Permits users to establish a foundation for systematic reasoning over the intercellular network. iX is a comprehensive high-resolution knowledgebase of directional intercellular interactions that was text-mined from all available PubMed abstracts across a broad range of disease conditions. Interactions captured by this method include (i) direct cytokine binding or secretion events and more distant, and (ii) indirect influencing relations, scored and filtered to emphasize precision.
A publicly available, multidisciplinary, cancer-focused knowledgebase developed to support cancer translational research and drug discovery. canSAR integrates genomic, protein, pharmacological, drug and chemical data with structural biology, protein networks and druggability data. canSAR is widely used to rapidly access information and help interpret experimental data in a translational and drug discovery context.
Provides experimentally determined kinetic data of protein–protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references.
Provides a corpus of scientific texts, used for BioCreative, a competition in which participants are given well defined text-mining or information extraction tasks in the biological domain. BC2GM-corpus consists mainly of the training and testing corpora from BioCreative I and the testing corpus for the current task consists of an additional 5,000 sentences that were held 'in reserve'.
Aims to collate any relevant data pertaining to any PE2-4 protein. Missing ProteinPedia permits to define, summarize and discuss all available data for the so-called missing proteins, emphasizing why they may be currently difficult to observe/find, using standard proteomics mass spectrometry (MS) and Ab-based techniques. It allows the generation of high confidence MS evidence for as many PE2-4 proteins as possible.
Provides a collection of definitions for the higher-level attributes. Genome Properties ascribes higher-level attributes to a species when a sufficient set of molecular markers are detected in its genome, or else reported jointly absent. It can help to summarize high-level traits of species biology from genome analysis. The method permits to understand metabolic context while trying to understand the roles of other proteins from the same species.
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.
A freely available web resource, listing expertise and molecular resource capabilities of research centres and biotechnology companies. The database is designed for researchers who require information on how to make best use of valuable biospecimens from biobanks and other sample collections, focusing on the choice of analytical techniques and the demands they make on the type of samples, pre-analytical sample preparation and amounts needed.
Provides comprehensive information about miRNAs affecting drug therapies. mTD is a database that provides the sentences describing the drug-miRNA interactions with links to corresponding publications for each drugmiRNA association. This resource can help to understand the mechanisms underlying drug actions better and design more efficient drug combinations, like the combination of miRNA inhibitors and drugs.
Provides clinically relevant somatic mutations. DIRECT enables a genetically informed approach to cancer medicine by providing clinicians access to tumor gene therapy-response information based on individual patient data published in the literature. It catalogs only patients with non-small cell lung cancers (NSCLCs) and published individual patient data on EGF receptor (EGFR) mutations.
Gathers species traits from several species. Traitpedia is a collaborative repository that contains trait information for about 180 eukaryotic species, with 15 traits per species, distributed in four categories: (1) general, (2) individual (phenotypical), (3) intraspecific (behavioral), and (4) Interspecific. Users can deposit simply formatted trait information. This database can assist in the mining of information and the extraction of trait correlations.
Contains data on the frequency of inherited human disorders. FIDD is useful in a clinical context, in medical research, for epidemiological studies, and for the planning of genetic services. It can be queried by the body system mainly affected by the disorder, the name of the disease or condition, its Online Mendelian Inheritance in Man (OMIM) number or the population surveyed. The database covers information of over 200 conditions.
A database of mutagenesis and mutation information on Human Immunodefiency Virus (HIV). Hivmut describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community.
An information network launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources, as data, software tools, materials, services, projects and organizations. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. dkNET provides an ideal environment for illustrating some of the opportunities and challenges associated with organizing and searching the new types of digital research objects, including dynamic databases, produced in support of biomedical research.
Collects full-text biomedical journal articles. CRAFT is a manually annotated corpus with all coreferential phenomena of identity and apposition. It also identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology.
Summarizes literature-curated information on levodopa-induced dyskinesia (LID) genetics. LIPDP is a publicly available web resource that investigates the LID-associated genes in a broader functional context through analysis of their relationships based on network models. It uses different underlying networks and allows to incorporate data into the analyses. The core of LIDPD is a set of Panel genes that have been associated with LID in the scientific literature. Different Highlight datasets provide additional gene annotations or associations with Parkinson's disease.
An online database to centralize aging research projects across numerous research disciplines. IARP integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research.
A text mining system for mutation-disease association extraction. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic patterns to extract mutation-disease associations. DiMeX includes a separate component that extracts mutation mentions in text and associates them with genes. The results indicate that our system outperforms the existing mutation-disease association tools, addressing the low precision problems suffered by most approaches. DiMeX was applied on a large set of abstracts from Medline to extract mutation-disease associations, as well as other relevant information including patient/cohort size and population data. We conclude that this high-throughput text-mining approach has the potential to significantly assist researchers and curators to enrich mutation databases.
Delivers large healthcare dataset expressed in the open electronic health record (openEHR) formalism. ORBA was constructed on the basis of nation-wide information of pseudo-anonymised patients from healthcare settings distributed across the twenty-seven Brazilian Federation Units. It is composed of more than 150 million records with information from approximately 55.47 million hospitalisation authorisations and 7.75 million patients.