Medical Text Indexer Output Help Information

Simple (Interactive)
Description The Interactive Simple output format breaks the terms out into their component sections (Suggested MeSH Heading, Suggested CheckTags, and Suggested SubHeadings).
Suggested MeSH Headings:
   -- Macaca

Suggested CheckTags:
   -- Animal

Suggested SubHeadings:
   -- No SubHeadings Recommended
Simple (Batch)
Description The Batch Simple output format is similar to the Interactive Simple format detailed above, except here, we add in the PMID and a field separator.
99999999|Suggested MeSH Headings:
99999999|   -- Macaca
99999999|Suggested CheckTags:
99999999|   -- Animal
99999999|Suggested SubHeadings:
99999999|   -- No SubHeadings Recommended
Description Detailed display showing all relevant information about all of the topN recommendations.
Format: PMID|Term|CUI|Score|Type|Misc|Location|Path(s)

PMID - PubMed assigned unique identifier.  If freetext, this is "0".

Term - MeSH Term.  If the term has an asterisk ("*") at the beginning, it
       denotes that the term was identified as coming from the Title section
       of a document.  This is an optional output item and requires the
       "-starMHTI" option being specified.

CUI  - Concept Unique Identifier for the MeSH Term.

Score - MTI score for this term.

Type - Type of the term:
            MH - MeSH Heading
            HM - Heading Mapped to
            ET - Entry Term
            NM - Supplemental Concept
            SH - MeSH SubHeading
            CT - MeSH CheckTag

Misc - If ET, this explains the replacement.  If not, blank.

Location - If term comes from MMI, we have location information showing
         where the term came from within the text.  "TI" - Title,
         "AB" - Abstract or "TI;AB" - comes from both Title and Abstract.

Path(s) - One or more designators showing which of the pathways recommended
         the term.

            MM - MetaMap's MMI
            RC - PubMed Related Citations
            TG - John Wilbur's Trigram Method
99999999|*Macaques|C0024398|36858|ET|Replaces "Macaca" - Alternative(s) (Macaque)|TI|MM;RC
99999999|Simian T-lymphotropic virus 1|C0038344|1758|MH|||RC
Full Listing with Detailed
Description The Full Listing format is the similar to the Detailed format outlined above. The differences are that the Full Listing shows the entire list and includes a number showing the list position for each recommendation.
Format: PMID|List position|Term|CUI|Score|Type|Misc|Location|Path(s)

The fields are defined as above in the "Detailed" output format.  The only
addition is as follows:

List position - One up number of the term's location in our hierarchical list.
99999999|11|Simian T-lymphotropic virus 1|C0038344|1758|MH|||RC
99999999|12|Monkey Diseases|C0026431|1026|MH|||RC
Just The Facts
Description The fields are the same as "Detailed" above except here we limit to just the first four fields.
Format: PMID|Term|CUI|Score
Description The DCMS List output format is a single line showing the PMID followed by zero or more recommended MeSH Terms and their associated data type.
Format:  PMID|Recommended MeSH Term:Data Type|
99999999|Macaca:MH|Hominidae:MH|Spumavirus:MH|Cercopithecus aethiops:MH|
Papio:MH|Retroviridae:MH|Pan troglodytes:MH|Retroviridae Infections:MH|
Primates:MH|Simian T-lymphotropic virus 1:MH|Monkey Diseases:MH|
Macaca mulatta:MH|Animals:MH|Macaca nemestrina:MH|Gorilla gorilla:MH|
Molecular Sequence Data:MH|Cercopithecus:MH|Deltaretrovirus Infections:MH|
Phylogeny:MH|Base Sequence:MH|Primate Diseases:MH|DNA Primers:MH|
SIV:MH|Antigens, Viral:MH|Polymerase Chain Reaction:MH|
Show "NO_TERMS" List
Description This is the same as the DCMS List above except if we have zero recommendations for a given PMID, we will print "NO_TERMS".
Format:  PMID|Recommended MeSH Term:Data Type|