1. www.flybase.orgflybase-help@morgan.harvard.edu Genetic Literature Curation at FlyBase-Cambridge Steven Marygold ABC meeting, December 2007 A Database of Drosophila Genes & Genomes

2. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

3. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

4. www.flybase.orgflybase-help@morgan.harvard.edu Group structure FlyBase FB-Indiana - website - fly stocks - image curation FB-Harvard - database - genome annotation - expression curation Group Manager Steven Marygold FB-Cambridge - bibliography - gene and phenotype curation - ontologies Literature Curators 3.25 FTEs GO Curator 1 FTE Reactome Curator 1 FTE Developer 1 FTE FB Ontology Editor 0.25 FTE Principal Investigators Michael Ashburner Nick Brown

5. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

6. www.flybase.orgflybase-help@morgan.harvard.edu Bibliography Search for string ‘Drosophil*’ in title, abstract or keywords Semi-automated search of publication databases –Medline, BIOSIS, ZooRec Manual searches of journal issues

7. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

8. www.flybase.orgflybase-help@morgan.harvard.edu Curation prioritization Types of publication curated: –Primary research papers –Supplemental information –Errata –Personal communications to FlyBase –Conference abstracts –Reviews –Books/Book chapters –Miscellaneous others

9. www.flybase.orgflybase-help@morgan.harvard.edu Curation prioritization 1.Prioritization of selected journals: Set of (~50) journals publishing on Drosophila biology Chronological, issue by issue curation 2.Prioritization of selected papers: Flagged by ‘skim curation’ Flagged by stock center Genes prioritized by GO project Alerted to by research community

10. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

11. www.flybase.orgflybase-help@morgan.harvard.edu Curation practice Access pdf Identify/select relevant paper Read abstract; skim-read intro 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

12. www.flybase.orgflybase-help@morgan.harvard.edu Curation practice Curated data classes (proforma types): –Publication –Gene –Allele –Aberration –Transgenic constructs –Transgenic insertions –Natural transposons

13. www.flybase.orgflybase-help@morgan.harvard.edu 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

14. www.flybase.orgflybase-help@morgan.harvard.edu 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

15. www.flybase.orgflybase-help@morgan.harvard.edu Curation practice ! GENE PROFORMAVersion 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 ! ALLELE PROFORMAVersion 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

16. www.flybase.orgflybase-help@morgan.harvard.edu Talk Outline 1.Group Structure 2.The FlyBase bibliography 3.Prioritizing curation 4.Curation practice 5.Curation support 6.Future directions

17. www.flybase.orgflybase-help@morgan.harvard.edu 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

18. www.flybase.orgflybase-help@morgan.harvard.edu 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

19. www.flybase.orgflybase-help@morgan.harvard.edu 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