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| [[WormBase-Caltech_Weekly_Calls_August_2019|August]] | | [[WormBase-Caltech_Weekly_Calls_August_2019|August]] |
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− | | + | [[WormBase-Caltech_Weekly_Calls_September_2019|September]] |
− | == September 12, 2019 ==
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− | === Update on SVM pipeline ===
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− | * New SVM pipeline: more analysis and more parameter tuning
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− | * avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
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− | * For example shown, "dumb" machine starts out with precision above 0.6
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− | * G-value (Michael's invention); does not depend on distribution of sets
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− | * Applied to various data types
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− | * Analysis: 10-fold cross validation
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− | ** Randomly select 10% pos and neg (without replacement) and repeat until all papers sampled
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− | * F-value changes over different p/n values; G-value does not (essentially flat)
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− | * Area Under the Curve (AUC): probability that a random positive scores higher than random negative
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− | * AUC values for many WB data types upper 80%'s into 90%'s
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− | * Ranjana: How many papers for a good training set? Michael: we don't know yet
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− | * Can't reproduce old training sets (for old SVM); provide Michael better training sets if you want improved SVM
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− | * If SVM still not good enough, Michael will work on deep neural networks (Tensor Flow)
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− | * Michael can provide training sets he has used recently
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− | | |
− | === Clarifying definitions of "defective" and "deficient" for phenotypes ===
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− | * WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
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− | * Have tried to create a logical definition pattern for these terms, but the vagueness of the meaning of "defective" and how it is distinct from "abnormal" has stalled the process
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− | * What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
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− | * Definitions include meanings or words:
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− | ** "Variations in the ability"
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− | ** "aberrant"
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− | ** "defect"
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− | ** "defective"
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− | ** "defects"
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− | ** "deficiency"
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− | ** "deficient"
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− | ** "disrupted"
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− | ** "impaired"
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− | ** "incompetent"
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− | ** "ineffective"
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− | ** "perturbation that disrupts"
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− | ** Failure to execute the characteristic response = abnormal?
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− | ** abnormal
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− | ** abnormality leading to specific outcomes
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− | ** fail to exhibit the same taxis behavior = abnormal?
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− | ** failure
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− | ** failure OR delayed
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− | ** failure, slower OR late
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− | ** failure/abnormal
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− | ** reduced
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− | ** slower
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− | | |
− | === Citace upload ===
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− | ** Tuesday, Sep 24th
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− | | |
− | === Strain to ID mapping ===
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− | * Waiting on Hinxton to send strain ID mapping file?
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− | * Hopefully we can all get that well before the upload deadline
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− | * Will do global replacement at time of citace upload (at least for now)
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− | | |
− | === New name server ===
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− | * When will this officially go live?
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− | * Will we now be able to request strain IDs through the server? Yes
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− | | |
− | === SObA Graphs ===
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− | * New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
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− | * A lot of whitespace padding above and below graph; maybe trim? trimming vertically would ultimately limit the view pane when user wants to zoom in, so we should leave as is for now
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− | * Diff tool: Raymond and Juancarlos created a prototype diff tool (for comparing two genes, for example)
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− | ** Paul: compared two genes that should be very similar, but there are a lot of differences; may reflect annotation coverage rather than biology
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− | | |
− | == September 19, 2019 ==
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− | === Strains ===
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− | * Need to wait for new strain IDs from Hinxton before running dumping scripts
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− | * Don't edit multi-ontology strain fields in OA for now!
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− | * Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
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− | * "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
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− | | |
− | === Alliance literature curation ===
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− | * Working group will be formed soon
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− | * Will work out general common pipelines for literature curation
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− | | |
− | === SObA Graph relations ===
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− | * Currently only integrating over "is a", "part of" and "regulates"
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− | * Maybe we could provide users an option to specify which relations to include, or maybe just exclude "regulates"
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− | | |
− | === Author First Pass ===
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− | * Putting together paper for AFP
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− | * Reviewing all user input for paper
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− | * Asking individual curators to check input
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− | | |
− | | |
− | == September 26, 2019 ==
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− | | |
− | === Data mining ===
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− | * Someone in Paul's lab asking to retrieve list of C. elegans orthologs from a list of human genes
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− | * Could we build a (simple) Alliance tool to do this?
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− | * Could SimpleMine do this? Could we build a SimpleMine-like tool for Alliance?
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− | | |
− | === Strains ===
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− | * Paul D generated WBStrains for the missing TransgeneOme objects
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− | * Working on a pipeline to identify new TransgeneOme strains at each upload
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− | * One TransgeneOme object had 2 strains. Possible solutions: dump 2 expression objects that differ only in the Strain or remove the UNIQUE tag in the data model
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− | ** Probably best to keep UNIQUE tag
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− | * Raymond: concerned about automatically generating strains based on imports from the group
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− | * Many odd strain names are coming from the TransgeneOme group; maybe we ought to have more discussions about generating official (following nomenclature standards) strain names from their imports
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− | * Quarantine strains on initial import; review and accept if pass standards
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− | | |
− | === Community phenotype requests August 2019 ===
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− | * Sent out new round of phenotype requests on August 20, 21, and 22, 2019
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− | * 2,626 emails/papers requested
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− | * 114 emails bounced; 5 resent to new addresses
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− | * 460 Phenotype OA community annotations; 181 RNAi OA annotations (641 annotations total)
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− | * From 94 papers (83 for Phenotype OA; 33 for RNAi; 22 for both)
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− | * By 81 distinct community curators (70 for Phenotype OA; 32 for RNAi OA; 21 for both)
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− | * 50 papers flagged as not having phenotypes (40 papers DO have phenotypes; 10 marked as negative; 80% failure rate!)
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− | ** Email states: "If there are no nematode phenotypes in this paper click the following link :"
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− | ** Maybe people are confused, or want to blow off the request
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− | ** Maybe we can programmatically generate short URLs for the link? May be difficult
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− | ** Provide a link to correct mistakes on confirmation page
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− | * 4 papers flagged for phenotypes (only 2 had curatable phenotypes; 1 had honey-induced phenotypes)
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− | * 115 papers with responses (5% response); 24 papers with input that were not main focus of request
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− | * Can we provide an opt-out link?
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− | | |
− | === Comparison SObA ===
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− | * Actually quite complicated; may require more consideration
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− | | |
− | === SObA graph and Ontology Browser for papers ===
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− | * May be able to modify/hack existing tools for genes and apply to papers
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− | * Paper-term matching powered by Textpresso
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