Literature managment training

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  • 1. VIB/BITS training:literature management
    Maté Ongenaert
    Center for Medical Genetics
    Ghent University Hospital, Belgium
  • 2. About the presenter
    Maté Ongenaert
    • Bio-engineer cell and gene biotechnology (2005)
    • 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
    • 6. Creator or PubMeth (database of DNA-methylation in cancer, based upon data extraction out of biomedical literature); mirnabodymap (miRNAs)
  • Contents
  • 7. Introduction
  • 8. Introduction
    Need for literature managment
    • Need for proper research paper management is obvious…
    • 9. How to efficiently manage, search, cite?
  • Introduction
    Examplein anacademic setting:
    I amworking on DNA-methylation in the cancerfield
    I spendhours of time, searching relevant literatureabout the genes and cancer types that interest me
    Time-consuming: inefficientsearches
    Inaccurate searches: I amnotaware of aliases of genes, synonyms,…
    Solution: based on automatedliteraturesearches and some basic but smart sorting and highlightingstrategies, I generate a database of DNA-methylationandcancer
  • 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
  • 21. Contents
    What
    Where
    How
    • Manually
    • 26. Automatically
  • Literaturesearching
    Articles
    PubMed
    Google Scholar
    Books
    Google Books
    Amazon
    Patents
    Esp@cenetPatenetlens
    EBI Patents
    Google Patents

    What
    Where
    How
    • Manually
    • 31. Automatically
  • Exercises
    Step-by-stepexercises on the use of advancedsearching options in PubMed
    Step-by-step RSS exercise
    Literaturesearching - PubMed
    PubMedprobably is the most usedliterature database and search engine
    Basic search > advanced search
    Limits
    Search fields([author];[title];[date])
    Query options (limit to human samples, published last year)
    Savesearchesandautomateexecution
    RSS options
  • 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,…
  • 39. Literaturesearching – automatedsearches
    Articles
    PubMed
    Automated (programmable) PubMed (NCBI) searches use E-Utils
    • E-Search
    Query > database query > ExecutionResult: list of primary IDs (PMIDs)
    • E-Fetch
    Given a list of PMIDs, retrieve all metadata in a structured (computer-readable) format (XML)
    What
    Where
    How
    • Manually
    • 44. Automatically
  • Literaturesearching - textmining
    TextMining efforts
    * Pre-indexed
    * Application-limited in most cases
    * Fast
    * User-friendly
    * Interpreted results
    * Scoring / prioritizing* Advanced visualization
    What
    Where
    How
    • Manually
    • 54. Automatically
  • Literaturesearching - textmining
  • 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
  • 58. Contents
    What
    Where
    How
    • Folder structure
    • 62. Management software
  • Literature storing
    Structure of a publication
    ‘Visible’ data in the abstract
    Title
    Abstract
    Journal
    Authors
    ‘Unvisable’ data in the abstract
    MeSHterms
    Link to Full Text
    DOI identifier
    Keywords
    Allthis information in a structured way = metadata
    Full text: text, figures, tables, supplementary data!
  • 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
  • 64. Literature storing
    Storing
    Mendeley
    • User-friendly (forscientists!) - stand-alone program and website
    • 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
    • 71. Shared libraries
  • Literature storing
    Storing
    Mendeley – presentation
    All information in thispresentation is in the ‘beginners guide’
    Manual included in Mendeleylibraryafterinstallation– readitandtryall features
    Alternatives:
    Zotero + ZotFile (configurationmightbean issue)
    CiteULike
     Both are supportedbyMendeley (1-way synchronisation)
    What
    Where
    How
    • Folder structure
    • 75. Management software
  • Literature storing
  • 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!
  • 79. Contents
    What
    Where
    How
    • On paper
    • 83. Work/home PC
    • 84. On the road: tablets
  • Reading
    What
    Where
    How
    • On paper
    • 88. Work/home PC
    • 89. On the road: tablets
  • Contents
    What
  • Contents - textmining
    User Input
    Extract information
    Do analysis
    Visualisation
  • 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