Data collections: recently updated

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NameNamespaceDefinition
ArrayMap arraymap arrayMap is a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data.
Benchmark Energy & Geometry Database begdb The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.
CAMEO cameo CAMEO continuously evaluate the accuracy and reliability of predictions.
SISu sisu The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in Finns. It provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland.
Natural Product-Drug Interaction Research Data Repository napdi The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).
FAIRsharing fairsharing The web-based FAIRSharing 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.
AGRICOLA agricola AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.
Human Endogenous Retrovirus Database erv Endogenous retroviruses (ERVs) are present in the genomes of practically all vertebrates, as a consequence of infiltration of the host germline lineages by circulating exogenous viruses. A typical mammalian genome contains tens to hundreds of thousands of ERV elements, most of which are evolutionarily old and sustained multiple mutation, deletions and rearrangements. Important roles both in physiology and disease processes have been described for some ERV elements, including regulation of host genes, taking part in placenta formation, and influencing immune responses.
NASA GeneLab ngl NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.
AOPWiki aop International repository of Adverse Outcome Pathways.
BioTools biotools Tool and data services registry.
MarDB mmp.db MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
MarCat mmp.cat MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.
restricted logoBioCyc biocyc BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.
MarRef mmp.ref MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.
CATH Protein Structural Domain Superfamily cath CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.
DOI doi The Digital Object Identifier System is for identifying content objects in the digital environment.
MetaCyc Compound metacyc.compound MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
MetaCyc Reaction metacyc.reaction MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
DataONE d1id DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.
GlyTouCan glytoucan GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.
restricted logoInChI inchi The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.
INSDC CDS insdc.cds The coding sequence or protein identifiers as maintained in INSDC.
Genome assembly database insdc.gca The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.
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.
30 of the most recently created or modified data collections.