Invited talk for a workshop for Dutch Genomics and Text Mining, Wageningen, 2007. (Scheduled just before drinks, it shows ;-) )

1. with AIDA Marco Roos , Scott Marshall, Sophia Katrenko, Edgar Meij, Willem van Hage, Pieter Adriaans AIDA demonstration Wageningen, 23/11/2007 Adaptation of Talk for Taverna/OMII-UK workshop, Hinxton, October 2007

2. About e-Science An e-science approach to mining biomedical literature

3. and beer… And how we relate it to beer…

4. Virtual Laboratory e-Science project

5. Wet laboratory analogy Data Data handling & Data integration Metadata Data analysis Data storage Expert knowledge

6. General framework of AID for VL-e Middleware for sharing resources Knowledge-based resource management

7. General framework of AID for VL-e Middleware for sharing resources Model based resource management TM TM TM TM TM TM

8. Theme An e-Science approach to mining biomedical literature

9. and beer… And how we relate it to beer…

10. 10/06/09 BioAID Which diseases may be associated with my protein of interest?

11. Biomedical knowledge repository 10/06/09 BioAID PubMed statistics http://www.ncbi.nlm.nih.gov/entrez >17 million citations >400,000 added/year ~70,000 searches/month … Does not compute Does not fit

12. Bioinformatics A bioinformatician

13. Bioinformatics A typical bioinformatician

14. Bioinformatics A biologist behind a computer who (just) learned perl

15. /* * determines ridges in htm expression table */ #include &quot;ridge.h&quot; int selecthtm(PGconn *conn, char *htmtablename, char *chromname, PGresult *htmtable) { char querystring[256]; sprintf(&quot;SELECT * FROM %s WHERE chrom = %s ORDER BY genstart&quot;, htmtablename, chromname); htmtable = PQexec(conn, querystring); return(validquery(htmtable, querystring)); } int is_ridge(PGresult *htmtable, int row, double exprthreshold, int mincount) /* determines if mincount genes in a row are (part of) a ridge */ /* pre: htmtable is valid and sorted on genStart (ascending) /* post: { if (mincount<=0) return TRUE; if (row>=PQntuples(htmtable)) return FALSE; if(PQgetvalue(htmtable, 0, PQfnumber(htmtable, &quot;movmed39expr&quot;)) < exprthreshold) { return FALSE; } return(is_ridge(htmtable, ++row, exprthreshold, --mincount)); } int main() { PGconn *conn; /* holds database connection */ char querystring[256]; /* query string */ PGresult *result; int i; conn = PQconnectdb(&quot;dbname=htm port=6400 user=mroos password=geheim&quot;); if (PQstatus(conn)==CONNECTION_BAD) { fprintf(stderr, &quot;connection to database failed.&quot;); fprintf(stderr, &quot;%s&quot;, PQerrorMessage(conn)); exit(1); } else printf(&quot;Connection ok&quot;); sprintf(querystring, &quot;SELECT * FROM chromosomes&quot;); printf(&quot;%s&quot;, querystring); result = PQexec(conn, querystring); if (validquery(result, querystring)) { printresults(result); } else { PQclear(result); PQfinish(conn); return FALSE; } PQclear(result); PQfinish(conn); return TRUE; } int printresults(PGresult *tuples) { int i; for (i=0; i< PQntuples(tuples) && i < 10; i++) { printf(&quot;%d, &quot;, i); printf(&quot;%s&quot;, PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(&quot; in validquery&quot;); if (PQresultStatus(result) != PGRES_TUPLES_OK) { printf(&quot;Query %s failed.&quot;, querystring); fprintf(stderr, &quot;Query %s failed.&quot;, querystring); return FALSE; } return TRUE; }

16. Theme No , that is not an e-Science approach to mining biomedical literature

17. Not e-science So 2000 (quoting Lennart Post)

18. Not e-science So 1980

19. Theme An e-Science approach to mining biomedical literature

21. e -Scientists Edgar Meij Information retrieval expert

22. e -Scientists Sophia Katrenko Machine learning (information extraction) expert

23. e -Scientists Willem van Hage Semantic web expert (and bass guitar player)

24. The AIDA toolbox for knowledge extraction and knowledge management in a virtual laboratory for e -Science

25. e -bioscience An e-bioscientist

26. Components of the AIDA toolbox used for Life Science knowledge extraction

27. Bio AID Disease Discovery workflow 10/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’

29. Sharing

30. with AIDA Live Demonstration Marco Roos , Scott Marshall, Sophia Katrenko, Edgar Meij, Willem van Hage, Pieter Adriaans AIDA demonstration Tavena/OMII-UK, Hinxton, October 2007

31. 10/06/09 BioAID Which diseases may be associated with my protein of interest?

32. 10/06/09 BioAID

33. Components of the AIDA toolbox used for Life Science knowledge extraction

34. 10/06/09 BioAID

35. Sharing

36. Bio AID Disease discovery workflow

37. Bio AID Disease discovery workflow 10/06/09 BioAID

38. Bio AID Disease discovery workflow from 100 abstracts: 29 proteins associated with 1280 diseases 10/06/09 BioAID

40. 10/06/09 BioAID Doesn’t EZH2 have synonyms?

41. “ Collaboration through web services” Bio-text mining expert Martijn Schuemie

42. “ Collaboration through web services” Synonym service

43. 10/06/09 BioAID EZH2 is only a small part of a very complex system, for my research I need more than lists

44. components... 10/06/09 BioAID

45. Workflow and semantics When running workflows Store how biological entities are related Combine results from different runs Recover ‘trails to evidence’

46. Example scenario of semantic approach Need a unique identifyer myModel myExtended Model

47. “ Collaboration through web services” 2 Bio-text mining expert Martijn Schuemie

48. getUniprotID Used as unique ID for proteins

49. 10/06/09 BioAID

50. 10/06/09 BioAID

51. Proto-ontology (Protégé Jambalaya plugin) 10/06/09 BioAID

52. Enriched ontology (snapshot) 10/06/09 BioAID

55. Modelling support Epigenetics (paramutation) Courtesy of Maike Stam Cell division Escherichia coli Courtesy of Tanneke den Blauwen HIV < TF M M M M M M M RDRP RdDM Pol reinforcement repression M M M M M M M TF TF Pol RDRP B'

56. Reuse and share knowledge MedLine Reuse and share biological knowledge TM

60. Why adopt e-science?

61. Why should I adopt e-Science? I don’t believe in e -Science I believe in Me -Science

62. Why adopt e-science? For determined sinners: ‘ The seven deadly sins of bioinformatics’ by Carole Goble http://www.slideshare.net/dullhunk/the-seven-deadly-sins-of-bioinformatics/

64. How does beer relate to BioAID? And how do we relate it to beer?

65. 10/06/09 BioAID

66. Thank you for your attention… Join the text mining network on myExperiment.org!!! AID information and resources http:// adaptivedisclosure.org W3C Semantic Web Health Care and Life Sciences Interest Group http://www.w3.org/2001/sw/hcls/ BioAID workflows available from http:// .org