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The Ontology for Biomedical Investigations
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Extension of OBI ontology with the term metabolite fingerprinting #953

Open korseby opened 6 years ago

korseby commented 6 years ago

Hi all + @proccaserra , @DSchober ,

I would like to request an extension of the OBI ontology.

Currently, it only includes the term “metabolite profiling” and lacks the term “metabolite fingerprinting”. The latter is used frequently as an approach in the research domain of “Eco-Metabolomics” [1].

Metabolite fingerprinting can be defined as follows:

The characterisation of metabolites following an untargeted approach without necessarily identifying metabolites.

Whereas metabolite profiling can be defined as follows:

The characterisation of metabolites following a semi-targeted approach that focus on specific groups of metabolites or specific pathways.

You can refer to my publication as reference [1]. The Book of Hall et al. contains a more detailed definition (page 39, available upon request) [2].

As suggested by @bpeters42 , ```I understand the need to capture targeted vs. non-targeted, but that should then be explained in the assay definition. Right now we have:

OBI_0000366 - metabolite profiling (synonym: metabolite assay), defined as: "Metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism"

This seems to also cover the fingerprinting you describe. So my suggestion would be to have one parent term (metabolite assay), and then have two children 'targeted metabolite assay' 'untargeted metabolite assay' or something like that. You are the expert in the domain, but for us it will be important to retain a parent term. I would also be interested what Philippe's opinion is on this who originally created the term. ```

Best wishes, *Kristian

[1] Peters et al. (2018) Int. J. Mol. Sci. 19(5), 1385; https://doi.org/10.3390/ijms19051385 [2] Hall, R.D. (Ed.) (2011) Biology of Plant Metabolomics; Annual Plant Reviews; Wiley-Blackwell: Oxford, UK; ISBN 978-1-4051-9954-4.

zhengj2007 commented 5 years ago

@bpeters42 Could you please look at this issue tracker?

bpeters42 commented 5 years ago

Based on the thread, I am trying to summarize the requests for new terms / term changes. Please provide concrete edits to the below if I am not getting it right.

metabolite profiling

OBI_0000366 - metabolite profiling (synonym: metabolite assay), defined as: "Metabolite profiling is an assay that aims to detect and identify material entities resulting from biochemical and cellular metabolism"

new term1) targeted metabolite profiling: A metabolite profiling assay that is set up to detect one or more specific metabolites

untargeted metabolite profiling assay: A metabolite profiling assay that is set up to detect a generic class of material entities, with the intention of detecting metabolites within them.

NEW TERM : metabolite profiling (synonym: metabolite assay), defined as: "Metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism"

The characterisation of metabolites following a semi-targeted approach that focus on specific groups of metabolites or specific pathways.

korseby commented 5 years ago

This sounds alright to me.

Maybe one minor addition.

I think that untargeted metabolite profiling assay could be changed to: A metabolite profiling assay that is set up to detect generic classes of material entities, with the intention of detecting metabolites or compound classes within them.

Following that,

The characterisation of metabolites following a semi-targeted approach that focus on specific compound classes, groups of metabolites or specific pathways.

Let me know if I can be of further help. Best wishes

bpeters42 commented 5 years ago

Neither 'generic classes' nor 'compound classes' are defined in OBI, and the word 'class' is highly overloaded already. I am not sure what the intended purpose of the edits is. Can you suggest edits with common language English that achieve the same ?

On Mon, Mar 18, 2019, 2:46 AM korseby notifications@github.com wrote:

This sounds alright to me.

Maybe one minor addition.

I think that untargeted metabolite profiling assay could be changed to: A metabolite profiling assay that is set up to detect generic classes of material entities, with the intention of detecting metabolites or compound classes within them.

Following that,

The characterisation of metabolites following a semi-targeted approach that focus on specific compound classes, groups of metabolites or specific pathways.

Let me know if I can be of further help. Best wishes

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obi-ontology/obi/issues/953#issuecomment-473839307, or mute the thread https://github.com/notifications/unsubscribe-auth/ANN9IjiipmYaXSUbWImc3WDZl4EmE82Fks5vX2B9gaJpZM4WHCdP .

korseby commented 5 years ago

The term "compound class" is commonly used in chemistry and biochemistry. The ChEBI ontology would be a good start (https://www.ncbi.nlm.nih.gov/pubmed/17932057).

bpeters42 commented 5 years ago

I am sorry, i cannot find a definition of 'compound class' in chebi. Can you please point me to it?

On Tue, Mar 26, 2019, 7:12 AM korseby notifications@github.com wrote:

The term "compound class" is commonly used in chemistry and biochemistry. The ChEBI ontology would be a good start ( https://www.ncbi.nlm.nih.gov/pubmed/17932057).

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