Symbolic Methods

These notes are for BINF 4003 - Methods III: Symbolic Methods, taught in the Fall of 2020 at Columbia University.

Overview

  1. Introduction: What are symbolic methods? Data-Information-Knowledge hierarchy, interoperability, “curly braces problem”.

  2. Knowledge representation: Medical knowledge representations, closed vs open world assumptions, reference vs interface terminologies, pre- vs post-coordination.

  3. Desiderata for medical vocabularies: Characteristics of high-quality controlled medical vocabularies.

Specific terminologies and tools

  1. ICD: Design, structure, limitations, adoption, versions: ICD-9, ICD-10, clinical modification.

  2. SNOMED: Design, structure, limitations, adoption, SNOMED clinical terms (SNOMED CT).

  3. RxNorm: Design, structure, data sources, use cases. RxNorm vs RxTerm.

  4. LOINC: Design, purpose, structure

  5. HPO: Human Phenotype Ontology

  6. UMLS: Three knowledge sources: Metathesaurus, Semantic Network, SPECIALIST Lexicon and Lexical Tools. Purpose, data sources, use cases.

  7. Concept mapping: MetaMap, Usagi, BioAnnotator

Symbolic Methods - Michael Zietz