# CaTIES May 2006 Adopter Coder Appraisal.

Feedback and actions taken regarding issues raised in the May 2006
Adoper Appraisal of Coding.

## Data Used

\<property name=\"factory.handle\"
value=\"http://165.123.243.205:8080/ogsa/services/caTIES/public_test\"/\>

\<property name=\"database.name\" value=\"caties_v_2_0_public_test\"/\>

\<property name=\"secure.connection\" value=\"true\"/\>

\<property name=\"document.sync.handle\"
value=\"http://165.123.243.205:8080/ogsa/services/caTIES/DocumentSyncerFactoryService\"/\>

This looks to be test reports coming from the Pitt CoPATH test set.
Later posted to Penn and analyzed by Tara McSherry and other caTIES
adopters.

## Bug Fix-like changes to the coder.

We say Fix-like here in that many of these fixes might have consequences
for other reports. In general we tried to focus on changes that
corrected behavior on the test set but seemed to have little foreseeable
impact on a greater class of unanalyzed reports.

-   Add **T190 \[Anatomical Abnormality\]** to our list of categorized
    Diagnosis

-   Add **T020 \[Acquired Abnormality\]** to our list of categorized
    Diagnosis

-   Remove **T020 \[Acquired Abnormality\]** form our list of
    categorized Organs

-   Add **T033 \[Finding\]** to our list of categorized Diagnoses.

-   Add **T042 \[Organ or Tissue Function\]** to our list of categorized
    Diagnosis

-   Remove **T042 \[Organ or Tissue Function\]** to our list of
    categorized Organs

-   Add **T080 \[Qualitative Concept\]** to our list of categorized
    Diagnosis

-   Add **T031 \[Body Substance\]** to our list of categorized Organs

-   Remove **Phenomenon or Process** from the CaTIES_ConceptFilter.jape

-   Remove **Temporal Concept** from CaTIES_ConceptFilter.jape

-   Remove **Classification** from CaTIES_ConceptFilter.jape

-   Remove **Physiologic Function** from CaTIES_ConceptFilter.jape

-   Remove **Organism Attribute** from CaTIES_ConceptFilter.jape

-   Add NegatedOrgan, and NegatedProcedure based on NegatedConcept. Now
    any concept in the 6 word negation will be mapped to the
    corresponding Negative Categories.

-   Take out the NegEx special treatment of Qualitative Concept

-   Make NegEx consider OutlineIdentifiers when determining how far it
    can proceed. The six word window was formerly only interrupted by
    SentenceEnd.

-   Add to NegEx

    -   Pre

    -   UNINVOLVED BY

    -   NON

    -   NOR

-   Post

    -   IS ABSENT

    -   WAS ABSENT

> (The following failed by negating good predecessor concepts after
> commas. so even though they are good post negation additions, limited
> empirical observation doesn\'t support their addition)

-   not specified

-   was not specified

-   is not specified

```{=html}
<!-- -->
```
-   Roll out a MMTx data version based on the very latest NCIM.

-   Send the MMTx developers a set of low level mappings that
    demonstrate MMTx tendency to ignore a stream of concepts in it\'s
    candidates list and only map a few of them.

-   Add additional OutlineIdentification The rule to be added is EOLN
    \\s\* {Letter\|Number}+ {:\|.}

-   DeID problems must be propagated to DeID Corp for analysis.

## 

## Reasoning for changes.

### Incorrectly Coded as General

This happens because we don\'t have this concept\'s semantic type in any
Organ, Diagnosis, or Procedure TUI list as expected by our human expert.
Moving more TUI\'s to these categories will increase sensitivity but
create more spurious results. Acutally Organ, Diagnosis, Procedure play
no part in searching for reports. They may hold meaning latter but, for
now, this is largely a deprecated notion. In general, we respond by
adding the set of TUI\'s that fix the problems in this report unless
some obvious cue suggests we leave it alone. We\'ll move toward more
sensitivity here, realizing the macroscopic effect is meaningless.

### False Positive

This can happen because of polysemy, particularly evident in \"weird\"
abbreviations. For instance, \"name\' as a Diagnoisis of NAME - Nevi,
atrial myxoma, skin myxoma, ephelides syndrome; fails through out. Not
entirely sure how to fix this since we need acronyms and abbrevs.

### Incorrect Organ, Procedure, Diagnosis

Often an extension of a false positive where a term is mapped to an
incorrect concept out of its polysemous possibilities and that concept
is then in the categorization map for Organ, Procedure, Diagnosis.

### Partial Coding

This happens because 1) aggregate concepts are not in the vocabulary 2)
MMTx has problems with continguous chunks of concepts 3) MMTx only works
in a phrase. In most of these cases there\'s not much we can do other
than report a list of what we think is insufficient coding behavior by
MMTx to the MMTx development team.

### False Negatives

Many false Negatives happen due to negation coding and in particular the
algorithmic extension that suggests that a Negated concept in the
category of either Organ and Disease should just be eliminated. The
original thinking

here was that No Organ and No procedure wouldn\'t make sense in the
context of the document. In fact, things like \"no exudates\" might be
beneficially coded as a NegatedOrgan. There are a couple ways to go on
this one

Add NegatedOrgan, NegatedProcedure and just NegatedConcept any concept
in the 6 word window mapping them approprietely to their categories.
Just make Negated Organs or Procedures ==\> Negated Concepts Just do 1
or 2 for Organs and make Procedures always revert to a positive. Revert
both Organs and Procedures to positives.

We have chosen (1) here since the categorizations are largely
unimportant for search we can gain a quicker look at how things work.

False negatives are also due to our use of concept filtering. Here we
filter on certain semantic type categories. Here we also move toward
more sensitivity by discontinuation of filtering on only those
troublesome filter concepts per this analysis.

False negatives are also due to MMTx apparent weakness in mapping longer
phrases of concept streams. It appears that in these cases MMTx only
takes a few of the potential concept mappings that it could derive from
its candidates.

False negatives are also due to concepts having been added to the NCIM
in a latter stage than what is available via a the EVS browser pages
version of NCIM. Solution here is to roll out a new MMTx data store.

False negatives are due to the former Negation elimination and bad
negation that fails to stop in the middle of an outline of within an
English phrase. We will add OutlineIdentifier to the mix in
CaTIES_NegEx.jape

## Log of Analysis

## 

Case \-- 9456609f-b9ec-11da-bf17-b1a4b49d6452

Sentence: COLON, ANASTOMOTIC POLYP, POLYPECTOMY-

FRAGMENTS OF HYPERPLASTIC POLYP

Incorrectly Coded As General:

Question:

FINAL DIAGNOSIS SECTION OF SPR:

Is \"POLYP\" a general concept? It is coded as one, yet \"HYPERPLASTIC
POLYP\" is coded as a diagnosis. This seems inconsistent to me

Answer:

POLYP is T190 Anatomical Abnormality. We currently do not have this in
our Diagnosis Categorization rule. We will add this.

Although the semantics of what we mean by Diagnosis comes into play. For
instance a benign Polyp may not be considered a disease. Seems like it
should be added. However. Even benign abnormalities are \"Diagnoses\"

Partial Coding:

Question

FINAL DIAGNOSIS SECTION OF SPR:

ASTOMOTIC POLYP is coded as 2 separate concepts ANASTOMOTIC = organ and
POLYP = general concept, but HYPERPLASTIC POLYP is coded as 1 concept (a
diagnosis).

GROSS DESCRIPTION SECTION OF SPR:

anastomotic polyp coded as 2 concepts (organ & general), while rectal
polyp was coded as 1 concept (a diagnosis)

Answer:

ASTOMOTIC POLYP is not in the vocabulary so MMTx derivates ASTOMOTIC to
it\'s noun form ASTOMOSIS with CUI =\> C0500470: Anastomosis

Body Space or Junction T030 which is in our Organ categorization list.

HYPERPLASTIC POLYP is a first class term coming from NCIT C0333983:
Hyperplastic Polyp MMTx favours longer concepts hence does not break it
up.

RECTAL POLYP is a first class term coming from NCIT C0034887: Rectal
Polyp

**In general the behaviour of categorization after morphological
dervivation is lenient. We have the ability to turn off certain
dervational functions of MMTx. Perhaps inferring an Organ from ASTOMOTIC
is reaching? But in general this is a good concept to get for
macroscopic value.**

GROSS DESCRIPTION SECTION OF SPR:

Patient\' s name, initials AIDIs AID considered PHI? (name is not shown
in SPR just AID)

Could be under scrubbing depending on whether HIPPA requires Patient
Initials be identified. We need to work with DeID on this case.

\#######################################################################################################################################

Case 9576ebeb-b9ec-11da-bf17-b1a4b49d6452

Incorrect General

Question: FINAL DIAGNOSIS & GROSS DESCRIPTION SECTIONS OF SPR:

• "POLYP" coded as general concept

Answer: Same argument as previous case.

False Positive:

GROSS DESCRIPTION SECTION OF SPR:

• "name" coded as diagnosis

This is a bizarre abbreviation coming from the NCIT CL110058: Carney
Syndrome

Disease of Syndrome T047.

NAME - Nevi, atrial myxoma, skin myxoma, ephelides syndrome

Why does MMTx pick this as it\'s best candidate map? Perhaps because we
prefer NCIT

as first choice source. In general we should keep a watch on weird
abbreviations. There

appears to be a way in MMTx to turn off full abreviation consideration.
I think the

flag might be to only consider unique abbreviations. Another problem may
be that we are capitolizing

sentences going into MMTx. Don\'t know if this makes a difference but we
should try

experiments with this sentence**. \[Turns out the capitalization is not
the issue.\]**

GROSS DESCRIPTION SECTION OF SPR:

"patient's name and initials MB" -- Is MB considered PHI? (name is not
shown in SPR just "MB")

Another underscrub in the same vien as last case.

\#######################################################################################################################################

Case 99a579e3-b9ec-11da-bf17-b1a4b49d6452

False Negatives

GROSS DESCRIPTION SECTION OF SPR:

• "left tonsil" not coded (however "right tonsil" is coded as an organ)

• "epithelial" is not coded

• "No fibrinopurulent exudates" is not coded

Left tonsil is negated because it\'s in a six word window of \"No\" - No
markings present to designate left tonsil

The since it doesn\'t make sense to talk about a negated organ we just
eliminate the concept. I\'m not sure about

the logic of this piece of the coding algorithm. In general we get LEFT
TONSIL and RIGHT TONISL in the FD so the

macroscopic coding of the report is good. It\'s hard even from a human
expert\'s perception how to code that negation

sentence. Basically throwing the code out there is probably
appropriete**. \[We have decided instead to explicitly negate Organ and
Procedures\]**

epithelial - Why are we missing this? It\'s first class concept
CL028674: Epithelial

This appears to be just a bad final mapping by MMTx. Here\'s what that
output to command line is.

Notice that epithelial is in the candidate list but not in the final map
for that phrase.

Processing 00000000.tx.1: It displays a pink-tan glistening epithelial
surface.

Phrase: \"It\"

Meta Candidates (0): \<none\>

Meta Mappings: \<none\>

Phrase: \"displays\"

Meta Candidates (1)

966 Display (Display {NCI}) \[Activity\]

Meta Mapping (966)

966 Display (Display {NCI}) \[Activity\]

Phrase: \"a pink-tan glistening epithelial surface.\"

Meta Candidates (8)

804 SURFACE (SURF {NCI,LNC}) \[Spatial Concept\]

637 TAN (2,2,6,6-Tetramethyl-4-oxopiperidine-1-oxyl {MSH,MTH})
\[Indicator, Reagent, or Diagnostic Aid,Organic Chemical,Pharma

cologic Substance\]

637 Epithelial (Epithelial {NCI,NCI-GLOSS}) \[Body System\]

604 Tanning (Tannings {MSH,MTH}) \[Occupational Activity\]

604 Tanning (Tanning {MTH}) \[Individual Behavior,Individual
Behavior,Organism Function\]

582 Epi (Adrenalin {MSH,UWDA,NCI,NCI-GLOSS,LNC}) \[Organic
Chemical,Pharmacologic Substance\]

582 EPI (Exocrine Pancreatic Insufficiency {MSH}) \[Disease or
Syndrome\]

566 Epithelium (Epithelium {MSH,NCI,UWDA,NCI-GLOSS}) \[Tissue\]

Meta Mapping (764)

637 TAN (2,2,6,6-Tetramethyl-4-oxopiperidine-1-oxyl {MSH,MTH})
\[Indicator, Reagent, or Diagnostic Aid,Organic Chemical,Pharma

cologic Substance\]

804 SURFACE (SURF {NCI,LNC}) \[Spatial Concept\]

No fibrinopurulent exudates These fall into the same category of negated
organs

Exudate C0015388: Exudate Body Substance Semantic Type: Body Substance

TUI: T031 In our Organ classification

fribronopurulent is itself not a concept but part of compound concept
that MMTx probably can\'t map.

This whole not negating organs may be a bad idea when we consider how
we\'re classifying things as

Organs. For instance No exudates should probably stay.

Matching Concepts

Exudate Body Substance

Exudate (Exudate (MMHCC)) Tissue

meningitis; fibrinopurulent Disease or Syndrome

pericarditis; fibrinopurulent Disease or Syndrome

Fibrinopurulent pleurisy Disease or Syndrome

GROSS DESCRIPTION SECTION OF SPR:

• "patient\'s name, initials EC" -- Is EC considered PHI? (name is not
shown in SPR just "EC")

Same under scrubbing problem

\#######################################################################################################################################

Case 9a1308ce-b9ec-11da-bf17-b1a4b49d6452

Incorrect General

\*FINAL DIAGNOSIS & GROSS DESCRIPTION SECTIONS OF SPR:

• "Benign" coded as general concept (should it be a diagnosis)

Benign by itself is a Qualitative Concept C0205183: Benign

Semantic Type: Qualitative Concept

TUI: T080

Definition: A concept which is an assessment of some quality, rather
than a direct measurement.

This is not in our disease or organ list.

**\[Add T080\]**

False Negative

\*FINAL DIAGNOSIS & GROSS DESCRIPTION SECTION OF SPR:

• "SIMPLE SEROUS CYST" not coded

Why are we missing this?

CL158879: Serous cyst Acquired Abnormality. We may be filtering this
semantic type?

Semantic Type: Acquired Abnormality

TUI: T020

Definition: An abnormal structure, or one that is abnormal in size or
location,

found in or deriving from a previously normal structure.

Acquired abnormalities are distinguished from diseases even though they
may result in pathological functioning

(e.g., \"hernias incarcerate\").

