search-url on two different places

[tschaka1904]

Dear OLS-Team,

the general term json model has a database_cross_reference, which contains a attribute search-url. I was looking at MI:0446 and the search-url attribute is empty. Instead it can be found in the obo_xrefobject.

Why is that?

Thanks,
Max

[simonjupp]

By default we just show properties and their values asserted in the ontology. So in this case

database_cross_reference is a property and the value is "search-url". You can see that in the sources.

We understand the some ontologies coming from OBO have a specific Xref pattern that OLS tries to detect, in cases where we spot this we add the obo_xref attribute. Note that most ontologies donct have this.

If you find an obo_xref you can probably ignore the database_cross_reference. We may even move to do that by default in the future so you wouldn't see database_cross_reference if there's a properly formatted boo xrefs in the raw ontology file.

[tschaka1904]

I understand that. It's just the fact that the old old-client just gave me the meta-data and I had all the existing information. Now I have basically to search it's existent. But I understand that not all files are formatted the same way. It is just difficult from a developer point of view, who uses the ols-ws, to collect all that information. Because the information can be on different places. Please don't take my tickets as any kind of bad feedback. I'm just trying to understand how I have to deal with the new OLS.

So you say that database_cross_reference might be removed in the near future? I guess theid-validation-regexp would, in that case, also end up in the obo_xref. Am I assuming that right?

[tschaka1904]

I was just checking out the MI obo file and looked at MI:0446
It looks like this:

So both id-validation-regexp and search-url are annotated with xref. But the JSON output the one is in the database_cross_reference and the other in the obo_xref.

Here is the JSON MI:0446