Information retrieval applications
Anni
Anni
An online tool to aid the biomedical researcher with a broad range of information needs.…
An online tool to aid the biomedical researcher with a broad range of information needs. Anni provides an ontology-based interface to MEDLINE and retrieves documents and associations for several classes of biomedical concepts, including genes, drugs…
Biblio-MetReS
Biblio-MetReS
Analyzes scientific documents to find the interactions between genes/proteins in order to…
Analyzes scientific documents to find the interactions between genes/proteins in order to reconstruct molecular networks. Biblio-MetReS relies on a central database with the genomes and gene annotation of more than 1000 organisms. It is this…
BioMedLib Search Engine
BioMedLib Search Engine
Takes your query and finds the best responses among millions of biomedical articles in…
Takes your query and finds the best responses among millions of biomedical articles in the National Library of Medicine's MEDLINE database. BioMedLib Search Engine finds relevant articles that other engines will miss. Furthermore, BioMedLib…
BIOSMILE Web Search
BIOSMILE Web Search
BWS
A web-based NCBI-PubMed search application, which can analyze articles for selected…
A web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves…
BioText Search Engine
BioText Search Engine
A freely available Web-based application that provides biologists with new ways to access…
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…
botXminer
botXminer
A publicly available application to search XML-formatted MEDLINE data in a complete,…
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…
CoPub
CoPub
A text mining tool that detects co-occuring biomedical concepts in abstracts from the…
A text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that…
Coremine Medical
Coremine Medical
A product of the PubGene Company designed to be used by anyone seeking information on…
A product of the PubGene Company designed to be used by anyone seeking information on health, medicine and biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to "drill down" to specific…
Deep Question Answering for Protein Annotation
Deep Question Answering for Protein Annotation
DeepQA4PA
A question-answering (QA) engines for protein annotation. Our QA engine with supervised…
A question-answering (QA) engines for protein annotation. Our QA engine with supervised macro-reading in MEDLINE achieved a top-precision ranging from 0.58 to 0.69 to answer functional proteomics questions, and Recall values up to 0.75 at R5 for…
EBI Search engine
EBI Search engine
A scalable text search engine that provides easy and uniform access to the biological…
A scalable text search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute (EMBL-EBI). The data resources represented in EBI Search include: nucleotide and protein sequences…
EBIMed
EBIMed
A web application that combines Information Retrieval and Extraction from Medline. EBIMed…
A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt…
extracting Functional Impact of Phosphorylation
extracting Functional Impact of Phosphorylation
eFIP
A tool to support article selection and information extraction of functional impact of…
A tool to support article selection and information extraction of functional impact of phosphorylated proteins. The current version focuses on protein-protein interactions (PPIs) as functional impact. In eFIP, PPIs refer to interactions between…
extracting Gene Information From Text
extracting Gene Information From Text
eGIFT
Identifies terms and documents that are relevant to a gene and its products. Additional…
Identifies terms and documents that are relevant to a gene and its products. Additional functionalities of eGIFT include finding terms in documents for a group of genes, finding genes sharing a specific term, finding related terms and related genes.
FABLE
FABLE
A model for tagging gene and protein mentions from text using the probabilistic sequence…
A model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). FABLE can identify gene and protein mentions with fairly high accuracy even without features containing…
Ferret
Ferret
A sentence-based search tool for accessing published research articles related to a set…
A sentence-based search tool for accessing published research articles related to a set of genes and concepts (keywords). Input may consist of several hundred genes and any number of concepts. Concepts can be simple keywords or more sophisticated…
Figurome
Figurome
A retrieval method that takes advantage of principles in image understanding, text mining…
A retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid…
Finding Associated Concepts with Text Analysis
Finding Associated Concepts with Text Analysis
FACTA+
A real-time text-mining system for finding and visualizing indirect associations between…
A real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and…
GeneE
GeneE
Expands your gene query to include all known synonyms to make sure you won't miss…
Expands your gene query to include all known synonyms to make sure you won't miss any documents. Highly ambiguous synonyms are combined with gene-specific keywords.
GeneValorization
GeneValorization
A web-based tool that gives a clear and handful overview of the bibliography available…
A web-based tool that gives a clear and handful overview of the bibliography available corresponding to the user input. Users provides as input a gene list (expressed by gene names or ids from EntrezGene), a context of study (expressed by keywords),…
GNSuite
GNSuite
Presents pre-processed input from the underlying parsing, protein recognition and DB…
Presents pre-processed input from the underlying parsing, protein recognition and DB identifier assignment systems. Eighteen thousand full text articles are indexed by GNSuite, and more than eighteen million abstracts from PubMed by MEDIE. The…
GoPubMed
GoPubMed
Allows users to explore PubMed search results with the Gene Ontology (GO), a…
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…
HighWire Press
HighWire Press
Provides powerful technology solutions to influential societies, university presses and…
Provides powerful technology solutions to influential societies, university presses and independent publishers who produce high-impact journals, books, and other scholarly publications. HighWire offers digital content development and hosting…
iHOP
iHOP
A network of concurring genes and proteins extends through the scientific literature…
A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. The iHOP system shows that distant medical and biological concepts can be related by surprisingly few…
iPapers
iPapers
An application that manages many PDF files of articles, whose information can be obtained…
An application that manages many PDF files of articles, whose information can be obtained by PubMed. iPapers automatically searches and imports the information of the imported articles from PubMed DB, e.g. name of authors, title, journal name,…
OSIRIS
OSIRIS
A search tool that integrates different sources of information with the aim to retrieve…
A search tool that integrates different sources of information with the aim to retrieve literature about sequence variation of a gene. In addition, it OSIRIS provides a method to link a dbSNP entry with the articles referring to it. OSIRISv1.2 can…
Quosa
Quosa
An end-to-end solution that can meet your most demanding scientific literature management…
An end-to-end solution that can meet your most demanding scientific literature management needs. QUOSA provides smart, flexible end-to-end solutions. Share the latest full-text scientific information faster, help drive information usage and control…
SeMedico
SeMedico
A semantic search engine for the life sciences. SeMedico is capable of document retrieval…
A semantic search engine for the life sciences. SeMedico is capable of document retrieval and text mining search. In its document retrieval mode, SeMedico is a search engine which is oriented towards a specialized scientific domain of discourse,…
Zotero
Zotero
A powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the…
A powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the writer to focus on content, rather than the tedious details of formatting citations and references. Zotero has new features including the ability to…