Hi Melanie,
We hope that all OBO projects will update to 1.2, unless they're already using BFO 2.0 Graz. We're willing to help them do it.
The problem you describe is exactly what we've been facing with OBI. We switched to ruttenberg-bfo2 a year ago, with the expectation that BFO 2.0 would soon be ready and that this change would help us prepare. Some of the ontologies we depend upon also made this change, while others didn't. We were left in a difficult position and it's slowing the development of OBI.
Compatibility between ontologies using BFO 1.2 and BFO 2.0 is designed to be good -- much better than the current state of affairs. With BFO 1.2 we can more easily test development versions of BFO 2.0, and then implement it when it's released.
At the beginning of December I wanted to figure out which ontologies are using which versions of BFO. Using Ontobee I discovered that a significant number of ontologies are already using the new IDs -- results are below. We want to consolidate on the new identifiers, and to do it sooner rather than later.
I see this as an opportunity to develop and debug OBO best-practices for upgrading our upper-level ontology. We haven't done anything like this before, but we'll have to do it again at some point in the future. There are clear benefits to doing it well and keeping our upper-level ontology in sync across the OBO library. I think we're better off starting small with a transition to BFO 1.2 before making the leap to BFO 2.0.
Best regards,
James
Ontobee now provides a "Ontologies that use the Class" section at the bottom of pages for terms, which will be more up-to-date than these results.
http://www.ifomis.org/bfo/1.1#Entity
1. Information Artifact Ontology
2. Ontology for General Medical Science
3. Ontology of Medically Related Social Entities
4. Influenza Ontology
5. eagle-i resource ontology
6. Interaction Network Ontology
7. Brucellosis Ontology
8. Chemical Information Ontology
9. NIF Gross Anatomy
10. Infectious disease
11. Ontology for Parasite LifeCycle
12. NIF Cell
13. ARG clinical encounter module
14. Oral Health and Disease Ontology
15. Reagent Ontology
http://purl.obolibrary.org/obo/BFO_0000001
1. Basic Formal Ontology
2. Adverse Event Reporting Ontology
3. Vaccine ontology
4. Ontology of Adverse Events
5. Relation ontology (dev)
6. OBI web service, development version
7. Oral Health and Disease Ontology
8. Ontology for biomedical investigations
The other 84 ontologies in Ontobee don't seem to use BFO.
Then I checked for the new and old "has_part" relations:
http://www.obofoundry.org/ro/ro.owl#has_part
1. Information Artifact Ontology
2. Suggested Ontology for Pharmacogenomics
3. Influenza Ontology
4. eagle-i resource ontology
5. Ontology of Adverse Events
6. Interaction Network Ontology
7. Brucellosis Ontology
8. Chemical Information Ontology
9. NIF Gross Anatomy
10. Infectious disease
11. NIF Cell
12. ARG clinical encounter module
13. microRNA Ontology
14. Software ontology
15. Oral Health and Disease Ontology
16. Reagent Ontology
http://purl.obolibrary.org/obo/BFO_0000050 (ruttenberg-bfo2 and RO)
1. Basic Formal Ontology
2. Fission Yeast Phenotype Ontology
3. Ontology for biomedical investigations
4. Zebrafish anatomy and development
5. Adverse Event Reporting Ontology
6. Vaccine ontology
7. Drosophila gross anatomy
8. Plant Ontology
9. uberon_collected_metazoa
10. Porifera Ontology
11. Uber anatomy ontology
12. OBI web service, development version
13. Oral Health and Disease Ontology
14. Vertebrate Skeletal Anatomy Ontology
15. Teleost Anatomy Ontology
16. Hymenoptera Anatomy Ontology
17. Ontology of Adverse Events
18. Gene Ontology