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BCHSI / philter-ucsf

Open source clinical text de-identification
BSD 3-Clause "New" or "Revised" License
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Issues with pathology terms #6

Open DSLituiev opened 4 years ago

DSLituiev commented 4 years ago

Here are examples where current version corrupts pathology terms:

Molecular markers

Ki-67 shows a high proliferative index in the poorly differentiated region (which accounts for 50-75% of the tumor).
===>
*****-67 shows a high proliferative index in the poorly  differentiated region (which accounts for 50-75% of the tumor).
Results in the tumor cell nuclei are:
MLH1 expression:  Present.       
MSH2 expression:  Present.
MSH6 expression:  Present.
PMS2 expression:  Present.
===>
Results in the tumor cell nuclei are:
***** expression:  Present. 
***** expression:  Present. 
***** expression:  Present.
***** expression:  Present.

Tumour staging

AJCC/UICC stage:  pT3N2b.
===> 
- AJCC/UICC stage: *****.

Positive lymph nodes

Are misinterpreted as dates

4.  Metastatic  adenocarcinoma in eleven of sixteen lymph nodes (11/16) 
and four satellite tumor nodules; see comment.
===>
4.Metastatic adenocarcinoma in eleven of sixteen lymph nodes (July 30) 
and four satellite tumor nodules; see comment.

Slide and Cassette numbers

CASSETTES:  Representative sections are submitted as follows:
B1:          Proximal surgical margin.
B2:          Distal surgical margin.
B3:          Appendix, cross-sections and distal tip, longitudinal.
B4-B5:          Surgical margins, separate small bowel segment.
B6:          Separate small bowel. 
B7:          Proximal terminal ileum.
B8:          Middle terminal ileum.
B9:          Distal terminal ileum.
B10:          Ascending colon polyps proximal to mass (smaller inked
blue).
B11-B12:     Closest approach of mass to radial surgical margin, full
thickness.
B13-B15:     Mass.

turns:

CASSETTES:
Representative sections are submitted as follows:
B1: Proximal surgical margin.
B2: Distal surgical margin.
*****: Appendix, cross-sections and distal tip, longitudinal.
*****-*****: Surgical margins, separate small bowel segment.
B6: Separate small bowel.
*****: Proximal terminal ileum.
*****: Middle terminal ileum.
*****: Distal terminal ileum.
*****: Ascending colon polyps proximal to mass (smaller inked blue).
*****-B12: Closest approach of mass to radial surgical margin, full thickness.
*****-*****: Mass