several terms need to be mireoted into OBI, including 'vaccine' and 'vaccination' from Vaccine Ontology, and 'host' and 'pathogen' from Infectious Disease Ontology (IDO).
couple of dependencies
1. purls not yet stable for VO, must be before mireot
2. IDO is prerelease so ids are not yet stable - must be before mireot or will need doing again.
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Just to precise before Alan complains :)
IDO IDs are stable (see file at http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl\), but this new version hasn't been released yet, so there is no SPARQL endpoint where we could fetch the info.
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Issue for host: we currently have:
- host role: OBI_0000725
- host of immune response role (which is not asserted under host role) OBI_1110083
- host: OBI_1110026 with definition "I thought we removed/edited this term? See OBI_1110083 below" and restriction organism and has role host role.
- pathogen role in OBI could be replaced by pathogen role in IDO (IDO_0000528)
Bjoern, can you check for the host issue (those are coming in from IEDB) ?
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- I clarified the label 'host' to be 'host of immune response', which is directly linked to the 'host of immune response role'. This is a separate term from than the one in IDO.
- I had discussed with Lindsay that the 'host role' in IDO would be renamed to 'host of symbiont role', to inter operate better, and I believe she agreed. Once that is done, we should import and replace our current host role (OBI_0000725). Will email to follow up.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
couple of dependencies
1. purls not yet stable for VO, must be before mireot
2. IDO is prerelease so ids are not yet stable - must be before mireot or will need doing again.
Just to precise before Alan complains :)
IDO IDs are stable (see file at http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl\), but this new version hasn't been released yet, so there is no SPARQL endpoint where we could fetch the info.
vaccine done
vaccination done
Issue for host: we currently have:
- host role: OBI_0000725
- host of immune response role (which is not asserted under host role) OBI_1110083
- host: OBI_1110026 with definition "I thought we removed/edited this term? See OBI_1110083 below" and restriction organism and has role host role.
- pathogen role in OBI could be replaced by pathogen role in IDO (IDO_0000528)
Bjoern, can you check for the host issue (those are coming in from IEDB) ?
- I clarified the label 'host' to be 'host of immune response', which is directly linked to the 'host of immune response role'. This is a separate term from than the one in IDO.
- I had discussed with Lindsay that the 'host role' in IDO would be renamed to 'host of symbiont role', to inter operate better, and I believe she agreed. Once that is done, we should import and replace our current host role (OBI_0000725). Will email to follow up.
Discussed on OBI call 2016-4-25. Will collect all IDO related OBI terms and discuss in the IDO-OBI alignment work.