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Minimum Information for the Reporting of an Ontology (MIRO) [3] associated with PGxO

PGxO reporting following MIRO guidelines [3]. For each guideline, we describe the value of the field to report.

Guideline (field to report) Description
A.1 Ontology name PGxO, v0.5
A.2 Ontology owner Adrien Coulet (https://members.loria.fr/ACoulet/)
A.3 Ontology license Creative Commons BY NC 4.0
A.4 Ontology URL http://pgxo.loria.fr/data/pgxo.owl
A.5 Ontology repository https://github.com/practikpharma/PGxO
A.6 Methodological framework Competency questions described in [1] and [2]
B.1 Need Reconciliation of pharmacogenomic knowledge units of various provenances, enabling further comparison
B.2 Competition SO-Pharm, PHARE, Genomic CDS, PO. Comparison in [2]
B.3 Target audience Bioinformaticians, knowledge engineers, clinical decision support systems. ANR PractiKPharma project (http://practikpharma.loria.fr)
C.1 Scope and coverage Representing, reconciling and tracing pharmacogenomic knowledge units.
C.2 Development community Adrien Coulet, Clément Jonquet, Pierre Monnin
C.3 Communication https://github.com/practikpharma/PGxO/issues
D.1 Knowledge acquisition methodology Described in [1] and [2]
D.2 Source knowledge location Described in [1] and [2]
D.3 Content selection Described in [1] and [2]
E.1 Knowledge Representation language  OWL 2 (OWL-XML syntax), Description Logics ALHI(D)
E.2 Development environment Protégé (https://protege.stanford.edu)
E.3 Ontology metrics 15 classes, 45 properties (44 object, 1 data), 149 axioms, 19KB
E.4 Incorporation of other ontologies  No ontologies are imported. OBO Relations Ontology, DUL and PROV-O are used. Mappings to NCIt, MeSH, SNOMED-CT, SO-Pharm, PO, PHARE and Genomic CDS
E.5 Entity naming convention Base URI: http://pgxo.loria.fr/
E.6 Identifier generation policy Append English rdfs:label to base URI
E.7 Entity metadata policy rdfs:label in English
E.8 Upper ontology None
E.9 Ontology relationships We use some relationships from OBO Relations Ontology, DUL and PROV-O. We defined 40 new relationships.
E.10 Axiom patterns None
E.11 Dereferenceable IRIs IRIs are dereferenceable to http://pgxo.loria.fr/. Preferred prefix is pgxo.
F.1 Sustainability plan The ontology is maintained by the PractiKPharma project (http://practikpharma.loria.fr/). No specific plan beyond the project span. Ontology is released on the NCBO BioPortal.
F.2 Entity deprecation strategy None
F.3 Versioning policy None
G.1 Testing Described in [1] and [2]
G.2 Evaluation Described in [1] and [2]
G.3 Example of use Described in [1] and [2]. Instantiation example available in https://raw.githubusercontent.com/practikpharma/PGxO/master/doc/pgxo_with_instances.owl
G.4 Institutional endorsement None
G.5 Evidence of use Used within the PractiKPharma project (http://practikpharma.loria.fr/)

References

  1. Monnin, P., Jonquet, C., Legrand, J., Napoli, A., & Coulet, A. (2017, October). PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. In Methods, tools & platforms for Personalized Medicine in the Big Data Era. Link
  2. Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A., Jonquet, C., Napoli, A., & Coulet, A. PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019). Link
  3. Matentzoglu, N., Malone, J., Mungall, C., Stevens, R.: MIRO: guidelines for minimum information for the reporting of an ontology. J. Biomedical Semantics 9(1), 6–1613 (2018). doi:10.1186/s13326-017-0172-7