From support at bioontology.org Mon May 3 21:17:32 2021 From: support at bioontology.org (support at bioontology.org) Date: Mon, 03 May 2021 21:17:32 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Song, Dongho Message-ID: <6090cadc44b69_53b22535ab455399@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue May 4 12:29:33 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 4 May 2021 19:29:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Clair Kronk In-Reply-To: <608c39dc85fd6_2c152483f30845b6@ncbo-prd-app-09.stanford.edu.mail> References: <608c39dc85fd6_2c152483f30845b6@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <7EDEFD68-9FD7-4089-8820-97B64B3FADD6@stanford.edu> Clair, When I execute your search, at first I just see the first screenshot below, showing only one term. But when I click on the '34 more from this ontology' bit in green, I see all the rest. Ignoring the strange-looking (and politically insensitive) indentation of all those terms under the one entry for 'nonbinary man', it looks like the terms have all been found (not that I know exactly how many it should find). This also matches the number found using the API: https://data.bioontology.org/search?q=nonbinary I think the choice of term that is presented first is random in this UI display?it is keeping the visible list short from each ontology, so that results from other ontologies can be seen, if any. Note that if you search for 'non-binary' in other ontologies (with the hyphen), many more terms are found. Does this match your experience? I had kicked off a reindexing of the ontology before I noticed the link in the green text, but I think all these additional concepts were always there. You may have noticed otherwise. Let me know if you have further problems. John [cid:7268AB42-D9E5-4DCB-B580-FB6EE6DEB3D5] [cid:15952C01-CAF6-40B2-A8A0-6249D4CCADD8] On Apr 30, 2021, at 10:09 AM, support at bioontology.org wrote: Name: Clair Kronk Email: clair.kronk at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fsearch%3Fq%3Dnonbinary%26ontologies%3D%26include_properties%3Dfalse%26include_views%3Dfalse%26includeObsolete%3Dfalse%26require_definition%3Dfalse%26exact_match%3Dfalse%26categories%3D Feedback: Hi! My name is Clair Kronk. I've noticed recently that I can't seem to get search results for the GSSO when searching BioPortal. Was there an issue with uploading the ontology? Thank you so much! _______________________________________________ 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 2021-05-04 at 12.20.02 PM.png Type: image/png Size: 31601 bytes Desc: Screen Shot 2021-05-04 at 12.20.02 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-05-04 at 12.26.14 PM.png Type: image/png Size: 147893 bytes Desc: Screen Shot 2021-05-04 at 12.26.14 PM.png URL: From jgraybeal at stanford.edu Tue May 4 16:59:03 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 4 May 2021 23:59:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Song, Dongho In-Reply-To: <6090cadc44b69_53b22535ab455399@ncbo-prd-app-09.stanford.edu.mail> References: <6090cadc44b69_53b22535ab455399@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <3C174A2A-F571-40A7-8E6B-9FA803A19787@stanford.edu> Hello, The ontology provider requested that downloads of this ontology be prohibited on BioPortal. I suggest you contact the provider directly, using the information on the summary page of the ontology: Contact Katia Laville, laville at icn.ch John On May 3, 2021, at 9:17 PM, support at bioontology.org wrote: Name: Song, Dongho Email: dhsong at kau.ac.kr Location: https%3A%2F%2Fbioportal.bioontology.org%2Frecommender Feedback: Hello, I wish I could have the following ontology by download to extend and SPARQL for my students in a class, however, it is blocked. Is there any way I can get a copy of this? https://bioportal.bioontology.org/ontologies/ICNP/?p=summary Thanks. Dongho Song, Prof. _______________________________________________ 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 May 5 09:26:05 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 05 May 2021 09:26:05 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Luis Gonzalez Message-ID: <6092c71d19edd_6afa1cf4120280cb@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From danielle.n.ndi at vumc.org Wed May 5 08:21:01 2021 From: danielle.n.ndi at vumc.org (Ndi, Danielle N) Date: Wed, 5 May 2021 15:21:01 +0000 Subject: [bioontology-support] Fw: ICD-10 Updated Needed In-Reply-To: References: Message-ID: Hello, Please see question below. Thank you, Danielle ________________________________ From: Ndi, Danielle N Sent: Tuesday, May 4, 2021 9:41 AM To: support at bioportal.org Cc: Ujwok, John A ; Markus, Tiffanie M Subject: ICD-10 Updated Needed Hello, I use the ICD10-CM ontology through REDCap. We are collecting COVID-19 data and have noticed the newest ICD10 updates, including COVID-19 codes added November 30, 2020, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update? Thank you, Danielle -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 5 13:01:14 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 5 May 2021 20:01:14 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Luis Gonzalez In-Reply-To: <6092c71d19edd_6afa1cf4120280cb@ncbo-prd-app-09.stanford.edu.mail> References: <6092c71d19edd_6afa1cf4120280cb@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <0CC8D50C-8157-4441-AB71-4461CA3DC4FA@stanford.edu> Hello Luis, You can go ahead and submit your new ontology whenever you want, and let us know as soon as you want to delete the old one (they can overlap). We perform the deletion on your behalf. John On May 5, 2021, at 9:26 AM, support at bioontology.org wrote: Name: Luis Gonzalez Email: lagonzalezmo at unal.edu.co Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCOLL%2Fedit Feedback: Hi I want deleted the ontology "Collembola Anatomy Ontology" (COLL) and resubmit a new ontology "Collembola Anatomy Ontology" with the new acronym CLAO, which is approved by The OBO Foundry. Thank you _______________________________________________ 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 Wed May 5 13:16:09 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 5 May 2021 20:16:09 +0000 Subject: [bioontology-support] ICD-10 Updated Needed In-Reply-To: References: Message-ID: <98DE7C94-2A7A-4523-AFDD-97EE9A2AA26B@stanford.edu> Hello Danielle, Thank you for this question. We uppdate all the UMLS vocabularies (our ICD10-CM is from UMLS) as soon as we can after the UMLS update is released. I see that the UMLS 2021AA release happened just Monday, so we will look at scheduling that as soon as possible. Unfortunately, it appears ICD10-CM is not updated in the 2021AA UMLS release, per the page https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html. I don't know why this would be, but if that's the case, we may not have any other means to get the latest ICD10-CM. I will do a little more investigation and let you know if I can find more positive news. John On May 5, 2021, at 8:21 AM, Ndi, Danielle N > wrote: Hello, Please see question below. Thank you, Danielle ________________________________ From: Ndi, Danielle N Sent: Tuesday, May 4, 2021 9:41 AM To: support at bioportal.org > Cc: Ujwok, John A >; Markus, Tiffanie M > Subject: ICD-10 Updated Needed Hello, I use the ICD10-CM ontology through REDCap. We are collecting COVID-19 data and have noticed the newest ICD10 updates, including COVID-19 codes added November 30, 2020, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update? Thank you, Danielle _______________________________________________ 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 Thu May 6 10:43:18 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 6 May 2021 17:43:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: References: <5f4387325d003_187c27ee53051630@ncbo-prd-app-08.stanford.edu.mail> <5A5E822B-1F9E-4850-9249-FE65654EBE6C@stanford.edu> Message-ID: <01155AF5-B2FD-488B-9394-5E8A05E90858@stanford.edu> Hi Karin, Just to clarify - the submit feedback form is presented in a modal dialog rather than a pop-up. Whether or not you?re blocking pop-ups should have no bearing on the modal dialog display. I?ve done some testing on my system with Chrome, Firefox, and Safari. Pop-ups are blocked in all 3 of the browsers and the submit feedback dialog displays properly for me in a modal dialog. In the original screenshot you sent, I noticed other oddities in your display. There are bullets showing up in the header and footer next to navigation links, and improper left-alignment of the ?cite us? and other links at the bottom. I?ve included your screenshot again below, along with a screenshot of how