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Request for new ontology pbpko #2563
Comments
Dear @Crispae, Thank you for your submission. The review will be executed as a two stage process:
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. You will be informed once your ontology is loaded in the OBO NOR Dashboard. Good luck! |
@Crispae |
Ontology version reviewed: 2024-04-05 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 Was the ontology developed for a very specific purpose or community? Terms with the new ontology prefix The correct pattern that would match the OBO identifier scheme is: The identifier scheme must be fixed. Are there terms with the same meaning available in another OBO Foundry ontology? 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? Correct use of imported terms Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment? Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense? Basic review of axiomatic patterns 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)”). Appropriate use of object properties - Responsiveness to suggested changes - General Comments: |
Note to OBO Foundry members: Clearly the lexical matching test is a work in progress. |
@addiehl Thank you for your comments. We will address the mentioned issues. If we need further assistance, we are counting on OBO Foundry. |
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
saurav.kumar@iispv.cat
Contact GitHub Username
Crispae
Contact ORCID Identifier
0000-0003-0593-2598
Formats
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
dc:license
annotation, serialised in RDF/XML.The text was updated successfully, but these errors were encountered: