Appendix 1: Syntactic conventions and Internationalized Resource Identifier (IRI) table

In order to improve readability, we will adopt the following syntactic conventions when discussing ontology terms. Relations are in bold font (e.g., concretizes, prescribed by), and classes are in italics with the first letter of each word capitalized (e.g., Plan Specification, Planned Process). Instances of classes (or individuals) are in lowercase italics, and often a hash sign followed by a number is used to uniquely specify individuals (e.g., plan #1, plan #2). For those ontology terms that have an Internationalized Resource Identifier (IRI), a table mapping the term to its IRI is provided in the table below.

* In the Core Ontology for Biology and Biomedicine (COB), the IRI for Completely Executed Planned Process is the same as the IRI for Ontology for Biomedical Investigation’s Planned Process class.

** In the Relation Ontology, the range of has input is specified as Material Entity. However, in our proposal, the range needs to be expanded.

*** In the Relation Ontology, the range of results in formation of is specified as Anatomical Entity. However, in our proposal, the range needs to include Disposition.

Appendix 2: specific and generic dependence

Instances of Specifically Dependent Continuants specifically depend on Independent Continuants, whereas instances of Generically Dependent Continuants generically depend on Independent Continuants. If a particular entity x specifically depends on another entity (or entities) y1, …, yn, x cannot exist unless entities y1, …, yn exist at every moment that x exists. Similar to specific dependence, if x generically depends on y1, …, yn, x cannot exist unless entities y1, …, yn exist. However, unlike specific dependence, each y1, …, yn does not have to exist at every moment x exists. For example, suppose x generically depends on y1 and y2, and for times t1 and t2, the following hold:

At t1, y1 and y2 exist.

At t2, y2 exists, but y1 does not.

Since x generically depends on y1 and y2, x exists at both t1 and t2. However, if x were to specifically depend on y1, x would have ceased to exist when y1 ceased to exist.

Appendix 3: usage of IAO Plan Specification

The following ontologies were extracted from Ontobee.org (https://ontobee.org/ontology/IAO?

iri = http://purl.obolibrary.org/obo/IAO_0000104) on 2024-05-16. After filtering for OBO Foundry ontologies, 40 ontologies were found to contain IAO’s Plan Specification term.

1. Agronomy Ontology.

2. Apollo Structured Vocabulary.

3. Biological Collections Ontology.

4. Chemical Methods Ontology.

5. Coronavirus Infectious Disease Ontology.

6. Cell Line Ontology.

7. Core Ontology for Biology and Biomedicine.

8. CTO: Core Ontology of Clinical Trials.

9. Data Use Ontology.

10. Evidence and Conclusion Ontology.

11. Environment Ontology.

12. Food Ontology.

13. FuTRES Ontology of Vertebrate Traits.

14. Gazetteer.

15. Genomics Cohorts Knowledge Ontology.

16. Genomic Epidemiology Ontology.

17. Health Surveillance Ontology.

18. Hypertension Ontology.

19. Informed consent Ontology.

20. Clinical LABoratory Ontology.

21. Model Card Report Ontology.

22. MIAPA Ontology.

23. Next Generation Biobanking Ontology.

24. Ontology of Biological and Clinical Statistics.

25. Ontology for Biomedical Investigations.

26. Ontology for Biobanking.

27. Oral Health and Disease Ontology.

28. Ontology of Host-Microbiome Interactions.

29. Ontology of Host Pathogen Interactions.

30. Ontology for Modeling and Representation of Social Entities.

31. Ontology for Nutritional Epidemiology.

32. Ontology for Nutritional Studies.

33. Obstetric and Neonatal Ontology.

34. Ontology of Organizational Structures of Trauma centers and Trauma systems.

35. Ontology of Precision Medicine and Investigation.

36. Ontology of RNA Sequencing.

37. The Prescription of Drugs Ontology.

38. Process Chemistry Ontology.

39. Radiation Biology Ontology.

40. Scientific Evidence and Provenance Information Ontology.

41. Space Life Sciences Ontology.

42. The Statistical Methods Ontology.

43. Software ontology.

44. Vaccine Ontology.

Appendix 4: usage of OBI Planned process

The following ontologies were extracted from Ontobee.org (https://ontobee.org/ontology/OBI?

iri = http://purl.obolibrary.org/obo/OBI_0000011) on 2024-05-16. After filtering for OBO Foundry ontologies, 61 ontologies were found to contain OBI’s Planned Process term.

