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.


Merged graph after embedding the corresponding FMA fragment to a non-lattice fragment in SNOMED CT’s Body Structure.
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f4-2092163: Merged graph after embedding the corresponding FMA fragment to a non-lattice fragment in SNOMED CT’s Body Structure.

Mentions: Given a non-lattice fragment in SNOMED CT’s Body Structure, the corresponding FMA fragment is embedded to the non-lattice fragment to visualize and compare the structures of the two fragments. For the embedding (or merging) of the two fragments, we not only need the matched concepts from both fragments, but also the matching relations. When mapping the relations, we distinguish matched “is-a” and mismatched “is-a” relation. A matched “is-a” relation is one that is in both SNOMED CT and FMA. A mismatched “is-a” relation is one that is in SNOMED CT but not in FMA (which could be relations other than “is-a”). Then, we merge the two fragments (both concepts and relations) together and render them using topological sort, a well-known rendering algorithm for directed acyclic graph. The rendering of the merged fragments is implemented using the svg (scalable vector graphics) drawing library D3 (http://www.d3js.org) (see Fig. 4 for an example of the merged fragments).


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)

Merged graph after embedding the corresponding FMA fragment to a non-lattice fragment in SNOMED CT’s Body Structure.
© Copyright Policy
Related In: Results  -  Collection

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

f4-2092163: Merged graph after embedding the corresponding FMA fragment to a non-lattice fragment in SNOMED CT’s Body Structure.
Mentions: Given a non-lattice fragment in SNOMED CT’s Body Structure, the corresponding FMA fragment is embedded to the non-lattice fragment to visualize and compare the structures of the two fragments. For the embedding (or merging) of the two fragments, we not only need the matched concepts from both fragments, but also the matching relations. When mapping the relations, we distinguish matched “is-a” and mismatched “is-a” relation. A matched “is-a” relation is one that is in both SNOMED CT and FMA. A mismatched “is-a” relation is one that is in SNOMED CT but not in FMA (which could be relations other than “is-a”). Then, we merge the two fragments (both concepts and relations) together and render them using topological sort, a well-known rendering algorithm for directed acyclic graph. The rendering of the merged fragments is implemented using the svg (scalable vector graphics) drawing library D3 (http://www.d3js.org) (see Fig. 4 for an example of the merged fragments).

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.