Request for new ontology - Intrinsically Disordered Proteins Ontology (IDPO)

[XimeAixa]

Title

Intrinsically Disordered Proteins Ontology

Short Description

The Intrinsically Disordered Proteins Ontology (IDPO) defines concepts and relationships for the states, transitions, and functional roles of intrinsically disordered proteins and regions.

Description

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are defined by amino acid sequences that do not fold into a stable tertiary structure but instead give rise to dynamic conformational ensembles. Unlike folded domains that mediate biological functions through well-structured molecular interactions, IDRs provide flexibility and adaptability that are essential in many cellular processes, including transcription, translation, signalling, and cell division. At the molecular scale, IDRs can act as flexible linkers, serve as tunable modules for molecular recognition, or function as binding interfaces capable of engaging multiple partners simultaneously. They can range from very short segments of 5–10 residues to long stretches exceeding 1,000 residues, and are often found as terminal tails or connecting linkers between folded domains. In addition, IDRs play a central role in the formation of biomolecular condensates through phase separation, further underscoring their structural and functional complexity.

Because of this high variability and multifunctionality, the characterization of IDPs and IDRs has required the development of rigorous and consistent standards within the IDP community to describe both their structural states and their biological roles. In this context, the Intrinsically Disordered Proteins Ontology (IDPO) was created, providing a standardized, controlled vocabulary that enables precise annotation, interoperability across databases, and integration into broader community frameworks.

IDPO captures three major aspects of intrinsic disorder:

• States: Encompass materials across a continuum of structural disorder and physical states.
• Transitions: Include structural shifts (disorder to order, order to disorder) and higher-order assembly processes such as liquid–liquid phase separation.
• Functional roles: Cover disorder-linked features (e.g., entropic chains), molecular recognition elements (short linear motifs and display sites), and roles in phase separation.

The ontology is designed to support research in structural biology, bioinformatics, molecular biology, and related fields by standardizing terminology across experimental and computational studies, facilitating data integration and interoperability, and enabling the annotation and analysis of IDP-related information in biological databases.

Identifier Space

IDPO

License

CC-BY 4.0

Domain

biochemistry

Source Code Repository

https://github.com/BioComputingUP/idpo

Homepage

https://github.com/BioComputingUP/idpo

Issue Tracker

https://github.com/BioComputingUP/idpo/issues

Contribution Guidelines

https://github.com/BioComputingUP/idpo/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/BioComputingUP/idpo/releases/latest/download/idpo.owl

Contact Name

Ximena Aixa Castro Naser

Contact Email

ximena.castro@unipd.it

Contact GitHub Username

XimeAixa

Contact ORCID Identifier

0000-0002-9211-1255

Formats

• OWL RDF/XML (.owl)
• OBO (.obo)
• OBO Graph JSON (.json)

Dependencies

bfo
ro
omo

Related

go

Usages

- user: https://disprot.org/
  description: "IDPO is used to annotate information about disordered regions from the literature."
  examples:
    - url: https://disprot.org/idpo/IDPO:0000002
      description: "All usages of IDPO:0000002 (disorder)"

Intended Use Cases and/or Related Projects

Intended Use Case
A key use case of the Intrinsically Disordered Proteins Ontology (IDPO) is its integration into DisProt, the reference database for manually curated annotations of IDPs and IDRs from the scientific literature. DisProt is organized such that each entry corresponds to a specific UniProt entry (or one of its isoforms) and provides detailed annotations of structural states, transitions, interactions, and functions. Through the use of IDPO terms, IDRs can be described in a standardized, semantically precise way and propagated to other public resources such as MobiDB. This alignment ensures that observations derived from experiments capture transitions between disordered and ordered states, conditional multistate behaviors, and functional roles. In a similar way, IDPO can support the annotation of IDP-related data across other resources, facilitating integration and interoperability among them.

Related Projects
IDPO was developed within the framework of the IDPfun2 Consortium and the ELIXIR IDP Community, reflecting a shared objective of the IDP community to create a dedicated ontology that can accurately describe protein disorder in both structural and functional terms. IDPO is also connected to the Gene Ontology (GO) Consortium, which provides functional context for IDPs in the DisProt database. Through this use case and related projects, IDPO serves as a community-driven standard that captures the unique complexity of protein disorder, ensuring broad adoption and long-term sustainability.

Data Sources

The ontology was developed in close collaboration with expert scientists and curators from the IDP Community to support data sharing practices that comply with the FAIR principles.

Some foundational studies demonstrating the biological significance of protein disorder that inspired the IDPO include:

• Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 2002 Apr;11(4):739-56
• Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci. 2002 Oct;27(10):527-33
• Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradović Z. Intrinsic disorder and protein function. Biochemistry. 2002 May 28;41(21):6573-82

Additional comments or remarks

In 2021, the IDP Community initiated a collaboration with the Gene Ontology (GO) Consortium to enhance the representation and annotation of IDPs/IDRs in DisProt. This collaboration focused on improving the coverage of molecular pathways involving IDPs, particularly in relation to their structural variability, functions, and interactions. Additionally, through this joint effort, several new GO terms were created to capture IDP-related functions and mechanisms that were not previously represented. However, while GO provides essential functional context, it does not comprehensively cover the full spectrum of structural and functional aspects of protein disorder. For this reason, a dedicated ontology such as IDPO remains necessary, as it is specifically designed to describe the conformational states and functional roles of IDPs and IDRs with the required granularity.

OBO Foundry Pre-registration Checklist

• I have read and understood the registration process instructions and the registration checklist.
• There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
• My term labels are in English and conform to the OBO Foundry Naming Conventions
• I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
• For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
• For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
• If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
• The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.

[pfabry]

Dear @XimeAixa,

Thank you for your submission. The review will be executed as a two stage process:

First, you will have to pass OBO NOR Dashboard. Pass means that no check apart from Users and Versioning may be red. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

After you have successfully passed the Dashboard you will be assigned an OBO Operations committee member to review the ontology. The assigned reviewer is to be considered the final arbiter of requirements; look to that reviewer's guidance regarding which suggestions made by other reviewers must be done, which suggestions are simply good to do but not required, and which should not be done.

Usually, the review will result in an opportunity for you to improve the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This gives other members of the committee the opportunity to assess your work.

When a decision is reached by the committee you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the case at hand.
Please let us know about any reasons you might have for increased urgency.

You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!

[XimeAixa]

Thank you @pfabry! Can you confirm whether IDPO is in the queue for the OBO Dashboard? A rough timeframe would be much appreciated.

[cthoyt]

@XimeAixa it's already there: https://obofoundry.org/obo-nor.github.io/dashboard/idpo/dashboard.html. The idea is you can iteratively address the issues the dashboard shows, since the dashboard is purely objective. Once they're satisfied, then review can begin.

[XimeAixa]

Thanks @cthoyt. Does this result mean we can proceed with the review, or is there anything we should fix first?

[pfabry]

Hi @XimeAixa, we have a meeting today and will get back to you shortly thereafter.

[nataled]

Hi @XimeAixa,
I'm not an official reviewer, but I took a quick look to see if there are any issues that pop out. I did find one general issue: the use of term labels that are way too broad for what is being defined. In general, these should be avoided, as per Principle 12, which states "make the primary labels to be as unambiguous as possible. Remember, your ontology may be used in a different context than that for which it was originally intended." Here are a few that I think could use some re-thinking:

IDPO:0000080 "transition" - obviously there are many types of transitions, but this one is defined in a way that is specific to proteins and parts thereof. Forgetting--for the moment--about the mention of proteins, at a minimum something like "state transition" should be used so that the term label is more closely relevant to what is being defined. Regarding the definition's protein-specific scope, there are two paths you could take. In one, the label is broadened (perhaps "protein state transition"). In the other, the definition is broadened to allow the term to apply to any state-transition situation. Whichever method is chosen, bear in mind the impact on child terms. For example, "higher-order assembly transition" doesn't specifically mention proteins.

IDPO:0000089 "state" - again, this label is very very broad for a definition that explicitly states it applies to proteins.

Renaming these will also alleviate term label clashes (for example, there are at least 3 ontologies with 'state' and 4 with 'transition').

This is not an exhaustive list (I see also 'disorder' and 'order', for example, that would better be termed 'disordered state' and 'ordered state', respectively, though again the definitions specifically mention they apply to proteins).

[XimeAixa]

Hi @nataled, thank you so much for the feedback. This is an aspect we can definitely improve. We’ll wait for the official reviewer’s comments before making any changes, but we’ll start exploring less ambiguous labels in the meantime.

[pfabry]

@XimeAixa
Your ontology is available in the OBO NOR Dashboard and has passed the technical review.
@addiehl has been assigned to review your ontology.

[XimeAixa]

Hi @pfabry, I have a question. Is there an estimated timeframe for when we can expect feedback? This would really help us better organize our work. Thanks!