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Histopatholgy reports
Introduction
In general, histopathology reports should be annotated in the same way as any other document. There are, however, some additional points to bear in mind. The way in which some entities are used is slightly different, to allow for the annotation of the investigations, results, and loci (and some addtional conditions) that predominate in histopathology reports. This section details the differences.
Investigations
- Histopathology reports may contain large lists of histochemistry and immunocytochemistry tests.
- These should be annotated as investigations.
- For example,
- "Mucin stains are focally positive."
- "Mucin stains" should be annotated as an investigation
- "Masson Fontana stain for melanin is negative"
- "Masson Fontana stain" should be annotated as an investigation
- Many tests are looking for the presence of specific surface antigens and markers. It can be unclear whether the text is referring to the antigen or the test. Where this is the case, the text should be marked as the test - i.e. an investigation.
- For example
- "SMA and desmin and MNF116 are negative."
- SMA, desmin and MNF116 should all be marked as investigations.
- Sometimes, these markers will be reported as part of a general histochemistry test
- For example
- "Immunohistochemistry shows these cells to be CD68 positive and MNF116 negative"
- "Immunohistochemistry", "CD68" and "MNF116" should all be annotated as investigations.
Results
- Histopathology reports may contain indications of the presence or absence of markers and stains.
- These should be annotated as results.
- For example,
- "Mucin stains are focally positive."
- "positive" should be annotated as a result
- "Masson Fontana stain for melanin is negative"
- "negative" should be annotated as a result
- In the case of surface antigen tests, the presence or absence of the specific surface antigens and markers should be annotated as results.
- For example
- "SMA and desmin and MNF116 are negative."
- "negative" should be marked as a result, linked to the three investigations.
- For example
- "Immunohistochemistry shows these cells to be CD68 positive and MNF116 negative"
- "positve" and "negative" should be annotated as results, linked to "CD68" and "MNF116" investigations respectively.
- There are many other ways of expressing positivity, which should also be marked as results of their repsective tests.
- For example
- "P53 stains some large cells" - "stains" should be marked as a result of the Investigation "P53"
- "large lymphoid cells immunoreactive for CD5" - "immunoreactive" should be marked as a result of the Investigation "CD5"
Locus
- In addition to the loci used in other reports, histopathology reports contain several other kinds of loci that should be annotated.
- Tissues
- For example
- "The subepithelial tissues are inflamed"
- "subepithelial tissue" should be annotated as a locus
- For example
- "endometrial stromal sarcoma"
- "endometrial stromal" should be annotated as a locus
- Cells
- For example,
- "HMB-45 immunostains are positive in these cells"
- "cells" should be annotated as a locus
- For example
- "many plump fibroblasts were seen"
- "fibroblasts" should be annotated as a locus
- For example
- "Mitotic figures are scanty"
- "Mitotic figures" should be annotated as a locus
- Sub-cellular components
- For example,
- "The nucleoli are prominent"
- "nucleoli" should be marked as a locus
Condition
- Histopathology reports sometimes mention cellular processes. These should be annotated as Conditions.
- For example,
- "There is a moderate proliferation fraction"
- "proliferation" should be annotated as a condition
- For example,
- "consistent with transformation of previous B-CLL"
- "transformation" should be annotated as a condition
has_finding relationship
- Histopathology reports may contain large lists of histochemistry and immunocytochemistry tests and results, indicating the presence or absence of markers and stains.
- These should be annotated as Investigations and Results, and related with a has_finding relation.
- For example,
- "Mucin stains are focally positive."
- A has_finding relation should link "Mucin stains" and "positive"
- "Masson Fontana stain for melanin is negative"
- A has_finding relation should link "Masson Fontana stain" and "negative"
- In the case of surface antigen tests, the presence or absence of the specific surface antigens and markers should be linked to results.
- For example
- "SMA and desmin and MNF116 are negative."
- "negative" should be linked to all three investigations, with has_finding relationships.
- For example
- "Immunohistochemistry shows these cells to be CD68 positive and MNF116 negative"
- "positve" and "negative" should be linked with has_finding relationships to "CD68" and "MNF116" investigations respectively.