[Psidev-ms-dev] PSI-MSS WG call minutes

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

Hi everyone, here are the minutes for the PSI-MSS WG telecon of
2008-07-21.

 

Present: Matt, Jim, Pierre-Alain, Eric

 

- validator mapping file

+ Marc Sturm asks about location of ms-mapping file. Eric will post.

+ Lennart reports that EBI has a working version of the validator and
will announce to the list very soon

 

- CV

+ Jim says we should add a CV entry for an SRF file

+ Jim will send to Eric an SRF file definition

+ Respond to Matt's query 7/7

 

- mzML support information table

+ Add TOPP

+ Add NCBI C++ toolkit

+ Add Proteios SE

 

- schema

+ Eric will reply to Marc Sturm's dataProcessing question

+ improve documentation based on that.

 

- nativeID formats?

+ Matt will create and send out a proposal for nailing this down

+ One different CV term for each possible style of nativeID?

 

- Next call

+ Next call same time in two weeks on August 4

 

 

Older notes from last call:

 

- CV status

+ Darren will check what Matt sent and then check it in

+ Eric received CV from David Sparkman

+ Lennart mentions that "% percent collision energy" is a child MS term
under UO parent

+ It is considered bad practice to add our own terms under someone
else's ontology

+ The UO ontology maintainer appears happy to add our own strange unit
terms

+ UO has some characters that OBO-Edit hates

+ Get in touch with the maintainer to fix some things in the UO

+ Darren will make a list of things to fix in UO and email to vocab list

+ Also fix all the warnings when OBO-Edit tries to save

 

+ Matt email: redo, removing duplicates. No lists, but do include the
singular concepts and repropose

+ Darren will remove all entries: synonym: "<new synonym>" RELATED []

+ Not sure what to do with Wilfred's suggestions. Ask how he wants to
use those.

+ Matt will remove extraneous \n in definitions

+ Consider that we may need to have a parent term to contain (m/z, mass,
ppm) but not yet

 

+ Matt will update the definition of scan time: start offset time of
beginning of the scan

+ Let's NOT check in the new terms that Matt is proposing yet. They
should not be all in root.

+ Lennart will send out a possible placement of Matt's terms.

 

+ Darren will check in minor fixing

+ Darren will then email to Lennart more controversial changes

 

- validator

+ Lennart and company will start working on this again this week

+ Lennart and Matt will work on updated rules

+ There are many back-end changes due to the MI group

+ Does the validator check that if there is an acquisition list, then
there would be a combination type (like sum of spectra) provided?

+ We will allow spectrum representation (like centroid/profile) in the
fileContent section

+ Need to incorporate the information in the OBO file (datatypes and
units)

+ Need to fix up the mapping file rules

+ Maybe need a rule that if a spectrum and if a mass spectrum, the need
mz array and similar

+ Need some sort of unit for intensity arrays

+ At the moment, we do not require any units for the array type. We
should add that?

+ Darren will explore that while adding has_units to CV

 

- Issue of generic binary array CV term issue

+ Marc Sturm wants to include his own custom binary data array types.
How should this be done?

+ Possible suggestion: there should be a special TOPP CV that they
maintain?

+ TOPP CV. These new terms live in TOPP CV, but also linked to MS binary
data array type

+ Lennart will ask Luisa et al. about this issue

 

- CV template updates to vendors

+ What's up with Thermo CVTerms and instrument attributes Excel sheet?

+ It helped Matt hand craft some nice code

+ Could have a separate CV for all this information. Or just a tsv/Excel
file

+ Start another round of vendor updates

 

- schema

+ No major schema changes planned

+ Let's keep a list of minor possibly desirable changes to make if there
needs to be an important change

+ One desirable addition is retention time in the index

+ Current examples show:
xmlns="http://psi.hupo.org/schema_revision/mzML_1.0.0"

  What should it be instead? Perhaps:
xmlns="http://psidev.info/schemas/mzML_1.0.0"

  Poll SG to get an answer

- Johannes Junker asks about supDataArrays. Should be fine as is. Ask
for clarification

 

- MIAPE example document?

+ Done and posted except for switching criteria and parameters for
creating peaklists

+ Pierre-Alain and Jim will get together and finish this

 

- documentation

+ Documentation is up to date

 

- website

+ Post the mapping file directly

+ Should we set up an mzML.org?

+ Instead of maintaining a separate page, set up a redirect?

 

- example files

+ Matt will take a stab at MALDI example and post it

+ Eric will remove tiny4 and point to "small" which includes LTQ-FT demo
usage

+ Fredrik sent to Eric nice examples of dta -> mzML and plgs -> mzML.
Eric will post.

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric & Matt some example RAW files and converted files
(including PDA, SRM)