Data collections: recently updated

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NameNamespaceDefinition
TAIR Locus tair.locus The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
Rat Genome Database rgd Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.
ENCODE: Encyclopedia of DNA Elements encode The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.
WormBase RNAi wb.rnai WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.
restricted logoWormBase wb WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.
restricted logoSGD sgd The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.
OCI oci Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information. OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus. OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312. OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.
FoodOn Food Ontology foodon FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.
Rebuilding a Kidney rbk (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.
Relation Ontology ro The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
Taxonomy taxonomy The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
CompTox Chemistry Dashboard comptox The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.
Complex Portal complexportal A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.
GUDMAP gudmap The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.
RNAcentral rnacentral RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.
CAMEO cameo The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.
Data Object Service dev.ga4ghdos Assists in resolving data across cloud resources.
Software Heritage swh Software Heritage is the universal archive of software source code.
AOPWiki (Key Event) aop.events International repository of Adverse Outcome Pathways.
AOPWiki (Key Event Relationship) aop.relationships International repository of Adverse Outcome Pathways.
AOPWiki (Stressor) aop.stressor International repository of Adverse Outcome Pathways.
FamPlex fplx FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
JRC Data Catalogue eu89h The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.
Protein Ontology pr The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.
Reactome reactome The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
MIRIAM Registry collection miriam.collection MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.
ICD icd The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.
PubMed pubmed PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.
HGNC hgnc The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.
PMC International pmc PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.
30 of the most recently created or modified data collections.