Added: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java?rev=1881995&view=auto ============================================================================== --- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java (added) +++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java Fri Sep 25 01:04:47 2020 @@ -0,0 +1,310 @@ +package org.apache.ctakes.gui.dictionary.cased.umls; + + +import org.apache.ctakes.core.util.StringUtil; +import org.apache.ctakes.core.util.annotation.SemanticTui; +import org.apache.ctakes.core.util.log.DotLogger; +import org.apache.ctakes.gui.dictionary.cased.Ranks; +import org.apache.ctakes.gui.dictionary.cased.term.CuiTerm; +import org.apache.ctakes.gui.dictionary.cased.umls.file.MrConso; +import org.apache.ctakes.gui.dictionary.cased.umls.file.Tty; +import org.apache.ctakes.gui.dictionary.umls.CuiCodeUtil; +import org.apache.log4j.Logger; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.util.*; +import java.util.stream.Collectors; + +import static org.apache.ctakes.gui.dictionary.cased.umls.file.MrConso.*; + +/** + * @author SPF , chip-nlp + * @version %I% + * @since 8/26/2020 + */ +public class UmlsParser { + + static private final Logger LOGGER = Logger.getLogger( "UmlsParser" ); + + + static public Collection<CuiTerm> createCuiTerms( final String consoPath, + final String styPath, + final String rankPath, + final Collection<SemanticTui> wantedTuis, + final Collection<String> wantedVocabularies, + final Collection<Tty> wantedTermTypes, + final Collection<String> wantedLanguages, + final Collection<String> writtenSchema ) { +// final Collection<Long> wantedCuis = getWantedCuis( styPath, wantedTuis ); + final Map<Long, Collection<SemanticTui>> wantedCuis = getWantedCuis( styPath, wantedTuis ); + if ( wantedCuis.isEmpty() ) { + return Collections.emptyList(); + } + final Map<Long, CuiTerm> cuiTerms + = buildTerms( consoPath, wantedCuis, wantedVocabularies, wantedTermTypes, wantedLanguages, writtenSchema ); + if ( cuiTerms.isEmpty() ) { + return Collections.emptyList(); + } + addTuis( cuiTerms, styPath, wantedTuis ); + + populateRanks( rankPath, wantedVocabularies, wantedTermTypes ); + + return cuiTerms.values(); + } + +// static private Collection<Long> getWantedCuis( final String styPath, +// final Collection<SemanticTui> wantedTuis ) { +// LOGGER.info( "Building valid CUI collection based upon TUIs in " + styPath ); +// final Collection<Long> wantedCuis = new HashSet<>(); +// try ( final BufferedReader reader = new BufferedReader( new FileReader( styPath ) ); +// DotLogger logger = new DotLogger() ) { +// String line = reader.readLine(); +// while ( line != null ) { +// final String[] columns = StringUtil.fastSplit( line, '|' ); +// final SemanticTui semanticTui = SemanticTui.getTuiFromCode( columns[ 1 ] ); +// if ( wantedTuis.contains( semanticTui ) ) { +// wantedCuis.add( CuiCodeUtil.getInstance().getCuiCode( columns[ 0 ] ) ); +// } +// line = reader.readLine(); +// } +// } catch ( IOException ioE ) { +// LOGGER.error( ioE.getMessage() ); +// } +// return wantedCuis; +// } + + static private Map<Long, Collection<SemanticTui>> getWantedCuis( final String styPath, + final Collection<SemanticTui> wantedTuis ) { + LOGGER.info( "Building valid CUI collection based upon TUIs in " + styPath ); + final Map<Long, Collection<SemanticTui>> wantedCuis = new HashMap<>(); + try ( final BufferedReader reader = new BufferedReader( new FileReader( styPath ) ); + DotLogger logger = new DotLogger() ) { + String line = reader.readLine(); + while ( line != null ) { + final String[] columns = StringUtil.fastSplit( line, '|' ); + final SemanticTui semanticTui = SemanticTui.getTuiFromCode( columns[ 1 ] ); + if ( wantedTuis.contains( semanticTui ) ) { + wantedCuis.computeIfAbsent( CuiCodeUtil.getInstance().getCuiCode( columns[ 0 ] ), + c -> EnumSet.noneOf( SemanticTui.class ) ) + .add( semanticTui ); + } + line = reader.readLine(); + } + } catch ( IOException ioE ) { + LOGGER.error( ioE.getMessage() ); + } + return wantedCuis; + } + + +// static private Map<Long,CuiTerm> buildTerms( final String consoPath, +// final Collection<Long> wantedCuis, +// final Collection<String> wantedVocabularies, +// final Collection<Tty> wantedTermTypes, +// final Collection<String> wantedLanguages, +// final Collection<String> writtenSchema ) { +// LOGGER.info( "Creating Terms from " + consoPath ); +// final Collection<String> wantedTextTypes = wantedTermTypes.stream().map( Tty::name ).collect( Collectors.toSet() ); +// +// final Map<Long, CuiTerm> cuiTerms = new HashMap<>(); +// +// try ( final BufferedReader reader = new BufferedReader( new FileReader( consoPath ) ); +// DotLogger logger = new DotLogger() ) { +// String line = reader.readLine(); +// while ( line != null ) { +// final String[] columns = StringUtil.fastSplit( line, '|' ); +// if ( !wantedTextTypes.contains( getMrConso( columns, TTY ) ) +// || !wantedVocabularies.contains( getMrConso( columns, SAB ) ) +// || !wantedLanguages.contains( getMrConso( columns, LAT ) ) ) { +// line = reader.readLine(); +// continue; +// } +// final String text = getMrConso( columns, STR ); +// if ( hasSpecialChars( text ) ) { +// line = reader.readLine(); +// continue; +// } +// final String cui = getMrConso( columns, CUI ); +// final long cuiCode = CuiCodeUtil.getInstance().getCuiCode( cui ); +// if ( wantedCuis.contains( cuiCode ) ) { +// final CuiTerm term +// = cuiTerms.computeIfAbsent( cuiCode, CuiTerm::new ); +// final String vocabulary = getMrConso( columns, SAB ); +// term.addSynonym( text, +// vocabulary, +// getMrConso( columns, TS ), +// getMrConso( columns, STT ), +// getMrConso( columns, TTY ) ); +// if ( writtenSchema.contains( vocabulary ) ) { +// term.addSchemaCode( vocabulary, getMrConso( columns, CODE ) ); +// } +// } +// line = reader.readLine(); +// } +// } catch ( IOException ioE ) { +// LOGGER.info( ioE.getMessage() ); +// } +// LOGGER.info( "Terms: " + cuiTerms.size() ); +// return cuiTerms; +// } + + static private Map<Long, CuiTerm> buildTerms( final String consoPath, + final Map<Long, Collection<SemanticTui>> wantedCuis, + final Collection<String> wantedVocabularies, + final Collection<Tty> wantedTermTypes, + final Collection<String> wantedLanguages, + final Collection<String> writtenSchema ) { + LOGGER.info( "Creating Terms from " + consoPath ); + final Collection<String> wantedTextTypes = wantedTermTypes.stream() + .map( Tty::name ) + .collect( Collectors.toSet() ); + + final Map<Long, CuiTerm> cuiTerms = new HashMap<>(); + + try ( final BufferedReader reader = new BufferedReader( new FileReader( consoPath ) ); + DotLogger logger = new DotLogger() ) { + String line = reader.readLine(); + while ( line != null ) { + final String[] columns = StringUtil.fastSplit( line, '|' ); + if ( !wantedTextTypes.contains( getMrConso( columns, TTY ) ) + || !wantedVocabularies.contains( getMrConso( columns, SAB ) ) + || !wantedLanguages.contains( getMrConso( columns, LAT ) ) ) { + line = reader.readLine(); + continue; + } + final String text = getMrConso( columns, STR ); + if ( hasSpecialChars( text ) ) { + line = reader.readLine(); + continue; + } + final String cui = getMrConso( columns, CUI ); + final long cuiCode = CuiCodeUtil.getInstance().getCuiCode( cui ); + final Collection<SemanticTui> tuis = wantedCuis.get( cuiCode ); + if ( tuis != null ) { + final CuiTerm term + = cuiTerms.computeIfAbsent( cuiCode, CuiTerm::new ); + final String vocabulary = getMrConso( columns, SAB ); + term.addSynonym( text, + vocabulary, + tuis, + getMrConso( columns, TS ), + getMrConso( columns, STT ), + getMrConso( columns, TTY ) ); + if ( writtenSchema.contains( vocabulary ) ) { + term.addSchemaCode( vocabulary, getMrConso( columns, CODE ) ); + } + } + line = reader.readLine(); + } + } catch ( IOException ioE ) { + LOGGER.info( ioE.getMessage() ); + } + LOGGER.info( "Terms: " + cuiTerms.size() ); + return cuiTerms; + } + + + static private String getMrConso( final String[] columns, + final MrConso conso ) { + return columns[ conso.ordinal() ]; + } + + static private boolean hasSpecialChars( final String text ) { + // strips off all non-ASCII characters + String txt = text.replaceAll( "[^\\x00-\\x7F]", "" ); + // erases all the ASCII control characters + txt = txt.replaceAll( "[\\p{Cntrl}&&[^\r\n\t]]", "" ); + // removes non-printable characters from Unicode + txt = txt.replaceAll( "\\p{C}", "" ); + return !text.equals( txt ); + } + + + static private void addTuis( final Map<Long, CuiTerm> cuiTerms, + final String styPath, + final Collection<SemanticTui> wantedTuis ) { + LOGGER.info( "Adding TUIs to Terms " + styPath ); + try ( final BufferedReader reader = new BufferedReader( new FileReader( styPath ) ); + DotLogger logger = new DotLogger() ) { + String line = reader.readLine(); + while ( line != null ) { + final String[] columns = StringUtil.fastSplit( line, '|' ); + final SemanticTui semanticTui = SemanticTui.getTuiFromCode( columns[ 1 ] ); + if ( wantedTuis.contains( semanticTui ) ) { + final CuiTerm cuiTerm = cuiTerms.get( CuiCodeUtil.getInstance().getCuiCode( columns[ 0 ] ) ); + if ( cuiTerm != null ) { + cuiTerm.addTui( semanticTui ); + } + } + line = reader.readLine(); + } + } catch ( IOException ioE ) { + LOGGER.error( ioE.getMessage() ); + } + } + + static private void populateRanks( final String rankPath, + final Collection<String> wantedVocabularies, + final Collection<Tty> wantedTextTypes ) { + LOGGER.info( "Ranking Vocabulary Text Types from " + rankPath ); + try ( final BufferedReader reader = new BufferedReader( new FileReader( rankPath ) ); + DotLogger logger = new DotLogger() ) { + String line = reader.readLine(); + while ( line != null ) { + final String[] columns = StringUtil.fastSplit( line, '|' ); + final Tty tty = Tty.getType( columns[ 2 ] ); + if ( wantedVocabularies.contains( columns[ 1 ] ) && wantedTextTypes.contains( tty ) ) { + try { + final int rank = Integer.parseInt( columns[ 0 ] ); + // 1 = Vocab name, 2 = Term Type (PT, AB, etc) + Ranks.getInstance().setUmlsRank( columns[ 1 ], columns[ 2 ], rank ); + } catch ( NumberFormatException nfE ) { + Ranks.getInstance().setUmlsRank( columns[ 1 ], columns[ 2 ], -1 ); + } + } + line = reader.readLine(); + } + } catch ( IOException ioE ) { + LOGGER.error( ioE.getMessage() ); + } + } + + + // TODO - allow User to blacklist +// +// // Pref Text | Cui | unwanted Synonym +// static public void removeUnwantedSynonyms( final String customUnwantedPath, +// final Map<String, CuiTerm> cuiTerms ) { +// if ( !new File( customUnwantedPath ).isFile() ) { +// LOGGER.warn( "No custom unwanted synonym file." ); +// return; +// } +// long count = 0; +// try ( final BufferedReader reader = new BufferedReader( new FileReader( customUnwantedPath ) ) ) { +// String line = reader.readLine(); +// while ( line != null ) { +// if ( !line.isEmpty() && !line.startsWith( "//" ) ) { +// final String[] columns = StringUtil.fastSplit( line, '|' ); +// if ( columns.length == 3 ) { +// final String cui = CuiUtil.getCui( columns[ 1 ] ); +// final CuiTerm term = cuiTerms.get( cui ); +// if ( term != null ) { +// term.addUnwantedSynonym( columns[ 2 ] ); +// count++; +// } +// } else { +// LOGGER.warn( "Poorly formed line: " + line ); +// } +// } +// line = reader.readLine(); +// } +// } catch ( IOException ioE ) { +// LOGGER.error( ioE.getMessage() ); +// } +// LOGGER.info( "Removed " + count + " unwanted term synonyms" ); +// } + + +}
Added: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Atn.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Atn.java?rev=1881995&view=auto ============================================================================== --- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Atn.java (added) +++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Atn.java Fri Sep 25 01:04:47 2020 @@ -0,0 +1,678 @@ +package org.apache.ctakes.gui.dictionary.cased.umls.abbreviation; + +/** + * Attribute Names + * https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/attribute_names.html + * + * @author SPF , chip-nlp + * @version %I% + * @since 12/18/2018 + */ +public enum Atn { + AAL_TERM, //AAL term + ACCEPTABILITYID, //Acceptability Id + ACCEPTED_THERAPEUTIC_USE_FOR, //Accepted therapeutic use for + ACTIVE, //Active + ADDED_MEANING, //Additional descriptive information + ADDITIONAL_GUIDELINE, //Additional explanatory text that is applicable to a concept (code/heading/subheading). + ADDON_CODE, //A "T" in this field indicates that it is an "Add-on" code, i.e. it is commonly carried out in addition to the primary procedure performed + AMBIGUITY_FLAG, //Source atom ambiguity flag + AMT, //AOT uses MeSH term + ANADA, //Abbreviated New Animal Drug application number for the generic drug for MTHSPL + ANATOMICAL_COORDINATE, //Anatomical coordinate + ANDA, //Abbreviated New (Generic) Drug application number for the MTHSPL drug + ANSWER_CODE_SYSTEM, //Answer code system + ANSWER_CODE, //Answer code + ANSWER_LIST_ID, //Answer list ID + ANSWER_LIST_NAME, //Answer list name + AN, //MeSH Annotation - an informative MeSH note written primarily for indexers or catalogers that may also be useful in explaining the use of a MeSH term to online searchers. + AQL, //MeSH Allowable Qualifier - list of allowable qualifier abbreviations for MeSH main headings (e.g. AA, CL, CS, DF, DU, IM, I,P ME, PK) + ASK_AT_ORDER_ENTRY, //Ask at Order Entry (AOE) observations for a clinical observation or laboratory test + ASSOC_OBSERVATIONS, //Associated observations + ATC_LEVEL, //ATC LEVEL + ATTRIBUTEDESCRIPTION, //Attribute Description + ATTRIBUTEORDER, //Attribute Order + ATTRIBUTETYPE, //Attribute Type + AUTHORITY, //Authority + BIOCARTA_ID, //BioCarta online maps of molecular pathways, adapted for NCI use ID + BLA, //Therapeutic Biologic Applications number for the MTHSPL drug + BLOCK, //Block code + BRAININFO_URL, //URL of the central directory page in BrainInfo + CASE_SIGNIFICANCE_ID, //Case significance ID + CAS_REGISTRY, //CAS Registry + CCDS_ID, //CCDS ID + CCF, //Canonical Clinical Problem Statement System (CCPSS) frequency - the number of times a CCPSS term appears in a patient record. + CCI, //ICD-9-CM code(s) clusters in a Clinical Classifications Software (CCS) category - individual ICD-9-CM codes (or ranges of such codes) classified into CCS categories. + CELL_APPENDAGE_TYPE, //Cell appendage type + CFR, //Code of Federal Regulation Number (e.g. 862.3220, 892.1610) + CHANGE_CLASS, //Identifies the type of change made to this version of the Code (i.e., changes from the prior version published in "CDT-2011-2012"), with the following meanings: 30 = No change to existing code, nomenclature or descriptor; 31 = New procedure code and nomenclature, and descriptor, if present; 35 = Revision in the nomenclature or descriptor (or both), or to indicate a revision to an entire subcategory. + CHANGE_REASON_PUBLIC, //Detailed explanation about special changes to the term over time. + CHAPTER, //Chapter code + CHARACTERISTIC_TYPE_ID, //Characteristic type ID + CHEBI_ID, //CHEBI ID + CHEMICAL_FORMULA, //Chemical Formula + CHROMOSOME_PAIRS_PER_NUCLEUS, //Chromosome pairs per nucleus + CITATION, //Citation + CMA_LABEL, //Center for Morphological Analysis + CNIDTYPE, //cNIDType - identifies whether an item is in the classical hierarchy of brains structures (value = h) or not (value = a for ancillary.Useful only to users of NeuroNames versions earlier than 2009. + CNID, //cNID - ID number useful only to users of NeuroNames versions earlier