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

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

Present: Jim, Florian, Steffen, Eric, Matt



1) Plans and agenda for spring PSI workshop in San Diego March 12-14



+ Likely attendance by some of the present

+ Please advertize this more and promote attendance.

+ Please register now and make hotel bookings



2) mzML status

3) TraML status



We need to update the web page with implementations

-       jTraML

-       Anubis

-       ATAQS

-       Metshot R package. Steffen will send.

-       More.



4) Discuss controlled vocabulary items.

+Here are some proposed modifications to Garhard’s latest from 8 hr ago:



************ def: field defined

[Term]

id: MS:1000836

name: dried droplet MALDI matrix preparation

def: "Dried droplet in MALDI matrix preparation." [PSI:MS]

is_a: MS:1000833 ! matrix application type



************ def: field defined

[Term]

id: MS:1000837

name: printed MALDI matrix preparation

def: "Printed MALDI matrix preparation." [PSI:MS]

is_a: MS:1000833 ! matrix application type



************ def: field defined

[Term]

id: MS:1000838

name: sprayed MALDI matrix preparation

def: "Sprayed MALDI matrix preparation." [PSI:MS]

is_a: MS:1000833 ! matrix application type



************ A new relation in "precolated plate": now also a "sample

plate type"; def: field defined

[Term]

id: MS:1000839

name: precoated MALDI sample plate

def: "Precoated MALDI sample plate." [PSI:MS]

is_a: MS:1000833 ! matrix application type

is_a: MS:1001938 ! sample plate type



[Term]

id: MS:1001915

name: leukocyte elastase

def: "Enzyme leukocyte elastase (EC 3.4.21.37)."

[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37

"BRENDA"]

is_a: MS:1001045 ! cleavage agent name

relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P)



We note for DOI, there is a regexp that could be applied in the validator,
but this is not done presently.



There was concern that “source sprayer type” should be a parent term and
not allow a value. But what

Should the children be??



[Term]

id: MS:1001934

name: source sprayer type

def: "The source sprayer type." [PSI:MS]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

relationship: part_of MS:1001933 ! source sprayer



Bring this topic up on the list.



Remove value type in:

[Term]

id: MS:1001938

name: sample plate type

def: "The sample plate type." [PSI:MS]

relationship: part_of MS:1001937 ! sample plate







  - Proposed commit from Gerhard

  - CXP, LECO instrument

  - cleavage agents

  - others?

5) MIAPE – MS

6) MIAPE – Quant



+ No discussion for now. Will discuss at future call and workshop.



Next meeting:

- Feb 14 8am Seattle Time?

+yes









*From:* Eric Deutsch [mailto:Eri...@sy...]
*Sent:* Monday, January 30, 2012 9:46 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI MSS WG call reminder



Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Plans and agenda for spring PSI workshop in San Diego March 12-14

2) mzML status

3) TraML status

4) Discuss controlled vocabulary items:

  - Proposed commit from Gerhard

  - CXP, LECO instrument

  - cleavage agents

  - others?

5) MIAPE – MS

6) MIAPE – Quant



Next meeting:

- Feb 14 8am Seattle Time?