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[bioontology-support] API access

Michael Dorf mdorf at stanford.edu
Thu Sep 16 16:11:02 PDT 2021


Hi Steph,

I’ve fixed the issue on our end, and the /ontologies_full endpoint is back to operational. Please contact us at support at bioontology.org<mailto:support at bioontology.org> if you require further assistance.

Thank you,

Michael

On Sep 16, 2021, at 8:42 AM, Jones, Stephanie (ELS-CBH) <stephanie at scibite.com<mailto:stephanie at scibite.com>> wrote:

Hi Michael,

I seem to be having the same error as before.

I am struggling to access the bioontology API – specifically, using the python requests library to accesshttp://data.bioontology.org/ontologies_full<https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies_full&data=04%7C01%7Cstephanie%40scibite.com%7C379f036448ae471e0cc008d94e185ab3%7C9274ee3f94254109a27f9fb15c10675d%7C0%7C0%7C637626688781984308%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=H4syTVzPZt9WxVj7GsV5b%2FW50fdRg0bh7v%2FMRNlyim4%3D&reserved=0>

Please can you help.

Thanks,
Steph


Stephanie Jones – Bioinformatician/Python Developer
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SciBite Limited BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR
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From: "Jones, Stephanie (ELS-CBH)" <stephanie at scibite.com<mailto:stephanie at scibite.com>>
Date: Friday, 30 July 2021 at 10:31
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Subject: Re: [bioontology-support] API access

Hi Michael,

Just wanted to say thanks for fixing this so quickly, much appreciated.

Steph

Stephanie Jones – Bioinformatician/Python Developer
<image007.jpg>
SciBite Limited BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR
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This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) You should not read, disclose, or copy it, (ii) Please notify sender of your receipt by reply email and delete this email and all attachments, (iii) SciBite does not accept or assume any liability or responsibility for any use of or reliance on this email. SciBite Ltd. Is a limited company registered in England. Registered number: 172552117. Registered office: BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR. Registered in England & Wales No. 07778456



From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Friday, 23 July 2021 at 21:27
To: "Jones, Stephanie (ELS-CBH)" <stephanie at scibite.com<mailto:stephanie at scibite.com>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] API access

Hi Stephanie,

Thank you for pointing this issue to us, and I apologize for the late reply. It took some investigating on my end to determine the cause of this behavior. I’ve fixed it for the moment, but there is a larger concern related to data integrity, which affects this endpoint. I’ve logged the details in this Github tracker:

https://github.com/ncbo/ontologies_api/issues/72<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fontologies_api%2Fissues%2F72&data=04%7C01%7Cstephanie%40scibite.com%7C379f036448ae471e0cc008d94e185ab3%7C9274ee3f94254109a27f9fb15c10675d%7C0%7C0%7C637626688781974309%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PwAelr51I1eoPcEhdRO0e22Fex%2FB0j1R%2FXYA2QugUAA%3D&reserved=0>

As a side note, this endpoint was developed for the CEDAR project (https://metadatacenter.org/<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmetadatacenter.org%2F&data=04%7C01%7Cstephanie%40scibite.com%7C379f036448ae471e0cc008d94e185ab3%7C9274ee3f94254109a27f9fb15c10675d%7C0%7C0%7C637626688781974309%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3w6KXoN7UWVo98THUNGLNklyS6NRvMNKnYhfdwFtRN4%3D&reserved=0>), which uses a number of proprietary BioPortal endpoints to perform specific tasks. While there is no restriction on its use, we don’t explicitly advertise it, as it is a bit heavy on resources and also somewhat slow for an industrial use.

I’ll try to look into the longer term solution soon, but again it is fixed for the time being. Let us know if you run into any further issues.

Thank you,

Michael


On Jul 22, 2021, at 1:07 AM, Jones, Stephanie (ELS-CBH) <stephanie at scibite.com<mailto:stephanie at scibite.com>> wrote:

Dear team,

I am struggling to access the bioontology API – specifically, using the python requests library to accesshttp://data.bioontology.org/ontologies_full<https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies_full&data=04%7C01%7Cstephanie%40scibite.com%7C379f036448ae471e0cc008d94e185ab3%7C9274ee3f94254109a27f9fb15c10675d%7C0%7C0%7C637626688781984308%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=H4syTVzPZt9WxVj7GsV5b%2FW50fdRg0bh7v%2FMRNlyim4%3D&reserved=0>

The error that I get back is a 500 error.

I have used the API before on previous occasions successfully and the code I have been using hasn’t changed so I’m wondering if anyone else has had any problems accessing the API.

Kind Regards,

Stephanie

Stephanie Jones – Bioinformatician/Python Developer
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SciBite Limited BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR
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