BioPortal displays on my system to underline the differences. Out of curiosity, have you tried clearing the cache for BioPortal to see if these issues persist? You could selectively clear the cache for just the BioPortal website in Chrome by doing the following: - Navigate to BioPortal - Click the three dots menu and choose More Tools -> Developer Tools to open the developer console - In the upper left corner of the browser window, right click on the reload icon and choose ?Empty Cache and Hard Reload? If you still see the same differences in display, could you provide more information about the version of Chrome or Firefox that you have installed, as well as what operating system you?re using? Kind regards, Jennifer [cid:A998C1E2-6A54-4CA4-86D3-296582972BC2 at lan] [cid:ADE38241-AE80-4614-B445-14E4D941C6B4 at lan] On Apr 29, 2021, at 12:54 AM, Karin Colsman > wrote: Hi John, thanks for getting back to me. I did not get a popup, so I guess all browsers are blocking it by default, and I did not notice them doing that. Maybe you could reprogram this without using a popup, or ensure it gets the space it needs when popups are blocked? Kind regards Karin From: John Graybeal > Sent: Thursday, 29 April, 2021 01:51 To: Karin Colsman > Cc: support at bioontology.org; Amnon Ptashek > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, Thank you for your request. We are investigating this error and will give you more information as soon as we can. (It is not anything obvious to me, but I will forward to our experts. It may be a day or two before we have further information, due to our current staffing limits. Apologies for that. I am not able to duplicate your issue with the support form?on my system it displays as a small pop-up form, without the footer. Is it possible you have blocked pop-ups? John On Apr 26, 2021, at 1:39 AM, Karin Colsman > wrote: Dear support team, we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be? I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them. Thank you very much for your time, Karin Colsman From: support at bioontology.org > Sent: Monday, 24 August, 2020 10:24 To: support at bioontology.org; Karin Colsman > Subject: [BioPortal] Feedback from Karin Colsman Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO _______________________________________________ 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 _______________________________________________ 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... 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Name: Screen Shot 2021-05-06 at 10.15.56 AM.png Type: image/png Size: 322601 bytes Desc: Screen Shot 2021-05-06 at 10.15.56 AM.png URL: From vendetti at stanford.edu Fri May 7 12:28:48 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 7 May 2021 19:28:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: <960de486aea34d6a9137832b6fa22432@osthus.com> References: <5f4387325d003_187c27ee53051630@ncbo-prd-app-08.stanford.edu.mail> <5A5E822B-1F9E-4850-9249-FE65654EBE6C@stanford.edu> <01155AF5-B2FD-488B-9394-5E8A05E90858@stanford.edu> <960de486aea34d6a9137832b6fa22432@osthus.com> Message-ID: <6E32C8C6-9D82-4B4C-AEFE-9DA4F2B317A7@stanford.edu> Hi Karin, OK - glad to hear the modal dialog is functioning for you. With regard to the footer layout, I?m not sure how to reproduce what you?re seeing. I used the BrowserStack cross-browser testing application with the inputs you gave (Windows, Chrome 90, resolutions 1920x1080), and the footer displays as intended: [cid:16C7243A-FA84-431A-8AEA-FF8275A912C2 at lan] I also used BrowserStack to look at the 1920x1080 resolution for the latest versions of tSafari, Edge, and Firefox, and they all looked OK. Are you running Windows 10? Kind regards, Jennifer On May 6, 2021, at 10:54 AM, Karin Colsman > wrote: Hi Jennifer, I?m getting the modal dialog now without any issues, in all my browsers (Firefox, Chrome, IE, Edge). No idea what went wrong at the time and why it is fixed now ? I didn?t do anything. The footer layout looks broken now though ? I am attaching a screenshot from Chrome Version 90.0.4430.93 (64-Bit) on Windows. A hard refresh doesn?t fix it. Thank you very much for spending time on this! Kind regards Karin [cid:5357B59E-3AF3-4456-83CD-53A47122D33D at lan] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-05-07 at 9.50.33 AM.png