No but we\'re calling Acquired Abnormality an Organ when it should be
disease

Here is the mapping

Processing 00000000.tx.1: LEFT OVARY WITH PHYSIOLOGIC CHANGES AND A
BENIGN SIMPLE SEROUS CYST (2.5

Phrase: \"LEFT OVARY\"

Meta Candidates (9)

1000 Left ovary (Structure of left ovary {LNC,UWDA,NCI}) \[Anatomical
Structure\]

861 OVARY (Genital System, Female, Ovary {NCI,LNC,MSH,UWDA,NCI-GLOSS})
\[Body Part, Organ, or Or

789 Ovarian (Ovarian {NCI,NCI-GLOSS}) \[Qualitative Concept,Spatial
Concept\]

694 Left (Levo- {NCI,UWDA}) \[Spatial Concept\]

661 Leaves (Plant Leaves {MSH,MTH}) \[Plant\]

638 LS (Basutoland {NCI,MSH}) \[Geographic Area\]

638 LS (LS {NCI,MSH}) \[Geographic Area\]

623 LV (Latvia {NCI,MSH}) \[Geographic Area\]

623 LV (Folix {NCI,MSH,NCI-GLOSS}) \[Pharmacologic Substance\]

Meta Mapping (1000)

1000 Left ovary (Structure of left ovary {LNC,UWDA,NCI}) \[Anatomical
Structure\]

Phrase: \"WITH PHYSIOLOGIC CHANGES\"

Meta Candidates (4)

827 Change (CHG {NCI}) \[Amino Acid, Peptide, or Protein,Neuroreactive
Substance or Biogenic Ami

694 Physiologic (Physiologic {NCI,NCI-GLOSS}) \[Qualitative Concept\]

623 PHYSIOLOGY (PHYSIOLOGY {MSH,NCI}) \[Biomedical Occupation or
Discipline,Functional Concept\]

594 Physiological (Physiological Diffuse Hyperplasia of the Mammary
Gland {NCI}) \[Neoplastic Pr

Meta Mapping (872)

694 Physiologic (Physiologic {NCI,NCI-GLOSS}) \[Qualitative Concept\]

827 Change (CHG {NCI}) \[Amino Acid, Peptide, or Protein,Neuroreactive
Substance or Biogenic Ami

Phrase: \"AND\"

Meta Candidates (2)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

1000 And (And {NCI}) \[Conceptual Entity\]

Meta Mapping (1000)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 And (And {NCI}) \[Conceptual Entity\]

Phrase: \"A BENIGN SIMPLE SEROUS CYST\"

Meta Candidates (4)

812 cyst (Cysts {MSH,MTH,NCI-GLOSS,NCI,LNC}) \[Anatomical
Abnormality,Finding\]

812 Serous (Serous {NCI,NCI-GLOSS}) \[Qualitative Concept\]

741 serum (Blood Serum {MSH,MTH,LNC,NCI-GLOSS,NCI,UWDA}) \[Body
Substance\]

645 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

Meta Mapping (791)

645 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

812 cyst (Cysts {MSH,MTH,NCI-GLOSS,NCI,LNC}) \[Anatomical
Abnormality,Finding\]

Phrase: \"(2.5 CM\"

Meta Candidates (6)

812 CM (CMR {NCI,MSH}) \[Geographic Area\]

812 CM (COMPLICATIONS {LNC,MTH,NCI}) \[Finding\]

812 CM (Cytometry {NCI}) \[Laboratory Procedure\]

812 CM (Cutaneous Mastocytosis {MSH,NCI}) \[Neoplastic Process\]

812 CM (Complicating {NCI}) \[Qualitative Concept\]

756 Curium (Curium {MSH}) \[Element, Ion, or Isotope\]

Meta Mapping (812)

812 CM (CMR {NCI,MSH}) \[Geographic Area\]

Meta Mapping (812)

812 CM (COMPLICATIONS {LNC,MTH,NCI}) \[Finding\]

Meta Mapping (812)

812 CM (Complicating {NCI}) \[Qualitative Concept\]

Meta Mapping (812)

812 CM (Cutaneous Mastocytosis {MSH,NCI}) \[Neoplastic Process\]

Meta Mapping (812)

812 CM (Cytometry {NCI}) \[Laboratory Procedure\]

Phrase: \").\"

Meta Candidates (0): \<none\>

Meta Mappings: \<none\>

Similar to epethial since the latter in a string of adjectives does not
make the

final map

Here is the server log of a re-code I just did\...

OK Here\'s what\'s happing\... When deriving the sentence from
underlying token stream we\'re throwing out punctuation and numbers so
that actual sentence

being sent is

Phrase: \"A BENIGN SIMPLE SEROUS CYST CM\"

Meta Candidates (10)

804 CM (CMR {NCI,MSH}) \[Geographic Area\]

804 CM (COMPLICATIONS {LNC,MTH,NCI}) \[Finding\]

804 CM (Cytometry {NCI}) \[Laboratory Procedure\]

804 CM (Cutaneous Mastocytosis {MSH,NCI}) \[Neoplastic Process\]

804 CM (Complicating {NCI}) \[Qualitative Concept\]

748 Curium (Curium {MSH}) \[Element, Ion, or Isotope\]

637 cyst (Cysts {MSH,MTH,NCI-GLOSS,NCI,LNC}) \[Anatomical
Abnormality,Finding\]

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

637 Serous (Serous {NCI,NCI-GLOSS}) \[Qualitative Concept\]

566 serum (Blood Serum {MSH,MTH,LNC,NCI-GLOSS,NCI,UWDA}) \[Body
Substance\]

Meta Mapping (786)

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

804 CM (CMR {NCI,MSH}) \[Geographic Area\]

Meta Mapping (786)

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

804 CM (COMPLICATIONS {LNC,MTH,NCI}) \[Finding\]

Meta Mapping (786)

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

804 CM (Cytometry {NCI}) \[Laboratory Procedure\]

Meta Mapping (786)

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

804 CM (Cutaneous Mastocytosis {MSH,NCI}) \[Neoplastic Process\]

Meta Mapping (786)

637 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

804 CM (Complicating {NCI}) \[Qualitative Concept\]

The same odd chain of adjectives before the main noun is happening.

Underscrubbed

\*GROSS DESCRIPTION SECTION OF SPR:

• "patient\'s name and initials B.S" -- Is B.S considered PHI? (name is
not shown in SPR just "B.S")

Same problem

\#######################################################################################################################################

Case: cfeee05b-b9ec-11da-bf17-b1a4b49d6452

False Negative

FINAL DIAGNOSIS SECTION OF SPR:

• "CRANIOTOMY" not coded

Again this is the notion that a Negated procedure concept just gets
thrown out. Basically the problem with this case is the NOT prefix to a
bunch of

meaningful concepts. Procedure is thrown out.

The main problem here is bad Negation. Can\'t be avoid with the NegEx
alogorithm as it is. It could

be improved with better phrase and NegEx coordination.

\#######################################################################################################################################

Case: a3ed9e1d-b9ec-11da-bf17-b1a4b49d6452

False Negative.

Question: Why nothing for TURBT?

Answer: because it\'s only source is SNOMED.

\#######################################################################################################################################

Case: a4187eb1-b9ec-11da-bf17-b1a4b49d6452

Incorrect Coding

\*FINAL DIAGNOSIS SECTION OF SPR:

• "ANGIOINVASION" coded as organ, but should be coded as diagnosis

This is coded as a Negated Concept it\'s semantic type is T033

Semantic Type: Finding

TUI: T033

Definition: That which is discovered by direct observation or
measurement of an

organism attribute or condition, including the clinical history of the
patient.

The history of the presence of a disease is a \'Finding\' and is
distinguished from the disease itself.

False Positive

\*FINAL DIAGNOSIS SECTION OF SPR:

• "Identified" coded as an organ

This is actually a T033 semantic type correct negegated by the prefix
negation NOT

The question I have is why FREE OF is negating ANGIOINVASION although it
get\'s the

correct result. It moves across sentence boundaries. Guess NegEx just
deals with

Tokens. Looks like it would improve NegEx to add some more stop types
like OutlineIdentifier.

Particularly outline identifier. FIX THIS\*\*\*\*

\#######################################################################################################################################

Case: b702b801-b9ec-11da-bf17-b1a4b49d6452

Incorrect Coding

•"Benign" located located in the final diagnosis section should be coded
as a diagnosis.

FIX THIS\*\*\* Add T080 to our diagnosis list

False Positive

"see" from "see comment" located the final diagnosis section is coded as
a Diagnosis.

This is a weird one C0042789: Vision

Organ or Tissue Function

Semantic Type: Organ or Tissue Function

TUI: T042

Definition: A physiologic function of a particular organ, organ system,
or tissue.

This should probably be Removeoved from our Organ list and definately
why is it in

the Diagnosis list?

Remove from diagnosis list.

False Negative

•"Cancerization" located in the final diagnosis section should be coded
as a diagnosis

This is probably just too hard given there is only one concept called

CL335272: Lobular Cancerization

Neoplastic Process

It would be great if MMTx could get this from CANCERIZATION OF LOBULES.
But perhaps just

fails.

Here\'s the mapping my question is why does the phrase finder correctly
keep in situ in the first

phrase when at other times I\'ve seen it fail?

Processing 00000000.tx.1: ductal carcinoma in situ, solid and cribriform
types with comedo necrosis and canceri

.

Phrase: \"ductal carcinoma in situ, solid\"

Meta Candidates (35)

804 Solid (Solid - descriptor {MTH,NCI}) \[Qualitative Concept\]

804 Solid (Solid Dosage Form {NCI,MTH}) \[Biomedical or Dental
Material\]

771 Ductal carcinoma in situ, NOS (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Pr

717 Carcinoma in situ, NOS (CIS {NCI-GLOSS,NCI,MSH,ICD9CM,ICD10})
\[Educational Activity,Intellectual Product

ss\]

673 Ductal carcinoma, NOS (Duct adenocarcinoma, NOS {NCI,MSH,NCI-GLOSS})
\[Neoplastic Process\]

673 Carcinoma, Ductal (Duct cell carcinoma {MSH}) \[Neoplastic Process\]

673 In Situ (In Situ {NCI}) \[Classification,Qualitative Concept,Spatial
Concept\]

637 carcinoma (Epitheliomas {MSH,NCI,NCI-GLOSS,MTH}) \[Neoplastic
Process\]

637 IN (IN {NCI,MSH}) \[Geographic Area,Geographic Area\]

637 IN (In element {LNC,MSH,MTH}) \[Element, Ion, or Isotope\]

637 Ductal (Ductal {NCI}) \[Conceptual Entity\]

637 Ductal (Ductal Hypoplasia of the Mammary Gland {NCI}) \[Disease or
Syndrome\]

637 Carcinoma (Carcinoma of the Prostate Gland {NCI}) \[Neoplastic
Process\]

637 Carcinoma (Carcinoma {NCI}) \[Neoplastic Process\]

604 ins (Chromosomal Insertion {NCI}) \[Cell or Molecular Dysfunction\]

604 INS (Nurse Informaticist {NCI}) \[Biomedical Occupation or
Discipline,Intellectual Product,Professional o

oup\]

604 INS (INS Gene {NCI}) \[Gene or Genome\]

582 CA (Factor IV {MSH,NCI,LNC,NCI-GLOSS,MTH}) \[Element, Ion, or
Isotope\]

582 CA (CA {NCI,MSH}) \[Geographic Area,Geographic Area\]

582 CA (Cancer, unspecified site
{NCI,MSH,NCI-GLOSS,LNC,MIM,ICD10,MTH,ICD9CM}) \[Neoplastic Process\]

582 Indexing (Indexing {MSH}) \[Occupational Activity\]

582 INSULIN (Unmodified insulin product {MSH,NCI,LNC,MTH}) \[Amino Acid,
Peptide, or Protein,Hormone,Pharmaco

582 INULIN (INULIN {LNC,MSH}) \[Biologically Active
Substance,Carbohydrate,Indicator, Reagent, or Diagnostic

582 CA (AC protocol {NCI,MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

582 Index (IX {NCI,MSH}) \[Intellectual Product\]

582 insulin (insulin {MTH}) \[Gene or Genome\]

582 Insulin (Insulin {NCI,NCI-GLOSS}) \[Amino Acid, Peptide, or
Protein,Hormone,Laboratory Procedure\]

582 CAS (CRKAS {NCI}) \[Gene or Genome\]

582 CAS (CRK-Associated Substrate {NCI}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

582 Insulin (Recombinant Insulin {NCI}) \[Amino Acid, Peptide, or
Protein,Pharmacologic Substance\]

582 CA (Cornu Ammonis {NCI}) \[Anatomical Structure,Body Part, Organ, or
Organ Component\]

566 duct (Ducts {UWDA,NCI-GLOSS,NCI}) \[Body Part, Organ, or Organ
Component\]

554 Iletin (Iletin {MSH}) \[Amino Acid, Peptide, or
Protein,Hormone,Pharmacologic Substance\]

537 carcinogen (chemical carcinogen {NCI,MSH,NCI-GLOSS}) \[Hazardous or
Poisonous Substance\]

537 Carcinogen (Chemical Carcinogen {NCI}) \[Hazardous or Poisonous
Substance\]

Meta Mapping (928)

771 Ductal carcinoma in situ, NOS (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Pr

804 Solid (Solid - descriptor {MTH,NCI}) \[Qualitative Concept\]

Meta Mapping (928)

771 Ductal carcinoma in situ, NOS (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Pr

804 Solid (Solid Dosage Form {NCI,MTH}) \[Biomedical or Dental
Material\]

Phrase: \"and\"

Meta Candidates (2)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

1000 And (And {NCI}) \[Conceptual Entity\]

Meta Mapping (1000)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 And (And {NCI}) \[Conceptual Entity\]

Phrase: \"cribriform types\"

Meta Candidates (2)

861 Types (With type {NCI,LNC}) \[Qualitative Concept\]

694 Cribriform (Cribs {MSH,NCI,NCI-GLOSS}) \[Qualitative Concept\]

Meta Mapping (888)

694 Cribriform (Cribs {MSH,NCI,NCI-GLOSS}) \[Qualitative Concept\]

861 Types (With type {NCI,LNC}) \[Qualitative Concept\]

Phrase: \"with comedo necrosis\"

Meta Candidates (3)

861 Necrosis NOS (Cellular necrosis {NCI,MSH,NCI-GLOSS}) \[Pathologic
Function\]

789 Necrotic (Necrotic {NCI}) \[Qualitative Concept\]

694 comedo (COMEDONE {NCI}) \[Disease or Syndrome,Qualitative Concept\]

Meta Mapping (888)

694 comedo (COMEDONE {NCI}) \[Disease or Syndrome,Qualitative Concept\]

861 Necrosis NOS (Cellular necrosis {NCI,MSH,NCI-GLOSS}) \[Pathologic
Function\]

Phrase: \"and\"

Meta Candidates (2)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

1000 And (And {NCI}) \[Conceptual Entity\]

Meta Mapping (1000)

1000 AND (AND {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 And (And {NCI}) \[Conceptual Entity\]

Phrase: \"cancerization\"

Meta Candidates (0): \<none\>

Meta Mappings: \<none\>

Phrase: \"of lobules.\"

Meta Candidates (2)

966 Lobule (Lobule {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or Organ
Component\]

916 Lobular (LBLR {NCI}) \[Qualitative Concept\]

Meta Mapping (966)

966 Lobule (Lobule {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or Organ
Component\]

I actually tried to use the quick composite phrases option for MMTx and
the composite

phrases. The composite phrases never returned. Hung. -Q returned on a
sub sentence

I gave it but the mapping was less satisfactory than the non-composite
configuration

E:\\\>java -cp
\"E:\\MMTx-2.4b\\nls\\mmtx\\lib\\mmtxProject.jar;E:\\MMTx-2.4b\\nls\\mmtx;E

nih.nlm.nls.mmtx.MMTx -Q=true

About to set the outputfile to standard output

MMTx (2.4.B release)

Control options:

tag_text

candidates

semantic_types

plain_syntax

mappings

stop_large_n

quick_composite_phrases (implies -zi)

strict_model

best_mappings_only

Using DataSet: 2004_strict

comedo necrosis and cancerization of lobules

Processing 00000000.tx.1: comedo necrosis and cancerization of lobules

Phrase: \"comedo necrosis and cancerization of lobules\"

Meta Candidates (3)

753 Necrosis (Necrosis {MSH}) \[Pathologic Function\]

586 Of (Within {MTH}) \[Spatial Concept\]

553 Lobule (Lobule {UWDA}) \[Body Part, Organ, or Organ Component\]

Meta Mapping (661)

753 Necrosis (Necrosis {MSH}) \[Pathologic Function\]

586 Of (Within {MTH}) \[Spatial Concept\]

553 Lobule (Lobule {UWDA}) \[Body Part, Organ, or Organ Component\]

The composite_phrase run finally returned and after taking hours on a
single sentence

came up with this erroneous mapping.

Processing 00000000.tx.1: ductal carcinoma in situ, solid and cribriform
types with comedo necrosis and cancerization of lobules

.

