Request for new ontology pbpko

[Crispae]

Title

Physiologically based pharmacokinetic modelling ontology

Short Description

Ontology aligned for PBPK modelling in life science domain

Description

The Physiologically-Based Pharmacokinetics (PBPK) ontology is a comprehensive framework designed to systematically capture and represent the intricate relationships and behaviors of pharmacokinetic processes within living organisms. At its core, the ontology encompasses a rich array of classes spanning physiological parameters, types of PBPK, biological compartments, and mathematical models that collectively contribute to the understanding of drug disposition and behavior in the body.the PBPK ontology serves as a unifying resource for researchers, clinicians, pharmacologists, and drug developers alike.By providing a structured vocabulary and semantic framework, it facilitates communication, data integration, and knowledge sharing across diverse research endeavors, thereby fostering collaboration and advancing scientific inquiry in pharmacokinetics and related disciplines.

Identifier Space

PBPKO

License

CC-BY 4.0

Domain

simulation

Source Code Repository

https://github.com/Crispae/pbpko

Homepage

https://crispae.github.io/pbpko/

Issue Tracker

https://github.com/Crispae/pbpko/issues

Contribution Guidelines

https://github.com/Crispae/pbpko/blob/main/docs/contributing.md

Ontology Download Link

https://github.com/Crispae/pbpko/blob/main/pbpko.owl

Contact Name

saurav kumar

Contact Email

[email protected]

Contact GitHub Username

Crispae

Contact ORCID Identifier

0000-0003-0593-2598

Formats

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

Dependencies

No response

Related

No response

Usages

No response

Intended Use Cases and/or Related Projects

PBPKO ontology will serve as a foundational resource for annotating and contextualizing Physiologically-Based Pharmacokinetics (PBPK) models within the domains of drug research and chemical risk assessment. PBPK model is a type of system biology model, hence direct integration of ontology with SBML allow automated annotation of model, if follow the standard approach.PBPK models is actively being develeoped in European project PARC.

Data Sources

PBPK expert community
Literature

Additional comments or remarks

As the PBPKO ontology is in the development phase, it benefits from continuous input and refinement by semantics.Requesting an Ontology ID space accelerates the process of integrating the ontology into models developed within the PARC project.

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 @Crispae,

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!

[pfabry]

@Crispae
Your ontology has been added to the OBO NOR Dashboard and has passed the technical review.
@addiehl has been assigned to review your ontology. 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.

[Crispae]

@pfabry Thanks for assigning the reviewer, we will co-ordinate with @addiehl to further refine the ontology.

[pfabry]

@Crispae @addiehl
The lexical matching did not find any duplicate term.

[addiehl]

Ontology version reviewed: 2024-04-05
Ontology reviewer: Alexander Diehl

To begin with, the OBO dashboard states that PBPKO is only missing one definition, whereas in reviewing the pbpko.owl file using Protege, I see that many classes are missing definitions, for instance the many classes that appear directly under entity: Falv, fSA_exposed, FSkin_e, PCAir, PCPoor, PCRich, Qair, and others. Also, many other classes at deeper levels in the hierarchy, such as Observed, Predicted, Residual error magnitude, Fcecum, Fcolon, intestinal transit time, linear elimination, and others are all undefined. I can only imagine there is some error in the OBO Dashboard code.

Ontology scope
Do the terms fall within the ontology’s stated target domain of knowledge?
Yes, based on my limited understanding of the intended domain.

Was the ontology developed for a very specific purpose or community?
The ontology was developed for the Physiologically-Based Pharmacokinetics (PBPK) modeling community, a branch of systems biology research.

Terms with the new ontology prefix
Do the terms follow the OBO identifier scheme?
No, there is a slight error
The identifier scheme used currently follows this pattern:
http://purl.obolibrary.org/obo/pbpko/PKPBO_00328

The correct pattern that would match the OBO identifier scheme is:
http://purl.obolibrary.org/obo/PKPBO_00328

The identifier scheme must be fixed.

Are there terms with the same meaning available in another OBO Foundry ontology?
Yes, for instance 'Excretion' (PKPBO:00225) is defined as "Removal of a compound from the body through various routes such as urine, feces, and exhalation."
The Gene Ontology has an 'excretion' class (GO:0007588) defined as "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds."
These definitions refer to the same process, and PBPKO must import the GO term.

PBPKO has 'goodness of fit' (PKPBO:00328), an undefined type of 'Statistical Method' (PKPBO:00001, also undefined).

