Re: [Psidev-ms-dev] mzML notes

[Eric D. <ede...@sy...>]

Hi everyone, we are now at the point where we begin the final push to =
complete mzML. I have cobbled together a calendar and assembled the list =
of to do items that I can think of. I hope we can have a well-attended =
call on Tuesday to review these items and hopefully get some volunteers =
to help with certain tasks. I then propose we continue to have calls =
every other week to keep the momentum going as best we can.


Feb 5 Agenda:
-----------------------
- Review current state of mzML
- Review/revise below schedule
- Review/revise below to do list and take on tasks


mzML Aims:
-----------------------
- Have all format changes complete by the Toledo meeting (hopefully =
sooner)
- Mop up documentation and loose threads at the meeting.
- 100.00% done by ASMS


Schedule:
-----------------------
Jan 25: mzML reviews returned. Official community review complete.
Feb=A0 1: ASMS abstracts due!
Feb=A0 5: mzML telecon 9:00am PST
Feb 19: mzML telecon 9:00am PST
Mar=A0 4: mzML telecon 9:00am PST
Mar 17: US HUPO meeting=20
Mar 25: mzML telecon 9:00am PST
Apr=A0 8: mzML telecon 9:00am PST
Apr 23: PSI meeting in Toledo
May
Jun 1-5: ASMS - Must be done and advertising it here!


News items:
-----------------------
- Official community reviews are in and sent around
- Abstract was submitted for ASMS. May be selected as a week-long =
display


To do list:
-----------------------

Schema changes:
---------------
- Incorporate Phil's suggested schema typing changes of 1/24
- Figure out how to implement datatype validation in cvParams
- For consistency binaryDataArray should be in List????
- Address suggestions from Darren 1/22
  - Fix instances in spec doc of instrumentType instead of instrument, =
etc.
  - Fix spectrumRef to point to id instead of scanNumber in example docs
  - Get full name "Proteomics Standards Initiative Mass Spectrometry =
Ontology" in obo file
  - Replace <referenceableParamGroup> with <paramGroup>
  - Remove <instrumentSoftwareRef> and use <softwareRef>
  - Change to: <cv id=3D"MS" ... >   ...    <cvParam cvRef=3D"MS" ...>
  - <sourceFile id=3D"1" sourceFileName=3D"tiny1.RAW"
        sourceFileLocation=3D"file://F:/data/Exp01" >
    should be shortened to:
    <sourceFile id=3D"1" name=3D"tiny1.RAW" =
location=3D"file://F:/data/Exp01" >
- Address the Mallick lab need for multiple precursors
  Allow multiple ionSelection elements
  allow terms for precursorIntensity
  score confidence
  see snippet on email thread 11/26
- Rune suggests allowing a range for the precursor like for MS^E
  (or technically there's always a window) See 12/7
- There was a discussion on 11/22 - 11/24 that essentially boils down =
to:
  Can we encode the MS inclusion list in an mzML file?
- Ask Randy how his "engineers are currently encoding chromatograms into
  mzData 1.05 using supplemental data vectors (not pretty)"
- Invite Mike MacCoss to help with chromatograms (via Parag)


Example files:
---------------
- Fix spectrumRef in examples
- mzML <--> MIAPE-MS mapping assessment. Build on work by Pierre-Alain & =
Frederik
- Get some of JimS's example files into a public area if he's willing
- Work with Waters to get MS^E examples made
- We need to develop a good MALDI example file with spot ids
- We need to develop a good example of a file created from individual =
dtas


Address reviewer comments:
---------------
- Address reviewer points in a document
- Angel's comments to the reviews
- Address the blunt criticisms summarized by Angel on 1/14


Validator:
---------------
- Make validator enforce this ascending scanNumber rule
- Update validator to check datatypes
- Update validator to 0.99.2


CV work:
---------------
- Figure out where we left off on CV
- Add "scan event" or similar to CV
- Need to get the relevant CV part into all vendors hands to update
- Various other CV open items to address
- Can we make the CV have the distinction between categories and terms?
- What do we do in a case like with MassWolf where it cannot know the
  instrument model?
- Coordinate submission of PSI-MS to OBO Foundry via Chris Mungall


Documentation:
---------------
- Clarify in spec doc that the binary data arrays are base64 encoded
- Should we get the indexing documented as an appendix?
- Include checksum definition
- Improve scanNumber ascending requirement in documentation
- Address locale issues in spec doc (offending example from mzData)
      <spectrumInstrument msLevel=3D"1" mzRangeStart=3D"75,00" =
mzRangeStop=3D"1000,00">
      <cvParam cvLabel=3D"psi" accession=3D"PSI:1000038" =
name=3D"TimeInMinutes" value=3D"0,033" />


Related software:
---------------
- Update ReAdW and Wolf for mzML 0.99.2
- Add support for mzML 0.99.2 to mzWiff and Hunter
- Finish off other converter loose ends
- Fix current indexing and binary encoding bugs reported by Darren 1/28
- Darren Kessner's msData C++ library reads/will read mzML
- Implement RAMP parser for mzML
- Get TPP / ISB workflow working with mzML
- Brian suggests a single C/C++ codebase with SWIG bindings to minimize =
implementation differences
- Other software?