Phrase: \"ductal carcinoma in situ, solid and cribriform types with
comedo necrosis and cancerization of lobules.\"

Meta Candidates (100)

745 \[M\]Solid carcinoma NOS (Solid carcinoma with mucin formation
{NCI}) \[Neoplastic Process,Neoplastic Process\]

733 Solid (Solid - descriptor {MTH,NCI}) \[Qualitative Concept\]

733 Solid (Solid Dosage Form {NCI,MTH}) \[Biomedical or Dental
Material\]

607 Ductal carcinoma in situ, NOS (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Process\]

593 Carcinoma in situ, NOS (CIS {NCI-GLOSS,NCI,MSH,ICD9CM,ICD10})
\[Educational Activity,Intellectual Product,Neoplastic Proce

ss\]

592 Ductal carcinoma, cribriform type (Ductal carcinoma, cribriform type
{MSH,NCI}) \[Neoplastic Process\]

579 Ductal carcinoma, NOS (Duct adenocarcinoma, NOS {NCI,MSH,NCI-GLOSS})
\[Neoplastic Process\]

579 Carcinoma, Ductal (Duct cell carcinoma {MSH}) \[Neoplastic Process\]

579 In Situ (In Situ {NCI}) \[Classification,Qualitative Concept,Spatial
Concept\]

578 Carcinoma, Cribriform (Ductal carcinoma, cribriform type {MSH,NCI})
\[Neoplastic Process\]

578 Comedo Carcinoma (Comedocarcinoma, NOS {NCI,NCI-GLOSS}) \[Neoplastic
Process\]

572 Solid Mammary Carcinoma (Solid Mammary Carcinoma {NCI}) \[Neoplastic
Process\]

567 AND (AND {NCI,MSH}) \[Geographic Area\]

567 carcinoma (Epitheliomas {MSH,NCI,NCI-GLOSS,MTH}) \[Neoplastic
Process\]

567 Cribriform (Cribs {MSH,NCI,NCI-GLOSS}) \[Qualitative Concept\]

567 IN (IN {NCI,MSH}) \[Geographic Area,Geographic Area\]

567 IN (In element {LNC,MSH,MTH}) \[Element, Ion, or Isotope\]

567 Necrosis NOS (Cellular necrosis {NCI,MSH,NCI-GLOSS}) \[Pathologic
Function\]

567 comedo (COMEDONE {NCI}) \[Disease or Syndrome,Qualitative Concept\]

567 Types (With type {NCI,LNC}) \[Qualitative Concept\]

567 Ductal (Ductal {NCI}) \[Conceptual Entity\]

567 Ductal (Ductal Hypoplasia of the Mammary Gland {NCI}) \[Disease or
Syndrome\]

567 Carcinoma (Carcinoma of the Prostate Gland {NCI}) \[Neoplastic
Process\]

567 Carcinoma (Carcinoma {NCI}) \[Neoplastic Process\]

567 And (And {NCI}) \[Conceptual Entity\]

563 With type (With type {NCI,LNC}) \[Qualitative Concept\]

563 Lobular carcinoma in situ, NOS (Lobular Breast Carcinoma In Situ
{NCI,NCI-GLOSS,ICD10}) \[Neoplastic Process\]

550 Solid Papillary Breast Carcinoma (Solid Papillary Carcinoma of the
Breast {NCI}) \[Neoplastic Process\]

548 Solid carcinoma with mucin formation (Solid carcinoma with mucin
formation {NCI}) \[Neoplastic Process,Neoplastic Process\]

545 Solid Pseudopapillary Carcinoma of Pancreas (Solid Pseudopapillary
Carcinoma of the Pancreas {NCI}) \[Neoplastic Process\]

545 Solid Mammary Carcinoma of Mouse (Solid Mammary Carcinoma {NCI})
\[Neoplastic Process\]

537 lobular carcinoma (Carcinomas, Lobular {MSH,NCI}) \[Neoplastic
Process\]

537 Lobular Cancerization (Lobular Cancerization {NCI}) \[Neoplastic
Process\]

533 Lobule (Lobule {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or Organ
Component\]

533 ins (Chromosomal Insertion {NCI}) \[Cell or Molecular Dysfunction\]

533 INS (Nurse Informaticist {NCI}) \[Biomedical Occupation or
Discipline,Intellectual Product,Professional or Occupational Gr

oup\]

533 INS (INS Gene {NCI}) \[Gene or Genome\]

523 Ductal Carcinoma in situ of Breast (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Process\]

511 CA (Factor IV {MSH,NCI,LNC,NCI-GLOSS,MTH}) \[Element, Ion, or
Isotope\]

511 CA (CA {NCI,MSH}) \[Geographic Area,Geographic Area\]

511 CA (Cancer, unspecified site
{NCI,MSH,NCI-GLOSS,LNC,MIM,ICD10,MTH,ICD9CM}) \[Neoplastic Process\]

511 Indexing (Indexing {MSH}) \[Occupational Activity\]

511 INSULIN (Unmodified insulin product {MSH,NCI,LNC,MTH}) \[Amino Acid,
Peptide, or Protein,Hormone,Pharmacologic Substance\]

511 INULIN (INULIN {LNC,MSH}) \[Biologically Active
Substance,Carbohydrate,Indicator, Reagent, or Diagnostic Aid\]

511 WS (WS {NCI,MSH,MTH}) \[Disease or Syndrome\]

511 CA (AC protocol {NCI,MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

511 WS (Navigator Islands {NCI,MSH}) \[Geographic Area\]

511 Index (IX {NCI,MSH}) \[Intellectual Product\]

511 insulin (insulin {MTH}) \[Gene or Genome\]

511 Insulin (Insulin {NCI,NCI-GLOSS}) \[Amino Acid, Peptide, or
Protein,Hormone,Laboratory Procedure\]

511 CAS (CRKAS {NCI}) \[Gene or Genome\]

511 CAS (CRK-Associated Substrate {NCI}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

511 Insulin (Recombinant Insulin {NCI}) \[Amino Acid, Peptide, or
Protein,Pharmacologic Substance\]

511 CA (Cornu Ammonis {NCI}) \[Anatomical Structure,Body Part, Organ, or
Organ Component\]

510 Solid Lung Carcinoma with Mucus Formation (Solid Lung Adenocarcinoma
with Mucin Production {NCI}) \[Neoplastic Process\]

510 Solid Papillary Carcinoma of the Breast (Solid Papillary Carcinoma
of the Breast {NCI}) \[Neoplastic Process\]

509 Pancreatic Solid Pseudopapillary Carcinoma (Solid Pseudopapillary
Carcinoma of the Pancreas {NCI}) \[Neoplastic Process\]

507 Circumscribed solid basal cell carcinoma (Circumscribed solid basal
cell carcinoma {NCI}) \[Neoplastic Process\]

507 Prostate Ductal Adenocarcinoma, Solid Pattern (Prostate Ductal
Adenocarcinoma, Solid Pattern {NCI}) \[Neoplastic Process\]

505 Lobular carcinoma in situ of breast (Lobular Breast Carcinoma In
Situ {NCI,NCI-GLOSS,ICD10}) \[Neoplastic Process\]

502 Carcinoma in situ of breast ductal (Ductal Breast Carcinoma In Situ
{NCI,NCI-GLOSS,MSH,ICD10}) \[Neoplastic Process\]

495 duct (Ducts {UWDA,NCI-GLOSS,NCI}) \[Body Part, Organ, or Organ
Component\]

495 Necrotic (Necrotic {NCI}) \[Qualitative Concept\]

494 Ductal carcinoma in situ, papillary (Ductal carcinoma in situ,
papillary {NCI}) \[Neoplastic Process\]

492 Non-Comedo Ductal Carcinoma in situ of Breast (Non-Invasive
Non-Comedo Ductal Carcinoma of the Breast {NCI}) \[Neoplastic

Process\]

491 Carcinoma in situ of esophagus (Esophagus Carcinoma in situ
{NCI,ICD9CM,ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of stomach (Gastric malignancy in situ
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of colon (Colonic Carcinoma in situ
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of rectum (Carcinoma in situ of the Rectum
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of anus NOS (Stage 0 Anal Canal Cancer
{ICD9CM,NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of larynx (Carcinoma in situ of the Larynx
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of Trachea (Carcinoma in situ of Trachea
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of skin (Cutaneous Carcinoma in situ
{NCI,ICD9CM,ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of breast (Carcinoma in situ of the Breast
{NCI,ICD10,ICD9CM,NCI-GLOSS}) \[Neoplastic Process\]

491 Carcinoma in situ of prostate (CIS - Carcinoma in situ of prostate
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of penis (Carcinoma in situ of penis
{ICD10,ICD9CM,NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of bladder (Flat CIS of the Urinary Bladder
{NCI,ICD10,ICD9CM}) \[Neoplastic Process\]

491 Carcinoma in situ of eye (Carcinoma in situ of eye {ICD10,ICD9CM})
\[Neoplastic Process\]

491 Carcinoma in situ of cervix (cervical intraepithelial neoplasia 3
{NCI,ICD10,ICD9CM,MSH}) \[Neoplastic Process\]

491 Carcinoma in situ of Vulva (FIGO Stage 0 Vulvar Carcinoma
{NCI,ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of cardia (Gastric Cardia Carcinoma In Situ {NCI})
\[Neoplastic Process\]

491 Carcinoma in situ of pylorus (Gastric Pylorus Carcinoma In Situ
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of gallbladder (Gallbladder Carcinoma in situ
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of bronchus (Carcinoma in situ of bronchus {NCI})
\[Neoplastic Process\]

491 Carcinoma in situ of endometrium (Endometrial carcinoma stage 0
{NCI,ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of mouth (Carcinoma in situ of the Oral Cavity
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of epipharynx (Carcinoma in situ of the
Nasopharynx {NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of pharynx (Carcinoma in situ of the Pharynx
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of mesopharynx (Carcinoma situ of oropharynx
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of hypopharynx (Carcinoma In Situ of the
Hypopharynx {NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of epiglottis (Epiglottis Carcinoma in situ {NCI})
\[Neoplastic Process\]

491 Carcinoma in situ of appendix (Carcinoma in situ of the Appendix
{NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of caecum (Cecum Carcinoma In Situ {NCI})
\[Neoplastic Process\]

491 Carcinoma in situ of ear (Carcinoma in situ of ear {ICD10,ICD9CM})
\[Neoplastic Process\]

491 Carcinoma in situ of endocervix (Carcinoma in situ of endocervix
{ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of exocervix (Carcinoma in situ of exocervix
{ICD10}) \[Neoplastic Process\]

491 Carcinoma in situ of vagina (Carcinoma in situ of vagina {ICD10})
\[Neoplastic Process,Neoplastic Process\]

491 Carcinoma in situ of Antrum (Gastric Antrum Carcinoma in situ {NCI})
\[Neoplastic Process\]

491 Carcinoma in situ of Hypopharynx (Carcinoma in situ of the
Hypopharynx {NCI}) \[Neoplastic Process\]

491 Carcinoma in situ of Vagina (FIGO Stage 0 Vaginal Carcinoma {NCI})
\[Neoplastic Process\]

Meta Mapping (799)

492 Non-Comedo Ductal Carcinoma in situ of Breast (Non-Invasive
Non-Comedo Ductal Carcinoma of the Breast {NCI}) \[Neoplastic

Process\]

733 Solid (Solid Dosage Form {NCI,MTH}) \[Biomedical or Dental
Material\]

567 Necrosis NOS (Cellular necrosis {NCI,MSH,NCI-GLOSS}) \[Pathologic
Function\]

Partial Coding

•"Breast" should be coded as "Breast, Right" in the Final Diagnosis
section.

MMTx Phrase Chunker.

•"Comedo Necrosis" should be coded together rather than as separate
terms in the Final Diagnosis section

There actually is no combined concept for Comedo Necrosis, MMTx does the
best it can. Which is pretty good.

\#######################################################################################################################################

Case: bf4a50fa-b9ec-11da-bf17-b1a4b49d6452

Incorrect Coded as General

•"breast mass" located in Part 1 of the gross description section (2
times) should be coded as organ.

Meta Mapping (824)

645 Inner (Inner {NCI}) \[Spatial Concept\]

861 Breast mass NOS (BREAST NODULE {NCI,ICD9CM,ICD10,LNC}) \[Finding\]

is labeled as \"right lower inner quadrant breast mass

This is coded as a Negated Concept it\'s semantic type is T033

Semantic Type: Finding

TUI: T033

Definition: That which is discovered by direct observation or
measuRemoveent of an

organism attribute or condition, including the clinical history of the
patient.

The history of the presence of a disease is a \'Finding\' and is
distinguished from the disease itself.

FIX THIS\*\*\*\* Add this to the diagnosis list.

False Positive Concept Should Not Be Coded but is.

• "well" from "well-circumscribed" located in Part 1of the gross
description section should not be coded as diagnosis.

Phrase: \"a well-circumscribed\"

Meta Candidates (3)

661 Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease or
Syndrome\]

661 Best (Best {NCI}) \[Disease or Syndrome,Qualitative Concept\]

623 Wellness (Wellness {MSH,NCI}) \[Idea or Concept\]

Meta Mapping (661)

661 Best (Best {NCI}) \[Disease or Syndrome,Qualitative Concept\]

Meta Mapping (661)

661 Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease or
Syndrome\]

• "linear" located in Part 1of the gross description section should not
be coded as diagnosis.

Phrase: \"with very fine linear chalky streaks.\"

Meta Candidates (4)

582 LIN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

566 Chalk (Chalk {MSH}) \[Inorganic Chemical,Pharmacologic Substance\]

566 LINE (LINE {LNC}) \[Medical Device\]

566 LINE (Long Interspersed Element {NCI}) \[Nucleotide Sequence\]

Meta Mapping (498)

582 LIN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

566 Chalk (Chalk {MSH}) \[Inorganic Chemical,Pharmacologic Substance\]

False Negative

• "Regional Lyimph Nodes" located in Part 1 D of the final diagnosis
section, although misspelled, should be coded as organ.

Spell Checker was not turned on. Probably shouldn\'t be

• "Distant Metastasis" located in Part 1 E of the final diagnosis
section should be coded as diagnosis.

DISTANT METASTASIS pMX CANNOT BE ASSESSED

This is the combination of the Negation Taggger not stopping at
OutlineIdentifiers and DISTANT METASTASIS is conded

in the window of pre-negation across the OutlineIdentifier boundary.

Phrase: \"DISTANT METASTASIS pMX\"

Meta Candidates (7)

901 Distant Metastasis (Distant Metastasis {NCI,NCI-GLOSS}) \[Phenomenon
or Process\]

827 METASTASIS (METASTATIC DISEASE {MSH,MTH,NCI}) \[Neoplastic Process\]

827 Metastasis (Tumor Cell Migration {NCI,NCI-GLOSS}) \[Phenomenon or
Process\]

827 Distant (DIS {NCI}) \[Intellectual Product,Spatial Concept\]

793 Metastases (CA - Secondary cancer {NCI,NCI-GLOSS}) \[Neoplastic
Process\]

755 Distance (Distances {MSH,NCI}) \[Quantitative Concept\]

755 metastatic (MT {NCI-GLOSS,NCI}) \[Finding,Gene or Genome,Geographic
Area\]

Meta Mapping (901)

901 Distant Metastasis (Distant Metastasis {NCI,NCI-GLOSS}) \[Phenomenon
or Process\]

Semantic Type: Phenomenon or Process

TUI: T067

This is filtered in the CaTIES_ConceptFilter otherwise it would be kept
a normal concept

or negated concept.

FIX THIS\*\*\*\* Remove Phenomen or Process from the filter??

Definition: A process or state which occurs naturally or as a result of
an activity.

({Concept.sty==\"Educational Activity\"}) \|

({Concept.sty==\"Machine Activity\"}) \|

({Concept.sty==\"Phenomenon or Process\"}) \|

Partial Coding

•"Breast" should be coded as "Breast, Right" in the Final Diagnosis
section.

Can\'t do it because of MMTx Phrase chunking word order etc.

•"Venous/Lymphatis Invasion" located in Part 1 G of the final diagnosis
section should be coded together as diagnosis

VENOUS LYMPHATIC INVASION ABSENT.

Meta Mapping (608)

645 Venous (VENS {NCI}) \[Qualitative Concept,Spatial Concept\]

645 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

645 Invasion (Tumour invasion {NCI}) \[Neoplastic Process,Pathologic
Function\]

This should get negated and it basically a MMTx thing that the concept
isn\'t discovered

the aggregate concept doesn\'t exist in the vocabulary.

Negation Issues

• "Venous/Lymphatic Invasion" located in Part 1 G of the final diagnosis
section should be coded as negated diagnosis.

• "Invasive Carcinoma" located in Part 1 F of the final diagnosis
section should be coded as a negated diagnosis.

\*\*\*FIX THIS ???

Category: ABSENT add as post negation

MARGINS UNINVOLVED BY CARCINOMA we could actually add this as pre
negation

\#######################################################################################################################################

Case: bbb6caa2-b9ec-11da-bf17-b1a4b49d6452

Incorrectly Coded as Organ

\"Thirty-Five (35)" located in Part 2 of the final diagnosis section
should not be coded as part of an organ , only "Benign Lymph Nodes"
should be coded.

NECK, RIGHT LEVELS THRU , NECK DISSECTION THIRTY-FIVE BENIGN LYMPH
NODES.

NECK, RIGHT LEVELS 2 THRU 4, NECK DISSECTION THIRTY-FIVE (35) BENIGN
LYMPH NODES.

This is a nasty one. MMTx will occassionally return overlapping
concepts. What it does here is consider

NECK \... LYMPH NODES to map to Cervical Lymph Node Structure. Which is
a good map but it sort of skips

over many concepts in the middle. MMTx also maps Benign out of the
middle. But in the CaTIES_ConceptFilter.jape

we Remove subsumed concepts. So all that\'s left is Cervical Lymph Node
structure.

