Wrong schema for indexedMzML?

[jpfeuffer]

Hi!

I get the following header

<?xml version="1.0" encoding="utf-8"?>
<indexedmzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml">
  <mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0" id="20120415_EXQ5_KiSh_SA_LabelFree_HeLa_pY_Noco_rep1">
    <cvList count="2">
...

when I run with "-f2"

Should it maybe be

<indexedmzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd" xmlns="http://psi.hupo.org/ms/mzml">
...

or similar?

[nielshulstaert]

Hi, my apologies for the late reply. Indeed the indexed schema used is 1.1.1 so I could change it to

<indexedmzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd" xmlns="http://psi.hupo.org/ms/mzml">

int the next release. I didn't find any 1.1.2 version, could you point me to it?

[jpfeuffer]

Hi! I am actually not sure anymore where I got it from 😄 I think I compared with msConvert. Let me check if 1.1.2 was correct. My main point was the "_idx" suffix, I think.

[ypriverol]

The mzML schemas are here:

• index: https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.1_idx.xsd

• non-index: https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd

[jpfeuffer]

Ok there is no 1.1.2 yet, right?

[edeutsch]

As far as I'm aware, there is no 1.1.2. The latest schemas are listed here: https://github.com/HUPO-PSI/mzML/tree/master/schema/schema_1.1

However, in looking at an output mzML files from msconvert, I see:

To make matters weirder, this URI: http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd is a valid redirect to the 1.1.1 schema. While this URI: http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd yields a 404.

Does @chambm or @javizca have any historical memory of this? Seems like the URI should be: http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd and that should be a redirect to: https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.1_idx.xsd

What do you think?

[chambm]

@edeutsch I'm afraid this may be an action item 8 years overdue :) https://sourceforge.net/p/psidev/mailman/psidev-ms-dev/thread/50D17F1D.9090508%40immun.lth.se/#msg30249870

[edeutsch]

haha, I have taken slothfulness to a new level!

I propose to check in mzML1.1.2_idx.xsd. I found a copy of it. And then I will ask @javizca to update the hyperlinks at psidev.info.

It looks like ProteoWizard has already implemented this for many years. And then we'll get ThermoRawFileParser to do the same.

Any objections?

[ypriverol]

@edeutsch actually you can do just a PR to github. We need to update the URLs in the library to github because the psi URLs are not working.

This goes nowhere http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd

[edeutsch]

@ypriverol I can certainly do a PR instead of direct checkin if you prefer that.

Although this goes nowhere: http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd This does: http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd (although to 1.1.1)

Which is why I said that after we have GitHub fixed, we need to ask @javizca to fix psidev.info. Or maybe you can do that?

[edeutsch]

okay chaps, I have created a PR at https://github.com/HUPO-PSI/mzML/pulls I would say that if we get approvals from @ypriverol and @chambm, we can merge it.

Sound okay?

[caetera]

It seems like the issue is still not fixed. Should I just update schema location to the current location on Github?

index: https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.1_idx.xsd

non-index: https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd

[edeutsch]

Sorry, I forgot to follow up on this. @javizca, would you make the links: http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd (currently a 404) http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd (currently points to the wrong file) do the right thing?

Correct content is in: https://github.com/HUPO-PSI/mzML/tree/master/schema/schema_1.1

[caetera]

This issue has not been active for quite a while, I will close it, but you're a welcome to reopen it if necessary.