The PHENIO Knowledge Graph provides the ontological backbone of the Monarch Knowledge Graph. It transforms the PHENIO (Phenomics Integrated Ontology) application ontology -- a curated integration of ontologies spanning phenotypes, anatomy, disease, and molecular biology -- into Biolink-compliant knowledge graph format with cross-species phenotype mappings from uPheno.
PHENIO integrates ontologies needed for cross-species phenotype comparison and analysis. See the PHENIO composition docs for detailed descriptions of each included ontology.
Phenotype terms from species-specific and cross-species phenotype ontologies. This is the largest category in the graph, reflecting PHENIO's primary purpose of enabling cross-species phenotype comparison.
- uPheno — Unified Phenotype Ontology (cross-species phenotype classes)
- HP — Human Phenotype Ontology
- MP — Mammalian Phenotype Ontology
- ZP — Zebrafish Phenotype Ontology
- XPO — Xenopus Phenotype Ontology
- WBPhenotype — C. elegans Phenotype Ontology
- FYPO — Fission Yeast Phenotype Ontology
- DDPHENO — Dictyostelium Phenotype Ontology
- DPO — Drosophila Phenotype Ontology
- OBA — Ontology of Biological Attributes
Anatomical structures from species-specific and cross-species anatomy ontologies, used as building blocks for phenotype definitions and expression data.
- UBERON — Integrated Cross-Species Anatomy Ontology
- FBbt — Drosophila Anatomy Ontology
- ZFA — Zebrafish Anatomy and Development Ontology
- EMAPA — Mouse Developmental Anatomy Ontology
- WBbt — C. elegans Gross Anatomy Ontology
- XAO — Xenopus Anatomy Ontology
- CL — Cell Ontology
- DDANAT — Dictyostelium Anatomy Ontology
Disease classification providing the disease hierarchy and disease-phenotype relationships used throughout the Monarch KG.
Medical actions and interventions from the Medical Action Ontology.
- MAXO — Medical Action Ontology
Gene Ontology terms representing biological processes, molecular functions, and cellular components.
- GO — Gene Ontology
Chemical entities relevant to phenotype and disease biology.
- CHEBI — Chemical Entities of Biological Interest
Gene identifiers used for disease-gene relationships within ontological axioms.
Taxonomy terms for the model organism species represented in the phenotype ontologies.
- NCBITaxon (slim) — NCBI Taxonomy
Developmental stage terms used to contextualize phenotype and expression data.
- HsapDv — Human Developmental Stages
- ZFS — Zebrafish Stage Ontology
- WBls — C. elegans Life Stages
- FBdv — Drosophila Developmental Stages
| Predicate | Description |
|---|---|
biolink:subclass_of |
Ontological hierarchy (is-a relationships) |
biolink:related_to |
Cross-ontology relationships derived from OWL axioms (part_of, has_part, develops_from, etc.) |
biolink:same_as |
Cross-species phenotype equivalences from uPheno SSSOM mappings |
biolink:has_phenotype |
Disease-to-phenotype associations from MONDO axioms |
biolink:disease_has_location |
Disease anatomical location from MONDO axioms |
PHENIO includes bridge axioms and mapping sets that enable cross-species inference:
- uPHENO bridge axioms — link species-specific phenotype ontologies to cross-species uPHENO classes
- uPHENO alignment axioms — integrate phenotype ontologies across species
- SSSOM mapping sets — standardized term mappings from Uberon (anatomy), CL (cell types), and uPHENO-OBA (phenotype-attribute)
These ontologies provide relational structure, quality descriptors, and upper-level categories rather than contributing primary nodes:
- BFO — Basic Formal Ontology (upper-level categories)
- RO — Relations Ontology (relationship types)
- PATO — Phenotypic Quality Ontology (qualities used in phenotype definitions)
- ECO — Evidence and Conclusion Ontology
- NBO — Neuro Behavior Ontology
- SO — Sequence Ontology (sequence features and attributes)
- Monochrom — Chromosome Ontology
- BSPO — Biological Spatial Ontology (spatial relationships)
- PR — Protein Ontology (slim)
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