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histology and Histopathology #853

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masciam opened this Issue Jul 27, 2017 · 8 comments

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masciam commented Jul 27, 2017

I am working on developing an ontology for histopathology reports.
In OBI histology has as synonym histopathology http://purl.obolibrary.org/obo/OBI_0600020
I think that these should be two different terms.
histology is as in OBI "The visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement"
But since not always histology is used for pathological specimen such as in the case of the lab test to check the location of some expression molecules I think that we should have two different term
With histopathology been an histology with the purpose of examine the pathological level of the specimen

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bpeters42 commented Jul 27, 2017

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masciam Jul 31, 2017

Histopathology is child of histology
proposed definition: Histopathology is an histology that has_specified_output some (information content entity and (is about some (disease)))
I think the difference between a general histology and the histopathology is the purpose the histopathology is performed to check the presence or the level of a specific disease.

masciam commented Jul 31, 2017

Histopathology is child of histology
proposed definition: Histopathology is an histology that has_specified_output some (information content entity and (is about some (disease)))
I think the difference between a general histology and the histopathology is the purpose the histopathology is performed to check the presence or the level of a specific disease.

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jamesaoverton Jul 31, 2017

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Discussed on the OBI call 2017-07-31. We were agreed that 'histology' is more general and 'histopathology' is focused on pathology, and that it would be good to have distinct terms.

We could also make a link to 'pathologist role'.

For the textual definition of 'histopathology', we suggest: "A histology assay that is intended to check for the presence or level of a specific disease".

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jamesaoverton commented Jul 31, 2017

Discussed on the OBI call 2017-07-31. We were agreed that 'histology' is more general and 'histopathology' is focused on pathology, and that it would be good to have distinct terms.

We could also make a link to 'pathologist role'.

For the textual definition of 'histopathology', we suggest: "A histology assay that is intended to check for the presence or level of a specific disease".

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mbrochhausen Aug 4, 2017

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I did add the term (30885d8), but I am going to keep the issue open, since there are two more things to fix, in my mind:

  1. delete alternative term 'histopathology' from 'histology'
  2. The definition know reads "A histology assay...". Either we should rename 'histology' to 'histology assay' (which I would suggest) and add 'histology' as an alternative term, or the definition should be changed to "A histology..."
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mbrochhausen commented Aug 4, 2017

I did add the term (30885d8), but I am going to keep the issue open, since there are two more things to fix, in my mind:

  1. delete alternative term 'histopathology' from 'histology'
  2. The definition know reads "A histology assay...". Either we should rename 'histology' to 'histology assay' (which I would suggest) and add 'histology' as an alternative term, or the definition should be changed to "A histology..."
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masciam Aug 4, 2017

masciam commented Aug 4, 2017

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masciam commented Aug 4, 2017

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turbomam May 21, 2018

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Inclined to add "assay" to the labels and then close. Speak up if it needs more attention.

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turbomam commented May 21, 2018

Inclined to add "assay" to the labels and then close. Speak up if it needs more attention.

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masciam May 21, 2018

masciam commented May 21, 2018

turbomam added a commit that referenced this issue May 21, 2018

jamesaoverton added a commit that referenced this issue May 22, 2018

Merge pull request #933 from obi-ontology/mam20180521
- demoted gene knockdown assay equivalence axiom to subClassOf #931
- alternative 'Genome Analyzer I term' for Illumina Genome Analyzer #832
- adding 'assay' to hitology and histpathology terms #853
- adding isoform sequencing #878
- updating def source for human and mouse nCounter 'arrays' #831
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