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NCIEVS Metaphrase API

NCIEVS Metaphrase API. Presented to the National Cancer Institute (NCI) Kim Ong 12/07/2001. Outline. Architecture Documentation Introduction Some API Classes Sample Code. EVS. Architecture (RMI). Metaphrase Java API. Java Client. RMI Server. Relational to Object mapping. RMI.

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NCIEVS Metaphrase API

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  1. NCIEVS Metaphrase API Presented to the National Cancer Institute (NCI) Kim Ong 12/07/2001

  2. Outline • Architecture • Documentation • Introduction • Some API Classes • Sample Code

  3. EVS Architecture (RMI) Metaphrase Java API Java Client RMI Server Relational to Object mapping RMI cache Oracle Database

  4. Two Versions of APIs • Remote Method Invocation (RMI) • Component Object Model (COM)

  5. Documentation

  6. Documentation

  7. Documentation

  8. Documentation

  9. Introduction • Source • A version of a local or external authority, such as PDQ, SNOMED, ICD-9, or CPT. • Concept • A unit of thought, a semantic unit or ‘meaning’ in the thesaurus. • Atom • An occurrence of a name in a source, typically associated with a Partition with a code. • Term • A set of atoms which belong to the same Concept and the same lexical class (i.e., have the same LUI)

  10. Introduction • Partition • A collection of meanings identified in a Source. • Code • The string which name a partition in a source. • Relationship • A directional link between two concepts

  11. Introduction • CUI • Concept Unique Identifier • LUI • Lexical class Unique Identifier • Term Group • A subset of atoms in a source; e.g., preferred term (PT), synonym (SY), abbreviation (AB) . • Preferred Name • The preferred name for a concept • Semantic Type • A classification of concepts

  12. Thesaurus Structure Preferred name of a concept term associative relationship concept Hierarchical relationship atom Preferred form of a term Each concept is identified by CUI Each term is identified by LUI

  13. Example CUI: C0007114 Skin neoplasm malignant NOS (CTEP-DIS) Skin Neoplasms, Malignant (NCI) Malignant Skin Neoplasm (NCIPDQ) PT Preferred name Cancer of the Skin (NCIPDQ) Skin Cancer (NCIPDQ) Malignant Skin Tumor (NCIPDQ) Skin Cancer (NCI) Skin Cancer, Including Melanoma (DBS-CODE) MELANOMA AND NON-MELANOMA SKIN CANCER (DCTD-CD) Skin Cancers (NIH) Malignant Neoplasm of the Skin (NCIPDQ) Malignant Tumor of the Skin (NCIPDQ) SY

  14. Some Details • For every relationship, there is an inverse relationship also. • Relationships between two concepts can be specified by multiple sources (e.g. NCI, SNOMED). SNOMED NCI

  15. NCI DBS DCB OCC DBS-KEY DBS-CODE DCB-BC DCB-BC1 DCB-BC2 Some Details • A source can have multiple sub-sources

  16. Some API Classes

  17. Metaphrase Class • Enumeration matches(String, SearchSpec) • searches database for the input string returning a list of match objects within the specified limit. • Concept getConcept(java.lang.String conceptID) • returns the Concept with the given ID. • Enumeration getSources() • returns a list of Source objects. These are the sources contained in metathesaurus. SubSources are not included in this list. • Enumeration getConcepts(Source source) • returns a list of Concept objects that contain atoms from the specified source. Note: The above list does not describe all the available methods for this class

  18. Concept Class • Atom[] atoms() • all the atoms that are contained in this concept. • Atom[] atoms(Source source) • all the atoms from the specified source that are contained in this concept. • Definition[] definitions() • the definitions for this concept. • String conceptID() • the ID for this concept. • String preferredName() • the preferred name of this concept. • Relationship[] relationships() • the links between this concept and other concepts. • Source[] sources() • the sources that have an atom in this concept. • Term[] synonyms() • the terms that are synonyms for this concept (basically the terms that are not in the PT termgroup). Note: The first element of this list is also the preferred term. Note: The above list does not describe all the available methods for this class

  19. Atom Class • Concept concept() • the concept that the atom belongs to. • String name() • the name of the atom. • String termgp() • the term group to which the atom belongs. • Source source() • the source that specified this atom. Note: The above list does not describe all the available methods for this class

