These tools will no longer be maintained as of December 31, 2024. Archived webpage can be found here. Indexing Initiative Github repository under development. Contact NLM Customer Service if you have questions.
These tools will no longer be maintained as of December 31, 2024. Archived webpage can be found here. Indexing Initiative Github repository under development. Contact NLM Customer Service if you have questions.
TOOLS
| Simple (Interactive) | |
| Description | The Interactive Simple output format breaks the terms out into their component sections (Suggested MeSH Heading, Suggested CheckTags, and Suggested SubHeadings). |
| Example |
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. |
| Example |
99999999|Suggested MeSH Headings: 99999999| -- Macaca 99999999| 99999999|Suggested CheckTags: 99999999| -- Animal 99999999| 99999999|Suggested SubHeadings: 99999999| -- No SubHeadings Recommended |
| Detailed | |
| 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
|
| Example |
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. |
| Example |
99999999|1|Macaca|C0024398|36858|MH||TI|MM;RC 99999999|2|Hominidae|C0019874|9762|MH||TI;AB|MM 99999999|3|Spumavirus|C0080180|7927|MH||AB|MM;RC 99999999|10|Primates|C0033147|1828|MH||AB|MM;RC 99999999|11|Simian T-lymphotropic virus 1|C0038344|1758|MH|||RC 99999999|12|Monkey Diseases|C0026431|1026|MH|||RC 99999999|13|transmission|C0040722|1011|SH||TI|MM |
| 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
|
| Example |
99999999|*Macaques|C0024398|36858 |
| DCMS List | |
| 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| |
| Example |
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| Human:CT|Animal:CT|transmission:SH| |
| 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| |
| Example |
99999999|NO_TERMS |