The two tables below present MetaMap2012's XML tags listed alphabetically and hierarchically; the two tables contain the same information, only arranged differently.

XML tags are characterized by structure (simple or complex) and number (unique or repeating):

Certain repeating tags also exist in plural form, denoting a series of one or more of the singular form of the tag, e.g.,
<AAs>, <AACUIs>, <Candidates>, <ConceptPIs>, <MappingCandidates>, <Mappings>, <MatchedWords>, <MatchMaps>, <MMOs>, <Negations>, <NegConcepts>, <NegConcPIs>, <NegTriggerPIs>, <Options>, <Phrases>, <SemTypes>, <Sources>, <SyntaxUnits>, <Tokens>, and <Utterances>.

Alphabetical listing of current XML tags

TagTypeDescription
<AAs
  Count="N">
<AA>		 CR All the data generated for an author-defined Acronym/Abbreviation (AA), consisting of
  • <AAText>: the text of the AA,
  • <AAExp>: its expansion,
  • <AATokenNum>: the number of tokens in the AA
  • <AALen>: the character length of the AA
  • <AAExpTokenNum>: the number of tokens in expansion
  • <AAExpLen>: the character length of its expansion, and
  • <AACUI>: any CUIs associated with the expansion of the AA
The following AA examples will use the text
polymerase chain reaction (PCR).
<AACUIs
  Count="N">
<AACUI>		 SR Any CUIs associated with the expansion of the AA.
<AAExp> SU The expansion of the AA (polymerase chain reaction)
<AAExpLen> SU The character length of the expansion of the AA (25, because polymerase chain reaction contains 25 characters)
<AAExpTokenNum> SU The number of tokens in the AA expansion (5, because polymerase chain reaction contains 5 tokens, including two blank tokens)
<AALen> SU The character length of the AA (3, because PCR contains 3 characters)
<AAText> SU The AA itself (PCR)
<AATokenNum> SU The number of tokens in the AA (1, because PCR contains 1 token)
<Candidates
  Total="T"
  Excluded="E"
  Pruned="P"
  Remaining="R">
<Candidate>		 CR All the data generated for a candidate concept, including
  • <CandidateScore>: the candidate's negative score,
  • <CandidateCUI>: its CUI,
  • <CandidateMatched>: the candidate matched,
  • <CandidatePreferred>: its preferred name,
  • <MatchedWords>: the text word(s) it matches,
  • <MatchMaps>: the matchmap(s),
  • <SemTypes>: the semantic type(s),
  • <IsHead>: IsHead (yes/no),
  • <IsOverMatch>: IsOverMatch (yes/no),
  • <Sources>: the UMLS source(s),
  • <ConceptPIs>: the positional information, and
  • <Status>: 0/1/2 depending on if candidate is retained/excluded/pruned
<CandidateCUI> SU The CUI of the candidate concept
<CandidateMatched> SU The candidate concept matched
<CandidatePreferred> SU The preferred name of the candidate concept
<CandidateScore> SU The negative score of the candidate concept; the computation of this value is explained on pp. 5-9 of MetaMap Evaluation.
<CmdLine> CU All the data about the command used to start MetaMap, consisting of
  • <Command>: the actual operating-system call used to start MetaMap, and
  • <Option>: any options passed to MetaMap
<Command> SU The actual operating-system call used to start MetaMap
<ConceptPIs
  Count="N">
<ConceptPI>		 CR The positional information of the concept, consisting of
  • <StartPos>: the 0-based character offset of the concept, counting from the beginning of the input text, and
  • <Length>: the character length of the string
<ConcMatchEnd> SU The position within the concept words of the last matching word
<ConcMatchStart> SU The position within the concept words of the first matching word
<InputMatch> SU The input word(s) making up the syntax unit
<IsHead> SU Yes/no value denoting if the candidate concept includes the head of the phrase containing it
<IsOverMatch> SU Yes/no value denoting if the candidate concept is an overmatch, i.e., if it contains words on one or both ends that do not match the input text.
<Length> SU The character length of the string
<LexCat> SU The lexical category of the syntax unit
<LexMatch> SU The lexical item(s) matched by the syntax unit
<LexVariation> SU The degree of lexical variation between the words in the candidate concept and the words in the phrase; the computation of this value is explained on pp. 2-3 of MetaMap Evaluation.
<MappingCandidates Total="N">
<Candidate>		 CU The candidate concepts participating in a mapping
<Mappings
  Count="N">
<Mapping>		 CR A set of candidate concepts making up the mapping for the phrase, consisting of
  • <MappingScore>: the negative score of the mapping, and
  • <MappingCandidates>: the candidate concept(s) participating in the mapping.
<MappingScore> SU The negative score of the mapping; the computation of this value is explained on pp. 9-10 of MetaMap Evaluation.
