The BioMart community portal: an innovative alternative to large, centralized data repositories
By D. Smedley, Syed Haider, S. Durinck, Luca Pandini, P. Provero, James E. Allen, O. Arnaiz, M. Awedh, R. Baldock, Giulia Barbiera and 95 more. Nucleic Acids Res., 2015
717 citations recorded by the source corpus.
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/312a8944cd54760dbf4d194471861b867f289ebf
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Citations in the corpus
- Mapping Transcriptomic Vector Fields of Single Cells (2022, neutral): “The database of human and mouse ortholog genes was retrieved from ensembl bioMart (Smedley et al., 2015).”
- SynGO: an evidence-based, expert-curated knowledgebase for the synapse (2019, methodology): “Total gene length was computed using the start_position and end_position BioMart attributes (gene start and end, in base pairs).”
- Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species (2017, methodology): “Ensembl Genomes data is also organised in additional databases, constructed using the BioMart data warehousing system (7), optimised around common gene-and variant-centric queries.”
- Genenames.org: the HGNC and VGNC resources in 2017 (2016, methodology): “download tools and BioMart (14) and RESTful web services.”
- Ensembl Genomes 2016: more genomes, more complexity (2015, methodology): “Ensembl Genomes data is also made available through a series of data warehouses, optimized around common (gene- and variant-centric) queries, using the BioMart data warehousing system (4).”
- Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition (2016, positive): “Enrichment for functions among optimal and non-optimal gene sets was performed by first mapping each gene to its Gene ontology (GO) (Ashburner et al, 2000) using Biomart (Smedley et al, 2015), restricting the onlotogies to "biological processes".”