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[bioontology-support] Access to a copy of the VMWare Virtual Appliance?

John Graybeal jgraybeal at stanford.edu
Wed Feb 13 12:39:16 PST 2019


No, BIoPortal is agnostic with regard to compliance with upper ontologies including BFO.

BioPortal does have one accommodation that relates to BFO. The class trees displayed by BioPortal do not show 'continuant' and 'occurent' classes at the head of these trees. because we found it confusing for many users over the years.

My warning is that opinions tend to be strongly held in this regard.

One bit of advice is to consider the tooling and community resources available when you choose to use (or not use) an ontology framework. Your ability to communicate, collaborate, and get advice about your ontology may be more important than the actual representations (and constraints) offered by a particular framework.

You may want to send an email to the Protege support list (see https://protege.stanford.edu/support.php) soliciting more advice, particularly if you want to put forward specific modeling concerns or goals of your effort. (You may also find out about existing related efforts via that support list.)

John


On Feb 13, 2019, at 1:51 AM, OSBORNE Jamie <Jamie.OSBORNE at swift.com<mailto:Jamie.OSBORNE at swift.com>> wrote:

Thanks John – downloading and getting setup now – One question that I have already after digging around on the online portal is whether the ontoportal technical stack has built-in any assumptions/requirements that ontologies are compliant with BFO?

While I appreciate the benefits of a foundational/operational ontology, we haven’t yet reached any agreement in Finance about which, if any, we will implement. Some of my peers have raised concerns that BFO is not well suited to our industry and have proposed (or developed) alternatives.

Do you have any thoughts, warnings, or expert advice for us?

Kind regards,

Jamie OSBORNE
Systems Architect
Standards Research
S.W.I.F.T. SCRL
Tel: +32 (0)2 655 3229
Mob: +32 (0)474 990 988
E-mail: jamie.osborne at swift.com<x-msg://73/jamie.osborne@swift.com>
Twitter: JamieAtSWIFT<http://twitter.com/#!/JamieAtSWIFT>
LinkedIn<https://www.linkedin.com/in/jamie-the-standards-nerd/>
*** Check out our new API Whitepaper<https://www.swift.com/news-events/news/delivering-a-global-platform-for-the-financial-services-api-economy> and API Developer Portal<https://developer.swift.com/> ***

þ Please consider the environment before printing
This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com<http://www.swift.com/> for more information about SWIFT.

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: 12 February 2019 23:33
To: OSBORNE Jamie
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Access to a copy of the VMWare Virtual Appliance?

Mail originates from outside SWIFT !
Be vigilant before you click on a link, open attachments or reply !
-------------------------------------------------------------------------
Hi again Jamie,

Thank you for providing your information with your request. You can now access this page that contains the download and documentation links:

  http://bioportal.bioontology.org/virtual_appliance

We are now providing version 2.5 of the Virtual Appliance, which implements a "call home" feature to determine whether there is an update available. I notice that you want to work with an AWS instance; unfortunately this is still at version 2.4. We hope to have a new AMI available before too long, but perhaps you'd like to contact me about your specific situation. Also, if you have any questions or thoughts about your use of the Virtual Appliance, please feel free to contact me. Our licensing may be change before too long and it will be good to give you an update on that as well.

For any questions about the installation or ontology population process, please email support at bioontology.org<mailto:support at bioontology.org>. And since requests for Virtual Appliance support are made through this NCBO Support email list, we suggest you sign up for the email list at
   https://mailman.stanford.edu/mailman/listinfo/bioontology-support.
This will help you keep up to date on the BioPortal and Virtual Appliance systems.

John

On Feb 10, 2019, at 12:52 PM, OSBORNE Jamie <Jamie.OSBORNE at swift.com<mailto:Jamie.OSBORNE at swift.com>> wrote:

Hi NCBO team,
Impressive work - I’d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I’m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022<https://www.iso20022.org/> and ISO 15022<https://www.iso20022.org/15022/iso-15022-home> financial information interchange standards.

Under ISO TC68/SC9/WG1<https://www.iso.org/committee/6534831.html>, I’m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance.

Our work is currently too experimental to be shared more broadly, so we’d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature.

Greatly appreciate your help to get up and running with a local instance. Thanks!

Kind regards,

Jamie OSBORNE
Systems Architect
Standards Research
S.W.I.F.T. SCRL
Tel: +32 (0)2 655 3229
Mob: +32 (0)474 990 988
E-mail: jamie.osborne at swift.com<x-msg://59/jamie.osborne@swift.com>
Twitter: JamieAtSWIFT<http://twitter.com/#!/JamieAtSWIFT>
LinkedIn<https://www.linkedin.com/in/jamie-the-standards-nerd/>
*** Check out our new API Whitepaper<https://www.swift.com/news-events/news/delivering-a-global-platform-for-the-financial-services-api-economy> and API Developer Portal<https://developer.swift.com/> ***

þ Please consider the environment before printing
This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com<http://www.swift.com/> for more information about SWIFT.

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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

========================
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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