From mohamed.keshk at gmail.com Tue Aug 10 15:29:37 2021 From: mohamed.keshk at gmail.com (Mohamed Keshk) Date: Tue, 10 Aug 2021 17:29:37 -0500 Subject: [bioontology-support] [BioPortal] Feedback from mohamed.keshk In-Reply-To: <6112e7508c2b_398f2f28350619e5@ncbo-prd-app-08.stanford.edu.mail> References: <6112e7508c2b_398f2f28350619e5@ncbo-prd-app-08.stanford.edu.mail> Message-ID: I'm really sorry, I cannot understand your reply. I need help on how to edit the ontology in my link: https://bioportal.bioontology.org/ontologies/PCL thanks, Mohamed On Tue, Aug 10, 2021 at 3:53 PM wrote: > Name: mohamed.keshk > > Email: mohamed.keshk at gmail.com > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount > > > *Feedback:* > > Hi, > I own the link for "Provisional Cell Ontology" under my > name Mohamed.Keshk, and my email mohamed.keshk at gmail.com at the link > https://bioportal.bioontology.org/ontologies/PCL > I'm not able to edit this ontology for a new update. > Can you help me on that? > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Aug 10 15:55:52 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 10 Aug 2021 22:55:52 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mohamed.keshk In-Reply-To: References: <6112e7508c2b_398f2f28350619e5@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <7DCDAAA1-E6CF-4881-9624-603141BEC6C5@stanford.edu> Mohamed, I apologize if we didn't respond to your earlier email, I don't have any record of it before now. I am sorry, I am not seeing you as a listed owner of this ontology in BioPortal, but I see you are one of the original authors. Can I suggest you contact Brian Aevermann to add you to the list of people who can administer the ontology? (Or he can email me directly.) You can contact me directly if that is not an option, I am at jgraybeal at stanford.edu. John On Aug 10, 2021, at 3:29 PM, Mohamed Keshk > wrote: I'm really sorry, I cannot understand your reply. I need help on how to edit the ontology in my link: https://bioportal.bioontology.org/ontologies/PCL thanks, Mohamed On Tue, Aug 10, 2021 at 3:53 PM > wrote: Name: mohamed.keshk Email: mohamed.keshk at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Hi, I own the link for "Provisional Cell Ontology" under my name Mohamed.Keshk, and my email mohamed.keshk at gmail.com at the link https://bioportal.bioontology.org/ontologies/PCL I'm not able to edit this ontology for a new update. Can you help me on that? _______________________________________________ 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 mecum at nceas.ucsb.edu Tue Aug 10 17:58:19 2021 From: mecum at nceas.ucsb.edu (Bryce Mecum) Date: Tue, 10 Aug 2021 16:58:19 -0800 Subject: [bioontology-support] [BioPortal] "Error Rdf" for new ontology submission Message-ID: Hey BioPortal folks, I just submitted a test ontology to check out how it works in BioPortal and I see it uploaded but didn't get any farther. It shows an "Error Rdf" status. [image: Screen Shot 2021-08-10 at 4.57.37 PM.png] Is there a way to check into the error on your end? Thanks, Bryce -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-08-10 at 4.57.37 PM.png Type: image/png Size: 18952 bytes Desc: not available URL: From mecum at nceas.ucsb.edu Tue Aug 10 18:04:10 2021 From: mecum at nceas.ucsb.edu (Bryce Mecum) Date: Tue, 10 Aug 2021 17:04:10 -0800 Subject: [bioontology-support] [BioPortal] "Error Rdf" for new ontology submission In-Reply-To: References: Message-ID: Sorry for not checking locally first: I just ran it through riot and I had a syntax error. Would it be possible to surface errors on the web interface? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Aug 10 22:48:26 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 11 Aug 2021 05:48:26 +0000 Subject: [bioontology-support] [BioPortal] "Error Rdf" for new ontology submission In-Reply-To: References: , Message-ID: That is an excellent suggestion that we hope to implement! I?m not able to predict when it will reach the top of the list though. Thanks for checking the parsing on your side! John ________________________________ From: bioontology-support on behalf of Bryce Mecum Sent: Tuesday, August 10, 2021 6:04:10 PM To: NCBO User Support Subject: Re: [bioontology-support] [BioPortal] "Error Rdf" for new ontology submission Sorry for not checking locally first: I just ran it through riot and I had a syntax error. Would it be possible to surface errors on the web interface? -------------- next part -------------- An HTML attachment was scrubbed... URL: From mecum at nceas.ucsb.edu Wed Aug 11 11:49:10 2021 From: mecum at nceas.ucsb.edu (Bryce Mecum) Date: Wed, 11 Aug 2021 10:49:10 -0800 Subject: [bioontology-support] [BioPortal] "Error Rdf" for new ontology submission In-Reply-To: References: Message-ID: Sounds great, thanks so much. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Aug 19 17:12:57 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 20 Aug 2021 00:12:57 +0000 Subject: [bioontology-support] CIDO in Bioportal In-Reply-To: <717A9731-A0E0-46A5-93AF-6C6067B9CA9B@stanford.edu> References: <717A9731-A0E0-46A5-93AF-6C6067B9CA9B@stanford.edu> Message-ID: Hi Oliver, There was a data discrepancy on our end that prevented new versions of CIDO from being created. The issue has been addressed, and the future versions will be pulled automatically. Meanwhile, the latest version of CIDO (1.0.255) has been downloaded and processed. Please let us know if you run into further issues. Thank you, Michael Begin forwarded message: From: "He, Oliver" > Subject: CIDO in Bioportal Date: August 19, 2021 at 12:01:40 PM PDT To: "'jgraybeal at stanford.edu'" > Hi John, Somehow CIDO in BioPortal has not been updated for a couple of months: https://bioportal.bioontology.org/ontologies/CIDO current version is v1.0.255 https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl could you help take a look and see what happens there? Thanks! Oliver Yongqun "Oliver" He, DVM, PhD Associate Professor Unit for Laboratory Animal Medicine Department of Microbiology and Immunology Center for Computational Medicine and Bioinformatics and Comprehensive Cancer Center University of Michigan Medical School Office: 2511F ARF, 1150 W. Medical Center Dr. Ann Arbor, MI 48109 Email: yongqunh at med.umich.edu Tel: 734-615-8231 (O) http://www.hegroup.org/ -----Original Message----- From: bioportal-announce > On Behalf Of bioportal-announce-request at lists.stanford.edu Sent: Saturday, April 11, 2020 3:00 PM To: bioportal-announce at lists.stanford.edu Subject: bioportal-announce Digest, Vol 57, Issue 1 External Email - Use Caution Send bioportal-announce mailing list submissions to bioportal-announce at lists.stanford.edu To subscribe or unsubscribe via the World Wide Web, visit https://mailman.stanford.edu/mailman/listinfo/bioportal-announce or, via email, send a message with subject or body 'help' to bioportal-announce-request at lists.stanford.edu You can reach the person managing the list at bioportal-announce-owner at lists.stanford.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of bioportal-announce digest..." Today's Topics: 1. BioPortal maintenance this weekend; minimal impact planned (John Graybeal) ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Apr 2020 23:00:08 +0000 From: John Graybeal To: "bioportal-announce at lists.stanford.edu" , "support at bioontology.org" Subject: [bioportal-announce] BioPortal maintenance this weekend; minimal impact planned Message-ID: <1450E9EE-141B-4334-AA3E-41EE3EE31A3D at stanford.edu> Content-Type: text/plain; charset="us-ascii" Hello everyone, This Saturday evening at 21:00 (GMT-7), we'll begin a maintenance upgrade activity on BioPortal which we hope will be almost transparent, with perhaps a brief interrupt in service. If there are problems, which we think highly unlikely, we need to reserve the next day for possible corrections. On Tuesday evening we'll be performing another maintenance upgrade, which is not expected to require any downtime or service interruptions. For more about why we're performing these barely-visible upgrades, visit https://www.bioontology.org/non-breaking-news-changes-coming-to-bioportal/. Some interesting things are coming to BioPortal. We look forward to sharing more about those soon. John ======================== 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: ------------------------------ Subject: Digest Footer _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce ------------------------------ End of bioportal-announce Digest, Vol 57, Issue 1 ************************************************* ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ======================== 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 yongqunh at med.umich.edu Thu Aug 19 19:03:04 2021 From: yongqunh at med.umich.edu (He, Oliver) Date: Fri, 20 Aug 2021 