The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth.
Provides a browser to highlight links between patents and scholar literature. PatCite proposes a search tool made by exploiting the information curated from the DocDB master database. It can be queried by two main ways: users can search scholar works quoted in patent literature or browse the patents that quotes scholarly articles. The platform can be queried through a text search or by submitting multiple ID such as PMID.
Offers a platform for facilitating researches through MEDLINE database. XplorMed is a web application that allows users to explore a set of abstracts. The application provides the main associations between the words in groups of abstracts and then authorizes users to select subsets based on selected groups of related words. The list generated can be hyperlinked to objects in multiple repositories such as OMIM or SWISS-PROT.
Allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the abstracts by category. Second, GoPubMed automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up.
An alternative search interface to the PubMed database of biomedical literature, incorporating external web services and providing functions to improve the efficiency of literature search, browsing and retrieval. Users can create and visualize clusters of related articles, export citation data in multiple formats, receive daily updates of publications in their areas of interest, navigate links to full text and other related resources, retrieve data from formatted bibliography lists, navigate citation links and store annotated metadata for articles of interest.
Offers a significant advance in the automated extraction of biological knowledge from sets of genes or abstracts. Martini is an easy-to-use tool that allows end-users to compare two gene sets using a sensitive, keyword-based method. It is based on keywords extracted from Medline abstracts and supports a much wider range of species than comparable tools. Martini is designed to be fast and easy-to-use, providing a quick first insight into the functional difference between two gene sets.
A publicly available application to search XML-formatted MEDLINE data in a complete, object-relational schema implemented in Oracle XML DB. An advantage offered by botXminer is that it can generate quantitative results with certain queries that are not feasible through the Entrez-PubMed interface. After retrieving citations associated with user-supplied search terms, MEDLINE fields (title, abstract, journal, MeSH and chemical) and terms (MeSH qualifiers and descriptors, keywords, author, gene symbol and chemical), these citations are grouped and displayed as tabulated or graphic results.
Facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. Omicseq uses an algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. It aims to enhance findability of omics datasets, to facilitate re-utilization, or re-purposing of existing data for secondary, tertiary analyses. The tool can facilitate discoveries using existing and emerging genomic datasets.
Mines literature data and access basic transcriptomic analyses about breast cancer data. BCNTB is composed of two main functions: BCNTB:Analytics, that investigates datasets and conducts a text search of titles and abstracts in PubMed using Boolean logical operators; and BNCTB:Miner which permits to build custom queries against all the genomics, methylomics, transcriptomics, proteomics and microRNA data.
Enables real-time responses to researchers’ queries. Olelo combines biomedical literature and terminologies in a fast in-memory database. It permits a fast and intelligent search through the ever-growing biomedical literature. The tool outputs an answer to a question and allows the user to further explore the corresponding documents. It provides a way to filter and narrow down relevant documents.
Provides a search algorithm for PubMed that takes advantage of the intelligence of users and cutting-edge machine-learning technology as an alternative to the traditional date sort order. Best Match was trained with past user searches with dozens of relevance-ranking signals (factors), the most important being the past usage of an article, publication date, relevance score, and type of article.
A freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated with each article.
A system for searching the MEDLINE database, implemented in a fully functional. Comparing with the most widely used PubMed system at NCBI, the iPubMed system contains two unique features: (i) being interactive, returning search results on the fly and allowing users to change queries adaptively, and (ii) allowing approximate search.
With an exponentially growing number of articles being published every year, scientists can use some help in determining which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work. Jane is a freely available web-based application that, on the basis of a sample text (e.g. the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.
A browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them.
Allows users to search and summarize RNA sequencing data. Snaptron is a search engine for querying splicing patterns in large, pre-analyzed collections about human. It lends valuable context and support to hypotheses related to splicing patterns in human. For each query, this tool combines the strengths of different indexing strategies: (1) R-trees; (2) B-trees; and (3) term-document inverted indices.
Allows biomedical data management, analysis, and visualization. SATORI is a web-based exploration system that combines search with visual browsing to provide an integrated exploration experience. The visualizations serve two purposes: supporting the information foraging loop and pattern discovery of attribute distributions, as well as ontology-guided semantic querying of the data repository.
Analyses and classifies cancer-related literature based on Hallmarks of Cancer (HoC). CHAT enables users to immediately analyse the correlation between any query term and the hallmarks and the associated process according to the detailed HoC taxonomy. This resource could be useful for classifying cancer related text and text mining associated biological processes, with a simple search query on cancer types, intrinsic or extrinsic factors, and therapeutics.
Allows automated data retrieval confined to publicly available citations and abstracts. Literature Lab interrogates the literature for associations between a list of genes and a list of key terms in an unbiased manner, for highlighting potentially important biological processes implicated by the gene list. The software was designed to aid in the analysis of microarray experiments. Literature Lab PLUS extends Literature Lab's reach by including comprehensive immunology as a domain of analysis.
