Download GENE PROFORMA Version 50: 05 Oct 2007!

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A Database of Drosophila Genes & Genomes
Genetic Literature Curation at
FlyBase-Cambridge
Steven Marygold
ABC meeting, December 2007
www.flybase.org
[email protected]
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Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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1.
2.
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5.
6.
Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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Group structure
FlyBase
FB-Harvard
FB-Cambridge
FB-Indiana
- database
- genome annotation
- expression curation
- bibliography
- gene and phenotype curation
- ontologies
- website
- fly stocks
- image curation
Principal Investigators
Michael Ashburner
Nick Brown
Reactome Curator
Group Manager
GO Curator
1 FTE
Steven Marygold
1 FTE
Literature Curators
Developer
FB Ontology Editor
3.25 FTEs
1 FTE
0.25 FTE
www.flybase.org
[email protected]
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1.
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6.
Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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Bibliography
• Search for string ‘Drosophil*’ in title,
abstract or keywords
• Semi-automated search of publication
databases
– Medline, BIOSIS, ZooRec
• Manual searches of journal issues
www.flybase.org
[email protected]
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1.
2.
3.
4.
5.
6.
Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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Curation prioritization
Types of publication curated:
– Primary research papers
– Supplemental information
– Errata
– Personal communications to FlyBase
– Conference abstracts
– Reviews
– Books/Book chapters
– Miscellaneous others
www.flybase.org
[email protected]
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Curation prioritization
1. Prioritization of selected journals:
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Set of (~50) journals publishing on Drosophila biology
Chronological, issue by issue curation
2. Prioritization of selected papers:
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Flagged by ‘skim curation’
Flagged by stock center
Genes prioritized by GO project
Alerted to by research community
www.flybase.org
[email protected]
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1.
2.
3.
4.
5.
6.
Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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Identify/select
relevant paper
Curation practice
Access pdf
Curate material into
individual ‘proformae’ to
form a ‘curation record’
Error-checking:
- spelling
- consistency
- validity
www.flybase.org
Read abstract;
skim-read intro
Highlight curatable
material within Results,
Methods, Figures &
legends, Tables
Completed records
submitted for loading
into Chado database
[email protected]
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Curation practice
Curated data classes (proforma types):
– Publication
– Gene
– Allele
– Aberration
– Transgenic constructs
– Transgenic insertions
– Natural transposons
www.flybase.org
[email protected]
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Curation practice
Gene-level curated data:
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valid FlyBase gene symbol/name
gene symbol/name used in paper
action gene rename or merge
action creation or deletion of gene
etymology of gene name
Sequence Ontology (SO) terms
cytological map position
relationship to cDNA/genomic clone
Gene Ontology (GO) terms
y/n flags to indicate paper has expression or
annotation information
www.flybase.org
[email protected]
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Curation practice
Allele-level curated data:
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valid FlyBase allele symbol/name
allele symbol/name used in paper
action allele rename or merge
action creation or deletion of allele
allele class
mutagen
nucleotide/amino acid changes
phenotype: class, anatomy, free text
genetic interaction: class, anatomy, free text
complementation data
associated transgenic construct/insertion
associated tag
www.flybase.org
[email protected]
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Curation practice
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GENE PROFORMA
Version 50: 05 Oct 2007!
G1a. Gene symbol to use in database
:ey
G1b. Gene symbol used in reference
:ey
G24a. GO -- Cellular component | evidence [CV] :
G24b. GO -- Molecular function | evidence [CV] :calcium channel
activity ; GO:0005262 | IDA
! G24c. GO -- Biological process | evidence [CV] :eye-antennal disc
development ; GO:0035214 | IMP
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ALLELE PROFORMA
Version 39: 6 July 2007!
GA1a. Allele symbol to use in database
:ey[46]
GA1b. Allele symbol used in paper
:ey[461]
GA56. Phenotypic | dominance class [bipartite CV] :visible |
recessive
! GA17. Phenotype [CV, body part(s) where manifest] :eye
anterior vertical bristle
www.flybase.org
[email protected]
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1.
2.
3.
4.
5.
6.
Talk Outline
Group Structure
The FlyBase bibliography
Prioritizing curation
Curation practice
Curation support
Future directions
www.flybase.org
[email protected]
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Curation support
• Curation support files
– Text files of data from latest DB instance
• Ontology files
– GO, SO, FB-anatomy, FB-phenotypes etc.
• PeeVeS
– Proforma Validation Software
• Other custom scripts
www.flybase.org
[email protected]
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Future directions
• More paper-by-paper prioritization
• ‘Skim curation’
– Manual curation
– Automated curation?
– User-submitted data
• Use of text-mining aids for ‘deep curation’
• Review breadth and depth of curation
• Enhanced curation interface
www.flybase.org
[email protected]
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Acknowledgements
FB-Cambridge:
Michael Ashburner (co-PI)
Nick Brown (co-PI)
Steven Marygold (Manager)
Gillian Millburn (Literature curator)
David Osumi-Sutherland (Ontology Editor and Literature curator)
Ruth Seal (Literature curator)
Peter McQuilton (Literature curator)
Paul Leyland (Developer)
Susan Tweedie (GO curator)
Mark Williams (Reactome curator)
Rachel Drysdale (former FB-Cambridge co-PI)
Genetics Dept., University of Cambridge, UK
The FlyBase Consortium
NHGRI at the NIH
www.flybase.org
[email protected]