The goal of the HUPO PSI-ID community is to develop the guidelines, controlled vocabularies and standardised formats to allow the unambiguous annotation of the basic structural and structure-function attributes of a disordered region
The main tasks of the PSI-IDP working group are to:
- define the community PSI-IDP XML, JSON and TAB exchange formats to permit the dissemination and storage of data relating to Intrinsically Disordered Proteins/Regions (IDP/IDR) structure and function.
- define the Minimum Information About Disordered Experiments (MIADE) guidelines to standardise the description of IDP experiments.
- create the ontologies and controlled vocabularies required to define the functional and structural aspects of IDRs, and the technical aspects of the exchange formats and minimum information guidelines.
- define the best practice guidelines for the curation of IDP literature and the annotation of IDP data.
- support the implementation of the PSI-ID exchange formats, controlled vocabularies and best practice guidelines by the tools and resources developed by the IDP community.
The on-going projects of the PSI-IDP working group are:
(i) definition and development of the Minimum Information About Disorder Experiments (MIADE) guidelines
The MIADE guidelines define the minimum level of information that is required to comprehend the results of an experiment investigating the structure of an IDR. As such, MIADE-compliant entries fall far short of the annotation of an IDR experiment to a level of detail that allows the experiment to be fully reproduced. The guidelines are a compromise between the excessive burden of the full annotation of an experiment and the capture of the most important information to clearly describe the key result of the experiment. Data annotated to this minimum common standard permits (i) unambiguous definition of experimental results, (ii) the deposition of the data into resources and (iii) the interchange of data between resources.
(ii) definition and development of the PSI-IDP exchange formats, working together with the PSI-MI workgroup.
The role of the PSI-ID TAB format is to represent, in a simple but unambiguous manner, an entry adhering to the MIADE guidelines for the description of the structural state of a protein region. This tabular format will facilitate many use cases by providing a format that is human-readable, easy to parse, and manipulatable in commonly used spreadsheet applications. The role of the PSI-IDP XML/JSON schema is to allow the experimental setup and results of an analysis of the structure state of a protein region to be unequivocally represented. A PSI-IDP XML/JSON entry allow but does not require annotation to that level and therefore the format is generally useful across a range of use cases. The PSI-IDP XML/JSON schema is based on the PSI-MI XML schema.
(iii) development of the PSI-ID controlled vocabulary to describe the technical aspects of IDP experiments and the sequence-level structural inferences derived from them.
Extensive controlled vocabulary (CV) development is required - Experimental methods and evidences; Structural terms for different “flavours” of IDRs; Functional terms for the structure from function; Transition and transition mechanism terms.
Planning document for the PSI-IDP workgroup - link
Draft PSI-IDP transfer formats - link
Presentation on the PSI-IDP workgroup - link
Chair: Norman Davey - The Institute of Cancer Research, London, UK (firstname.lastname@example.org)
Co-Chairs: Silvio C. E. Tosatto - University of Padua, Padua, Italy (email@example.com); Zsuzsanna Dosztányi - Eötvös Loránd University, Budapest, Hungary (firstname.lastname@example.org)
Secretary: Bálint Mészáros - European Molecular Biology Laboratory, Heidelberg, Germany (email@example.com)
Editor(s): Nicolás Palopoli - Universidad Nacional de Quilmes, Buenos Aires, Argentina (firstname.lastname@example.org), Rita Pancsa - Research Centre for Natural Sciences, HAS, Budapest, Hungary (email@example.com), Kim Van Roey - European Molecular Biology Laboratory, Heidelberg, Germany (firstname.lastname@example.org)
Minimal Reporting Requirements Coordinator(s): Norman Davey - The Institute of Cancer Research, London, UK (email@example.com)
Ontology Coordinator(s): Toby Gibson - European Molecular Biology Laboratory, Heidelberg, Germany (firstname.lastname@example.org); Peter Tompa - Vrije Universiteit Brussel, Brussels, Belgium (email@example.com)
Website Maintainer(s): Damiano Piovesan - University of Padua, Padua, Italy (firstname.lastname@example.org)