02:03:04 +0000 Subject: [bioontology-support] CIDO in Bioportal In-Reply-To: References: <717A9731-A0E0-46A5-93AF-6C6067B9CA9B@stanford.edu> Message-ID: <392550321a874d8baecad2bbd6f2ed20@med.umich.edu> HI Michael, That's great. Thanks! Oliver From: Michael Dorf Sent: Thursday, August 19, 2021 8:13 PM To: He, Oliver Cc: John Graybeal ; support at bioontology.org Subject: Re: CIDO in Bioportal External Email - Use Caution Hi Oliver, There was a data discrepancy on our end that prevented new versions of CIDO from being created. The issue has been addressed, and the future versions will be pulled automatically. Meanwhile, the latest version of CIDO (1.0.255) has been downloaded and processed. Please let us know if you run into further issues. Thank you, Michael Begin forwarded message: From: "He, Oliver" > Subject: CIDO in Bioportal Date: August 19, 2021 at 12:01:40 PM PDT To: "'jgraybeal at stanford.edu'" > Hi John, Somehow CIDO in BioPortal has not been updated for a couple of months: https://bioportal.bioontology.org/ontologies/CIDO current version is v1.0.255 https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl could you help take a look and see what happens there? Thanks! Oliver Yongqun "Oliver" He, DVM, PhD Associate Professor Unit for Laboratory Animal Medicine Department of Microbiology and Immunology Center for Computational Medicine and Bioinformatics and Comprehensive Cancer Center University of Michigan Medical School Office: 2511F ARF, 1150 W. Medical Center Dr. Ann Arbor, MI 48109 Email: yongqunh at med.umich.edu Tel: 734-615-8231 (O) http://www.hegroup.org/ -----Original Message----- From: bioportal-announce > On Behalf Of bioportal-announce-request at lists.stanford.edu Sent: Saturday, April 11, 2020 3:00 PM To: bioportal-announce at lists.stanford.edu Subject: bioportal-announce Digest, Vol 57, Issue 1 External Email - Use Caution Send bioportal-announce mailing list submissions to bioportal-announce at lists.stanford.edu To subscribe or unsubscribe via the World Wide Web, visit https://mailman.stanford.edu/mailman/listinfo/bioportal-announce or, via email, send a message with subject or body 'help' to bioportal-announce-request at lists.stanford.edu You can reach the person managing the list at bioportal-announce-owner at lists.stanford.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of bioportal-announce digest..." Today's Topics: 1. BioPortal maintenance this weekend; minimal impact planned (John Graybeal) ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Apr 2020 23:00:08 +0000 From: John Graybeal > To: "bioportal-announce at lists.stanford.edu" >, "support at bioontology.org" > Subject: [bioportal-announce] BioPortal maintenance this weekend; minimal impact planned Message-ID: <1450E9EE-141B-4334-AA3E-41EE3EE31A3D at stanford.edu> Content-Type: text/plain; charset="us-ascii" Hello everyone, This Saturday evening at 21:00 (GMT-7), we'll begin a maintenance upgrade activity on BioPortal which we hope will be almost transparent, with perhaps a brief interrupt in service. If there are problems, which we think highly unlikely, we need to reserve the next day for possible corrections. On Tuesday evening we'll be performing another maintenance upgrade, which is not expected to require any downtime or service interruptions. For more about why we're performing these barely-visible upgrades, visit https://www.bioontology.org/non-breaking-news-changes-coming-to-bioportal/. Some interesting things are coming to BioPortal. We look forward to sharing more about those soon. John ======================== 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: ------------------------------ Subject: Digest Footer _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce ------------------------------ End of bioportal-announce Digest, Vol 57, Issue 1 ************************************************* ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ======================== 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues -------------- next part -------------- An HTML attachment was scrubbed... URL: From w.sloof at umcg.nl Wed Aug 25 07:07:41 2021 From: w.sloof at umcg.nl (Sloof, W (epi)) Date: Wed, 25 Aug 2021 14:07:41 +0000 Subject: [bioontology-support] Problem with drug names retrieval with CHEBI ontology Message-ID: <6eb72480ac99465f90a84f1da1043c44@umcg.nl> Dear Sir/Madam, We experience some problems retrieving drug names