Nick Reo initiated the following email exchange requesting a new field be added. This issue is partitioned into several other related issues that will jointly solve the problem. They will also refer to this email.

Email from Nick Reo

I would prefer that the field name does not suggest one choice. I want to this include multiple entries, since many metabolites are found in multiple sample types. Maybe something like "Samples that contain compound".

On Oct 20, 2011, at 3:45 PM, Eric Moyer wrote:

That field is doable. I imagine it will be a day or two of work for Dan and I.

For the user interface, we can stick to single-letter abbreviations (or maybe check-boxes?) to ease data entry, but I think that in the actual file we should write out what they mean. This will aid later expansion. We might want to add cytoplasm, extracellular, kidney, pancreas, marrow, bladder, nerve, etc depending on what tissues/areas become interesting. This process will be easier if we don't always need to come up with a new one-letter code.

My suggestion for the field name is "Samples where compound was found" and semantically, the absence of a sample type should not mean that the compound will never be found there, just that we haven't recorded its presence in that type of sample.

Dan: This will involve updating CompoundBin, EditMetabMap, and FilterMetabMap. I can take CB and FMM and you can do EMM.

I separate out EMM because I'd like to see a modification to allow the working bin to just replace the entry from which it came without creating a new bin. This will need to happen under the hood because any modification to this new field will need to be propagated to the other bins for the same metabolite.

I'm also thinking that the CompoundBin class ought to be renamed Resonance, as in, this Resonance is from metabolite x, it is a Resonance found in 1H spectra, it is a mutiplet, it is usually found in the bin [right,left] ...

--Eric

From: Nick Reo To: Eric Moyer; Dan Wlodarski Andrew Neuforth Sent: Thursday, October 20, 2011 10:01 AM Subject: targeted deconvolution

Guys

I want to add another field to the targeted deconvolution master metabolite database. We are preparing to expand this database with additional metabolites that may only be prevalent in certain sample types such as brain extracts, serum, urine, etc. I would like to add this information to the database. Maybe we can add it to an existing field, but it might be best to construct a new field for this info.

Here's what I'd like it to look like:

U = urine S = serum B = brain L = liver F = fecal

I suggest that we use the abbreviations only. If metabolite "X" is likely to be present in urine, serum, and fecal samples, then data would be entered into the field as: U, S, F. The title of the field could be "Sample Source" or something like that??

It might be best to make a separate field. Then a user can filter the metabolite list to include only metabolites that are expected to be found in their particular sample. For instance, if I am working with a serum sample, then I can ask the software to display only metabolites found in serum.

Let me know your thoughts. Thanks for all your hard work on this project!!

Nick PS. Andy, we will need to provide this information about metabolites to Eric and Dan. You probably have some of this info already, but I can help with some more resources.

BiRG / Metabolomics-Analysis-Toolbox

Metabmap should include field "Samples that contain compound" #98

Email from Nick Reo