Introduction of ATDB 2.0 Ontology System
ATDB 2.0 Ontology System
ATDB 2.0 Ontology System includes two ontologies, Toxin Ontology (TO) and Ion Channel Ontology (IO), to classify and annotate toxins and ion channel respectively. Each ontology contains 3 layers in architecture: Vocabulary, Name space and Ontology. Vocabularies are the basic elements of the ontology system defining certain properties of molecules, which are linked hierarchically by two type relationships: 'is' and 'contains'. Name spaces are top branches of Ontology. Each of them contains a tree of hierarchic terms and usually was designed to answer a certain biological question. Most of toxins and ion channels in ATDB are mapped to the TO and IO system. User can browse annotation information via tree views for name spaces. The OBO file of TO definition can be downloaded from here.
Toxin Ontology (TO)
Toxin ontology is a special ontology for annotation toxin molecule. It was constructed by four parts: Category, Pathogenesis, Target and Symptom, for answering distinct biological questions about toxin molecular: I) what is the category of the toxin(s)? (Category); II) what is the biological mechanism of the toxin(s) (Pathogenesis); III) what is the target of the toxin(s) (Target); IV) what are the symptoms induced by toxin(s) (Symptom). In last version, 3820 toxin sequences have been annotated with 14069 annotation information by manually in ATDB 2.0. The OBO file of definition can be downloaded from here.
Category term space handles the issue of toxin classification including eight top branches: functional categories and species categories. The first one is common classification system for function across species. The second one follows species classification firstly and then structure or functional characters, which are accepted by related community.
Pathogenesis term space covers most ways toxin takes effect, such as Cytolysis, Membrane interaction, Channel transport regulation, Vesicle transport regulation.
Target term space has three branches to describe the targets of toxin. Organism mentions the species or tissues affected by toxin. A toxin has the Mammal term (TX:0000075) means the toxin has some affection to mammals. The branch inherited from the Cell term describes the type of the cell and organelles affected by toxin. Ligand contains a detailed classification of the molecules which intact with toxins such as Enzyme, GPCR or ion channels.
Symptom term space has two branches. The first one (individual symptom) describes the symptoms appeared in an animal individuals. The other is Physiological model symptom which records the symptom of certain physiological preparation (such as nerve-muscle preparation) induced by toxins.
Ion channel ontology (IO)
Ion channel ontology is a special ontology for annotation ion channel molecular. It has constructed by six parts: Classification, Activity Site, Pharmacological, Physiological, Stimulation and Distribution, for answering distinct biological questions about ion channel molecular. I) what is the category of ion channel? (Classification); II) what are the active sites of channel? (Activity Site); III) what is the pharmacology function of ion channel? (Pharmacology); IV) what is the normal physiological function of ion channels? (Physiology); V) what is the environment/stimulation when ion channel has been activated or inactivated in vivo? (Stimulation); VI) what is the tissue specificity of ion channels? (Distribution). In the last version, 1252 channel sequences have been annotated with 7972 annotation information by manually in ATDB 2.0.
Classification term space handles the issue of ion channel classification including five top branches: Epithelial Na+ channel, G protein-coupled receptor, Ligand-gated Ion channel, Mechanosensitive ion channel and Voltage-gated Ion channel, as a common classification system for function across species.
Activity Site term space covers common integrate site of ion channel which include: Block gate range, Domain, Key residue, Voltage-sensitivity range.
Pharmacology Function term space has five branches (Disease, Drug site, Potential using, System Effect and Treatment) to describe the property in pharmacology.
Physiological Function term space has 27 status of ion channel which include normal and un-normal status in physiology.
Stimulation term space has five branches (Activation, Activators, Gating inhibitors, Inactivation and Inhibitors) to describe the the environment/stimulation in vivo..
Distribution term space has three branches (Knub, Nerve system, Organisestatus) to describe the distribution of ion channel in vivo.
As the function and characters of toxins are rather heterogeneous, how to balance the compactness and integrality is a very hard problem. We are interested in knowing what term should be included in the next version and we need you suggestions. You can contact us via email: firstname.lastname@example.org