www.flybase.org community curation in flybase 10 ways that researchers can help improve flybase data
TRANSCRIPT
www.flybase.org
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
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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
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Fast Track Your Paper
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Current Methods (cont.)
4. Submit corrections to gene model annotations
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Fast Track Your Paper
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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)
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Current Methods (cont.)
6. Help reduce the number of ’orphan genes’ in FlyBase
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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
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GENETICS links
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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
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Current Methods (cont.)
9. Declare the FlyBase and/or Genome Annotation ‘Release’ numbers in your papers
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Future Methods
10. Gene Summary wikis (coming soon)
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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)