  20. Term Class • Concept concept() • the concept that contains this term. • String preferredForm() • the string representation of this term. Note: The above list does not describe all the available methods for this class

  21. Definition Class • String text() • the text of the definition. • Source source() • the source that specified this definition. Note: The above list does not describe all the available methods for this class

  22. Relationship Class • String rel() • the type of relationship: RN or CHD = narrow, RB or PAR = broader, RO or RL = related. • String rela() • more details pertaining to the relationship: e.g., ‘is part of’. • Concept concept1() • the first concept that is part of the relationship. • Concept concept2() • the second concept that is part of the relationship. • Source source() • the source that specified this relationship. Note: The above list does not describe all the available methods for this class

  23. Source Class • String description() • description of the source • String SAB() • an abbreviation that representes the source, e.g., NCI represents National Cancer Institute. • Subsource[] children() • the subsources of this source. Note: The above list does not describe all the available methods for this class

  24. Match Class • Atom matched() • the atom that matched the search string. • Atom preferred() • the preferred atom for the concept that contains the matched atom. • Concept concept() • the concept that contains the matched atom. • int score() • the match score. The higher the score the better the match. • Term matchedTerm() • the term that matched the search string. • Term preferredTerm() • the preferred term for the concept that contains the matched term. Note: The above list does not describe all the available methods for this class

  25. Sample Code

  26. Example • Connect to EVS metaphrase server • Perform Search for “Skin Cancer” and identify matched concepts • Get synonyms for each matched concept • Get relationships for each matched concept • Compile & Run

  27. Constructor RMIMetaphrase(String serverURL, String DBName, String userName, String passWord) Example try { metaphrase = new RMIMetaphrase("//"+"ncievs.nci.nih.gov"+"/RemoteMetaphrase", "NCI", "guest", "NCI-EVS"); } catch (MetaphraseException me) { } Step 1: Connect to EVS - Create an instance of RMIMetaphrase

  28. Methods Enumeration Metaphrase.matches(String s, SearchSpecspec) Atom Match.matched(); Atom Match.preferred() String Atom.name() Example try { SearchSpec spec = new SearchSpec(); spec.setLimit(10); String s = “Skin Cancer”; Enumeration matches = metaphrase.matches(s, spec); while (matches.hasMoreElements()) { Match match = (Match) matches.nextElement(); Term matched_Term = match.matchedTerm(); int score = match.score(); String matchAtom = matched_Term.preferredForm(); Concept concept = matched_Term.concept(); String CUI = concept.conceptID(); } catch (MetaphraseException me) { } Step 2: Perform Search - Use the matches function

  29. Methods Term[] Concept.synonyms() String Term.preferredForm() Example while (match.hasMoreElements()) { Concept concept = ((Match) match.nextElement()).concept(); try { Term[] syns = concept.synonyms(); for (int I=0;I<syns.length;I++) System.out.println(syns[I].preferredForm()); } catch (MetaphraseException me) { } } Step 3: Get Synonyms - Call on Concept.synonyms for each matched concept

  30. Methods Relationship[] Concept.relationships() String Relationship.rel(); Concept Relationship.concept1(); Example while (match.hasMoreElements()) { Concept concept = ((Match) match.nextElement()).concept(); try { Relationship[] rels = concept.relationships(); for (int I=0;I<rels.length;I++) System.out.println(rels[I].concept1().preferredName() + “ “ rels[I].rel() + “ “ + rels[I].concept2().preferredName()); } catch (MetaphraseException me) { } } Step 4: Get Relationships - Call on Concept.relationships for each matched concept

  31. Step 5: Compile & Run (RMI) Compile javac -deprecation -classpath %classpath%; c:\metaphrase\Metaphrase2.jar test.java Run java -classpath %classpath%; c:\metaphrase\Metaphrase2.jar test

  32. Step 5: Compile (COM) javac -deprecation -classpath %CLASSPATH%; c:\Metaphrase\commetaphrase.zip; c:\Metaphrase\xerces.jar; c:\Metaphrase\Tbv5vbjn.zip; c:\metaphrase\metaphrase2.jar; c:\jswdk-1.0.1\lib\servlet.jar test.java

  33. Step 5: Run (COM) if "%OS%" == "Windows_NT" setlocal set BASE=%1 set TERM=%2 jview -cp %BASE%commetaphrase.zip; %BASE%xerces.jar test pause

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