dictyBase Literature Curation

dictyBase Literature Curation and How Authors can Help. This presentation highlights the time consuming strain curation and how authors may help with adding tables; it also describes the possibility to use textmining when annotating Gene Ontology, and how authors can insure that results are described in a complete way and easy to interpret for textmining tools. At the SAB meeting it was then decided to create a community annotation form. At the end of the talk a floor vote was taken that indicated people would respond to community curation requests.

Transcript

1. dictyBase Literature Curation and how Authors can Help Dicty 2012 Conference 1. August, 2012 Madrid, Spain
2. •  Literature topics (broad categories of biological entities) •  Mutant strains •  Phenotypes of mutant strains •  Molecular functions (GO) •  Biological processes (GO) •  Cellular components (GO) •  Gene names/Protein names •  Free-text descriptions, notes, summaries •  Gene structure Literature Curation at dictyBase
3. Why Curating Literature? •  Makes experimental results easily accessible on Gene Pages •  Widely distributes annotations (GO; TrEMBL…) •  Manually annotated genomes provide ‘gold standard’ for electronic annotations of related genomes •  Systematic annotations amenable for computational analyses •  Increases visibility for publications, as every experimental annotation is linked to a PubMed reference •  Leads to increase in citations
4. Literature Curation progress 0 1000 2000 3000 4000 5000 6000 7000 8000 total papers in dictyBase curated papers End of Year Number of papers
5. Literature Curation progress 0 1000 2000 3000 4000 5000 6000 7000 8000 total papers in dictyBase curated papers Karen Pascale Bob End of Year Number of papers
6. Literature Curation progress 0 1000 2000 3000 4000 5000 6000 7000 8000 total papers in dictyBase curated papers Karen Pascale Bob End of Year Number of papers Gene Model Curation Focus
7. Ways to Increase Curation Efficiency 1. Hire more Curators! UNREALISTIC
8. Ways to Increase Curation Efficiency 1. Hire more Curators! UNREALISTIC 2. Create a Full Community Annotation Tool! UNREALISTIC 1. Hire more Curators!
9. Ways to Increase Curation Efficiency 1. Hire more Curators! UNREALISTIC 2. Create a Full Community Annotation Tool! UNREALISTIC 3. Authors Help by Writing Curatable Papers! Let’s Try! 1. Hire more Curators! 2. Create a Full Community Annotation Tool!
10. •  Literature topics (broad categories of biological entities) •  Mutant strains •  Phenotypes of mutant strains •  Molecular functions (GO) •  Biological processes (GO) •  Cellular components (GO) •  Gene names/Protein names •  Free-text descriptions, notes, summaries •  Gene structure Literature Curation at dictyBase
11. Strain Annotation •  Strain Descriptor •  Strain Name(s) •  Systematic Name •  Strain Summary •  Genotype •  Genetic Modification •  Mutagenesis Method •  Strain Characteristics •  Depositor (IA) •  Parental Strain •  Species •  Plasmid •  Reference(s) •  Associated Gene(s) Strain Details
12. Strain Annotation •  Strain Descriptor •  Strain Name(s) •  Systematic Name •  Strain Summary •  Genotype •  Genetic Modification •  Mutagenesis Method •  Strain Characteristics •  Depositor (IA) •  Parental Strain •  Species •  Plasmid •  Reference(s) •  Associated Gene(s) Phenotype and Strain Details
13. Strain Information in Papers - 1
14. Strain Information in Papers - 1 FIGURE LEGEND
15. Strain Information in Papers - 1 FIGURE LEGEND RESULTS
16. Strain Information in Papers - 1 FIGURE LEGEND RESULTS Parental Strain Info Missing!
17. Strain List from Paper 1 New strains created: •  - zak2- •  - zak2-/[act15]:GFP •  - zak2-/[ecmA]:LacZ •  - zak2-/[ecmA]:zakA •  - zak2-/[ecmB]:LacZ •  - zakA-/[ecmA]:LacZ •  - zakA-/[ecmB]:LacZ •  - gskA-/[ecmA]:LacZ •  - gskA-/[ecmB]:LacZ •  - gskA-/act15]:gskA(Y214F) Existing strains used: •  - zakA- •  - gskA-
18. Strain Information in Papers - 2
19. Strain Information in Papers - 2 Numerous complex strains
20. Strain List from Paper 2 Strains with phenotypes created in this paper: •  myoK-/[act15]:myoK •  myoK-/[act15]:pakB(1-337:563-852) •  myoK-/[act15]:YFP:myoK(1-121:262-858) •  myoK-/[act15]:GFP:myoK(114-272) •  [act15]:GFP:myoK(801-858) •  [act15]:myoK:Myc •  abpE- •  abpE-/[act15]:abpE •  [act15]:pakB(1-337:563-852) Expression strains for localization studies: •  GFP-myoB •  YFP-myoC •  GFP-dymA
21. How Authors May Help Strain  name(s)/ descriptor   Parent  strain   Muta5on  /   Characteris5cs   Promoter/ Construct   Resistance   marker   asf1-­‐       HSM345   JH10   Null,  homologous   recombina=on   thy-­‐ construct   NA   grlK-­‐/grlK:GFP   ABC56   grlk-­‐   overexpression   ac=n  15,   pDXA-­‐GFP   neoR   iksA-­‐/iksA(T123A,   S234A)   iksA-­‐   gene  replacement,   point  muta=ons   iksA   neoR   fimA-­‐/fimC-­‐/fimD-­‐   GFA376   fimA-­‐/fimC-­‐   null,  loxP   floxed  BsR   casseYe   BsR   Strain Table
22. How Authors may Help Strain List •  dymA-/[dymA]:dymA, null, rescue, bsR •  lvsA-/[act6]:GFP:lvsA(659- 3619), knock-in, bsR •  AX3/[act15]:cAR1(I104D), point mutation, bsR •  AX2/Δ(1-75;119-579)-golvesin(C)-GFP, pDEX-GFP, act15p, neoR Add parental info here or in Materials &Methods
