Tag: classification

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 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.

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 ...

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 ...

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 ...

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

The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The anti ...

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

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

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

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 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 ...

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 ...

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 ...

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 is a a database of inherited disorders, other (single-locus) traits, and genes 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.

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.

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 ...

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 ...

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 Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. You can browse the ontologies through the website as well as programmatically via the OLS API.

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 ...

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 ...

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

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 ...

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 ...

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 ...

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 ...

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 ...

The International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3) is used principally in tumour or cancer registries for coding the site (topography) and the histology (morphology) of neoplasms, usually obtained from a pathology report ...

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 ...

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

The International Classification of External Causes of Injury (ICECI) was created to enable the classification of external causes of injuries. It is designed to help researchers and prevention practitioners to describe, measure and monitor the occurr ...

The Encyclopedia of Life (EOL) is a collaborative encyclopedia to describe all known living species. It identifies sources of biodiversity knowledge that are legally and practically shareable; integrates them with other sources and adds metadata; pro ...

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

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.

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 ...

The Library of Congress Medium of Performance Thesaurus (LCMPT) for Music is a stand-alone vocabulary that provides terminology to describe the instruments, voices, etc., used in the performance of musical works. The core terms in LCMPT are based chi ...

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 ...

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 ...