Phrase: \"NECK DISSECTION THIRTY-FIVE BENIGN LYMPH NODES\"

Meta Candidates (26)

872 Cervical lymph nodes (Cervical lymph node structure {UWDA,NCI})
\[Anatomical Structure\]

818 Nodes, Lymph (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or Organ Component\]

795 lymph (Reticuloendothelial System, Lymph {NCI,NCI-GLOSS,MSH,UWDA})
\[Body Substance\]

795 LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

762 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

762 Node (TreeNode {NCI}) \[Intellectual Product\]

747 LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part,
Organ, or Organ Component\]

747 LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

729 Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI}) \[Anatomical
Structure,Body Part, Organ, or Organ Comp

724 Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA}) \[Body System\]

724 Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part, Organ, or
Organ Component\]

724 Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional Concept,Qualitative
Concept\]

724 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

712 Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

695 NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

695 Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

689 NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

651 neck dissection (Dissections, Neck {MSH,NCI-GLOSS,NCI})
\[Therapeutic or Preventive Procedure\]

629 dissection (Dissections {MSH,NCI}) \[Functional Concept,Therapeutic
or Preventive Procedure\]

629 neck (Necks {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or Region\]

629 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

573 CERVICAL (Cx - Cervical {NCI-GLOSS,NCI}) \[Spatial Concept\]

536 Cervix, NOS (Genital System, Female, Cervix
{NCI,NCI-GLOSS,MSH,UWDA,LNC}) \[Body Part, Organ, or Organ Comp

536 Cervix (Cervix Uteri {NCI}) \[Tissue\]

523 CX (Canton and Enderbury Islands {NCI,MSH}) \[Geographic Area\]

523 CX (CX {NCI,LNC,MTH}) \[Laboratory Procedure\]

Meta Mapping (809)

872 Cervical lymph nodes (Cervical lymph node structure {UWDA,NCI})
\[Anatomical Structure\]

629 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

Now I also tried this with \--prefer_multiple_concepts=true and the
result isn\'t tha

appealing in that the multiple adjective problem arises and ignores
LYMPH. You would

like to get LYMPH NODES, BENIGN, NECK DISSECTION.

Phrase: \"NECK DISSECTION THIRTY-FIVE BENIGN LYMPH NODES\"

Meta Candidates (26)

738 Cervical lymph nodes (Cervical lymph node structure {UWDA,NCI})
\[Anatomical Structure\]

689 Nodes, Lymph (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or Organ

680 lymph (Reticuloendothelial System, Lymph {NCI,NCI-GLOSS,MSH,UWDA})
\[Body Substance\]

680 LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

646 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

646 Node (TreeNode {NCI}) \[Intellectual Product\]

617 LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part,
Organ, or Organ Component

617 LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

608 Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA}) \[Body S

608 Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part, Organ, or
Organ Component\]

608 Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional Concept,Qualitative
Concept\]

608 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

600 Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI}) \[Anatomical
Structure,Body Part, Org

596 Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

580 NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

580 Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

574 NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

522 neck dissection (Dissections, Neck {MSH,NCI-GLOSS,NCI})
\[Therapeutic or Preventive Proced

513 dissection (Dissections {MSH,NCI}) \[Functional Concept,Therapeutic
or Preventive Procedur

513 neck (Necks {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or Region\]

513 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

458 CERVICAL (Cx - Cervical {NCI-GLOSS,NCI}) \[Spatial Concept\]

421 Cervix, NOS (Genital System, Female, Cervix
{NCI,NCI-GLOSS,MSH,UWDA,LNC}) \[Body Part, Org

421 Cervix (Cervix Uteri {NCI}) \[Tissue\]

407 CX (Canton and Enderbury Islands {NCI,MSH}) \[Geographic Area\]

407 CX (CX {NCI,LNC,MTH}) \[Laboratory Procedure\]

Meta Mapping (922)

513 neck (Necks {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or Region\]

513 dissection (Dissections {MSH,NCI}) \[Functional Concept,Therapeutic
or Preventive Procedur

513 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

646 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

Meta Mapping (922)

513 neck (Necks {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or Region\]

513 dissection (Dissections {MSH,NCI}) \[Functional Concept,Therapeutic
or Preventive Procedur

513 BENIGN (Bgn - Benign {NCI-GLOSS,NCI}) \[Qualitative Concept\]

646 Node (TreeNode {NCI}) \[Intellectual Product\]

Incorrectly coded Diagnosis

• \"Lip", located in the final diagnosis Part 5 section, should be coded
as an organ

Phrase: \"LIP,\"

Meta Candidates (2)

1000 lip (Lip structure {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or
Region\]

1000 LIP (LIP - Lymphoid interstitial pneumonitis {NCI}) \[Neoplastic
Process\]

Meta Mapping (1000)

1000 LIP (LIP - Lymphoid interstitial pneumonitis {NCI}) \[Neoplastic
Process\]

Meta Mapping (1000)

1000 lip (Lip structure {UWDA,MSH,MTH,NCI,LNC}) \[Body Location or
Region\]

This is a polysemous disease abbreviation that randomly beats out the
body part in one sentence

and not in the sentence a few down. Not much to do since we really
can\'t turn off abbreviations

in MMTx.

Incorrect Coding as general concept.

• "Positive Lymph", located in Pard 3 B of the final diagnosis section,
should not be coded as a general concept. "Lymph" should be coded with
the following term as an organ.

Actually here I might disagree. Perhaps this should be categorized
Diagnosis. It is of TUI T033 Finding which we are considering

adding to the diagnosis list. That would make this more plausible.

• "Fibrosis", located in Part 3 C of the final diagnosis section, should
be coded as a diagnosis.

T033 added will fix this.

• "Inflammation", located in Part 3 C of the final diagnosis section,
should be coded as a diagnosis

T033 added will fix this.

• "Blood Clot", located in Part 4 of the final diagnosis section, should
be coded as a diagnosis.

T033 will fix this.

False Positive:

• "See" from "See parts", located in Part 5 D of the final diagnosis
section, is coded as a negated diagnosis.

This is the same problem with SEE being a disease abbreviation. In the
scope of a Negation prefix. Fix this by Removeoving

that semantic type from the disease list.

• "Parts" from "See parts", located in Part 5 D of the final diagnosis
section, is coded as an organ.

Not confirmed.

False Negatives

• "Lymph Node", located in Part 4 of the final diagnosis is missed.
Should be coded as an organ.

This is due to the current algorithm of purging negated organs and
procedures. The new algorithm will probably

be to un-negate them

• "Exophytic", located in Part 4 of the final diagnosis section, is not
coded

MMTx just can\'t get this. It\'s in two long concepts from ICD10 and
NCIT.

Partial Coding

• "Composite", located in Part 5 of the final diagnosis section should
be coded together with the following term as the procedure "Composite
Resection"

There\'s no Combined concept for this in the vocabulary. However it\'s
odd that MMTx can\'t map composite. Which is the case.

• "Chronic", located in Part 3 C of the final diagnosis section, should
be coded with "Inflammation" as a diagnosis ("Chronic Inflammation").

The reason we miss Chronic Inflammation is because it comes as a whole
only from SNOMED. MMTx gets both discrete concepts but Chronic

is a Temporal Concept that we filter in the CaTIES_Concept filter.

\*\*\*Fix This??? Don\'t filter Temporal concepts.

• "Right", located under final diagnosis Part 5, should be coded
together as "Right Mandible"

No Right Mandible combined concept

• "Left", located under final diagnosis Part 1, should be coded together
as "Neck, Left" as organ

The MMTx phrase processor makes this impossible.

• "Extranodal", located under final diagnosis Part 1, is incorrectly
coded as an organ. Should be code together with the following term as a
negated diagnosis ("Extranodal spread")

Spreading only comes from SNOMED there is no combined concept for
Extranodal Spread. Does get a negated Extranodal.

• "Lymph", located in Part 3 B of the final diagnosis section, should be
coded together as "Lymph Nodes"

This is part of that POSITIVE LYMPH NODES for which there is an NCIGLOSS
combined concept.

Actually the plural causes MMTx to botch this notice

Processing 00000000.tx.1: POSITIVE LYMPH NODE

Phrase: \"POSITIVE LYMPH NODE\"

Meta Candidates (18)

1000 Positive Lymph Node (Positive Lymph Node {NCI,NCI-GLOSS})
\[Finding\]

901 lymph node (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or

845 LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part,
Organ, or Organ Co

845 LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

827 lymph (Reticuloendothelial System, Lymph {NCI,NCI-GLOSS,MSH,UWDA})
\[Body Substance

827 LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

827 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

827 Node (TreeNode {NCI}) \[Intellectual Product\]

815 Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI}) \[Anatomical
Structure,Body Pa

755 Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA})

755 Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part, Organ, or
Organ Componen

755 Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional Concept,Qualitative
Concept\]

755 Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

755 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

734 NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

727 NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

727 Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

660 POSITIVE (POSITIVE {NCI}) \[Qualitative Concept\]

Meta Mapping (1000)

1000 Positive Lymph Node (Positive Lymph Node {NCI,NCI-GLOSS})
\[Finding\]

POSITIVE LYMPH NODES

Processing 00000000.tx.1: POSITIVE LYMPH NODES

Phrase: \"POSITIVE LYMPH NODES\"

Meta Candidates (19)

901 Nodes, Lymph (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, o

901 Positive Lymph Node (Positive Lymph Node {NCI,NCI-GLOSS})
\[Finding\]

829 LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part,
Organ, or Organ Co

829 LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

827 lymph (Reticuloendothelial System, Lymph {NCI,NCI-GLOSS,MSH,UWDA})
\[Body Substance

827 lymph node (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or

827 LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

812 Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI}) \[Anatomical
Structure,Body Pa

793 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

793 Node (TreeNode {NCI}) \[Intellectual Product\]

755 Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA})

755 Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part, Organ, or
Organ Componen

755 Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional Concept,Qualitative
Concept\]

755 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

743 Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

727 NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

727 Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

721 NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

660 POSITIVE (POSITIVE {NCI}) \[Qualitative Concept\]

Meta Mapping (901)

660 POSITIVE (POSITIVE {NCI}) \[Qualitative Concept\]

901 Nodes, Lymph (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, o

And MMTx is not consistant in that earlier it broke it up differently.
Not much to do here.

\#######################################################################################################################################

Case: 99605a8b-b9ec-11da-bf17-b1a4b49d6452

Incorrect Coding - ORGAN

• \"submitted", located in the gross description section, should not be
coded as an organ

submitted appears to be a negated concept. which is wrong. but not an
organ?

Incorrect Coding - DIAGNOSIS

• \"soft fibroconnective tissue", located in the gross description
section, should be coded as an organ.

MMTx actually get soft tissue here disregarding the fibroconnective.
This TUI of Functional Concept from NCIT.

Also it\'s not coded as diagnosis. So I\'m wondering if Tara\'s comments
here are in sync with the doc I\'m looking at.

False Negative

• \"Sacs", located in the final diagnosis section should be coded
together with the previous term as a diagnosis ("Hernia Sacs")

GROSS DIAGNOSIS Right and left inguinal soft tissue, excision HERNIA
SACS.

Here we lose from excluding SNOMED Hernia Sac is a snomed term.

Also mentioned SACS in partial coding. Same explanation.

\#######################################################################################################################################

Case: a8d6073f-b9ec-11da-bf17-b1a4b49d6452

Incorrect Coding as Organ

• \"Identified\" from Final Diagnosis Section is coded as a Organ.

• "Submitted\" from Final Diagnosis Section is coded as a Organ.

Not seeing this?

Incorrect Coding as Diagnosis

• \"well\" has been incorrectly coded as Diagnosis in the Gross
Description Section.

C0343101: Eosinophilic cellulitis

Phrase: \"well-circumscribed,\"

Meta Candidates (3)

661 Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease or
Syndrome\]

661 Best (Best {NCI}) \[Disease or Syndrome,Qualitative Concept\]

623 Wellness (Wellness {MSH,NCI}) \[Idea or Concept\]

Meta Mapping (661)

661 Best (Best {NCI}) \[Disease or Syndrome,Qualitative Concept\]

Meta Mapping (661)

661 Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease or
Syndrome\]

Yet it\'s getting this cui C9051935. And I can\'t find where it coming
from? Definately an NCIM concept should

be CL051935 Ok it\'s coming from NCIT Best CL051935: Best Qualitative
Concept

Source Definition

NCI2006_01C H

Yet there is also a Best that is a Disease of Syndrome

C1411990: Best

Disease or Syndrome

This is troublesome for so many reasons.

Here\'s the map again

Processing 00000000.tx.1: well-circumscribed

Phrase: \"well-circumscribed\"

Meta Candidates (3)

661 C0343101:Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease
or Syndrome\]

661 C9051935:Best (Best {NCI}) \[Disease or Syndrome,Qualitative
Concept\]

623 C0018684:Wellness (Wellness {MSH,NCI}) \[Idea or Concept\]

Meta Mapping (661)

661 C9051935:Best (Best {NCI}) \[Disease or Syndrome,Qualitative
Concept\]

Meta Mapping (661)

661 C0343101:Wells (Eosinophilic cellulitis \[Wells\] {ICD10}) \[Disease
or Syndrome\]

It seems like this \"Best\" should not be included in the TUI list.

C1411990: Best

Disease or Syndrome

Somehow the TUIs and CUIs are being switched. There may be something we
can do in addSemanticTypeFeatures routine

of the EvsMMTx class. Because that concept pointer should NOT have two
semantic type categories.

False Negatives

(all in Gross Description)

• Renal vein should be coded as an Organ.

THis is in negation scope and again new algorithm to not negate an organ
in the Negation scope should work here.

• Perirenal should be coded as Organ.

perirenal adipose tissue doesn\'t have a combined concept and perirenal
is only existant with other combined concepts.

• Perirenal fat should be coded as Organ.

This is in window of Negation but should be ignored in the new algorithm
to un-negate organ.

Negation Issues

• Non-neoplastic has been been incorrectly coded. (Neoplastic has been
coded as a diagnosis)

Non can this be added as a prenegation phrase? Maybe not.

\#######################################################################################################################################

Case: a94ae925-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ

• \"Identified\" from Final Diagnosis Section is coded as a Organ.

Not seeing this happen?

Incorrect Diagnosis

• \"well\" has been incorrectly coded as Diagnosis in the Gross
Description Section.

Almost certainly same issue as previous case. No additional
investigation here.

Partial Coding

•"invasion" located in Part 1of the final diagnosis section is coded by
itself. "angiolymphatic invasion" should be coded together.

•\"well-circumscribed\" should be coded together as a General Concept

\#######################################################################################################################################

Case: be54ce54-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ

• \"Identified\" from Final Diagnosis Section is coded as a Organ.

Not seeing where this is happening?

False Positive

• "see" from "see above" located in Part 2 of the final diagnosis
section is coded as a Diagnosis.

This is the same organ problem noted many times. \*\*\*Fix this ???

• "above" from "see above" located in Part 2 of the final diagnosis
section is coded as a Diagnosis.

Looks to be just a positive concept. Obviously shouldn\'t be coded at
all since it\'s a short hand.

In the Final Diagnosis Section, Lymphatic has been coded as an Organ and
Invasion as a Diagnosis concept. \"Lymphatic Invasion\" should be coded
together as Diagnosis

This is a hard one because it looks like it should be there since
Lymphatic Invasion is a first class concept from NCIT. The only
explanation

I have is that the version of NCIT might be too old NCI2006_01C

• "Breast, Right" should be coded as organ (instead of only just Breast)
in Final Diagnosis Section.

Can\'t get this because of phraser.

\#######################################################################################################################################

Case: 963a6310-b9ec-11da-bf17-b1a4b49d6452

False Negative

• In the Gross Description section, \"Fibroadipose\" should be coded.

IS LABELED RIGHT BREAST TISSUE AND CONSISTS OF A BROWNISH-YELLOW
FIBROADIPOSE AND BREAST TISSUE MEASRING X X CM.

Fibroadipose is only associated with SNOMED terms and only as a
constituent of bigger concepts. Thus

No concept in the vocabulary for Fibroadipose.

\#######################################################################################################################################

Case: a1f417d6-b9ec-11da-bf17-b1a4b49d6452

False Negative

• In the Gross Description section, \"Fibroadipose\" should be coded.

Same argument as previous case. Not in vocabulary.