The Ontology of Biological and Clinical Statistics has also a 'goodness of fit' (http://purl.obolibrary.org/obo/OBCS_0000030) subclass of 'inferential statistical data analysis' a type of planned process, defined as "An inferential statistical data analysis used to analyze how well a statistical model fits a set of observations; measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model in question."

The The Statistical Methods Ontology has 'goodness of fit statistical test' (http://purl.obolibrary.org/obo/STATO_0000191) defined as "A goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input."

PBPKO should import their statistical test classes from an established ontology.

Is there another OBO Foundry ontology whose scope covers any of the new terms?
yes, see above for the statistical terms.

Correct use of imported terms
If the ontology reuses terms from other OBO ontologies, are they used accurately?
No, the BFO hierarchy is imported in PBPKO and ignored completely for all the PBPKO native classes, which include both continuants and occurrents.

Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment?
The few GO terms that are imported are in the proper place under BFO:process.

Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense?
There are no additional axioms.

Basic review of axiomatic patterns
Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.)
There is no attempt at adding axioms to any PBPKO classes.

Are existential restrictions used correctly? (Typical mistakes include “R some (A and B and C)” to mean “(R some A and R some B and R some C)”).
There is no attempt at adding axioms to any PBPKO classes.

Appropriate use of object properties -
Are object properties used in a manner consistent with their definitions, domain, and range? (Examples of incorrect usage include those based on some interpretation of the label of the object property but not actually fitting the property definition or domain and range.)
There are no object properties employed.

Responsiveness to suggested changes -
Have the developers been willing to fix any identified issues during the review?
Let's see.

General Comments:
PBPKO should developed along the OBI model as it is full of assays. I recommend the developers of PBPKO study OBI and consider how best to refactor PBPKO. Also, the term names in PBPKO have insufficient face value (they should be more descriptive), and all classes should be defined.

[addiehl]

Note to OBO Foundry members: Clearly the lexical matching test is a work in progress.

[Crispae]

@addiehl Thank you for your comments. We will address the mentioned issues. If we need further assistance, we are counting on OBO Foundry.

[Crispae]

@addiehl

Thank you for your comments, Apology for the delay in response, we need to restructure the ontology involving the domain experts.

Following your suggestions, we reviewed our ontology PBPKO, which is being developed for the Physiologically Based Pharmacokinetic Modelling community, and made the necessary changes accordingly.
Some of these are:

We now adopted the ROBOT tool to develop the reviewed version of the PBPKO.
The identifier scheme, which was previously http://purl.obolibrary.org/obo/pbpko/PKPBO_00328, has been updated to the corrected pattern http://purl.obolibrary.org/obo/PKPBO_00328 in accordance with the OBO guidelines.

We included the definition for the terms which were missing earlier. Though, some of the terms still does not have the definitions; we will address this issue soon on discussion with wider PBPK community of the project.

The terms which had the same meaning were included from other OBO Foundry ontologies such as Gene Ontology, OBCIS, UBERON. And the annotation properties were included from IAO.

Also, the BFO ontology which was imported and not used, was removed correctly to avoid any irregularities in the ontology.
The ontology was restructured to define the parent class and subclasses more logically, ensuring correct placements and a more rational organization.

Also, documentation page was added for the ontology which can be viewed at https://crispae.github.io/pbpko/. It will be further enriched with detailed descriptions.

NOTE:
As we have used ROBOT, we define all versions and IRI manually, Our current version of ontology can be downloaded from https://github.com/Crispae/pbpko/releases/download/v1.0.0/pbpko_15_07_2024.owl

Please let us know if any additional changes are needed so we can further refine our ontology.

[addiehl]

Thanks for your detailed description of your revisions. I will review your changes and get back to you soon.

[nlharris]

Hi @addiehl, have you had a chance to look at this?

[Crispae]

Hi @addiehl, any update of review process . We need to implement this ontology in our ongoing project (PARC), some of our use cases depends on it.

Please let us know, if further changes required, we will try to accommodate those ASAP.

[addiehl]

I apologize for my delay.

Re-review comments:

1. The IRIs appear to be fixed. Good.

2. There is still duplication, rather that import of terms from other OBO Foundry ontologies. This is particularly true for anatomy terms. Some upper level anatomy terms are taken from Uberon, but the child terms are still local to pbpko, even when they could have come from Uberon. Bad. This needs to be fixed.

Similarly the statistical terms should be imported, not created de novo.

3. Most terms appear to be defined, but there are a few missing definitions still, such as 'Nails'. This should be an easy fix.

Overall, the ontology structure is still closer to a mind map, rather than a proper ontology.

Without addressing point 2 above, I cannot recommend this ontology should be admitted to the OBO Foundry.

--Alex

[addiehl]

Also, one minor change that is required is that the Ontology IRI needs to be changed from
"https://github.com/Crispae/pbpko/blob/main/pbpko.owl"
to
"http://purl.obolibrary.org/obo/pbpko.owl"

This will enable the ontology to pass the new ontology dashboard check for URIs.

[jamesaoverton]

In the initial description above, the Ontology Download Link is https://github.com/Crispae/pbpko/blob/main/pbpko.owl, but that URL no longer resolves. So I believe that the report from the New Ontology Requests Dashboard is out-of-date: https://obofoundry.org/obo-nor.github.io/dashboard/pbpko/dashboard.html.

@Crispae Please provide us with a working Ontology Download Link.

[Crispae]

Also, one minor change that is required is that the Ontology IRI needs to be changed from "https://github.com/Crispae/pbpko/blob/main/pbpko.owl" to "http://purl.obolibrary.org/obo/pbpko.owl"

This will enable the ontology to pass the new ontology dashboard check for URIs.

Thank you for the clarification, @addiehl !

We initially held off on using a PURL URL since we hadn't been assigned one, and the ontology is still under review. However, we will proceed with updating the Ontology IRI to http://purl.obolibrary.org/obo/pbpko.owl .

[Crispae]

In the initial description above, the Ontology Download Link is https://github.com/Crispae/pbpko/blob/main/pbpko.owl, but that URL no longer resolves. So I believe that the report from the New Ontology Requests Dashboard is out-of-date: https://obofoundry.org/obo-nor.github.io/dashboard/pbpko/dashboard.html.

@Crispae Please provide us with a working Ontology Download Link.

@jamesaoverton thanks for catching this, here is the updated link with latest version

https://github.com/Crispae/pbpko/releases/download/v1.0.1/pbpko_10_09_2024.owl

[Crispae]

I apologize for my delay.

Re-review comments:

1. The IRIs appear to be fixed.  Good.

2. There is still duplication, rather that import of terms from other OBO Foundry ontologies.  This is particularly true for anatomy terms.  Some upper level anatomy terms are taken from Uberon, but the child terms are still local to pbpko, even when they could have come from Uberon.  Bad.  This needs to be fixed.

Similarly the statistical terms should be imported, not created de novo.

3. Most terms appear to be defined, but there are a few missing definitions still, such as 'Nails'.  This should be an easy fix.

Overall, the ontology structure is still closer to a mind map, rather than a proper ontology.

Without addressing point 2 above, I cannot recommend this ontology should be admitted to the OBO Foundry.

--Alex

@addiehl Thanks for your comments, For the Uberon terms, we’re currently in discussions with PBPK experts to determine the best approach. While importing all relevant terms from Uberon would address duplication, there's some concern that the standard Uberon terminology might not fully capture the contextual nuances specific to PBPK modeling.

Definitions issue will be updated.

Assigning object properties and applying restrictions are ongoing discussions with PBPK experts, and we will keep you updated on this and might come with next release of the ontology.

Thanks for you feedback, and we’ll follow up with further updates.

[addiehl]

For the Uberon import, ideally you should create a list of the required Uberon terms and use a MIREOT tool to extract the terms you want from Uberon and their parents to root. You can use the extract tool in ROBOT with the MIREOT option or use ONTOFOX to do this.

The resulting owl file of Uberon terms can be used as an imported ontology for pbpko or directly merged with pbpko. Keeping it as a separate file is preferable, as you can easily update it later if Uberon changes.

You can also use the Ontology Development Kit to manage imports, but this is a more involved approach to set up.

If there are nuances about anatomical parts you want to capture in pbpko that are missing from Uberon, there are a couple ways to reference related Uberon terms:

1. make a request to Uberon for a new subclass of an existing Uberon term if you think there is a missing term in Uberon with the required specificity.
2. If Uberon rejects your request, after considering their reasons, import the Uberon parent and create your own term under it.

Keep in mind that ontologies that are part of the OBO Foundry commit to following the OBO Foundry Principles; these include Principle 5 Scope and Principle 10 Commitment to Collaboration. If you create your own anatomy terms (or statistical terms, for that matter), then you are expanding the scope of your ontology into the scope of Uberon. If instead you import Uberon terms and collaborate with the Uberon developers, then you comply with both principle 5 and 10.

[nlharris]

Hi @Crispae, are you working on the suggested revisions?

[Crispae]

Hi @nlharris

We are currently addressing the comments provided by @addiehl and will keep you updated with the latest developments on the ontology.
For your information, we have recently moved the ontology repository to the organization level: https://github.com/InSilicoVida-Research-Lab/pbpko.