Like Gene Ontology (GO), biomedical ontology such as phenotype ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Biomedical ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
- Worm Phenotype (WP) Ontology WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology Based on YP which is the major contributor to the ‘Ascomycete phenotype ontology’, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Xenopus Anatomy (XA) Ontology XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- UniProtKB KeyWords (KW) Ontology Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- CTD Diseases (CD) Ontology CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
- CTD Chemicals (CC) Ontology CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).
DO Hierarchy (disease ontology from University of Maryland)
WP Hierarchy (worm phenotype from Wormbase Release WS226)
YP Hierarchy (yeast phenotype from Ascomycete phenotype ontology)
XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)
KW Hierarchy (Keywords from UniProtKB)
CD Hierarchy (CTD diseases from Comparative Toxicogenomics Database)
CC Hierarchy (CTD chemicals from Comparative Toxicogenomics Database)
1. DO Hierarchy (disease ontology from University of Maryland)
4. WP Hierarchy (worm phenotype from Wormbase Release WS226)
5. YP Hierarchy (yeast phenotype from Ascomycete phenotype ontology)
9. XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)
13. KW Hierarchy (Keywords from UniProtKB)
15. CD Hierarchy (CTD diseases from Comparative Toxicogenomics Database)
16. CC Hierarchy (CTD chemicals from Comparative Toxicogenomics Database)