From support at bioontology.org Sat Jan 1 13:59:50 2022 From: support at bioontology.org (support at bioontology.org) Date: Sat, 01 Jan 2022 13:59:50 -0800 Subject: [bioontology-support] [BioPortal] Feedback from mabablue Message-ID: <61d0ced68a73a_1b3713d86cc55536@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 3 04:34:50 2022 From: support at bioontology.org (support at bioontology.org) Date: Mon, 03 Jan 2022 04:34:50 -0800 Subject: [bioontology-support] [BioPortal] Feedback from mabablue Message-ID: <61d2ed6a559_76fb2990654718aa@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 3 12:07:31 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 3 Jan 2022 20:07:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mabablue In-Reply-To: <61d0ced68a73a_1b3713d86cc55536@ncbo-prd-app-08.stanford.edu.mail> References: <61d0ced68a73a_1b3713d86cc55536@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <0F0A536A-68C9-4C9B-B19D-329830A2012A@stanford.edu> Hello Barbara, On Jan 1, 2022, at 1:59 PM, support at bioontology.org wrote: I have problems to get eLTER Controlled Lists running on BioPortal: https://bioportal.bioontology.org/ontologies/ELTER_CL. Can you please help? I looked at the submission information you entered for ELTER_CL. The value you enter in the ?Load from URL? text box needs to point directly to the ontology source file. You had entered this URL: https://github.com/LTER-Europe/eLTER_CL/blob/main/vocabulary.ttl ? which points to an HTML page at GitHub that displays the content of vocabulary.ttl, as well as other GitHub specific information. Instead, you need to click the ?Raw? button on that GitHub page to get the URL that points directly to the ontology source file: https://raw.githubusercontent.com/LTER-Europe/eLTER_CL/main/vocabulary.ttl I created a new submission for ELTER_CL with this new URL and BioPortal has loaded / processed the ontology, and it?s fully available to view now. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 3 12:14:33 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 3 Jan 2022 20:14:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mabablue In-Reply-To: <61d2ed6a559_76fb2990654718aa@ncbo-prd-app-09.stanford.edu.mail> References: <61d2ed6a559_76fb2990654718aa@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <2EE83CDB-9002-4189-BB2C-BCF997FE3969@stanford.edu> Hello Barbara, On Jan 3, 2022, at 4:34 AM, support at bioontology.org wrote: I uploaded the Envthes Thesaurus and it seems that has parsed the skos ttl file but it still has problems to show the classes, why? I?m looking at ENVTHES in BioPortal now, and the classes appear to display without issue. Could you let us know if you?re still experiencing difficulty? Kind regards, Jennifer [cid:41716BA2-CD35-492F-B463-9A62404A1544] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-01-03 at 12.13.44 PM.png Type: image/png Size: 131759 bytes Desc: Screen Shot 2022-01-03 at 12.13.44 PM.png URL: From Barbara.Magagna at umweltbundesamt.at Mon Jan 3 12:15:48 2022 From: Barbara.Magagna at umweltbundesamt.at (Magagna Barbara) Date: Mon, 3 Jan 2022 20:15:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mabablue In-Reply-To: <2EE83CDB-9002-4189-BB2C-BCF997FE3969@stanford.edu> References: <61d2ed6a559_76fb2990654718aa@ncbo-prd-app-09.stanford.edu.mail> <2EE83CDB-9002-4189-BB2C-BCF997FE3969@stanford.edu> Message-ID: Dear Jennifer, now all works, thank you very much for your help. Cheers, Barbara Von: Jennifer Leigh Vendetti Gesendet: Montag, 3. J?nner 2022 21:15 An: NCBO User Support Cc: Magagna Barbara Betreff: Re: [bioontology-support] [BioPortal] Feedback from mabablue Hello Barbara, On Jan 3, 2022, at 4:34 AM, support at bioontology.org wrote: I uploaded the Envthes Thesaurus and it seems that has parsed the skos ttl file but it still has problems to show the classes, why? I?m looking at ENVTHES in BioPortal now, and the classes appear to display without issue. Could you let us know if you?re still experiencing difficulty? Kind regards, Jennifer [cid:image001.png at 01D800E7.12F01940] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 131759 bytes Desc: image001.png URL: From support at bioontology.org Tue Jan 4 06:56:57 2022 From: support at bioontology.org (support at bioontology.org) Date: Tue, 04 Jan 2022 06:56:57 -0800 Subject: [bioontology-support] [BioPortal] Feedback from maggiesun Message-ID: <61d460391bd8e_44b1e96d9886981@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jan 4 10:57:12 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 4 Jan 2022 18:57:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from DG_Allotrope_AFO In-Reply-To: <61c19555d2efe_26451f646a81534@ncbo-prd-app-09.stanford.edu.mail> References: <61c19555d2efe_26451f646a81534@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <18086064-E74D-4175-9D33-124280304AA5@stanford.edu> Hi Karin, Thank you for your inquiry. There was a strange data discrepancy with AFO ontology that prevented you from submitting a new version. This error happens occasionally, and we haven?t had the means to track it down yet. I?ve addressed the issue in our backend and re-submitted the latest version of your ontology, pulled directly from http://purl.allotrope.org/voc/afo/latest.ttl. It?s now fully processed and ready for use. Let us know if you experience further issues. Thank you for your patience. Michael On Dec 21, 2021, at 12:50 AM, support at bioontology.org wrote: Name: DG_Allotrope_AFO Email: DG_Allotrope_AFO at osthus.