* indicates the 28 systems surveyed in Lu, Database 2011

# indicates other systems added to the list after the above publication through request or regular update (last update: Feburary 2012)

Tool Selection Filters

Seeking relevant words or concepts for focused reading
Seeking retrieval results ranked by relevance
Semantic search with biological concepts
Looking for experts;reviewers; and collaborators
Seeking assistance in gene list analysis and/or curation
Identifying similar publications
Visualization of search results in literature networks
Searching with natural language questions
Seeking instant results while typing queries
Seeking automatic updates on saved searches
Searching in languages other than English
Seeking assistance in terminology development

Reporting New Tools Here:

System Name:
System URL:
Author/Developer Names:
Link to publication/description:
Brief highlight (no more than 10 words):
Contact email:


Biomedical Literature Search Tools

* PubMed (Sayers et al., 2011)
: A service of the National Center for Biotechnology Information (NCBI)
# BioMedLib (2011)
:  Does both keyword-based and meaning-based search
# BibliMed (2011)
:  Providing contextual help like MeSH terms organized by qualifiers
: Uses gene sets and SVM to rank literature search results
*iPubMed (Wang et al., 2010)
: Supports fuzzy type-ahead searches
# MEDPILOT (Daumke et al., 2010)
: A service provided by the Geman National Library of Medicine (ZB MED)
#MARTINI (Soldatos et al., 2010)
: Searches literature and uses keywords to compare gene sets.
*RefMed (Yu et al., 2010)
: Enabling multi-level relevance feedback for PubMed searches
#Semantic MEDLINE Prototype (Kilicoglu et al., 2010)
: Summarizing and visualizing semantic relations extracted from literature
# LigerCat (Sarkar et al., 2009)
: Generating "MeSH Clouds" for exploring search results
*MiSearch (States et al., 2009)
: Ranks citations based on implicit user feedback
*MedlineRanker (Fontaine et al., 2009)
: Flexible ranking of biomedical literature
*Quertle® (2009)
: Relationship-driven search and supports searches with categorical concepts
*MScanner (Poulter et al., 2008)
: A classfier for retrieving Medline citations
*Anne O'Tate (Smalheiser et al., 2008)
: Clustering by important words, topics, journals, authors, etc.
*Medline.Cognition (Goldsmith et al., 2008)
: Powered by Cognition's proprietary search technology
*hakia (2008)
: Part of the semantic search engine hakia.com
*MedEvi (Kim et al., 2008)
: Providing textual evidence of semantic relations in output
*EBIMed (Rebholz-Schuhmann et al., 2007)
: Offers associations between protein/genes, GO annotations, drugs and species.
*McSyBi (Yamamoto and Takagi, 2007)
: Biomedical knowledge navigation by literature clustering
*PICO (Schardt et al., 2007)
: Using Patient, Intervention, Comparison, Outcome (PICO) framework for clinical questions
*eTBLAST (Errami et al., 2007)
: Finding documents similar to input text
*PubGet (2007)
: Retrieving results in PDFs
*HubMed (Eaton 2006)
: Incorporating external web services for improving search efficiency
*PubFocus (Plikus et al., 2006)
: Semantic analytics through integration of controlled bio-dictionaries and ranking algorithm
*BabelMeSH (Liu et al., 2006)
: a cross-language tool for MEDLINE/PubMed
#CISMeF (Neveol et al., 2006; Thirion et al., 2007)
: Providing access to MEDLINE/PubMed using queries in French
*MEDIE (Ohta et al., 2006)
: Extracting text fragments matching queried semantics
: EBI's tool for integrating biomedical literature and data
*Twease (Dorff et al., 2006)
: Expands search queries and automatically discovers common abbreviations
# MEDSUM (2005)
: The MEDLINE summary tool
*PubNet (Douglas et al., 2005)
: A flexible system for visualizing literature derived networks
*GoPubMed (Doms and Schroeder, 2005)
: Exploring PubMed with the Gene Ontology
*askMEDLINE (Fontelo et al., 2005)
: This tool would translate a question into an efficient search
*SLIM (Muin et al., 2005)
: Features interactive slider bars in the search form
*ClusterMedTM (2004)
: A demo service by Vivisimo®
*XplorMed (Perez-Iratxeta et al., 2003; Perez-Iratxeta et al., 2001)
: Summarizing the subjects contained in the search results
*PubCrawler (Hokamp and Wolfe, 1999; Hokamp and Wolfe, 2004)
: Alerting users with new articles based on saved searches
Systems Last Update
(assessed on 08/23/10)
Service Provider Profile Source Code Available System Output Format PubMed ID Links Full Text Links Related Article Links Export Search Results
RefMed 2010AcademicList
iPubMed CurrentAcademicList
Quertle 2010PrivateList
MiSearch CurrentAcademicList
MedlineRanker CurrentAcademicList
MScanner 2007AcademicList
Anne O'Tate CurrentAcademicList
Medline.Cognition 8/6/2010PrivateList
hakia 2010PrivateList
MedEvi 2010GovernmentTable
EBIMed 2010GovernmentTable
McSyBi CurrentAcademicList
PICO CurrentGovernmentList
eTBLAST 2010AcademicList
PubGet CurrentPrivateList
HubMed CurrentPrivateList
PubFocus CurrentPrivateList
BabelMeSH 2010GovernmentList
MEDIE 12/10/2009AcademicList
CiteXplore CurrentGovernmentList
Twease CurrentAcademicList
PubNet CurrentAcademicGraph
GoPubMed CurrentPrivateList
askMEDLINE 2010GovernmentList
SLIM CurrentGovernmentList
ClusterMedTM CurrentPrivateList
XplorMed CurrentAcademicList
PubCrawler CurrentAcademicList
MEDPILOT 2010GovernmentList
LigerCat CurrentAcademicWord cloudn/an/an/an/a
BioMedLib 2010PrivateList
CISMeF 2006AcademicListn/an/an/an/a
Semantic MEDLINE CurrentGovernmentGraph
MARTINI CurrentGovernmentTable
CAIPIRINI CurrentAcademicTable
BibliMed CurrentPrivateList
MEDSUM CurrentAcademicSummary Statsn/an/an/an/a