Database Tools
Bioinformatics Applications Developed by the ABCC/CISB group that utilize CISB's data warehouse of publicly available databases.
AVIA logoAVIA is web-based annotation and visualization pipeline from genomic variations. AVIA provides integrated access to genomic and proteomic databases and functional annotations. In addition, the availability of a wider range of input options, including gene lists and protein mutations, classification of potentially significant SNPs and genes, and pathway visualization layered with annotation data distinguishes itself from other annotation servers. This tool is available at avia.abcc.ncifcrf.gov.
BioDataBioData is a web-based tool that can be used to explore the variety of databases available through ABCC. Since we have automated the update process, users can get the most up-to-date information. If users are interested in exploratory analysis of these databases, this application will help query and craft SQL queries, which can later be used in downstream applications. This service is available at biodata.abcc.ncifcrf.gov. There are also web APIs available.
bioDBnet logobiological DataBase network, or bioDBnet, is an application integrating a vast number of biological databases including Gene, UniProt, Ensembl, GO, Affy, RefSeq etc. The databases are created by downloading data from various public resources. They are formatted and maintained in a relational structure at the Advanced Biomedical Computing Center (ABCC)
CyPRUSCyPRUS is a web-based tool that allows users to do more specific queries within Uniprot. This tool uses a Mongo database to quickly search Uniprot based on features, such as point mutations using a gene-based position variants. Also, by allowing users customize their views, results can be imported directly into other applications for use. We are currently using this feature in AVIA. This tool is available here.
totem logoToTeM is a web-based tool that allows users to do full text searching on Medline Abstracts. It uses Lucene and Solr for text indexing for fast retrieval. This service is available by clicking here.