ncievs metaphrase api presented to the national cancer institute (nci) kim ong 12/07/2001

NCIEVS Metaphrase API

Presented to the National Cancer Institute (NCI)

Kim Ong

12/07/2001

Outline

• Architecture

• Documentation

• Introduction

• Some API Classes

• Sample Code

Architecture (RMI)

EVS

OracleDatabase

MetaphraseJavaAPIRelational

to Objectmapping

JavaClientRMI

RMIServer

cache

Two Versions of APIs

• Remote Method Invocation (RMI)

• Component Object Model (COM)

Documentation

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)

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

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

Thesaurus Structure

concept

term

atom

Preferred nameof a concept

Preferred formof a term

Hierarchicalrelationship

associativerelationship

Each concept is identified by CUIEach term is identified by LUI

Example

CUI: C0007114

Skin neoplasm malignant NOS (CTEP-DIS)Skin Neoplasms, Malignant (NCI)Malignant Skin Neoplasm (NCIPDQ)

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)

PT

SY

Preferredname

Some Details

NCI SNOMED

• For every relationship, there is an inverse relationship also.

• Relationships between two concepts can be specified by multiple sources (e.g. NCI, SNOMED).

Some Details

NCI

DBS DCB OCC

DBS-KEY DBS-CODE DCB-BC

DCB-BC2DCB-BC1

• A source can have multiple sub-sources

Some API Classes

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

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.


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.


Term Class• Concept concept()

– the concept that contains this term.

• String preferredForm()– the string representation of this term.


Definition Class• String text()

– the text of the definition.

• Source source()– the source that specified this definition.


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.


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.


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.


Sample Code

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

Step 1: Connect to EVS

- Create an instance of RMIMetaphrase

RMIMetaphrase(String serverURL, String DBName, String userName, String passWord)

Constructor

try { metaphrase = new RMIMetaphrase("//"+"ncievs.nci.nih.gov"+"/RemoteMetaphrase", "NCI", "guest", "NCI-EVS");} catch (MetaphraseException me) { }

Example

Step 2: Perform Search- Use the matches function

Enumeration Metaphrase.matches(String s, SearchSpec spec)Atom Match.matched(); Atom Match.preferred()String Atom.name()

Methods

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) { }

Example

Step 3: Get Synonyms

- Call on Concept.synonyms for each matched concept

Term[] Concept.synonyms()String Term.preferredForm()

Methods

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) { }}

Example

Step 4: Get Relationships

- Call on Concept.relationships for each matched concept

Relationship[] Concept.relationships()String Relationship.rel(); Concept Relationship.concept1();

Methods

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) { }}

Example

Step 5: Compile & Run (RMI)

javac -deprecation -classpath %classpath%;c:\metaphrase\Metaphrase2.jar test.java

Compile

java -classpath %classpath%;c:\metaphrase\Metaphrase2.jar test

Run

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

Step 5: Run (COM)

if "%OS%" == "Windows_NT" setlocalset BASE=%1set TERM=%2

jview -cp %BASE%commetaphrase.zip;%BASE%xerces.jar testpause

ncievs metaphrase api presented to the national cancer institute (nci) kim ong 12/07/2001

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