Pure Science

Comparative Data Analysis Ontology

"CDAO stands for "Comparative Data Analysis Ontology", a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science. In general, ontologies are designed to support formal or automated reasoning. Our aim in developing CDAO is to provide the language support for representing, and reasoning over, phylogenetic data and metadata.

Environment Ontology

"The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material." EnvO enables "a concise, standardised, and comprehensive description of environment that is key to the integration, archiving and federated searching of environmental data. As a tool for the life sciences, we see EnvO bringing benefits similar to those of the Gene Ontology (GO).

Chemical Entities of Biological Interest

"Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Ontology for Genetic Interval

"Using realistic ontology BFO as its top ontology's framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) that have a liner primary sequence sturcture. It is either a proper part of an chromosome or a RNA molecule or an artificial genetic interval."

Neurobehavior Ontology

"The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GO’s process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. NBO’s prime application is to provide the vocabulary that is required to integrate behavior observations within and across species.

Mobile Genetic Element Ontology

"MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME.
Please note that some terms in the ontology are there transiently as markers or awaiting future incorporation in the sequence ontology (SO). The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up."

A Classification of Mobile Genetic Elements

"ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. There are 122154 proteins found in 2326 MGEs. Total number of host is 811 (Version 0.4)."

"ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. There are 122154 proteins found in 2326 MGEs. Total number of host is 811 (Version 0.4)."

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