HUPO PSI-PAR: standard format for protein affinity reagents

List of Contents

  1. News
  2. Introduction to the PSI-PAR format
  3. Purpose of this web page
  4. MIAPAR (Minimum Information About a Protein Affinity Reagent)
  5. XML schema
  6. Controlled Vocabularies
  7. User manual
  8. Example data in PSI-PAR
  9. Software and tools
  10. Meetings
  11. Release schedule
  12. List of planned features
  13. Links
  14. Contact

 

News

  • The PSI-PAR is available in Pubmed

Report: A community standard format for the representation of protein affinity reagents.
Gloriam DE, Orchard S, Bertinetti D, Bjorling E, Bongcam-Rudloff E, Bourbeillon J, Bradbury AR, de Daruvar A, Dubel S, Frank R, Gibson TJ, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, van der Maarel S, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Uhlen M, Wingren C, Gold L, Woollard P, Sherman DJ, Hermjakob H.
Mol Cell Proteomics. 2009 Aug 14.
  • The PSI-PAR format has been approved by PSI after a document review

  • The manuscript describing MIAPAR was published by Nature Methods in 2010

 

Introduction to the PSI-PAR format

The work on PSI-PAR was initiated as part of the ProteomeBinders project and carried out by EMBL-EBI and the PSI-MI work group. 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.

The PSI-PAR format is a standardized means of representing protein affinity reagent data and is designed to facilitate the exchange of information between different databases and/or LIMS systems. PSI-PAR is not a proposed database structure. The PSI-PAR format consists of the PSI-MI XML2.5 schema (originally designed for molecular interactions) and the PSI-PAR controlled vocabulary. In addition, PSI-PAR documentation and examples are available on this web page. The scope of PSI-PAR is PAR and target protein production and characterization.

 

Purpose of this web page

  • Help database and LIMS system administrators get started with PSI-PAR for import and/ors export of their data. To this end we recommend reading the manuscript, example files, user manual, schema documentation and presentations from the PSI-PAR training day .
  • Aid experimentalists by providing guidelines in form of MIAPAR and information about the benefit of a community standard (PSI-PAR)

 

Minimum Information about a Protein Affinity Reagent (MIAPAR)

The Minimum Information about a Protein Affinity Reagent MIAPAR is available for public comment. MIAPAR is intended to be used as a guideline for experimentalists who wish to unambiguously describe protein affinity reagents and their protein targets. Please send any feedback to orchard@ebi.ac.uk.

 

XML schema

The XML schema is used to standardize the structure of the data representation. The PSI-PAR format utilizes the PSI-MI XML2.5 schema with no changes to the structure as this is the only way to ensure compatibility with the existing software and tools. The use of the PSI-MI XML2.5 schema, which was developed for molecular interaction data, is motivated by the fact that the binding of PARs to protein targets is a type of molecular interaction.

However, the PAR data has introduced information that has not been captured in the PSI-MI XML2.5 schema previously such as the production of PARs and target proteins and annotation of experimental materials and experimental control reagents. To better describe how the PSI-MI XML2.5 schema is used for the representation of PAR data see we have modified the schema element descriptions ("annotations") and made this new schema documentation available for download. It is also recommended to read the user manual and examples.

 

Controlled Vocabularies

To standardize the semantics of data representation, i.e. ensuring common terminology, controlled vocabularies (CVs) are used to populate the elements of the schema. Each CV outlines a list of terms with a standardized name, a definition and one or more aliases. The PSI-PAR CV contains the majority of the terms from the PSI-MI CV and in addition approximately 200 new terms. The PSI-PAR CV can be browsed on the ontology lookup service (OLS) or downloaded in obo format. Apart from the PSI-PAR CV the PSI-MI XML2.5 schema utilizes a number of external CVs/ontologies that can also be found on the OLS including the Gene Ontology, NCB I taxonomy ontology, BioSapiens Annotations and Unit Ontology. A table showing which CV to use for which schema element is available here.

 

User manual

The user manual does not require previous knowledge and systematically describes the use of the PSI-MI XML2.5 schema elements for the representation of PAR data. It is intended to aid database and LIMS system administrators that wish to use the PSI-PAR format to export and/or import protein affinity reagent data.

 

Example data represented in PSI-PAR

This section provides examples of data from published articles that have been captured in the PSI-PAR format. The examples (below) are available as both PSI-MI XML2.5 files and HTML files. Overviews of the examples are also supplied in the manuscript and in this spreadsheet.

  • Characterization of monoclonal antibodies to human group B rotavirus and their use in an antigen detection enzyme-linked immunosorbent assay.
  • Burns JW, Welch SK, Nakata S, Estes MK
  • J Clin Microbiol 1989, 27(2):245-250.
  • Download     XML     HTML
  • A proteomics-based approach for monoclonal antibody characterization.
  • Weiler T, Sauder P, Cheng K, Ens W, Standing K, Wilkins JAs
  • Anal Biochem 2003, 321(2):217-225
  • Download:    XML     HTML
  • A designed ankyrin repeat protein evolved to picomolar affinity to Her2.
  • Zahnd C, Wyler E, Schwenk JM, Steiner D, Lawrence MC, McKern NM, Pecorari F, Ward CW, Joos TO, Pluckthun A
  • J Mol Biol 2007, 369(4):1015-1028
  • Download:    XML     HTML

 

Software and tools

A number of tools have been developed for the PSI-MI XML2.5 schema and below is a summary of the relevant ones to PSI-PAR. A complete description can be found on the PSI-MI web site.

  • Validating tools have been developed that can interface with ontologies/CVs and perform semantic validation on PSI-MI XML2.5 files. Validation can be carried out by (1) a Java API that enables the embedding of the validator into any third party application, (2) a command line interface and (3) a web application that allows the uploading of a PSI-MI data file and reporting of both syntactic and semantic discrepancies.
  • The Ontology Lookup Service (OLS) is an ontology viewer with browsing and search functionality. It comprises the PSI-PAR CV and a number of additional CVs that are used in conjugation with the PSI-MI XML2.5 schema such as the Gene Ontology, BioSapiens Annotations and Unit Ontology.
  • A Java XML parser has been developed that allow for import and export of PSI-MI XML2.5 files to and from databases. It comprises a Java library and may also be used to develop any type of software reading and/or writing PSI-MI XML2.5 data.
  • XML stylesheets(XLSTs) are available that can convert PSI-MI XML2.5 data files to HTML, thus providing user friendly human readable representation.
  • Finally, a complete, open source database implementation providing reading, writing, and interactive editing of data in PSI-MI XML 2.5 schema, exists, the IntAct molecular interaction database.

 

Meetings

 

Release schedule

The PSI-PAR format underwent document review by PSI. This process resulted in the first stable version of PSI-PAR, pulished in 2009 (PMID:19674966), publication of MIAPAR is planned 2009/10. The next version, 3.0, of the PSI-MI XML format is planned to be released between 2010 and 2012 and will be backwards compatible with version 2.5. For further information, see the release schedule for the PSI-MI XML schema.

 

List of planned features

Because we are following a levelled approach, we are interested in knowing what the community wishes to be included in the next level. New suggestions can be added on the PSI-MI tracker, where also existing suggestions can be viewed.

 

Links to further information

 

Contact

PSI-PAR master; email

 

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