Genetic Literature Curation at FlyBaseCambridge

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Genetic Literature Curation at FlyBase-Cambridge
A Database of Drosophila Genes Genomes

• Steven Marygold
• ABC meeting, December 2007

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Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

3
Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

4
Group structure
FlyBase

• FB-Indiana
• website
• fly stocks
• image curation

• FB-Harvard
• database
• genome annotation
• expression curation

• FB-Cambridge
• bibliography
• gene and phenotype curation
• ontologies

Principal Investigators Michael Ashburner Nick
Brown
Group Manager Steven Marygold
GO Curator 1 FTE
Reactome Curator 1 FTE
Literature Curators 3.25 FTEs
Developer 1 FTE
FB Ontology Editor 0.25 FTE
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Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

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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

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Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

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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

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Curation prioritization

• Prioritization of selected journals
• Set of (50) journals publishing on Drosophila
  biology
• Chronological, issue by issue curation
• Prioritization of selected papers
• Flagged by skim curation
• Flagged by stock center
• Genes prioritized by GO project
• Alerted to by research community

10
Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

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Curation practice
Read abstract skim-read intro
Identify/select relevant paper
Access pdf
Highlight curatable material within Results,
Methods, Figures legends, Tables
Curate material into individual proformae to
form a curation record

• Error-checking
• spelling
• consistency
• validity

Completed records submitted for loading into
Chado database
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Curation practice

• Curated data classes (proforma types)
• Publication
• Gene
• Allele
• Aberration
• Transgenic constructs
• Transgenic insertions
• Natural transposons

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Curation practice

• Gene-level curated data
• 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

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Curation practice

• Allele-level curated data
• 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

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Curation practice

• ! 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 GO0005262 IDA
• ! G24c. GO -- Biological process evidence CV
  eye-antennal disc development GO0035214 IMP
• ! ALLELE PROFORMA Version 39 6 July 2007!
• ! GA1a. Allele symbol to use in database
  ey46
• ! GA1b. Allele symbol used in paper
  ey461
• ! GA56. Phenotypic dominance class bipartite
  CV visible recessive
• ! GA17. Phenotype CV, body part(s) where
  manifest eye
• anterior vertical bristle

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Talk Outline

• Group Structure
• The FlyBase bibliography
• Prioritizing curation
• Curation practice
• Curation support
• Future directions

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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

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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

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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