and codes from the CHEBI ontology. Researchers from our institute reported this to us when collecting medication data in our REDCap EDC system. As of today some drug names are not auto-completed anymore and return with no results. Earlier this was not the case. Specific drug names like clozapine or olanzapine cannot be found anymore. While testing, many other drug names still return plenty results, so the CHEBI ontology service in general is accessible and functional. Changing ontology services is risky because this will result in (partial) data loss in the ongoing study. Please could you help us and look into this matter? We would be thankful if you can solve our problem. Best Regards, Wessel Sloof Datamanager Team Research Datamanagement IMO/IM-MIT University Medical Centre Groningen The Netherlands ________________________________ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Aug 19 20:34:15 2021 From: support at bioontology.org (support at bioontology.org) Date: Thu, 19 Aug 2021 20:34:15 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Ramona Walls Message-ID: <611f22b723038_2467238a214889b9@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Aug 18 17:41:07 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 18 Aug 2021 17:41:07 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Jo-Jo Feng Message-ID: <611da8a339d51_74c3243fd8045974@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Aug 11 13:54:29 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 11 Aug 2021 13:54:29 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Karthik Message-ID: <61143905b8308_4d0e22c92449621a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Aug 10 11:55:11 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 10 Aug 2021 18:55:11 -0000 Subject: [bioontology-support] [BioPortal] Feedback from Mubeen Message-ID: <6112cb81168b7_2027282969455519@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From niva at dtu.dk Tue Aug 17 22:18:01 2021 From: niva at dtu.dk (Nikola Vasiljevic) Date: Wed, 18 Aug 2021 05:18:01 +0000 Subject: [bioontology-support] [BioPortal] Load from URL failure for ZonMw Controlled Vocabulary of Subjects In-Reply-To: <611c6004f12d0_4069229471061712@ncbo-prd-app-31.stanford.edu.mail> References: <611c6004f12d0_4069229471061712@ncbo-prd-app-31.stanford.edu.mail> Message-ID: Hi there, As we created new vocabulary, feel free to remove: 1. ZONMW-SUBJECTS: http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECTS 2. ZONMW-SUBJECT http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECT >From BioPortal. Many thanks, Nikola Nikola Vasiljevi?, PhD RDA Ambassador Special consultant for Digitalization ORCID: 0000-0002-9381-9693 ResearcherID: L-4445-2016 GoogleScholar Mobile: +45 5180 1452 Email: niva at dtu.dk DTU Wind Energy Frederiksborgvej 399 Building 125 4000 Roskilde www.vindenergi.dtu.dk/english ________________________________ From: admin at bioontology.org Sent: Wednesday, August 18, 2021 3:19:00 AM To: jam.belien at amsterdamumc.nl; Nikola Vasiljevic Subject: [BioPortal] Load from URL failure for ZonMw Controlled Vocabulary of Subjects BioPortal failed to load ZonMw Controlled Vocabulary of Subjects (ZONMW-SUBJECTS) from URL: https://raw.githubusercontent.com/fair-data-collective/zonmw-subjects/master/vocabulary.ttl. Please verify the URL you provided for daily loading of your ontology: 1. Make sure you are signed in to BioPortal. 2. Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECTS. 3. Click the "Edit submission information" link. 4. In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area. If you need further assistance, please contact us via the BioPortal support mailing list. Thank you, The BioPortal Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 25 15:04:11 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 25 Aug 2021 22:04:11 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karthik In-Reply-To: <61143905b8308_4d0e22c92449621a@ncbo-prd-app-09.stanford.edu.mail> References: <61143905b8308_4d0e22c92449621a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Karthik, Apologies for this late reply. We have a REST API that you could use to download the subclasses of the ?cancer" class in the DOID ontology. The call would look something like the following: https://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_162/children?display_links=false&display_context=false The result set includes the IDs