572 Biochemistry

Beta Cell Genomics Ontology

"Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies.

"Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies.

DrugBank

"The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8246 drug entries including 2012 FDA-approved small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries.

"The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8246 drug entries including 2012 FDA-approved small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries.

UniProtKB Keywords

"UniProtKB Keywords constitute a controlled vocabulary with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest. Keywords are classified in 10 categories: Biological process, Cellular component, Coding sequence diversity, Developmental stage, Disease, Domain, Ligand, Molecular function, Post-translational modification, Technical term. An entry often contains several keywords. Inside a category, the keywords are stored in alphabetical order.

"UniProtKB Keywords constitute a controlled vocabulary with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest. Keywords are classified in 10 categories: Biological process, Cellular component, Coding sequence diversity, Developmental stage, Disease, Domain, Ligand, Molecular function, Post-translational modification, Technical term. An entry often contains several keywords. Inside a category, the keywords are stored in alphabetical order.

Lipid Classification System

"The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own sublassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's (LM_ID) which reflects their position in the classification hierarchy."

"The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own sublassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's (LM_ID) which reflects their position in the classification hierarchy."

PANTHER Classification System

"The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. Proteins have been classified according to: Family and subfamily: families are groups of evolutionarily related proteins; subfamilies are related proteins that also have the same function. Molecular function: the function of the protein by itself or with directly interacting proteins at a biochemical level, e.g. a protein kinase.

Enzyme Nomenclature

"By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes.

"By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes.

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