Sub-Term Mapping Tools

Synonym Norm Development

I. Requirements
Use normalization to aggressively map a term to its synonyms by abstracting away from

• g: Genitive
• rs: parenthetical plural forms (s), (es), (ies)
• o: Punctuation
• l: cases
• Ct: spelling variants and inflectional variants

• remove duplicated spaces
• trim
• duplicated results

II. Developments

• Approach 1 (Ct on input term):
  • use lvg -f:g:rs:o:l:Ct
  • Ct is to get the citation form on the input term
  • fast performance
  • lower coverage rate (98% of method bellows)
  • Example 1:

    ID	Term	norm term	synonym substitutions	CUI
    KP102818	CLOTTING FACTOR DEFICIENCY, CONGENITAL	...	not found

• Approach 2 (Ct on every words of input term):
  • Use lvg -f:g:rs:o:l:Ct
  • Customize Ct to get the citation form on every words of the input term
  • More mutation and results slower performance and high coverage rate
  • Example 1:

    ID	Term	norm term	synonym substitutions	CUI
    KP102818	CLOTTING FACTOR DEFICIENCY, CONGENITAL	clot factor deficiency congenital	coagulation factor deficiency hereditary ...	C0272316

  • However, still misses some mapping when the citation form has punctuation, such as "carcino-embryonic" is the citation of "carcinoembryonic"
  • Example 2:

    ID	Term	norm term	synonym substitutions	CUI
    KP194142	Elevated carcinoembryonic antigen	elevate carcino-embryonic antigen	increase carcino-embryonic antigen increased carcino-embryonic antigen high carcino-embryonic antigen ...	C0549371

• Approach 3 (Move Ct before removing punctuation):
  • Use lvg -f:g:rs:Ct:l:o
  • Example 2:

    ID	Term	norm term	synonym substitutions	CUI
    KP194142	Elevated carcinoembryonic antigen	elevate carcino embryonic antigen	increase carcino embryonic antigen increased carcino embryonic antigen high carcino embryonic antigen ...	C0549371
    			elevate cea	C0742014

  • Add remove genitive after Ct:
    • E0000135|Addison's disease|Addisons disease
    • There are no records with CT has (s), (es), (ies), so no need for -f:rs
    • Use Database for CUI mapping to improve performance

III. Comparisons

	Approach 1 (Ct on term)	Approach 2 (CuiMap)	Approach 3 (Smt)
Performance	Fast KP: 27 min. VA: 23 min.	Slow KP: 78 min. VA: 321 min.	Fast KP: 22 min. VA: 68 min.
Coverage-KP (26890 terms)	CUI with Norm: 12165 - 45.24% CUI with 1 synonyms: 1673 - 6.22% CUI with 2 synonyms: 168 - 0.62% No CUI found: 12884 - 47.91% Total term-CUIs found: 31643	CUI with Norm: 12165 - 45.24% CUI with 1 synonyms: 1692 - 6.29% CUI with 2 synonyms: 174 - 0.65% No CUI found: 12859 - 47.82% Total term-CUIs found: 31660	CUI with Norm: 12165 - 45.24% CUI with 1 synonyms: 1692 - 6.29% CUI with 2 synonyms: 174 - 0.65% No CUI found: 12859 - 47.82% Total term-CUIs found: 31661
Coverage-VA (21221 terms)	CUI with Norm: 16937 - 79.81% CUI with 1 synonyms: 221 - 1.04% CUI with 2 synonyms: 12 - 0.06% No CUI found: 4051 - 19.09% Total term-CUIs found: 27478	CUI with Norm: 16937 - 79.81% CUI with 1 synonyms: 228 - 1.07% CUI with 2 synonyms: 15 - 0.07% No CUI found: 4041 - 19.04% Total term-CUIs found: 27498	CUI with Norm: 16937 - 79.81% CUI with 1 synonyms: 228 - 1.07% CUI with 2 synonyms: 15 - 0.07% No CUI found: 4041 - 19.04% Total term-CUIs found: 27498

IV. Notes
In practice, we only normalize key of the synonym pair. This might cause non-symmetric issues. For example:
synonym pair: impaired|abnormality are stored as follows in the database table:

normalized key	synonym
impair	abnormality
abnormality	impaired impair|abnormality

The mapping results in non-symmetric lookup:

• abnormality -> abnormality -> impaired
• impair -> impair -> abnormality (not symmetric)
• impaired -> impair -> abnormality