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Note: List of resources along with their features are provided here to help the scientific community. Please help us by contributing any additional information you may have. Comments, suggestions or personal experiences regarding any of the tools listed are welcome.

Bio-literature search engines	Comments

Simple summary scanners
askMEDLINE	Allows MEDLINE/PubMed queries in the form of simple questions. The tool also provides links to PICO (Patient, Intervention, Comparison, Outcome) interface & Babel MesH - (Multilanguage search for MEDLINE/PubMed).
eTBLAST	Online system that offers the easiest and most effective method of published literature search with abstracts, rather than words and phrases as query components. The set of utilities at eTBLAST can hierarchically list articles with high similarity to the query paragraph as well as the journals and authors frequently associated with such related articles
PubMed	Widely used bio-literature search engine developed from NCBI. It is a free interface for searching Medline database.It also covers other NLM databases.
PubMed Interact	It is an interactive interface for MEDLINE/PubMed and follows the search and syntax rules of PubMed. This interactive site from NCBI presents ‘slider bars’ to enable quicker settings and re-settings of different parameters involved in the search strategy.The tool seems to be in its beta version.
ReleMed	ReleMed categorizes each retrieved citation into 8 different levels of relevance, depending on the frequency of occurrence of the search terms within the title, sentences of abstract & MeSH. Has efficient Automatic term mapping feature.
MiSearch Adaptive PubMed Search Tool	Ranks the retrieved citations based on an estimated likelihood of a user choosing to view them. User’s citation choices are acquired by the program during browsing.
MedKit	The tool seems to be developed to overcome the following limitations of PubMed.
PubMed Informer	It is a tool for monitoring topics of interest from MEDLINE/PubMed using five tracking methods: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds
Info-PubMed	Info-PubMed is based on Natural Language Processing and Text Mining techniques
Whatizit	A sister application from EBI that can be useful in a wide variety of advanced searches. This engine, which may also be accessed programmatically, can search specific terms in molecular biology in given texts and link them to publicly available databases.
CiteSeerX (beta version)	It is a search engine for the scientific literature and academic papers.
Novoseek	It is a biomedical search engine. It indexes articles from PubMed and open access articles from PubMed Central.
Web of Science	Is a commercial search engine from Thomson Reuters, known for its citation tracking ability.
Full-text scanners
Google Scholar (GS)	A full text search engine for retrieval of scholarly articles. Scans the full text of the articles and displays 1000 citations in the order of relevance determined by the number of times cited.
HighWire Press (HWP)	A full text search engine from Stanford University. Additonal features like 'Citation map' and 'Match maker' among the others are noteworthy.
PubMed Central	A full-text search engine developed by NCBI. It provides access to the full-text of articles sponsored by NIH.
Scirus	Is a free full text scanner from Elseiver. Provides patent related information.
Customized Life Science Search Engine (Brij.in)	A Google powered and hosted search engine customized for life sciences can scan complete documents from different sources.
OvidSP	Searches full-text ejournals and ebooks, within the OvidSP platform.
Summary scanners that can process the citations for further information
ALIBABA	ALIBABA interfaces with PubMed, analyses a set of retrieved abstracts and presents the extracted information on biomedical objects, as well as their relationship, an easily perceptible graphical format.
BioAsk	BioAsk searches MEDLINE, categorizes the citations based on biological entities identified within and provides a graphical output indicating the distribution and links of results across different categories.
BioIE	A search program developed to extract information from PubMed citations.It retrieves sentences within PubMed abstracts that refer to structure, function, diseases and therapeutic compounds, localization, or familial relationships of biological entities (mainly proteins).
CiteXplore	A literature search engine developed from EMBL-EBI. It also includes text mining tools.It retrieves citations from Medline abstracts, patent abstracts etc.One major feature of the tool is that it cross-links to EMBL-EBI’s biological databases.
ClusterMed	Useful clustering of the results based on authors, affiliation, publication dates, MeSH terms etc.
EBIMed	EBIMed is a search engine from European Bioinformatics Institute with many attributes, particularly the query options, automatic processing of citations and the display features. It finds abstracts in the PubMed-way, analyses them and presents a complete overview of associations between the biological entities found within the abstracts.
