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Request for new ontology [PRIDE] #2652

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nithujohn opened this issue Nov 12, 2024 · 31 comments
Open
13 of 14 tasks

Request for new ontology [PRIDE] #2652

nithujohn opened this issue Nov 12, 2024 · 31 comments
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@ddooley
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new ontology - submitter action needed New ontology requests that have been reviewed and need changes in order to be accepted new ontology Use for new ontology registration requests

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@nithujohn
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nithujohn commented Nov 12, 2024 •
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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

[email protected]

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.
@nithujohn nithujohn added the new ontology Use for new ontology registration requests label Nov 12, 2024
@pfabry
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pfabry commented Nov 12, 2024

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
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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
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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
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ValWood commented Nov 12, 2024

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

@cmungall
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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
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nataled commented Nov 12, 2024

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

@nlharris nlharris added new ontology - reviewer response required Reviewer of this ontology needs to respond to an update or question. new ontology - submitter action needed New ontology requests that have been reviewed and need changes in order to be accepted and removed new ontology - reviewer response required Reviewer of this ontology needs to respond to an update or question. labels Nov 24, 2024
@ypriverol
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@nlharris We are working on some of the issues at the moment, @nithujohn will get back to you and other reviewers soon.

@pfabry
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pfabry commented Nov 25, 2024

@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
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@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.

@nithujohn
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@zhengj2007 We have made the changes for the mentioned issues. Please have a look, Thanks!

@zhengj2007 zhengj2007 added new ontology - reviewer required Indicates that an ontology is ready for review new ontology - submitter action needed New ontology requests that have been reviewed and need changes in order to be accepted and removed new ontology - submitter action needed New ontology requests that have been reviewed and need changes in order to be accepted new ontology - reviewer required Indicates that an ontology is ready for review labels Feb 14, 2025
@zhengj2007
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Thanks, @nithujohn

Hi @pfabry, The last dashboard check was on February 10, 2025, which was before the latest PRIDE changes were made. Could you please rerun the dashboard? Thanks!

@pfabry
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pfabry commented Feb 17, 2025

Dashboard updated. There is still a missing license annotation in the ontology, and the version IRI does not follow the "YYYY-MM-DD" format.

@zhengj2007
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Thanks! @pfabry

@nithujohn Could you please add the license information and fix version IRI in the ontology? See previous comment.

@ypriverol
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@pfabry @zhengj2007 Thanks for the update. we will fix all of them. Can you let me know how I can create a Dashboard like that locally or trigger myself to be sure that I do not need to bother you again?

@pfabry
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pfabry commented Feb 17, 2025

@ypriverol First, you are not bothering me :) Second, you can find information about how to run your own dashboad here.

@zhengj2007
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@ypriverol I think all errors in the ontology can be identified by Robot report. Two issues reported by the Dashboard can be identified by ROBOT tool as well. It might be easy to setup than Dashboard.

Am I right? @pfabry

@ypriverol
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Thanks, @zhengj2007 @pfabry. I have managed to setup everything locally, the next ping should be all greens!!! Working with @nithujohn on that right now. Thanks a lot to both of you.

@ypriverol
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ypriverol commented Feb 17, 2025 •
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@pfabry @zhengj2007 you can trigger the Dashboard report; it should be way better now.

@pfabry
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pfabry commented Feb 18, 2025

@ypriverol @zhengj2007
I just updated the dashboard:

  • The "open" check is still red due to a mismatch between the license in the ontology (CC 4.0) and the one in the submission form in this issue (CC0).
  • The reason for the "URI" check remaining red is unclear. The ontology’s URIs are valid, so this may be a dashboard issue.
  • Also, there seems to be a typo in one of the root classes of the ontology: BF_0000001 instead of BFO_0000001.

@ypriverol
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@pfabry Thanks a lot:

  • @nithujohn will be updating the license from CC 0 -> CC 4.0.
  • I have no idea how to fix this error URI.
  • I have updated it and fixed the terms for BF.

Do you know what is the next step.

@anitacaron
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anitacaron commented Feb 18, 2025 via email

@ypriverol
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@anitacaron do you know what field I have to define in the OBO to make sure that when Im converting to OWL file that value get picked.

@anitacaron
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anitacaron commented Feb 18, 2025 via email

@ypriverol
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Yes. I though also that, I have been following some existing ontologies, and all of them are http://purl.obolibrary.org/obo/{ontology}.owl

@ypriverol
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@anitacaron @pfabry @ddooley what is the next step?

@pfabry
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pfabry commented Feb 18, 2025

@ypriverol @anitacaron

I've done some test on my own. The "URI" check is still red because the identifier in the dashboard_config file is still "pride_cv" and has not been changed yet to "pride". I will update the dashboard accordingly.

The next step is now for @ddooley to review the ontology.

@ypriverol
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Actually, for a long time we have been using pride_cv.owl https://github.com/PRIDE-Archive/pride-ontology/blob/master/pride_cv.owl and the file is actually like that. Is the one use by OLS and other services which use now the PRIDE ontology. My question is do we have to change the file name?

@nataled
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nataled commented Feb 18, 2025

You do not have to change the file name. The PURL for your ontology http://purl.obolibrary.org/obo/pride.owl will need to be set to point to https://github.com/PRIDE-Archive/pride-ontology/blob/master/pride_cv.owl. This is done in the PURL configuration YAML file for your ontology, which will need to be created if the ontology is accepted.

@lschriml
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Awaiting Damion's review.

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