Introduction of Toxin Ontology (TO)
What is Toxin Ontology (TO)?
Toxin Ontology project provides classification and controlled vocabulary to describe toxin function and attributes in any organism. It contains four term spaces (Category, Bio-activity, Symptom and Target) and more than 700 distinct terms. All of toxins in ATDB are annotated by more than 7000 term matches manually. The OBO file of TO definition can be downloaded from here.
About term spaces
Liking Gene Ontology (GO) which has three term spaces to handle different perspectives of gene function, Toxin Ontology (TO) contains four term spaces for answering distinct biological questions about toxin: What is the classification of the toxin? (Category); what is the biological activity of toxin taking effect (Activity); what organism, cell, molecules does the toxin interact with (Target); what is the symptom of toxin injuring (Symptom). Users can access the four term spaces via user-friend view in the website.
Outline
Category term space handles the issue of toxin classification including two top branches: functional categories and species categories. The first one is common classification system for function across species. The later one follows species classification firstly and then structure or functional characters, which are accepted by related community.
Activity term space cover most of ways toxin take 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. These effects were divided into two parts: local/regional effects and systemical effects. The other is Physiological model symptom which records the symptom of certain physiological preparation (such as nerve-muscle preparation) induced by toxins.
Future works
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 need you suggestions. You can contact us via the email: hqyone@hotmail.com
