Released October, 2006
Last maintenance update, April 2013
Table of Contents
- OBO PSI CVs by working groups
- Recommendation for PSI CVs
- Common PSI CVs
- Mapping between exchange schema and CVs
- Further information and relevant links
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.
- PSI-MI CVs are available here, send comment to email@example.com
- PSI-MS CV supporting the mzML, TraML, mzIdentML, mzQuantML and mzTab schemas is available here, send comment to firstname.lastname@example.org
- PSI-MOD CVs are available here and documented here, send comment to email@example.com
- PSI-GEL is supported by the SEP ontology, documented here, the CVs are available here, and comment can be sent to firstname.lastname@example.org.
- The old PSI-PI CV is available here, issues can be posted here.
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 email@example.com
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.
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.
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.
- Ontology lookup service (OLS)
- OBO Foundry portal
- GeneOntology (GO)
- Ontology for Biomedical Investigations (OBI)
- The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary
- Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
Gerhard Mayer, mayerg97 :at: rub.de, April 2013