OBI ids not available to assays used for MoTrPAC

[jimmyzhen]

When using the OBI lookup service for terms relevant to targeted/untargeted metabolomics and proteomics assays used in MoTrPAC data, I wasn't able to find the terms for the following:

Targeted 3-Hydroxyisobutyric Acid (3-HIB)
Targeted Acyl-CoA
Targeted Acylcarnitines
Targeted Amines
Targeted Amino Acids
Targeted Beta-Aminoisobutyric Acid
Targeted Ceramide
Targeted Conventional
Targeted Ethanolamides
Targeted Keto Acids
Targeted Nucleotides
Targeted Organic Acids
Targeted Oxylipins
Targeted Sphingomyelin
Targeted Tricarboxylic Acid Cycle
Untargeted HILIC-Positive
Untargeted Ion-Pair Negative
Untargeted Lipidomics, Reversed-Phase Negative
Untargeted Lipidomics, Reversed-Phase Positive
Untargeted Reversed-Phase Negative
Untargeted Reversed-Phase Positive
Global Proteomics
Phosphoproteomics
Acetyl Proteomics
Protein Ubiquitination

Please let me know if there are any questions. Thank you.

[mgiglio99]

Hi Jimmy, Sorry for the delay on this. As we look over the list, we are interpreting the targeted terms as being assays for those specific compounds/analytes. Thus the OBI terms that we would create would be, for example: 3-hydroxyisobutyric acid assay acyl-CoA assay etc. And the definitions would have the structure: "An analyte assay that measures the abundance of 3-hydroxyisobutyric acid" "An analyte assay that measures the abundance of acyl-CoA" etc. These terms would be children of the OBI term 'analyte assay' OBI:0000443 Does this sound correct for the targeted terms? Question on one targeted term request: "Targeted Tricarboxylic Acid Cycle" - does this one mean that there is a focus on just metabolytes that are part of the TCA cycle? If so, not sure how we would structure this one.

For the untargeted terms, these six we are not sure about: Untargeted HILIC-Positive Untargeted Ion-Pair Negative Untargeted Lipidomics, Reversed-Phase Negative Untargeted Lipidomics, Reversed-Phase Positive Untargeted Reversed-Phase Negative Untargeted Reversed-Phase Positive We think they are liquid chromatography techniques but we would need to be more explicit in the term names about what they are. If you can provide some definitions for these it will help us to understand what you mean by each and place them correctly in OBI.

For the "Global Proteomics" term, will this existing OBI term work? 'protein expression profiling assay' OBI:0000615, defined as "An assay that determines protein expression and translation activity using protein extracts collected from a material entity." with an alternate term name 'proteomic analysis'

For these three: Phosphoproteomics Acetyl Proteomics Protein Ubiquitination We are thinking that these refer to assaying for proteins with specific modifications. Is that correct? We would need a bit more information about them in order to define them properly. Our initial thought is that these could be children of OBI term: 'protein state assay' OBI:0002953 definition: "A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc." Let us know if this sounds good to you.

Thanks so much,

Michelle and Suvvi

[jimmyzhen]

Hi @mgiglio99, thank you and Suvvi for looking into this. I have asked my colleague David (whom you met back in April) to help addressing the questions you shared here. Will keep you posted.

[biodavidjm]

Hi Michelle and Suvvi,

Before we get into the details, all those assays are mass spectrometry (MS) based metabolomics and proteomics, which are very frequently used for the large-scale analysis of proteins and metabolites. I would guess that those terms should already exist. I am not an expert in ontology terms, so I did a search on Google and I found these examples that could apply to

• Proteomics TMT quantification
• tandem mass spectrometry
• liquid chromatography mass spectrometry assay

However, I am sure that I am not searching in the right place.

I also wonder about the granularity. Would we need something like this?

