2. Why do we need Community
Curation?
• Increasing number of papers
• Backlog of existing papers
15,000 Papers
Primary data papers without
variation phenotype data
Primary data papers with
possible variation phenotype
data
Curated
3. The Solution
• Changes in curation software & database
infrastructure = more curation!
We Need Your Help!
4. Community Curation System
• Easy to use.
• Autocomplete functions.
• Remembers you.
• Enforced standards across all forms.
5. Benefits to the Submitter
• You know your data best.
• Vested interest in public availability of data.
• Automated inclusion in the database.
• Attribution on public website.
Allele phenotype (AP) used to demonstrate why we need cc. WB 15 years. AP only in last 7 yrs, so backlog already existed. Challenging data class – allele name hidden in paper, terms used not always consistent, new terms adopted.
45% of identified papers flagged for AP, of which about 15% curated. At 170 papers per year = over 30 years
he second, delightful, pressure is an increase in data and results generated by the C. elegans and nematode communities. While we are handling this increase by changes in our software for curation, the database infrastructure, and the website, we do need your help. Many of you have helped us over the last few years to identify data in your papers or by sending us data directly. We now need you to help with a few types of information by submitting the data via specially designed, user-friendly forms that ensure good quality and the use of standard terminology. In particular, we have a large backlog of uncurated information associating alleles with phenotypes. We pledge to make this process as painless as possible, and to improve WormBase’s description of phenotypes with your feedback, starting at this meeting at the WormBase booth, workshops and posters. With your help, continual improvement of our efficiency, and additional sources of funding, we are optimistic that we can do much more with even somewhat less effort.
We have improved curation tools. But not enough.
New wormbase form – top tab – link to allele phenotype and to other forms. Screen shot of tab showing the options (time delay screen shot)
Allele sequence form
Allele phenotype form
Animation showing optional opened up and with link to allele sequence form
Animation showing green pop up on right.
Auto complete when name recognised (transferred to other forms when same computer is used). Allele name checked and user encouraged to submit new alleles to us if necessary. Phenotpye links to ontology, user can be sure using best term
Optional.
Auto complete when name recognised (transferred to other forms when same computer is used). Allele name checked and user encouraged to submit new alleles to us if necessary. Phenotpye links to ontology, user can be sure using best term
Optional.
Allele sequence form
happens after submission
- acknowledgement to submitter
- email to relevant curators
- triage - automated (ish)
- curation
Website
Need a time line