Difference between revisions of "WormBase-Caltech Weekly Calls"
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**1) Metrics and quality control | **1) Metrics and quality control | ||
***Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage") | ***Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage") | ||
− | ****SVM form (in development) vs Curation Status form (needs work/update); numbers for coverage | + | ****SVM form (in development) vs Curation Status form (needs work/update); can generate numbers for coverage to display on the web? |
****What is the vision of a new Curation Status form? (Daniela will write something) | ****What is the vision of a new Curation Status form? (Daniela will write something) | ||
+ | ****Stats with new SVM results on pre-2000 papers: state them in grant as pre-2000 corpus | ||
***Quality Control: How do we demonstrate that our curation is correct/accurate? | ***Quality Control: How do we demonstrate that our curation is correct/accurate? | ||
− | ****Sampling First-pass curation (false negative estimates) | + | ****Sampling First-pass curation (false negative estimates) |
****WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics | ****WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics | ||
****Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass | ****Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass | ||
Line 88: | Line 89: | ||
**Migrate to Chado? Do we need detailed plan for this? | **Migrate to Chado? Do we need detailed plan for this? | ||
**FlyBase has migrated; they like Chado, but the migration was painful | **FlyBase has migrated; they like Chado, but the migration was painful | ||
+ | |||
+ | |||
+ | WOrm Breeder's Gazette & WormBook outreach | ||
+ | *Mass mailings should be an Opt-in system, as opposed to blanket mass mailings | ||
+ | *One mass mail for each to ask about Opting-in to e-mail alerts? | ||
+ | *Regional & International worm meetings; hand all e-mails over to meeting organizers? | ||
+ | |||
+ | |||
+ | Itai Yanai expression datasets | ||
+ | *Including images from microarray expression data | ||
+ | |||
+ | |||
+ | Phenotype Images? |
Revision as of 19:06, 13 September 2012
2012 Meetings
September 6, 2012
Canopus
- Will become a server (heavy outside access)
- Raymond will take precautions to restore properly; should take a week or less
- Used for:
- Picture curation
- Virtual worm web page & FTP
Grant Writing
- Approach & future plans - do we need to discuss and add more to proposal?
- Virtual worm access to data
- Browsing data
- Browse genes/proteins by class/GO annotation
- Intermine queries
- Queries can be saved and used again later (available to other users)
- Results can be stored and displayed on web pages
- Displaying large scale expression (microarray) data (from SPELL)
- SPELL data currently stored in relational (MySQL?) form
- We could extend the WormBase web app to interact with SPELL data
- RESTful-compliant data serving would be best
Migration away from ACEDB?
- Scalability - ACEDB does not scale to genome-scale studies
- We (EBI & OICR) spend a lot of time building ACEDB database
- ACEDB not actually used so much
- Makes more sense to adopt a more central database
- Migration would take place over entire grant cycle
- We should continue extending models as we see fit, in the meantime
Massmails
- Discuss again with Paul about Worm Breeder's Gazette and WormBook.
September 13, 2012
Grant
- Two things to work on:
- 1) Metrics and quality control
- Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
- SVM form (in development) vs Curation Status form (needs work/update); can generate numbers for coverage to display on the web?
- What is the vision of a new Curation Status form? (Daniela will write something)
- Stats with new SVM results on pre-2000 papers: state them in grant as pre-2000 corpus
- Quality Control: How do we demonstrate that our curation is correct/accurate?
- Sampling First-pass curation (false negative estimates)
- WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics
- Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass
- Data-type specific issues
- Internal consistency checks
- Ontology based curation checks (granularity; branch-consistency)
- Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
- 2) Training and user interaction
- Screencasts and FAQs list (Chris will write some sentences)
- User guide status? Currently needs major revamp and new information (old Wiki User Guide is now obsolete)
- Online chat: has been broken for months; should it only be allowed for logged-in users?
- 1) Metrics and quality control
- Daily updates with low-connectivity data (not relying on sequence mapping) from PostgreSQL database?
- Have different CGI forms to populate the data on the website?
- Are we committed to migrating away from ACEDB? Who then is responsible for managing data models?
- Migrate to Chado? Do we need detailed plan for this?
- FlyBase has migrated; they like Chado, but the migration was painful
WOrm Breeder's Gazette & WormBook outreach
- Mass mailings should be an Opt-in system, as opposed to blanket mass mailings
- One mass mail for each to ask about Opting-in to e-mail alerts?
- Regional & International worm meetings; hand all e-mails over to meeting organizers?
Itai Yanai expression datasets
- Including images from microarray expression data
Phenotype Images?