Released December 5, 2005
Last maintenance update
June 1, 2006,
to version 2.5.3
Table of Contents
- Purpose of the PSI MI XML format
- Purpose of this document
- Directory structure
- Release schedule
- Changes from PSI MI 1.0 to 2.5
- Maintenance releases
- Detailed Documentation
- Use of external controlled vocabularies
- List of planned features
- How to comment
- Available data
- Data submission
- Further information and relevant links
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. For detailed information on all PSI activities, please see PSI Home Page.
This document decribes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. This document describes level 2.5. For documentation of the previous level 1.0 please see Version 1.0 Documentation.
Level 2.0 beta was never officially released. This version, 2.5, is the released successor of 1.0.
PSI MI was designed by a consortium of molecular interaction data providers from both academia and industry, including BIND, DIP, IntAct, MINT, MIPS, GlaxoSmithKline, CellZome, Hybrigenics, Universities of Bielefeld, Bordeaux, Cambridge, and others.
The PSI MI format is a data exchange format for molecular interactions. It is not a proposed database structure.
The purpose of this document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. For the detailed and most up-to-date description please see the auto-generated documentation. This documentation will also provide additional information, e.g. sample data.
The XML schema is located at http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd
This document is in the root directory of the PSI MI 2.5 release. Subdirectories are
doc/Auto-generated documentation of the PSI MI XML schema
src/Source code for schema and related software
tools/Data management tools
- Level 2.5 has been released in early December 2005. It is now supported by most PSI partners.
- Level 1.0 support is planned to be continued until summer 2007.
Changes in the PSI MI XML format and controlled vocabularies from version 1.0 to 2.5 are documented in this page.
Minor updates as a result of the PSI spring meeting in San Francisco, April 2006:
- updated entrySet@minorVersion to 3
- bioSourceType@taxId now mandatory. This was inadvertedly made non-mandatory with 2.5.2.
- featuretype@id now mandatory. This was inadvertedly made non-mandatory with 2.5.2.
- Optional attribute parameter/uncertainty added.
- Added participant/parameterList and participant/attributeList to allow more complex modelling of participants.
- Deleted XML constraints on entry level. They were not working due to syntax errors, and few XML validators can check them. This validation level will be performed by the PSI XML validator in the future.
There were some inconsistencies in the naming of complex types in 2.5.1. These have been fixed. This has no impact on the XML data files. The only impact for users is a facilitation if they use code generators. Concrete changes:
- complex type interactorType to interactorElementType
- complex type interactionType to interactionElementType
- complex type featureType to featureElementType
- featureType@id has been moved into the complex type featureElementType and typed as xs:int
- bioSourceType@ncbiTaxId has been moved into the complex type bioSourceType and typed as xs:int
- updated entrySet@minorVersion to 2
At the PSI meeting in Geneva, September 2005, it was discussed that participant/experimentalFormList/experimentalForm should have the possibility to assign a position, e.g. to describe an n-terminal protein modification in an experiment. It was decided to implement this using the existing featureType. The controlled vocabulary has been updated accordingly, but the change in the XML schema was not implemented. This required the maintenance release 2.5.1, with the following changes:
- Added entrySet@minorVersion, fixed to 1
- Deleted participant/experimentalFormList/experimentalForm
Where possible, external controlled vocabularies are referenced from PSI MI. External controlled vocabularies are used in two forms:
- Open controlled vocabularies: We think that no existing controlled vocabulary provides all necessary terms for the given attribute in the PSI MI format. In this case, it is up to the data provider to choose a controlled vocabulary, or to provide a free text string if no appropriate controlled vocabulary exists.
- Closed controlled vocabularies: We think that there is a controlled vocabulary which appropriately covers all necessary terms for the given attribute. In this case, only terms from the defined vocabulary should be used.
We now support only the new OBO format, not any more the previous DAG-edit format.
The closed controlled vocabularies referenced by PSI MI are listed in the table below. All vocabularies are contained in a files in OBO flat file format: psi-mi25.obo. They can be browsed at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI. The correctness of references to external controlled vocabularies is currently not enforced by the PSI MI schema. It is the responsibility of the data provider to ensure that only existing terms at an up-to-date data source are referenced.
PSI MI XML level 2.5 data element
participant identification method
interaction detection method
feature detection method
feature range status
In the previous DAG format, which was split into *.dag and *.def files, obsolete MI terms were reported as children of the node “obsolete (MI:0431)”. The newer OBO format has a special class “obsolete”, to which all obsolete PSI MI terms are assigned.
Mapping from OBO to MIF25 format
We recommend the following mapping from the file psi-mi25.obo to PSI MI 2.5 XML files:
OBO format element
PSI MI 2.5 XML file element
Mapping controlled vocabularies between PSI 1.0 and 2.5
The major change from PSI 1.0 to 2.5 requires a remapping of controlled vocabularies.
Proposed mappings from PSI 1.0 to 2.5 CVs are described in cv-1to25mapping.doc.
The reverse mapping is described in cv-25to1mapping.txt. This file is presented in plain text format to facilitate parsing.
Both files are available here.
Because we are following a leveled approach, we are interested in knowing what the community wishes to be included in the next level.
The latest list of features to discuss/include in the future can be found here:
If you would like to comment on this document, the PSI MI XML specification, please send a mail to:
- IntAct: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/
- MINT: http://mint.bio.uniroma2.it/mint/download.do
- MIPS: http://mips.gsf.de/genre/proj/mpact
- Sample data is available in the sampleData subdirectory
- PSI-MI XML 2.5 Java Parser : to read and write interaction data from and to file.
- PSI-MITAB 2.5 Java Parser : to read and write interaction data in tab-delimited format.
- XMLMakerFlattener to convert PSI MI XML format into tab-delimited ASCII format (flat-files) and vice versa.
- The PSI MI controlled vocabularies can be browsed at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI
- PSI XML Validator: Semantic validator for PSI MI files. It validates correct use of PSI MI ontologies in a data file, plus additional semantic consistency rules. The current beta version can be downloaded from http://sourceforge.net/project/showfiles.php?group_id=65472&package_id=176724
- MIF25_compact.xsl : conversion from the expanded to the compact form of the PSI 2.5 format.
- MIF25_expand.xsl : conversion from the compact to the expanded form.
- MIF25_view.xsl : conversion from xml into “draft” html.
Henning Hermjakob, firstname.lastname@example.org, 22-MAY-2006