PSI Spring Meeting 2008 in Toledo, Spain, April 23-25, 2008. |
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Topics In addition to the workgroup-specific further development of PSI standards and tools, a major theme in the PSI spring workshop 2008 in Toledo, Spain, will be the planning of further interaction with the community in general, and journals in particular, to increase the public availability of proteomics data. The following activities are planned for the different PSI work groups:
Molecular InteractionsIn 2007, key deliverables of the PSI MI work group have been published with contributions from a broad range of authors:
While the PSI MI 2.5 format has now been stable for two years, the controlled vocabularies are under dynamic maintenance and help adapting the PSI MI XML format to new data types. In this workshop, we will discuss PSI MI applications to antibody-antigen interactions, drug-target interactions, and observation of detailed binding parameters. In continuation of the focus topic of the last meeting we will assess progress in the provision of "gold standard" interaction datasets and interaction confidence scoring. We also aim to finalise the definition of PSICQUIC, the PSI Common QUery InterfaCe. Controlled VocabulariesAt the Toledo meeting we will present the beta version of PSI Validator framework that tackles the issue of automatically checking that experimental data reported using a specific PSI format and various bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) or CVs are indeed compliant with the overall MIAPE recommendations. The semantic validator enforces many rules regarding the use of controlled vocabulary terms, it verifies that the terms mentioned exist in its source CV, and more importantly that the correct terms are used in the correct location of a document. This framework can be adapted to any standard just by customizing the parameters it requires: an XML Schema Definition (XSD), one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. At the meeting we will present the implementations of the validator to related to the mz.ML and to the PSI-MI standards. We aim to refine the existing PSI validator implementations and extend the validator framework to other working group; thus continue the effort of CVs alignment in the Proteomics Informatic and in the Sample Process group. Mass Spectrometry
One of the main deliverables of the Mass Spectrometry working group is mzML, a standard for storing and exchanging the result of a mass spectrometry experiment. mzML is issued from the need of a merge between the PSI mzData format and the Institute for Systems Biology mzXML format. The public review period of the version 0.99 is behind us. We therefore target to prepare a release candidate ready to be discussed in Toledo, and hopefully be prepared for releasing version 1 by June 1st. Prior to the Toledo meeting: At the Toledo meeting: Proteomics InformaticsThe goals of the group are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The main current deliverable of the Proteomics Informatics working group is the analysisML data exchange standard, which, at a minimum encapsulates the results from an MS, MS-MS, MSn, tag database or denovo search. Work on analysisML started in the Summer of 2005, and in spite of significant effort from a small number of people a standard has not yet been released. In 2005, peptide and protein identification were the dominant requirements but other results such as quantitation data have become increasingly important since then. The current state is a draft release of an XML schema based on FuGE, using a model driven architecture which aims to support all types of proteomics experiments in a single instance document. There have been repeated requests for analysisML to be more general and cover non-proteomic experiments. It has also been suggested that we use separate standards for types different results. Finally, there have been comments that using a model driven architecture (MDA) is too complex for those involved in the development of analysisML and that this is slowing down development. One of the goals of this meeting is to 'step back' and: One of the key deliverables from the meeting will be to produce a roadmap with clear milestones, deliverables and resources (volunteers!). Once agreement on this is reached, there will be further work on the schema, example instance documents, controlled vocabulary and documentation. Gel electrophoresis and sample processing
The Gel / SP workgroups are developing minimum reporting requirements, data exchange formats and controlled vocabularies for gel electrophoresis, column chromatography and other separation techniques used in proteomics. The Gel track has recently completed the MIAPE GE requirements document, and the supporting GelML exchange format, for describing gel electrophoresis experimental protocols. During the meeting, plans for publicising and implementing GelML will be discussed. The Gel track is also developing reporting requirements and a data exchange format for the results of gel image analysis: MIAPE GI and GelInfoML, the former will be worked on intensively during the meeting. An early draft of a reporting requirements document for data analysis has been drawn up, which will be discussed. The SP track has completed a reporting requirements document for column chromatography, MIAPE CC, and is developing a supporting data exchange format: spML. The further development of spML will be a focal point of the meeting. Across the Gel/SP track, the sepCV (controlled vocabulary) has been developed to supply terms for GelML / spML, any outstanding issues with sepCV can be raised during the meeting. Summary of objectives:
Meeting format The meeting will commence on 23rd April and run through the evening of 25th April, with common sessions and four parallel tracks in alternation. Registration is now closedPRACTICAL INFORMATION GUIDE: (pdf) VENUE. The meeting will take place at Beatriz Toledo Hotel, Toledo, Spain www.hotelbeatriztoledo.com You can download the kmz file (Google Earth file) with the location of the hotel here HOTELS. As for previous PSI meetings, we ask you to make the reservation by your own. BEATRIZ TOLEDO H**** We agreed a special price, so we highly recommend it: Other accommodation options are: Single: 105 € Double: 125 € C/ Concilios de Toledo, 1 Tlf. +34925 289 800 Fax +34925 289 808 http://www.buenavistatoledo.hilton.com/ Close to meeting venue ALFONSO VI H**** Single: 60 € Double: 120 € General Moscardó, 2 Tlf. 925 22 26 00 Fax 925 21 44 58 http://www.hotelalfonsovi.com/index.html City centre, 1,5 Km from meeting venue LAS CONCHAS H*** Single: 55 € Double: 78 € Juan Labrador, 8 Tlf. 925 21 07 60 Fax 925 22 42 71 http://www.lasconchas.com/ City centre, 1,5 Km from meeting venue Alternative hotels can be found here Organization:
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Toledo Agenda.xls
Signups closed for this event
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| Toledo Agenda.xls | 48.5 KB |