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bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
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Chromatography is a major contributor to variance, we should add metadata from that #33

Closed mwalzer closed 4 years ago

mwalzer commented 5 years ago

see #32

mwalzer commented 5 years ago

But do we need Temperature and Pressure?

mwalzer commented 5 years ago

Is it conceivable to drive non-linear gradients?

ypriverol commented 4 years ago

@mwalzer can you do a PR where you suggest in the specification how to encode additional metadata related with the Chromatograms, here the place to put the information (https://github.com/bigbio/proteomics-metadata-standard/blob/master/experimental-design/README.adoc#4-msrun-technical-details-properties)

lisavetasol commented 4 years ago

You have added many things about chromatography, but it seems the fractionation type is still missing. It could be the same types as for separation before MS (like RP, HILIC and so on), but with additional common fractionation types (high pH RP, SDS PAGE, off-gel electrophoresis, SCX). Also, maybe consider adding the information about concatenation method (with concatenation / without concatenation).

ypriverol commented 4 years ago

This ontology term separation

Can be used to add different separation methods. We can add a new term called fractionation type and under that term all the methods we would like to add. Can you list @lisavetasol all the methods you would like to add. ?

lisavetasol commented 4 years ago

I'm mostly familiar with the bottom-up approach and probably there are some other types for top-down/middle-down, so I suspect my list isn't complete.

  1. SDS PAGE / Gel electrophoresis (the second one is more general)
  2. Off-gel electrophoresis
  3. HiRIEF / Isoelectric focusing (the second one is more general)
  4. HILIC (ERLIC can be a separate type or just a sub-type)
  5. Ion-exchange chromatography (SCX/WCX and SAX/WAX can be sub-types)
  6. Size-exclusion chromatography
  7. RP (high-pH RP can be a separate type or just a sub-type) Also, it should be possible to specify two types together for 2D separation.
ypriverol commented 4 years ago

@mwalzer will be updating our ontology. Mathias, when you finish the annotation, can you do a PR to be review by me.

ypriverol commented 4 years ago

This has been done. https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo#L3673 @lisavetasol check all the terms.

lisavetasol commented 4 years ago

Looks great!

  1. I think this one id: PRIDE:0000556 name: Ion-exchange chromatography is redundant since you already specified SCX, SCA, WSX and WSA. Propose to delete it or add a relation is_a: PRIDE:0000556!Ion-exchange chromatography.
  2. I wouldn't use LC for id: PRIDE:0000562 name: Normal-phase liquid chromatography (LC) because LC usually means just liquid chromatography (not a normal-phase one). So a better way would be "NP" to be consistent with "RP".
  3. id: PRIDE:0000554 name: Hydrophilic interaction chromatography (HILIC) can be as well is_a: PRIDE:0000551 ! Separation method.
  4. [Term] id: PRIDE:0000122 name: Two Dimensional Polyacrylamide Gel Electrophoresis should be is_a: PRIDE:0000550 ! Fractionation method but not separation according to @mwalzer

    I assumed separation is where can be directly coupled to MS.

  5. Not sure if id: PRIDE:0000565 name: High-performance liquid chromatography should have is_a relations, but they are missing. If it's meant to be as Separation and Fractionation, I think it may be confusing since there are already specific types (RP, hpHRP, HILIC and so on).

Beside these, it looks good to me :)

ypriverol commented 4 years ago

@lisavetasol we have solved all the issues in the last PR.

lisavetasol commented 4 years ago

I think these ones id: PRIDE:0000562 name: Normal-phase liquid chromatography (NP) id: PRIDE:0000563 name: Reversed-phase chromatography (RP) aren't ion-exchange ones. They are is_a: PRIDE:0000565 name: High-performance liquid chromatography if you wish or just
is_a: PRIDE:0000550 ! Fractionation method and is_a: PRIDE:0000551 ! Separation method

ypriverol commented 4 years ago

Done thanks for the feedback @lisavetasol

ypriverol commented 4 years ago

@mwalzer @lisavetasol the new terms have been updated in PRIDE https://www.ebi.ac.uk/ols/ontologies/pride . Please can you have a look?

lisavetasol commented 4 years ago

Cool, I think it's enough terms :) Just maybe the relations, between them, are a little bit incorrect. I sketched the way I think they are related. Not sure if that's a better way, but I highlighted in red the stuff I think may be confusing in the current version. Pride ontology fractionation methods

ypriverol commented 4 years ago

@lisavetasol I will include these changes. @lisavetasol when do you think you will be able to push the first datasets?

lisavetasol commented 4 years ago

@ypriverol hopefully this week :)