1. VIB/BITS training:literature management Maté Ongenaert Center for Medical Genetics Ghent University Hospital, Belgium

3. PhD in Applied biological sciences, cell and gene biotechology (2009)

4. Currently postdoctoral researcher at CMGG (Ghent University)

5. Both in academic and industrial settings, involved in automated literature searches and integration of data analysis with literature results

7. Introduction

10. Introduction

11. Introduction

12. Introduction

13. Introduction Examplein anacademic setting: I amworking in the field of micro-RNAs, which have been described in variouscancer types What is knownaboutonemicroRNA, what are itsdescribed targets, where is itlocated, what is the expression level in specific tissue types Are theregeneswhoseexpression profile in (negatievely) correlatedwith the miRNA www.mirnabodymap.org Includes a literature search: database containsall abstracts with a microRNAmentioned in  allowsfastsearching

14. Introduction

15. Introduction Relevant example in anindustrial setting: We performed a micro-array experiment, comparingcisplatin-resistant and sensitive ovariancancercelllines; in the analysis, 308 probes are differentially methylated What is knownabout these genesin Ovariancancer? Platinum-resistance? Are these protectedby patents worldwide? Please, give me the overview… Do it FAST and ACCURATE

16. Introduction

17. Introduction

18. Introduction Different levels of ‘TextMining’

19. Introduction

20. Introduction

22. Books

23. Patents

27. Books

28. Patents

32. Literaturesearching - PubMed PubMedadvanced options Pubmed: one of the databases from the NCBI PubMed: both the database, containingall information AND the interface (web-basedandothers) Advanced search Making full use of the capabilities of the interface to the database (use of AND / OR / NOT) and NCBI-specific features Use of the * (Check details forgeneratedterms) Fields (Author – Date – title- …) Set limits (restrictresultsbased on fields) MeSH (Medical Subject Headers)

33. Literaturesearching - PubMed

34. Literaturesearching - PubMed

35. Literaturesearching - PubMed PubMedadvanced options Savesearchesandautomateexecution MyNCBI: save searchesand plan execution of queries Get resultsby e-mail at specifiedtimes RSS options RSS (Really Simple Syndication) is a way to get information in a synchronized way – in a web browser, an email client or news reader Exercises Sign up foran RSS feed and display results in a news reader (such as Google Reader)

36. Literaturesearching – Google scholar Exercises Search Google scholarandtry out if the ‘full text search’ and meeting abstracts work

37. Literaturesearching – Publish or perish Exercises Find “Publish or Perish”, find out howitworksandcalculate the h-factor foranauthor / journal / …

38. Literaturesearching – Patents Exercises Find patents: check if the gene of your interest is described in a patent / check ifyour supervisor is on a patent,…

40. Books

41. Patents

45. EBI-Med

46. Chilibot

47. GoPubMed

48. PolySearch

50. Books

51. Patents

55. Literaturesearching - textmining

56. Literaturesearching - textmining

57. Literaturesearching General: obtaining full-textandreferring Unique identifiers are a goodideato share references PubMed ID DOI (canbeusedforany object on the web – is permanentlyavailable – permalink) How to get the full text? PubMed / Google Scholar -> link to full text Through the site of the publisher / author’sgroup Using SFX (Institution has to support this) Google making use of the titleand “doctype:pdf” Ask the authornicely Open access Makessurethateveryonecan access yourwork at any time Drasticallyimproves the impact of your research work

59. Abstract

63. Literature storing Storing Software that deals withliterature User-friendly (forscientists!) Metadataand full-text Fastseachesand filters Read andcitein one program Collaboratewithothers Commerciallyavailable EndNote Reference Manager In general excellent CITATION software Freelyavailable Zotero (Firefox plugin) Mendeley

65. Metadataand full-tekst

66. Includes PDF reader and annotator

67. Fastseachesand filters

68. PDFs are indexedandallowfastsearching

69. Read andcitein one program (Word / bibTex / OpenOffice)

70. Collaboratewithothers

72. Abstract

76. Literature storing

77. Literature storing Exercises Register and download Mendeley – while reading through the instruction manual, just do it.... Alsotryimporting / exporting

78. Literature storing Storing Addpublications Add a file Add a folder Set ‘watched folders’ AllPDFs in this folder are added, metadataextractedandindexed Import (fromEndNote / …) Import yourexistinglibrariesfromEndnoteandothers Through the ‘web-importer’ Rememeber ‘where’ whensearching: online – whynot managing yourreferenceswhereyou browse them: in your webbrowser!

80. Make annotations

83. Work/home PC

85. Make annotations

88. Work/home PC

90. OpenOffice

92. Literaturemining Literature mining tools are in most cases based on the following tasks Translate your query Execute the query Internal database or querying system External (PubMed) Get the results from the query in a structured format (XML – ready to parse) Parse (extract information) from the results Do analysis on the results (counting, sorting, highlighting) Present the results or summaries

93. Literaturemining Literature mining tools are in most cases based on the following tasks: Translate your query Execute the query Get the results Parse (extract information) from the results Do analysis on the results Present the results or summaries These steps will be present in most tools that deal with literature Demonstration: creating a web-application

94. Literaturemining Demonstration Web-application Translate query – find aliases for human genes and incorporate them in the search Query NCBI PubMed using E-fetch Get the results and process them Count Highlight Rank Visualisation