# 16 Alternative PubMed Search

WHAT?
The default database for finding scientific medical articles is PUBMED

PubMed

The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Ovid, Dialog, EBSCO, Knowledge Finder and many other commercial, non-commercial, and academic providers. As of October 2008, more than 500 licences had been issued, more than 200 of them to non-US providers.

As licences to use MEDLINE data are available for free, the NLM in effect provides a free testing ground for a wide range of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option.

WHY?

Lu identifies a sample of 28 current and free web based PubMed versions, requiring no installation or registration, which are grouped into four categories:

• Ranking search results (10 systems):
• eTBLAST; Hakia; MedlineRanker; MiSearch; MScanner; PubFocus; Quertle; RefMed; SemanticMedline; TWEASE;

• Clustering results by topics, authors, journals etc. (5 systems):

Anne O'Tate; ClusterMed; GoPubMed; McSyBi; XplorMed

• Enhancing semantics and visualisation (5 systems):

CiteXplore; EBIMed; MedEvi; MEDIE; PubNet

• Improved search interface and retrieval experience (8 systems):

askMEDLINE; BabelMeSH; HubMed; iPubMed; PICO; PubCrawler; Pubget; SLIM

         (Lu's database: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/)


Major free Search engines that ALSO search Mddline/PubMed:

• Webicina PeRSSonalized Medicine
• ScienceRoll Medical Search
• HealthMash
• Mednar
• Scirus
• Trip Database

Some Apps that search PubMed:

• Papers
• Orkov
• Pubmed Clip
• Pubmed Library
• Pubsearch Plus
• Pubmed on Tap
• Mobile Abstracts

Discovery excercises:

• Have a look at GoPubMed and PubGet. What are their main features?
• Choose 2 other Alternative PubMed Interfaces and compare them with eachother (ánd with PubMed)
  Make a short summary of your findings and share them with the group via Facebook Page & the Google Doc Folder of NBAMHI
• Try Webicina PeRSSonalized Medicine. This service can offer search, alerts & rss on your specific topic or speciality, without having to go elsewhere.
• ScienceRoll Medical Search
• MedPilot, a semantic search engines based on pubMed but more! (by the ZB MED Germany

All in one big list ...

Biomedical Literature Search Tools

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PubMed (Sayers et al., 2011) : A service of the National Center for Biotechnology Information (NCBI)

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BioMedLib (2011) : Does both keyword-based and meaning-based search

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CAIPIRINI (2010) : Uses gene sets and SVM to rank literature search results

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iPubMed (Wang et al., 2010) : Supports fuzzy type-ahead searches

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MEDPILOT (Daumke et al., 2010) : A service provided by the Geman National Library of Medicine (ZB MED)

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MARTINI (Soldatos et al., 2010) : Searches literature and uses keywords to compare gene sets.

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RefMed (Yu et al., 2010) : Enabling multi-level relevance feedback for PubMed searches

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Semantic MEDLINE Prototype (Kilicoglu et al., 2010) : Summarizing and visualizing semantic relations extracted from literature

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LigerCat (Sarkar et al., 2009) : Generating "MeSH Clouds" for exploring search results

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MiSearch (States et al., 2009) : Ranks citations based on implicit user feedback

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MedlineRanker (Fontaine et al., 2009) : Flexible ranking of biomedical literature

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Quertle® (2009) : Relationship-driven search and supports searches with categorical concepts

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MScanner (Poulter et al., 2008) : A classfier for retrieving Medline citations

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Anne O'Tate (Smalheiser et al., 2008) : Clustering by important words, topics, journals, authors, etc.

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Medline.Cognition (Goldsmith et al., 2008) : Powered by Cognition's proprietary search technology

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hakia (2008) : Part of the semantic search engine hakia.com

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MedEvi (Kim et al., 2008) : Providing textual evidence of semantic relations in output

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EBIMed (Rebholz-Schuhmann et al., 2007) : Offers associations between protein/genes, GO annotations, drugs and species.

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McSyBi (Yamamoto and Takagi, 2007) : Biomedical knowledge navigation by literature clustering

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PICO (Schardt et al., 2007) : Using Patient, Intervention, Comparison, Outcome (PICO) framework for clinical questions

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eTBLAST (Errami et al., 2007) : Finding documents similar to input text

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PubGet (2007) : Retrieving results in PDFs

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HubMed (Eaton 2006) : Incorporating external web services for improving search efficiency

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PubFocus (Plikus et al., 2006) : Semantic analytics through integration of controlled bio-dictionaries and ranking algorithm

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BabelMeSH (Liu et al., 2006) : a cross-language tool for MEDLINE/PubMed

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CISMeF (Neveol et al., 2006; Thirion et al., 2007) : Providing access to MEDLINE/PubMed using queries in French

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MEDIE (Ohta et al., 2006) : Extracting text fragments matching queried semantics

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CiteXplore : EBI's tool for integrating biomedical literature and data

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Twease (Dorff et al., 2006) : Expands search queries and automatically discovers common abbreviations

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PubNet (Douglas et al., 2005) : A flexible system for visualizing literature derived networks

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GoPubMed (Doms and Schroeder, 2005) : Exploring PubMed with the Gene Ontology

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askMEDLINE (Fontelo et al., 2005) : This tool would translate a question into an efficient search

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SLIM (Muin et al., 2005) : Features interactive slider bars in the search form

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ClusterMedTM (2004) : A demo service by Vivisimo®

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XplorMed (Perez-Iratxeta et al., 2003; Perez-Iratxeta et al., 2001) : Summarizing the subjects contained in the search results

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PubCrawler (Hokamp and Wolfe, 1999; Hokamp and Wolfe, 2004) : Alerting users with new articles based on saved searches