<MatchedWords
  Count="N">
<MatchedWord>		 SR The word(s) in the input text matched by the candidate
<MatchMaps
  Count="N">
<MatchMap>		 CR A data structure representing
  • the correspondence of words in the candidate concept (<TextMatchStart> and <TextMatchEnd>) and words in the phrase (<ConcMatchStart> and <ConcMatchEnd>), and
  • the lexical variation (<LexVariation>) between the words in the candidate concept and the words in the phrase.
For example, given the input text obstructive sleep apnea and the candidate concept sleep apnea, the matching words sleep and apnea are
  • the 2nd and 3rd words of the text, and
  • the 1st and 2nd words of the concept.
There is no lexical variation, so the matchmap would therefore be [[[2,3],[1,2],0]]. For the candidate concept sleep apneas, the MatchMap would be the same, other than having lexical variation of 1 instead of 0.
<MMOs>
<MMO>		 CR All the XML output generated for an entire input record or citation, consisting of
  • <CmdLine>: the command used to start MetaMap,
  • <AA>: any acronyms/abbreviation(s) found in the text,
  • <Negation>: any negation(s) found in the text, and
  • <Utterances>: the utterance(s) found in the text
<Negations
  Count="N">
<Negation>		 CR All the data generated for a negation, including
  • <NegType>: the negation type,
  • <NegTrigger>: the negation trigger,
  • <NegTriggerPI>: the negation trigger's positional information,
  • <NegConcepts>: the negated concept(s), and
  • <NegConcPIs>: the negated concept's StartPos/Length positional information
For more information about MetaMap's implementation of NegEx, see the MetaMap09 Release Notes.
<NegConcCUI> SU The CUI associated with the negated concept
<NegConcepts
  Count="N">
<NegConcept>		 CR The negated concept(s), consisting of
  • <NegConcCUI>: the negated concept's CUI, and
  • <NegConcMatched>: the negated concept's name
<NegConcMatched> SU The name of the negated concept
<NegConcPIs
  Count="N">
<NegConcPI>		 CR The StartPos/Length positional information of the negated concept
<NegTrigger> SU The negation trigger
<NegTriggerPIs
  Count="N">
<NegTriggerPI>		 CR The StartPos/Length positional information of the negation trigger
<NegType> SU The negation type
<Options
  Count="N">
<Option>		 CR The option(s) passed to MetaMap, consisting of
  • <OptName>: the option's name, and
  • <OptValue>: the option's value.
<OptName> SU The name of the command-line option
<OptValue> SU The value of the command-line option (can be null)
<Phrases
  Count="N">
<Phrase>		 CR The syntactic subcomponent of the utterance, consisting of
  • <PhraseText>: the text of the phrase,
  • <SyntaxUnits>: the syntax unit(s),
  • <PhraseStartPos>: the 0-based character offset of the phrase, counting from the beginning of the input text
  • <PhraseLength>: the character length of the phrase,
  • <Candidate>: any candidate concepts identified in the phrase, and
  • <Mapping>: any mappings created
<PhraseLength> SU The character length of the phrase
<PhraseStartPos> SU The 0-based character offset of the phrase, counting from the beginning of the input text
<PhraseText> SU The text of the phrase
<PMID> SU The PubMed ID of the citation containing the utterance
<SemTypes
  Count="N">
<SemType>		 SR The semantic type(s) of the candidate
<Sources
  Count="N">
<Source>		 SR The UMLS vocabulary/ies in which the concept was found
<StartPos> SU The 0-based character offset of the string, counting from the beginning of the input text
<Status> SU 0, 1, or 2, representing if candidate was retained (0), excluded (1), or pruned (2)
<SyntaxType> SU The syntactic type of the syntax unit (e.g., head, mod, verb, etc.)
