Tag: molecular entity

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 ...

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 ...

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 ...

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 ...

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.

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-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 ...

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

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 ...

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.

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

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 ...

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 ...

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 ...

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 ...

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 ...

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

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. ...

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 ...

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 ...

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.

The BioModels Ontology is an OWL Representation of the models in the BioModels repository. This resource has not been updated recently within BioPortal, and no official homepage can be found, therefore we have marked its status as Uncertain. Please g ...

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

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 ...

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 ...

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 ...

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 ...

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 ...

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

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

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

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" 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. ...