nuclear assays, non morphological abnormalities

[obophenotype-user]

The annotator wanted to record something to the effect of: "abnormality on FDG PET scan with hypometabolism of the thalami." and suggested that we include "nuclear medicine type studies such as PET scans performed in the evaluation of neurodegenerative disorders." In this case, they also annotated 'NOT morphological abnormality of the central nervous system'. The supposition is that the metabolism is altered rather than the morphology as assayed by PET (as many other radioactive tracers can be used in PET to image tissue concentration of other types of molecules). PET can of course also be used for morphology too. They can't annotate to 'abnormality of the thalamus' because this implies a morphological abnormality and is a descendent of 'morphological abnormality of the central nervous system'.

Perhaps we need a series of abnormal metabolism in X terms? and have the abnormality of X anatomical structure not always be subclasses of abnormal morphology?

lots to discuss!

These types of imaging assay terms are requested a lot, we should try to think of a way to address them in a general way.

Reported by: mellybelly

Original Ticket: obo/human-phenotype-requests/270

[obophenotype-user]

• summary: nuclear assays --> nuclear assays, non morphological abnormalities
• Description has changed:

Diff:

--- old
+++ new
@@ -1,7 +1,8 @@
-This requires discussion. 
+The annotator wanted to record something to the effect of: "abnormality on FDG PET scan with hypometabolism of the thalami." and suggested that we include "nuclear medicine type studies such as PET scans performed in the evaluation of neurodegenerative disorders." In this case, they also annotated 'NOT morphological abnormality of the central nervous system'. The supposition is that the metabolism is altered rather than the morphology as assayed by PET (as many other radioactive tracers can be used in PET to image tissue concentration of other types of molecules). PET can of course also be used for morphology too. They can't annotate to 'abnormality of the thalamus' because this implies a morphological abnormality and is a descendent of 'morphological abnormality of the central nervous system'. 

-The annotator wanted to record something to the effect of: "abnormality on FDG PET scan with hypometabolism of the thalami." and suggested that we include "nuclear medicine type studies such as PET scans performed in the evaluation of neurodegenerative disorders." In this case, they also annotated 'NOT morphological abnormality of the central nervous system'
+Perhaps we need a series of abnormal metabolism in X terms? and have the abnormality of X anatomical structure not always be subclasses of abnormal morphology? 

-The suggestion is that the metabolism is altered rather than the morphology as assayed by PET (as many other radioactive tracers can be used in PET to image tissue concentration of other types of molecules). Perhaps we need a series of abnormal metabolism in X terms? PET can of course also be used for morphology too.
+lots to discuss!
+

 These types of imaging assay terms are requested a lot, we should try to think of a way to address them in a general way.

Original comment by: mellybelly

[obophenotype-user]

• status: unread --> closed-accepted
• assigned_to: Peter N. Robinson

Original comment by: pnrobinson

[obophenotype-user]

after some thought, I would propose the following solution. I have created a term

HP:0012657 Abnormal brain positron emission tomography in the hierarchy "Abnormality of nervous system physiology". The term is defined: A functional brain anomaly detectable by positron emission tomography (PET). PET scanning is a method for functional brain imaging, and its measurements reflect the amount of brain activity in the various regions of the brain. Comment: Note that while structural brain anomalies can cause abnormal brain PET scan results, structural abnormalities are detectable by multiple neuroimaging modalities and should be coded using terms from the hierarchy under 'Abnormality of nervous system morphology' (HP:0012639). There is a child term HP:0012658 Abnormal brain FDG positron emission tomography Def: An anomaly detectable in [18F]-fluorodeoxyglucose (FDG) positron emission tomography (PET) brain scans. Glucose uptake measured with FDG-PET is a marker of neuronal metabolic activity. And under this three (for now) children for prefrontal, thalamus, hypothalamus.

Essentially, the abnormalities measured by PET are only observable via this method, and therefore, like the EEG subhierarchy, deserve their own terms (it is an inference that they represet brain metabolism -- correct probably in the great majority of cases). The different tracers measure subtly different things.

We should expanded the PET terms, and also add fMRI terms.

Please let me know if you have any suggestions/comments/cautions!

Original comment by: pnrobinson

[obophenotype-user]

This is perfect, thanks very much. The comment is key - need to annotate in addition if abnormal structure is seen.

I agree, we need to expand these terms and include all the cross products with major brain regions. Perhaps we can set up a term genie instance for this?

Original comment by: mellybelly