From jgraybeal at stanford.edu Mon Feb 1 15:05:02 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 1 Feb 2021 23:05:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maarten Boers In-Reply-To: <601404aff1b42_6eae20215b4495c@ncbo-prd-app-09.stanford.edu.mail> References: <601404aff1b42_6eae20215b4495c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <74FE1BF4-9027-459E-99B7-2616004607C9@stanford.edu> Marrten, Sorry, this problem is due to some issues we are having processing the MedDRA file from UMLS. We are investigating the cause of the issue, and meanwhile can only show the search bar for this ontology. You can follow our progress on the ticket https://github.com/ncbo/bioportal-project/issues/202. John On Jan 29, 2021, at 4:50 AM, support at bioontology.org wrote: Name: Maarten Boers Email: m.boers at amsterdamumc.nl Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Droot Feedback: Hi, I'm ising the bioportal to search Meddra for academic use. Prviously I used the tree to explore terms, but I can't access it any more,I only get a search field to search classes. How do I regain access to the tree? Thx, M _______________________________________________ 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 vendetti at stanford.edu Mon Feb 1 15:47:15 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 1 Feb 2021 23:47:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Miller In-Reply-To: <60122575cf588_1e5726c080c842ba@ncbo-prd-app-08.stanford.edu.mail> References: <60122575cf588_1e5726c080c842ba@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <38EBE74F-FA70-4E17-A0BA-8F52353E8F7B@stanford.edu> Hello Mark, On Jan 27, 2021, at 6:46 PM, support at bioontology.org wrote: Name: Mark Miller Email: mark.miller at igedla.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fsearch Feedback: How do I apply for or get an API key? Thanks Instructions are available on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Feb 1 15:59:53 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 1 Feb 2021 23:59:53 +0000 Subject: [bioontology-support] Download DRON as OWL? In-Reply-To: References: Message-ID: <169D6D55-58A6-4849-A814-BE68DDE96D90@stanford.edu> Hello Mason, I reproduced the issue in Chrome - it?s a mixed content error: Mixed Content: The site at 'https://bioportal.bioontology.org/' was loaded over a secure connection, but the file at 'http://data.bioontology.org/ontologies/DRON/submissions/12/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb' was redirected through an insecure connection. This file should be served over HTTPS. This download has been blocked. See https://blog.chromium.org/2020/02/protecting-users-from-insecure.html for more details. The problem is on our end, and we?ll need to get this fixed. In the mean time though, you should be able to use Firefox or Safari to download the file successfully. Apologies for the inconvenience. Kind regards, Jennifer On Jan 28, 2021, at 11:39 AM, Edmison, Mason > wrote: Hello, I am trying to download the Drug Ontology (from < https://bioportal.bioontology.org/ontologies/DRON>) as OWL but the download never starts. Is this something you can help me with? Best, Mason _______________________________________________ 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 Thu Feb 4 09:09:30 2021 From: support at bioontology.org (support at bioontology.org) Date: Thu, 04 Feb 2021 09:09:30 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Daniel Chang Message-ID: <601c2a4aa50ce_364e28a0230620cb@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 4 09:24:03 2021 From: support at bioontology.org (support at bioontology.org) Date: Thu, 04 Feb 2021 09:24:03 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Daniel Chang Message-ID: <601c2db3bb234_4c7826f07009946@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Feb 4 14:31:59 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 4 Feb 2021 22:31:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Daniel Chang In-Reply-To: <601c2db3bb234_4c7826f07009946@ncbo-prd-app-09.stanford.edu.mail> References: <601c2db3bb234_4c7826f07009946@ncbo-prd-app-09.stanford.edu.mail> Message-ID: No problem Daniel. I see that you have an account under your email address, with the account name of "Hope Biosciences Stem Cell Research Foundation". Have you tried logging in to that account? The 5-word account name with spaces is what you will need to use to log in, and since it has spaces you might also try "Hope\ Biosciences\ Stem\ Cell\ Research\ Foundation". I just created an account twice without any difficulty. Since it just requires filling out all the fields, my guess is that BioPortal had a brief hiccup while you were creating the account, and cached the error result, either within BioPortal or within your system. (I thought it might be that you were using the same email address, but I created both my accounts with the same email address.) But the user name that you enter has to be different, of course. If you don't have access to the account we found above (as it's an unusually long account name), we have flushed the caches on our end, so I suggest you flush your browser cache, or perhaps better, start from a different browser, and try again. If you send us a screenshot of the filled out form that might help us troubleshoot. John On Feb 4, 2021, at 9:24 AM, support at bioontology.org wrote: Name: Daniel Chang Email: daniel at hopebio.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Sorry. I just sent a previous inquiry w/o much context. I am representing on behalf of Hope Biosciences Stem Cell Research Foundation, a non-profit org and active member of the REDCap Consortium. We use REDCap EDC to support our clinical research and came across a module that can greatly help benefit our coding standardization: https://github.com/ctsit/ae_and_conmeds We learned that we need the BioPortal Token to enable the biomedical ontology search feature on our REDCap instance. We tried creating an account, but was prompted with an error. If you can please share what must be done to successfully onboard to the bioportal platform, it would be much appreciated. Thank you, Daniel 832-438-6222 _______________________________________________ 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 heike.goerzig at helmholtz-berlin.de Fri Feb 5 01:57:13 2021 From: heike.goerzig at helmholtz-berlin.de (=?utf-8?B?R8O2cnppZywgSGVpa2U=?=) Date: Fri, 5 Feb 2021 09:57:13 +0000 Subject: [bioontology-support] preventing wrong mappings Message-ID: Dear bioontology Team, we are creating an ontology we are planning to upload to the bioportal. As the mapping is done automatically on labels and maybe the description, there might be created some false mappings. We would like to prevent this. Would owl:disjointWith along a related ontologie be an option? Thanks, Heike -- Heike G?rzig Helmholtz-Zentrum Berlin f?r Materialien und Energie (HZB) Albert-Einstein-Str. 15, 12489 Berlin Tel.: +49 30 8062 42683 -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 6785 bytes Desc: not available URL: From lore at illinois.edu Fri Feb 5 14:55:21 2021 From: lore at illinois.edu (Lore, Michelle H) Date: Fri, 5 Feb 2021 22:55:21 +0000 Subject: [bioontology-support] API Security Message-ID: Hello, I'm a REDCap administrator at University of Illinois at Urbana-Champaign. We're looking to enable the biomedical ontology auto-suggest functionality that REDCap provides, and our campus security is requesting information about the API security of the BioPortal API. I looked on the API documentation page and throughout the NCBO website and could not find anything explicitly about API security. Any additional information you can provide is appreciated. Thank you, Michelle Michelle Lore, MS (she/her) REDCap Application Specialist Interdisciplinary Health Sciences Institute University of Illinois | Urbana-Champaign 901 W. University Avenue, Suite 201 | MC-261 | Urbana, IL 61801 Phone: (217) 244-9666 | Email: lore at illinois.edu Website: https://healthinstitute.illinois.edu/ Twitter: https://twitter.com/IllinoisIHSI -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Feb 5 19:25:30 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 6 Feb 2021 03:25:30 +0000 Subject: [bioontology-support] preventing wrong mappings In-Reply-To: References: Message-ID: <90D9423D-7FB6-4A90-96B9-341B1594A2FE@stanford.edu> Heike, That's a great idea! But no, unfortunately the automated mappings are pretty simple-minded, without any particular augmentation. While we find the mappings are about 85% valid, it is understood by most who use them that they are more in the way of discovery tools, not so much modeling tools. (The mappings created in this way are noted as LOOM mappings in the UI and the API, so they can be identified.) It is of course still useful information to signal readers and machines that any similarity mappings should be ignored for those relations, and maybe we could pick upon it when we find resources to improve the mappings algorithm. It is not a perfect solution however; there will be cases where two classes should not be mapped as being similar, but in fact their may be some instances that could belong to both classes. Another challenge is that our automated mappings are done across ontologies (not within ontologies, to my knowledge); and you would have to update your disjoint statements regularly to reflect incorrect mappings to newly added ontology terms in BioPortal. John On Feb 5, 2021, at 1:57 AM, G?rzig, Heike > wrote: Dear bioontology Team, we are creating an ontology we are planning to upload to the bioportal. As the mapping is done automatically on labels and maybe the description, there might be created some false mappings. We would like to prevent this. Would owl:disjointWith along a related ontologie be an option? Thanks, Heike -- Heike G?rzig > Helmholtz-Zentrum Berlin f?r Materialien und Energie (HZB) Albert-Einstein-Str. 15, 12489 Berlin Tel.: +49 30 8062 42683 _______________________________________________ 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 jgraybeal at stanford.edu Fri Feb 5 19:38:41 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 6 Feb 2021 03:38:41 +0000 Subject: [bioontology-support] API Security In-Reply-To: References: Message-ID: <02774914-7237-4851-8898-78C9DFED6D4F@stanford.edu> Michelle, I'm sorry, but despite some awareness of security concerns, I'm not familiar with the precise meaning of the term "API security". The top few references on the web indicate it is a bit of an abstract concept, e.g., "the application of any security best practice applied to web APIs." So that doesn't help you too much, but I can give you a few pieces of information you can pass along to your campus security. We use REST API services with per-user API keys, TLS encryption (https) and rate limits. (There are some public services that do not require API keys.) We do not additionally encrypt our message packets, since the TLS encryption provides encryption for them (and also enforces appropriately secure signatures on the transaction). I hope that is enough information for you and them. We are used by upwards of 75 university and similar installations, and we have not had concerns expressed or security questions asked (to my knowledge), so I hope but can not promise that is some indication of the suitability of our security for this heavily accessed research system. John On Feb 5, 2021, at 2:55 PM, Lore, Michelle H > wrote: Hello, I?m a REDCap administrator at University of Illinois at Urbana-Champaign. We?re looking to enable the biomedical ontology auto-suggest functionality that REDCap provides, and our campus security is requesting information about the API security of the BioPortal API. I looked on the API documentation page and throughout the NCBO website and could not find anything explicitly about API security. Any additional information you can provide is appreciated. Thank you, Michelle Michelle Lore, MS (she/her) REDCap Application Specialist Interdisciplinary Health Sciences Institute University of Illinois | Urbana-Champaign 901 W. University Avenue, Suite 201 | MC-261 | Urbana, IL 61801 Phone: (217) 244-9666 | Email: lore at illinois.edu Website: https://healthinstitute.illinois.edu/ Twitter: https://twitter.com/IllinoisIHSI _______________________________________________ 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 Sun Feb 7 09:20:26 2021 From: support at bioontology.org (support at bioontology.org) Date: Sun, 07 Feb 2021 09:20:26 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Kirstin Fearnhead Message-ID: <6020215a598a5_3b23297fb6029641@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From lore at illinois.edu Mon Feb 8 06:35:56 2021 From: lore at illinois.edu (Lore, Michelle H) Date: Mon, 8 Feb 2021 14:35:56 +0000 Subject: [bioontology-support] API Security In-Reply-To: <02774914-7237-4851-8898-78C9DFED6D4F@stanford.edu> References: <02774914-7237-4851-8898-78C9DFED6D4F@stanford.edu> Message-ID: Thank you, John! I appreciate your response. Thanks again, Michelle From: John Graybeal Sent: Friday, February 5, 2021 9:39 PM To: Lore, Michelle H Cc: support at bioontology.org Subject: Re: [bioontology-support] API Security Michelle, I'm sorry, but despite some awareness of security concerns, I'm not familiar with the precise meaning of the term "API security". The top few references on the web indicate it is a bit of an abstract concept, e.g., "the application of any security best practice applied to web APIs." So that doesn't help you too much, but I can give you a few pieces of information you can pass along to your campus security. We use REST API services with per-user API keys, TLS encryption (https) and rate limits. (There are some public services that do not require API keys.) We do not additionally encrypt our message packets, since the TLS encryption provides encryption for them (and also enforces appropriately secure signatures on the transaction). I hope that is enough information for you and them. We are used by upwards of 75 university and similar installations, and we have not had concerns expressed or security questions asked (to my knowledge), so I hope but can not promise that is some indication of the suitability of our security for this heavily accessed research system. John On Feb 5, 2021, at 2:55 PM, Lore, Michelle H > wrote: Hello, I?m a REDCap administrator at University of Illinois at Urbana-Champaign. We?re looking to enable the biomedical ontology auto-suggest functionality that REDCap provides, and our campus security is requesting information about the API security of the BioPortal API. I looked on the API documentation page and throughout the NCBO website and could not find anything explicitly about API security. Any additional information you can provide is appreciated. Thank you, Michelle Michelle Lore, MS (she/her) REDCap Application Specialist Interdisciplinary Health Sciences Institute University of Illinois | Urbana-Champaign 901 W. University Avenue, Suite 201 | MC-261 | Urbana, IL 61801 Phone: (217) 244-9666 | Email: lore at illinois.edu Website: https://healthinstitute.illinois.edu/ Twitter: https://twitter.com/IllinoisIHSI _______________________________________________ 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 Mon Feb 8 10:34:46 2021 From: support at bioontology.org (support at bioontology.org) Date: Mon, 08 Feb 2021 10:34:46 -0800 Subject: [bioontology-support] [BioPortal] Feedback from mriyayi Message-ID: <60218446926ad_5cf725226449519@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From MRIYAYI at hotmail.com Mon Feb 8 10:38:52 2021 From: MRIYAYI at hotmail.com (DANIEL IYAYI) Date: Mon, 8 Feb 2021 18:38:52 +0000 Subject: [bioontology-support] Error Message - https://bioportal.bioontology.org/ontologies/PANET Message-ID: Hi, I have uploaded an OWL file to https://bioportal.bioontology.org/ontologies/PANET. It is intermittently showing an error 'problem retrieving classes'. [cid:9668f2a6-5c05-462c-9728-5aedd51af245] It worked last Friday and nothing has changed since then. Please can you investigate Kind regards Dan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 29600 bytes Desc: image.png URL: From jgraybeal at stanford.edu Mon Feb 8 14:15:55 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 8 Feb 2021 22:15:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Kirstin Fearnhead In-Reply-To: <6020215a598a5_3b23297fb6029641@ncbo-prd-app-08.stanford.edu.mail> References: <6020215a598a5_3b23297fb6029641@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Kirstin, I believe we'll need some more precise description, with examples, of how you are searching for/looking up these codes, with examples of what you would expect and what does not seem to be working, with more detail about the two systems on which you are looking up these codes. I can see (on my Mac) that some terms, e.g., Carcinoma (http://purl.bioontology.org/ontology/SNOMEDCT/68453008) have a code in the attribute 'ICD-O-3 Code' which appears to be the M code of which you speak. (We are not familiar with the domain ourselves but this seemed consistent based on Google research. ;->) But I can't tell exactly what steps you are performing in order to try to duplicate the problem you are seeing. John On Feb 7, 2021, at 9:20 AM, support at bioontology.org wrote: Name: Kirstin Fearnhead Email: kirsty at drkf.co.za Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F711329002 Feedback: I was using this site to look up the SNOMED morphology M-codes. For some reason when i search on My MAcbook i get these codes when i search and can look them up, but on my other laptop the M-codes will just not appear. Where do i find them or what setting do i change in order for them to come up? _______________________________________________ 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 jgraybeal at stanford.edu Mon Feb 8 16:29:15 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 9 Feb 2021 00:29:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mriyayi In-Reply-To: <60218446926ad_5cf725226449519@ncbo-prd-app-08.stanford.edu.mail> References: <60218446926ad_5cf725226449519@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <87CB7063-37FE-4E6D-AB4A-FC1ABE0229F0@stanford.edu> Hello Dan, i'm responding here to both your contacts from today, they each had useful information. The ontology Classes tab is consistently showing an error for me as of mid-day Pacific Time today. I have a theory about why it seemed to change "later", and a theory about what's wrong, but I'm not 100% confident in either. Unfortunately I'm not an ontology expert and we are a very resource-limited, but this will hopefully provide some insight about what has happened and what you might try. ** What's failing ** I'll start with the reason BioPortal is failing to display the ontology classes: it is unable to find the root class for your ontology tree. So it displays one or another error. If I open your ontology in Protege, I see that there is an apparent root class, OBI_0000070. But it seems Protege is not recognizing your entities below that?it is showing the full string for them within angle brackets < >. ** Ontology diagnosis ** The ExPaNDS:' notation would expand into a full IRI if it could, but ExPaNDS is not included in the ontology prefixes. So these may not be expanding into valid IRIs. (Protege often does its best to parse cases like this anyway, so the absence of errors does not mean the ontology is well-formed.) In addition, there are unescaped spaces in your IRI terms, I verified some of this by plugging your ontology into http://visualdataweb.de/validator/validate, which indicated in the first parser that it tried (RDF) that the expansion in line 51 did not result in an appropriate IRI. Removing the space seemed to fix that issue. I didn't try removing all the spaces for lack of time. You might want ** Why you didn't see this Friday ** I am guessing what changed 'after Friday' is that when you first made changes to your ontology on Friday, they had not been fully reflected in the Classes page display, which can be cached internally in BioPortal for some hours, or even in your browser cache. So you could have been seeing working data from a previous submission, which eventually went away after the cache expired in BioPortal and/or in your browser. I apologize that these delays sometimes happen, I know it is annoyingly confusing. ** What you can try ** Of course you can try eliminating all the spaces and providing the prefix expansion for that ExPaNDS notation, that might take care of it. Getting the file to pass the validator is probably an important step. Or, if you go back to an ontology you know worked, you could resubmit it and see if (after an appropriate period of time, I'd say that's 2 hours followed by clearing your browser cache) BioPortal begins showing classes again. If you are unable to make the ontology work after addressing those issues, resubmit your question with the current symptoms and we'll see if there's anything we can add. John [cid:085101EB-0DF0-4D82-BD29-9D264A187BCE] [cid:B9ED41D0-2E20-4BF6-9BD8-3399FE02F457] On Feb 8, 2021, at 10:34 AM, support at bioontology.org wrote: Name: mriyayi Email: mriyayi at hotmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPANET Feedback: Hi, Regarding https://bioportal.bioontology.org/ontologies/PANET. The Classes tab is intermittently showing 'Problem retrieving classes'. The OWL file uploaded seems to be fine. Please can you investigate and let us know. Kind regards Dan From: DANIEL IYAYI > Subject: [bioontology-support] Error Message - https://bioportal.bioontology.org/ontologies/PANET Date: February 8, 2021 at 10:38:52 AM PST To: "support at bioontology.org" >, "Collins, Steve (DLSLtd,RAL,SCI)" > Hi, I have uploaded an OWL file to https://bioportal.bioontology.org/ontologies/PANET. It is intermittently showing an error 'problem retrieving classes'. [cid:9668f2a6-5c05-462c-9728-5aedd51af245] It worked last Friday and nothing has changed since then. Please can you investigate Kind regards Dan _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-02-08 at 4.04.46 PM.png Type: image/png Size: 225491 bytes Desc: Screen Shot 2021-02-08 at 4.04.46 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... 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URL: From support at bioontology.org Mon Feb 15 10:46:55 2021 From: support at bioontology.org (support at bioontology.org) Date: Mon, 15 Feb 2021 18:46:55 -0000 Subject: [bioontology-support] [BioPortal] Feedback from Ray Lee Message-ID: <602ac1917c8de_1fbd24fe4c4867e1@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Lisa.Hopcroft at phs.scot Mon Feb 22 08:03:32 2021 From: Lisa.Hopcroft at phs.scot (Lisa Hopcroft) Date: Mon, 22 Feb 2021 16:03:32 +0000 Subject: [bioontology-support] Question regarding MedDRA hierarchy viewing Message-ID: Hello, I used to be able to view a MedDRA preferred term in the context of the MedDRA hierarchy, and therefore be able to map the preferred term to an System of Classification (SoC) term. This seems to have been removed from the website, is this accidental or has this functionality purposefully been removed? Thank you, Lisa Lisa Hopcroft Principal Information Analyst / Clinical Trials Statistician Public Health Scotland Phone: 0141 282 2119 E-mail: Lisa.Hopcroft at phs.scot Please note my new email address. [Teams-20x20] Chat with me on teams [email-sig] -------------------------------------------------------------------------------------------------------------------------------------------------------- This email is intended for the named recipient only. If you have received it by mistake, please (i) contact the sender by email reply; (ii) delete the email from your system; . and (iii) do not copy the email or disclose its contents to anyone. -------------------------------------------------------------------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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URL: From mriyayi at hotmail.com Thu Feb 11 23:28:28 2021 From: mriyayi at hotmail.com (DANIEL IYAYI) Date: Fri, 12 Feb 2021 07:28:28 -0000 Subject: [bioontology-support] [BioPortal] Feedback from mriyayi In-Reply-To: <87CB7063-37FE-4E6D-AB4A-FC1ABE0229F0@stanford.edu> References: <60218446926ad_5cf725226449519@ncbo-prd-app-08.stanford.edu.mail>, <87CB7063-37FE-4E6D-AB4A-FC1ABE0229F0@stanford.edu> Message-ID: Thanks John, I have made some alterations, and uploaded a new version. I have yet to create the expands namespace but the plan is to use purl or w3 to do this (perhaps this is the root cause of the problem) Initially, I was able to see the classes in Bioportal when I use google chrome (see below) but when I cleared the cache it disappeared. It was not visible when I use internet explorer or microsoft edge as a browser. [cid:052a72f8-15e9-4954-a801-83fb0bb54048] My collegues cannot see the classes in any browser. Kind regards Dan ________________________________ From: John Graybeal Sent: 09 February 2021 00:29 To: support at bioontology.org Cc: mriyayi at hotmail.com Subject: Re: [bioontology-support] [BioPortal] Feedback from mriyayi Hello Dan, i'm responding here to both your contacts from today, they each had useful information. The ontology Classes tab is consistently showing an error for me as of mid-day Pacific Time today. I have a theory about why it seemed to change "later", and a theory about what's wrong, but I'm not 100% confident in either. Unfortunately I'm not an ontology expert and we are a very resource-limited, but this will hopefully provide some insight about what has happened and what you might try. ** What's failing ** I'll start with the reason BioPortal is failing to display the ontology classes: it is unable to find the root class for your ontology tree. So it displays one or another error. If I open your ontology in Protege, I see that there is an apparent root class, OBI_0000070. But it seems Protege is not recognizing your entities below that?it is showing the full string for them within angle brackets < >. ** Ontology diagnosis ** The ExPaNDS:' notation would expand into a full IRI if it could, but ExPaNDS is not included in the ontology prefixes. So these may not be expanding into valid IRIs. (Protege often does its best to parse cases like this anyway, so the absence of errors does not mean the ontology is well-formed.) In addition, there are unescaped spaces in your IRI terms, I verified some of this by plugging your ontology into http://visualdataweb.de/validator/validate, which indicated in the first parser that it tried (RDF) that the expansion in line 51 did not result in an appropriate IRI. Removing the space seemed to fix that issue. I didn't try removing all the spaces for lack of time. You might want ** Why you didn't see this Friday ** I am guessing what changed 'after Friday' is that when you first made changes to your ontology on Friday, they had not been fully reflected in the Classes page display, which can be cached internally in BioPortal for some hours, or even in your browser cache. So you could have been seeing