HUPO-PSI-IDP

Formats and standards for the HUPO-PSI intrinsically disordered proteins community

We're looking for community input:

Document for community input on XML schema here

An XSD of HUPO-PSI-IDP XML format is available here

An example of the HUPO-PSI-IDP v4 XML format holding a IDR annotation is available here

Planning document for MIADE-compliant DisProt implementation here

Document for community input on MIADE guideline here

The goals of the community are:

The PSI-IDP working group is composed of academic, government, and industry researchers, software developers and database curators and managers. The main goals of the PSI-IDP working group are to:

• define the community PSI-IDP XML exchange format and associated controlled vocabularies to permit the dissemination and storage of data relating to IDR structure and function.
• define the Minimum Information About Disorder Experiments (MIADE) guidelines to standardise the description of intrinsically disordered protein (IDP) experiments.
• support the integration of the developed standards, exchange formats and controlled vocabularies into IDP tools and resources.
• define the rules and guidelines for the curation of IDP literature and the annotation of IDP data.

Current projects of the PSI-IDP working group are:

• definition and development of the MIADE guidelines.
• definition and development of the PSI-ID XML format and the PSI-IDP TAB format, working together with the PSI-MI workgroup.
• development of the PSI-IDP controlled vocabulary.

The slides on current plans/progress:

ELIXIR IDP community slides here

Slides from HUPO-PSI annual meeting 2021

Introduction here

Overview (Norman Davey)here

MIADE (Norman Davey) here

DisProt Curation (Federica Quaglia) here

Experiment CV (Bálint Mészáros) here

Functional CV (Nico Palopoli) here

Use Cases (Bálint Mészáros) here

Milestones:

Milestone 1 Submission of a manuscript to a journal in the field to announce the PSI-IDP WG

Goal 1: Completion of the MIADE standard defining the minimal fundamental parameters to describe a structural disorder experiment, based on simple use cases

Goal 2: Completion of the 1.0 version of the PSI-IDP TAB format 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

Goal 3: Completion of the 1.0 version of the PSI-IDP XML format to allow the experimental setup and results of an analysis of the structure state of a protein region to be unequivocally represented

Milestone 2: Setting up the WG website/GitHub page to serve as a platform for dissemination of developed formats and standards

Goal 4: Work together with the PSI-MI WG to set up a protocol for integrating IDP interaction data into core data resources of molecular interactions

Goal 5: Defining the scope and priorities for version 1.0 of the CV for IDPs

HUPO-PSI guidelines and standards:

Thsis directory contains describing HUPO-PSI guidelines and standards. All documents are in draft form and have not been submitted by the HUPO-PSI review process. We are happy to have new contriibutors to the project.

Report on the HUPO-PSI guidelines and standards:

Report on ELIXIR funded project to define preliminary draft of the standards and guidelines for the exchange of structural data relating to intrinsically disordered protein region here.

HUPO-PSI MIADE guidelines:

Draft document of the MIADE guidelines here.

HUPO-PSI-ID XML format:

An XSD of HUPO-PSI-IDP XML format is available here

An example of the HUPO-PSI-IDP v4 XML format holding a IDR annotation is available here

HUPO-PSI-ID TAB format:

An annotated example of the HUPO-PSI-IDP TAB format is available here

Administrative:

Group Name: HUPO PSI Intrinsic Disorder Protein Working Group (PSI-IDP WG)

Chair (with affiliation and current email address): Norman Davey - The Institute of Cancer Research, London, UK

Co-Chairs (1 or 2) (with affiliation and current email address): Silvio C. E. Tosatto - University of Padua, Padua, Italy; Zsuzsanna Dosztányi - Eötvös Loránd University, Budapest, Hungary

Secretary: Bálint Mészáros - Eötvös Loránd University, Budapest, Hungary

Other officers (optional) (with affiliation and current email address):

Editor(s): Nicolás Palopoli - Universidad Nacional de Quilmes, Buenos Aires, Argentina; Rita Pancsa - Research Centre for Natural Sciences, HAS, Budapest, Hungary; Kim van Roey(?)

Minimal Reporting Requirements Coordinator(s): Norman Davey - The Institute of Cancer Research, London, UK

Ontology Coordinator(s): Toby Gibson - European Molecular Biology Laboratory, Heidelberg, Germany; Peter Tompa - Vrije Universiteit Brussel, Brussels, Belgium

Web site Maintainer(s): Damiano Piovesan - University of Padua, Padua, Italy (damiano.piovesan@unipd.it)

Funding:

This project was initialised with funding from ELIXIR for the implementation study: “Integration and standardisation of intrinsically disordered protein data”.

Useful Software

A free, open-source ontology editor and framework for building intelligent systems here