23. •  Literature topics (broad categories of biological entities) •  Mutant strains •  Phenotypes of mutant strains •  Molecular functions (GO) •  Biological processes (GO) •  Cellular components (GO) •  Gene names/Protein names •  Free-text descriptions, notes, summaries •  Gene structure Literature Curation at dictyBase
24. Gene Ontology (GO) Annotations •  Captures 3 biological aspects: molecular functions, biological processes, cellular components •  Controlled vocabularies: consistent descriptions of gene products in different databases •  Collaborative effort across a wide range of groups •  Allows extracting biological knowledge from large data sets •  GO Browser AmiGO: Search and browse GO and the gene products that member databases have annotated using GO terms •  Enables the use of text mining to assist manual annotation hYp://www.geneontology.org/  
25. GO Annotations in dictyBase
26. Textpresso Annotation Flow Textpresso colleagues at WormBase download papers weekly from our server
27. Textpresso Annotation Flow Textpresso colleagues at WormBase download papers weekly from our server Full text GO annotation pipeline
28. Textpresso Annotation Flow Textpresso colleagues at WormBase download papers weekly from our server Full text GO annotation pipeline Presentation of textpresso output to dictyBase and annotation by Curator
29. Textpresso Annotation Flow Textpresso colleagues at WormBase download papers weekly from our server Full text GO annotation pipeline Presentation of textpresso output to dictyBase and annotation by Curator GO annotation file added to dictyBase annotations
30. Textpresso for GO Components Full text marked up with categories: “DDB_G0289429 is localized at the nuclear envelope when expressed as a green fluorescent protein (GFP) fusion protein.” Gene Verb Cellular Component Assay
31. Textpresso Category Examples •  Components: nucleolus, spindle, plasma membrane •  Assays: GFP-tagged, antibodies, staining •  Verbs: expressed, co-localized, observed
32. Textpresso Annotation Tool
33. Problems Encountered…
34. Missing Category Term Statement in paper correctly describes localization but is missing a term from one of the required categories: Missing Gene Product “Staining shows it localizes to the plasma membrane.” Missing Assay term “DGAP1 is found at the plasma membrane.”
35. Missing Category Term Statement in paper correctly describes localization but is missing a term from one of the required categories: Missing Gene Product “Staining shows it localizes to the plasma membrane.” Missing Assay term “DGAP1 is found at the plasma membrane.”
36. Missing Category Term Statement in paper correctly describes localization but is missing a term from one of the required categories: Missing Gene Product “Staining shows it localizes to the plasma membrane.” “Staining shows ABC localizes to the plasma membrane.” Missing Assay term “DGAP1 is found at the plasma membrane.” “DGAP1 localizes to the plasma membrane.”
37. Problematic Nomenclature Gene product names not in dictyBase Unknown gene product names Gene/protein names might have an extra hyphen or any small difference from what is in dictyBase, e.g. using myosin 1D instead of myosin-1D
38. Problematic Nomenclature Gene product names not in dictyBase Unknown gene product names Gene/protein names might have an extra hyphen or any small difference from what is in dictyBase, e.g. using myosin 1D instead of myosin-1D Greek or special characters “GFP-β1/2 colocalizes with clathrin and with punctae of AP2α at the cell periphery” β1/2 = beta adaptin1/2; gene ap1b1, DDB_G0279141
39. Problematic Nomenclature Gene product names not in dictyBase Unknown gene product names Gene/protein names might have an extra hyphen or any small difference from what is in dictyBase, e.g. using myosin 1D instead of myosin-1D Greek or special characters “GFP-β1/2 colocalizes with clathrin and with punctae of AP2α at the cell periphery” β1/2 = beta adaptin1/2; gene ap1b1, DDB_G0279141
40. GO Term not Identified Component terms not in GO: Term not there at all e.g. “protruding regions” Might be “pseudopodium” Term not represented in GO as such e.g. “microtubule-organizing center” In GO: “microtubule organizing center”  
41. Wish List •  Describe all essential strain properties •  When describing more than a couple of strains, list new strains in a table or simple list. •  Use exact gene/protein identifiers that are in -, or communicated to dictyBase •  When preferring a simple/short, special character name throughout the paper, use common name or gene ID at least once for the description of each result •  Spread the message to lab members, colleagues!
42. 2012 dictyBase Scientific Advisory Board: Create Community Annotation Form
43. Thank You! The dictyBase team •  Rex Chisholm •  Warren Kibbe •  Petra Fey •  Robert Dodson •  Siddhartha Basu •  Yogesh Pandit •  Ismail Mitchell (software volunteer) •  Kerry Sheppard (DSC) •  Kanaka Harkare (DSC temp) •  Pascale (consultant) Textpresso Collaborators •  Kimberly Van Auken •  Yuling Li •  Michael Mueller Funding •  NIH (NIGMS and NHGRI) •  GO Consortium