The Cyc system has a large knowledge base with detailed knowledge about its concepts. Cyc has axioms and rules for common-sense real-world knowledge embedded in a large taxonomy covering everything. This is used with Cyc’s logical inference engine to cover medical subject matter in conceptual depth with machine-usable semantics. Cyc’s semantic definitions of relationships are more detailed than those in other systems. For gross anatomy we described the spatial positions, orientations, and functions of, as well as relationships between, bones, muscles, vessels, nerves, organs, etc. Cyc knows which junctions of vessels are distal to which others, which organs are directly served, etc. Several general Knowledge Representation and ontology issues arose while we described human gross anatomy to Cyc including: logical representation of prototypical relations, connections, and alignments; composite informative names versus opaque name-tokens; abstract versus concrete series; body regions and anatomical directions; non-exact mappings to external standard terms; directness of functional service by vessels; body systems versus locations in the body; specialized prototypes; and the veterinary organ taxonomy problem.