Method and system for text understanding in an ontology driven platform
Embodiments of methods and systems for informatics systems are disclosed. Such informatics systems may utilize a unifying format to represent text to facilitate linking between data from the text and one or more ontologies, and the commensurate ability to mine such data.
1. A system, comprising:
an informatics system coupled to one or more data sources, the informatics system comprising a processor and a non-transitory computer readable medium comprising instructions for:
receiving a clinical text as input from a data source;
creating a parse graph of the input, wherein creating the parse graph comprises parsing the input to create the parse graph by segmenting the input into a set of evidence spaces based on one or more identifiers within the input, ordering the set of evidence spaces, and chunking each of the set of evidence spaces into one or more chunks, each chunk comprising a permutation of tokens of the evidence space within a distance of one another in the evidence space;
obtaining a graph representation of a domain ontology, wherein the domain ontology comprises a set of concepts and a set of relationships; and
mapping the parse graph to the graph representation of the domain ontology to create a unified graph comprising the graph representation of the input and the graph of the domain ontology, wherein mapping the parse graph to the graph representation of the domain ontology comprises matching a set of concepts represented by the parse graph to one or more of the set of concepts of the domain ontology.
2. The system of claim 1 , wherein the input is parsed based on a graph representation of a syntax ontology and the syntax ontology comprises the one or more identifiers.
3. The system of claim 1 , wherein the distance is five plus or minus two.
4. The system of claim 1 , wherein the instructions are further for:
constructing a query based on at least one of the set of concepts or at least one of the set of relationships of the domain ontology; and
searching the unified graph based on the query to obtain data of the input associated with the at least one concept or the at least one relationship.
5. A method, comprising:
receiving a clinical text as input from a data source;
creating a parse graph of the input, wherein creating the parse graph comprises parsing the input to create the parse graph by segmenting the input into a set of evidence spaces based on one or more identifiers within the input;
obtaining a graph representation of a domain ontology, wherein the domain ontology comprises a set of concepts and a set of relationships; and
mapping the parse graph to the graph representation of the domain ontology to create a unified graph comprising the graph representation of the input and the graph of the domain ontology;
creating a parse graph of the input, wherein creating the parse graph comprises parsing the input to create the parse graph by segmenting the input into a set of evidence spaces based on one or more identifiers within the input, ordering the set of evidence spaces, and chunking each of the set of evidence spaces into one or more chunks, each chunk comprising a permutation of tokens of the evidence space within a distance of one another in the evidence space;
obtaining a graph representation of a domain ontology, wherein the domain ontology comprises a set of concepts and a set of relationships; and
mapping the parse graph to the graph representation of the domain ontology to create a unified graph comprising the graph representation of the input and the graph of the domain ontology, wherein mapping the parse graph to the graph representation of the domain ontology comprises matching a set of concepts represented by the parse graph to one or more of the set of concepts of the domain ontology.
6. The method of claim 5 , wherein the input is parsed based on a graph representation of a syntax ontology and the syntax ontology comprises the one or more identifiers.
7. The method of claim 5 , wherein the distance is five plus or minus two.
8. The method of claim 5 , further comprising:
constructing a query based on at least one of the set of concepts or at least one of the set of relationships of the domain ontology; and
searching the unified graph based on the query to obtain data of the input associated with the at least one concept or the at least one relationship.
9. A non-transitory computer readable medium comprising instructions for:
receiving a clinical text as input from a data source;
creating a parse graph of the input, wherein creating the parse graph comprises parsing the input to create the parse graph by segmenting the input into a set of evidence spaces based on one or more identifiers within the input, ordering the set of evidence spaces, and chunking each of the set of evidence spaces into one or more chunks, each chunk comprising a permutation of tokens of the evidence space within a distance of one another in the evidence space;
obtaining a graph representation of a domain ontology, wherein the domain ontology comprises a set of concepts and a set of relationships; and
mapping the parse graph to the graph representation of the domain ontology to create a unified graph comprising the graph representation of the input and the graph of the domain ontology, wherein mapping the parse graph to the graph representation of the domain ontology comprises matching a set of concepts represented by the parse graph to one or more of the set of concepts of the domain ontology.
10. The computer readable medium of claim 9 , wherein the input is parsed based on a graph representation of a syntax ontology and the syntax ontology comprises the one or more identifiers.
11. The computer readable medium of claim 9 , wherein the distance is five plus or minus two.
12. The computer readable medium of claim 9 , wherein the instructions are further for:
constructing a query based on at least one of the set of concepts or at least one of the set of relationships of the domain ontology; and
searching the unified graph based on the query to obtain data of the input associated with the at least one concept or the at least one relationship.