Partial Coding

• "Breast, Right" should be coded together as organ (instead of Breast
as Organ and right as a General concept) in Final Diagnosis Section.

Consistent inability of MMTx phrase finder. Comma separates these into
phrases.

\#######################################################################################################################################

Case: bf83896e-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ

• \"mass\" has been incorrectly coded as an Organ in the Gross
Description section.

T020 problem. Acquired Abnormality should be a Diagnosis not an Organ

Partial Coding

• "left breast" should be coded together as organ (instead of Breast as
Organ and left as a General concept) in Gross Description Section.

This is just an anomaly of the MMTx phrase parser. For some reason each
word gets it\'s own phrase here. \"left breast\" is a first

class LOINC concept and if put directly into MMTx like the left breast
has DCIS. It performs correctly. Really can\'t fix this.

\#######################################################################################################################################

Case: ec9e2b57-b9ec-11da-bf17-b1a4b49d6452

False Negatives

• \"Distant Metastasis\" should be coded as a Diagnosis in the final
diagnosis section.

This is coded as Phenomenon Or Process from NCIT and we currently filter
this in the CaTIES_ConceptFilter.jape

Should we remove this TUI filter?

Incorrect General

• \"Pathologic Staging\" should be coded as a General Concept in the
final diagnosis section.

This is coded as a Classification TUI that is being filtered with the
concept filter.

Don't filter classification

\#######################################################################################################################################

Case: ed6b3f64-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ

• \"identified\" has been incorrectly coded as an Organ in the final
diagnosis section.

This is discussed in an earlier case.

• \"Axillary\" has been incorrectly coded as an Organ in the final
diagnosis section.

Not seeing this. Looks like Axillary is coded as Negated concept.
Appropriate Coding

• "Complete Excision" should be coded together as Procedure (instead of
Excision as Procedure and complete being coded as a General Concept) in
Final Diagnosis Section.

This is unexplainable since Complete Excision is a first class NCIT
concept. It also comes from SNOMED. The only explanation

is that Complete Excision did not enter NCIM until before 2006_01.

\*\*\*Fix this??? Try regenerating the Data Source. Against the very
latest NCIM.

Spelling

• The spell checker has not corrected the spelling for \"Lyimph\". This
has resulted in incorrect coding of Organ concept \"Regional Lymph
Nodes\"

We\'re not running the spell checker.

\#######################################################################################################################################

Case: ee03d5ed-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ:

• \"frozen section\" has been incorrectly coded as an Organ in the gross
description section.

C0016741: Frozen Sections

Tissue Semantic Type: Tissue

TUI: T024

Definition: An aggregation of similarly specialized cells and the
associated intercellular substance. Tissues are relatively non-localized
in comparison to body parts, organs or organ components.

So this is ok.

• \"cavity\" has been incorrectly coded as an Organ in the gross
description section.

Semantic Type: Body Space or Junction

TUI: T030

Definition: An area enclosed or surrounded by body parts or organs or
the place where two anatomical structures meet or connect.

We include this as an Organ. Really what we mean by Organ is probably
Anatomy_Kind

• \"mass\" has been incorrectly coded as an Organ in the gross
description section.

This is T020 that should be changed to Diagnosis. \*\*\*Fix this???

False Negatives

• \"INTERVILLOUSITIS\" should be coded as a General Concept in the final
diagnosis section.

We miss this because it only appears in SNOMED

• In Gross Description section, \"thymus\" should be coded as an Organ

Not seeing thymus anywhere in this report?

\#######################################################################################################################################

Case: 9b064287-b9ec-11da-bf17-b1a4b49d6452

False Negatives:

• \"Allograft ileal biopsy\" should be coded as a procedure in the Final
Diagnosis section.

• \"Allograft\" should be coded as a procedure as well, in the Final
Diagnosis section.

This is weird

Sentence incoming is\...

Allograft ileal biopsy second allograft, months , NO EVIDENCE OF ACUTE
CELLULAR REJECTION OR VIRAL INCLUSIONS

MMTx just makes a mess of this. Choosing a Dental Material as the
semantic type for allograft.

Processing 00000000.tx.1: Allograft ileal biopsy second allograft,
months , NO EVIDEN

INCLUSIONS

Phrase: \"Allograft ileal biopsy second allograft,\"

Meta Candidates (11)

637 Biopsy NOS (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

637 Second (2nd {NCI}) \[Functional Concept\]

637 Allograft (Allograft surgical material {MTH}) \[Biomedical or Dental
Material\]

637 allograft (Allografts {MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

637 Second (Sekund {NCI}) \[Quantitative Concept\]

582 SEC (enterotoxin C, staphylococcal {MSH,NCI}) \[Amino Acid, Peptide,
or Protein,Imm

582 Sec (3-Selenylalanine {MSH,NCI}) \[Amino Acid, Peptide, or
Protein,Biologically Act

582 SEC (Secondary to {NCI}) \[Classification,Qualitative Concept\]

582 SEC (Section {NCI}) \[Conceptual Entity\]

566 Ileum (Ileum {MSH,NCI,UWDA}) \[Body Part, Organ, or Organ
Component,Tissue\]

554 ilium (Bone structure of ilium {UWDA,MSH,NCI}) \[Anatomical
Structure\]

Meta Mapping (597)

637 Allograft (Allograft surgical material {MTH}) \[Biomedical or Dental
Material\]

637 Second (2nd {NCI}) \[Functional Concept\]

Meta Mapping (597)

637 Allograft (Allograft surgical material {MTH}) \[Biomedical or Dental
Material\]

637 Second (Sekund {NCI}) \[Quantitative Concept\]

Meta Mapping (597)

637 allograft (Allografts {MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

637 Second (2nd {NCI}) \[Functional Concept\]

Meta Mapping (597)

637 allograft (Allografts {MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

637 Second (Sekund {NCI}) \[Quantitative Concept\]

This should be sent to NLM perhaps.

• \"Acute cellular rejection\" should be coded as a concept.

Same sentence

Phrase: \"OF ACUTE CELLULAR REJECTION\"

Meta Candidates (8)

827 Rejection (Rejections {MSH}) \[Social Behavior\]

660 ACUTE (ACUTE {NCI-GLOSS,NCI}) \[Classification,Qualitative
Concept,Temporal Concept\]

604 ACS (Cancer Society, American {MSH,NCI}) \[Health Care Related
Organization\]

604 AC (AC {NCI,MSH}) \[Geographic Area\]

604 ACS (ACS {NCI}) \[Spatial Concept\]

604 ACS (American College of Surgeons {NCI}) \[Professional Society\]

589 cell (Cell Types {NCI,LNC,MSH,MTH,NCI-GLOSS,UWDA}) \[Cell\]

589 Cellularity (Cellularity {NCI}) \[Conceptual Entity\]

Meta Mapping (828)

660 ACUTE (ACUTE {NCI-GLOSS,NCI}) \[Classification,Qualitative
Concept,Temporal Concept\]

589 cell (Cell Types {NCI,LNC,MSH,MTH,NCI-GLOSS,UWDA}) \[Cell\]

827 Rejection (Rejections {MSH}) \[Social Behavior\]

Meta Mapping (828)

660 ACUTE (ACUTE {NCI-GLOSS,NCI}) \[Classification,Qualitative
Concept,Temporal Concept\]

589 Cellularity (Cellularity {NCI}) \[Conceptual Entity\]

827 Rejection (Rejections {MSH}) \[Social Behavior\]

Note the poor semantic types that our CaTIES_ConceptFilter.jape throws
out.

We can do better by not throwing out Classification or Temporal Concept.
Qualitative Concept is second

in the list for ACUTE otherwise it would be included. This is a problem
seen regarding \"well\" in previous

cases. \*\*\*Fix This??? add Classification and Temporal Concept. There
really is no combined concept for

acute cellular rejection so if we could just do better on the
constituents it would be a best case improvement.

\#######################################################################################################################################

Case: 9fa98c5b-b9ec-11da-bf17-b1a4b49d6452

Incorrect Diagnosis:

• \"Autolyzed\" has been incorrectly coded as Diagnosis in the Final
Diagnosis section.

This has TUI T046 Pathologic Function which get\'s a diagnosis. Probably
correct.

• \"Duplication\" has been incorrectly coded as Diagnosis in the Final
Diagnosis section.

T049 Cell or molecular dysfunction. This is probably a polysomous coding
error. There is

\"Duplication\" Quantitative Concept coming from SNOMED so including
SNOMED here might help.

\*\*\*Fix this??? Included SNOMED. But in general there is no combined
concept for ILEAL DUPLICATION CYST.

\#######################################################################################################################################

Case: a4c42815-b9ec-11da-bf17-b1a4b49d6452

False negatives

• \"Cystoprostatectomy\" should be coded as a procedure in the Final
Diagnosis section.

There is a Radical Cystoprostatectomy in NCIT but my guess is that it\'s
new to 0601 we are at 0511.

MDR-60 and SNODMED have it and I believe we don\'t include either of
these. Actually I tried the OTS

MMTx with cystoprostatectomy and got nothing as well.
SNOMEDCT_2004_01_31, MDR-60, NCI2006_01C

has a Radical Cystoprostatectomy. We\'re just missing this.

• \"Urothelium\" should be coded as Organ in the Final Diagnosis
section.

URINARY BLADDER, POSTMORTEM DONOR CYSTOPROSTATECTOMY - UROTHELIUM LINED
BLADDER TISSUE WITH MILD CHRONIC CYSTITIS.

NO EVIDENCE OF UROTHELIAL CARCINOMA IN SITU (CIS) NOR INVASIVE
UROTHELIAL CARCINOMA SEEN.

URINARY BLADDER, POSTMORTEM DONOR CYSTOPROSTATECTOMY - UROTHELIUM LINED
BLADDER TISSUE WITH MILD CHRONIC CYSTITIS

Processing 00000000.tx.1: URINARY BLADDER, POSTMORTEM DONOR
CYSTOPROSTATECTOMY - UROTHELIUM LINED BLADDER TISSUE WITH MILD

IC CYSTITIS

Phrase: \"URINARY BLADDER,\"

Meta Candidates (6)

1000 Urinary bladder, NOS (BLAD {NCI,MSH,NCI-GLOSS,UWDA,LNC}) \[Body
Part, Organ, or Organ Component\]

861 bladder (BLAD {NCI,MSH,NCI-GLOSS,UWDA,LNC}) \[Body Part, Organ, or
Organ Component\]

861 URINARY (Urinary system structure {NCI,UWDA,MSH,NCI-GLOSS,LNC})
\[Body Part, Organ, or Organ Component\]

861 Urinary (URNY {NCI,NCI-GLOSS}) \[Qualitative Concept\]

789 URINE (Urinary System, Urine {NCI,LNC,NCI-GLOSS,MSH,UWDA}) \[Body
Substance\]

789 Urine (Urine {NCI}) \[Tissue\]

Meta Mapping (1000)

1000 Urinary bladder, NOS (BLAD {NCI,MSH,NCI-GLOSS,UWDA,LNC}) \[Body
Part, Organ, or Organ Component\]

Phrase: \"POSTMORTEM DONOR CYSTOPROSTATECTOMY - UROTHELIUM LINED BLADDER
TISSUE\"

Meta Candidates (8)

818 Bladder Tissue (Bladder Tissue {NCI}) \[Tissue\]

795 tissue (Body tissue structure {MTH,UWDA,LNC,NCI,MSH,NCI-GLOSS})
\[Tissue\]

629 postmortem (Autopsy {NCI,ICD9CM,MSH}) \[Diagnostic Procedure\]

629 bladder (BLAD {NCI,MSH,NCI-GLOSS,UWDA,LNC}) \[Body Part, Organ, or
Organ Component\]

629 donor (Donors {ICD9CM,MSH,NCI,LNC}) \[Population Group\]

629 Urothelium (Urothelium {MSH,NCI,UWDA,NCI-GLOSS}) \[Tissue\]

595 LINE (LINE {LNC}) \[Medical Device\]

595 LINE (Long Interspersed Element {NCI}) \[Nucleotide Sequence\]

Meta Mapping (801)

629 postmortem (Autopsy {NCI,ICD9CM,MSH}) \[Diagnostic Procedure\]

818 Bladder Tissue (Bladder Tissue {NCI}) \[Tissue\]

Phrase: \"WITH MILD CHRONIC CYSTITIS\"

Meta Candidates (3)

901 Chronic cystitis NOS (Cystitis chronic NOS {NCI}) \[Disease or
Syndrome\]

827 Cystitis NOS (Cystitis, unspecified {ICD10,ICD9CM,MSH,NCI})
\[Disease or Syndrome\]

660 CHRONIC (CHR {NCI,NCI-GLOSS}) \[Classification,Qualitative
Concept,Temporal Concept\]

Meta Mapping (901)

901 Chronic cystitis NOS (Cystitis chronic NOS {NCI}) \[Disease or
Syndrome\]

Looks like urithelium should be mapped above. Same multi-adjective
pattern seen earlier with MMTx

epithelial.

False Negatives

\"• The Invasive part of \"\"Invasive Urothelial Carcinoma\"\" has not
been coded in the Final Diagnosis section.

When just submitting Invasive Urothelial Carcinoma it gets both Invasive
and Urothelial Carcinoma. Of course this

should be negated. But why is Invasive not showing up when it looks like
it is mapped?

Processing 00000000.tx.1: NO EVIDENCE OF UROTHELIAL CARCINOMA IN SITU
CIS NOR INVASIVE UROTHELIAL CARCINOMA S

Phrase: \"NO EVIDENCE\"

Meta Candidates (2)

861 Evidence (Evidence {NCI}) \[Functional Concept\]

694 NO (NO {NCI,MSH}) \[Geographic Area\]

Meta Mapping (888)

694 NO (NO {NCI,MSH}) \[Geographic Area\]

861 Evidence (Evidence {NCI}) \[Functional Concept\]

Phrase: \"OF UROTHELIAL CARCINOMA IN SITU CIS\"

Meta Candidates (38)

804 CIS (CIS {NCI-GLOSS,NCI,MSH,ICD9CM,ICD10}) \[Educational
Activity,Intellectual Product,Neoplastic Process

804 CIS (Commonwealth of Independent States {MSH,MTH}) \[Geographic
Area\]

804 CIS (G18 {NCI,MSH,MTH}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

804 Cis (Genus Cis {MTH}) \[Invertebrate\]

771 CI (CL {NCI,MSH}) \[Biologically Active Substance,Element, Ion, or
Isotope,Geographic Area\]

771 CI (CI {MSH,NCI}) \[Geographic Area\]

771 Urothelial Carcinoma in situ (Urothelial Carcinoma in situ {NCI})
\[Neoplastic Process\]

771 CI (CI Term Type {NCI}) \[Conceptual Entity\]

717 Carcinoma in situ, NOS (CIS {NCI-GLOSS,NCI,MSH,ICD9CM,ICD10})
\[Educational Activity,Intellectual Product

ss\]

673 Urothelial carcinoma (Cell Carcinoma, Transitional
{MSH,NCI-GLOSS,NCI}) \[Neoplastic Process\]

673 Urothelial carcinoma, NOS (BLADDER CANCER TRANSITIONAL CELL {NCI})
\[Neoplastic Process\]

673 In Situ (In Situ {NCI}) \[Classification,Qualitative Concept,Spatial
Concept\]

637 carcinoma (Epitheliomas {MSH,NCI,NCI-GLOSS,MTH}) \[Neoplastic
Process\]

637 IN (IN {NCI,MSH}) \[Geographic Area,Geographic Area\]

637 IN (In element {LNC,MSH,MTH}) \[Element, Ion, or Isotope\]

637 Carcinoma (Carcinoma of the Prostate Gland {NCI}) \[Neoplastic
Process\]

637 Carcinoma (Carcinoma {NCI}) \[Neoplastic Process\]

604 ins (Chromosomal Insertion {NCI}) \[Cell or Molecular Dysfunction\]

604 INS (Nurse Informaticist {NCI}) \[Biomedical Occupation or
Discipline,Intellectual Product,Professional o

oup\]