A text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature.
Comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
A unique, free, information resource for biomedical and health researchers. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Europe PMC offers RESTful web services to access both articles and grants, powerful search tools such as citation-count sort order and data citation features, a service to add publications to your ORCID, a variety of export formats, and an External Links service that enables any related resource to be linked from Europe PMC content.
A free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). As an archive, PubMed Central is designed to provide permanent access to all of its content, even as technology evolves and current digital literature formats potentially become obsolete.
Provides access to information about eukaryotic DNA replication. DNAReplication is a database that provides (i) model pages, (ii) proteins essential for DNA replication, showing association with replication factors, or having been implicated in repair of damage resulting from replication defects, (iii) replication concepts and abbreviations and (iv) links to other relevant webpages and to labs involved in DNA replication.
Aims to provide the most relevant results and the best quality information in PubMed. PubMed Labs is an online resource that assists users to identify and find articles of interest. It includes a functionality called “snippets” that shows highlights from the article abstract that are related to researchers’ query. Moreover, it is possible to specify text availability (only abstract, free full text, or full text).
Provides ‘omics’ information about genes and proteins expressed in the normal liver and hepatic disease. LiverAtlas was constructed thanks to existing biological databases and biomedical literature. It contains liver-related data with quality scores and high-quality data. The database is accessible thanks to a web interface that provides convenient browsing, searching, downloading and visualizing functions.
Filters target articles with ontology name and concept. Biotea Explorer facilitates the processing of biomedical literature by delivering a semantic dataset for PubMed Central (PMC) and its open-access subset. This subset has been improved with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.
Provides a publicly available integrative resource in the field of hematopoiesis. HSC-explorer is a manually curated database collecting literature-derived knowledge about the different hematopoietic stem cell subpopulations and their behavior in repopulation activity, self-renewal and quiescence and how these processes are regulated by intrinsic and extrinsic factors. The database covers the early steps of differentiation. It aims to present biological findings in form of a comprehensive and intuitive graphical network allowing scientists to explore hematopoiesis in a systems-oriented approach.
Facilitates sharing of medical data models. MDM-Portal is a registered German and European information infrastructure that provides a multilingual platform for exchange and discussion of data models in medicine, both for medical research and healthcare. The database contains more than 4000 data models. Most contents of the MDM portal were derived from clinical trials and each data model can be tagged with one or several keywords from the MeSH thesaurus.
Gathers information about worldwide publications about Crows, Ravens, Jays, and Magpies. CLD intends to register publications from journals, short notes, books, theses and field guides dealing with corvids. Each file is tagged with specific keywords according to corvid taxa, topics, language used, countries, abstract and link to full document. The database compiles almost 500 years of ornithological research, starting in 1544 with Turner.
Provides a biomedical search corpus based on citations on platforms such as Medline, Pubmed or Google Scholar. SciRide Finder proposes an open-access search engine to improve text mining and literature searches. The application allows users to constrain their results to Cited Statements only as well as find data to build evidence-based narratives for their own research.
Permits users to search several types of information. Elsevier DataSearch is a platform that works with a search engine. Results of a query send back toward dataset such as ScienceDirect or arXiv. Several filters are available to classify results of a query.
Gathers more than 4700 papers from scientific literature dealing with transcranial direct current stimulation (tDCS). tDCS-OD is a communautary open source platform that extracts and reports each stimulation parameters, (such as intensity or electrode size), in a single repository and allows users to investigate each paper according them. It also includes utilities to filter and extract data as well as an export function to generate CSV and XLS files.
Displays an interactive map that represents the arXiv repository for scientific research papers. Paperscape represents each paper by a circle, with the size of a circle related to how often that paper has been cited.
Contains bibliographic information and abstracts of health-related articles, reports, surveys, and other resource documents pertaining to the health and health care of American Indians, Alaska Natives, and Canadian First Nations. The Native Health Database provides information for the benefit, use, and education of organizations and individuals with an interest in health-related issues, programs, and initiatives regarding North American indigenous peoples.
Scans daily updates of medical databases. PubCrawler offers a database that helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. It looks for matches to text (Medline and GenBank annotation), not sequences, and writes its output as a WWW page.
Allows consultation of preprint articles. PrePubMed is a method for finding biology preprints until an institution develops a better method. It indexes new preprints daily. This homepage works similarly to PubMed but has no affiliation with the NCBI. The homepage contains a search engine which works on two modes: a general research and an advanced research (adjustable according to authors, title, abstract, and affiliation).
Regroups open access journals and articles. Paperity is multi-disciplinary and aims to facilitate access to literature. The goal of the platforms is to regroup integrality of open access literature. It permits to disseminate discoveries more effectively and maximize research impact.