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Dear Bioportal team, We are having a problem with getting our newest version of AFO published. The autoupdate from http://purl.allotrope.org/voc/afo/latest.ttl did not produce a new version, although the file was updated on Friday. I tried submitting the new file manually via https://bioportal.bioontology.org/ontologies/AFO/submissions, but I am blocked by the following error message: Errors On Form [:error, #>] Could you please take a look? Thank you! Karin Colsman _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jan 4 11:40:59 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 4 Jan 2022 19:40:59 +0000 Subject: [bioontology-support] bioontology-support: CTCAE version and dutch farmacotherapeutisch kompas In-Reply-To: <4c85c09d226a4b28bdfd6588ab97983d@umcg.nl> References: <4c85c09d226a4b28bdfd6588ab97983d@umcg.nl> Message-ID: Hi Olga, Thank you for your inquiry. The version of CTCAE I am seeing in BioPortal does say ?5.0?. The original filename also stipulates "NCIt_CTCAE_5.0.owl?. Are you saying that the actual contents of the file contains an earlier version? https://bioportal.bioontology.org/ontologies/CTCAE The contact for this ontology is listed as: CTCAE Help, ncictcaehelp at mail.nih.gov Enterpise Vocabulary Services, NCIThesaurus at mail.nih.gov I am assuming they are the ones who maintain the BioPortal submissions of CTCAE. It?s best to reach out to them in case you are seeing a discrepancy between theirs and our versions of CTCAE. Regarding your question on "farmacotherapeutisch komas?, a potential issue may be the publisher licensing terms that restrict the public distribution of the ontology. Again, the best way to approach this is to contact them directly and explain your use case to see if they would allow their ontology to be uploaded to BioPortal. Their contact form is located here: https://www.farmacotherapeutischkompas.nl/algemeen/contact The majority of the ontologies we host aren?t actually published and maintained by us. They are managed directly by either their creators or their administrative staff. If it turns out that the Healthcare Institute of Netherlands prohibits their content to be distributed openly, an alternative may be to ask them whether they would allow having your own ?private" copy of "farmacotherapeutisch komas? to be hosted in BioPortal. If so, you can upload their ontology under your account and designate it as ?private?, so that only you could view and interact with it. Hope this helps. Michael On Dec 21, 2021, at 2:04 AM, Eriks, OLV > wrote: Dear Sir/Madam, Researchers from our institute use preferably the CTCAE codelist of the ontology service in REDCap. However, we find out that this CTCAE in this portal is an older version (3.5). We would really appreciate to work with a more recent version (5.0). Is it possible for you to realize this upload? An other question is, is there a possibility to upload a Dutch codelist ?farmacotherapeutisch komas? in the bioontology portal?. And if yes, what should we do to realize this. Thank you very much in advance. Kind regards, Olga Eriks ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jan 4 11:52:09 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 4 Jan 2022 19:52:09 +0000 Subject: [bioontology-support] [BioPortal] Feedback from maggiesun In-Reply-To: <61d460391bd8e_44b1e96d9886981@ncbo-prd-app-08.stanford.edu.mail> References: <61d460391bd8e_44b1e96d9886981@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Maggie, Thank you for contacting us. Can you please provide more detail on what specific endpoint you were calling, what method was used (POST/GET), and what parameters you were passing to the API call (except for the value of your private API key)? If you can send me your actual code snippet so I can reproduce the issue on my end, that would be ideal. Thank you, Michael On Jan 4, 2022, at 6:56 AM, support at bioontology.org wrote: Name: maggiesun Email: sunrmin.ele at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Email: sunrmin.ele at gmail.com Hello, I was trying to download mapping information by using the API.But I always receive "ConnectionResetError: [Errno 54] Connection reset by peer". Can I know why I get this error and how I can solve the issue? Thanks. Look forward to your response. Best, Maggie _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghardallou.m at gmail.com Wed Jan 5 00:37:33 2022 From: ghardallou.m at gmail.com (Meriam Ghardallou) Date: Wed, 5 Jan 2022 09:37:33 +0100 Subject: [bioontology-support] error with bioportal Message-ID: Dear sir/madam I ?m asking about the error message that I obtained when I tried to submit a new version of ontologies; It is indicated ? Error Diff ? and ? Problem retrieving classes" Following screen shots of the error message and the URL of the page https://bioportal.bioontology.org/ontologies/VODANA-MPA Thank you so much for your help -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture d?e?cran 2022-01-05 a? 09.34.37.png Type: image/png Size: 204250 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture d?e?cran 2022-01-05 a? 09.36.31.png Type: image/png Size: 119675 bytes Desc: not available URL: From mdorf at stanford.edu Wed Jan 5 08:50:12 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 5 Jan 2022 16:50:12 +0000 Subject: [bioontology-support] error with bioportal In-Reply-To: References: Message-ID: <839DC201-9DBC-47DE-A9F8-1E92B2DDD8B4@stanford.edu> Hi Meriam, Thank you for contacting us. I?ve checked your ontology, and the classes display correctly on my end. It?s possible that the error you saw was due to our production caches not having been fully refreshed after your ontology had been processed. Error Diff can be ignored for the moment. The error