GoPubMed	Categorizes PubMed citations based on GO(Gene Ontology) and MeSH (Medical Subject Headings) vocabulary. Also, provides statistical details pertaining to the search topic.
PubFocus	Provide ranked list of citations and assist in deciding authors and journals of related interests. PubFocus also indicates distribution of NCI ontology and gene orthology terms
PubMed Assistant	PubMed Assistant is a Java application (requires Java 1.4.2 or later versions, with web-start) that interfaces with MEDLINE. It has several useful functions. Provides ‘auto-refine’ option for the query based on user selected list of citations.
Scopus	A paid tool which is a summary scanner developed by Elseiver. It provides an extensive coverage of scientific resources. Its citation mapping ability is worthy of mention.
XplorMed	XplorMed is a server that allows query in the PubMed format, as a file or a database entry. The tool can be useful to group abstracts based on the associations between the words within them. The output will first show the PMIDs of the first 500 abstracts categorized under 16 MeSH categories.
PubWindows	Allows browsing of PubMed citations with MeSH terms. It allows easy set up of RSS feeds based on subject searches and easy citation exporting in popular formats: RIS/EndNote, BibTex, RDF, MODS, RefWorks.
MEDSUM	Provides a simple way to count PubMed citations under different categories like the time of publication, occurrence of MeSH terms, authors, journals and other PubMed pre-defined subsets.
Anne O'Tate	The tool organizes the results according to pre-defined categories. The categories include the biological terms found in titles or abstracts, topics, journals, authors, publication years and affiliations.
HubMed	Alternative interface to the PubMed database with additional options (e.g. visualization of links between articels TouchGraph)
PubReMiner	PubReMiner can query PubMed, retrieve citations and generate frequency tables based on journals, authors, words in T/A, MeSH headings etc. But we have not been able to use this tool successfully, except for gene name search.
PubMed Gold	PubMed Gold is a PubMed interface that finds PDFs for PubMed citations by automatically searching Google. Links to free full text articles indexed by PubMed are also displayed with some citations.
PubFinder	Designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic.
Text-mining tools
PubGene	Retrieves associate information on genes, proteins, biological terms [chemicals (based on PubMed chemicals), molecular processes, biological functions and cellular components) based on GO & diseases (based on MeSH)]
iHOP	It allows searching the literature with a gene name and extracts the related biological information.
iProLink (integrated Protein Literature, information and knowledge)	Provides curated data sources for text mining research in the areas of bibliography mapping, annotation extraction, protein named entity recognition, and protein ontology development.
Chilibot	Search PubMed abstracts for specific relationships between proteins, genes, or keywords. It can also show the results as a graph.
Bitola	A biomedical discovery support system that aims to assist biomedical researchers in detecting potential relations between biomedical concepts (currently contains MeSH and HUGO).
G2D	A platform that allows searching human genomic regions for genes related to inherited diseases
ARROWSMITH	Extended MEDLINE search tool.
Dragon	Dragon Plant Explorer, text mining tool for plant related literature from PubMed.
ConceptLink	ConceptLink creates visual images for medical concepts. It allows the user to explore concept relationships visually. ConceptLink is also a visual interface for PubMed.
LitMiner	Extracts, and performs statistical analysis of co-occurrence of annotated entities (genes, compounds, disorders and tissues), from the abstracts retrieved in response to a query using one of these entities.
Textpresso	Organism specific literature search tool that enables the user to search for one or a combination of categories of biological concepts and classes, and/or keywords within an entire literature.
Search engines related to clinical activities
CancerLit	An interface to PubMed provided by the National Cancer Institute of USA
CAMbase	It allows easy search of literature of Complementary and Alternative Medicine (CAM) in different ressources.
Cochrane Central Register of Controlled Trials (CENTRAL)	Contains approx. 500,000 records towards “independent evidence to inform healthcare decision-making” (from Cochrane and other systematic reviews, clinical trials etc).
Cumulative Index to Nursing and Allied Health (CINAHL)	This database covers nursing and allied health.