| MTI Parameter Information |
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| Filtering | |||
| Parameter | Default Value | Option | Notes |
|---|---|---|---|
| Pre-Packaged Filtering: | |||
| Default for MEDLINE Citations (intended for use with MEDLINE citations) |
OFF | -defaultL_MTI | This option incorporates
the following options: Default Filtering, Add CheckTags,
Add Geographics, Add USA, Remove "Do Not Index With" Terms, Limit
Results for Title Only Citations, Limit Results via Publication Types,
Star MHs that come from the Title, Rank Score Filtering for Title
Only Citations, Show Term Unique Identifers, Use Latest Supplemental
Concepts, Perform Aged/Human Review, use WSD, and we use the
"justFacts" Output option.
Please Note: This option is intended for use with MEDLINE citations. This option uses the PMID to request related citations from PubMed. If you are processing non-MEDLINE text and using your own PMIDs, please use the option below - you will get much better results. |
| Default for Non-MEDLINE Text (intended for use with Non-MEDLINE text) |
OFF | -default_MTI | This option is the same as the above option except it is intended for use with Non-MEDLINE text. This option uses a backup method of identifying related citations based on the text and not the PMID. |
| MeSH on Demand | OFF | -MoD_PP | This option uses the MeSH on Demand filtering and provides a list of the top 10 related citations in PubMed as it's first line followed by each MeSH term summarizing the input text. Each MeSH term also includes the MeSH Unique Identifier (DUI/CUI), UMLS Concept Identifier (CUI), and a MTI score. This is not intended to be a replacement for using the existing MeSH on Demand web page which provides a richer output. |
| Special Output (raw results) | OFF | -Special_Output | This is the option that we use internally to create a static data set from which to work from with MTI. This option overrides everything else that you might set. The reason is that this simply takes the input from the various input paths and performs a simple filtering of the data (removing excluded terms, etc.). The remaining terms are provided as a result with all of the relevant data. |
| Option-1 for MEDLINE Citations (intended for use with MEDLINE citations) |
ON | -opt1L_DCMS | This is the same as the Default Processing, except we use
the "Detailed" Output option instead of "List".
Please Note: This option is intended for use with MEDLINE citations. This option uses the PMID to request related citations from PubMed. If you are processing non-MEDLINE text and using your own PMIDs, please use the option below - you will get much better results. |
| Option-1 Processing for Non-MEDLINE Text (intended for use with Non-MEDLINE text) |
ON | -opt1_DCMS | This option is the same as the above option except it is intended for use with Non-MEDLINE text. This option uses a backup method of identifying related citations based on the text and not the PMID. |
| Do No Filtering, Adds, or Forced | OFF | -doNoAddForced | This option turns off all of the special filtering, additions, and the use of any of the lookup lists for MTI. This allows you to evaluate basic performance of the paths without the interference of the post-processing we do in MTI. |
| Basic Filtering: | |||
| Default Filtering | OFF | Basic MTI processing based on the default values for all options. | |
| Medium Filtering | OFF | -medFilter | Remove items from the list of recommendations based on specific heuristics. |
| Strict Filtering | OFF | -strictFilter | Remove all items from the list of recommendations that are not recommended by both MetaMap and PubMed Related Citations. |
| Filtering Modifiers: | |||
| Force MTI as First Line Indexer (MTIFL) | OFF | -forceMTIFL | Forces MTI to use MTIFL filtering. |
| Post Processing | |||
| Parameter | Default Value | Option | Notes |
| Star MHs that come from the Title | ON | -starMHTI | Add "*" to each MeSH Term that was identified from the Title. This is similar to IM term identification. |
| Add CheckTags | ON | -addCTs | Add from a list of CheckTags based on review of actual text and the list of CheckTags. |
| Add Geographics | ON | -addGEOs | Add from a list of Geographic Locations based on review of actual text and the list of Geographics. |
| Add USA if Triggered | ON | -addUSA | If the MeSH Heading United States is not already assigned and we any of the items from the USA triggers list in the article or list of results, we will add Unites States. |
| Remove "Do Not Index With" Terms | ON | -remMHs | Remove MeSH Terms which have been indicated as "Do Not Index With" from our list of recommendations and prior to scoring. |
| Show Headings Mapped to (HM) | ON | -showHMs | Display MeSH Headings that are in fact "Headings Mapped to" with a "HM" notation versus normal MeSH Headings "MH" notation. |
| Show Entry Terms (ET) | ON | -showETs | Replace MeSH Headings with their corresponding Entry Term where applicable. |
| Show Treecodes | OFF | -showTreecodes | In the detailed outputs, add in the treecodes for each result if we have them (everything above the line will have the information). |
| Show Term Unique Identifiers | ON | -showTUIs | Normally only used in our overnight DCMS processing. The TUIs map to a specific term in the MeSH vocabulary and allow the DCMS personnel to map to the appropriate MeSH term even when the spelling of a term changes. |
| Perform Aged/Human Review | ON | -doAgedReview | Make sure we don't add age related checktags if we already have the CheckTag Animals set and Humans not set. If Animals is not set, and we have age related CheckTags recommended, we need to add Humans. Age related CheckTags include: "Adolescent", "Adult", "Aged", "Child", "Infant", and "Infant, Newborn". If Animals is set, we will remove any of these age related CheckTags. |
| Bypass Related Citations Results Exclusion | ON | -nocheckRC | Do not process the results obtained via the PubMed Related Citations through our MH_exclude list. |
| Limit Recommendations via Publication Types | ON | -limitPTs | Reduce the number of recommendations from the default when a citation is identified by specific Publication Types. Currently this is set as follows: PT equals "Review" or "News", we limit the number of returned terms to 14. If the PT equals "Editorial", we limit to 9, and if the PT equals "Letter", we limit to 8. |
| Limit Recommendations for Title Only Citations | ON | -limitTitleOnly | Reduce the number of recommendations from the default when a citation only has a title field and no abstract. This is currently calculated based on the number of words in the title: 0-2 words limits the number to 7, 3 or 4 limit to 8, 5 or 6 limit to 10, 7 - 10 limit to 11, 11-14 limit to 12, 15 - 18 limit to 13, 19 - 21 limit to 14, and anything larger then 21 words in the title is limited to 13 items. |
| Rank Score Filtering for Title Only Citations | ON | -RSfilterTO | If this is a title only abstract/citation AND the term is ranked 11 or below on the list of recommendations AND if the score is less then 190, we will stop the list. |
| Rank Score Filtering for Title & Abstract Citations | ON | -RSfilterALL | If this is a title AND abstract citation AND the term is ranked 14 or below on the list of recommendations AND if the score is less then 203, we will stop the list. |
| Use Latest Supplemental Concepts | ON | -doSuppChemUpdate | Every Monday morning the MeSH Vocabulary is updated. This usually only involves the Supplement Concepts. Each week we create a lookup list telling how to handle the changes (replace or remove). This option says to use this updated lookup list and apply any relevant changes. If you don't use this option, the results will be from the static MeSH Vocabulary created at the beginning of each MeSH Indexing year. |
| Show MeSH DUIs | OFF | -showDUIs | In the detailed output, add in the MeSH Unique Identifier for each result if we have it. |
| Use Word Sense Disambiguation (WSD) | ON | -useWSD | This option turns on the WSD option for the MetaMap path to MTI. MetaMap uses WSD to limit ambiguous UMLS Concepts it finds in the text being processed. |
| Output | |||
|
Please Note: There is now a new help page just for
the output options which shows examples for each output type. MTI Output Help Information page |
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| Parameter | Default Value | Option | Notes |
| Simple | OFF | -display_simple2 (Interactive) -display_simple3 (Batch) |
Simple display with only the names of the MeSH Headings, CheckTags, and SubHeadings being displayed in scoring order and with annotations. This was the default output for the old Interactive MTI web page. The current options better reflect the actual program. |
| Detailed | ON | <blank> or -detail |
Detailed display showing all relevant information about all of the topN recommendations. This includes: name of the item, CUI, final score, type, where item was found in the text, and who recommended the term. In the case of CheckTags and SubHeadings, the field after the type (CT/SH) contains the triggering information - who caused this item to be included in the recommendations. Recommendations are displayed in scoring order. |
| Full Listing with Detailed | OFF | -display_full | 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. |
| Just The Facts | OFF | -justFacts | The fields are the same as "Detailed" above except here we limit to just the first four fields - PMID|Term|CUI|Score |
| Default List | OFF | -detail_list | The Default List output format is a single line showing the PMID followed by zero or more recommended MeSH Terms and their associated data type. |
| Show "NO_TERMS" List | OFF | -detail_listII | This is the same as the DCMS List above except if we have zero recommendations for a given PMID, we will print "NO_TERMS". |
| XML | OFF | -xml | In the XML output format, we enclose all the terms with XML tags. The list has "<KEYWORD_LIST>" and "</KEYWORD_LIST>" tags denoting start and end respectively. Each recommended term, regardless of type is then enclosed within the tags. |
| Debugging | |||
| Parameter | Default Value | Option | Notes |
| Detailed Display of Path Inputs | OFF | -debug1 | Detailed information for applying Medium Filtering. Usually used for |
| Show Decisions during Medium Filtering | OFF | -medFilterR | Detailed information for applying Medium Filtering. Usually used for debugging purposes. Identifies how items are saved and removed. NOTE: This option turns on Medium Filtering. |
| Show Decisions during Aged/Human Review | OFF | -showAgedReview | Detailed information for applying Aged/Human Review. Usually used for debugging purposes. Identifies how items are saved and removed. NOTE: This option turns on the Aged/Human Review. |
| Show Decisions during ET Substitution | OFF | -showETsD | Detailed information for applying ET Substitution. Usually used for debugging purposes. Identifies how items are identified. NOTE: This option turns on the Show Entry Terms. |
| Show Decisions during HM Substitution | OFF | -showHMsD | Detailed information for applying HM Substitution. Usually used for debugging purposes. Identifies how items are identified. NOTE: This option turns on the Show Headings Mapped to. |
| Show Decisions during Restrict to MeSH | OFF | -RTM_Debug | Detailed information for we convert UMLS Concepts to MeSH Terms via the Restrict to MeSH process. Usually used for debugging purposes. |
| Show Timing during Processing | OFF | -doTiming | Shows how long various sections of the MTI processing take during the processing of an item. |
| Show Interim Weight Breakout by Path | OFF | -showInterimBreakout | Shows the raw list of results from the various paths before any scoring, clustering, and filtering has been done. The display breaks out how the various paths contribute to the overall weight for each list item. |
| Show Decision Point in Rank Score Filtering | OFF | -showRSfilter | Shows the list item that triggers the Rank Score Filtering to kick-in. This works for both RSfilterTO and RSfilterALL. |
| Show MTI Explanation Information | OFF | -showJust | Shows information about all of the recommendations made by MTI. The information here is similar to the Expanded Detail output format. |
| Advanced Options | |||
| Number of MeSH Terms to Display | |||
| Parameter | Default Value | Option | Notes |
| Number of MeSH Terms to Display | 25 | -topn <int> | Max Number of Recommendations to Display - roughly. This number dictates the number of terms returned and then we add some terms depending on the options you select (addGEOs, addCTs, etc.). The options that add terms can push the number of terms over this number. The valid range here is again 0 to 32,767. 0 would not be very helpful though. |
| Path Weight | |||
| Parameter | Default Value | Option | Notes |
| MetaMap | 7 | -mmi <float> | Path Weight for MetaMap Range: 0 to 32,767. 0 turns off |
| Related Citations | 2 | -pub <float> | Path Weight for Related Citations Range: 0 to 32,767. 0 turns off |
| Trigram | 0 | -trg <float> | Path Weight for Trigram Range: 0 to 32,767. 0 turns off |
| Related Citation | |||
| Parameter | Default Value | Option | Notes |
| Number of Citations | 10 | -cit <int> | Number of related citations to use from PubMed. Range: 0 to 100. 0 effectively turns off the RC path |
| MeSH major topic | 1.00 | -im <float> | Relevance scoring for MeSH major topic items returned from the Related Citations method. Range: 0.00 to 1.00 |
| MeSH term | 0.80 | -nim <float> | Relevance scoring for normal MeSH items returned from the Related Citations method. Range: 0.00 to 1.00 |
| Nav Weight | |||
| Used in calculating the NavScore part of the Clustering Algorithm. The NavScore is the confidence in navigating from a UMLS term to a MeSH Heading. | |||
| Parameter | Default Value | Option | Notes |
| Direct Match | 1.00 | -dir <float> | Relevance scoring for term identified as having a "Direct Match" to a MeSH Heading via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| ATX | 1.00 | -atx <float> | Relevance scoring for term identified as having an "Associated Expression" relationship to a MeSH Heading via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| Parent/Broader | 0.90 | -par <float> | Relevance scoring for term identified as having an "Parent" relationship (term is the parent of the MeSH Heading), or "Broader" relationship (term is a broader term then the MeSH Heading) via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| Child/Narrower | 0.75 | -chd <float> | Relevance scoring for term identified as having a "Child" relationship (term is the child of the MeSH Heading), or "Narrower" relationship (term is a narrower then the MeSH Heading) via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| Sibling | 0.70 | -sib <float> | Relevance scoring for term identified as having a "Sibling" relationship to the MeSH Heading via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| Other Related | 0.50 | -oth <float> | Relevance scoring for term identified as having an "Other Related" relationship (not synonyous, narrower, or broader) to the MeSH Heading via lookup in the UMLS MRREL file. Range: 0.00 to 1.00 |
| Ranking | |||
| Parameter | Default Value | Option | Notes |
| Co-occurrences Factor | 10000 | -cot <int> | Relevance scoring for terms identified as co-occurring with another term. Co-occurrences are concepts that occur together in the same "entries" in some information source. Co-occurrence is identified using the UMLS MRCOC file. Valid range is 0 to 32,767 where 0 turns it off. |
| Title Factor | 20 | -ti <int> | Booster for MeSH Headings identified as coming from the Title field of the citation being processed. Value is a percentage of the current score to add. For example, the default is 20. We would multiply the current score by 120%. NOTE: Not currently used! This parameter has been superceded by the "Emphasize Titles" factor which is a defined doubling of the score for items found in the Title field of the citation. This emphasis is done after ranking and clustering. |
| Related Term Factor | 100 | -rel <int> | Relevance scoring for terms identified as being related via the MeSH tree structure. This is used during the Clustering phase and figures into the overall RankScore for an item. Valid range is 0 to 32,767 where 0 turns it off. |
| Misc. | |||
| Parameter | Default Value | Option | Notes |
| Emphasize HSTAR | 0.00 | -emp_hstar <float> | Boost the scoring for MeSH terms found in the following MeSH
tree hierarachies: N01 - N05, G02 - G03, L01. score = current_score + (current_score * HSTAR_FACTOR) We have had limited success with a HSTAR_FACTOR of 20. Valid range is 0.00 and up. 0.00 turns it off. |
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