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[bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Michael Dorf mdorf at stanford.edu
Wed Oct 3 14:42:04 PDT 2018


Hi Chen,

I see your email from September 19th with three questions. To be honest, I’m not sure why it fell through our radar, but I’ll do my best to address it here. Please see my answers inline in BLUE:

1) I was going to get the permanent link of class "Case studies" in ONE, then I clicked the icon next to "class mappings"but get the ID of "Case studies": "http://purl.bioontology.org/ontology/ONE/standards#caseStudies". I cannot reach the class by the link. Could you please check?

The correct permanent link should be: http://purl.bioontology.org/ontology/ONE?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FONE%2Fstandards%23caseStudies<http://purl.bioontology.org/ontology/ONE?conceptid=http://purl.bioontology.org/ontology/ONE/standards#caseStudies>

It’s a bug in our system that results in a wrong link whenever the default classes view is loaded. Once you click on another class and come back to the original one, the permanent link will be correct. I’ve logged this behavior here:

https://github.com/ncbo/bioportal_web_ui/issues/84

2) But is it possible to set the ID as permanent link? For MeSH ontology, it works (e.g. "http://purl.bioontology.org/ontology/MESH/D000602" can be used to reach the class on BioPortal). The IDs of my Classes also start with "http://purl.bioontology.org/ontology/“.

MeSH is part of a group of UMLS ontologies that we import periodically into our system from a publicly available relational database. The import process generates our own permalinks and handles them accordingly for each ontology in this set. The rest of the ontologies use their original class IDs that are found in the ontology source file. Our uniform permalink structure for ALL ontologies is in the format:

http://purl.bioontology.org/ontology/<ONTOLOGY_ACRONYM>?conceptid=<URL_ENCODED_CONCEPT_ID>

3) For ONE, the mappings are still a problem. I reported it before. https://github.com/ncbo/ontologies_api/issues/50

This remains an open issue.  We’re a small team, so our development schedule is highly selective. Unfortunately, fixing this issue hasn’t hit the top of our priority list to date.

Thanks again for contacting us and sorry about the delay in responding.

Michael



----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Oct 3, 2018, at 1:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

Dear,
I sent my questions 2 weeks ago (17 September, 2018). However, I have not got your answer yet.
Regards,
Chen

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