of each subclass (screenshot below). Our REST API is documented here: http://data.bioontology.org/documentation Instructions for getting an API key are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Let us know if you need further assistance. Kind regards, Jennifer [cid:2787BD21-2687-4A9C-A2F2-4B1FE803D3B5 at lan] On Aug 11, 2021, at 1:54 PM, support at bioontology.org wrote: Hi, I want to download all the instances of all the subclasses under the class "cancer" with their ID. Could you please explain how to do it. Thanks _______________________________________________ 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 2021-08-25 at 2.55.20 PM.png Type: image/png Size: 241120 bytes Desc: Screen Shot 2021-08-25 at 2.55.20 PM.png URL: From vendetti at stanford.edu Wed Aug 25 15:09:07 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 25 Aug 2021 22:09:07 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mubeen In-Reply-To: <6112cb81168b7_2027282969455519@ncbo-prd-app-08.stanford.edu.mail> References: <6112cb81168b7_2027282969455519@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Mubeen, Thank you for reaching out. We?re aware of this issue, which is documented here in our issue tracker: https://github.com/ncbo/bioportal-project/issues/202 Unfortunately, we?ve not had the resources to be able to address this yet. If you have a GitHub account, you could subscribe to notifications for this issue to monitor any progress. Kind regards, Jennifer On Aug 10, 2021, at 11:54 AM, support at bioontology.org wrote: Name: Mubeen Hi, re the weblink https://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root could you please return your old configuration and show the full hierarchy under "Classes". Use of autosearch/autoencoding via the "Jump to" feature is like shooting in the dark, with risks of omissions and misclassifications. Thanks! _______________________________________________ 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 vendetti at stanford.edu Wed Aug 25 15:15:43 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 25 Aug 2021 22:15:43 +0000 Subject: [bioontology-support] [BioPortal] Load from URL failure for ZonMw Controlled Vocabulary of Subjects In-Reply-To: References: <611c6004f12d0_4069229471061712@ncbo-prd-app-31.stanford.edu.mail> Message-ID: Hi Nikola, Sure, no problem. ZONMW-SUBJECTS and ZONMW-SUBJECT have been deleted. Kind regards, Jennifer On Aug 17, 2021, at 10:18 PM, Nikola Vasiljevic > wrote: Hi there, As we created new vocabulary, feel free to remove: 1. ZONMW-SUBJECTS: http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECTS 2. ZONMW-SUBJECT http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECT From BioPortal. Many thanks, Nikola Nikola Vasiljevi?, PhD RDA Ambassador Special consultant for Digitalization ORCID: 0000-0002-9381-9693 ResearcherID: L-4445-2016 GoogleScholar Mobile: +45 5180 1452 Email: niva at dtu.dk DTU Wind Energy Frederiksborgvej 399 Building 125 4000 Roskilde www.vindenergi.dtu.dk/english ________________________________ From: admin at bioontology.org > Sent: Wednesday, August 18, 2021 3:19:00 AM To: jam.belien at amsterdamumc.nl; Nikola Vasiljevic Subject: [BioPortal] Load from URL failure for ZonMw Controlled Vocabulary of Subjects BioPortal failed to load ZonMw Controlled Vocabulary of Subjects (ZONMW-SUBJECTS) from URL: https://raw.githubusercontent.com/fair-data-collective/zonmw-subjects/master/vocabulary.ttl. Please verify the URL you provided for daily loading of your ontology: 1. Make sure you are signed in to BioPortal. 2. Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/ZONMW-SUBJECTS. 3. Click the "Edit submission information" link. 4. In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area. If you need further assistance, please contact us via the BioPortal support mailing list. Thank you, The BioPortal Team _______________________________________________ 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 vendetti at stanford.edu Wed Aug 25 15:38:44 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 25 Aug 2021 22:38:44 +0000 Subject: [bioontology-support] Problem with drug names retrieval with CHEBI ontology In-Reply-To: <6eb72480ac99465f90a84f1da1043c44@umcg.nl> References: <6eb72480ac99465f90a84f1da1043c44@umcg.nl> Message-ID: <85BC1D72-DD59-403D-8B54-B451B64626EC@stanford.edu> Hello Wessel, On Aug 25, 2021, at 7:07 AM, Sloof, W (epi) > wrote: Dear Sir/Madam, We experience some problems retrieving drug names and codes from the CHEBI ontology. Researchers from our institute reported this to us when collecting medication data in our REDCap EDC system. As of today some drug names are not auto-completed anymore and return with no results. Earlier this was not the case. Specific drug names like clozapine or olanzapine cannot be found anymore. While testing, many other drug names still return plenty results, so the CHEBI ontology service in general is accessible and functional. Changing ontology services is risky because this will result in (partial) data loss in the ongoing study. Please could you help us and look into this matter? We would be thankful if you can solve our problem. I looked at the CHEBI ontology today. A new version was uploaded on August 1st. An error occurred during processing and the ontology terms failed to index. I?ve fully re-indexed CHEBI just now and tested the search service. I?m seeing results for clozapine and olanzapine. Apologies for the inconvenience. Let us know if you experience any other issues. Kind regards, Jennifer [cid:E74D7994-A018-4276-B800-C4D2D9011EC6 at lan] [cid:AE1E6CF1-FA8B-4B6F-87A2-DEB79DB1D675 at lan] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-08-25 at 3.37.04 PM.png Type: image/png Size: 54260 bytes Desc: Screen Shot 2021-08-25 at 3.37.04 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-08-25 at 3.37.45 PM.png Type: image/png Size: 53828 bytes Desc: Screen Shot 2021-08-25 at 3.37.45 PM.png URL: From amy.dang at deakin.edu.au Thu Aug 26 23:29:37 2021 From: amy.dang at deakin.edu.au (Amy Dang) Date: Fri, 27 Aug 2021 06:29:37 +0000 Subject: [bioontology-support] Can I please find out what version of MedDRA are we using in REDCap? Message-ID: H Bio Ontology team, Can I please find out what version of MedDRA are we using? We used the MedDRA coding in the RECap provided and when I went to the link it said version 2021AA, is the updated version in REDCap? Do you automatically update the latest versions in REDCap and is this the correct place to find that detail? https://bioportal.bioontology.org/ontologies/MEDDRA?p=summary Please see screen shot below. Many thanks, Amy [cid:image004.png at 01D79B5F.462EA760] [cid:image005.png at 01D79B60.04708E50] Amy Dang Project Officer HERB (Health Education and Research Building) Level 2, 299 Ryrie Street, Geelong VIC 3220 PH: 0432 322 723 Email: amy.dang at deakin.edu.au or arrowtrial at deakin.edu.au [cidimage001.png at 01D732B7.79AAA730][Icon Description automatically generated][A picture containing logo Description automatically generated] Important Notice: The contents of this email transmission, including any attachments, are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents and any attachments is expressly prohibited. If you have received this transmission in error, please delete it and any attachments from your system immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free. Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 14421 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 274949 bytes Desc: image002.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 52260 bytes Desc: image003.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image004.png Type: image/png Size: 82035 bytes Desc: image004.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image005.png Type: image/png Size: 109795 bytes Desc: image005.png URL: From support at bioontology.org Fri Aug 27 09:47:34 2021 From: support at bioontology.org (support at bioontology.org) Date: Fri, 27 Aug 2021 09:47:34 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Zach Smith Message-ID: <61291726305b4_33de281ee9c63925@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Aug 27 10:01:16 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 27 Aug 2021 17:01:16 +0000 Subject: [bioontology-support] Can I please find out what version of MedDRA are we using in REDCap? In-Reply-To: References: Message-ID: Hi Amy, On Aug 26, 2021, at 11:29 PM, Amy Dang > wrote: H Bio Ontology team, Can I please find out what version of MedDRA are we using? We import MedDRA into BioPortal from the National Library of Medicine?s UMLS: https://www.nlm.nih.gov/research/umls/quickstart.html We used the MedDRA coding in the RECap provided and when I went to the link it said version 2021AA, 2021AA refers to the UMLS release version, not the MedDRA version. If