Literature managment training

VIB/BITS training:literature management

Maté Ongenaert

Center for Medical GeneticsGhent University Hospital, Belgium

About the presenter

Maté Ongenaert

Bio-engineer cell and gene biotechnology (2005) PhD in Applied biological sciences, cell and gene

biotechology (2009) Currently postdoctoral researcher at CMGG (Ghent

University) Both in academic and industrial settings, involved in

automated literature searches and integration of data analysis with literature results

Creator or PubMeth (database of DNA-methylation in cancer, based upon data extraction out of biomedical literature); mirnabodymap (miRNAs)

Contents

Introduction

Literature management

Practical exercises

Search Store

ReadWrite

Introduction

Introduction

Need for literature managment

Need for proper research paper management is obvious… How to efficiently manage, search, cite?

Introduction

Example in an academic setting:

I am working on DNA-methylation in the cancer field I spend hours of time, searching relevant literature about the

genes and cancer types that interest me

Time-consuming: inefficient searches Inaccurate searches: I am not aware of aliases of genes,

synonyms,…

Solution: based on automated literature searches and some basic but smart sorting and highlighting strategies, I generate a database of DNA-methylation and cancer

Introduction

Introduction

Introduction

Introduction

Example in an academic setting:

I am working in the field of micro-RNAs, which have been described in various cancer types

What is known about one microRNA, what are its described targets, where is it located, what is the expression level in specific tissue types

Are there genes whose expression profile in (negatievely) correlated with the miRNA

www.mirnabodymap.org Includes a literature search: database contains all abstracts with a

microRNA mentioned in allows fast searching

Introduction

Introduction

Relevant example in an industrial setting:

We performed a micro-array experiment, comparing cisplatin-resistant and sensitive ovarian cancer cell lines; in the analysis, 308 probes are differentially methylated

What is known about these genes in Ovarian cancer? Platinum-resistance? Are these protected by patents worldwide? Please, give me the overview… Do it FAST and ACCURATE

Introduction

Introduction

Introduction

Different levels of ‘TextMining’

Introduction

Introduction

Contents

Search Store

ReadWrite

What- Articles- Books- Patents- Official documents

Where- Library- Online

How- Manually- Automatically

Literature searching


ArticlesPubMed

Google Scholar

BooksGoogle Books

Amazon

PatentsEsp@cenetPatenetlensEBI Patents

Google Patents…



Exercises Step-by-step exercises on the use of advanced searching options

in PubMed Step-by-step RSS exercise

Literature searching - PubMed

PubMed probably is the most used literature database and search engine

Basic search > advanced search Limits Search fields ([author];[title];[date]) Query options (limit to human samples, published last year) Save searches and automate execution RSS options


PubMed advanced options

Pubmed: one of the databases from the NCBI PubMed: both the database, containing all information AND the

interface (web-based and others)

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 for generated terms) Fields (Author – Date – title - …) Set limits (restrict results based on fields) MeSH (Medical Subject Headers)




PubMed advanced options

Save searches and automate execution MyNCBI: save searches and plan execution of queries Get results by e-mail at specified times

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 for an RSS feed and display results in a news reader (such

as Google Reader)

Literature searching – Google scholar

Exercises Search Google scholar and try out if the ‘full text search’ and

meeting abstracts work

Literature searching – Publish or perish

Exercises Find “Publish or Perish”, find out how it works and calculate the h-

factor for an author / journal / …

Literature searching – Patents

Exercises Find patents: check if the gene of your interest is described in a

patent / check if your supervisor is on a patent,…

Literature searching – automated searches


ArticlesPubMed

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)



Literature searching - textmining


TextMining efforts

* Pre-indexed* Application-limited in most cases

* Fast* User-friendly

* Interpreted results* Scoring / prioritizing

* Advanced visualization

- iHOP- EBI-Med- Chilibot

- GoPubMed- PolySearch- PubGene






Literature searching

General: obtaining full-text and referring

Unique identifiers are a good idea to share references• PubMed ID• DOI (can be used for any object on the web – is permanently available –

permalink) How to get the full text?

• PubMed / Google Scholar -> link to full text• Through the site of the publisher / author’s group• Using SFX (Institution has to support this)• Google making use of the title and “doctype:pdf”• Ask the author nicely

Open access• Makes sure that everyone can access your work at any time• Drastically improves the impact of your research work

Contents

Search Store

ReadWrite

What- Metadata- Abstract- Full text (PDF)

Where- Off-line- Online

How- Folder structure- Management software

Literature storing

Structure of a publication

‘Visible’ data in the abstract• Title• Abstract• Journal• Authors

‘Unvisable’ data in the abstract• MeSH terms• Link to Full Text• DOI identifier• Keywords

All this information in a structured way = metadata Full text: text, figures, tables, supplementary data!

Literature storing

Storing

Software that deals with literature• User-friendly (for scientists!)• Metadata and full-text• Fast seaches and filters• Read and cite in one program• Collaborate with others

Commercially available• EndNote• Reference Manager• In general excellent CITATION software

Freely available• Zotero (Firefox plugin)• Mendeley

Literature storing

Storing

Mendeley User-friendly (for scientists!) - stand-alone program and website

Metadata and full-tekst Includes PDF reader and annotator

Fast seaches and filters PDFs are indexed and allow fast searching

Read and cite in one program (Word / bibTex / OpenOffice)

Collaborate with others Shared libraries

Literature storing

Storing

Mendeley – presentation All information in this presentation is

in the ‘beginners guide’ Manual included in Mendeley library

after installation – read it and try all features

Alternatives: Zotero + ZotFile (configuration might

be an issue) CiteULike Both are supported by Mendeley (1-way synchronisation)

What- Metadata- Abstract- Full text (PDF)


How- Folder structure- Management software

Literature storing

Literature storing

Literature storing

Exercises Register and download Mendeley – while reading through the

instruction manual, just do it.... Also try importing / exporting

Literature storing

Storing

Add publications• Add a file• Add a folder• Set ‘watched folders’• All PDFs in this folder are added, metadata extracted and indexed

• Import (from EndNote / …)• Import your existing libraries from Endnote and others

• Through the ‘web-importer’• Rememeber ‘where’ when searching: online – why not managing your

references where you browse them: in your webbrowser!

Contents

Search Store

ReadWrite

What- PDF- Make annotations- Highlight items


How- On paper- Work/home PC- On the road: tablets

Reading

What- PDF- Make annotations- Highlight items


How- On paper- Work/home PC- On the road: tablets

Contents

Search Store

ReadWrite

What- MS Word- OpenOffice- bibTex

Contents - textmining

Search Store

ReadWrite

User Input

Extract information

Do analysis

Visualisation

Literature mining

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

Literature mining

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

http://localhost/

Literature mining

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

Date post:	17-Nov-2014
Category:	Devices & Hardware
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Literature managment training

Devices & Hardware