Databases

This section contains databases of literature texts or data mined from literature sources.

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BioNumbersDatabase Content

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BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

ccPDBDatabase Content

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ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is complied from the literature and the Protein Data Bank (PDB), where all datasets were derived from PDB.

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CharProtDBDatabase Content

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CharProtDB is a curated database of biochemically characterized proteins. The initial data set in CharProtDB was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.

CIViC - Clinical Interpretation of Variants in CancerResource Content

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Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Realizing precision medicine will require this information to be centralized, debated and interpreted for application in the

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DGIdb - Mining the Druggable GenomeResource Content

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The Drug-Gene Interaction database (DGIdb) mines existing resources that generate hypotheses about how genes might be targeted therapeutically or prioritized for drug development. It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially 'druggable' genes.

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TitlePublication YearGoogle Scholar Citation Count

genenames.orgDatabase Content

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genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.

This content is being maintained by HGNC.

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MINTDatabase Content

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Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The full MINT dataset can be freely downloaded.

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TitlePublication YearGoogle Scholar Citation Count
MINT, the molecular interaction database: 2012 update20125

NBRP resourcesDatabase Content

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The National BioResource Project (NBRP) is a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones, etc. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
NBRP databases: databases of biological resources in Japan201011

NCBI ResourcesDatabase Content

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The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.

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Protein Naming UtilityDatabase Content

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The Protein Naming Utility (PNU) is a web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. The PNU allows users to generate and manage collections of naming rules, optionally building upon the growing body of rules generated at the J. Craig Venter Institute (JCVI). Users can check their protein names against a selected PNU rule collection, generating both statistics and corrected names. The PNU can also be used to correct GenBank table files prior to submission to GenBank.

SCRIPDBResource Content

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Patents are a rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. SCRIPDB is a chemical structure database designed to make this data available.

UKPMCDatabase Content

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UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
UKPMC: a full text article resource for the life sciences20118
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