indicates that there is no file in our system to compare the latest version to. This should fix itself with future versions of the ontology. Let us know if you run into further issues. Michael On Jan 5, 2022, at 12:37 AM, Meriam Ghardallou > wrote: Dear sir/madam I ?m asking about the error message that I obtained when I tried to submit a new version of ontologies; It is indicated ? Error Diff ? and ? Problem retrieving classes" Following screen shots of the error message and the URL of the page https://bioportal.bioontology.org/ontologies/VODANA-MPA Thank you so much for your help _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Jan 7 16:05:12 2022 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 8 Jan 2022 00:05:12 +0000 Subject: [bioontology-support] error with bioportal In-Reply-To: <839DC201-9DBC-47DE-A9F8-1E92B2DDD8B4@stanford.edu> References: <839DC201-9DBC-47DE-A9F8-1E92B2DDD8B4@stanford.edu> Message-ID: Thanks Misha. I'll just add to this that my experience is that if I check the ontology page quickly after submission (but before full processing is complete), I get "Problem retrieving classes." It can then take quite some time before that disappears, and involves refreshing my browser cache for that page *and* that BioPortal's cache has been updated also, which should happen every 2 hours or so I believe. Sorry we haven't had time to chase that down more precisely, but it may give you an idea how to proceed. john On Jan 5, 2022, at 8:50 AM, Michael Dorf > wrote: Hi Meriam, Thank you for contacting us. I?ve checked your ontology, and the classes display correctly on my end. It?s possible that the error you saw was due to our production caches not having been fully refreshed after your ontology had been processed. Error Diff can be ignored for the moment. The error indicates that there is no file in our system to compare the latest version to. This should fix itself with future versions of the ontology. Let us know if you run into further issues. Michael On Jan 5, 2022, at 12:37 AM, Meriam Ghardallou > wrote: Dear sir/madam I ?m asking about the error message that I obtained when I tried to submit a new version of ontologies; It is indicated ? Error Diff ? and ? Problem retrieving classes" Following screen shots of the error message and the URL of the page https://bioportal.bioontology.org/ontologies/VODANA-MPA Thank you so much for your help _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 12 03:30:59 2022 From: support at bioontology.org (support at bioontology.org) Date: Wed, 12 Jan 2022 03:30:59 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Muhammad Yahya Message-ID: <61debbf39e87e_340723fc4e09974@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From rcoop at adventhp.com Wed Jan 12 06:46:55 2022 From: rcoop at adventhp.com (Robert Coop) Date: Wed, 12 Jan 2022 14:46:55 +0000 Subject: [bioontology-support] FW: license request for OntoPortal In-Reply-To: References: <9DC18F9F-EAE8-464D-A6E3-C5E280D0311D@stanford.edu> Message-ID: Hi Jennifer and others! I had previously been working with John on the below issue but was wondering if you could handle this in his absence. Please let me know. Thanks! Coop, Ph.D. | Chief Al Officer Advent Health Partners, Inc. | 301 Plus Park Blvd., Suite 500, Nashville, TN 37217 (615) 933-0526 | AdventHP.com Access my calendar to schedule a meeting with me Connect with me on LinkedIn [https://adventhp.com/logo-advent-health/] [https://adventhp.com/adv-inc-5000-2020_esig/] Confidentiality Notice: The information contained in this transmission is privileged and confidential and/or protected health information (PHI) and may be subject to protection under the law, including the Health Insurance Portability and Accountability Act of 1996, as amended (HIPAA). This transmission is intended for the sole use of the individual or entity to whom it is addressed. If you are not the intended recipient, you are notified that any use, dissemination, distribution, printing or copying of this transmission is strictly prohibited and may subject you to criminal or civil penalties. If you have received this transmission in error, please contact the sender immediately by replying to this email and deleting/expunging this email and any attachments from any computer. From: Robert Coop Sent: Wednesday, January 12, 2022 8:45 AM To: John Graybeal Subject: RE: license request for OntoPortal Hi John! I recently submitted a new license request for Appliance ID: 8f637575-1240-49bd-b26f-5612e821ded3 . This is not a second deployment; I tried to customize some parts of the ontoportal code and completely broke my distribution. I re-deployed from the AMI but my previous key had expired. Can you approve this request? Thanks! Coop, Ph.D. | Chief Al Officer Advent Health Partners, Inc. | 301 Plus Park Blvd., Suite 500, Nashville, TN 37217 (615) 933-0526 | AdventHP.com Access my calendar to schedule a meeting with me Connect with me on LinkedIn [https://adventhp.com/logo-advent-health/] [https://adventhp.com/adv-inc-5000-2020_esig/] Confidentiality Notice: The information contained in this transmission is privileged and confidential and/or protected health information (PHI) and may be subject to protection under the law, including the Health Insurance Portability and Accountability Act of 1996, as amended (HIPAA). This transmission is intended for the sole use of the individual or entity to whom it is addressed. If you are not the intended recipient, you are notified that any use, dissemination, distribution, printing or copying of this transmission is strictly prohibited and may subject you to criminal or civil penalties. If you have received this transmission in error, please contact the sender immediately by replying to this email and deleting/expunging this email and any attachments from any computer. From: John Graybeal > Sent: Saturday, December 11, 2021 1:24 PM To: Robert Coop > Subject: license request for OntoPortal You don't often get email from jgraybeal at stanford.edu. Learn why this is important CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hello, I received and approved your license request for the OntoPortal Appliance, on the understanding that this is an evaluation period for your use of the software. Please let me know if you have any trouble, or you can send requests to the public support list support at bioontology.org, where more people can see and respond to it. Should you wish to use the software in your commercial enterprise, we ask that you contact us to discuss regular licensing arrangements. We like to come to reasonable agreements that help us keep the software maintained and upgraded as needed for current semantic technologies. In case you are interested, we also run the OntoPortal Alliance (https://ontoportal.org), an organization that supports the public use and improvement of the OntoPortal Appliance. Participation is free to those who are using the Appliance as a publicly visible repository, and terms can be negotiated for commercial organizations who wish to play an active role in the Alliance. Please contact me if you are interested in further information about participating in the OntoPortal Appliance. Thank you for your interest and support! John ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ BioPortal and OntoPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 12 09:52:37 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 12 Jan 2022 17:52:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Muhammad Yahya In-Reply-To: <61debbf39e87e_340723fc4e09974@ncbo-prd-app-08.stanford.edu.mail> References: <61debbf39e87e_340723fc4e09974@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <6661E1AE-151B-41BD-BE90-59881B8C4481@stanford.edu> Hello Muhammad, I?ve searched our system extensively and don?t see any ontologies either with an ?MY? acronym, or a name of ?Muhammad yahya?. What is the full URL of your ontology summary page? I?m wondering if you are perhaps interacting with a different OntoPortal installation. Kind regards, Jennifer On Jan 12, 2022, at 3:30 AM, support at bioontology.org wrote: Name: Muhammad Yahya Email: muhammad.yahya at insight-centre.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I recently submitted an ontology with the name Muhammad yahya and the acronym MY. Can you please change its name to Reference Generalized Ontological model and its acronym to RGOM. I could not get it in the beginning and upload it with my name. Thank you. Regards, Muhammad Yahya _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From diller17 at ufl.edu Wed Jan 12 13:10:52 2022 From: diller17 at ufl.edu (Diller,Matthew A) Date: Wed, 12 Jan 2022 21:10:52 +0000 Subject: [bioontology-support] Fail to Load Ontology Error Message-ID: <2EA06050-CBE2-4D8F-B37C-AD08EE7D3413@ufl.edu> To who this may concern, I recently indexed an ontology in Bioportal and just received an email notifying me that there was an issue loading it from the URL I provided, despite this problem not appearing when I first created the Bioportal page for my ontology or in the month following that. I?m wondering if there is something on my end that needs to be done to fix this since there is nothing wrong with the URL I provided (it is still working and points at the correct file) or if this is a bug on your end. The URL in question is https://raw.githubusercontent.com/ufbmi/ORCS/master/orcs.owl and it is for the ORCS ontology (http://bioportal.bioontology.org/ontologies/ORCS). Thanks, Matt Diller PhD Candidate Department of Health Outcomes and Biomedical Informatics College of Medicine | University of Florida 2004 Mowry Road, Gainesville, FL 32603 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 12 14:16:47 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 12 Jan 2022 22:16:47 +0000 Subject: [bioontology-support] Fail to Load Ontology Error In-Reply-To: <2EA06050-CBE2-4D8F-B37C-AD08EE7D3413@ufl.edu> References: <2EA06050-CBE2-4D8F-B37C-AD08EE7D3413@ufl.edu> Message-ID: <06067223-4181-413D-8D76-54636046300A@stanford.edu> Hi Matt, I noticed a large number of load failures starting to come through last night, all of which involved ontology files served from the raw.githubusercontent.com domain. I checked a few of the URLs manually by entering them in a browser and none were accessible. I believe the problem was on GitHub?s end. Nevertheless, I?ll keep an eye on the load process again this evening to see if the same type of errors are occurring. Kind regards, Jennifer On Jan 12, 2022, at 1:10 PM, Diller,Matthew A > wrote: To who this may concern, I recently indexed an ontology in Bioportal and just received an email notifying me that there was an issue loading it from the URL I provided, despite this problem not appearing when I first created the Bioportal page for my ontology or in the month following that. I?m wondering if there is something on my end that needs to be done to fix this since there is nothing wrong with the URL I provided (it is still working and points at the correct file) or if this is a bug on your end. The URL in question is https://raw.githubusercontent.com/ufbmi/ORCS/master/orcs.owl and it is for the ORCS ontology (http://bioportal.bioontology.org/ontologies/ORCS). Thanks, Matt Diller PhD Candidate Department