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 |