psidev-ms-dev

Re: [Psidev-ms-dev] Gettings started with the MS Standard

[Gerhard M. <Ger...@ru...>]

Hello proteomics community,

just for information I forward you the mail from Mark Bean from the 
AnIML group.

Best Regards,
Gerhard

Am 09.05.2012 18:24, schrieb Mark Bean:
> Dear Gerhard
>
> In that case, I am pleased to establish contact!  Thank you for the links.  I have subscribed silently to Psidev-pi-dev mailings for ages, but haven't kept up.  I should have, and now it is a bit harder to get started.
>
> AnIML has been going a long time (encapsulating all of analytical chemistry through volunteer efforts isn't the fastest car on the highway), perhaps too long.  Our web presence has been intentionally small because one or two of the major analytical companies started selling products that "supported AnIML" long before we had a standard.  However, we do have the beginnings of a useful website at http://animl.sourceforge.net/ (or http://www.animl.org/ which is the same).
>
> The AnIML schemas are locked, undergoing a final punch-list review prior to documentation (we have funds for this from various instrument and pharmaceutical companies).  There are two schemas:  one constrains all AnIML data files and is immutable, the other constrains the Technique Definitions or Technique Extensions that the committee or other people create.  The Technique Definitions in turn also constrain the AnIML files for terminology, units, content for each Technique used.  And herein is a bit of an oddity in that xml AnIML files are constrained by another xml Technique Definition, which is not a schema, forcing us to create our own validator.
>
> So far we have UV-Vis, Chromatography techniques completed, and are currently working on NMR and MS.  When those are completed, we will ballot the standard and make it public through ASTM.  Originally we were working in collaboration with IUPAC, but I'm not sure how active their participation is these days.
>
> The chief architect of AnIML is Burkhard Schaefer (his father is a computer science professor in your country), based on work Burkhard did at the National Institute of Standards (NIST) in Washington, DC.  His e-mail is b.s...@bs...
>
> Best regards, and thanks for the fast response!  I hope to have more discussions in the future.
>
> Mark
>
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Wednesday, May 09, 2012 11:59 AM
> To: Mark Bean
> Subject: Re: Gettings started with the MS Standard
>
> Hello Mark,
>
> I think we didn't met or talked before, but of course any cooperation
> between AnIML and psi-ms is always welcome.
> As I understood AnIML is about spectroscopy of small molecules. Is that
> correct?
> Can you please send me back an official link to the AnIML?
>
> Since this year I am coordinating the psi-ms.obo ontology.
> You can find it at
> http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> You can open the .obo file in any text editor or by use of OBO-Edit
> http://oboedit.org/
>
> We have also a mailing list, which you can subscribe, so that you stay
> informed with the latest developments of psi-ms.obo:
> psi...@li...
>
> Best Regards,
> Gerhard
>
> Am 09.05.2012 17:19, schrieb Mark Bean:
>> ASTM E13 Committee on Analytical Data Standards (AnIML)
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Gettings started with the MS Standard

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

Hi Gerhard, thank you for forwarding the communication. I presented our
work on mzML and related at one of their telecons a few years ago.

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Thursday, May 10, 2012 2:24 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Gettings started with the MS Standard
>
> Hello proteomics community,
>
> just for information I forward you the mail from Mark Bean from the
> AnIML group.
>
> Best Regards,
> Gerhard
>
> Am 09.05.2012 18:24, schrieb Mark Bean:
> > Dear Gerhard
> >
> > In that case, I am pleased to establish contact!  Thank you for the
> links.  I have subscribed silently to Psidev-pi-dev mailings for ages,
> but haven't kept up.  I should have, and now it is a bit harder to get
> started.
> >
> > AnIML has been going a long time (encapsulating all of analytical
> chemistry through volunteer efforts isn't the fastest car on the
> highway), perhaps too long.  Our web presence has been intentionally
> small because one or two of the major analytical companies started
> selling products that "supported AnIML" long before we had a standard.
> However, we do have the beginnings of a useful website at
> http://animl.sourceforge.net/ (or http://www.animl.org/ which is the
> same).
> >
> > The AnIML schemas are locked, undergoing a final punch-list review
> prior to documentation (we have funds for this from various instrument
> and pharmaceutical companies).  There are two schemas:  one constrains
> all AnIML data files and is immutable, the other constrains the
> Technique Definitions or Technique Extensions that the committee or
> other people create.  The Technique Definitions in turn also constrain
> the AnIML files for terminology, units, content for each Technique
> used.  And herein is a bit of an oddity in that xml AnIML files are
> constrained by another xml Technique Definition, which is not a schema,
> forcing us to create our own validator.
> >
> > So far we have UV-Vis, Chromatography techniques completed, and are
> currently working on NMR and MS.  When those are completed, we will
> ballot the standard and make it public through ASTM.  Originally we
> were working in collaboration with IUPAC, but I'm not sure how active
> their participation is these days.
> >
> > The chief architect of AnIML is Burkhard Schaefer (his father is a
> computer science professor in your country), based on work Burkhard did
> at the National Institute of Standards (NIST) in Washington, DC.  His
> e-mail is b.s...@bs...
> >
> > Best regards, and thanks for the fast response!  I hope to have more
> discussions in the future.
> >
> > Mark
> >
> >
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Wednesday, May 09, 2012 11:59 AM
> > To: Mark Bean
> > Subject: Re: Gettings started with the MS Standard
> >
> > Hello Mark,
> >
> > I think we didn't met or talked before, but of course any cooperation
> > between AnIML and psi-ms is always welcome.
> > As I understood AnIML is about spectroscopy of small molecules. Is
> that
> > correct?
> > Can you please send me back an official link to the AnIML?
> >
> > Since this year I am coordinating the psi-ms.obo ontology.
> > You can find it at
> > http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-
> ms/mzML/controlledVocabulary/psi-ms.obo
> > You can open the .obo file in any text editor or by use of OBO-Edit
> > http://oboedit.org/
> >
> > We have also a mailing list, which you can subscribe, so that you
> stay
> > informed with the latest developments of psi-ms.obo:
> > psi...@li...
> >
> > Best Regards,
> > Gerhard
> >
> > Am 09.05.2012 17:19, schrieb Mark Bean:
> >> ASTM E13 Committee on Analytical Data Standards (AnIML)
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
>
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