of Health Outcomes and Biomedical Informatics College of Medicine | University of Florida 2004 Mowry Road, Gainesville, FL 32603 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From elena.gelain at meyer.it Fri Jan 14 02:20:26 2022 From: elena.gelain at meyer.it (Elena Gelain) Date: Fri, 14 Jan 2022 11:20:26 +0100 (CET) Subject: [bioontology-support] getting information Message-ID: <200855028.20891916.1642155626354.JavaMail.zimbra@meyer.it> Dear all, this is just an explorative email to ask how the portal works. If I correctly understand the information (BioPortal help) web page, the browsing of the whole repository is free but the use of the ontologies for the mappings is not permitted for the locked or private repositories, such as SNOMED CT. Hence, to use the terminology I should refer to each Organization. Looking forward for your reply, I thank you for your attention, best regards, Elena Gelain Rare Diseases Unit Meyer Children?s Hospital Viale Pieraccini 24, 50139 Firenze, Italy e-mail: elena.gelain at meyer.it From vendetti at stanford.edu Fri Jan 14 09:28:49 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 14 Jan 2022 17:28:49 +0000 Subject: [bioontology-support] getting information In-Reply-To: <200855028.20891916.1642155626354.JavaMail.zimbra@meyer.it> References: <200855028.20891916.1642155626354.JavaMail.zimbra@meyer.it> Message-ID: <6DAAF6C6-68EB-4FC3-B936-AC91548E6EAF@stanford.edu> Hello Elena, On Jan 14, 2022, at 2:20 AM, Elena Gelain > wrote: Dear all, this is just an explorative email to ask how the portal works. If I correctly understand the information (BioPortal help) web page, the browsing of the whole repository is free but the use of the ontologies for the mappings is not permitted for the locked or private repositories, such as SNOMED CT. Hence, to use the terminology I should refer to each Organization. If an ontology is marked as ?private? in BioPortal, the content is only visible to those user accounts that have been granted access to the ontology entry. There are other ontologies like SNOMEDCT that are marked as ?public?, but licensing restrictions prohibit us from providing the ontology source files for download by end users. In other words, there are no ?Downloads? columns in the ?Submissions? tables on the ontology summary pages. However, that doesn?t mean that you can?t browse the ontology content for SNOMEDCT in BioPortal. For example, you can see the list of ontologies that have mappings to SNOMEDCT: https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=mappings ? and, you can see mappings between individual classes, e.g.: https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F362981000#mappings The mappings are also available via the BioPortal REST API, e.g.: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006/mappings Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From Huey.Hum at fda.hhs.gov Wed Jan 19 07:27:28 2022 From: Huey.Hum at fda.hhs.gov (Hum, Huey *) Date: Wed, 19 Jan 2022 15:27:28 +0000 Subject: [bioontology-support] Requesting latest MedDRA V.24.1 .ttl file for FDA Message-ID: Hi, My name is Huey and I work with the FDA Search 360 team which is an intra FDA search engine. We are looking to update the search terms on our platform to MedDRA V.24.1. Do you have the latest .ttl file that would cover the terms in V.24.1 release that we can leverage? Thank you for your help in advance. Best regards, Huey Hum FDA CDER | Contractor Office of Business Informatics (OBI) huey.hum at fda.hhs.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Jan 21 08:41:22 2022 From: support at bioontology.org (support at bioontology.org) Date: Fri, 21 Jan 2022 08:41:22 -0800 Subject: [bioontology-support] [BioPortal] Feedback from shawntanzk Message-ID: <61eae2328bc04_6fb31ed9bfc63455@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Jan 21 12:13:44 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 21 Jan 2022 20:13:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shawntanzk In-Reply-To: <61eae2328bc04_6fb31ed9bfc63455@ncbo-prd-app-08.stanford.edu.mail> References: <61eae2328bc04_6fb31ed9bfc63455@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <66F08EC5-0715-4144-8AAE-7B088F27DE97@stanford.edu> Hello, On Jan 21, 2022, at 8:41 AM, support at bioontology.org wrote: I refer to the provisional cell ontology which I am now managing. I have been trying to get the preferred name to use "http://www.w3.org/2000/01/rdf-schema#label" instead but have not been able to successfully do it despite putting that in the preferred name entry - instead it is still using http://www.w3.org/2004/02/skos/core#prefLabel. Wondering if I could get some help on this. I was able to reproduce the behavior here, even after fully reprocessing the ontology and flushing the application caches. I?ve entered an issue in our tracker for this problem: https://github.com/ncbo/ontologies_linked_data/issues/125 We?re short staffed at the moment, but will try to get to this as soon as we can. Apologies for the inconvenience. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From karin.colsman.contractor at osthus.com Mon Jan 24 01:14:31 2022 From: karin.colsman.contractor at osthus.com (Karin Colsman) Date: Mon, 24 Jan 2022 09:14:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from DG_Allotrope_AFO In-Reply-To: <18086064-E74D-4175-9D33-124280304AA5@stanford.edu> References: <61c19555d2efe_26451f646a81534@ncbo-prd-app-09.stanford.edu.mail> <18086064-E74D-4175-9D33-124280304AA5@stanford.edu> Message-ID: <24d5834d347e4cb0bcb34ee35ae26dc4@osthus.com> Dear Michael, it all looks good, thanks for fixing! Kind regards Karin From: Michael Dorf Sent: Dienstag, 4. Januar 2022 19:57 To: support at bioontology.org Cc: DG_Allotrope_AFO Subject: Re: [bioontology-support] [BioPortal] Feedback from DG_Allotrope_AFO Hi Karin, Thank you for your inquiry. There was a strange data discrepancy with AFO ontology that prevented you from submitting a new version. This error happens occasionally, and we haven?t had the means to track it down yet. I?ve addressed the issue in our backend and re-submitted the latest version of your ontology, pulled directly from http://purl.allotrope.org/voc/afo/latest.ttl. It?s now fully processed and ready for use. Let us know if you experience further issues. Thank you for your patience. Michael On Dec 21, 2021, at 12:50 AM, support at bioontology.org wrote: Name: DG_Allotrope_AFO Email: DG_Allotrope_AFO at osthus.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Dear Bioportal team, We are having a problem with getting our newest version of AFO published. The autoupdate from http://purl.allotrope.org/voc/afo/latest.ttl did not produce a new version, although the file was updated on Friday. I tried submitting the new file manually via https://bioportal.bioontology.org/ontologies/AFO/submissions, but I am blocked by the following error message: Errors On Form [:error, #>] Could you please take a look? Thank you! Karin Colsman _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.x.wan at gsk.com Tue Jan 25 08:25:39 2022 From: stephen.x.wan at gsk.com (Stephen Wan) Date: Tue, 25 Jan 2022 16:25:39 +0000 Subject: [bioontology-support] Server Error Message-ID: Hi, I'm currently developing a Python program to find the latest version of ontologies. I was able to successfully get the info until today. I'm currently getting the below errors, via API, browser and browser. Can you please check my account (login swan) to see if there are any issues. Thank you in advance. API error returned (API key was ok this morning) status":401,"error":"You must provide a valid API Key. Your API Key can be obtained by logging in at bioportal.bioontology.org/account Browser Error when Signing into account swan 500 Internal Server Error If you are the administrator of this website, then please read this web application's log file and/or the web server's log file to find out what went wrong. Regards, Stephen Wan Senior Engineer, Data Quality & Governance R&D Data Platform and Solutions GSK GlaxoSmithKline | Gunnelswood Road | Stevenage | Herts | SG1 2NY | UK Email stephen.x.wan at gsk.com gsk.com | Twitter | YouTube | Facebook | Flickr [cid:image001.png at 01D81208.2FF58ED0] [Misc_Responsibility_DG_POS_RGB.png] Please consider the environment before printing this email GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation. ________________________________ This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 17326 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 1449 bytes Desc: image002.png URL: From plwhetzel at gmail.com Tue Jan 25 09:22:17 2022 From: plwhetzel at gmail.com (Trish Whetzel) Date: Tue, 25 Jan 2022 09:22:17 -0800 Subject: [bioontology-support] BioPortal is down Message-ID: Hi all, I'm trying to access BioPortal from the web, but I'm getting an error message that something has gone wrong. Is there a known downtime today? Best, Trish -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jan 25 09:59:33 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 25 Jan 2022 17:59:33 +0000 Subject: [bioontology-support] BioPortal is down In-Reply-To: References: Message-ID: <64D3815E-C144-4236-8A09-992ACFB5FF2A@stanford.edu> Hi Trish, Hope you?re doing well, it?s great to hear from you! Sorry, but we experienced an unscheduled downtime earlier this morning. The system is now back up. Let us know if are still seeing anything abnormal. Thank you, Michael On Jan 25, 2022, at 9:22 AM, Trish Whetzel > wrote: Hi all, I'm trying to access BioPortal from the web, but I'm getting an error message that something has gone wrong. Is there a known downtime today? Best, Trish _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jan 25 10:04:00 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 25 Jan 2022 18:04:00 +0000 Subject: [bioontology-support] Server Error In-Reply-To: References: Message-ID: Hi Stephen, We?ve had an unscheduled downtime this morning, which affected both the front- and back-end BioPortal services. The system has now been restored. Please let us know if your issue persists. Thank you, --- Michael Dorf Chief Software Architect National Center for Biomedical Ontology (NCBO) Stanford Center for Biomedical Informatics Research (BMIR) Stanford University mdorf at stanford.edu 650-723-0357 On Jan 25, 2022, at 8:25 AM, Stephen Wan > wrote: Hi, I?m currently developing a Python program to find the latest version of ontologies. I was able to successfully get the info until today. I?m currently getting the below errors, via API, browser and browser. Can you please check my account (login swan) to see if there are any issues. Thank you in advance. API error returned (API key was ok this morning) status":401,"error":"You must provide a valid API Key. Your API Key can be obtained by logging in at bioportal.bioontology.org/account Browser Error when Signing into account swan 500 Internal Server Error If you are the administrator of this website, then please read this web application's log file and/or the web server's log file to find out what went wrong. Regards, Stephen Wan Senior Engineer, Data Quality & Governance R&D Data Platform and Solutions GSK GlaxoSmithKline | Gunnelswood Road | Stevenage | Herts | SG1 2NY | UK Email stephen.x.wan at