than 2009. + CNU, //ISO 3166-1 standard country code in numeric (three-digit) format + COATING, //FDA Structured Product Label imprint attribute for coating + CODE_ALSO, //Instructs that 2 codes may be required to fully describe a condition but the sequencing of the two codes is discretionary, depending on the severity of the conditions and the reason for the encounter. + CODE_FIRST, //Certain conditions have both an underlying etiology and multiple body system manifestations due to the underlying etiology. ICD-10-CM has a coding convention that requires the underlying condition be sequenced first followed by the manifestation. Wherever such a combination exists there is a "code first" note at the manifestation code. These instructional notes indicate the proper sequencing order of the codes, etiology followed by manifestation. In most cases the manifestation codes will have in the code title, "in diseases classified elsewhere." Codes with this title are a component of the etiology/manifestation convention. The code title indicates that it is a manifestation code. "In diseases classified elsewhere" codes are never permitted to be used as first listed or principle diagnosis codes. They must be used in conjunction with an underlying condition code and they must be listed following the underlying condition. + CODING_TIP, //Coding Tip + COLORTEXT, //FDA Structured Product Label imprint attribute for color text + COLOR, //FDA Structured Product Label imprint attribute for color + COMBO_SCORE_NO_TOP_WORDS, //Combo Score that has no top words + COMBO_SCORE, //Combo Score + COMMENT, //Comment + COMMON_ORDER_RANK, //Ranking of approximately 300 common orders performed by laboratories in USA + COMMON_SI_TEST_RANK, //Corresponding SI terms for 2000 common tests performed by laboratories in USA + COMMON_TEST_RANK, //Numeric ranking of approximately 2,000 common tests performed by hospitals + CONCEPT_TYPE, //Concept type + CONDITIONAL_NADA, //Conditional Nada + CONSIDER, //Codes to consider before definitive diagnosis + CONSUMER_NAME, //An experimental (beta) consumer friendly name + CONTEXT_SCORE, //Context Score + CONTRIBUTING_AUTHOR, //contributing author + COPYRIGHT, //Copyright + CORRELATIONID, //Correlation Id + CPF, //CPT Full Description - complete text of the CPT full description, in cases where the CPT term in the "STR" field of MRCON has been trimmed from its original form. + CPTLINK_CONCEPT_ID, //CPT Link concept identifier + CPT_LEVEL, //For headings, a value ranging from H1 (a top-level heading such as Surgery) to H6 (a 6th-level subheading) and HS (a heading for a small family of related codes). For CPT codes, either PC for Parent Code or CC for Child Code. + CTV3ID, //The Read Code for a SNOMED CT concept taken from the United Kingdom?s Clinical Terms Version 3 terminology. + CUI_SCORE, //CUI Score + CV_ALGORITHM, //Content view algorithm + CV_CATEGORY, //Content view category + CV_CLASS, //Content view class + CV_CODE, //Content view code + CV_CONTRIBUTOR_DATE, //Date corresponding to the contributor version of this concept view + CV_CONTRIBUTOR_URL, //URL corresponding to the contributor version of this concept view + CV_CONTRIBUTOR_VERSION, //Version of this content view submitted by the contributor + CV_CONTRIBUTOR, //Content view contributor + CV_DESCRIPTION, //Content view description + CV_INCLUDE_OBSOLETE, //Content view includes obsolete data: YN + CV_IS_GENERATED, //Content view generated: Y/N + CV_MAINTAINER_DATE, //Date corresponding to the maintainer version of this concept view + CV_MAINTAINER_URL, //URL corresponding to the maintainer version of this concept view + CV_MAINTAINER_VERSION, //Version of this content view submitted by the maintainer + CV_MAINTAINER, //Content view maintainer + CV_MEMBER, //Describes the membership for an atom belonging to a particular content view. The value for this attribute is a tilde-delimited microsyntax. The first field is the content view bitflag (e.g. 2048), followed by field name-value pairs describing the member. + CV_PREVIOUS_META, //Previous UMLS Metathesaurus version used to generate content view. A null value means the content view is generated based on current UMLS Metathesaurus version. + CX, //MeSH Consider Also Note - other word roots or prefixes that should be consulted for concepts related to this MeSH concept, e.g., the value for "Heart" is "consider also terms at cardi- and myocardi-". + CYTOGENETIC_LOCATION, //Cytogenetic location of the gene + DATE_CREATED, //Date created + DATE_FIRST_PUBLISHED, //Date first published + DATE_LAST_MODIFIED, //Date last modified + DATE_MODIFIED, //Date Modified + DATE_NAME_CHANGED, //Date name changed + DATE_SYMBOL_CHANGED, //Date symbol changed + DAYS_POST_FERTILIZATION, //Days post fertilization + DAYS_RESTRICTION, //Days restriction + DA, //Metathesaurus Date of entry - YYYYMMDD, e.g., 19920830 - date of entry of the concept into the Metathesaurus. + DB_XR_ID, //Database cross-reference ID + DCSA, //Controlled Substance Act designation code (e.g. 0,2,3n) + DC, //MeSH Descriptor class - type of MeSH term the concept name represents. + DDFA, //Drug Doseform Abbreviation (e.g. SOLN) + DDF, //Drug Doseform (e.g. chewable tablet) + DEFAULT_LANGUAGECODE, //Default language code value + DEFAULT_MODULE_ID, //Default module ID + DEFINITION_STATUS_ID, //Definition status ID + DESCRIPTIONFORMAT, //Description Format + DESCRIPTIONLENGTH, //Description Length + DESCRIPTION_FORMAT, //Description format + DESCRIPTION_LENGTH, //Description length + DESCRIPTOR_ELEMENT, //Elements of a multi-paragraph descriptor, such as, E&M, lab panels, and molecular pathology + DESCRIPTOR_EXTENSION, //Extension of full description of the concept + DESIGN_NOTE, //Design note. + DESI_DESC, //Source drug efficacy study implementation indicator + DEVTYPE, //Device Type + DHJC, //Multum HCPCS J-code Multum clinical drugs linked to HCPCS J-codes where applicable (e.g. J7507) + DID, //Descriptor Identifier + DIMENSION, //Dimension code + DISJOINT_FROM, //Disjoint from + DISPARAGED, //Disparaged + DIV, //NCBI Division/Phyla (e.g. DIV[NCBI]Viruses) + DM_SPL_ID, //DailyMed internal identifier for MTHSPL atom + DPC, //Multum Pregnancy Hazard Classification Code assigned to Multum clinical drugs. (e.g. X, D) + DQ, //MeSH Date Qualifier Established YYYYMMDD - date the qualifier became available for indexing MEDLARS citations. + DRTA, //Drug Route of Administration Abbreviation (e.g. INJ) + DRT, //Drug Route of Administration (e.g. Injection (systemic) ) + DRUG_CLASS_TYPE, //VA Drug class type - Values can be "Major","Minor","Sub Class", or "0","1","2" respectively + DST, //Drug Strength (e.g. 0.01%, 0.02 MG, 0.02 MG/ML) + DX, //MeSH Date major descriptor established YYYYMMDD - first day of the Index Medicus publication month in which the descriptor (in any form) was available for searching as a major descriptor. + EC, //Specifies the MeSH main heading to be used instead of the Descriptor/Qualifier combination specified in the EC_OF attribute. + EFFECTIVE_TIME, //Effective time + ENA, //International Nucleotide Sequence Database Collaboration accession number(s) + ENSEMBLGENE_ID, //Ensembl gene ID + ENTREZGENE_ID, //EntrezGene ID + EPONYM, //Eponym + ESSENTIAL_AMINO_ACID, //Essential Amino Acid + ESSENTIAL_FATTY_ACID, //Essential Fatty Acid + EUPROSTATE16, //Euprostate 16 + EUPROSTATE27, //Euprostate 27 + EXAMPLE_UCUM_UNITS, //The Unified Code for Units of Measure (UCUM) + EXAMPLE_UNITS, //Example units + EXCLUDES1, //A pure excludes. It means "NOT CODED HERE!" Indicates that the code excluded should never be used at the same time as the code above the Excludes1 note. Used for when two conditions cannot occur together, such as a congenital form versus an acquired form of the same condition. + EXCLUDES2, //Represents "Not included here". Indicates that the condition excluded is not part of the condition it is excluded from but a patient may have both conditions at the same time. When an Excludes2 note appears under a code it is acceptable to use both the code and the excluded code together. + EXCLUDE_DI_CHECK, //Exclude drug interaction check + EXEMPT_DEVICE, //Exempt Device + EXEMPT_MOD, //Contains 51 or 63 for codes where Modifier 51 or 63 is Exempt + EXPORT_ONLY, //Export Only + EXTENSIBLE_LIST, //Extensible List + EXTERNAL_COPYRIGHT_LINK, //External copyright link + EZ, //Enzyme Commission Number - International Union of Biochemists Enzyme Commission number for an enzyme concept. + FDA_APPROVAL_PENDING, //T for codes marked with the FDA approval pending symbol + FDA_TABLE, //FDA Table + FDA_UNII_CODE, //FDA UNII Code + FIRST_IN_SUBSET, //Version of subset first containing this concept + FOURTHLEVEL, //Fourth Level code + FREESURFER_TERM, //Freesurfer term + FREQUENCY, //Frequency + FROMRSAB, //Root source abbreviation for the "from" identifiers of a map set + FROMVSAB, //Versioned source abbreviation for the "from" identifiers of a map set + FR, //MeSH Frequency + FX, //MeSH MH Mapping - maps a MeSH MH to a 'See Related' MH. + GENBANK_ACCESSION_NUMBER, //GenBank Accession Number + GENELOCUS, //Gene Locus + GENESYMBOL, //Gene Symbol + GENE_ENCODES_PRODUCT, //Gene Encodes Product + GENE_FAM_DESC, //Gene family description + GENE_FAM_ID, //ID used to designate a gene family or group + GESTATION_AGE_WEEKS, //Gestation Age Weeeks + GLOBAL_PERIOD_CODE, //Global period code + GO_COMMENT, //GO Comment field data + GO_NAMESPACE, //Go Namespace field data + GO_SUBSET, //Go Subset field data + GUIDELINE, //Guideline + GXR, //GO Cross Reference to external databases (e.g. MetaCyc:TRNA-CHARGING-PWY) + HAC, //HCPCS action code - code denoting the change made to a procedure or modifier code within the HCPCS system. + HAD, //HCPCS Action Effective Date - effective date of action to a procedure or modifier code. + HAQ, //HCPCS Anesthesia Base Unit Quantity - base unit represents the level of intensity for anesthesia procedure services that reflects all activities except time. + HAS_BOUNDARY, //Has boundary + HAS_DIMENSION, //Has dimension + HAS_DIRECT_CELL_LAYER, //Has direct cell layer + HAS_DIRECT_PLOIDY, //Has direct ploidy + HAS_DIRECT_SHAPE_TYPE, //Has direct shape type + HAS_INHERENT_3D_SHAPE, //has inherent 3d shape + HAS_MASS, //Has mass + HBT, //HCPCS Berenson-Eggers Type of Service Code - BETOS for the procedure code based on generally agreed upon clinically meaningful groupings of procedures and services. + HCC, //HCPCS Coverage Code - code denoting Medicare coverage status. There are two subelements separated by "=". + HCD, //HCPCS Code Added Date - year the HCPCS code was added to the HCFA Common Procedure Coding System. + HCO, //HL7 Comment + HGNC_ID, //HGNC ID + HIR, //HCPCS Coverage Issues Manual Reference Section Number - number identifying the Reference Section of the Coverage Issues Manual. + HIT, //HL7 Interpretation: German Interpretation according to the German HL/ user group + HL7AI, //HL7 approved indicator + HL7AP, //HL7 associated concept property + HL7AR, //HL7 package artifact + HL7AT, //HL7 applies to + HL7BR, //HL7 binding realm name + HL7CC, //HL7 complete codes indicator + HL7CD, //HL7 conductible + HL7CI, //HL7 package combined Id + HL7CO, //HL7 contributor + HL7CP, //HL7 copyright owner + HL7CSC, //HL7 conceptual space for class code + HL7CST, //HL7 coding strength + HL7CS, //HL7 code status + HL7CY, //HL7 copyright years + HL7DC, //HL7 is document characteristic + HL7DH, //HL7 default handling code + HL7DI, //HL7 deprecation info + HL7DK, //HL7 definition kind + HL7DV, //HL7 default value + HL7ED, //HL7 effective date + HL7HA, //HL7 how applies + HL7HI, //HL7 history item + HL7ID, //HL7 internal Id + HL7II, //HL7 is immutable + HL7IM, //HL7 is mandatory indicator + HL7IN, //HL7 inverse name + HL7IR, //HL7 inverse relationship + HL7IS, //HL7 is selectable + HL7LT, //HL7 license terms + HL7MI, //HL7 maintained indicator + HL7MN, //HL7 vocabulary model name + HL7NA, //HL7 is navigable + HL7NO, //HL7 notation + HL7OAN, //HL7 other annotation + HL7OA, //HL7 owning affiliate + HL7OD, //HL7 OID + HL7OI, //HL7 open issue + HL7PK, //HL7 package kind + HL7PL, //HL7 preferred for language + HL7PR, //HL7 package root + HL7PV, //HL7 publisher version Id + HL7RA, //HL7 rendering application + HL7RD, //HL7 release date + HL7RF, //HL7 reflexivity + HL7RG, //HL7 responsible group organization name + HL7RK, //HL7 relationship kind + HL7RN, //HL7 package realm namespace + HL7RT, //HL7 rendering time + HL7SCS, //HL7 supported code system + HL7SL, //HL7 supported language + HL7SV, //HL7 schema version + HL7SY, //HL7 symmetry + HL7TI, //HL7 title + HL7TR, //HL7 transitive + HL7TY, //HL7 property type + HL7VC, //HL7 value set content + HL7VD, //HL7 version date + HL7VE, //HL7 package version + HL7VP, //HL7 versioning policy + HL7XN, //HL7 xml namespace + HL7_ATTACHMENT_REQUEST, //HL7 attachment request + HL7_ATTACHMENT_STRUCTURE, //HL7 attachment structure + HL7_FIELD_SUBFIELD_ID, //A value which indicates the content should be delivered in the named field/subfield of the HL7 message. When NULL, the data should be sent in an OBX segment with this LOINC code stored in OBX-3 and with the value in the OBX-5 + HLC, //HCPCS Lab Certification Code - code used to classify laboratory procedures according to the specialty certification categories listed by CMS(formerly HCFA). + HMP, //HCPCS Multiple Pricing Indicator Code - code used to identify instances where a procedure could be priced. + HMR, //HCPCS Medicare Carriers Manual reference section number - number identifying a section of the Medicare Carriers Manual. + HM, //MeSH Heading Mapped To - heading mapped to attribute in C-MeSH containing repeating (MH or MH/SH) elements (e.g. HM = PYRROLIDINONES, HM = *TARTRATES, HM = ESTRONE/* analogs & derivatives) + HN, //History Note - for MeSH history notes, the year when the current form of the MeSH term was established as a major and/or minor descriptor. + HOMOLOGOUS_GENE, //Homologous Gene + HPD, //HCPCS ASC payment group effective date - date the procedure is assigned to the ASC payment group. + HPG, //HCPCS ASC payment group code which represents the dollar amount of the facility charge payable by Medicare for the procedure. + HPI, //HCPCS Pricing Indicator Code - used to identify the appropriate methodology for developing unique pricing amounts under Part B. + HPN, //HCPCS processing note number identifying the processing note contained in Appendix A of the HCPCS Manual. + HPO_COMMENT, //HPO Comment + HSE, //HL7 Section: Chapter + HSNU, //HL7 Sort Number: Number for sorting the values according to the official document + HSN, //HCPCS Statute Number identifying statute reference for coverage or noncoverage of procedure or service. + HTA, //HL7 Anchor: HTML-Reference to the Standard + HTD, //HCPCS Termination Date - last date for which a procedure or code may be used by Medicare Providers. + HTG, //HL7 Generate: Yes/No + HTID, //HL7 Table ID + HTS, //HCPCS Type of Service Code - carrier assigned HCFA Type of Service which describes the particular kind(s) of service represented by the procedure code. + HTT, //HL7 Table Type: Number specifying the type of this table (user defined, HL7 defined, ..) + HUS, //HL7 Usage: How is this data element used (Original, Added, Deleted) + HXR, //HCPCS Cross reference code - an explicit reference crosswalking a deleted code or a code that is not valid for Medicare to a valid current code (or range of codes). + IAA, //ICD10AM Abbreviated Descriptor + IAC, //ICD10AM Australian Code - Contains a flag "1" for codes that have been exclusively developed in Australia. + IAD, //ICD10AM Effective from - indicates the date that the code is effective from. + IAH, //ICD10AM Age Edit, higher limit - minimum age is expressed as a three digit field. + IAL, //ICD10AM Age Edit, lower limit - minimum age is expressed as a three digit field. + IAN, //Annotation or Usage Note - a value of "+" or "DAGGER," denotes a code describing the etiology or underlying cause of the disease; an "*" or "ASTERISK," denotes a code describing the manifestation of a disease. A value of "DEFAULT" indicates that dual coding is not indicated. + IAR, //ICD10AM Relationship Note - code embedded in the term, may have a * or +. + IAS, //ICD10AM Sex Edit flag to indicate whether the code is valid for a particular sex. Sex flags are 1 (male) or 2 (female). + IAT, //ICD10AM Sex Edit Type - all sex flagged codes are followed by a "sex edit type" flag. The sex edit type flags are 1 (fatal) or 2 (warning). + IAY, //ICD10AM Age Edit Type - all age flagged codes are followed by an age edit type flag. The age edit type flags are 1 (fatal) or 2 (warning). + ICA, //ICD Additional Codes Note - an ICD-9-CM instruction to signal the coder that an additional code should be used if the information is available to provide a more complete picture of that diagnoses or procedure. + ICC, //ICD Code Also Note - an ICD-9-CM instruction to signal the coder to code additional information. + ICD_O_3_CODE( "ICD-O-3_CODE" ), //ICD-O-3 Code + ICE, //ICD Entry Term (e.g. Diarrhea:{dysenteric; epidemic}; Infectious diarrheal disease) + ICF, //ICD Fifth-digit Code Note - instruction to coders indicating use of a fifth-digit code. + ICNP_TYPE, //ICNP Type Codes: Defines if the code is a Diagnosis/Outcome (DC), Intervention (IC) + ICN, //ICD Note - instruction providing additional coding information. + ICPCCODE, //ICPC Code + IDNR, //Original ID number for source file + IEEE_CF_CODE10, //IEEE CF Code10 + IEEE_DESCRIPTION, //IEEE description + IEEE_DIM, //IEEE DIM + IEEE_REFID, //IEEE REF ID + IEEE_UOM_UCUM, //IEEE UOM UCUM + II, //MeSH Indexing Information - for MeSH chemical terms (Term Type=NM), MeSH headings that may be relevant to articles that are also assigned the NM term. + IMAGING_DOCUMENT_VALUE_SET, //A value of "TRUE" indicates that the LOINC NUM is a member of the Imaging Documents Value Set + IMPRINT_CODE, //Imprint Code + INACTIVATION_INDICATOR, //Inactivation indicator + INC, //ICD10AM Neoplasm code (e.g. C34.- ) + IND_CODE, //IND Code + IND, //IND + INFOODS, //Infoods + IPX, //ICD10 code related to an ICPC code - a + indicates that the ICD10 code is broader than the ICPC code; a - indicates that the ICD10 code is narrower than the ICPC code. + ISLEAF, //Leaf flag: 0 for hierarchical nodes, 1 for leaf nodes + IS_DRUG_CLASS, //Is Drug Class + IS_RETIRED_FROM_SUBSET, //In future, some concepts will be marked retired if they are retired by IHTSDO or no longer considered to be useful e.g. when there are more appropriate SNOMED CT concepts + JHU_DTI_81( "JHU_DTI-81" ), //JHU DTI-81 + JHU_WHITE_MATTER_TRACTOGRAPHY_ATLAS, //JHU white matter tractography atlas + JXR, //OMIM code that is related to Jablonski term. + KEGG_ID, //Kyoto Encyclopedia of Genes and Genomes (KEGG), KEGG Pathway Database, adapted for NCI use ID + LABELER, //FDA Structured Product Label Manufacturer/Distributor/Supplier name + LABEL_TYPE, //DailyMed label type + LANGUAGECODE, //SNOMED CT string identifying a language and, if appropriate, a dialect in which this description is valid. + LANGUAGE, //Language + LAST_IN_SUBSET, //The version of Subset last containing this concept. + LATERALITY, //Laterality + LCD, //LOINC CDISC common tests + LCL, //LOINC Class - arbitrary classification of terms in LOINC designed to assist LOINC development and to group related observations together (e.g. ABXBACT = Antibiotic susceptibility) + LCN, //LOINC Classtype - 1 = Laboratory Class; 2 = Clinical Class; 3 = Claims Attachment; 4 = Surveys + LCS, //LOINC status - valid values are "ACTIVE," "TRIAL," "DISCOURAGED," "DEPRECATED." For "DEPRECATED" or "DISCOURAGED" concepts, the term that should now be used may appear in the LMP element. + LCT, //LOINC Change Type Code - type of change made to a LOINC term. + LEA, //LOINC Example Answers - for some tests and measurements, LOINC has supplied examples of valid answers. These values differ from those in the ANSWERLIST field because that details possible values for nominal scale terms. + LEGALLY_MARKETED_UNAPPROVED_NEW_ANIMAL_DRUGS_FOR_MINOR_SPECIES, //Legally Marketed Unapproved New Animal Drugs for Minor Species + LEVEL, //RXNORM: Specifies the type of drug concepts - Values can be "Ingredient", "VA Class", or "VA Product"; ICF: hierarchical level number + LFO, //LOINC Formula - regression equation details for many OB.US calculated terms. + LMP, //LOINC Map to Code of the term that has superseded a term with a LCS value of DEPRECATED. + LOCUS_GROUP, //Locus group + LOCUS_SPECIFIC_DB_XR, //Locus specific database cross-reference + LOCUS_TYPE, //Locus Type + LOE, //Level of effort + LOINC_COMPONENT, //LOINC component + LOINC_METHOD_TYP, //LOINC method type + LOINC_PROPERTY, //LOINC property + LOINC_SCALE_TYP, //LOINC scale type + LOINC_SCORE, //A numeric score associated with a LOINC answer ('LA') concept. + LOINC_SYSTEM, //LOINC system + LOINC_TIME_ASPECT, //LOINC time aspect + LOR, //LOINC ORDER_OBS field. Defines term as order only, observation only, or both. Values are: BOTH OBSERVATION ORDER. A fourth category, Subset, is used for terms that are subsets of a panel but do not represent a package that is known to be orderable. + LQS, //Survey Question Source + LQT, //Survey Question Text + LRN2, //Related names 2 + LSP, //LOINC Species code + LSU, //Submitted Units + LT, //Indicates if a chemicals or medical device is a tradename (present in older versions of the Metathesaurus and was discontinued, then brought back starting in 2002AD) + LUR, //Units required when used as OBX segment - a Y/N field that indicates that units are required when this LOINC is included as an OBX segment in a HIPAA attachment + MACRONUTRIENT, //Macronutrient + MANUFACTURER_STATUS, //Manufacturer Status + MAPADVICE, //Map Advice + MAPCATEGORYID, //Map Category Id + MAPGROUP, //Map Group + MAPPED_UCSC_ID, //UCSC ID (mapped data) + MAPPRIORITY, //Map Priority + MAPRULE, //Map Rule + MAPSETGRAMMAR, //Grammar used to describe boolean expressions used in a map set + MAPSETNAME, //Official name of a map set + MAPSETRSAB, //Root source abbreviation for a map set + MAPSETSID, //Source asserted identifier for a map set + MAPSETTYPE, //Indicates the nature of a map set. Its value is map set specific. It can be used to indicate the inclusion of one to one, one to many and choices of maps. + MAPSETVERSION, //Version of the map set + MAPSETVSAB, //Versioned source abbreviation for a map set + MAPSETXRTARGETID, //Map set target identifier used for XR mappings. + MAPTARGET, //Map Target + MARKETING_CATEGORY, //Marketing category + MARKETING_EFFECTIVE_TIME_HIGH, //The date the MTHSPL drug became active + MARKETING_EFFECTIVE_TIME_LOW, //The date the MTHSPL drug became completed + MARKETING_STATUS, //The Marketing Status of the MTHSPL drug + MDA, //MeSH date of entry YYYYMMDD - date the term was added to the MeSH file, which is prior to the date the term became available for indexing and searching MEDLARS citations. Terms that have been part of MeSH for many years may have no value in this element. + MEASURE_DEVELOPER, //Name of the measure developer associated with the Category II code + MEA, //In NOC, the "measurement scale" used for a particular outcome. + MENU_PARENT, //Link information to Term Menu parent. This may not always be the same as the TermParent. Element will not exist for top level menus, e.g. cancer. + MENU_TYPE, //Values are Clinical Trials--Cancer Type, Clinical Trials--Drug, or Cancer Information. + MESH_DEFINITION, //MeSH definition for MeSH main heading + MESH_DUI, //The MeSH descriptor unique identifier to which the given NDFRT term maps + MESH_NAME, //MeSH name + MESH_UI, //The MeSH Unique Identifier to which the given NDFRT term maps + MGD_ID, //MGD ID + MGI_ACCESSION_ID, //MGI Accession ID + MICRONUTRIENT, //Micronutrient + MIMTYPEMEANING, //OMIM MimType Meaning + MIMTYPEVALUE, //OMIM MimType Value + MIMTYPE, //OMIM Entry Type + MIRBASE_ID, //miRBase ID + MISO, //MedDRA Serial Code International SOC Sort Order Digit (01-26) + MMR, //MeSH revision date YYYYMMDD - date of the last major revision to the term's MeSH record. + MMX_RXO, //Micromedex Product Category Code + MN, //MeSH hierarchical number for the concept in the MeSH tree structures. This number also appears in the HCD subelement of the REL and CXT elements. + MODIFIER_ID, //Modifier ID + MODIFIER, //Modifier + MODULE_ID, //Module ID + MONOGRAPH_OFFICIAL_DATE, //Monograph Official Date + MONOGRAPH_STATUS, //Monograph Status + MOVED_FROM, //Moved from + MPS, //MedDRA primary SOC (PTs may have multiple treepositions, but each has a primary soc) + MP_GROUP_URL, //MEDLINEPLUS group URL + MP_HEALTH_TOPIC_URL, //MEDLINEPLUS health topic URL + MP_OTHER_LANGUAGE_URL, //MEDLINEPLUS health topic other-language URL + MP_PRIMARY_INSTITUTE_URL, //MEDLINEPLUS health topic primary-institute URL + MR, //Major revision date YYYYMMDD - date the Metathesaurus entry for the concept underwent any revision in content. + MSC, //Minimal Standard (Terminology) Class + MSP, //SPN Medical Specialty Panel (responsible for reviewing the product). + MTH_MAPFROMCOMPLEXITY, //Indicates the complexity of "from" expressions used in a map set + MTH_MAPFROMEXHAUSTIVE, //Indicates whether or not the "from" source of a map set is completely mapped + MTH_MAPSETCOMPLEXITY, //Indicates the overall complexity of a map set + MTH_MAPTOCOMPLEXITY, //Indicates the complexity of "to" expressions in a map set + MTH_MAPTOEXHAUSTIVE, //Indicates whether or not the "to" source is completely mapped + NADA, //New Animal Drug Application number for MTHSPL drug + NCBI_TAXON_ID, //NCBI_Taxon_ID + NCI_ID, //NCI thesaurus concept id + NDA_AUTHORIZED_GENERIC, //New Drug Application number for authorized generic MTHSPL drug + NDA, //New Drug Application number for MTHSPL drug + NDC, //National Drug Code corresponding to a clinical drug (e.g. 000023082503) + NDFRT_KIND, //NDFRT kind + NDF_TRANSMIT_TO_CMOP, //NDF Transmit to Consolidated Mail Outpatient Pharmacy (CMOP) + NDF_UNITS, //NDF units + NEOPLASTIC_STATUS, //Neoplastic Status + NEUROLEX_ID, //Neurolex ID + NEUROQUANT, //Neuroquant + NFI, //National formulary indicator - "YES" or "NO" indicating whether a drug is in the VA's National Formulary + NF_INACTIVATE, //National Formulary Inactivation Date - the date a drug was removed from the VA's National Formulary + NF_NAME, //National Formulary Name + NICHD_HIERARCHY_TERM, //NICHD Hierarchy Term + NON_VACCINE, //Non Vaccine + NOTE, //Note + NSC_CODE, //NSC Code + NSR, //Neuronames Species Restriction - indication that a Neuronames concept applies to humans, macaques, primates, rats, etc. Most Neuronames concepts have no species restriction. + NUI, //NDFRT numerical unique identifier + NUTRIENT, //Nutrient + OCCURRENCE, //Number of institutions having this concept on their problem list (from 1 to 7), not populated for concepts retired from Subset + OID, //Answer list OID + OL, //MeSH Online Note - information helpful to online searchers of MEDLINE, especially when the history of a term or cross-reference has implications for online searching. This is a potential source of useful information for rules for search interface programs. + OMIM_ID, //OMIM ID + OMIM_NUMBER, //OMIM Number + ORDER_NO, //Order number + ORIG_CODE, //Original code associated with this string + ORIG_SOURCE, //Original source associated with this string + ORIG_STY, //Original semantic type + OR_GROUP, //Indicates that relationships with the same CUI2 and RG are disjunctive expressions + OTC_MONOGRAPH_FINAL, //FDA Structured Product Label OTC monograph status + OTC_MONOGRAPH_NOT_FINAL, //FDA Structured Product Label OTC monograph status + OUTDATED_MEANING, //Outdated Meaning + PANEL_TYPE, //Panel type + PARENT_CLASS, //VA Internal entry number of the parent class + PARTITION, //Partition + PART_SEQ_ORDER, //Part sequence order + PART_TYPE, //Part type + PA, //Pharmacologic Action of MeSH main headings (MH) for drugs and supplementary concept names (NM). The information in this element is also represented by an "isa" relationship between the MH or NM concept and the MeSH concept name for the class of drugs with a particular pharmacologic action. + PCL, //Pharmacy Practice Activity Classification (PPAC) Category - all terms are assigned to one of five categories, which connote their hierarchy. + PDC, //SPN Product Device Class (level of CDRH regulation: class 1, 2, or 3). + PDQ_CLOSED_TRIAL_SEARCH_ID, //PDQ Closed Trial Search ID + PDQ_OPEN_TRIAL_SEARCH_ID, //PDQ Open Trial Search ID + PHYSICAL_STATE, //Physical state + PID_ID, //National Cancer Institute Nature Pathway Interaction Database ID + PID, //Legacy PDQ ID + PIRADSV2, //Piradsv 2 + PI, //MeSH heading or heading/subheading combination(s) followed by a date range in parentheses (YYYY). + PLACE_OF_SERVICE_CODE, //Place of service code + PLR, //Pharmacy Practice Activity Classification (PPAC) Last Revision Date (Format: M/DD/YY time) + PMID, //Pubmed ID + PM, //Public MeSH note - combines key information from the HN and PI elements in a format that is printed in the MeSH publications. + POLARITY, //Polarity + PRC, //Product Third Party Review Code from SPN. + PREF_FLAG_ID, //Preferred flag + PREMARKET_APPLICATION, //Premarket Application + PREMARKET_NOTIFICATION, //FDA Structured Product Label premarket notification + PREV_NAME, //Previous name + PREV_SYMBOL, //Previous symbol + PROPRIETARY_NAME, //Proprietary name + PTR, //SPN Product Tier (level of CDRH triage: 1, 2, 3, or E{xempt}). + PUBLISH_VALUE_SET, //publish value set + PUBMEDID_PRIMARY_REFERENCE, //PubMedID Primary Reference + PXC, //PDQ Protocol Exclusion Criteria - terms with type "exclusion criteria," which may be indexed on protocol records to identify conditions that exclude a patient from eligibility. + PYR, //PsychInfo year designation + RADLEX_ID, //RadLex ID + RADLEX_PLAYBOOK_LONG_NAME, //RadLex Playbook long name + RADLEX_PREF_NAME, //RadLex preferred name + RANK, //NCBI Rank (e.g. RANK[NCBI]species) + REFSEQ_ID, //RefSeq ID + REFSET_PATTERN, //Refset pattern + REF, //References or citations related to a given atom or concept. + REMARKS, //Specific coding instructions + REPLACED_BY_SNOMED_CID, //Current version SNOMEDCT concept id this concept is replaced by + REPORTABLE, //Indicates whether a code is reportable + RGD_ID, //Rat genome database gene ID + RID, //Read Codes Term_id - identifier assigned to a Read term, used in referring to the term in the Read file structure, and may be used in clinical information systems. + RNA_CENTRAL_ID, //RNA Central ID + RN, //Registry Number - series of numbers and hyphens (any leading zeros in an RN are dropped) or a series of numbers and periods, preceded by EC + RPID, //RadLex Playbook ID + RR, //The Chemical Abstracts Registry numbers for salts, optical isomers, or isotope-labeled versions of the concept followed by the relationship of this RR to the RN (in parentheses.) Applies to chemicals only. These numbers can be used as links to information in a number of chemical and toxicological databases. + RVU_FACILITY_PRACTICE_EXPENSE_DISCONTINUED, //RVU facility practice expense discontinued + RVU_FACILITY_PRACTICE_EXPENSE_PROFESSIONAL, //RVU facility practice expense professional + RVU_FACILITY_PRACTICE_EXPENSE_TECHNICAL, //RVU facility practice expense technical + RVU_FACILITY_PRACTICE_EXPENSE, //RVU facility practice expense + RVU_MEDICARE_GLOBAL_PERIOD_DISCONTINUED, //RVU Medicare global period discontinued + RVU_MEDICARE_GLOBAL_PERIOD_PROFESSIONAL, //RVU Medicare global period professional + RVU_MEDICARE_GLOBAL_PERIOD_TECHNICAL, //RVU Medicare global period technical + RVU_MEDICARE_GLOBAL_PERIOD, //RVU Medicare global period + RVU_NONFACILITY_PRACTICE_EXPENSE_DISCONTINUED, //RVU nonfacility practice expense discontinued + RVU_NONFACILITY_PRACTICE_EXPENSE_PROFESSIONAL, //RVU nonfacility practice expense professional + RVU_NONFACILITY_PRACTICE_EXPENSE_TECHNICAL, //RVU nonfacility practice expense technical + RVU_NONFACILITY_PRACTICE_EXPENSE, //RVU nonfacility practice expense + RVU_PLI_DISCONTINUED, //RVU PLI discontinued + RVU_PLI_PROFESSIONAL, //RVU PLI professional + RVU_PLI_TECHNICAL, //RVU PLI technical + RVU_PLI, //RVU PLI + RVU_TOTAL_FACILITY_DISCONTINUED, //RVU total facility discontinued + RVU_TOTAL_FACILITY_PROFESSIONAL, //RVU total facility professional + RVU_TOTAL_FACILITY_TECHNICAL, //RVU total facility technical + RVU_TOTAL_FACILITY, //RVU total facility + RVU_TOTAL_NONFACILITY_DISCONTINUED, //RVU total nonfacility discontinued + RVU_TOTAL_NONFACILITY_PROFESSIONAL, //RVU total nonfacility professional + RVU_TOTAL_NONFACILITY_TECHNICAL, //RVU total nonfacility technical + RVU_TOTAL_NONFACILITY, //RVU total nonfacility + RVU_WORK_DISCONTINUED, //RVU work discontinued + RVU_WORK_PROFESSIONAL, //RVU work professional + RVU_WORK_TECHNICAL, //RVU work technical + RVU_WORK, //RVU work + RXAUI, //RxNorm atom identifier for the atom it is connected to + RXCUI, //RxNorm concept identifier for the atom this is connected to + RXN_ACTIVATED, //Date the RxNorm atom was reactivated + RXN_AVAILABLE_STRENGTH, //Available drug strengths listed in the order of ingredients from the drug + RXN_BN_CARDINALITY, //Cardinality of RxNorm Brand Name Atom + RXN_BOSS_AI, //RXN Boss AI + RXN_BOSS_AM, //RXN Boss AM + RXN_BOSS_FROM, //RXN Boss From + RXN_BOSS_STRENGTH_DENOM_UNIT, //RXN Boss Strength Denom Unit + RXN_BOSS_STRENGTH_DENOM_VALUE, //RXN Boss Strength Denom Value + RXN_BOSS_STRENGTH_NUM_UNIT, //RXN Boss Strength Num Unit + RXN_BOSS_STRENGTH_NUM_VALUE, //RXN Boss Strength Num Value + RXN_HUMAN_DRUG, //Drug available for use in Humans + RXN_IN_EXPRESSED_FLAG, //Strength Expressed As Precise Flag + RXN_OBSOLETED, //Date the RxNorm atom became obsolete + RXN_QUALITATIVE_DISTINCTION, //RXN Qualitative Distinction + RXN_QUANTITY, //Normal Form quantity factor + RXN_STRENGTH, //Strength plus unit of SCDC + RXN_VET_DRUG, //Drug available for use in animals + RXR, //Replacement: cross reference from obsolete code to current code + RXTERM_FORM, //The RxTerm dose form name for this drug + SB, //SNOMED International subset indicator - valid values: * =can code using two T codes or G code for laterality B Bethesda system (Morphology); IC= ICDO (Oncology) related; N=Nursing; N* =Nursing, provisional; U=Ultrastructure (Morphology); V= Veterinary; V* =Veterinary AND can code using two T codes or G code for laterality (Topography) + SCORE, //FDA Structured Product Label imprint attribute for score + SC, //MeSH Supplemental record class. + SECONDLEVEL, //Second Level code + SEQ_NO, //Sequence number + SHAPETEXT, //FDA Structured Product Label imprint attribute for shape text + SHAPE, //FDA Structured Product Label imprint attribute for shape + SHF, //SNOMED Hospital Formulary Code - the American Hospital Formulary Code for a chemical contained in SNOMED International (e.g. 84:24:12) + SIC, //SNOMED ICD9CM Reference - the ICD9CM code or codes listed as relevant to the meaning of the concept in SNOMED International. + SID, //Secondary GO ID (e.g. GO:0020034) + SIZE, //FDA Structured Product Label imprint attribute for size + SLOT_SYNONYM, //slot synonym + SMQ_ALGO, //Standardised MedDRA Query (SMQ) Algorithm. Boolean expression of algorithm for the SMQ. "N" if the SMQ does not utilize an algorithm. + SMQ_LEVEL, //Standardised MedDRA Query (SMQ) Level. Value between 1 and 5 identifying the level of the SMQ within the hierarchy of SMQs; 1 is the most general, 5 is the most narrow. + SMQ_SOURCE, //Standardised MedDRA Query (SMQ) Source. Source for the development of the SMQ, e.g. medical references. + SMQ_STATUS, //Standardised MedDRA Query (SMQ) Status. "A" = active; "I" = inactive. + SMQ_TERM_ADDVERSION, //Standardised MedDRA Query (SMQ) Addition Version. Version of MedDRA in which term was added to the SMQ. + SMQ_TERM_CAT, //Standardised MedDRA Query (SMQ) Term Category. A single alphabetical letter indicating the category of the term for application of the SMQ algorithm. If the SMQ does not use algorithms, then all Term_category values are assigned "A." For a child SMQ, this field is assigned "S." + SMQ_TERM_LEVEL, //Standardised MedDRA Query (SMQ) Term Level. The MedDRA hierarchy level of a term (4=PT, 5=LLT) or 0 (zero) for a child SMQ. + SMQ_TERM_LMVERSION, //Standardised MedDRA Query (SMQ) Last Modified Version. Version of MedDRA in which term was last modified in the SMQ. + SMQ_TERM_SCOPE, //Standardised MedDRA Query (SMQ) Term Scope. Defines the MedDRA term as a member of the broad scope (1), narrow scope (2) of the SMQ search, or a child SMQ (0) (zero). + SMQ_TERM_STATUS, //Standardised MedDRA Query (SMQ) Term Status. Identifies a term as active ("A") or inactive ("I") within this SMQ. + SMQ_TERM_WEIGHT, //Standardised MedDRA Query (SMQ) Term Weight. Used for some SMQ algorithms; "0" is used as default. + SMX, //SNOMED Multiaxial coding - an alphanumeric string that includes hyphens, parentheses, and sometimes ellipses. + SNGL_OR_MULT_SRC_PRD, //Single or multi-source product + SNOMED_CHILD, //SNOMED CHILD + SNOMED_CID, //SNOMED-CT concept ID mapping for NDFRT disease name term + SNOMED_PARENT, //SNOMED PARENT + SORT, //Sort field + SOS, //Scope Statement + SOURCEEFFECTIVETIME, //Source Effective Time + SOURCE_EFFECTIVE_TIME, //Source effective time + SOURCE_UI, //Unique identifier from the source + SPECIALTY, //Specialty + SPECIES, //Species + SPL_SET_ID, //FDA Structured Product Label SET_ID code + SRC, //MeSH Literature source of chemical name - a citation to an article in a journal indexed for MEDLINE in which the chemical has been identified. (Note: Not to be confused with source abbreviation of SRC) + STATE_OF_DETERMINATION, //State of determination + STATUS_REASON, //Classification of the reason for concept status in LOINC + STATUS_TEXT, //Explanation of concept status in narrative text in LOINC + STRENGTH, //NDF strength + ST, //Concept Attributes Status - valid values: R Reviewed, U Unreviewed + SUBCATEGORY, //Subcategory + SUBSEQUENT_TEXT_PROMPT, //Subsequent text prompt + SUBSET_MEMBER, //Subset member + SWISS_PROT, //Swiss Prot + SWP, //Swiss Protein Number + SYCODE, //Synonym Code + SYMBOL, //FDA Structured Product Label imprint attribute for symbol + SYN_QUALIFIER, //Synonym qualifier + TALAIRACH_TERM, //Talairach Term + TARGETCOMPONENT, //Target Component + TARGETEFFECTIVETIME, //Target Effective Time + TARGET_EFFECTIVE_TIME, //Target effective time + TA_ID, //TAID + TELEMEDICINE, //Telemedicine + TERMCODE, //Term Code + TERMID, //Term identifier + TERMSTATUS, //Term status + TERMUI, //Term unique identifier + TERM_BROWSER_VALUE_SET_DESCRIPTION, //Term browser value