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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.
EBI Search engine
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 at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property.
A semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. To semantically enrich these articles and provide convenient user access, GeneView uses several inter-operating components: (i) named entity recognition and PPI extraction modules; (ii) an inverted index for efficient searching; (iii) a customizable ranking algorithm taking the extracted entity-centric information into account and (iv) a web front end for querying and visualization.
DigSee / Disease gene Search engine with evidence sentences
A search engine to find explicit association between genes and cancer through biological events. Although several Web-based text-mining systems are available to extract implicit relationship between genes and cancer, most of them do not provide fine-grained information about the molecular context of gene–disease association. DigSee is a unique system in this aspect, and its accuracy was validated using manually curated evidence sentences.
A web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions.
CCT / Current Comparative Table
Enables to automate customized bioinformatics searches, typically of remote sequence or hidden Markov model (HMM) databases. CCT is useful to scientists who study large sets of molecules in today’s evolving information landscape because it color-codes all result files by age and highlights even tiny changes in sequence or annotation. It can be easily configured to automatically download new versions of databases and to run any number of bioinformatics searches on the new data. This software then organizes the results in a table containing hyperlinks color-coded by result age, making it simple to pick out recently changed results.
SALSA / Searching with Assembly of Local Sequence Alignments
Computes a gapped alignment of two sequences. SALSA uses dynamic programming to build an accurate alignment based on the fragments initially identified. It produces a good estimate of the optimal score, without a substantial increase in computation time. The software is implemented as a multi-threaded application using POSIX threads, which allows it to fully take advantage of multiple CPUs in symmetric multiprocessing (SMP) computers.
Provides the bioinformatics community with annotated Web services descriptions in diverse formats. BioSWR is a web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional Web Service Definition Language (WSDL) based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language.
Allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term cooccurrence. PubMatrix is a web-based toll that provides previous searches using common useful lists of keyword terms. It is a simple intuitive multiplex comparison tool requiring no user understanding of algorithm design, perl, or scripting, and minimal instruction time. It allows automatic systematic searching of PubMed followed by a quick intuitive survey of results, and as such, dramatically reduces the investigator time needed to query PubMed as compared to a gene-by-gene approach.
G-Bean / Graph based Biomedical search engine
A Web-based literature retrieval tool to query documents in MEDLINE database. The major contributions of G-Bean are three folds: 1) G-Bean uses a multithreaded parallel algorithm to automatically generate the document index to address the inefficiency of the PubMed's manual indexing process; this automated index generation scheme allows incremental index update for timely index maintenance; 2) it merges multiple biomedical ontologies into a single ontology graph and uses all concepts in this ontology graph to index documents, ameliorating PubMed's low concept coverage problem of using only MeSH terms for indexing; 3) G-Bean automatically retrieves additional relevant articles based on user's current selection and ranks them according to their semantic similarities with all articles selected so far while PubMed can recommend a list of articles matching the same keywords with only the current viewing article.
BOSS / Biomedical Object Search System
Fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good scalability, just as with conventional document search engines, because it is designed to use a standard document-indexing model with minimal modifications. Considering the features, BOSS notches up the technological level of traditional solutions for search on biomedical information.
Smart Drug Search
A search engine in assistance of antimicrobial research. Smart Drug Search is use for the screening of literature related to antimicrobial resistance, microbial virulence and topics alike. The search engine combines state-of-the-art web technologies and frameworks with text mining tools so that literature monitoring is active and efficient, and user experience may be easily customized and refined. It was implemented as a web-based application, being designed as a common three-layered architecture where the bottom layer is responsible for accessing the database, the middle layer supports the main functionalities of the web search engine and the top layer is in charge of providing the end-user interface
A web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. Genes2WordCloud provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.
Permits to conduct searches of the medical literature and retrieving full-text PDFs. Pubget’s search functionality and add-on features are evaluated to determine potential for library instruction and promotion. With many libraries relying on OpenURL link resolvers to connect searchers with institutional subscriptions, Pubget offers an alternative by combining search, article-level link resolving, and authentication in a single platform. The tool is a search engine designed for life sciences researchers.
