Limits...
NEO: Systematic Non-Lattice Embedding of Ontologies for Comparing the Subsumption Relationship in SNOMED CT and in FMA Using MapReduce.

Zhu W, Zhang GQ, Tao S, Sun M, Cui L - AMIA Jt Summits Transl Sci Proc (2015)

Bottom Line: After identifying 8,428 equivalent concepts between the collection of over 30,000 concepts in Body Structure and the collection of over 83,000 concepts in FMA using UMLS equivalent concept mappings, 2,117 shared is-a relations and 5,715 mismatched relations were found.Among Body Structure's 90,465 non-lattice fragments, 65,968 (73%) contained one or more is-a relations that are in SNOMED CT but not in FMA, even though they have equivalent source and target concepts.This shows that SNOMED CT may be more liberal in classifying a relation as is-a, a potential explanation for the fragments not conforming to the lattice property.

View Article: PubMed Central - PubMed

Affiliation: Department of EECS, Case Western Reserve University, Cleveland, OH Division of Medical Informatics, Case Western Reserve University, Cleveland, OH.

ABSTRACT
A structural disparity of the subsumption relationship between FMA and SNOMED CT's Body Structure sub-hierarchy is that while the is-a relation in FMA has a tree structure, the corresponding relation in Body Structure is not even a lattice. This paper introduces a method called NEO, for non-lattice embedding of FMA fragments into the Body Structure sub-hierarchy to understand (1) this structural disparity, and (2) its potential utility in analyzing non-lattice fragments in SNOMED CT. NEO consists of four steps. First, transitive, upper- and down-closures are computed for FMA and SNOMED CT using MapReduce, a modern scalable distributed computing technique. Secondly, UMLS mappings between FMA and SNOMED CT concepts are used to identify equivalent concepts in non-lattice fragments from Body Structure. Then, non-lattice fragments in the Body Structure sub-hierarchy are extracted, and FMA concepts matching those in the non-lattice fragments are used as the seeds to generate the corresponding FMA fragments. Lastly, the corresponding FMA fragments are embedded to the non-lattice fragments for comparative visualization and analysis. After identifying 8,428 equivalent concepts between the collection of over 30,000 concepts in Body Structure and the collection of over 83,000 concepts in FMA using UMLS equivalent concept mappings, 2,117 shared is-a relations and 5,715 mismatched relations were found. Among Body Structure's 90,465 non-lattice fragments, 65,968 (73%) contained one or more is-a relations that are in SNOMED CT but not in FMA, even though they have equivalent source and target concepts. This shows that SNOMED CT may be more liberal in classifying a relation as is-a, a potential explanation for the fragments not conforming to the lattice property.

No MeSH data available.


A non-lattice fragment in SNOMED CT (solid lines) [10]. Adding the dashed node “Tissue specimen from trunk” and substituting the dashed edges for the solid edges to “Tissue specimen” would result in a lattice fragment.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4525277&req=5

f2-2092163: A non-lattice fragment in SNOMED CT (solid lines) [10]. Adding the dashed node “Tissue specimen from trunk” and substituting the dashed edges for the solid edges to “Tissue specimen” would result in a lattice fragment.

Mentions: The purpose of this paper is to provide a systematic study of such a structural disparity between FMA and SNOMED CT, motivated by the observation that the is-a relation in FMA has a tree structure, but the corresponding relation in SNOMED CT is not even a lattice (see Fig. 2 in Background). We introduce a method called NEO, Non-Lattice Embedding of Ontologies, for systematic structural embedding of FMA fragments into the Body Structure sub-hierarchy, to understand this structural disparity and its potential utility in analyzing non-lattice fragments (Fig. 2) in SNOMED CT.


NEO: Systematic Non-Lattice Embedding of Ontologies for Comparing the Subsumption Relationship in SNOMED CT and in FMA Using MapReduce.

Zhu W, Zhang GQ, Tao S, Sun M, Cui L - AMIA Jt Summits Transl Sci Proc (2015)

A non-lattice fragment in SNOMED CT (solid lines) [10]. Adding the dashed node “Tissue specimen from trunk” and substituting the dashed edges for the solid edges to “Tissue specimen” would result in a lattice fragment.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4525277&req=5

f2-2092163: A non-lattice fragment in SNOMED CT (solid lines) [10]. Adding the dashed node “Tissue specimen from trunk” and substituting the dashed edges for the solid edges to “Tissue specimen” would result in a lattice fragment.
Mentions: The purpose of this paper is to provide a systematic study of such a structural disparity between FMA and SNOMED CT, motivated by the observation that the is-a relation in FMA has a tree structure, but the corresponding relation in SNOMED CT is not even a lattice (see Fig. 2 in Background). We introduce a method called NEO, Non-Lattice Embedding of Ontologies, for systematic structural embedding of FMA fragments into the Body Structure sub-hierarchy, to understand this structural disparity and its potential utility in analyzing non-lattice fragments (Fig. 2) in SNOMED CT.

Bottom Line: After identifying 8,428 equivalent concepts between the collection of over 30,000 concepts in Body Structure and the collection of over 83,000 concepts in FMA using UMLS equivalent concept mappings, 2,117 shared is-a relations and 5,715 mismatched relations were found.Among Body Structure's 90,465 non-lattice fragments, 65,968 (73%) contained one or more is-a relations that are in SNOMED CT but not in FMA, even though they have equivalent source and target concepts.This shows that SNOMED CT may be more liberal in classifying a relation as is-a, a potential explanation for the fragments not conforming to the lattice property.

View Article: PubMed Central - PubMed

Affiliation: Department of EECS, Case Western Reserve University, Cleveland, OH Division of Medical Informatics, Case Western Reserve University, Cleveland, OH.

ABSTRACT
A structural disparity of the subsumption relationship between FMA and SNOMED CT's Body Structure sub-hierarchy is that while the is-a relation in FMA has a tree structure, the corresponding relation in Body Structure is not even a lattice. This paper introduces a method called NEO, for non-lattice embedding of FMA fragments into the Body Structure sub-hierarchy to understand (1) this structural disparity, and (2) its potential utility in analyzing non-lattice fragments in SNOMED CT. NEO consists of four steps. First, transitive, upper- and down-closures are computed for FMA and SNOMED CT using MapReduce, a modern scalable distributed computing technique. Secondly, UMLS mappings between FMA and SNOMED CT concepts are used to identify equivalent concepts in non-lattice fragments from Body Structure. Then, non-lattice fragments in the Body Structure sub-hierarchy are extracted, and FMA concepts matching those in the non-lattice fragments are used as the seeds to generate the corresponding FMA fragments. Lastly, the corresponding FMA fragments are embedded to the non-lattice fragments for comparative visualization and analysis. After identifying 8,428 equivalent concepts between the collection of over 30,000 concepts in Body Structure and the collection of over 83,000 concepts in FMA using UMLS equivalent concept mappings, 2,117 shared is-a relations and 5,715 mismatched relations were found. Among Body Structure's 90,465 non-lattice fragments, 65,968 (73%) contained one or more is-a relations that are in SNOMED CT but not in FMA, even though they have equivalent source and target concepts. This shows that SNOMED CT may be more liberal in classifying a relation as is-a, a potential explanation for the fragments not conforming to the lattice property.

No MeSH data available.