Type: image/png Size: 532958 bytes Desc: Screen Shot 2021-05-07 at 9.50.33 AM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bioportal-footer-display-issue.png Type: image/png Size: 147755 bytes Desc: bioportal-footer-display-issue.png URL: From support at bioontology.org Tue May 11 14:43:17 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 11 May 2021 14:43:17 -0700 Subject: [bioontology-support] [BioPortal] Feedback from gilberto fragoso Message-ID: <609afa75295b8_1a1d26cd2c83532a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 12 08:48:15 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 12 May 2021 15:48:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from gilberto fragoso In-Reply-To: <609afa75295b8_1a1d26cd2c83532a@ncbo-prd-app-09.stanford.edu.mail> References: <609afa75295b8_1a1d26cd2c83532a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <0CC70F0A-CFCA-4AA4-B071-29C07C9F767F@stanford.edu> Hi Gilberto, Thanks for the question. The answer is a little bit complicated (different people created those two views), so I will contact you offline to discuss this further. John On May 11, 2021, at 2:43 PM, support at bioontology.org wrote: Name: gilberto fragoso Email: fragosog at mail.nih.gov Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT Feedback: Hi all, We just noticed there are two views of the NCIt in https://bioportal.bioontology.org/ontologies/NCIT. They are quite old, don't know how the views were generated, but we publish those branches as well in our ftp site. What's the best way to update these views? thanks, Gilberto _______________________________________________ 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 hujie at njmu.edu.cn Tue May 11 20:35:40 2021 From: hujie at njmu.edu.cn (=?UTF-8?B?6IOh5p2w?=) Date: Wed, 12 May 2021 11:35:40 +0800 (GMT+08:00) Subject: [bioontology-support] How to edit the Acronym and Description of my uploaded ontology? Message-ID: <317a9773.2e51.1795ea4f7f9.Coremail.hujie@njmu.edu.cn> Dear manager: I have uploaded a ontology to bioportal, but I want to reedit the Acronym and Description, how can I do. Thanks very much! -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 12 14:05:02 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 12 May 2021 21:05:02 +0000 Subject: [bioontology-support] How to edit the Acronym and Description of my uploaded ontology? In-Reply-To: <317a9773.2e51.1795ea4f7f9.Coremail.hujie@njmu.edu.cn> References: <317a9773.2e51.1795ea4f7f9.Coremail.hujie@njmu.edu.cn> Message-ID: <0F8EE20B-D1C7-466A-8743-8CA1C94FDB54@stanford.edu> Hello, You can not edit the Acronym, because it serves as the primary identifier for the ontology throughout BioPortal. If you want to change it, you could resubmit your ontology under the new Acronym, and then ask us to delete the existing ontology. You can edit the description and other metadata for any ontology you manage by going to the Summary page for the ontology, and in the Submissions section, clicking on the 'person with pencil' icon (the blue on at the end of the line). You can edit the Description for the ontology there, then click on the Save submission button at the bottom of the page. [cid:6966A24F-1BC2-47EC-B003-B231A3668D32] John On May 11, 2021, at 8:35 PM, ?? > wrote: Dear manager: I have uploaded a ontology to bioportal, but I want to reedit the Acronym and Description, how can I do. Thanks very much! _______________________________________________ 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 2021-05-12 at 2.02.56 PM.png Type: image/png Size: 38468 bytes Desc: Screen Shot 2021-05-12 at 2.02.56 PM.png URL: From Bushra.Samad at ucsf.edu Fri May 21 16:45:34 2021 From: Bushra.Samad at ucsf.edu (Samad, Bushra) Date: Fri, 21 May 2021 23:45:34 +0000 Subject: [bioontology-support] Updated BioPortal Ontologies Message-ID: Hi, I am not sure who to contact I wanted to check when the COVID vaccine data (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html) will be available in RxNorm in BioPortal. I did not see it in REDcap and the UCSF REDcap administrator said they have no control over the updates of the BioPortal Ontologies available on REDcap. I contacted NLM support and they directed me to contact you. Thanks Bushra -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon May 24 11:22:31 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 