[Psidev-qc-dev] REVIEW PHASE ENDS SOON! HUPO PSI recommendation document (file format PSI-MI XML 3.0.0), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

 

The 60-days public comments and external 

review phase for PSI-MI XML 3.0.0 ends soon! (29th September 2017).

 

  Best regards 

    Martin Eisenacher (PSI Editor)

 

 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Freitag, 28. Juli 2017 17:10
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
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<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format PSI-MI XML 3.0.0),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

There has been a submission to the PSI Document Process 

by the Molecular Interactions workgroup updating the 

PSI-MI format to version 3.0.0 

(from long-time stable XML 2.5, released 2005).

 

The submission (incl. current version of the specification document) can

be found here:

http://www.psidev.info/PSI-MI-in-docproc

 

After having passed a review of the PSI steering group 

with minor changes, the proposed document version 3.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 29th September 2017).

 

Purpose of the format (excerpt from the spec. doc.):

“The existing XML standard (PSI-MI XML2.5) has proven to be, 

and will continue to be, capable of capturing the vast majority 

of molecular interaction data, which are generated by 

techniques such as protein complementation assays, 

affinity capture, biophysical measurements and enzyme assays. 

However, use cases have arisen which cannot be adequately 

described within this XML schema, for example allosteric 

interactions, abstracted interactions and dynamic interactions. 

In order to meet these specialist use cases, a new version of

the XML format has been developed, PSI-MI XML3.0.”

 

Specification document: attached and at

http://www.psidev.info/PSI-MI-in-docproc

Schema MIF300.xsd:
https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd 

Schema documentation (Schema browser):
<https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html>
https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html

Schema documentation and use case examples (as Word docs.): 

See appendix documents

at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub 

or
<https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0>
https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0

(details of appendices in the spec. doc. and below).

 

 PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/PSI-MI-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 


1.      Appendices


Example files showing how the schema meets each of the use cases listed in
section 1.3. Note, all examples available in the IntAct database (
<http://www.ebi.ac.uk/intact> www.ebi.ac.uk/intact) unless otherwise stated


1.1         Appendix 1 Schema documentation for MIF300.xsd


1.2         Appendix 2 Example file showing the representation of all
molecular interaction data from a single publication (PMID: 26919541) in
PSI-MI XML3.0 – note, includes use case 1.3k, rewrite of bibliography
section


1.3         Appendix 3 Representation of a negative feature range (use case
1.3a)


1.4         Appendix 4 Representation of the sequence change caused by
introduction of a mutation (use case 1.3b)


1.5         Appendix 5 Representation of multiple feature detection methods
and feature roles (use cases 1.3c, 1.3d)


1.6         Appendix 6 Representation of kinetic parameters added at feature
level (use case 1.3e)


1.7         Appendix 7 Representation of variable conditions (dynamic
interactions) in an experiment (use case 1.3f)


1.8         Appendix 8 Representation of an abstracted interaction, a
manually curated protein complex, in PSI-MI XML3.0 (use case 1.3g)


1.9         Appendix 9 Representation of a cooperative interaction in PSI-MI
XML3.0 (Use case 1.3h)


1.10     Appendix 10 Representation of molecule sets i.e. cases where a
participant may be one of a list of molecules (use case 1.3i)


1.11     Appendix 11 Representation of the systematic capture of the
stoichiometry of molecules within an interaction (use case 1.3j)


 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de