<SyntaxUnits
  Count="N">
<SyntaxUnit>		 CR The syntactic subcomponent of the phrase, consisting of
  • <SyntaxType>: the syntactic type of the syntax unit (e.g., head, mod, verb, etc.,
  • <LexMatch>: the lexical item(s),
  • <InputMatch>: the input word(s),
  • <LexCat>: the lexical category, and
  • <Tokens>: the token(s) making up the lexical items
<TextMatchEnd> SU The position within the phrase words of the last matching word
<TextMatchStart> SU The position within the phrase words of the first matching word
<Tokens
  Count="N">
<Token>		 SR The tokens making up the lexical items
<Utterances
  Count="N">
<Utterance>		 CR All the data generated for an utterance, including
  • <PMID>: the utterance's PubMed ID,
  • <UttSection>: the section type (e.g., title or abstract),
  • <UttNum>: the 1-based utterance number within the section,
  • <UttText>: the text of the utterance,
  • <UttStartPos>: the 0-based character offset of the utterance, counting from the beginning of the input text
  • <UttLength>: the length, and
  • <Phrases>: the phrase(s) making up the utterance
<UttLength> SU The character length of the utterance
<UttNum> SU The 1-based numerical position of the utterance within the section
<UttSection> SU The section type (e.g., title or abstract) of the utterance
<UttStartPos> SU The 0-based character offset of the utterance, counting from the beginning of the input text
<UttText> SU The text of the utterance

Hierarchical listing of current XML tags

TagTypeDescription
<MMOs>
<MMO>		 CR All the XML output generated for an entire input record or citation, consisting of
  • <CmdLine>: the command used to start MetaMap,
  • <AA>: any acronyms/abbreviation(s) found in the text,
  • <Negation>: any negation(s) found in the text, and
  • <Utterances>: the utterance(s) found in the text
<CmdLine> CU All the data about the command used to start MetaMap, consisting of
  • <Command>: the actual operating-system call used to start MetaMap, and
  • <Option>: any options passed to MetaMap
<Command> SU The actual operating-system call used to start MetaMap
<Options
  Count="N">
<Option>		 CR The option(s) passed to MetaMap, consisting of
  • <OptName>: the option's name, and
  • <OptValue>: the option's value.
<OptName> SU The name of the command-line option
<OptValue> SU The value of the command-line option (can be null)
<AAs
  Count="N">
<AA>		 CR All the data generated for an author-defined Acronym/Abbreviation (AA), consisting of
  • <AAText>: the text of the AA,
  • <AAExp>: its expansion,
  • <AATokenNum>: the number of tokens in the AA
  • <AALen>: the character length of the AA
  • <AAExpTokenNum>: the number of tokens in expansion
  • <AAExpLen>: the character length of its expansion, and
  • <AACUI>: any CUIs associated with the expansion of the AA
The following AA examples will use the text
polymerase chain reaction (PCR).
<AAText> SU The AA itself (PCR)
<AAExp> SU The expansion of the AA (polymerase chain reaction)
<AATokenNum> SU The number of tokens in the AA (1, because PCR contains 1 token)
<AALen> SU The character length of the AA (3, because PCR contains 3 characters)
<AAExpTokenNum> SU The number of tokens in the AA expansion (5, because polymerase chain reaction contains 5 tokens, including two blank tokens)
<AAExpLen> SU The character length of the expansion of the AA (25, because polymerase chain reaction contains 25 characters)
<AACUIs
  Count="N">
<AACUI>		 SR Any CUIs associated with the expansion of the AA.
<Negations
  Count="N">
<Negation>		 CR All the data generated for a negation, including
  • <NegType>: the negation type,
  • <NegTrigger>: the negation trigger,
  • <NegTriggerPIs>: the negation trigger's positional information,
  • <NegConcepts>: the negated concept(s), and
  • <NegConcPIs>: the negated concept's StartPos/Length positional information
For more information about MetaMap's implementation of NegEx, see the MetaMap09 Release Notes.
<NegType> SU The negation type
<NegTrigger> SU The negation trigger
<NegTriggerPIs
  Count="N">
<NegTriggerPI>		 CR The StartPos/Length positional information of the negation trigger
<NegConcepts
  Count="N">
<NegConcept>		 CR The negated concept(s), consisting of
  • <NegConcCUI>: the negated concept's CUI, and
  • <NegConcMatched>: the negated concept's name
<NegConcCUI> SU The CUI associated with the negated concept
<NegConcMatched> SU The name of the negated concept
<NegConcPIs
  Count="N">
<NegConcPI>		 CR The StartPos/Length positional information of the negated concept
<Utterances
  Count="N">
<Utterance>		 CR All the data generated for an utterance, including
  • <PMID>: the utterance's PubMed ID,
  • <UttSection>: the section type (e.g., title or abstract),
  • <UttNum>: the 1-based utterance number within the section,
  • <UttText>: the text of the utterance,
  • <UttStartPos>: the 0-based character offset of the utterance, counting from the beginning of the input text
  • <UttLength>: the length, and
  • <Phrases>: the phrase(s) making up the utterance
<PMID> SU The PubMed ID of the citation containing the utterance
<UttSection> SU The section type (e.g., title or abstract) of the utterance
<UttNum> SU The 1-based numerical position of the utterance within the section
<UttText> SU The text of the utterance
<UttStartPos> SU The 0-based character offset of the utterance, counting from the beginning of the input text
<UttLength> SU The character length of the utterance
<Phrases
  Count="N">
<Phrase>		 CR The syntactic subcomponent of the utterance, consisting of
  • <PhraseText>: the text of the phrase,
  • <SyntaxUnits>: the syntax unit(s),
  • <PhraseStartPos>: the 0-based character offset of the phrase, counting from the beginning of the input text
  • <PhraseLength>: the character length of the phrase,
  • <Candidate>: any candidate concepts identified in the phrase, and
  • <Mapping>: any mappings created
<PhraseText> SU The text of the phrase
<SyntaxUnits
  Count="N">
<SyntaxUnit>		 CR The syntactic subcomponent of the phrase, consisting of
  • <SyntaxType>: the syntactic type of the syntax unit (e.g., head, mod, verb, etc.,
  • <LexMatch>: the lexical item(s),
  • <InputMatch>: the input word(s),
  • <LexCat>: the lexical category, and
  • <Tokens>: the token(s) making up the lexical items
<SyntaxType> SU The syntactic type of the syntax unit (e.g., head, mod, verb, etc.)
