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BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). The system can be used with any type of data and comes with a range of query interfaces and administration tools, including 'out of the ... [More]
GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More]
FlyGATE is a knowledge database dedicated to the transposable element (TEs) sequences of the Drosophila melanogaster genome.
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.
The python modules hosted here are the core of Cistrome Database, developed by Shirley's Lab in Dana-Farber Cancer Institute. The Cistrome Database aims to provide a data storage framework and common analysis tools for ChIP-chip/ChIP-seq data.
The Microbial Phenotype Ontology and Database is an effort to bring a well-defined controlled vocabulary to the assignment of properties to various microbes (predominantly Bacteria & Archaea). Aside from a formal ontology of terms, software and human curation of term-specie associations are being developed.
A web database and bioinformatics analysis tool for gene families involved in antigenic variation and immune system evasion in pathogens.