Transcript Cambridge Workshop November 2008

Community Curation in FlyBase
10 ways that researchers can help improve
FlyBase data
www.flybase.org
Introduction
What is ‘Community Curation’?
– Annotation/revision of data in FlyBase by fly researchers
Why do it?
– Authors/researchers are the experts in their fields
– Limited number of FlyBase curators, and increasing amount and
variety of data being published
– Improves FlyBase utility for everyone
www.flybase.org
Current Methods
1. Add a relevant publication not in FlyBase
2. Associate genes with an uncurated publication
3. Flag data types in an uncurated publication
www.flybase.org
Fast Track Your Paper
www.flybase.org
Current Methods (cont.)
4. Submit corrections to gene model annotations
www.flybase.org
Fast Track Your Paper
www.flybase.org
Current Methods (cont.)
5. Work with FlyBase to revise and improve annotation
of a particular subject / data type
Recent examples:
-
GO annotation of ‘hearing genes’ (AGOA group)
rationalization of nomenclature for Traf genes (Leptin and
colleagues)
modENCODE data sets
protein interaction data (DPiM)
www.flybase.org
Current Methods (cont.)
6. Help reduce the number of ’orphan genes’ in FlyBase
Data type
Number (FB2011_03)
Dmel Gene Reports
30,193
- localized to genome
15,191 (50%)
- not localized to genome
15,002 (50%)
Data type
Number (FB2011_03)
Dmel protein coding genes
13,922
- with no functional data
2133 (15%)
www.flybase.org
Current Methods (cont.)
7. Use FlyBase gene symbols/names in your papers
–
–
–
Unique identifier (e.g. CG number or FBgn) also useful
Contact FlyBase prior to publication if naming a gene
Contact FlyBase if the FlyBase symbol is ‘wrong’ (e.g. inaccurate,
misleading, or doesn’t reflect common usage)
Advantages include:
–
–
–
Consistency and clarity between literature and FlyBase
Faster, more accurate curation into FlyBase
Makes automatic curation/linking possible
www.flybase.org
GENETICS links
www.flybase.org
Current Methods (cont.)
8. Provide accurate and clear references for alleles,
transgenes etc. used in your papers
–
And/or use FlyBase symbols or another unique identifier (e.g. FBid
number)
Advantages include:
–
–
–
Faster, more accurate curation into FlyBase
Minimize duplicate Reports in FlyBase
Other researchers know exactly which reagents you’ve used
www.flybase.org
Current Methods (cont.)
9. Declare the FlyBase and/or Genome Annotation
‘Release’ numbers in your papers
www.flybase.org
Future Methods
10. Gene Summary wikis (coming soon)
www.flybase.org
Summary
1. Add relevant publications to FlyBase
2. Associate genes with uncurated publications
3. Flag data types in uncurated publications
4. Submit revisions to gene models
5. Work with FlyBase curators to improve specific areas
6. Annotate / clean up 'gene orphans’
7. Use FlyBase symbols in your papers
8. Provide accurate references for reagents in your papers
9. Declare FlyBase release numbers in your papers
10. Contribute to Gene Summary wikis (coming soon)
www.flybase.org