<LexMatch> SU The lexical item(s) matched by the syntax unit
<InputMatch> SU The input word(s) making up the syntax unit
<LexCat> SU The lexical category of the syntax unit
<Tokens
  Count="N">
<Token>		 SR The tokens making up the lexical items
<PhraseStartPos> SU The 0-based character offset of the phrase, counting from the beginning of the input text
<PhraseLength> SU The character length of the phrase
<Candidates
  Total="T"
  Excluded="E"
  Pruned="P"
  Remaining="R">
<Candidate>		 CR Total="T" All the data generated for a candidate concept, including
  • <CandidateScore>: the candidate's negative score,
  • <CandidateCUI>: its CUI,
  • <CandidateMatched>: the candidate matched,
  • <CandidatePreferred>: its preferred name,
  • <MatchedWords>: the text word(s) it matches,
  • <MatchMaps>: the matchmap(s),
  • <SemTypes>: the semantic type(s),
  • <IsHead>: IsHead (yes/no),
  • <IsOverMatch>: IsOverMatch (yes/no),
  • <Sources>: the UMLS source(s),
  • <ConceptPIs>: the positional information, and
  • <Status>: 0/1/2 depending on if candidate is retained/excluded/pruned
<CandidateScore> SU The negative score of the candidate concept; the computation of this value is explained on pp. 5-9 of MetaMap Evaluation.
<CandidateCUI> SU The CUI of the candidate concept
<CandidateMatched> SU The candidate concept matched
<CandidatePreferred> SU The preferred name of the candidate concept
<MatchedWords
  Count="N">
<MatchedWord>		 SR The word(s) in the input text matched by the candidate
<SemTypes
  Count="N">
<SemType>		 SR The semantic type(s) of the candidate
<MatchMaps
  Count="N">
<MatchMap>		 CR A data structure representing
  • the correspondence of words in the candidate concept (<TextMatchStart> and <TextMatchEnd>) and words in the phrase (<ConcMatchStart> and <ConcMatchEnd>), and
  • the lexical variation (<LexVariation>) between the words in the candidate concept and the words in the phrase.
For example, given the input text obstructive sleep apnea and the candidate concept sleep apnea, the matching words sleep and apnea are
  • the 2nd and 3rd words of the text, and
  • the 1st and 2nd words of the concept.
There is no lexical variation, so the matchmap would therefore be [[[2,3],[1,2],0]]. For the candidate concept sleep apneas, the MatchMap would be the same, other than having lexical variation of 1 instead of 0.
<TextMatchStart> SU The position within the phrase words of the first matching word
<TextMatchEnd> SU The position within the phrase words of the last matching word
<ConcMatchStart> SU The position within the concept words of the first matching word
<ConcMatchEnd> SU The position within the concept words of the last matching word
<LexVariation> SU The degree of lexical variation between the words in the candidate concept and the words in the phrase; the computation of this value is explained on pp. 2-3 of MetaMap Evaluation.
<IsHead> SU Yes/no value denoting if the candidate concept includes the head of the phrase containing it
<IsOverMatch> SU Yes/no value denoting if the candidate concept is an overmatch, i.e., if it contains words on one or both ends that do not match the input text.
<Sources
  Count="N">
<Source>		 SR The UMLS vocabulary/ies in which the concept was found
<ConceptPIs
  Count="N">
<ConceptPI>		 CR The positional information of the concept, consisting of
  • <StartPos>: the 0-based character offset of the concept, counting from the beginning of the input text, and
  • <Length>: the character length of the string
<StartPos> SU The 0-based character offset of the string, counting from the beginning of the input text
<Length> SU The character length of the string
<Status> SU 0, 1, or 2, representing if candidate was retained (0), excluded (1), or pruned (2)
<Mappings
  Count="N">
<Mapping>		 CR A set of candidate concepts making up the mapping for the phrase, consisting of
  • <MappingScore>: the negative score of the mapping, and
  • <MappingCandidates>: the candidate concept(s) participating in the mapping
<MappingScore> SU The negative score of the mapping; the computation of this value is explained on pp. 9-10 of MetaMap Evaluation.
<MappingCandidates Total="N">
<Candidate>		 CU The candidate concepts participating in a mapping