working data from a previous submission, which eventually went away after the cache expired in BioPortal and/or in your browser. I apologize that these delays sometimes happen, I know it is annoyingly confusing. ** What you can try ** Of course you can try eliminating all the spaces and providing the prefix expansion for that ExPaNDS notation, that might take care of it. Getting the file to pass the validator is probably an important step. Or, if you go back to an ontology you know worked, you could resubmit it and see if (after an appropriate period of time, I'd say that's 2 hours followed by clearing your browser cache) BioPortal begins showing classes again. If you are unable to make the ontology work after addressing those issues, resubmit your question with the current symptoms and we'll see if there's anything we can add. John [cid:085101EB-0DF0-4D82-BD29-9D264A187BCE] [cid:B9ED41D0-2E20-4BF6-9BD8-3399FE02F457] On Feb 8, 2021, at 10:34 AM, support at bioontology.org wrote: Name: mriyayi Email: mriyayi at hotmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPANET Feedback: Hi, Regarding https://bioportal.bioontology.org/ontologies/PANET. The Classes tab is intermittently showing 'Problem retrieving classes'. The OWL file uploaded seems to be fine. Please can you investigate and let us know. Kind regards Dan From: DANIEL IYAYI > Subject: [bioontology-support] Error Message - https://bioportal.bioontology.org/ontologies/PANET Date: February 8, 2021 at 10:38:52 AM PST To: "support at bioontology.org" >, "Collins, Steve (DLSLtd,RAL,SCI)" > Hi, I have uploaded an OWL file to https://bioportal.bioontology.org/ontologies/PANET. It is intermittently showing an error 'problem retrieving classes'. [cid:9668f2a6-5c05-462c-9728-5aedd51af245] It worked last Friday and nothing has changed since then. Please can you investigate Kind regards Dan _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-02-08 at 4.04.46 PM.png Type: image/png Size: 225491 bytes Desc: Screen Shot 2021-02-08 at 4.04.46 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-02-08 at 4.05.17 PM.png Type: image/png Size: 25544 bytes Desc: Screen Shot 2021-02-08 at 4.05.17 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 39049 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 31879 bytes Desc: image.png URL: From sierra.miller at nist.gov Fri Feb 12 06:57:43 2021 From: sierra.miller at nist.gov (Miller, Sierra D. (Fed)) Date: Fri, 12 Feb 2021 14:57:43 -0000 Subject: [bioontology-support] Relationships Between Terms in BioPortal Message-ID: Hello, I am trying to flesh out our ontology (NIST_GEL) a bit more by adding relationship entries. I?m new to this work so I?m not sure how this works or if BioPortal even supports this type of mapping but I am attaching the view of my Prot?g? build where it shows the relationship entry of one of the terms. I did this for a few terms and then uploaded this file to our BioPortal listing as a test to see if we could link terms. I uploaded this yesterday afternoon and I?m not seeing anything in BioPortal mentioning the relationship entry. Is this something that is observable? _______ Sierra D. Miller Bioinformatician Biomarker and Genomic Sciences Group Biosystems and Biomaterials Division National Institute of Standards and Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-02-12 at 9.54.33 AM.png Type: image/png Size: 160808 bytes Desc: Screen Shot 2021-02-12 at 9.54.33 AM.png URL: From olamide at plateaumed.com Thu Feb 18 05:42:14 2021 From: olamide at plateaumed.com (olamide adebayo) Date: Thu, 18 Feb 2021 14:42:14 +0100 Subject: [bioontology-support] Issue Uploading Ontology Locally Message-ID: <4CEB34DF-6578-4BE2-937F-30F16565AA06@plateaumed.com> Good day, I hope this meets you well. I am trying to upload the SNOMED CT ontology(by file upload) to my local Virtual Appliance but I keep getting a select location validation error despite literally selecting a location as per form requirements. Even when I tried uploading via URl, the system always hang and it never gets uploaded. Kindly assist. Secondly, does your system support the Expression Constraint Language(ECL) in SNOMED CT?? Kind Regards, Olamide -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Feb 14 17:41:02 2021 From: support at bioontology.org (support at bioontology.org) Date: Mon, 15 Feb 2021 01:41:02 -0000 Subject: [bioontology-support] [BioPortal] Feedback from STEPHEN COATES Message-ID: <6029d123b4afb_41f5218c8f4706f0@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: