TODO (after PSI-MS meeting 25-26-27 June 2007)
====      
  
 Additional instance documents
 -----------------------------
  - One that demonstrates the use of the acquisitionList and acquisition (essentially, one precursor scan, three MS/MS scans, that are then combined)
  - Make an example that shows a nice usage of CV in the 'sample' element (NEWT, Brenda, Cell Type Ontology, ...)
  - The existing examples have some changed CV terms. These need to be updated (after the identifiers for these terms have have been fixed).


 Validator ToDo's
 ----------------
  - scan_numbers must be always increasing but need not be consecutive
  - spectrum ids must be unique within a file
  - scan numbers unique within run, identifiers unique within file
  - Instrument should have at least one 'model' cvParam. This has to be validated by the validator as it is really hard to do on the schema.
  - SourceFileType has an attribute 'fileType' which should be verified against the CV.
  - 'BinaryArrayDataType', attributes 'dataType' and 'compressionType' should come from the CV.
  - 'Acquisition' - 'methodOfCombination' should come from the CV.
  - Split between 'Attribute' and 'Action' changes the way attribute validation should be done.  


  
 Release schedule
 ----------------
  July 1  limited circulation for comment
  August 1 Submission to Doc Proc
  September 1 Start of 60 day public review
  Oct 6 HUPO
  
  - When we send out the beta version of mzML for testing, send it to David Fenyo, Jayson, Randy, ISB, Patrick
  - We should get Rolf or someone to announce to whole assembly about mzML being in community review in Seoul (if indeed true)

 
 Web site
 --------
  - Please post your notes. I don't need to review them, but can if you want.
  - I wonder if it makes sense and is easy to create a separate Lyon page and a separate EBI page so post notes and the state after those meetings, separate from the latest?   
  - We should post the results on the web site soon.  
  - Revise the links to point into CVS
   

 Items done
 ----------
   - tiny1 in filecontent no SIM just MSn only <DONE --LENNART>
   - cvList count is wrong. should be 1 <DONE --LENNART>
   - Commit changes to tiny1 <DONE --LENNART> 
   - I failed to get the psi-ms-dev and psi-ms-wg admin password. Luisa thought she knew it but didn't.  Forgot to catch Chris Taylor who might know it. Can you ask around and dig it up? <DONE --LENNART>
   - would be useful to start making a text list of unusual validator rules <DONE --LENNART>
   - Check my CVS access <DONE --LENNART; developer login is 'edeutsch'>

 
    
 Remaining list from Eric
 ------------------------
 
  - Add mechanism to specify external sample LSID ref

  - never did make an acquisition list example

  - Consider the addition of nestedCvParam tag (with order?)

  - Can we come up with a reasonable example where this might be useful outside of sample?  which probably shouldn't be extensive anyway

  - What about retention time? attribute or CvParam?

  - Anything else that should be an attribute instead of a cvParam?

  - Consider a way to annotate the min/max pH of a band for the run

  - Put together a document showing indexing

  - Email mzML state to Josh and ask him to update ReAdW & RAMP

  - index contains ?: spectrum_id="" run_id="" scan_number="" offset=""
 
  - Jimmy points out that mzXML encodes MRMs effectively like tiny MS2 scans with scanType=”MRM”

  - Let’s remember that the transition list will change over time within a run

  - Now that we’re allowing multiple runs in a file, how will the index look to handle this?

  - Matt Chambers asks for better definition of run 6/20

  - Matt chambers asks about start/stop time, absolute time, order issues with dataProcessingList

  - Randy reminds that is important: mzML be stable and easy to support. Minimize “more than one way to do it”