Difference between revisions of "WormBase-Caltech Weekly Calls"
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| + | = 2019 Meetings = | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_January_2019|January]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_February_2019|February]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_March_2019|March]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_April_2019|April]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_May_2019|May]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_June_2019|June]] | ||
| − | + | [[WormBase-Caltech_Weekly_Calls_July_2019|July]] | |
| − | + | [[WormBase-Caltech_Weekly_Calls_August_2019|August]] | |
| − | |||
| − | |||
| − | == | + | == 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" | ||
| + | ** "aberrant" | ||
| + | ** "defect" | ||
| + | ** "defective" | ||
| + | ** "defects" | ||
| + | ** "deficiency" | ||
| + | ** "deficient" | ||
| + | ** "disrupted" | ||
| + | ** "impaired" | ||
| + | ** "incompetent" | ||
| + | ** "ineffective" | ||
| + | ** "perturbation that disrupts" | ||
| + | ** Failure to execute the characteristic response = abnormal? | ||
| + | ** abnormal | ||
| + | ** abnormality leading to specific outcomes | ||
| + | ** fail to exhibit the same taxis behavior = abnormal? | ||
| + | ** failure | ||
| + | ** failure OR delayed | ||
| + | ** failure, slower OR late | ||
| + | ** failure/abnormal | ||
| + | ** reduced | ||
| + | ** slower | ||
| − | == | + | === Citace upload === |
| + | ** 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 | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | === SObA Graphs === | |
| + | * 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 == | |
| − | |||
| − | === | + | === Strains === |
| − | * | + | * 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 | |
| − | |||
| − | |||
| − | |||
| − | * | ||
| − | |||
Revision as of 16:39, 19 September 2019
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
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"
- "aberrant"
- "defect"
- "defective"
- "defects"
- "deficiency"
- "deficient"
- "disrupted"
- "impaired"
- "incompetent"
- "ineffective"
- "perturbation that disrupts"
- Failure to execute the characteristic response = abnormal?
- abnormal
- abnormality leading to specific outcomes
- fail to exhibit the same taxis behavior = abnormal?
- failure
- failure OR delayed
- failure, slower OR late
- failure/abnormal
- reduced
- slower
Citace upload
- 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
SObA Graphs
- 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
Strains
- 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
