Tag: classification

Found 49 sources
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Disease Ontology

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

CATH Protein Structure Classification

The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class ( ...

Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

The Carbohydrate-Active enZYmes Database

The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

Pharmacogenomics Knowledge Base

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...


SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.


ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are fi ...


ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

GABI-Kat SimpleSearch

T-DNA insertions in Arabidopsis and their flanking sequence tags.

Virulence Factor Database

VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).


PLAZA is a platform for comparative, evolutionary, and functional genomics. The platform consists of multiple instances, where each instance contains additional genomes, improved genome annotations, new software tools, etc.

Enzyme nomenclature database

ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each t ...

Integrated relational Enzyme database

IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification ...

Human Oral Microbiome Database

The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provi ...

Human Endogenous Retrovirus database

This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. The database makes it possible to continuously improve classification and characterization of retroviral families. The HERV database no ...

Online Mendelian Inheritance in Animals

Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).


HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

Assembling the Fungal Tree of Life

The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life.


Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The database can be used to predict protein structures that have not yet been identified. Genome3D uses structural ...


ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the ty ...


TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) re ...


The Enzyme Database was developed as a new way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards.

Chemical Component Dictionary

The Chemical Component Dictionary is an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, sma ...


The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant ima ...


MycoBank is a database created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations ). Pairwise sequence alignments ...

Description of Plant Viruses

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences a ...

Infectious Disease Ontology Core

The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedi ...

International Classification of Diseases Version 10 - Procedure Coding System

The ICD-10 Procedure Coding System (ICD-10-PCS) is an international system of medical classification used for procedural coding. The ICD-10-PCS is a procedure classification published by the United States for classifying procedures performed in hospi ...


Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family class ...

EcoliWiki: A Wiki-based community resource for Escherichia coli

Community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

BCCM/MUCL Agro-food & Environmental Fungal Collection

BCCM/MUCL is a generalist fungal culture collection of over 30 000 filamentous fungi, yeasts and arbuscular mycorrhizal fungi including type, reference and test strains. The collections activities include the distribution of its holdings, the accessi ...

CareLex Controlled Vocabulary

Contains controlled vocabulary terms from National Cancer Institute used to classify clinical trial electronic content (documents, images, etc). A Content model contains content classification categories (classes) and metadata properties (data proper ...

Functional Therapeutic Chemical Classification System

The Functional Therapeutic Chemical Classification System (FTC) defines over 20,000 mechanisms and modes of action for approved drugs. The resource abstracts away from the traditional chemical structure-based approach and focuses solely on the mode o ...

Database Of Local Biomolecular Conformers

Dolbico, the Database Of Local Biomolecular Conformers, stores DNA structural data including the information about DNA local spatial arrangement. The main aim of Dolbico is the exploration of DNA structure at a local level. The analysis of local DNA ...

Autism DSM-ADI-R ontology

The Autism DSM-ADI-R (ADAR) ontology uses SWRL rules to infer phenotypes from ADI-R items. It includes OWL class definitions representing DSM IV diagnostic criteria for autistic disorder and ASD criteria for Autism Spectrum Disorder. The goal is to c ...

BCCM/ULC Cyanobacteria Collection

BCCM/ULC is a small and dedicated public collection, currently containing one of the largest collections of documented (sub)polar cyanobacteria worldwide. The BCCM/ULC collection is hosted by the Centre for Protein Engineering (the Unit) of the Unive ...

International Classification of Diseases for Oncology 3rd Revision

The International Classification of Diseases for Oncology (ICD-0) has been used for nearly 25 years, principally in tumor or cancer registries, for coding the site (topography) and the histology (morphology) of the neoplasm, usually obtained from a p ...

Data Documentation Initiative Lifecycle (DDI-Lifecycle)

Data Documentation Initiative (DDI) Lifecycle (DDI-Lifecycle, DDI-L) is designed to document and manage data across the entire life cycle, from conceptualization to data publication, analysis and beyond. The freely available international DDI standar ...

Protein Classification Benchmark Collection

The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.

Catalog of Fishes Genus Database

The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database.

Reference list of Metabolite names

RefMet provides a standardized reference nomenclature for both discrete metabolite structures and metabolite species identified by spectroscopic techniques in metabolomics experiments. This is an essential prerequisite for the ability to compare and ...


AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.

Enzyme Commission Number

In its report in 1961, the first Enzyme Commission devised a system for enzyme classification that also serves as a basis for assigning code numbers. These code numbers, prefixed by EC, contain four elements separated by points / full stops and are n ...

Domain Resource Application Ontology

The Domain Resource Application Ontology (DRAO) is an application ontology describing cross-discipline research domains used within FAIRsharing records by curators and the user community. It is built in conjunction with the Subject Resource Applicati ...

Subject Resource Application Ontology

The Subject Resource Application Ontology (SRAO) is an application ontology describing subject areas / academic disciplines used within FAIRsharing records by curators and the user community. It is built in conjunction with the Domain Resource Applic ...

Encyclopedia of Life

Our knowledge of the many life-forms on Earth - of animals, plants, fungi, protists and bacteria - is scattered around the world in books, journals, databases, websites, specimen collections, and in the minds of people everywhere. Imagine what it wou ...

IUPAC-IUB Commission on Biochemical Nomenclature - Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents

The Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents, created by the IIUPAC-IUB Commission on Biochemical Nomenclature, formalizes the naming scheme for simple nucleotides; nucleotide coenzymes and related substance ...

IUPAC-IUB Joint Commission on Biochemical Nomenclature - Nomenclature and Symbolism for Amino Acids and Peptides

The Nomenclature and Symbolism for Amino Acids and Peptides, created by the IUPAC-IUB Joint Commission on Biochemical Nomenclature, formalizes the naming scheme for amino acids, non-peptide derivatives of amino acids and peptides as well as peptide d ...


The PLANKTON*NET data provider at the Alfred Wegener Institute for Polar and Marine Research is an open access repository for plankton-related information. It covers all types of phytoplankton and zooplankton from marine and freshwater areas. PLANKT ...

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