24 May 2021 18:22:31 +0000 Subject: [bioontology-support] Updated BioPortal Ontologies In-Reply-To: References: Message-ID: Hello Bushra, On May 21, 2021, at 4:45 PM, Samad, Bushra > wrote: Hi, I am not sure who to contact I wanted to check when the COVID vaccine data (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html) will be available in RxNorm in BioPortal. I did not see it in REDcap and the UCSF REDcap administrator said they have no control over the updates of the BioPortal Ontologies available on REDcap. I contacted NLM support and they directed me to contact you. We ingest RxNorm from the UMLS Metathesaurus [1]. They do releases twice per year, and we just finished importing the 2021AA release [2]. According to their documentation, the 2021AA release contains RxNorm version 20AA_210301F [3]. I ran a couple of test searches and did find some of the content you asked about has been pulled in, e.g.: RXCUI 2470234 (Moderna COVID-19 Vaccine): https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2470234 RXCUI 2468235 (Pfizer-BioNTech COVID-19 Vaccine): https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2468235 However, there are other RXCUIs that don?t appear to be part of this RxNorm release, e.g., the Janssen vaccine (RXCUI 2479835). Apologies, but I?m not aware of any plans to ingest a new version of RxNorm until the UMLS Metathesaurus 2021AB release in November of this year. Kind regards, Jennifer [1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html [2] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html [3] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/metadata.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From Bushra.Samad at ucsf.edu Mon May 24 11:28:55 2021 From: Bushra.Samad at ucsf.edu (Samad, Bushra) Date: Mon, 24 May 2021 18:28:55 +0000 Subject: [bioontology-support] Updated BioPortal Ontologies In-Reply-To: References: Message-ID: Thanks for the prompt response and the clear explanation Jennifer. I see the updates on REDcap. Thanks again Bushra From: Jennifer Leigh Vendetti Date: Monday, May 24, 2021 at 11:22 AM To: "Samad, Bushra" Cc: "support at bioontology.org" Subject: Re: [bioontology-support] Updated BioPortal Ontologies Hello Bushra, On May 21, 2021, at 4:45 PM, Samad, Bushra wrote: Hi, I am not sure who to contact I wanted to check when the COVID vaccine data (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hello Bushra, On May 21, 2021, at 4:45 PM, Samad, Bushra > wrote: Hi, I am not sure who to contact I wanted to check when the COVID vaccine data (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html) will be available in RxNorm in BioPortal. I did not see it in REDcap and the UCSF REDcap administrator said they have no control over the updates of the BioPortal Ontologies available on REDcap. I contacted NLM support and they directed me to contact you. We ingest RxNorm from the UMLS Metathesaurus [1]. They do releases twice per year, and we just finished importing the 2021AA release [2]. According to their documentation, the 2021AA release contains RxNorm version 20AA_210301F [3]. I ran a couple of test searches and did find some of the content you asked about has been pulled in, e.g.: RXCUI 2470234 (Moderna COVID-19 Vaccine): https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2470234 RXCUI 2468235 (Pfizer-BioNTech COVID-19 Vaccine): https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2468235 However, there are other RXCUIs that don?t appear to be part of this RxNorm release, e.g., the Janssen vaccine (RXCUI 2479835). Apologies, but I?m not aware of any plans to ingest a new version of RxNorm until the UMLS Metathesaurus 2021AB release in November of this year. Kind regards, Jennifer [1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html [2] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html [3] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/metadata.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From naveen.ponnuswamy at novartis.com Tue May 25 05:28:00 2021 From: naveen.ponnuswamy at novartis.com (Ponnuswamy, Naveen) Date: Tue, 25 May 2021 12:28:00 +0000 Subject: [bioontology-support] API Key Message-ID: Hello Team, Good day! Can you please help with the process around getting the API key to connect to Bio Portal ontologies. Regards, Naveen Ponnuswamy Ontologist - DaaS - CTS CONEXTS Novartis Healthcare Pvt. Ltd, Telangana 500 032 INDIA M: +91 96864 22300 E-mail: naveen.ponnuswamy at novartis.com www.novartis.