gsk.com gsk.com | Twitter | YouTube | Facebook | Flickr Please consider the environment before printing this email GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation. ________________________________ This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 26 01:02:54 2022 From: support at bioontology.org (support at bioontology.org) Date: Wed, 26 Jan 2022 01:02:54 -0800 Subject: [bioontology-support] [BioPortal] Feedback from felix engel Message-ID: <61f10e3e2301f_66bb148e3f080d7@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 26 10:13:40 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 26 Jan 2022 18:13:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from felix engel In-Reply-To: <61f10e3e2301f_66bb148e3f080d7@ncbo-prd-app-09.stanford.edu.mail> References: <61f10e3e2301f_66bb148e3f080d7@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Felix, Thank you for your nice comment. Without knowing your specific application of BioPortal, it?s a bit subjective for me to give you a pointed answer. You can do a general search for ?BioPortal? on Google Scholar, which yields a number of relevant publications: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=bioportal&btnG= Though some of these are dated, the general purpose of BioPortal has remained unchanged: provide an online repository and tools for biomedical ontologies. Here is a relevant research paper: https://www.sciencedirect.com/science/article/pii/S153204641730120X You can also check out our Projects page, which has a sampling of third party resources that utilize BioPortal: https://bioportal.bioontology.org/projects Another resource to consider is the OntoPortal Alliance, which uses the BioPortal technology to promote semantic services in scientific research: https://ontoportal.org/ If you are interested in the technical aspects of BioPortal, we publish a virtual appliance that you can install and configure locally. Browse the relevant documentation here: https://ontoportal.github.io/administration/ Hope this helps. Thank you, --- Michael Dorf Chief Software Architect National Center for Biomedical Ontology (NCBO) Stanford Center for Biomedical Informatics Research (BMIR) Stanford University mdorf at stanford.edu 650-723-0357 On Jan 26, 2022, at 1:02 AM, support at bioontology.org wrote: Name: felix engel Email: felix.engel at tib.eu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fhelp Feedback: Hi, first of all, many thanks to provide such a great tool! I am employed at the TIB in Hannover Germany and we are working heavily with ontologies and terminologies, in general with respect to the engineering domain. I am interested in some more infromation about the general usage of BioPortal. Is there a publication or a link that you can provide me? many thanks nd all the best Felix _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From Felix.Engel at tib.eu Thu Jan 27 00:21:15 2022 From: Felix.Engel at tib.eu (Engel, Felix) Date: Thu, 27 Jan 2022 08:21:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from felix engel In-Reply-To: References: <61f10e3e2301f_66bb148e3f080d7@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <84bf2eb085324b3883d2742f21884231@tib.eu> Hi Michael, many thanks for your swift reply! I was aware of most of the links you send in your reply. I haven?t read ?An empirical analysis of ontology reuse in BioPortal? which is really interesting. So thanks again for this. Concerning my background: I am working on a Terminology Service for engineers for a big German RDM Infrastructure initiative. Currently on basis of OLS, please have a look if you are interested: https://terminology.nfdi4ing.de/ts4ing/index I am aware of BioPortal since many years and really enjoyed its development an clearly structured interfaces. However, the engineering domain is quite different compared to the Biomedical one. Now, I am quite interested to understand better who is using yours and other Terminology Services, for what reasons. I found an interesting UMLS related paper: https://academic.oup.com/jamia/article/27/10/1606/5873605?login=false and was wondering if there is something similar available for BioPortal? All the best Felix Von: Michael Dorf [mailto:mdorf at stanford.edu] Gesendet: Mittwoch, 26. Januar 2022 19:14 An: support at bioontology.org Cc: Engel, Felix Betreff: Re: [bioontology-support] [BioPortal] Feedback from felix engel Hi Felix, Thank you for your nice comment. Without knowing your specific application of BioPortal, it?s a bit subjective for me to give you a pointed answer. You can do a general search for ?BioPortal? on Google Scholar, which yields a number of relevant publications: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=bioportal&btnG= Though some of these are dated, the general purpose of BioPortal has remained unchanged: provide an online repository and tools for biomedical ontologies. Here is a relevant research paper: https://www.sciencedirect.com/science/article/pii/S153204641730120X You can also check out our Projects page, which has a sampling of third party resources that utilize BioPortal: https://bioportal.bioontology.org/projects Another resource to consider is the OntoPortal Alliance, which uses the BioPortal technology to promote semantic services in scientific research: https://ontoportal.org/ If you are interested in the technical aspects of BioPortal, we publish a virtual appliance that you can install and configure locally. Browse the relevant documentation here: https://ontoportal.github.io/administration/ Hope this helps. Thank you, --- Michael Dorf Chief Software Architect National Center for Biomedical