Tag: data mining

The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public ...

The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

BRENDA is the main collection of enzyme functional data available to the scientific community.

The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has fun ...

LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure inform ...

The PDB_REDO databank contains alternative (in many cases higher quality) versions of Protein Data Bank (PDB) structure models that were optimised by model refinement and rebuilding. The structure models are supplemented by validation data that desc ...

Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global orderin ...

Integrated database of mammalian genomes, phenotypes, strains and cell lines

MarRef is a manually curated marine microbial genome database that contains complete genomes.

Includes all non-complete marine microbial genomes regardless of the level of completeness.

MarCat is a gene (protein) catalogue of uncultivable and cultivable marine microorganisms derived from metagenomics samples.

Database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for uniq ...

A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.

TUPDB (Target-Unrelated Peptide Data Bank) is a comprehensive database of target-unrelated peptides (TUPs) and TUP motifs. It contains extensive information extracted from research articles and public databases.

DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.

EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments t ...

The largest integrated microbial knowledge base.

Forensic loci allele database.

Enhanced biochemical coverage for peak identification in untargeted metabolomics.

A comprehensive bipolar disorder database for genetic research.

It is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text.

Top ‱ cited papers from PUBMED. Unicorn Papers are based on an equal contribution (EC) citation model in which the total number of citations had been divided by the number of the authors. Currently, the list contains 3405 papers with ECcit ≥ 847.0 ( ...