HUPO Proteomics Standards Initiative
HUPO Proteomics Standards Initiative - Protein Separation Workgroup (PSI-PS)
The group has been formed following a merger of the PSI-GEL and SP (sample processing and separations) workgroups
PS Group Charter
The PSI Protein Separation work group is a collaboration of researchers from academia, industrial partners and software vendors. The group aims to develop reporting requirements that supplement the MIAPE parent document, describing the minimum information that should be reported about gel-based, and non-gel based separation technologies employed for proteins and peptides in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about these technologies and supporting controlled vocabularies.
1. MIAPE documents
- MIAPE GE
The MIAPE module for Gel Electrophoresis (GE) has been published in Nature biotechology entitled Guidelines for reporting the use of gel electrophoresis in proteomics (Nature Biotechnology 26, 863 - 864 (2008), doi:10.1038/nbt0808-863).
The MIAPE GE module identifies the guidelines for the minimum information to report about the use of n-dimensional gel electrophoresis in a proteomics experiment, in a manner compliant with the aims as laid out in the MIAPE principles document.
The most recent version of the MIAPE GE specification can be found here:
MIAPEGelDB, a web-based tool to edit and store MIAPE Gel electrophoresis document (http://miapegeldb.expasy.org/)
**NEW: ProteoRed has developed a MIAPE Generator tool accessible by via the ProteoRed portal: http://www.proteored.org/MIAPETool.asp **
- MIAPE GI (Gel Informatics)
MIAPE: Gel Informatics v1.0
- MIAPE CC (Column Chromatography)
- MIAPE CE (Capillary Electrophoresis)
- MIAPE SPPE (Sample Preparation for a Phosphoproteomics Experiment)
2. Data formats
- GelML
GelML is a data exchange format for describing the results of gel electrophoresis experiments.
In late 2007, GelML completed the PSI document process and was released as a stable version 1.
"Some small modifications are being made to GelML in light of problems identified during implementation, which will result in a release of a version 1.1 schema. Implementers should work with the version of the schema hosted on googlecode, here: http://code.google.com/p/gelml/ "
Format Status Download GelML Version 1 release
Version 1.1 (under development)
Previous milestone releases can be found here: Specification document (milestone 2) and here: Specification document (milestone 1)
- spML
Data and metadata produced in different places may be in different formats, making comparison and exchange difficult. We therefore seek to develop consensus interchange formats (XML Schema based) to facilitate the development of effective search and analysis tools, simplifying both the dissemination and exchange of data. These XML Schemata are derived from application-specific object models (themselves subclassed from the generic FuGE object model). The development process will draw on the wisdom and experience of a wide range of concerned people, both in academia and industry.
Format Scope Status spML Liquid and gas chromatography, centrifugation, rotofors, capillary electrophoresis, general sample handling and chemical modifications Milestone 1 release
- Specification document
- UML model (best viewed with theMagicDraw free community edition
- Demonstration XML Schema (proof of concept only)
- Example XML instance file
- Directory of sample files
spML Liquid and gas chromatography, capillary electrophoresis, general sample handling and chemical modifications Milestone 2 release
- Specification document
- UML model (best viewed with the MagicDraw free community edition (version 10.5 and above)
- Save as spML_milestone2.mdzip, also requires AndroMDA Profiles (Unzip archive and provide location of file when requested by MagicDraw)
- spML milestone 2 instances and XML Schema (zip archive)
3. Ontology
-
sepCV
The sepCV is an ontlogy for sample preparation and processing and covers terminology required for gel electrophoresis and gel informatic investigations. More details on sepCV can be found on the sepCV page
4. Meetings and Logistics
On-going communication between all participants will be achieved via the mailing list (currently mailto:psidev-gps-dev@lists.sourceforge.net).
Every few weeks a telephone conference will be organised to allow discussion of the progress and direction of the working group. Details of the next meeting will be posted here as soon as they are available.
The group will meet face to face each year at the Spring PSI conference and other meetings will be arranged as necessary.
Next Meeting / Teleconference
- To be arranged
Meeting Minutes
- Minutes from past calls can be found on the list archive
- Spring PSI Meeting, San Francisco, CA, USA. April 2006.
5. Mailing lists
In the spirit of the HUPO Proteomics Standards Initiative, this working group is not exclusive and all interested parties are encouraged to join. For further details, please email the current mailing list (mailto:psidev-gps-dev@lists.sourceforge.net) to which you can subscribe.
Details of the teleconferences will be posted to the mailing list. You are encouraged to join these discussions should you wish to contribute.
6. Group Structure (2009)
Role
Chair Juan-Pablo Albar Co-chair Andy Jones MIAPE Co-ordinator Christine Hoogland and Montserrat Carrascal Ontology Co-ordinator Alberto Medina Editor Salvador Martínez de Bartolomé Secretary Sang-Yun Cho
Last update by: Salvador Martínez de Bartolomé, 20-Jul-2009