Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Two things to work on: | *Two things to work on: | ||
**1) Metrics and quality control | **1) Metrics and quality control | ||
− | ***Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments 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 vs Curation Status form; numbers for coverage | + | ****SVM form (in development) vs Curation Status form (needs work/update); numbers for coverage |
+ | ****What is the vision of a new Curation Status form? (Daniela will write something) | ||
+ | ***Quality Control: How do we demonstrate that our curation is correct? | ||
+ | ****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? | ||
+ | ****Contact senior author on a paper to check the quality of data from a paper | ||
+ | |||
**2) Training and user interaction | **2) Training and user interaction | ||
***Screencasts and FAQs list (Chris will write some sentences) | ***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) | ***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? | ***Online chat: has been broken for months; should it only be allowed for logged-in users? |
Revision as of 18:28, 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); numbers for coverage
- What is the vision of a new Curation Status form? (Daniela will write something)
- Quality Control: How do we demonstrate that our curation is correct?
- 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?
- Contact senior author on a paper to check the quality of data from a paper
- Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
- 1) Metrics and quality control
- 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?
- 2) Training and user interaction