Controlled Vocabularies

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Proteomics Standards Initiative

Controlled Vocabularies

Released October, 2006

Last maintenance update, April 2013

Table of Contents

  1. Introduction
  2. OBO PSI CVs by working groups
  3. Recommendation for PSI CVs
  4. Common PSI CVs
  5. Mapping between exchange schema and CVs
  6. Further information and relevant links
  7. References

 

Introduction

The Controlled Vocabularies (CVs) of the Proteomic Standard Initiative (PSI) provide a consensus annotation system to standardize the meaning, syntax and formalism of terms used across proteomics, as required by the PSI Working Groups Each PSI working group develop the CVs required by the technology or data type it aims to standardize, following common recommendations for devoplement and maintenance. At the PSI meeting in Washington (Science 296, 827), it was decided that all PSI working groups should adopt the same CVs standardizing some overlapping concepts (units and resources). Finally, we propose a common mapping schema to describe for each exchange schema the associations between its specific elements and the PSI CVs or other external ontology resources. Such mapping support the validation of XML files.

 

OBO PSI CVs by working groups

 

Recommendation for PSI CVs

The recommendations for creation and maintenance of PSI CVs are defined in the Guidelines for the development of Controlled Vocabularies. Please send any comment to psidev-onto-dev@lists.sourceforge.net

 

Common PSI CVs

Developing CVs is a process of collecting, and if necessary defining terms. Every effort must be made to adopt and re-use existing ontologies or CVs where they exist, to avoid “re-inventing the wheel”. As stated by OBO “we would strive for community acceptance of a single ontology for one domain, rather than encouraging rivalry between ontologies”.Therefore it is recommended to represent the following concepts as described.

Units It is RECOMMENDED to use, and to contribute to the Unit ontology by requesting required terms via their mailing list .

Chemical Entities For the representation of Chemical entities it is RECOMMENDED to use terms from Chemical Entities of Biological Interest ChEBI. ChEBI is also available from the OBO Foundry website.

Phenotypic quality For the representation of Phenotypic quality (e.g. age, color, shape etc..) it is RECOMMENDED to use terms from the quality ontology and request any missing term via the dedicated mailing list.

As common reference system for databases MIRIAM resource is recommended.

 

Mapping between exchange schema and CVs

The mapping of the exchange schema elements supported by CVs with a common mechanism would greatly increase the cross-compatibility of the PSI resources and facilitate joint development of data validation tools. Therefore we propose a simple XML schema , providing a pattern to write a mapping file (see also the documentation and an example file for MI WG). A validation tool based on this mapping documentation is being developed for both MI and MS WGs.

 

Further information and relevant links

 

References

Gerhard Mayer,  mayerg97 :at: rub.de, April 2013