SKR/MetaMap:
  1. Valid Data Models include: A, B, C.
    Where "A" represents Strict Model, "B" represents Moderate Model, and "C" represents Relaxed Model. Default is "A" Strict Model

  2. Valid Knowledge Sources: 02, 03, 04, and 05.
    Where the numbers represent the last two-digits of the UMLS Knowledge Sources year. For example,
    02 would be 2002 UMLS Knowledge Source. Default is 05 for 2005.

  3. Valid Priority values: 0, 1, 2.
    Where "0" represents Normal priority - most likely priority, "1" represents Medium, and "2" represents High priority.
    Medium and High priorities are reserved and you must have the proper permissions to use them. Default is 0 for Normal priority.

  4. You may elect to use "Restrict to Sources" OR "Exclude Sources", but, not both.

  5. You may elect to use "Restrict to Semantic Type(s)" OR "Exclude Semantic Type(s)", but not both.

  6. Specifying the "Threshold Number" will automatically set the Threshold (-r) option.

  7. For more in-depth information about the SKR/MetaMap options, please refer to the following document:
    PDF - Description of SKR/MetaMap Options Description of SKR/MetaMap Options (280 kb)

  8. The following are the options we normally use, and have set as defaults from the SKR web site:

    General Description Arg Short Name
    Plain Syntax p plain_syntax
    Candidates c candidates
    Semantic Types s semantic_types
    Mappings m mappings
    Tag Text t tag_text
    Adj/Noun Derivational Variants D an_derivational_variants
    No Acronym/Abbreviation Variants a no_acros_abbrs
    Stop Large N l stop_large_n
    Best Mappings Only b best_mappings_only
    Which equates to skr05 -ApcsmtDalb


  9. The following list details all of the SKR API available options for the SKR/MetaMap program:
General Description Arg Short Name Form Name Default Type
Data Model to Use - DMOption DMOption "A" String
Knowledge Source Selection - KSource KSource "05" String
Plain Syntax p plain_syntax Defaults7 false Boolean
Candidates c candidates Defaults2 false Boolean
Semantic Types s semantic_types Defaults4 false Boolean
Mappings m mappings Defaults6 false Boolean
Tag Text t tag_text Defaults1 false Boolean
Adj/Noun Derivational Variants D an_derivational_variants CB30 false Boolean
No Acronym/Abbreviation Variants a no_acros_abbrs CB3 false Boolean
Stop Large N l stop_large_n Defaults3 false Boolean
Best Mappings Only b best_mappings_only Defaults5 false Boolean
Restrict to Semantic Types List - Jstypes Jstypes "" String
Display Phrases Only - Phrases Phrases false Boolean
Restrict to Sources List - Rsources Rsources "" String
Threshold Number - Threshold Number Threshold "" String
Data Version to Use - Version Version "" String
Exclude Sources List - esources esources "" String
Exclude Semantic Types List - kstypes kstypes "" String
Formal Tagger Output F formal_tagger_output CB33 false Boolean
Show Concept's Sources [2006+] G sources DSP_SRC false Boolean
Show Original Phrases [2006+] H display_original_phrases DSP_OP false Boolean
Show CUIs I show_cuis CB100 false Boolean
Restrict to Semantic Type(s) J restrict_to_sts New03_3 false Boolean
Ignore Stop Phrases K ignore_stop_phrases CB54 false Boolean
MMI Output M mmi_output Output2 false Boolean
Fielded MMI output N fielded_mmi_output New03_12 false Boolean
Show Preferred Names Only [2005+] O show_preferred_names_only SPNOutput false Boolean
Composite Phrases P composite_phrases CB31 false Boolean
Quick Composite Phrases Q quick_composite_phrases CB51 false Boolean
Restrict to Sources R restrict_to_sources New03_1 false Boolean
SemRep Output S semrep_output Output3 false Boolean
Tagger Output T tagger_output Output1 false Boolean
Data Version V mm_data_version DV false Boolean
Show Preferred Name Sources W preferred_name_sources New03_5 false Boolean
Truncate Candidates Mapping X truncate_candidates_mappings CB52 false Boolean
Prefer Multiple Concepts Y prefer_multiple_concepts CB32 false Boolean
No Derivational Variants d no_derivational_variants CB2 false Boolean
Exclude Sources e exclude_sources New03_2 false Boolean
Fielded Output f fielded_output FO1 false Boolean
Allow Concept Gaps g allow_concept_gaps Browse3 false Boolean
Ignore Word Order i ignore_word_order Browse4 false Boolean
Show Acronym/Abbreviations [2006+] j dump_aas DSP_AAS false Boolean
Exclude Semantic Type(s) k exclude_sts New03_4 false Boolean
Number Candidates n number_the_candidates CB5 false Boolean
Allow Overmatches o allow_overmatches Browse2 false Boolean
Machine Output q machine_output CB6 false Boolean
Threshold Option r threshold CB8 false Boolean
Unique Acronym/Abbrev Variants u unique_acros_abbrs_only CB4 false Boolean
Variants v variants CB7 false Boolean
Syntax x syntax CB1 false Boolean
Term Processing z term_processing Browse1 false Boolean
 