604 INS (INS Gene {NCI}) \[Gene or Genome\]

582 CA (Factor IV {MSH,NCI,LNC,NCI-GLOSS,MTH}) \[Element, Ion, or
Isotope\]

582 CA (CA {NCI,MSH}) \[Geographic Area,Geographic Area\]

582 CA (Cancer, unspecified site
{NCI,MSH,NCI-GLOSS,LNC,MIM,ICD10,MTH,ICD9CM}) \[Neoplastic Process\]

582 Indexing (Indexing {MSH}) \[Occupational Activity\]

582 INSULIN (Unmodified insulin product {MSH,NCI,LNC,MTH}) \[Amino Acid,
Peptide, or Protein,Hormone,Pharmaco

582 INULIN (INULIN {LNC,MSH}) \[Biologically Active
Substance,Carbohydrate,Indicator, Reagent, or Diagnostic

582 CA (AC protocol {NCI,MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

582 Index (IX {NCI,MSH}) \[Intellectual Product\]

582 insulin (insulin {MTH}) \[Gene or Genome\]

582 Insulin (Insulin {NCI,NCI-GLOSS}) \[Amino Acid, Peptide, or
Protein,Hormone,Laboratory Procedure\]

582 CAS (CRKAS {NCI}) \[Gene or Genome\]

582 CAS (CRK-Associated Substrate {NCI}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

582 Insulin (Recombinant Insulin {NCI}) \[Amino Acid, Peptide, or
Protein,Pharmacologic Substance\]

582 CA (Cornu Ammonis {NCI}) \[Anatomical Structure,Body Part, Organ, or
Organ Component\]

566 Urothelium (Urothelium {MSH,NCI,UWDA,NCI-GLOSS}) \[Tissue\]

554 Iletin (Iletin {MSH}) \[Amino Acid, Peptide, or
Protein,Hormone,Pharmacologic Substance\]

537 carcinogen (chemical carcinogen {NCI,MSH,NCI-GLOSS}) \[Hazardous or
Poisonous Substance\]

537 Carcinogen (Chemical Carcinogen {NCI}) \[Hazardous or Poisonous
Substance\]

Meta Mapping (928)

771 Urothelial Carcinoma in situ (Urothelial Carcinoma in situ {NCI})
\[Neoplastic Process\]

804 CIS (CIS {NCI-GLOSS,NCI,MSH,ICD9CM,ICD10}) \[Educational
Activity,Intellectual Product,Neoplastic Process

Meta Mapping (928)

771 Urothelial Carcinoma in situ (Urothelial Carcinoma in situ {NCI})
\[Neoplastic Process\]

804 CIS (Commonwealth of Independent States {MSH,MTH}) \[Geographic
Area\]

Meta Mapping (928)

771 Urothelial Carcinoma in situ (Urothelial Carcinoma in situ {NCI})
\[Neoplastic Process\]

804 CIS (G18 {NCI,MSH,MTH}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

Meta Mapping (928)

771 Urothelial Carcinoma in situ (Urothelial Carcinoma in situ {NCI})
\[Neoplastic Process\]

804 Cis (Genus Cis {MTH}) \[Invertebrate\]

Phrase: \"NOR\"

Meta Candidates (2)

1000 NOR (NO {NCI,MSH}) \[Geographic Area\]

1000 NOR (NOR {NCI}) \[Mammal\]

Meta Mapping (1000)

1000 NOR (NO {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 NOR (NOR {NCI}) \[Mammal\]

Phrase: \"INVASIVE UROTHELIAL CARCINOMA\"

Meta Candidates (21)

913 Invasive Carcinoma (Invasive Carcinoma {NCI}) \[Neoplastic Process\]

913 Invasive carcinoma NOS (Undifferentiated Invasive Carcinoma of the
Prostate Gland {NCI}) \[Neoplastic Pro

901 Urothelial carcinoma (Cell Carcinoma, Transitional
{MSH,NCI-GLOSS,NCI}) \[Neoplastic Process\]

901 Urothelial carcinoma, NOS (BLADDER CANCER TRANSITIONAL CELL {NCI})
\[Neoplastic Process\]

827 carcinoma (Epitheliomas {MSH,NCI,NCI-GLOSS,MTH}) \[Neoplastic
Process\]

827 Carcinoma (Carcinoma of the Prostate Gland {NCI}) \[Neoplastic
Process\]

827 Carcinoma (Carcinoma {NCI}) \[Neoplastic Process\]

771 CA (Factor IV {MSH,NCI,LNC,NCI-GLOSS,MTH}) \[Element, Ion, or
Isotope\]

771 CA (CA {NCI,MSH}) \[Geographic Area,Geographic Area\]

771 CA (Cancer, unspecified site
{NCI,MSH,NCI-GLOSS,LNC,MIM,ICD10,MTH,ICD9CM}) \[Neoplastic Process\]

771 CA (AC protocol {NCI,MSH,MTH}) \[Therapeutic or Preventive
Procedure\]

771 CAS (CRKAS {NCI}) \[Gene or Genome\]

771 CAS (CRK-Associated Substrate {NCI}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance\]

771 CA (Cornu Ammonis {NCI}) \[Anatomical Structure,Body Part, Organ, or
Organ Component\]

727 carcinogen (chemical carcinogen {NCI,MSH,NCI-GLOSS}) \[Hazardous or
Poisonous Substance\]

727 Carcinogen (Chemical Carcinogen {NCI}) \[Hazardous or Poisonous
Substance\]

660 Invasive (INV {NCI}) \[Qualitative Concept,Qualitative Concept\]

604 IV (CI {MSH,NCI}) \[Geographic Area\]

604 IV (IV - Intravenous {NCI,NCI-GLOSS}) \[Spatial Concept\]

604 IV (IV {NCI}) \[Functional Concept,Quantitative Concept\]

589 Urothelium (Urothelium {MSH,NCI,UWDA,NCI-GLOSS}) \[Tissue\]

Meta Mapping (901)

660 Invasive (INV {NCI}) \[Qualitative Concept,Qualitative Concept\]

901 Urothelial carcinoma (Cell Carcinoma, Transitional
{MSH,NCI-GLOSS,NCI}) \[Neoplastic Process\]

Meta Mapping (901)

660 Invasive (INV {NCI}) \[Qualitative Concept,Qualitative Concept\]

901 Urothelial carcinoma, NOS (BLADDER CANCER TRANSITIONAL CELL {NCI})
\[Neoplastic Process\]

Phrase: \"SEEN\"

Meta Candidates (2)

966 seeing (visual perception {MSH,MTH,LNC}) \[Organ or Tissue
Function\]

916 SEER (SEER Program {NCI,MSH}) \[Research Activity\]

Meta Mapping (966)

966 seeing (visual perception {MSH,MTH,LNC}) \[Organ or Tissue
Function\]

• \"\"Urothelium\"\" should be coded as Organ in the Final Diagnosis
section.\"

OK here\'s what\'s happing. In the CaTIES_NegEx.jape \"Invasive\" is
negated. And there\'s a special case

made for Qualitative Concepts that simply Remove them if they\'re
negated this was probably because other

kinds of Qualitative Concepts didn\'t make sense as negated concepts.
Maybe it\'s better to put this

back in or at least move the functionality over to the
ConceptCategorizer that does additional post

Negation cleanup for Procedures and Organs. \*\*Fix this???

Negation Problems

\"Invasive Urothelial Carcinoma\" should be coded as a Negated Diagnosis
in the Final Diagnosis section. (\"Urothelial Carcinoma\" has been coded
as Diagnosis) \*\*\*Fix this??? Add \"nor\" to the prenegation list.

\#######################################################################################################################################

Case: a239372e-b9ec-11da-bf17-b1a4b49d6452

False negative

• \"Paracortical\" should be coded as a Organ/General Concept in the
Final Diagnosis section.

There\'s only one combined concept that MMTx apparently just can\'t pare
down. If given the exace termonology

it gets it.

Processing 00000000.tx.1: Lymph node paracortical region

Phrase: \"Lymph node paracortical region\"

Meta Candidates (24)

1000 Lymph Node Paracortical Region (Lymph Node Paracortical Region
{NCI}) \[Anatomical Structure\]

812 REGION (REGION {LNC,NCI}) \[Spatial Concept\]

756 REG (REG {NCI}) \[Professional or Occupational Group,Qualitative
Concept\]

756 REG (Registered {NCI}) \[Qualitative Concept\]

756 REG (Registering {NCI}) \[Occupational Activity\]

756 REG (Registration {NCI}) \[Conceptual Entity,Health Care Activity\]

756 REG (EXTR1 {NCI}) \[Gene or Genome\]

741 Regional (RGN {NCI,NCI-GLOSS}) \[Spatial Concept\]

694 lymph node (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or Organ Component\]

645 lymph (Reticuloendothelial System, Lymph {NCI,NCI-GLOSS,MSH,UWDA})
\[Body Substance\]

645 LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

645 Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

645 Node (TreeNode {NCI}) \[Intellectual Product\]

638 LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part,
Organ, or Organ Component\]

638 LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic Process\]

608 Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI}) \[Anatomical
Structure,Body Part, Organ, or Organ Componen

574 Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA}) \[Body System\]

574 Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part, Organ, or
Organ Component\]

574 Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional Concept,Qualitative
Concept\]

574 Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

574 Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

553 NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

545 NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

545 Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

Meta Mapping (1000)

1000 Lymph Node Paracortical Region (Lymph Node Paracortical Region
{NCI}) \[Anatomical Structure\]

• The Invasive part of \"Invasive Urothelial Carcinoma\" has not been
coded in the Final Diagnosis section.

This looks like a faulty duplication from a previous case observation.

\#######################################################################################################################################

Case: ac8fb341-b9ec-11da-bf17-b1a4b49d6452

Partial coding

• \"Rectal biopsy\" should be coded together as a procedure as opposed
to \"Rectal\" being coded as a General Concept and \"biopsy\" as a
Procedure in both final diagnosis and gross description sections.

This is a first class NCIT concept but it may be new to NCI2006_01C.
\*\*\*Fix this?? Built a new data source.

\#######################################################################################################################################

Case: cd1ed031-b9ec-11da-bf17-b1a4b49d6452

False Negative

\"• \"\"left tonsil" located in the gross description section should be
coded as an Organ.

No markings present to designate left tonsil from right tonsil.

left tonsil is in the scope of a pre negation. \*\*\*Fix this?? the new
negation rule to not eliminate but insteand un-negate

a negated organ might fix this. Although it\'s odd here.

•"exudate" located in the gross description section should be coded as a
General Concept.

Same as last. exudate is an Organ and eliminated.

•"No fibrinopurulent" located in the gross description section should be
coded as a Negated Diagnosis.\"

No fibrinopurulent exudates These fall into the same category of negated
organs

Exudate C0015388: Exudate Body Substance Semantic Type: Body Substance

TUI: T031 In our Organ classification

fribronopurulent is itself not a concept but part of compound concept
that MMTx probably can\'t map.

This whole not negating organs may be a bad idea when we consider how
we\'re classifying things as

Organs. For instance No exudates should probably stay.

\#######################################################################################################################################

Case: cf754381-b9ec-11da-bf17-b1a4b49d6452

False Negative

• \"Appendix\" should be coded as an Organ in the Final Diagnosis
section.

\*\*\*\*Fix this? Again organ rule. Eliminates negated organ

\#######################################################################################################################################

Case:

Incorrect genereal Should me organ

• \"Esophageal\" should be coded as an Organ instead of a General
Concept in the Final Diagnosis section.

is received in formalin, labeled with the patient\'s name, and is
designated esophageal biopsy

Phrase: \"esophageal biopsy\"

Meta Candidates (4)

861 Biopsy NOS (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

694 Esophageal (Esophagus Disorders {MSH,ICD9CM,MTH,ICD10,NCI})
\[Disease or Syndrome\]

694 ESOPHAGEAL (ESOPHAGEAL {NCI-GLOSS,NCI}) \[Qualitative Concept\]

623 Esophagus, NOS (Gastrointestinal Tract, Esophagus
{NCI,UWDA,NCI-GLOSS,MSH,LNC}) \[Body

Meta Mapping (888)

694 ESOPHAGEAL (ESOPHAGEAL {NCI-GLOSS,NCI}) \[Qualitative Concept\]

861 Biopsy NOS (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

Meta Mapping (888)

694 Esophageal (Esophagus Disorders {MSH,ICD9CM,MTH,ICD10,NCI})
\[Disease or Syndrome\]

861 Biopsy NOS (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

As seen by this map MMTx could go with either an Esophagial Qualitative
Concept or a Disease. Either

randomly or based on a source priority list it chooses Qualitative
Concept T080 which we don\'t map

to Organ. This is the best we can do with this.

\#######################################################################################################################################

Case: 9b384f0c-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ Coding

• \"Involvement\" has been incorrectly coded as an Organ in the final
diagnosis section.

Not seeing this it is correct coded as a Negated Concept

Incorrect General

• \"Pleura\" should be coded as an Organ but has been coded as a General
Concept in the gross description sections.

Because of shoddy outlining the chunker run the entire sentence
together. includes the phrase

pleuraH mass which gets mapped to a Finding. If we include this as a
diagnosis then this would get placed as

a diagnosis. We could alter the outline identifiers but this case is
just messy. Not much to do here.

False Negative

\"• \"\"Lymph node\"\" should be coded as an Organ both in the final
diagnosis and gross description sections.

In FD Lymph node gets negated by the previous line item. Introducing
outline identifiers into NegEx will fix this. \*\*\*Fix This???

In GD Lymph nodes are apparently missed with that big mis-chunked
sentence because of MMTx\'s propensity to take

big rich conceptual phrases and only include the two concepts in the map

Phrase: \"A frozen section portion B parabronchial lymph nodes C
bronchial resection margin D vascular resection margin E-G mass\"

Meta Candidates (82)

848 C0746921:Lymph Node Mass (NODAL MASS {NCI}) \[Finding\]

810 C0746921:NODAL MASS (NODAL MASS {NCI}) \[Finding\]

798 C9106225:Resected Mass (Resected Mass {NCI}) \[Finding\]

784 C0577559:Mass NOS (Observation of a mass {MTH,NCI}) \[Acquired
Abnormality\]

784 C9106224:Resectable Mass (Resectable Mass {NCI}) \[Finding\]

784 C9314318:MASS (MASS {NCI}) \[Functional Concept,Quantitative
Concept\]

624 C0016741:Section, Frozen (Frozen Sections {MSH}) \[Tissue\]

624 C0024204:Nodes, Lymph (Lymph node proper
{NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body Part, Organ, or Organ C

