Sample Processing Workgroup

The Sample Processing Working Group has been merged with
the gel group into a Protein Separation working group 

 


Statement of purpose

The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be 'classical' one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, 'tagging' proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics.
  • Minimum reporting requirements
    The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME).
  • XML formats for data exchange
    Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a 'parent' FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals.
  • Controlled vocabularies (CVs) and ontology
    Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO).



The MIAPE minimum reporting requirements

The context-sensitive nature of transcriptome, metabolome and proteome data necessitates the capture of a richer set of metadata (data about the data) than is required for basic genetic sequence, where usually knowing the organism of origin will suffice. The use of paper citations as proxies for actual metadata hinders the reassessment of data sets, and obstructs non-standard searching (e.g. by the order that different liquid chromatography columns were coupled). The requirements of the various journals also differ, so important detail may be lacking in some cases, or presented in an esoteric fashion.

There is then a need for public repositories that contain information from whole proteomics experiments; making explicit both where samples came from, and how analyses of them were performed. It is therefore appropriate to attempt to define the minimum set of information about a proteomics experiment that would be required by such a repository.

Working drafts (see also the MIAPE home page):

The MIAPE 'Parent Document' (gives basic principles and context)
MIAPE: CC v1.1.0 (Column Chromatography)
MIAPE: CE v0.7.0 (Capillary Electrophoresis)
MIAPE: SP v0.1 (Sample preparation and handling)




Exchange format development

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.

FormatScopeStatus
spMLLiquid and gas chromatography, centrifugation, rotofors, capillary electrophoresis, general sample handling and chemical modificationsMilestone 1 release
spMLLiquid and gas chromatography, capillary electrophoresis, general sample handling and chemical modificationsMilestone 2 release
The FuGE object model provides the set of 'superclasses' from which all objects in spML will be subclassed.

spML will also have a dedicated controlled vocabulary file to accompany it, the terms from which will be integrated into the overall PSI CV and contributed to the FuGO project.

History corner: Once upon a time there was the PSI-OM (erstwhile child of the PEDRo object model), which for completeness is still viewable (but no longer under development): Rose version -- Acrobat PDF -- GIF (big...)




Controlled vocabulary development

Update to follow soon.




Meeting reports

Update to follow soon.




Moderated email discussion list

This list caters to the activities of the Gel and Sample Processing WGs, providing a central organising point for announcements and discussion.




Contact details (organisers)

Any queries or grumbles should be emailed to Chris Taylor, chris.taylor[@]ebi.ac.uk.

 


Chris Taylor, chris.taylor[@]ebi.ac.uk, August 8th, 2006. - Salvador Martínez de Bartolomé, smartinez@proteored.org, June 16th, 2009



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