Data collections: recently updated

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NameNamespaceDefinition
MultiCellDS collection multicellds.collection MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).
MultiCellDS Digital snapshot multicellds.snapshot MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.
MultiCellDS Digital Cell Line multicellds.cell_line MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.
World Register of Marine Species worms The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.
restricted logoInChIKey inchikey The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.
Systems Biology Ontology sbo The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.
restricted logoKyoto Encyclopedia of Genes and Genomes kegg Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
OMIM omim Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.
DOI doi The Digital Object Identifier System is for identifying content objects in the digital environment.
RRID rrid The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.
Mammalian Phenotype Ontology mp The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.
Protein Modification Ontology mod The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.
Unit Ontology uo Ontology of standardized units
Plant Environment Ontology eo The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.
Human Phenotype Ontology hp The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
Plant Transcription Factor Database planttfdb The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.
JWS Online jws JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.
Relation Ontology ro The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
Japan Chemical Substance Dictionary jcsd The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).
GPCRDB gpcrdb The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.
ProbOnto probonto ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.
DATF datf DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.
Molbase molbase Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.
MatrixDB matrixdb.association MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.
DisProt disprot The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
STOREDB storedb STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.
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.
Taxonomy taxonomy The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
Reactome reactome The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
KEGG Reaction kegg.reaction KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.
30 of the most recently created or modified data collections.