UMLS Concept and Relation Mapping

Mapping Open Resources to UMLS Concepts

The goal of mapping the annotations to ontologies is to extend the expressivity and richness of the SemRep annotations. An example is shown in Figure 1 below. The gray nodes connected by the inhibits, treats, and ISA edges illustrate three annotations provided by SemRep. All other nodes and edges are those that will be added to as a result of this project.

Figure 1. Mapping open resources and ontology identifiers to SemRep concept and relation annotations

The table below illustrates the mappings we intend to make between the UMLS resources we are including and ontologies. The second half of the table is specifically focused on the mappings between Semantic Network relations and ontologies. Information source. Please note that the mappings from the Semantic Network Relations to the OBO ontologies is still in progress.

Source	Mapping	Notes
CONCEPT ANNOTATIONS
Anatomical Therapeutic Chemical (ATC)	ChEBI, GO, UBERON	Using concept identifiers as well as creating mappings to external concept identifiers
DrugBank	ChEBI	Internally using concept identifiers to map to external identifiers
Gene Ontology (GO)	Sources included in dbxref mappings	Using concept identifiers
HUGO Gene Nomenclature Committee (HGNC)	Ensembl	Using concept identifiers as well as creating mappings to external concept identifiers
Human Phenotype Ontology (HPO)	Sources included in dbxref mappings	Using concept identifiers
The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9-CM)	DOID, HPO	Internally mapping to external concept identifiers
The International Classification of Diseases, Tenth Revision (ICD10)	ATC, ChEBI	Internally mapping to external concept identifiers. Will use mappings from the Jensen Lab
The International Classification of Diseases, Tenth Revision, Procedure Coding System (ICD10-PCS)	LOINC	Internally mapping to external concept identifiers
The Logical Observation Identifiers Names and Codes terminology (LOINC)	ATC, ChEBI, CL, CSSO, DOID, DRON, DINTO, GO, HPO, SYMP, UBERON	Using concept identifiers as well as creating mappings to external concept identifiers
NCBI Taxonomy	Sources included in dbxref mappings	Using concept identifiers
National Drug File - Reference Terminology	ATC, ChEBI	Internally mapping concept identifiers to external concept identifiers
Foundational Model of Anatomy (FMA)	UBERON	Internally mapping to external concept identifiers
The Healthcare Common Procedure Coding System (HCPCS)	LOINC	Internally mapping to external concept identifiers
Online Mendelian Inheritance in Man (OMIM)	DOID, HPO	Internally mapping concept identifiers to external concept identifiers
RELATION ANNOTATIONS (n= 68)
ISA	rdfs:subClassOf	Confident mapping
PART_OF	obo:BFO_0000050	Confident mapping to part of
PROCESS_OF	obo:BFO_0000066	Confident mapping to occurs in
TREATS	obo:RO_0002606; obo:RO_0002599	Confident mappings, but mappings must be made according to subject and object concept types. If subject is a chemical, then use is substance that treats. If subject is a procedure, then use capable of inhibiting or preventing pathological process
LOCATION_OF	obo:RO_0001015; obo:BFO_0000067	Confident mappings, but mappings must be made according to subject and object concept types. If subjects and objects are continuants, then use location of. If subject is a continuant and object is a occurrent, then use contains process
INTERACTS_WITH	obo:RO_0002434	Confident mapping to interacts with
PRECEDES	obo:BFO_0000063	Confident mapping to precedes
PREP	NONE	Not including this relation (n= 6 predications)
SPEC	NONE	Not including this relation (n= 1 predications)
NOM	NONE	Not including this relation (n= 2 predications)
258	NONE	Not including this relation (n= 1 predications)
394	NONE	Not including this relation (n= 1 predications)
240	NONE	Not including this relation (n= 1 predications)
1176	NONE	Not including this relation (n= 2 predications)

Acronyms:

• Anatomical Therapeutic Chemical (ATC);
  
• Cell Ontology (CL);
  
• Chemical Entities of Biological Interest (ChEBI);
  
• Clinical Signs and Symptoms Ontology (CSSO);
  
• Human Disease Ontology (DOID);
  
• Drug Ontology (DRON);
  
• Drug-Drug Interactions Ontology (DINTO);
  
• Gene Ontology (GO);
  
• Human Phenotype Ontology (HPO);
  
• Logical Observation Identifiers Names and Codes terminology (LOINC);
  
• Symptom Ontology (SYMP);
  
• Uber Anatomy Ontology (UBERON)