Data collections: recently updated

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NameNamespaceDefinition
MetaNetX reaction metanetx.reaction MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.
MetaNetX chemical metanetx.chemical MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.
MetaNetX compartment metanetx.compartment MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.
Transport Classification Database tcdb The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.
OMIT omit The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).
Genomic Data Commons Data Portal gdc The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.
Information Artifact Ontology iao An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
Sequence Read Archive insdc.sra The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.
FAIRsharing fairsharing The web-based BioSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.
Reactome reactome The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
dbGaP dbgap The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.
COSMIC Gene cosmic COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.
Nucleotide Sequence Database insdc The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.
ProteomeXchange px The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.
PRINTS prints PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
Progenetix pgx The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).
UniProt Knowledgebase uniprot The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.
Identifiers.org Registry mir The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.
Cellosaurus cellosaurus The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.
E-cyanobacterium entity ecyano.entity E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.
E-cyanobacterium rule ecyano.rule E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.
BioAssay Ontology bao The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.
LINCS Small Molecule lincs.smallmolecule The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).
LINCS Cell lincs.cell The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.
SEED Compound seed.compound This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.
PIRSF pirsf The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
GRID grid International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.
MedGen medgen MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.
National Bibliography Number nbn The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.
Ontology for Biomedical Investigations obi The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).
30 of the most recently created or modified data collections.