621 C0017725:D-Glucose (D-glucose preparation
{MSH,NCI,LNC,NCI-GLOSS,MTH}) \[Biologically Active Substanc

617 C0005847:vascular (Blood vessel structure
{UWDA,MSH,MTH,NCI-GLOSS,NCI,LNC}) \[Body Part, Organ, or Or

617 C0015252:Resection (Surgical Removeoval {NCI,NCI-GLOSS})
\[Therapeutic or Preventive Procedure\]

617 C0024202:lymph (Reticuloendothelial System, Lymph
{NCI,NCI-GLOSS,MSH,UWDA}) \[Body Substance\]

617 C0024264:LYMPH (Lymphocytic {NCI,LNC,MTH,MSH,NCI-GLOSS}) \[Cell\]

617 C0205039:BRONCHIAL (BRO {LNC,MTH,NCI}) \[Body Part, Organ, or Organ
Component\]

617 C0719022:Bronchial (Bronchial {MTH}) \[Organic
Chemical,Pharmacologic Substance\]

617 C9052662:Section (Section {NCI}) \[Conceptual Entity\]

617 C9107728:Margin (Border {NCI}) \[Spatial Concept,Spatial Concept\]

617 C9127933:margin (Surgical Margins {NCI,NCI-GLOSS}) \[Spatial
Concept\]

617 C9317951:Vascular (Vascular {NCI}) \[Qualitative Concept\]

591 C0085188:Freeze Sectioning (Freeze Sectioning {MSH}) \[Laboratory
Procedure\]

584 C0004683:BS (BS {NCI,MSH}) \[Gene or Genome,Geographic Area\]

584 C0007886:CS (CS {LNC,MSH,MTH}) \[Cell Component,Element, Ion, or
Isotope,Geographic Area,Geographic A

584 C0013754:ES (ES {NCI,MSH}) \[Geographic Area\]

584 C0016701:freezing (Freezings {MSH}) \[Natural Phenomenon or
Process\]

584 C0037747:ES (ESP {NCI,MSH}) \[Geographic Area\]

584 C0057936:DS (Diethyl Sulfate {NCI,MSH}) \[Organic
Chemical,Pharmacologic Substance\]

584 C0162832:GS (Genes, APC {MSH,MTH,NCI,LNC}) \[Gene or Genome\]

584 C0700320:sectioning (Sectioning technique {MTH}) \[Laboratory
Procedure\]

584 C0746922:Node (Node {NCI}) \[Body Part, Organ, or Organ Component\]

584 C1442488:BS (BSL {NCI,LNC,MTH}) \[Conceptual Entity\]

584 C9017727:GS (GS {NCI}) \[Geographic Area\]

584 C9320112:DS (DS {NCI}) \[Gene or Genome\]

584 C9322513:ES (Endosinusial {NCI}) \[Spatial Concept\]

584 C9337348:Node (TreeNode {NCI}) \[Intellectual Product\]

564 C0005802:Blood Glucose (Blood Sugar {MSH,MTH}) \[Carbohydrate\]

562 C0004587:Bacilli (Bacterial rods {MSH,MTH}) \[Bacterium\]

562 C0004927:behavior (Finding relating to behaviour {MSH,NCI,LNC})
\[Behavior\]

562 C0007009:Carbon (C element {MSH}) \[Element, Ion, or Isotope\]

562 C0009498:COMPLEMENT (COMPLEMENT {LNC,MSH,NCI}) \[Amino Acid,
Peptide, or Protein,Immunologic Factor\]

562 C0009563:Compliance (Compliance {MSH,MTH}) \[Quantitative Concept\]

562 C0010715:Cytidine (Cytosine Riboside {MSH,NCI}) \[Nucleic Acid,
Nucleoside, or Nucleotide\]

562 C0010843:CYTOSINE (CYTOSINE {NCI,MSH}) \[Biologically Active
Substance,Organic Chemical\]

562 C0011530:Deoxyribose (D-erythro-Pentose, 2-deoxy- {MSH})
\[Biologically Active Substance,Carbohydrate

562 C0017725:GLUCOSE (D-glucose preparation {MSH,NCI,LNC,NCI-GLOSS,MTH})
\[Biologically Active Substance,

562 C0017890:GLYCINE (Aminoacetic Acid {MSH,LNC,NCI,MTH}) \[Amino Acid,
Peptide, or Protein\]

562 C0018320:guanidine (Guanidines {MSH,MTH}) \[Organic Chemical\]

562 C0018330:Guanosine (Guanosine {MSH,NCI}) \[Biologically Active
Substance,Nucleic Acid, Nucleoside, or

562 C0061856:GRAM (Gram Stain {NCI,MSH,MTH}) \[Indicator, Reagent, or
Diagnostic Aid,Laboratory Procedure

562 C0120446:Guanidine (Guanidinium {MSH,NCI,MTH}) \[Organic
Chemical,Pharmacologic Substance\]

562 C0150141:Bath (Baths {MSH,LNC,MTH}) \[Medical Device,Therapeutic or
Preventive Procedure\]

562 C0242264:capacitance (Electric Capacitance {MSH}) \[Quantitative
Concept\]

562 C0282189:Gravities (Gravity {MSH}) \[Natural Phenomenon or Process\]

562 C0337438:Glucose (Glucose {MTH}) \[Laboratory Procedure\]

562 C0337527:brother (Brothers {MSH,NCI,LNC}) \[Family Group\]

562 C0439228:day (d - day {NCI,LNC}) \[Temporal Concept\]

562 C0522461:Glycine (Glycine {MTH}) \[Plant\]

562 C0596544:Expectation (Expectation {NCI}) \[Mental Process\]

562 C1040746:Bacilli (Bacilli {MTH}) \[Bacterium\]

562 C1301886:DIAMETER (Bore {NCI,LNC,NCI-GLOSS}) \[Quantitative
Concept\]

562 C1321605:COMPLIANCE (Cooperation, Patient {MSH,MTH,NCI})
\[Individual Behavior\]

562 C9158123:Contact (Contact {NCI}) \[Spatial Concept\]

562 C9331893:Celsius (Celsius Scale {NCI}) \[Intellectual Product\]

562 C9337316:Coulomb (Ampere second {NCI}) \[Quantitative Concept\]

553 C0024204:LN (Lymph node proper {NCI,NCI-GLOSS,LNC,MSH,UWDA}) \[Body
Part, Organ, or Organ Component\]

553 C9055296:LN (Lobular Intraepithelial Neoplasia {NCI}) \[Neoplastic
Process\]

546 C0006255:bronchi (Bronchus, NOS {NCI-GLOSS,MSH,MTH,NCI,UWDA}) \[Body
Part, Organ, or Organ Component\]

546 C0013741:Einsteinium (Einsteinium {MSH}) \[Element, Ion, or
Isotope\]

546 C0024235:Lymphatic (Reticuloendothelial System, Lymphatic System
{NCI,MSH,NCI-GLOSS,UWDA}) \[Body Sys

546 C0229889:Lymphatic (Vessels, Lymphatic {MSH,UWDA,LNC}) \[Body Part,
Organ, or Organ Component\]

546 C1235659:Bronchus (Bronchus {MTH}) \[Invertebrate\]

546 C9054717:Resected (RES {NCI,NCI-GLOSS}) \[Qualitative Concept\]

546 C9084262:Lymphoid (Lymphoid {NCI,NCI-GLOSS}) \[Functional
Concept,Qualitative Concept\]

546 C9324601:Lymphatic, NOS (LYMPT {NCI}) \[Qualitative Concept\]

536 C0229654:Lymphoid nodule (Nodular lymphoid tissue {UWDA,NCI})
\[Anatomical Structure,Body Part, Organ

534 C9017709:BV (BVT {NCI}) \[Geographic Area\]

534 C9110875:Nodal (Nodal {NCI}) \[Qualitative Concept,Spatial Concept\]

517 C0005767:BLOOD (BLD {LNC,MSH,MTH,NCI,UWDA,NCI-GLOSS}) \[Body
Substance\]

517 C0085243:NOD (Diabetic Mouse, Nonobese {MSH,NCI}) \[Mammal\]

517 C0524631:Lymphatism (Lymphatism {MSH}) \[Disease or Syndrome\]

517 C9052628:Resectable (Resectable {NCI,NCI-GLOSS}) \[Qualitative
Concept\]

511 C0018966:Haem (Ferroprotoporphyrin {MSH,NCI}) \[Biologically Active
Substance,Organic Chemical\]

511 C0028259:NODULE (NDUL {NCI,NCI-GLOSS}) \[Finding\]

Meta Mapping (791)

624 C0016741:Section, Frozen (Frozen Sections {MSH}) \[Tissue\]

784 C0577559:Mass NOS (Observation of a mass {MTH,NCI}) \[Acquired
Abnormality\]

Meta Mapping (791)

624 C0016741:Section, Frozen (Frozen Sections {MSH}) \[Tissue\]

784 C9314318:MASS (MASS {NCI}) \[Functional Concept,Quantitative
Concept\]

Meta Mapping (791)

• \"\"parabronchial lymph nodes\"\" should be coded as an Organ in the
gross description section.

Since it can\'t get it at all it can\'t categorize it as an organ.

• \"\"bronchial\"\" and \"\"bronchus\"\" should be coded as an Organ in
the gross description section.

These are both in the run on sentence.

• \"\"vascular\"\" should be coded as an Organ in the gross description
section.

same sentence

• \"\"resection\"\" should be coded as a Procedure in the gross
description section\"

same sentence

Negation Issue

• tumor should be coded as Negated Diagnosis. (it has been coded as a
diagnosis)

This is because FOPR (i.e., FOR) is missspelled and we\'re not running
the spell checker

Miscillaneous

• the spell checker has not corrected the spelling for \"Negatve\". This
has resulted in incorrect coding of a Negated Diagnosis concept as
Diagnosis.

\#######################################################################################################################################

Case: 9dab7231-b9ec-11da-bf17-b1a4b49d6452

Incorrect General

• \"\"Lymph Node\"\" should be coded as an Organ and \"\"Positive\"\" as
a General Concept but \"\"Lymph Nodes Positive\"\" has been coded as a
General Concept in the final diagnosis section.\"

Actually this is preferred because its a long map of diagnosis. Trouble
is this is a \"Finding\" T033 which we are going

to change to be a diagnosis. \*\*\*Fix This???

Partial Coding

• "Lung, Right" should be coded together as organ (instead of Lung as
Organ and right as a General concept) in Final Diagnosis Section.

Phraser of MMTx Can\'t fix.

\#######################################################################################################################################

Case: 9ed57364-b9ec-11da-bf17-b1a4b49d6452

False negatives

\"Lymph node\" should be coded as an Organ in the gross description
section.

• \"parabronchial lymph nodes\" should be coded as an Organ in the gross
description section.

• \"bronchial\" and \"bronchus\" should be coded as an Organ in the
gross description section.

• \"vascular\" should be coded as an Organ in the gross description
section.

• \"resection\" should be coded as a Procedure in the gross description
section.

• \"anthracoctic\" should be coded as a Diagnosis in the gross
description section.

Actually it is coded as a Diagnosis?

\#######################################################################################################################################

Case: b1973d1f-b9ec-11da-bf17-b1a4b49d6452

False Negative:

• \"Lymph node\" should be coded as an Organ in the final diagnosis
section.

This is the negated organ problem but here Lymph node infiltrate Test.

infiltrate should make it in as a Negated Concept, however it doesn\'t
because

the Physiologic Function is concept filtered. \*\*\*Fix this???

\#######################################################################################################################################

Case: bffd264a-b9ec-11da-bf17-b1a4b49d6452

Incorrect organs

• \"exudes\" has been incorrectly coded as an Organ. (it should be a
General Concept).

Mapped to exudate which is a Tissue. Actually reasonable

• \"identified\" has been incorrectly coded as an Organ.

identified seems to be correctly coded as a negated concept. This will
become a negated diagnosis

if we change Finding here.

• \"frozen section\" has been incorrectly coded as an Organ.

frozen section actually maps to Tissue semantic type so this is
correctly coded as Organ.

False Negative

• \"Segmentectomy\" should be coded as a Procedure in the gross
description section.

Processing 00000000.tx.1: The specimen is received unfixed labeled with
the patient s name and upper division segmente

ft upper lobe, suture at lesion

Phrase: \"The specimen\"

Meta Candidates (1)

1000 C0370003:SPECIMEN (Sample {NCI,LNC}) \[Physical Object,Substance\]

Meta Mapping (1000)

1000 C0370003:SPECIMEN (Sample {NCI,LNC}) \[Physical Object,Substance\]

Phrase: \"is\"

Meta Candidates (0): \<none\>

Meta Mappings: \<none\>

Phrase: \"received\"

Meta Candidates (1)

1000 C9052596:Received (Received {NCI}) \[Conceptual Entity,Functional
Concept\]

Meta Mapping (1000)

1000 C9052596:Received (Received {NCI}) \[Conceptual Entity,Functional
Concept\]

Phrase: \"unfixed\"

Meta Candidates (0): \<none\>

Meta Mappings: \<none\>

Phrase: \"labeled\"

Meta Candidates (3)

1000 C9337421:Labeled (Tagged {NCI}) \[Functional Concept\]

966 C0181496:Label (Pharmaceutical Product Label {NCI,MSH})
\[Manufactured Object\]

966 C9031994:Label (Label {NCI,NCI-GLOSS}) \[Indicator, Reagent, or
Diagnostic Aid\]

Meta Mapping (1000)

1000 C9337421:Labeled (Tagged {NCI}) \[Functional Concept\]

Phrase: \"with the patient s name\"

Meta Candidates (9)

827 C0027365:Name (Names {MSH,NCI,LNC}) \[Intellectual Product\]

827 C9110058:NAME (Carney Syndrome {NCI}) \[Disease or Syndrome\]

827 C9333581:Name (Scientific Name {NCI}) \[Intellectual Product\]

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C0205436:Second (2nd {NCI}) \[Functional Concept\]

604 C9333091:Second (Sekund {NCI}) \[Quantitative Concept\]

589 C0037659:SOMATOSTATIN (Somatostatin-14 {NCI,MSH,LNC,MTH}) \[Amino
Acid, Peptide, or Protein,Pharmacologic Substanc

589 C1335871:somatostatin (SST gene {MTH}) \[Gene or Genome\]

589 C9101872:Somatostatin (SST {NCI}) \[Amino Acid, Peptide, or
Protein,Hormone,Manufactured Object\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C0205436:Second (2nd {NCI}) \[Functional Concept\]

827 C0027365:Name (Names {MSH,NCI,LNC}) \[Intellectual Product\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C0205436:Second (2nd {NCI}) \[Functional Concept\]

827 C9110058:NAME (Carney Syndrome {NCI}) \[Disease or Syndrome\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C0205436:Second (2nd {NCI}) \[Functional Concept\]

827 C9333581:Name (Scientific Name {NCI}) \[Intellectual Product\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C9333091:Second (Sekund {NCI}) \[Quantitative Concept\]

827 C0027365:Name (Names {MSH,NCI,LNC}) \[Intellectual Product\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C9333091:Second (Sekund {NCI}) \[Quantitative Concept\]

827 C9110058:NAME (Carney Syndrome {NCI}) \[Disease or Syndrome\]

Meta Mapping (833)

660 C0030705:patient (PT {NCI,MSH,LNC}) \[Patient or Disabled
Group,Temporal Concept\]

604 C9333091:Second (Sekund {NCI}) \[Quantitative Concept\]

827 C9333581:Name (Scientific Name {NCI}) \[Intellectual Product\]

Phrase: \"and\"

Meta Candidates (2)

1000 C0002838:AND (AND {NCI,MSH}) \[Geographic Area\]

1000 C9337427:And (And {NCI}) \[Conceptual Entity\]

Meta Mapping (1000)

1000 C0002838:AND (AND {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 C9337427:And (And {NCI}) \[Conceptual Entity\]

Phrase: \"upper division segmentectomy left upper lobe,\"

Meta Candidates (11)

861 C1261076:Left upper lobe (Upper Lobe of the Left Lung-LUL
{NCI,UWDA}) \[Anatomical Structure,Body Part, Organ, or

mponent\]

799 C0450424:Left (Levo- {NCI,UWDA}) \[Spatial Concept\]

799 C0796494:Lobe (Lobe {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or
Organ Component\]

766 C0242724:Leaves (Plant Leaves {MSH,MTH}) \[Plant\]

743 C0023376:LS (Basutoland {NCI,MSH}) \[Geographic Area\]

743 C0023668:LS (LS {NCI,MSH}) \[Geographic Area\]

727 C0023128:LV (Latvia {NCI,MSH}) \[Geographic Area\]

727 C0023413:LV (Folix {NCI,MSH,NCI-GLOSS}) \[Pharmacologic Substance\]

727 C9052334:Lobar (Lobar {NCI}) \[Qualitative Concept\]

632 C0024885:Segmentectomy (Segmentectomy {MSH,NCI,NCI-GLOSS})
\[Therapeutic or Preventive Procedure\]

632 C9111427:Upper (Above {NCI}) \[Spatial Concept\]

Meta Mapping (836)

632 C9111427:Upper (Above {NCI}) \[Spatial Concept\]

861 C1261076:Left upper lobe (Upper Lobe of the Left Lung-LUL
{NCI,UWDA}) \[Anatomical Structure,Body Part, Organ, or

mponent\]

Phrase: \"suture\"

Meta Candidates (2)

1000 C0038969:SUTURE (SUTURE {NCI,MSH,MTH}) \[Medical Device\]

1000 C0502420:Suture (Suture Joint {MTH,UWDA}) \[Body Space or
Junction\]

Meta Mapping (1000)

1000 C0038969:SUTURE (SUTURE {NCI,MSH,MTH}) \[Medical Device\]

Meta Mapping (1000)

1000 C0502420:Suture (Suture Joint {MTH,UWDA}) \[Body Space or
Junction\]

Phrase: \"at lesion\"

Meta Candidates (1)

1000 C0221198:LESION (LESION {NCI-GLOSS,NCI}) \[Finding\]

Meta Mapping (1000)

1000 C0221198:LESION (LESION {NCI-GLOSS,NCI}) \[Finding\]

MMTx misses segmentectomy

\*\*\*Fix this??? Should be reported to NLM developers.

\#######################################################################################################################################

Case: c31255cb-b9ec-11da-bf17-b1a4b49d6452

Incorrect Organ

\"• \"\"fragmented\"\" has been incorrectly coded as an Organ. (it
should be a General Concept).

This is Body Substance T031 which is in our Organ list.

• \"\"identified\"\" has been incorrectly coded as an Organ.

Again seeing not identified coded as Negated concept. Finding. If we add
Finding as Diagnosis this will

become a negated diagnosis which is more or less incorrect. \*\*\*\*Fix
this?

• \"\"external\"\" has been incorrectly coded as an Organ.\"

Not seeing this?

Incorrect Diagnosis

• in gross description section, \"testes\"(Organ) has been incorrectly
coded as a Diagnosis concept.

Phrase: \"testes.\"

Meta Candidates (2)

1000 C0039584:TESTES (Disorder testicle {MSH,MTH,NCI,LNC}) \[Disease or
Syndrome\]

1000 C0039597:testes (Genital System, Male, Testis
{NCI,MSH,MTH,UWDA,NCI-GLOSS,LNC}) \[Body Part, Organ, or Organ
Component\]

Meta Mapping (1000)

1000 C0039584:TESTES (Disorder testicle {MSH,MTH,NCI,LNC}) \[Disease or
Syndrome\]

Meta Mapping (1000)

1000 C0039597:testes (Genital System, Male, Testis
{NCI,MSH,MTH,UWDA,NCI-GLOSS,LNC}) \[Body Part, Organ, or Organ
Component\]

Looks like it could go either way but why testes would be a disease of
syndrome I can\'t figure.

False Positive

• \"see" from "see comment" located in the final diagnosis section is
coded as a Diagnosis.

See earlier explanation and Fix

False Negative

\"• \"\"Gestational\"\" should be coded as a General Concept in the
final diagnosis section.

Gestational Age gets coded as a single concept but then is filter by
CaTIES_ConceptFilter.jape

\*\*\*Fix this??? Remove \[Organism Attribute\] from filter list.

• \"\"perivillous fibrin\"\" should be coded as a General Concept in the
final diagnosis section.

Processing 00000000.tx.1: RETROPLACENTAL HEMORRHAGE WITH ADJACENT
PERIVILLOUS FIBRIN DEPOSITION

Phrase: \"RETROPLACENTAL HEMORRHAGE\"

Meta Candidates (2)

861 C0019080:Haemorrhage (Extravasation of blood {MSH,NCI,MTH,ICD9CM})
\[Finding\]

789 C9108732:Haemorrhagic (Hemorrhagic Change {NCI}) \[Finding\]

Meta Mapping (861)

861 C0019080:Haemorrhage (Extravasation of blood {MSH,NCI,MTH,ICD9CM})
\[Finding\]

Phrase: \"WITH ADJACENT PERIVILLOUS FIBRIN DEPOSITION\"

Meta Candidates (6)

812 C9159187:Deposition (DEPS {NCI}) \[Finding\]

645 C0015982:fibrin (Fibrins {MSH,NCI}) \[Anatomical Structure\]

645 C9124273:Adjacent (Next to {NCI}) \[Conceptual Entity\]

545 C0016006:fibrinogen (Fibrinogens {MSH,MTH,NCI,LNC}) \[Amino Acid,
Peptide, or Protein,Biologically Active Substance\]

545 C0337428:Fibrinogen (Fibrinogen assay {MTH}) \[Finding,Laboratory
Procedure\]

534 C0016703:FG (GF {NCI,MSH}) \[Geographic Area\]

Meta Mapping (791)

645 C9124273:Adjacent (Next to {NCI}) \[Conceptual Entity\]

812 C9159187:Deposition (DEPS {NCI}) \[Finding\]

• \"\"INTERVILLOUSITIS\"\" should be coded as a General Concept in the
final diagnosis section.

This isn\'t really in the NCIM as a descrete concept.

• In Gross Description section, \"\"thymus\"\" should be coded as an
Organ\"

Thymus gets coded as a Biologically active substance T123

\*\*\*Fix this??? We filter this. Remove this from the filter and add
this T123 to our Organ list.

This is problematic because Thymus can be the Body Part or the thing
secreted from it.

Processing 00000000.tx.1: thymus

Phrase: \"thymus\"

Meta Candidates (2)

1000 C0040112:THYMUS (Extracts, Thymus {MSH,MTH}) \[Biologically Active
Substance\]

1000 C0040113:THYMUS (Thymus Proper {NCI,MSH,UWDA,MTH,NCI-GLOSS}) \[Body
Part, Organ, or Organ Component,Pharmacologic Substanc

e\]

Meta Mapping (1000)

1000 C0040112:THYMUS (Extracts, Thymus {MSH,MTH}) \[Biologically Active
Substance\]

Meta Mapping (1000)

1000 C0040113:THYMUS (Thymus Proper {NCI,MSH,UWDA,MTH,NCI-GLOSS}) \[Body
Part, Organ, or Organ Component,Pharmacologic Substanc

e\]

Looks like we may have to lose this one.

DeID

• a couple of dates have not been Removeoved from the Gross Description
section.

\*\*DATE\[Feb 2 06\]

\*\*DATE\[Jun 14 06\]

These aren\'t offset or anything.

\#######################################################################################################################################

Case: bfbcc1e4-b9ec-11da-bf17-b1a4b49d6452

General should be Diagnosis

• \"fibrosis\" has been incorrectly coded as a General Concept in the
final diagnosis section. (it should be a Diagnosis)

This is a Finding T033 should make diagnosis \*\*\*Fix this???

Partial Coding

\"• "Lung, Left" should be coded together as organ (instead of Lung as
Organ and left as a General concept) in Final Diagnosis Section.

• "upper lower lobest" should be coded together as organ (instead of
lobes as Organ and upper, lower as a General concept) in Final Diagnosis
Section.

• "Wedge Biopsy" should be coded together as Procedure (instead of
Biopsy as Procedure and wedge not being coded) in Final Diagnosis
Section.\"

See below. Again this just was too much for MMTx. Even though wedge
biopsy looks to be first class NCIT concept MMTx

cannot map to it.

This is just mapped this way by the phrase analyzer in MMTx

Processing 00000000.tx.1: LUNG, LEFT UPPER LOWER LOBES, WEDGE BIOPSIES
OSS PATH-NUMBER, USUAL INTERSTITIAL PNEUMONIA PA

TTERN OF FIBROSIS ASSOCIATED WITH ALVEOLAR PROTEINOSIS AND CHOLESTEROL
GRANULOMAS see comment

Phrase: \"LUNG,\"

Meta Candidates (14)

1000 C0024109:lung (Set of lungs {UWDA,MSH,NCI,LNC}) \[Body Part, Organ,
or Organ Component\]

944 C9317978:Pulmonary, NOS (PULM {NCI,NCI-GLOSS,LNC}) \[Qualitative
Concept\]

907 C0032285:pneumonia (Pulmonary Inflammations
{MSH,NCI-GLOSS,NCI,ICD10}) \[Disease or Syndrome\]

893 C0030125:PAS (Benzoic acid, 4-amino-2-hydroxy- {MSH}) \[Organic
Chemical,Pharmacologic Substance\]

893 C0030193:PN (Dolor {MSH,MTH,NCI,LNC,ICD10}) \[Sign or Symptom\]

893 C0030266:PA (PA {NCI,MSH}) \[Geographic Area,Geographic Area\]

893 C0030853:PA (Pennsylvania {MSH,NCI}) \[Geographic Area\]

893 C0031995:PN (Pitcairn Islands {NCI,MSH}) \[Geographic Area\]

893 C0206417:PNS (Systems, Peripheral Nervous {MSH,UWDA,MTH,NCI}) \[Body
System\]

893 C0681477:PA (Program Announcements, NIH {NCI}) \[Governmental or
Regulatory Activity,Intellectual Product\]

893 C1455752:PN (PN {LNC}) \[Qualitative Concept,Quantitative Concept\]

893 C9100596:PNS (PNS {NCI}) \[Therapeutic or Preventive Procedure\]

893 C9110592:Pa (Pascal {NCI}) \[Quantitative Concept\]

893 C9233807:PAS (Periodic Acid Schiff {NCI}) \[Laboratory Procedure\]

Meta Mapping (1000)

1000 C0024109:lung (Set of lungs {UWDA,MSH,NCI,LNC}) \[Body Part, Organ,
or Organ Component\]

Phrase: \"LEFT\"

Meta Candidates (4)

1000 C0450424:Left (Levo- {NCI,UWDA}) \[Spatial Concept\]

966 C0242724:Leaves (Plant Leaves {MSH,MTH}) \[Plant\]

928 C0023128:LV (Latvia {NCI,MSH}) \[Geographic Area\]

928 C0023413:LV (Folix {NCI,MSH,NCI-GLOSS}) \[Pharmacologic Substance\]

Meta Mapping (1000)

1000 C0450424:Left (Levo- {NCI,UWDA}) \[Spatial Concept\]

Phrase: \"UPPER LOWER LOBES,\"

Meta Candidates (6)

793 C0796494:Lobe (Lobe {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or
Organ Component\]

743 C9052334:Lobar (Lobar {NCI}) \[Qualitative Concept\]

660 C9110734:Lower (Lower {NCI}) \[Qualitative Concept\]

660 C9111427:Upper (Above {NCI}) \[Spatial Concept\]

627 C9333589:Lowest (Nadir {NCI}) \[Qualitative Concept\]

589 C0206579:LO (LO {NCI,MSH}) \[Geographic Area\]

Meta Mapping (840)

660 C9111427:Upper (Above {NCI}) \[Spatial Concept\]

660 C9110734:Lower (Lower {NCI}) \[Qualitative Concept\]

793 C0796494:Lobe (Lobe {NCI,UWDA,NCI-GLOSS}) \[Body Part, Organ, or
Organ Component\]

Phrase: \"WEDGE BIOPSIES OSS PATH-NUMBER,\"

Meta Candidates (5)

804 C0237753:Number (NUMS {NCI,LNC,MTH}) \[Quantitative Concept\]

721 C0020580:Numbness (\[D\]Hypoaesthesia {MSH,MTH}) \[Sign or Symptom\]

721 C0028643:\[D\]Numbness (\[D\]Numbness {NCI,MTH}) \[Sign or Symptom\]

637 C0005558:biopsies (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

637 C0205469:PATH (PATH {LNC,NCI}) \[Biomedical Occupation or
Discipline\]

Meta Mapping (764)

637 C0005558:biopsies (BX {NCI,MSH,NCI-GLOSS}) \[Diagnostic
Procedure,Geographic Area\]

804 C0237753:Number (NUMS {NCI,LNC,MTH}) \[Quantitative Concept\]

Phrase: \"USUAL INTERSTITIAL PNEUMONIA PATTERN\"

Meta Candidates (13)

812 C0449774:pattern (PATT {NCI}) \[Spatial Concept\]

756 C0085786:Usual interstitial pneumonia (Idiopathic fibrosing
alveolitis {ICD9CM,MSH,NCI}) \[Disease or Syndrome\]

756 C9066984:Usual Interstitial Pneumonia (Usual Interstitial Pneumonia
{NCI}) \[Disease or Syndrome\]

694 C0206061:Interstitial pneumonia (PNEUMONITIS INTERSTITIAL {MSH,NCI})
\[Disease or Syndrome\]

645 C0032285:pneumonia (Pulmonary Inflammations
{MSH,NCI-GLOSS,NCI,ICD10}) \[Disease or Syndrome\]

645 C0596790:Interstitial (Interstitial {NCI}) \[Functional Concept\]

590 C0030193:PN (Dolor {MSH,MTH,NCI,LNC,ICD10}) \[Sign or Symptom\]

590 C0031995:PN (Pitcairn Islands {NCI,MSH}) \[Geographic Area\]

590 C0206417:PNS (Systems, Peripheral Nervous {MSH,UWDA,MTH,NCI}) \[Body
System\]

590 C1455752:PN (PN {LNC}) \[Qualitative Concept,Quantitative Concept\]

590 C9100596:PNS (PNS {NCI}) \[Therapeutic or Preventive Procedure\]

553 C0024109:lung (Set of lungs {UWDA,MSH,NCI,LNC}) \[Body Part, Organ,
or Organ Component\]

539 C9317978:Pulmonary, NOS (PULM {NCI,NCI-GLOSS,LNC}) \[Qualitative
Concept\]

Meta Mapping (916)

756 C0085786:Usual interstitial pneumonia (Idiopathic fibrosing
alveolitis {ICD9CM,MSH,NCI}) \[Disease or Syndrome\]

812 C0449774:pattern (PATT {NCI}) \[Spatial Concept\]

Meta Mapping (916)

756 C9066984:Usual Interstitial Pneumonia (Usual Interstitial Pneumonia
{NCI}) \[Disease or Syndrome\]

812 C0449774:pattern (PATT {NCI}) \[Spatial Concept\]

Phrase: \"OF FIBROSIS\"

Meta Candidates (1)

1000 C0016059:Fibrosis NOS (Fibrous thickening {MSH,NCI,NCI-GLOSS,MTH})
\[Finding\]

Meta Mapping (1000)

1000 C0016059:Fibrosis NOS (Fibrous thickening {MSH,NCI,NCI-GLOSS,MTH})
\[Finding\]

Phrase: \"ASSOCIATED\"

Meta Candidates (4)

1000 C0332281:Associated (AW {NCI}) \[Idea or Concept,Qualitative
Concept\]

916 C0004083:association (Associations {MSH,MTH}) \[Mental Process\]

916 C0699792:association (association {MTH}) \[Social Behavior\]

916 C9335171:Association (NCI Thesaurus Association {NCI}) \[Conceptual
Entity\]

Meta Mapping (1000)

1000 C0332281:Associated (AW {NCI}) \[Idea or Concept,Qualitative
Concept\]

Phrase: \"WITH ALVEOLAR PROTEINOSIS\"

Meta Candidates (8)

1000 C0034050:Alveolar proteinosis (Alveolar Proteinosis, Pulmonary
{MSH,ICD9CM}) \[Disease or Syndrome\]

944 C0052059:ALP (BLPI {NCI,MSH}) \[Amino Acid, Peptide, or
Protein,Biologically Active Substance,Gene or Genome\]

944 C0102159:AlP (ruberythric acid {MSH}) \[Organic
Chemical,Pharmacologic Substance\]

944 C9101409:ALP (ESKINE {NCI}) \[Gene or Genome\]

944 C9107230:ALPS (Canale-Smith Syndrome {NCI}) \[Disease or Syndrome\]

861 C1440080:Alveolar (Alveolar {LNC}) \[Body Part, Organ, or Organ
Component,Qualitative Concept\]

789 C9068966:Alveoli (Alveoli {NCI,NCI-GLOSS}) \[Body Part, Organ, or
Organ Component\]

789 C9318893:Alveolus (Alveolus {NCI}) \[Tissue\]

Meta Mapping (1000)

1000 C0034050:Alveolar proteinosis (Alveolar Proteinosis, Pulmonary
{MSH,ICD9CM}) \[Disease or Syndrome\]

Phrase: \"AND\"

Meta Candidates (2)

1000 C0002838:AND (AND {NCI,MSH}) \[Geographic Area\]

1000 C9337427:And (And {NCI}) \[Conceptual Entity\]

Meta Mapping (1000)

1000 C0002838:AND (AND {NCI,MSH}) \[Geographic Area\]

Meta Mapping (1000)

1000 C9337427:And (And {NCI}) \[Conceptual Entity\]

Phrase: \"CHOLESTEROL GRANULOMAS\"

Meta Candidates (4)

983 C9108736:Cholesterol Granuloma (Cholesterinic granuloma {NCI})
\[Finding\]

861 C0008377:CHOLESTEROL (CHOL {NCI,MSH,LNC,MTH}) \[Biologically Active
Substance,Steroid\]

861 C0018188:Granulomas (Epithelioid granuloma {MSH,NCI}) \[Finding\]

827 C9318248:Granuloma (Granuloma of the Mammary Gland {NCI})
\[Neoplastic Process\]

Meta Mapping (983)

983 C9108736:Cholesterol Granuloma (Cholesterinic granuloma {NCI})
\[Finding\]

Phrase: \"see\"

Meta Candidates (2)

966 C0042789:seeing (visual perception {MSH,MTH,LNC}) \[Organ or Tissue
Function\]

928 C0242638:SEER (SEER Program {NCI,MSH}) \[Research Activity\]

Meta Mapping (966)

966 C0042789:seeing (visual perception {MSH,MTH,LNC}) \[Organ or Tissue
Function\]

Phrase: \"comment\"

Meta Candidates (2)

1000 C0282411:Comment (Comment {MSH,MTH}) \[Intellectual Product\]

1000 C0947611:Comment (Comments {NCI,MTH,LNC}) \[Intellectual Product\]

Meta Mapping (1000)

1000 C0282411:Comment (Comment {MSH,MTH}) \[Intellectual Product\]

Meta Mapping (1000)

1000 C0947611:Comment (Comments {NCI,MTH,LNC}) \[Intellectual Product\]