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Community Curation WormBase Workshop International Worm Meeting 2017
- 1. Community Curation Enabling the research community to contribute annotations directly to WormBase Mary Ann Tuli
- 2. 2 years ago……… • Increasing number of curatable papers • Backlog of existing papers Why do we need Community Curation?
- 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.
- 6. Expedious Processing More Data in WormBase Benefits Whole Scientific Community
- 9. Phenotype Submission Can view existing data Autofill
- 10. Phenotype Submission Click on ? to see help
- 11. Phenotype Submission Submission of new alleles encouraged
- 12. Phenotype Submission Links to ontologies encourage standardised terms Links to ontologies encourage standardised terms
- 14. Allele Sequence Submission Same functions as Allele Phenotype form
- 15. Pipeline • Acknowledgement to submitter. • Email notification sent to relevant curators. • Curator validates submission. • Website – Attribution
- 16. Results from past 12 months - Phenotypes 1584 emails sent (one per paper) 237 replies (15%) 31 other 2056 phenotype annotations (29% of all phenotype annotations) 268 papers
- 17. Recognition!
- 18. Recognition!
- 19. Results – Gene Descriptions 0 10 20 30 40 50 60 70 2015 2016 2017 (predicted)
- 20. Recognition!
- 21. Thank you help@wormbase.org Juancarlos Chan Chris Grove Ranjana Kishore
Editor's Notes
- A lot of the work of Chris Grove
- 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 the 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.
- Obvious button to go to all the forms
- 4 forms. I’m mainly using phenotype to demonstrate the functionality of the forms. Micropublication is going to be presented in more details by Daniela
- 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
- Targeted approach. Past year. 7134 phenotype annotations (2056 from CC) From 394 papers (268 CC) 1584 emails sent (one per paper) Community phenotype curation. 237 responded (15%) 31 other papers (15 requested from author first pass) = 268 papers in total (2056 phenotype annotations from 209 unique contributors).
- Allele sequence form
- 2015, 27 2016, 32 2017 (so far) = 64 predicte not widely marketed yet, due to working on reconciling manual and automated descriptions.