Proteomics

• Quantitative proteomics: The use of mass spectrometry to measure the abundance of proteins in a sample.
• Tandem mass tag (TMT): A technique for labeling proteins with multiple isotopes, which allows for the relative quantification of proteins in a sample.
• Global protein abundance: The total amount of protein present in a sample.
• Relative quantification: The comparison of the abundance of proteins in two or more samples.
• Phosphoproteomics: The study of the phosphorylation state of proteins.
• Phosphopeptide: A peptide that contains a phosphate group.
• Isotope-labeling technique: A technique for labeling molecules with isotopes, which allows for the identification and quantification of those molecules.
• etc

Metabolomics

Untargeted Metabolomics

Untargeted metabolomics is a global approach that aims to measure as many metabolites as possible in a biological sample, without any pre-selection of the metabolites of interest.

Untargeted Metabolomics, HILIC-Positive

Hydrophilic interaction liquid chromatography (HILIC) is a chromatography method used to separate polar and hydrophilic compounds, which are often challenging to separate with reverse-phase chromatography. The term "positive" likely refers to the ionization mode used in mass spectrometry. Possible terms:

• Untargeted metabolomics: The comprehensive analysis of all the measurable analytes in a sample, including chemical unknowns.
• Hydrophilic interaction liquid chromatography (HILIC): A type of liquid chromatography that is used to separate hydrophilic molecules.
• Positive mode: A mode of mass spectrometry in which the analyte is ionized by adding protons.
• Metabolite: A low-molecular-weight organic compound that is involved in the metabolism of an organism.

(And same for all the other untargeted assays)

Targeted Metabolomics

Targeted metabolomics focuses on a specific subset of metabolites, typically those known to be involved in certain biological pathways or associated with particular biological questions. It is characterized by its focus on the quantitative analysis of this predefined set of metabolites.

In a targeted metabolomics approach, only the metabolites of interest are measured, which can provide more accurate and sensitive measurements compared to untargeted metabolomics.

We could need terms for

• Targeted metabolomics: The analysis of a specific set of metabolites in a sample.
• Mass spectrometry-based targeted metabolomics: A method for measuring the abundance of specific metabolites in a sample using mass spectrometry.
• Isotope-labeled internal standard: A compound that is added to a sample to help with the quantification of metabolites.
• Metabolite profiling: The measurement of the relative abundance of a set of metabolites in a sample.
• Quantitative metabolomics: The measurement of the absolute abundance of metabolites in a sample.

My question is: what other CFDE projects have generated Proteomics and Metabolomics datasets? I guess we should be able to reuse some of the ontology terms.

Thanks!

[mgiglio99]

Hello @biodavidjm and @jimmyzhen

Apologies for the huge delay in getting back to this issue. The summer was over-the-top busy.

Thanks for the additional information. There are a lot of elements to tease apart and this will take some thought/work. Initial impressions: We'll focus our initial effort in seeing what exists already around the following nodes: -'mass spectrometry assay' http://purl.obolibrary.org/obo/OBI_0000470 -'protein expression profiling assay' http://purl.obolibrary.org/obo/OBI_0000615 -'metabolite profiling assay' http://purl.obolibrary.org/obo/OBI_0000366 We'll also look for terms related to the above that might not yet be linked to them. Quick note - some of the items in your list above (e.g. Metabolite, Isotope-labeled internal standard) are not assays but rather are other types of entities. Thus, while we can explore finding/making terms to capture those, it would not be something you could put into the assay field for C2M2.

If you need terms to use for submission until we can get the specific ones you need, the three above are good general terms (that will be parents to the specific terms we eventually make for you) that you could use.

It will be a few weeks before we'll have time available to delve into these (deadlines in other areas). And at that point, it might make sense to arrange a zoom so that we can talk about them - might make things go more quickly.

Best, Michelle

[biodavidjm]

Hi Michelle,

We will follow your suggestion and use:

Proteomics assays

'protein expression profiling assay' http://purl.obolibrary.org/obo/OBI_0000615

The term seems appropriate for describing untargeted proteomics assays. Untargeted proteomics assays are broad in scope, focusing on the identification and quantification of as many proteins as possible in a sample, without pre-selecting specific targets.

Metabolomics assays:

'metabolite profiling assay' http://purl.obolibrary.org/obo/OBI_0000366

The term is suitable for both targeted and untargeted metabolomics studies. The definition provided encompasses the goals of both targeted and untargeted metabolomics approaches.

I'm curious about the terms used by other consortia for these assays. It would be beneficial for us to ensure consistency in terminology across all groups involved.