The goal of the HUPO PSI-IDP 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 an intrinsically disordered region. The main tasks of the PSI-IDP working group are to:
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- Maintain the Minimum Information About Disordered Experiments (MIADE) guidelines to standardise the description of IDP experiments.
- Define the best practice guidelines for the curation of IDP literature and the annotation of IDP data.
- 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 community PSI-ID 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.
- 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.
Minimum Information About Disorder Experiments (MIADE) guidelines
An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. The Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data.
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions
Mészáros et al. Nature Methods (2023) – https://doi.org/10.1038/s41592-023-01915-x
Current projects
Definition and development of the PSI-ID exchange formats
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-ID 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-IDPXML/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-ID XML/JSON schema is based on the PSI-MI XML schema.
Development of the PSI-ID controlled vocabulary
Extensive controlled vocabulary (CV) development is required – Most of IDP functions are now represented into the Gene Ontology (GO) and all experimental methods and evidences have been recently integrated into the Evidence and Conclusions Ontology (ECO). Structural terms for different “flavours” of IDRs and functional terms for the structural transition mechanism terms are not represented in any recognized ontology.
Useful links
- Presentation on the PSI-IDP workgroup – link (Norman Davey)
- Planning document for the PSI-IDP workgroup – link
- MIADE guidelines article – Nature Methods – link
- MIADE presentations at the HUPO-PSI meeting 2022 (11 – 13 May 2022) – link1 (Federica Quaglia), link2 (Edoardo Salladini)
- Draft PSI-IDP transfer formats – link
Group members
- Chair
Damiano Piovesan – University of Padova, Padua, Italy (damiano.piovesan@unipd.it) - Co-Chairs
Maria Cristina Aspromonte – University of Padova, Padua, Italy (mariacristina.aspromonte@unipd.it)
Federica Quaglia – National Research Council, Italy (f.quaglia@ibiom.cnr.it) - Minimal Reporting Requirements Coordinator
Maria Victoria Nugnes – University of Padova, Padua, Italy (mariacristina.aspromonte@unipd.it) - Ontology Coordinator
Maria Cristina Aspromonte – University of Padova, Padua, Italy (mariacristina.aspromonte@unipd.it)
Federica Quaglia – National Research Council, Italy (f.quaglia@ibiom.cnr.it) - Editor
Nicolas Palopoli – Universidad Nacional de Quilmes, Buenos Aires, Argentina (nicopalo@gmail.com) - Website Maintainer
Damiano Piovesan – University of Padova, Padua, Italy (damiano.piovesan@unipd.it)