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Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online. [5] Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. [6] Ensembl and Ensembl Genomes software uses an Apache 2.0 license [7] license.
Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, [7] and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data.
[1] [5] [6] The GeneCards database provides access to free Web resources about more than 350,000 known and predicted human genes, integrated from >150 data resources, such as HGNC, Ensembl, and NCBI. The core gene list is based on NCBI, Ensembl and approved gene symbols published by the HUGO Gene Nomenclature Committee (HGNC).
GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project.. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). [2]
Users can select various types of identifiers such as CCDS ID, gene ID, gene symbol, nucleotide ID and protein ID to search for specific CCDS information. [1] The CCDS reports (Figure 1) are presented in a table format, providing links to specific resources, such as a history report, Entrez Gene [ 10 ] or re-query the CCDS data set.
The literature-derived human gene-disease network (LHGDN) is a text mining derived database with focus on extracting and classifying gene-disease associations with respect to several biomolecular conditions. It uses a machine learning based algorithm to extract semantic gene-disease relations from a textual source of interest.
The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database (also known as EMBL-bank). [2] The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the ...
For each model organism, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. RefSeq is limited to major organisms for which sufficient data are available (121,461 distinct "named" organisms as of July 2022), [ 4 ] while GenBank includes sequences for any ...