Tag: molecular entity

Found 39 sources
Source Match ReputationScore*

Chemical Entities of Biological Interest

Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, et ...

Systems Biology Markup Language

The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By su ...

Systems Biology Graphical Notation

The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biolo ...

Biological Magnetic Resonance Databank

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

BioAssay Ontology

The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.

IUPAC International Chemical Identifier

Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is a machine-readable string generated from a chemical structure. InChIs are unique to the compound they descri ...

NMR Self-defining Text Archive and Retrieval format

NMR-STAR is an extension of the STAR file format to store the results of biological NMR experiments.


The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

Minimum Information About a Bioactive Entity

MIABE is intended to be used as a guideline which should be consulted prior to the publication of data describing small molecules and their interactions with one or more target molecules. It was developed by representatives of pharmaceutical companie ...

Toxin and Toxin Target Database

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.


GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

CHEMical INFormation Ontology

The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic ...

macromolecular Crystallographic Information File

PDBx/mmCIF is a dictionary of data archiving macromolecule crystallographic experiments and their results.

Simplified Molecular Input Line Entry Specification Format

This format is an open specification version of the SMILES language, a typographical line notation for specifying chemical structure. It is hosted under the banner of the Blue Obelisk project, with the intent to solicit contributions and comments fro ...

Pathway Ontology

The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes o ...

KEGG Mark-up Language

The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and mo ...

Chemical Markup Language

CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. ...

BioModels Ontology

OWL Representation of the models in the BioModels repository.

Ontology for MicroRNA Target

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 techno ...

NanoParticle Ontology

An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.

Global Alliance for Genomics and Health Metadata Model

The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data.

MDL molfile Format

An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. Each molfile describes a single molecular structure which can contain disjoint fragments. The V3000 molfile and V3000 rxnfile ...

Enzyme Mechanism Ontology

The "Enzyme Mechanism Ontology " describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.


ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching ...

Hierarchical Editing Language for Macromolecules

HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules (e.g. proteins, nucleotides, antibody drug conjugates) whose size and complexity render existing small-molecule and sequence-based info ...


This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.

Collaborative Computing Project for NMR

The CCPN Data Model for macromolecular NMR is intended to cover all data needed for macromolecular NMR spectroscopy from the initial experimental data to the final validation. It serves for exchange of data between programs, for storage, data harvest ...

Structure Data Format

Structure Data Format (SDF) is a chemical file formats to represent multiple chemical structure records and associated data fields. SDF was developed and published by Molecular Design Limited (MDL) and became the most widely used standard for importi ...

Melanoma Molecular Map Project

A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.


ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properti ...


LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.

CHARMM Card File Format

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a computational package used for classical, quantum and hybrid quantum/classical simulations. The CHARMM Card File Format (.CRD) stores the standard Cartesian coordinates of the atoms in the s ...

ChemDraw Native File Format

CDX is the native file format of ChemDraw, and is guaranteed to save anything drawn in ChemDraw without loss of data. At the same time, however, its architecture was carefully designed to make it a flexible and general-purpose chemical format. It is ...

MolMeDB: Molecules on Membranes Database

MolMeDB is an open chemistry database concerning the interaction of molecules with membranes.

Imperial College Research Data Repository

A lightweight digital repository for data based on the concepts of collections of filesets. Both the collection and the fileset are assigned a DOI by the DataCite organisation which can be quoted in articles

ICM binary file Format

ICM binary file Format is used in databases pertaining to structural biology and protein families. This format can be used for the graphical representation of RNA, DNA, and proteins interactions.

MDL reaction Format

MDL reaction Format is used to describe the kinetics of chemical reactions and the chemical structure of the reactants and products.

Minimum Information about a Molecular Interaction Causal Statement

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines describe the minimum and necessary information to depict causal interactions in molecular biology, as well as contextual details. The aim is to homogenize the ...

BRIX generated O Format

"BRIX generated O Format" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://www.doe-mbi.ucla.edu/Software/o_man/node306.html. ...

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