Request for new ontology [PRIDE]

[nithujohn]

Title

Proteomics Identification Ontology

Short Description

The Proteomics Identification Ontology (PRIDE ontology) provides a model for describing, sharing and integrating of proteomics data mainly for mass spectrometry based experiments.

Description

The PRIDE Ontology is used to standardize and organize the annotation of data in the PRoteomics IDEntifications Database (PRIDE), which is a public repository for proteomics data.
The ontology ensures consistency in the way proteomics data, such as protein identifications, peptide sequences, experimental conditions, instruments, and protein modifications, are described. It is part of a collection of controlled vocabularies and ontologies developed and used by the Proteomics Standards Initiative (PSI) to standardize the description of proteomics data. PRIDE Ontology is a crucial tool for ensuring that proteomics data are properly annotated, making it easier for researchers to share, compare, and analyze proteomics data across different studies and experiments.

Identifier Space

PRIDE

License

CC 4.0

Domain

biochemistry

Source Code Repository

OBOFoundry.github.io

Homepage

https://github.com/PRIDE-Archive/pride-ontology

Issue Tracker

https://github.com/PRIDE-Archive/pride-ontology/issues

Contribution Guidelines

https://github.com/PRIDE-Archive/pride-ontology/blob/master/CONTRIBUTING.md

Ontology Download Link

https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo

Contact Name

Nithu Sara John

Contact Email

nithu@ebi.ac.uk

Contact GitHub Username

nithujohn

Contact ORCID Identifier

0000-0002-4823-6210

Formats

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

Dependencies

-efo -chmo

Related

No response

Usages

No response

Intended Use Cases and/or Related Projects

No response

Data Sources

No response

Additional comments or remarks

No response

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 @nithujohn,

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.

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!

[bpeters42]

After Dashboard is passed, @ddooley will serve as reviewer.
Maybe also consider to have a different name then 'PRIDE' to differentiate the project from the Ontology?

[ypriverol]

Hi @bpeters42, I think it is almost impossible to change PRIDE at this moment. This ontology has more than 15 years. It is used all over the place in PRIDE and OLS. Then, it will be difficult to do that major refactoring.

[ValWood]

Hi, What is the scope? It isn't clear from the submission. The description also seems to be about the database rather than the ontology?

[ypriverol]

When reading the issue I realised that we created wrongly some of the sections, we will modify the issue accordingly.

[cmungall]

Maybe also consider to have a different name then 'PRIDE' to differentiate the project from the Ontology?

This is the current state of things in bioregistry:

https://bioregistry.io/registry/pride, e.g. pride:0000006 (the vocabulary/ontology)
https://bioregistry.io/registry/pride.project, e.g. pride.project:PXD000440, (the PRIDE datasets)

This was inherited from identifiers.org some time ago.

so the id spaces are clearly distinguished. I agree though that this is pretty suboptimal and confusing. The database should be "primary", the proteomics community think of the project IDs (PDXs) as "PRIDE IDs". But here we are, short of a time machine or major refactoring there is no way to fix this.

[nataled]

Hi @ypriverol,
While I am not the official reviewer, I did take a quick look at the ontology. Without doing any deep diving, I saw two big violations of OBO Principles right away: (1) There appear to be many missing definitions at the top of the hierarchy (violation of Principle 6); and (2) the term names violate OBO standards against capitalization, as outlined in Principle 12.

[nlharris]

Hi @ypriverol, please let us know when you've fixed those issues so we can take a look at your ontology.

[ypriverol]

@nlharris We are working on some of the issues at the moment, @nithujohn will get back to you and other reviewers soon.

[pfabry]

@ypriverol
Your ontology has been added to the OBO NOR Dashboard.
The result of the lexical matching is available here: PRIDE lexmatch 20241125.txt

[zhengj2007]

@ypriverol and @nithujohn: Any progress on addressing the issues? If we don't get the response by March 1st, we are going to close the issue. You can reopen the issue when you are ready for reviewing.