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[bioontology-support] [BioPortal] Feedback from Tatsuya Kushida

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Dec 7 14:32:40 PST 2018


Hello Tatsuya,

I should have added previously that in order to use the API, you’ll need to get an API key. Instructions for doing so are on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer


On Dec 7, 2018, at 2:29 PM, Tatsuya Kushida <kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>> wrote:

Hello Jennifer, and John,

Thank you for your quick response. I'm afraid that I can't use the
SPARQL endpoint, but I will attempt to use the API.

Best regards,
Tatsuya
2018年12月8日(土) 3:22 Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>:

Hello Tatsuya,

You might be interested to look at BioPortal's REST API. The API is actively supported and allows you to access your current ontology data, e.g.:

http://data.bioontology.org/ontologies/IOBC

The API is documented here:

http://data.bioontology.org/documentation

Kind regards,
Jennifer



On Dec 7, 2018, at 7:47 AM, John Graybeal <jgraybeal at stanford.edu> wrote:

Hello,

We're sorry, but we have not updated the Beta SPARQL end point for quite some time. We hope to bring up a new endpoint in the future, but the SPARQL endpoint is not currently a supported product for BioPortal.

John


On Dec 7, 2018, at 1:10 AM, support at bioontology.org wrote:

Name: Tatsuya Kushida

Email: kushida at biosciencedbc.jp

Location: http://sparql.bioontology.org/


Feedback:

I'm a researcher from National Bioscience Database Center of Japan Science and Technology Agency. I registered my ontology "IOBC" (http://bioportal.bioontology.org/ontologies/IOBC) in BioPortal. However when I performed the following SPARQL query using BioPortal SPARQL endpoint (http://sparql.bioontology.org/), I couldn't find "IOBC". How can I find "IOBC"?

### my performed SPARQL query ###
PREFIX omv:
PREFIX xsd:
SELECT distinct *
WHERE {
?ont a omv:Ontology .
?ont omv:acronym "IOBC"^^xsd:string .
}


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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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--
櫛田達矢(Tatsuya Kushida)
国立研究開発法人 科学技術振興機構(JST)
バイオサイエンスデータベースセンター(NBDC)
102-0081 東京都千代田区四番町5-3
TEL: 03-5214-8491 FAX: 03-5214-8470
mob: 090-6199-2657
kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>

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