Section 1: Introduction to Core Concepts -- Introduction -- History of Terminology and Ontology -- Knowledge Representation and the Logical Basis of Ontology -- Theoretical Foundations of Terminology -- Terminology Requirements and Standards Development -- Terminology Design -- Maintenance -- Quality Control -- Section 2: Realist Ontology -- Realism Based Ontology -- What is an ontology? -- Ontology vs. terminology -- Ontology vs. taxonomy -- Ontologies and databases -- Ontology and the Semantic Web -- Ontology in biomedical informatics -- Bad ontologies -- The concept orientation -- Why ontologies so often fail -- Recipes for success -- Examples of successful ontologies and of how they are being used -- The place of Referent Tracking in Biomedical Informatics -- Introduction: what is Referent Tracking (RT)? How does it relate to ontology? What does it aim to achieve? Why does it matter? -- Basic principles: how RT is build on top of three important distinctions made in realism-basedontology: particulars types, continuants occurrents, referents references -- Syntax and semantics of RT-expressions -- RT as a development tool for ontologies -- Using RT to detect and prevent flaws in scientific research and ambiguities and inconsistencies in reports and papers -- RT as a solution for semantic interoperability -- Werner Ceusters -- Bioontology in Service of Translational Science -- Introduction to Bioontologies and the OBO Foundry -- The Gene Ontology -- Overview of GO Content and Structure -- GO annotation -- Term Enrichment/Pathway Analysis -- Success Stories -- Challenges -- Bioontologies and Data Annotation Systems -- ImmPort/HIPC -- Kidney Precision Medicine Project -- GEO and Array Express -- Disease and Phenotype Annotation for Translational Studies -- Use of Ontologies at Mouse Genome Informatics -- HPO and the Monarch Project -- Compositionality: An Implementation Guide -- Section 3: Terminologies and their Implementation -- Interface Terminologies -- SNOMED CT -- RxNorm andNDF-RT and ATC codes -- LOINC -- SOLOR -- ICD -- CPT -- HCC Codes / Risk Adjustment and MACRA / MIPS -- DRGs -- NCI EVS -- Nursing Terminologies -- RED / MED -- UMLS Metathesauras and knowledge sources -- Section 4: Terminology Services, APIs and Methods -- Terminological Systems -- HL7 FHIR and APIs -- Section 5: Summing it All Up -- Lessons Learned and Suggested Research Agenda -- The future of coding and coding systems -- Conclusion.