1. Alzheimer’s Disease Ontology.

2. Agronomy Ontology.

3. Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM).

4. Apollo Structured Vocabulary.

5. Biological Collections Ontology.

6. Chemical Methods Ontology.

7. Coronavirus Infectious Disease Ontology.

8. Cell Line Ontology.

9. Core Ontology for Biology and Biomedicine.

10. CTO: Core Ontology of Clinical Trials.

11. The Drug Ontology.

12. Data Use Ontology.

13. Evidence and Conclusion Ontology.

14. An ontology of core ecological entities.

15. Environmental conditions, treatments and exposures ontology.

16. Environment Ontology.

17. Epilepsy Ontology.

18. Food Ontology.

19. FuTRES Ontology of Vertebrate Traits.

20. Gazetteer.

21. Genomics Cohorts Knowledge Ontology.

22. Genomic Epidemiology Ontology.

23. Genotype Ontology.

24. Health Surveillance Ontology.

25. Hypertension Ontology.

26. Information Artifact Ontology.

27. Informed consent Ontology.

28. Clinical LABoratory Ontology.

29. Medical Action Ontology.

30. Microbial Conditions Ontology.

31. Model Card Report Ontology.

32. Mental Disease Ontology.

33. Next Generation Biobanking Ontology.

34. Ontology of Adverse Events.

35. Ontology of Biological and Clinical Statistics.

36. Ontology for Biobanking.

37. Occupation Ontology.

38. Ontology for General Medical Science.

39. Oral Health and Disease Ontology.

40. Ontology of Host-Microbiome Interactions.

41. Ontology of Host Pathogen Interactions.

42. Ontology for Modeling and Representation of Social Entities.

43. Ontology for Nutritional Epidemiology.

44. Ontology for Nutritional Studies.

45. Obstetric and Neonatal Ontology.

46. Ontology of Organizational Structures of Trauma centers and Trauma systems.

47. Ontology of Precision Medicine and Investigation.

48. Ontology of RNA Sequencing.

49. Ontology of Vaccine Adverse Events.

50. The Prescription of Drugs Ontology.

51. Planaria-ontology.

52. Plant Phenology Ontology.

53. Process Chemistry Ontology.

54. Radiation Biology Ontology.

55. Relation Ontology.

56. Name Reaction Ontology.

57. Scientific Evidence and Provenance Information Ontology.

58. Space Life Sciences Ontology.

59. The Statistical Methods Ontology.

60. Software ontology.

61. Vaccine Ontology.

Appendix 5: axioms Associated with figures

In order to address ambiguities that may arise from the figures, we include axioms associated with each figure that define how the figure is to be interpreted.

Appendix 5.1. Axioms for Fig. 2

plan specification #1 instance of Plan Specification.

process #1 instance of Planned Process.

agent #1 instance of Agent.

concretization #1 instance of Realizable Entity.

concretization #1 concretizes plan specification #1.

plan specification #1 generically depends on agent #1.

concretization #1 characteristic of agent #1.

process #1 realizes concretization #1.

agent #1 participates in process #1.

Appendix 5.2: axioms for Fig. 4

restorative treatment specification #1 instance of Plan Specification.

root canal specification #1 instance of Plan Specification.

restorative concretization #1 instance of Quality.

root canal concretization #1 instance of Quality.

restorative concretization #1 concretizes restorative treatment specification #1.

root canal concretization #1 concretizes root canal specification #1.

dentist #1 instance of Dentist.

restorative concretization #1 characteristic of dentist #1.

root canal concretization #1 characteristic of dentist #1.

Appendix 5.3: axioms for Fig. 6

plan specification #1 instance of Plan Specification.

process #1 instance of Process.

agent #1 instance of Agent.

plan specification #1 generically depends on agent #1.

process #1 prescribed by plan specification #1.

agent #1 participates in process #1.

Appendix 5.4: axioms for Fig. 7

plan creation process #1 instance of Plan Creation Process.

plan specification #1 instance of Plan Specification.

process #1 instance of Process.

agent #1 instance of Agent.

plan #1 instance of Plan.

plan concretization #1 concretizes plan specification #1.

plan creation process #1 has input plan concretization #1.

plan creation process #1 results in formation of plan #1.

agent #1 participates in process #1.

plan #1 characteristic of agent #1.

process #1 realizes plan #1.