 
MTI:
  1. For more in-depth information about the MTI options, please refer to the following document:
    Description of MTI Options (html)
General Description Arg Short Name Form Name Default Type
Number of MeSH Terms to Display - topn <int> topn 25 Boolean
Default DCMS Processing - default_DCMS Filtering false Boolean
Option-1 DCMS Processing - opt1_DCMS Filtering false Boolean
Default Gateway Processing - default_NewGateway Filtering false Boolean
Option-1 Gateway Processing - opt1_NewGateway Filtering false Boolean
Special Output (raw results) - Special_Output Filtering false Boolean
Default Filtering - <blank> Filtering false Boolean
Medium Filtering - medFilter Filtering false Boolean
Strict Filtering - strictFilter Filtering false Boolean
Star MHs that come from the Title - starMHTI starMHTI false Boolean
Add CheckTags - addCTs addCTs false Boolean
Add Geographics - addGEOs addGEOs false Boolean
Add USA if Triggered - addUSA addUSA false Boolean
Remove "Do Not Index With" Terms - remMHs remMHs false Boolean
Show Headings Mapped to (HM) - showHMs showHMs false Boolean
Show Entry Terms (ET) - showETs showETs false Boolean
Show Treecodes - showTreecodes showTreecodes false Boolean
Show Term Unique Identifiers - showTUIs showTUIs false Boolean
Perform Aged/Human Review - doAgedReview doAgedReview false Boolean
Bypass Related Citations Results Exclusion/td> - nocheckRC nocheckRC false Boolean
Limit Recommendations via Publication Types - limitPTs limitPTs false Boolean
Limit Recommendations for Title Only Citations - limitTitleOnly limitTitleOnly false Boolean
Rank Score Filtering for Title Only Citations - RSfilterTO RSfilterTO false Boolean
Rank Score Filtering for Title & Abstract Citations - RSfilterALL RSfilterALL false Boolean
Use Latest Supplemental Concepts - doSuppChemUpdate doSuppChemUpdate false Boolean
Show MeSH DUIs - showDUIs showDUIs false Boolean
Simple/Default - display_simple2 Output false Boolean
Detailed - <blank> or detail Output true Boolean
Expanded Detailed - detail2 Output false Boolean
Full Listing w/ Detailed - detail_list Output false Boolean
Show "NO_TERMS" List - detail_listII Output false Boolean
XML Output - xml Output false Boolean
Detailed Display of Path Inputs - debug1 debug1 false Boolean
Show Decisions during Medium Filtering - medFilterR medFilterR false Boolean
Show Decisions during Aged/Human Review - showAgedReview showAgedReview false Boolean
Show Decisions during ET Substitution - showETsD showETsD false Boolean
Show Decisions during HM Substitution - showHMsD showHMsD false Boolean
Show Decisions during Restrict to MeSH - RTM_Debug RTM_Debug false Boolean
Show Timing during Processing - doTiming doTiming false Boolean
Show Interim Weight Breakout by Path - showInterimBreakout showInterimBreakout false Boolean
Show Decision Point in Rank Score Filtering - showRSfilter showRSfilter false Boolean
MetaMap - mmi <float> mmi 7 String
Related Citations - pub <float> pub 2 String
Trigram - trg <float> trg 0 String
Number of Citations - cit <int> cit 10 String
MeSH major topic - im <float> im 1.00 String
MeSH term - nim <float> nim 0.80 String
Direct Match - dir <float> dir 1.00 String
ATX - atx <float> atx 1.00 String
Parent/Broader - par <float> par 0.90 String
Child/Narrower - chd <float> chd 0.75 String
Sibling - sib <float> sib 0.70 String
Other Related - oth <float> oth 0.50 String
Co-occurrences Factor - cot <int> cot 10000 String
Title Factor - ti <int> ti 20 String
Related Term Factor - rel <int> rel 100 String
Emphasize HSTAR - emp_hstar <float> emp_hstar 0.00 String
 
SemGen:
General Description Arg Short Name Form Name Default Type
Full Fielded Output D FullFielded FullFielded false Boolean
 
SemRep:
General Description Arg Short Name Form Name Default Type
Full Fielded Output D FullFielded FullFielded false Boolean
 
Generic:
  1. There is NO Interactive facility for Generic jobs.

  2. Generic jobs must have commands that reside in /nfsvol/nls/bin.

  3. Commands for the Generic jobs must not have ".." embedded in their path.

  4. Generic jobs can be normal (without validation), or with validation where the Scheduler expects an "<<< EOT >>>"
    end of result marker on a line by itself, so it can verify it received a complete result. To specify whether you want to use
    validation or not, you change the boolean value of the initial job object creation. "false" indicates that you want normal
    Generic Batch processing, while "true" indicates that you want Generic Batch with Validation processing.

    GenericObject myGenericObj = new GenericObject(false);
    GenericObject myGenericObj = new GenericObject(true);

  5. Generic jobs also allow you to specify any special environment variables you might need inorder to run your command.
    Specified via the Batch_Env field. For example,

    setField("Batch_Env", "NLS=/nfsvol/nls#CC=gcc");.

    Where each environment variable is separated by a "#".
General Description Arg Short Name Form Name Default Type
Batch Command - Batch_Command Batch_Command "" String
Batch Environment - Batch_Env Batch_Env "" String