BioMart Central Portal—unified access to biological data

By Syed Haider, B. Ballester, D. Smedley, Junjun Zhang, Peter M. Rice, Arek Kasprzyk. Nucleic Acids Res., 2009

368 citations recorded by the source corpus.

BioMart Central Portal (www.biomart.org) offers a one-stop shop solution to access a wide array of biological databases. These include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase and PRIDE; for a complete list, visit, http://www.biomart.org/biomart/martview. Moreover, the web server features seamless data federation making cross querying of these data sources in a user friendly and unified way. The web server not only provides access through a web interface (MartView), it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services. The website is free and open to all users and there is no login requirement.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/63cb645be55347cffb6c90791a6b9b4ec133ea8b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The human gene damage index as a gene-level approach to prioritizing exome variants (2015, methodology): “We also demonstrated a strong association between gene damage and the number of paralogs (27, 28): genes with high GDI had significantly larger numbers of paralogs than human genes generally (P = 3.”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, methodology): “For more detailed description of all the interfaces please refer to earlier publications (1,7).”
Ensembl’s 10th year (2009, methodology): “In addition to their availability through the Ensembl web site, the Ensembl BioMart is also available from the main BioMart Portal (17).”
BioMart: driving a paradigm change in biological data management (2011, background): “…introduced a new innovative way of creating large multi-database repositories that avoid the need to store all the data in a single location (2), and finally it proved that large-scale projects involving next generation sequencing data can be managed efficiently in a distributed environment…”
The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease (2012, neutral): “15) (Haider et al., 2009; Kenan et al., 1991).”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, methodology): “We retrieve the gene annotation and gene-ID relations from KEGG Genes and BioMart (37).”
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer (2009, positive): “One of the strengths of Biomart is its ability to federalize several independent systems and query them together returning a coherent dataset combined from all.”
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer (2010, methodology): “A Biomart is now available allowing more automated data mining and integration with other biological databases.”
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, methodology): “Mappings between Ensembl gene IDs, Ensembl transcript IDs, Ensembl protein IDs, Entrez Gene IDs and UniProt accessions as used by DomainGraph were downloaded via the corresponding Ensembl BioMart versions (6).”
International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data (2011, methodology): “The architecture of the ICGC data management system has been modeled on the BioMart Central Portal (3, 4).”