Remove OMIA hyperlinks in OLS "has_dbxref" display?

[franknic]

When viewing VBO in EBI's OLS, I have noticed that the hyperlinks for OMIA in "has_dbxref" link to OMIA phenes rather than to OMIA breed information. For example, the two hyperlinks for Labrador Retriever (Dog) VBO:02000800 are for OMIA breed ids 387 and 75. But the hyperlinks actually point to the phenes OMIA:000387 : Fecundity, Java (redundant) and OMIA:000075 : Coat colour, ashen. Since there is no easy way to link directly to OMIA breed information; since there is no utility in doing so; and since our longer-term aim is to have only VBO as the source of breed information in OMIA, I think the best option would be to simply delete the hyperlinks. While we are still checking the actual links between OMIA breed ids and VBO ids, it would be useful to retain the actual OMIA breed ids, but to remove the hyperlinks. If the "has_dbxref" section requires a hyperlink, then it's probably best to delete the OMIA breed ids from the "has_dbxref" OLS display. Until we have fully integrated all OMIA breeds into VBO, it would, however, be helpful to retain the OMIA breed ids in the VBO spreadsheets, if that is feasible. Including http://omia.org/ as a (historic) source is still fine.

[sabrinatoro]

OMIA x-refs represent OMIA's internal ID for breeds. We agreed to add them to help OMIA with their breed mapping to VBO, and we agreed to remove them once these mappings were done in OMIA (and OMIA uses VBO id instead of their internal id). If OMIA is done with their breed mapping, we can remove them now. But if OMIA mapping to VBO is not done, removing them will impede OMIA's ability to do these mappings.

@franknic and @ImkeTammen please let me know how you would like to proceed at this point.

[franknic]

Thank you very much, Sabrina. Yes, we certainly want to retain the x-refs until the OMIA mapping has been completed. The actual problem is with the hyperlinks to the OMIA x-refs. Having had a closer look, I can see that it is possible to show x-refs in OLS without any hyperlink. For example, with Labrador Retriever (Dog): VBO02000800, there are five x-refs but only three have hyperlinks: neither FCI:122 nor VeNom:14631 has a hyperlink. So, if the hyperlinks could be removed for OMIA, the problem would be solved. In other words, it would be great if the OMIA x-refs could be treated in the same way as FCI and VeNom x-refs. It would be fine to retain the present OMIA hyperlinks that are shown by mousing-over the circled i that is adjacent to the actual x-refs, because these are generic.

[sabrinatoro]

The reason why FCI and VeNom do not link out is because we haven't "defined" where these IDs should linked out. However, OMIA ids have been defined; if we remove the ability to link to OMIA for VBO, we will also remove it for Mondo (I think). @matentzn, could you please advise on how to proceed? Thank you

[sabrinatoro]

@franknic We can remove these omia x-refs from the release (especially if these are internal x-refs). We will still have the corresponding OMIA-VBO in our spreadsheets, ready for you to use whenever you need them, but the public will not see them. This might be the best way to handle these at this point. IF you want to indicate (in a public version) that OMIA refers to these breeds, we could add omia as a source for the breed, but not show the id itself. Would this be better?

[franknic]

Thank you very much, Sabrina Yes, removing the OMIA breed x-refs from the release but leaving them in the spreadsheets is one possibility. However, I am wondering whether there might be a better approach. The OMIA breed x-refs are just like the VeNom x-refs; each VeNom x-ref includes a unique id for each breed, but it is not possible to create a hyperlink that will take you to the actual source of that unique VeNom id. So, the VeNom x-refs are listed under the OLS heading "has_dbxref" but they are not hyperlinked because it is not possible to define where these unique x-refs should be linked to. (The only feasible URL for the Venom x-refs is https://venomcoding.org/venom-codes/, which takes users to the VeNom home page, as distinct from an actual source for a specific VeNom breed id. This generic URL appears when anyone mouses-over the circled i that is adjacent to the all VeNom x-refs for any breed.) In contrast, for FCI x-refs and iDog x-refs, it is possible to create a hyperlink that takes you directly to the source of that unique FCI id or iDog id. For iDog x-refs, the specific hyperlinks are included for each iDog x-ref under the OLS heading "has_dbxref". For FCI x-refs, the specific hyperlinks are included in the circled i but could also be included as actual hyperlinks to the FCI x-ref. All of this suggests that it should be possible to treat OMIA breed x-refs in the same manner as VeNom x-refs. Is this feasible? For completeness, I should mention that, unlike OMIA breed ids, OMIA phene ids can be hyperlinked, because each of them has a specific URL that is a simple function of the phene id, e.g. the URL for OMIA phene 001893 is https://omia.org/OMIA001893/. I hope this is helpful.

[sabrinatoro]

@franknic I discussed this with colleagues working in OLS, and they confirmed that if an x-ref comes from a source that is in the bioregistry, it will be linked out (and there is no work around this). The reason why xrefs from VeNom and FCI do not link out is because these sources are not yet in bioregistry. OMIA is in the bioregistry, which will allow hyperlinks to diseases (when we have them in Mondo), but also add hyperlink to every OMIA x-refs. _if/when VeNom and FCI are in the bioregistry, we might need to review how we include them in VBO_

Our colleagues also agree that internal x-refs (ie IDs that should not be linked out) should not be included in the ontology. Therefore, the solution is to remove the OMIA breed x-ref from VBO. These will still be available in our internal spreadsheet when you need them.

I will remove the OMIA id from the next VBO release.

[franknic]

Thank you very much, Sabrina. I am very grateful for your efforts in contacting folk at OLS. And it is great to have an explanation in terms of bioregistry. Imke and I have discussed this, and we agree with your strategy of removing the OMIA breed ids from VBO but retaining them in the VBO spreadsheets. Yes, we are likely to encounter exactly the same issue with VeNom if it is included in bioregistry because it is just not possible to provide a direct link to the source of a particular VeNom id, whilever VeNom remains only in a spreadsheet. With many thanks Frank