2017 ==
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| − | | |
| − | === Biocuration meeting ===
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| − | * Mary Ann (or someone who is available) will present the micropublications poster
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| − | * Can share posters here: https://f1000research.com/channels/biocuration
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| − | | |
| − | === Person curation AGR curator call ===
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| − | * Person curation is topic of next AGR curator call (April 12th)
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| − | * Cecilia can present on person curation (persons, paper-person connections)
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| − | * Karen can help
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| − | * Could discuss authors vs. persons in WormBase
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| − | * Chris can discuss experience with online chat service
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| − | | |
| − | === Potential AGR all-hands call on April 5th ===
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| − | * Stacia Engel will let people know
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| − | * Would have short presentations from working groups
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| − | | |
| − | === Karen part time as of April 1st ===
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| − | * Grant came through (congratulations!), so Karen will be part time as of Apr 1
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| − | * Someone should take over transgene and molecule curation
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| − | * Transgenes
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| − | ** Relevant curators already have training on how to curate
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| − | ** How much of these curation processes are on auto-pilot?
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| − | ** CGC sends strain info (with trangenes) to Mary Ann
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| − | ** Can we automate the transgene-strain connections coming from CGC?
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| − | ** Mary Ann can take over manual transgene curation
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| − | ** Could have summer student (undergard or high school) to help?
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| − | * Molecules
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| − | ** Ranjana, Wen, & Chris can take over molecule curation
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| − | ** Should we automate the dumping process? Wen will take over dumping the data
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| − | | |
| − | === Micropublications ===
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| − | * Minipublication from Tim Schedl's lab
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| − | ** Narrative of multiple micropublications
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| − | ** Requesting a DOI for each individual data set
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| − | ** Need a process to submit everything at once (through forms)
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| − | ** Grad student submitting 2 allele-phenotypes and 2 expression patterns
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| − | * Working on grant rebuttal
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| − | ** Need to demonstrate sustainability of micropublication process; persistence if funding goes away? how does the pipeline scale?
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| − | ** How much will the data be used?
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| − | ** What is the setup cost for Xenbase (or other database)? Setting up the forms initially, processing data and having reviewers longer term
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| − | ** Request submitters to suggest reviewers; also have a pool of willing reviewers
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| − | ** Submitters can be included in reviewer pool
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| − | | |
| − | | |
| − | == March 30, 2017 ==
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| − | | |
| − | === Biocuration meeting ===
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| − | * Received good feedback from meeting
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| − | * Micropublication poster won poster prize (go Daniela!)
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| − | * Lots of precision medicine
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| − | * Great keynote talks
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| − | * Disease meeting at Biocuration meeting
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| − | ** Discussed layout for gene report page for AGR 0.6
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| − | ** Need to clarify association type
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| − | * Good feedback about automated decriptions talk
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| − | * SGD outreach (Kevin MacPherson)
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| − | ** Systematically posting blogs posts and twitter
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| − | ** Write articles
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| − | ** Yeast research blog posts
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| − | ** First of the month webinars
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| − | * For WormBase outreach, we could write articles, news & views
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| − | ** Can post blogs about worm researcher's work
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| − | ** Community write articles?
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| − | ** Newsletter (used to send out emails), bring back? People used to feel like it was spamming
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| − | ** We can have Facebook page (Google + ?)
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| − | ** We need public education, can/should be fun content
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| − | ** Sarah Torres willing to post things on social media, but we need to send her the content
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| − | ** Ask Barbara Perry about writing/editing some articles? Two person job, writing and editing
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| − | ** Create content for lay public
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| − | ** Random Twitter posts putting some people off
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| − | ** Would be good to have someone tweeting hot topics from worm meetings
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| − | * Phenotypes
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| − | ** From Melissa Haendel, try INCA(?) instead of using EQ/post-composed terms?
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| − | * Curating pratices; better (or more fun) than WormBase?
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| − | ** PDF highlighting tools
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| − | * Community curation feedback
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| − | ** People were impressed with participation rates (16% response rate)
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| − | ** Should revisit Textpresso/automated extraction of relevant sentences, present to authors to check off correct connections
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| − | * FlyBase asking community to write concise desriptions (20% response rate)
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| − | | |
| − | === Micropublications ===
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| − | * Grant review: Questions about sustainability, high throughput data, and how people will use the data
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| − | * Minipublications as small narratives
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| − | | |
| − | === IWM ===
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| − | * Paul giving brief plenary talk about WormBase
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| − | * We could wear some identifiable WormBase gear
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| − | ** Hats, ties, bowties, ascots, scarfs, t-shirts, bandanna, ribbon?
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| − | | |
| − | === Textpresso Central ===
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| − | * Ready for the public
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| − | * C. elegans corpus updated weekly
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| − | * "Data not shown" pipeline working for Daniela
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