View stunning SlideShares in full-screen with the new iOS app!Introducing SlideShare for AndroidExplore all your favorite topics in the SlideShare appGet the SlideShare app to Save for Later — even offline
View stunning SlideShares in full-screen with the new Android app!View stunning SlideShares in full-screen with the new iOS app!
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
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
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
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
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)
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)
Literaturesearching – Google scholar Exercises Search Google scholarandtry out if the ‘full text search’ and meeting abstracts work
Literaturesearching – Publish or perish Exercises Find “Publish or Perish”, find out howitworksandcalculate the h-factor foranauthor / journal / …
Literaturesearching – Patents Exercises Find patents: check if the gene of your interest is described in a patent / check ifyour supervisor is on a patent,…
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
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!
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
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
Literature storing Exercises Register and download Mendeley – while reading through the instruction manual, just do it.... Alsotryimporting / exporting
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!
Contents - textmining User Input Extract information Do analysis Visualisation
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
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
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