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