PSI-MI XML 3.0.0 in DocProc [handling editor: Martin Eisenacher]

 1.) Original submission (after steering group review)

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).

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: see below as attachment of this page

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

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

PLEASE ADD COMMENTS to this submission page 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)

 

Appendices

at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub
or https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0

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 (www.ebi.ac.uk/intact) unless otherwise stated

Appendix 1 Schema documentation for MIF300.xsd

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

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

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

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

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

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

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

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

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

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

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