set description + TERM_STATUS, //Term Status + THIRDLEVEL, //Third Level code + TH, //MeSH Thesaurus ID - identifies thesauri other than MeSH in which the MeSH heading or cross-reference is included. + TOLERABLE_LEVEL, //Tolerable Level + TOP_2000_LAB_RESULTS_SI, //Top 2000 lab results SI + TOP_2000_LAB_RESULTS_US, //Top 2000 lab results US + TORSAB, //Root source abbreviation for the "to" identifiers of a map set + TOVSAB, //Versioned source abbreviation for the "to" identifiers of a map set + TRANSLATION, //Translated name of the neuroanatomical structure + TYPE_ID, //Type ID + TYPE, //Multum Medical Supply Category (e.g. natural supplements) + UMLSRELA, //UMLS relationship attribute + UMLSREL, //The UMLS Metathesaurus REL relationship (SY, CHD, RN, RB, RO) assigned to SNOMED CT relationship identifiers. + UNAPPROVED_DRUG_OTHER, //Marketing category unapproved_drug_other for MTHSPL atom + UNAPPROVED_HOMEOPATHIC, //Unapproved Homeopathic + UNAPPROVED_MEDICAL_GAS, //Unapproved Medical Gas + UNITS_AND_RANGE, //Units and range + UNIT, //Unit + UNIVERSAL_LAB_ORDERS_VALUE_SET, //A value of "TRUE" indicates that the LOINC NUM is a member of the LOINC Universal Lab Orders Value Set + UPC, //Universal Product Code + USAGE, //The average usage percentage among all institutions (i.e. sum of individual usage percentages divided by 7), not populated for concepts retired from Subset + USDA_ID, //USDA ID + USE_ADDITIONAL, //Certain conditions have both an underlying etiology and multiple body system manifestations due to the underlying etiology. ICD-10-CM has a coding convention that requires the underlying condition be sequenced first followed by the manifestation. Wherever such a combination exists there is a "use additional code" note at the etiology code. These instructional notes indicate the proper sequencing order of the codes, etiology followed by manifestation. In most cases the manifestation codes will have in the code title, "in diseases classified elsewhere." Codes with this title are a component of the etiology/ manifestation convention. The code title indicates that it is a manifestation code. "In diseases classified elsewhere" codes are never permitted to be used as first listed or principle diagnosis codes. They must be used in conjunction with an underlying condition code and they must be listed following the underlying condition. + USE_FOR, //Use for + US_RECOMMENDED_INTAKE, //US Recommended Intake + UWT, //A semantic type provided from terms from the University of Washington Digital Anatomist + VACCINE_STATUS, //Vaccine status. CVX codes for inactive vaccines allow transmission of historical immunization records. + VAC, //VA Class - the code of an NDF/HT drug class name (e.g. AM110) + VALUEID, //Value Id + VANDF_RECORD, //Concatenated triple of VANDF file number, VANDF file IEN, VANDF file record status + VA_CLASS_NAME, //VA class name + VA_DISPENSE_UNIT, //VA dispense unit + VA_GENERIC_NAME, //VA generic name + VA_IEN, //VA individual entry number + VEGA_ID, //VEGA ID + VERSION_FIRST_RELEASED, //Version first released + VERSION_LAST_CHANGED, //Version last changed + VIEW, //View + VMO, //VA CMOP (central mail - order pharmacy) ID + VUID; //VHA unique identifier assigned to the product + + private final String _name; + + Atn() { + this( "" ); + } + + Atn( String name ) { + _name = name; + } + + public String getName() { + if ( _name.isEmpty() ) { + return this.name(); + } + return _name; + } + + +} Added: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/IsPref.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/IsPref.java?rev=1881995&view=auto ============================================================================== --- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/IsPref.java (added) +++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/IsPref.java Fri Sep 25 01:04:47 2020 @@ -0,0 +1,11 @@ +package org.apache.ctakes.gui.dictionary.cased.umls.abbreviation; + +/** + * @author SPF , chip-nlp + * @version %I% + * @since 12/18/2018 + */ +public enum IsPref { + N, // Seems to actually mean that a synonym is preferred + Y; // Seems to indicate that a synonym is NOT preferred +} Added: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Lat.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Lat.java?rev=1881995&view=auto ============================================================================== --- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Lat.java (added) +++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Lat.java Fri Sep 25 01:04:47 2020 @@ -0,0 +1,48 @@ +package org.apache.ctakes.gui.dictionary.cased.umls.abbreviation; + +/** + * https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html + * + * @author SPF , chip-nlp + * @version %I% + * @since 12/18/2018 + */ +public enum Lat { + BAQ( "Basque" ), + CHI( "Chinese" ), + CZE( "Czech" ), + DAN( "Danish" ), + DUT( "Dutch" ), + ENG( "English" ), + EST( "Estonian" ), + FIN( "Finnish" ), + FRE( "French" ), + GER( "German" ), + GRE( "Greek" ), + HEB( "Hebrew" ), + HUN( "Hungarian" ), + ITA( "Italian" ), + JPN( "Japanese" ), + KOR( "Korean" ), + LAV( "Latvian" ), + NOR( "Norwegian" ), + POL( "Polish" ), + POR( "Portuguese" ), + RUS( "Russian" ), + SCR( "Croatian" ), + SPA( "Spanish" ), + SWE( "Swedish" ), + TUR( "Turkish" ); + + + private final String _name; + + Lat( String name ) { + _name = name; + } + + public String getName() { + return _name; + } + +} Added: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rel.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rel.java?rev=1881995&view=auto ============================================================================== --- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rel.java (added) +++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rel.java Fri Sep 25 01:04:47 2020 @@ -0,0 +1,56 @@ +package org.apache.ctakes.gui.dictionary.cased.umls.abbreviation; + +import java.util.Arrays; + +/** + * Relationship + * https:// www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html + * + * @author SPF , chip-nlp + * @version %I% + * @since 12/18/2018 + */ +public enum Rel { + AQ, // Allowed qualifier + CHD, // has child relationship in a Metathesaurus source vocabulary --> If there is no relation name (Rela) then Rela ~ isa + DEL( false ), // Deleted concept + PAR, // has parent relationship in a Metathesaurus source vocabulary + QB, // can be qualified by + RB, // has a broader relationship + RL( false ), // the relationship is similar or alike. the two concepts are similar or "alike". In the current edition of the Metathesaurus, most relationships with this attribute are mappings provided by a source, named in SAB and SL; hence concepts linked by this relationship may be synonymous, i.e. self-referential: CUI1 = CUI2. In previous releases, some MeSH Supplementary Concept relationships were represented in this way. + RN, // has a narrower relationship + RO, // has relationship other than synonymous, narrower, or broader + RQ( false ), // related and possibly synonymous + RU( false ), // Related, unspecified + SIB( false ), // has sibling relationship in a Metathesaurus source vocabulary + SY( false ), // source asserted synonymy + XR( false ), // Not related, no mapping" ); + UNKNOWN( false ); + + private final boolean _wanted; + + Rel() { + this( true ); + } + + Rel( final boolean wanted ) { + _wanted = wanted; + } + + public boolean isWanted() { + return _wanted; + } + + static public Rel getRel( final String name ) { + return Arrays.stream( values() ) + .filter( s -> name.equalsIgnoreCase( s.name() ) ) + .findFirst() + .orElse( UNKNOWN ); + } + + static public boolean isWanted( final String name ) { + return getRel( name ).isWanted(); + } + + +}