Ontology (NCBO) Stanford Center for Biomedical Informatics Research (BMIR) Stanford University mdorf at stanford.edu 650-723-0357 On Jan 26, 2022, at 1:02 AM, support at bioontology.org wrote: Name: felix engel Email: felix.engel at tib.eu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fhelp Feedback: Hi, first of all, many thanks to provide such a great tool! I am employed at the TIB in Hannover Germany and we are working heavily with ontologies and terminologies, in general with respect to the engineering domain. I am interested in some more infromation about the general usage of BioPortal. Is there a publication or a link that you can provide me? many thanks nd all the best Felix _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From rob.taylor at vumc.org Thu Jan 27 07:32:19 2022 From: rob.taylor at vumc.org (Taylor, Rob) Date: Thu, 27 Jan 2022 15:32:19 +0000 Subject: [bioontology-support] [BioPortal] Issues with HGNC ontology search Message-ID: Hi John, We've had some reports recently from REDCap users in which searches to the HGNC ontology via https://bioportal.bioontology.org/search do not seem to return any results, even when typing a known keyword that should return results. We were just wondering if you or your folks who run the service are aware of this issue. Thanks for any help you can provide. Rob Taylor Manager of Application Development Vanderbilt University Medical Center, VICTR 2525 West End Ave, Suite 1060 | Nashville, TN 37203 Email: rob.taylor at vumc.org Website: https://projectredcap.org [REDCap logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 9092 bytes Desc: image001.png URL: From mdorf at stanford.edu Fri Jan 28 11:20:11 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Jan 2022 19:20:11 +0000 Subject: [bioontology-support] [BioPortal] Issues with HGNC ontology search In-Reply-To: References: Message-ID: <8386CF0F-247A-42F7-A43B-253EB322813F@stanford.edu> Hi Rob, I?ve run a few searches on HGNC ontology on my end, and they all yielded results (screenshot below). We did have a brief outage earlier in the week; it?s possible that it may have coincided with the users? attempts at searches. Are you still experiencing this issue? [cid:7FAD0554-53EC-4316-BA8D-ADD39D6EF322] Thank you, --- Michael Dorf Chief Software Architect National Center for Biomedical Ontology (NCBO) Stanford Center for Biomedical Informatics Research (BMIR) Stanford University mdorf at stanford.edu 650-723-0357 On Jan 27, 2022, at 7:32 AM, Taylor, Rob > wrote: Hi John, We?ve had some reports recently from REDCap users in which searches to the HGNC ontology via https://bioportal.bioontology.org/search do not seem to return any results, even when typing a known keyword that should return results. We were just wondering if you or your folks who run the service are aware of this issue. Thanks for any help you can provide. Rob Taylor Manager of Application Development Vanderbilt University Medical Center, VICTR 2525 West End Ave, Suite 1060 | Nashville, TN 37203 Email: rob.taylor at vumc.org Website: https://projectredcap.org _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-01-28 at 11.14.59 AM.png Type: image/png Size: 223985 bytes Desc: Screen Shot 2022-01-28 at 11.14.59 AM.png URL: From rob.taylor at vumc.org Fri Jan 28 12:02:05 2022 From: rob.taylor at vumc.org (Taylor, Rob) Date: Fri, 28 Jan 2022 20:02:05 +0000 Subject: [bioontology-support] [BioPortal] Issues with HGNC ontology search In-Reply-To: <8386CF0F-247A-42F7-A43B-253EB322813F@stanford.edu> References: <8386CF0F-247A-42F7-A43B-253EB322813F@stanford.edu> Message-ID: Michael, Thanks for responding quickly. Yes, I can confirm that it's working again. It must've been the outage affecting our users. It's all good now. Thanks so much! Rob Taylor Manager of Application Development Vanderbilt University Medical Center, VICTR 2525 West End Ave, Suite 1060 | Nashville, TN 37203 Email: rob.taylor at vumc.org Website: https://projectredcap.org [REDCap logo] From: Michael Dorf Sent: Friday, January 28, 2022 1:20 PM To: Taylor, Rob Cc: John Graybeal ; support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Issues with HGNC ontology search Hi Rob, I've run a few searches on HGNC ontology on my end, and they all yielded results (screenshot below). We did have a brief outage earlier in the week; it's possible that it may have coincided with the users' attempts at searches. Are you still experiencing this issue? [cid:image002.png at 01D8144F.A0D53990] Thank you, --- Michael Dorf Chief Software Architect National Center for Biomedical Ontology (NCBO) Stanford Center for Biomedical Informatics Research (BMIR) Stanford University mdorf at stanford.edu 650-723-0357 On Jan 27, 2022, at 7:32 AM, Taylor, Rob > wrote: Hi John, We've had some reports recently from REDCap users in which searches to the HGNC ontology via https://bioportal.bioontology.org/search do not seem to return any results, even when typing a known keyword that should return results. We were just wondering if you or your folks who run the service are aware of this issue. Thanks for any help you can provide. Rob Taylor Manager of Application Development Vanderbilt University Medical Center, VICTR 2525 West End Ave, Suite 1060 | Nashville, TN 37203 Email: rob.taylor at vumc.org Website: https://projectredcap.org _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support [ WARNING : This email came from an external source. Please treat this message with additional caution.] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 12854 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 223985 bytes Desc: image002.png URL: