We are calling for curation teams to produce a document describing their curation process as it starts from selection of articles for curation (as journal articles or abstracts) culminating in database entries.
As a help in this important enterprise, we have put together two resources:
OUTLINE for Description of Biocuration Workflow
- Introduction a. Overall philosophy and what information is captured.
- Encoding methods a. How is the information captured to make it machine readable?
- Information access a. When a curator runs into a problem or a difficult case what kind of information is needed to solve it?
- Use of text mining tools a. What text mining tools do you currently employ in your workflow and what problems do these algorithms solve for you?
b. What use is being made of this information or is envisioned for this information?
c. The current workflow of the operation.
d. How are the links to biomedical literature captured?
b. What entities are involved and how are they entered in the database?
c. What relationships are involved and how are they symbolized?
d. What standardized or controlled vocabularies are used?
e. Give examples of a variety of data elements and how they appear in the database.
b. What kind of internet searching is used most often in difficult cases? dictionary? wikipedia? other database?
b. What problems do you have that are not currently solved, but which you think could be amenable to a text mining solution (i.e., for which steps text mining could overcome current bottlenecks in the existing pipeline)?
Your description of your workflow and any available annotated corpora will be valuable for considering workflows and challenge tasks for the future BioCreative IV challenge.
Document format
The file should be up to 6 pages, including figures; Word or .rtf files would be preferred.
Important Dates
Item | Deadline | Submit via | Comment |
---|---|---|---|
Team Registration | November 15, 2011 | web | register here |
Submission of Biocuration Workflow | December 31, 2011 | email to lynette@mitre.org | Subject:BioCreative-2012 Track II |
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