A user-friendly, cross-platform application that allows users to retrieve and download data files from all bioinformatics databases. PubData uses keywords to search for specific biomedical data much like PubMed searches biomedical literature. Multiple databases are queried at once to produce optimal results in a timely manner and avoid the hassle of manually searching each source one by one. PubData utilizes novel natural language processing and artificial intelligence algorithms to not only query multiple databases at once in order to produce accurate results in a timely and efficient manner, but also to adapt to user preferences via a collaborative filtering recommender system.
Djeen / Database for Joomla's Extensible Engine
Allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Djeen is a new Research Information Management System (RIMS) for collaborative projects. It is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance.
Biovista Vizit
Helps biomedical scientists with their research and discovery work. Biovista Vizit is a visual bibliography search tool based on PubMed that permits to collaborate and helps to share information. User can start with a gene and asks to show pathways or diseases related to it. This online resource also allows to explore relationships by expanding and browsing the graph of links based on feedback. It provides genes, pathways, cell lines, post-translational modifications (PTMs) and diseases in more of 30 categories.
Finds public databases by data type. drfinddata searches the Data Resource Catalogue to find entries with EDAM data terms matching a query string. The first search is of the EDAM ontology data namespace, using the term names and their synonyms. All child terms are automatically included in the set of matches inless the -nosubclasses qualifier is used. The -sensitive qualifier also searches the definition strings. The set of EDAM terms are then compared to entries in the Data Resource Catalogue, searching the 'edat' EDAM data index.
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Provides information on over 190 published online cellular pathway and network databases. Pathguide is organised around approximate categories and a database can be stored in multiple categories if it contains multiple data types. The main categories for databases are: Protein–protein interaction (PPI), Metabolic pathway, Signaling pathway, Gene regulation network (GRN), Genetic pathway and Pathway diagram. The database includes a number of protein-sequence databases that store pathway information as secondary information.
Allows exploration of biological databases utilizing semantic web methods. BioCarian is a search engine that browses several selected public databases. The databases consist in a sample collection of DNA-level data (dbSNP, GWAS, Ensembl), protein data (UniProt), pathway data (KEGG, Reactome), disease data (OMIM, DisGeNET) and a private database containing viral integration sites in the liver cancer patients. BioCarian can be used to do a primary analysis of data and act as means of an independent, orthogonal verification of an analysis result.
Assists with large-scale data-mining related to gene function in Caenorhabditis elegans. GExplore contains information about the domain organization of the proteomes of 9 nematode species, can display the location of Caenorhabditis elegans mutations with respect to the domain organization of the proteins, and includes stage-specific RNAseq gene expression data generated by the modENCODE project. The database has been organized to facilitate independent updates of the different parts of the database and to allow the addition of novel data sets in the future.
DESHCV / Dragon Exploratory System on Hepatitis C Virus
Provides a biomedical text-mining and relationship exploring knowledgebase. DESHCV is a comprehensive Hepatitis C Virus (HCV) online web resource. Users can retrieve information using specified concepts, keywords and phrases. It also offers option of either viewing the retrieved abstracts with or without embedded tagged concepts. It leads to the identification of possible new discovery and augments efforts in the search for diagnostic or even therapeutic targets.
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.
Bioz, Inc
Mines hundreds of millions of pages of complex, dense and unstructured life-sciences papers, and then uses Natural Language Processing and Machine Learning to clean, tag and structure the data. Bioz's platform incorporates semantic analysis engine and relevancy ranking of results, research-relevant correlations, reagent product ratings, and researcher collaboration optimization. By using this database, scientists are able to reduce the cost of reagents and equipment, shorten the amount of time required for successful experimentation, and most importantly, improve the quality of their research.
An online tool to explore established and potential gene-disease associations in the context of other biomedical relations. Knowledge.bio provides access to a network of interconnected concepts mined from more than 20,000,000 PubMed abstracts. We integrate explicit connections identified by the SemRep system from the US National Library of Medicine with the Implicitome from the Leiden University Medical Center. The Implicitome provides predicted relationships between genes and diseases based on 'concept profile' technology.
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