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue May 25 10:49:06 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 25 May 2021 17:49:06 +0000 Subject: [bioontology-support] API Key In-Reply-To: References: Message-ID: Hi Naveen, There are some instructions on the wiki for getting an API key: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer On May 25, 2021, at 5:28 AM, Ponnuswamy, Naveen > wrote: Hello Team, Good day! Can you please help with the process around getting the API key to connect to Bio Portal ontologies. Regards, Naveen Ponnuswamy Ontologist ? DaaS ? CTS CONEXTS Novartis Healthcare Pvt. Ltd, Telangana 500 032 INDIA M: +91 96864 22300 E-mail: naveen.ponnuswamy at novartis.com www.novartis.com _______________________________________________ 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 Fri May 28 05:08:19 2021 From: support at bioontology.org (support at bioontology.org) Date: Fri, 28 May 2021 05:08:19 -0700 Subject: [bioontology-support] [BioPortal] Feedback from WTulleken Message-ID: <60b0dd333e13e_753725205742552c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri May 28 09:59:31 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 28 May 2021 16:59:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from WTulleken In-Reply-To: <60b0dd333e13e_753725205742552c@ncbo-prd-app-09.stanford.edu.mail> References: <60b0dd333e13e_753725205742552c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <4A839E25-F086-499B-AD23-2FD1B1C400A3@stanford.edu> Hello Wesley, Can you be more specific about what?s not working? I checked the BioPortal page that allows you to register for a new account: https://bioportal.bioontology.org/accounts/new ? and it appears to be functioning. Jennifer On May 28, 2021, at 5:08 AM, support at bioontology.org wrote: Name: WTulleken Email: wesley.tulleken at up.ac.za Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hi. Im trying to get an API to use with RedCap, but its not working. Can you assist? I basically cant register at the moment. Can you assist? Thanks Wesley wesley.tulleken at up.ac.za _______________________________________________ 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 wesley.tulleken at up.ac.za Mon May 31 02:03:27 2021 From: wesley.tulleken at up.ac.za (Wesley Van Hougenhouck-Tulleken) Date: Mon, 31 May 2021 11:03:27 +0200 Subject: [bioontology-support] [BioPortal] Feedback from WTulleken In-Reply-To: <4A839E25-F086-499B-AD23-2FD1B1C400A3@stanford.edu> References: <60b0dd333e13e_753725205742552c@ncbo-prd-app-09.stanford.edu.mail> <4A839E25-F086-499B-AD23-2FD1B1C400A3@stanford.edu> Message-ID: Hi Jennifer Many thanks for your email. The problem I had on friday seems to have resolved. I am able to access the BioPortal easily now. My query now is that I am using RedCap to create a database for clinical data. I have been advised to use the ontological function in RedCap for ICD10 coding, and when I try to enable it, RedCap requests an API token. I have attached a screenshot. If you could advise, or guide me to the correct person, I would be very grateful. Many thanks On Fri, 28 May 2021 at 18:59, Jennifer Leigh Vendetti wrote: > Hello Wesley, > > Can you be more specific about what?s not working? I checked the BioPortal > page that allows you to register for a new account: > > https://bioportal.bioontology.org/accounts/new > > ? and it appears to be functioning. > > Jennifer > > > > On May 28, 2021, at 5:08 AM, support at bioontology.org wrote: > > Name: WTulleken > > Email: wesley.tulleken at up.ac.za > > Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 > > > *Feedback:* > > Hi. Im trying to get an API to use with RedCap, but its not working. Can > you assist? > > I basically cant register at the moment. Can you assist? > > Thanks > Wesley > > wesley.tulleken at up.ac.za > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -- This message and attachments are subject to a disclaimer. Please refer to? http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf ?for full details. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2021-05-31 at 10.53.23.png Type: image/png Size: 276638 bytes Desc: not available URL: