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Gene Wiki+ for integrative queries
mwsync
OMIM
PharmGKB
{{#ask:
[[Category:Human_proteins]]
[[is_associated_with::
<q>[[Category:Breast_cancer]
]</q>]]
[[HasSNP::
…
<q>[[is_associated_with::
http://genewikiplus.org](https://image.slidesharecdn.com/20120816isi-120817113128-phpapp01/85/Crowdsourcing-to-structure-biological-knowledge-USC-ISI-22-320.jpg)
Uploaded byAndrew Su
Crowdsourcing to structure biological knowledge (USC/ISI)
This document discusses using crowdsourcing to improve biological knowledge by structuring gene annotations. It notes that few genes are well annotated currently, with most attention given to a small number of prominent genes. Biocuration is a bottleneck that limits greater annotation. The document proposes harnessing the "Long Tail" of scientists through a Gene Wiki and biological games to directly involve more researchers in annotation. This could scale up annotation to the rate of new data generation and literature. Structured data from crowdsourcing could enable new integrative queries and predictive models across genes, diseases, and genotypes.
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Crowdsourcing to structure biological knowledge (USC/ISI)
- 1. Crowdsourcing to structurebiological knowledge Andrew Su, Ph.D. Department of Molecular and Experimental Medicine The Scripps Research Institute ISI, USC August 16, 2012
- 2. 2 Human genetics underlieshuman health Molecular understanding of: • Biological function • Genetic variation • Mutation “Gene • Deletion annotation” • Amplification • … ~3 billion ~23,000 bases genes Molecular diagnostics & therapeutics
- 3. 3 Structured gene annotationsenable computation Structured annotations
- 4. 4 Few genes arewell annotated TP53 TNF APOE MTHFR IL6 HLA-DRB1 Counts VEGFA EGFR TGFB1 59% ACE PubMed 38% 23,278 protein- coding genes Gene ontology (GO) Genes, sorted by decreasing counts Data: NCBI gene2pubmed, August 2010
- 5. 5 Biocuration is akey annotation bottleneck Number of PubMed-indexed articles 1,000,000 800,000 600,000 400,000 200,000 0 1979 1984 1989 1994 1999 2004 2009
- 6. 6 311,696 articles (1.5%of PubMed) have been cited by GO annotations
- 7. 7 Sooner or later, the research community will need to be involved in the 0 annotation effort to scale up to the rate of data generation.
- 8. 8 The Long Tailis a prolific source of content Short Head Content produced Long Tail Contributors (sorted) News : Newspapers Blogs Video: TV/Hollywood YouTube Product reviews: Consumer reports Amazon reviews Food reviews: Food critics Yelp Talent judging: Olympics American Idol
- 9. 9 Wecan harness the Long Tail of scientists to directly participate in the gene annotation process.
- 10. 10 From crowdsourcing tostructured data The Gene Wiki Biological Games
- 11. 11 10,000 gene“stubs” within Wikipedia Utility Users Contributors Protein structure Gene summary Symbols and identifiers Gene Ontology annotations Protein interactions Tissue expression Linked pattern references Links to structured databases Huss, PLoS Biol, 2008
- 12. 12 Gene Wikihas a critical mass of readers Total: 4.0 million views / month Huss, PLoS Biol, 2008; Good, NAR, 2011
- 13. 13 Gene Wikihas a critical mass of editors Editor count Editors Edit count Edits Increase of ~10,000 words / month from >1,000 edits Currently 1.42 million words Approximately equal to 230 full-length articles Good, NAR, 2011
- 14. 14 A review articlefor every gene is powerful Reelin: 68 editors, 543 edits since July 2002 Heparin: 175 editors, 320 edits since June 2003 AMPK: 44 editors, 84 edits since March 2004 RNAi: 232 editors, 708 edits since October 2002 References to the literature Hyperlinks to related concepts
- 15. Filtering, extracting, andsummarizing PubMed Documents Concepts
- 16. 16 Document- and concept-centrictext mining Predicate Subject Object
- 17. 17 Simple text miningfor gene annotations NCBI Entrez Gene: 334 Gene Wiki mapping Wikilink Candidate assertion GO:0006897 GO exact match 6319 novel Gene Ontology annotations 2147 novel Disease Ontology annotations
- 18. 18 Gene Wiki+ forintegrative queries mwsync http://genewikiplus.org
- 19. 19 Dynamic queries acrossgenes, diseases, SNPs
- 20.
- 21.
- 22. 22 Gene Wiki+ forintegrative queries mwsync OMIM PharmGKB {{#ask: [[Category:Human_proteins]] [[is_associated_with:: <q>[[Category:Breast_cancer] ]</q>]] [[HasSNP:: … <q>[[is_associated_with:: http://genewikiplus.org
- 23. 23 Gene Wiki+ forintegrative queries mwsync OMIM PharmGKB http://genewikiplus.org
- 24. 24 From crowdsourcing tostructured data The Gene Wiki Biological Games
- 25. 25 Not just thebiomedical literature…
- 26. 26 BioGPS aggregates gene-centricinformation http://biogps.org
- 27. 27 The plugin interfaceis simple and universal Pubmed http://www.ncbi.nlm.nih.gov/sites/entrez?...&Term={{Symbol}} STRING http://string-db.org/newstring_cgi?...&identifier={{EnsemblGene}} KEGG http://www.genome.jp/dbget-bin/www_bget?hsa:{{EntrezGene}} URL template Rendered URL Gene entity
- 28. 28 The plugin interfaceis simple and universal
- 29. 29 The plugin interfaceis simple and universal
- 30. 30 The plugin interfaceis simple and universal
- 31. 31 The plugin interfaceis simple and universal
- 32. 32 The plugin interfaceis simple and universal Total of 389 gene-centric online databases registered as BioGPS plugins
- 33. 33 BioGPS has acritical mass of users Daily pageviews • > 4100 registered users Top 10 organizations • 4000 unique visitors per week 1. Harvard 6. Cambridge 2. NIH 7. U Penn • 40,000 page views per week 3. UCSD 8. Stanford 4. Scripps 9. Wash U 5. MIT 10. UNC
- 34. 34 All resources shouldprovide RDF…
- 35. 35 Mining structured contentfrom HTML
- 36. 36 Defining a dataextraction template TP53 TNF APOE IL6 VEGF EGFR TGFB1 … …
- 37. 37 The BioGPS SemanticAnnotator http://50.112.124.237
- 38. 38 All resources shouldprovide flat files…
- 39. 39 From crowdsourcing tostructured data The Gene Wiki Biological Games
- 40. 40 Seven million humanhours http://www.flickr.com/photos/archana3k1/4124330493/
- 41. 41 Twenty million humanhours http://www.flickr.com/photos/ableman/2171326385/
- 42. 42 - 150 billion human hours per year http://www.flickr.com/photos/rvp-cw/6243289302/
- 43. 43 Using games tofold proteins Fold.it players have successfully: • Outperformed state of the art protein folding algorithms (Cooper, Nature, 2010) • Solved a previously-intractable crystal structure (Khatib, Nat Struct Mol Biol, 2011) • Designed an improved protein folding algorithm (Khatib, PNAS, 2011) • Improved enzyme activity of de novo designed enzyme (Eiben, Nat Biotechnol, 2011)
- 44. 44 Using games tofold RNAs http://eterna.cmu.edu/
- 45. 45 Using games toalign sequences http://phylo.cs.mcgill.ca
- 46. 46 Using games toannotate gene-disease links hurry! then on to the next question If its ‘right’, you get points Click the related disease http://genegames.org
- 47. 47 Dizeez players seempretty smart… In total: • 207 unique gamers • 1045 games played • 8525 guesses # Occurrences Gene Disease Pubmed OMIM PharmGKB Gene Wiki 7 GAST gastrinoma 7 RBP3 retinoblastoma 7 SSX1 synovial sarcoma 6 TG Graves' disease 6 CRYGC Cataract 6 SOX8 mental retardation 6 WRN Werner syndrome 6 ABL1 leukemia 6 MLL3 leukemia 6 SNAI2 breast carcinoma
- 48. 48 Dizeez players seempretty smart… In total: • 207 unique gamers • 1045 games played • 8525 guesses # Occurrences Gene Disease Pubmed OMIM PharmGKB Gene Wiki 5 MECOM sarcoma 4 ATF7 cancer 3 ABCB5 acute myeloid leukemia 3 SART1 glioblastoma 3 NCK1 leukemia 3 NEK1 cancer
- 49.
- 50. 50 COMBO: Genomic predictorsfor disease make predictions on cancer normal new samples find patterns cancer normal
- 51. 51 COMBO: Genomic predictorsfor disease
- 52. 52 COMBO: Genomic predictorsfor disease
- 53. 53 COMBO: Genomic predictorsfor disease
- 54. 54 COMBO: Genomic predictorsfor disease
- 55. 55 COMBO: Genomic predictorsfor disease
- 56. 56 COMBO: Genomic predictorsfor disease
- 57. 57 Wecan harness the Long Tail of scientists to directly participate in the gene annotation process.
- 58. 58 Collaborators Group members Doug Howe, ZFIN Erik Clarke Ian Macleod John Hogenesch, U Penn Jon Huss, GNF Ben Good Chunlei Wu Luca de Alfaro, UCSC Salvatore Loguercio Angel Pizzaro, U Penn Faramarz Valafar, SDSU Pierre Lindenbaum, Fondation Jean Dausset Summer internships for students! Michael Martone, Rush Konrad Koehler, Karo Bio Warren Kibbe, Simon Lim, Northwestern Many Wikipedia editors WP:MCB Project Contact http://sulab.org Recruiting graduate students asu@scripps.edu in quantitative biology! See @andrewsu http://education.scripps.edu/ +Andrew Su Funding and Support (BioGPS: GM83924, Gene Wiki: GM089820)
Editor's Notes
- #5 We are very early in our efforts to comprehensively annotate human gene functionWhy important? Genome-scale surveys aren’t biased toward well studied genes, huge opportunity for biomedical discovery59% have 5 or fewer references38% have one or no references
- #7 Much knowledge is locked up in biomedical literature – our goal is to make it computableIf you believe that greater than 1.5% of articles have relevance to gene function, then it says there is a bottleneck in in our curation effortsNumbers updated 7/15/2011
- #11 For each resourceBriefly describe the unstructured resourceDescribe the structuring approach
- #16 Relying on the entire community of scientists to digest the biomedical literature: identification filtering extraction summarization
- #25 For each resourceBriefly describe the unstructured resourceDescribe the structuring approach
- #29 MODs and portals
- #30 Genetics resources
- #31 Literature resources
- #32 Protein resources
- #33 Pathway and expression databases
- #40 For each resourceBriefly describe the unstructured resourceDescribe the structuring approach
- #41 Empire state building