you want to know what version of MedDRA is included in the 2021AA UMLS release, you can look at this page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html It?s MedDRA version 23.1. is the updated version in REDCap? Do you automatically update the latest versions in REDCap and is this the correct place to find that detail? https://bioportal.bioontology.org/ontologies/MEDDRA?p=summary We?re the developers and maintainers of the BioPortal application, not REDCap. What I can say is that BioPortal only serves the most recent version of any given ontology. I assume that REDCap uses the BioPortal REST API to retrieve ontology data, so I?d guess they are also serving the most recent version of MedDRA. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Aug 27 10:15:45 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 27 Aug 2021 17:15:45 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zach Smith In-Reply-To: <61291726305b4_33de281ee9c63925@ncbo-prd-app-08.stanford.edu.mail> References: <61291726305b4_33de281ee9c63925@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <8BC7ECCC-1B2B-4D34-BBC6-B53190467150@stanford.edu> Hello Zach, On Aug 27, 2021, at 9:47 AM, support at bioontology.org wrote: Hello Sir or Madam, I am currently utilizing the bioontology API for MedDRA through RedCAP. There is a question around the update cycle and current version for reporting. A few questions: 1) How often is the MedDRA version updated? We import MedDRA into BioPortal from the National Library of Medicine?s UMLS. The UMLS is updated twice per year in May (the ?AA? release) and November (the ?AB? release), e.g., this year will be 2021AA and 2021AB. Although we host MedDRA, we?re not the authors and/or maintainers of the vocabulary. I don?t know whether each UMLS release contains a new version of MedDRA. The UMLS provides a vocabulary documentation page where you can find information about when each vocabulary was last updated: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html In particular, this page shows the metadata for MedDRA: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/index.html 2) Confirming the current version, is it 23.1? Yes 3) Is there a regular cycle for MedDRA updates? You may want to check with the authors / maintainers of MedDRA directly to get an answer to this question: https://www.meddra.org/contact Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Aug 27 13:24:23 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 27 Aug 2021 20:24:23 +0000 Subject: [bioontology-support] Can I please find out what version of MedDRA are we using in REDCap? In-Reply-To: References:

Message-ID: Amy, Jessica, If I may add to this excellent summary, we know that MedDRA itself (at the MedDRA site) has been updated to version 24. We do not know why MedDRA is not updated every 6 months in UMLS, but because it is not updated in UMLS, and we get MedDRA only through UMLS, we are unable to provide version 24 of MedDRA in BioPortal. We have not been able to find any other ontological source for MedDRA that can legally be put on BioPortal, so we do not anticipate the latest version of MedDRA itself being on BioPortal until late this year, likely late November. John On Aug 27, 2021, at 10:01 AM, Jennifer Leigh Vendetti > wrote: Hi Amy, On Aug 26, 2021, at 11:29 PM, Amy Dang > wrote: H Bio Ontology team, Can I please find out what version of MedDRA are we using? We import MedDRA into BioPortal from the National Library of Medicine?s UMLS: https://www.nlm.nih.gov/research/umls/quickstart.html We used the MedDRA coding in the RECap provided and when I went to the link it said version 2021AA, 2021AA refers to the UMLS release version, not the MedDRA version. If you want to know what version of MedDRA is included in the 2021AA UMLS release, you can look at this page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html It?s MedDRA version 23.1. is the updated version in REDCap? Do you automatically update the latest versions in REDCap and is this the correct place to find that detail? https://bioportal.bioontology.org/ontologies/MEDDRA?p=summary We?re the developers and maintainers of the BioPortal application, not REDCap. What I can say is that BioPortal only serves the most recent version of any given ontology. I assume that REDCap uses the BioPortal REST API to retrieve ontology data, so I?d guess they are also serving the most recent version of MedDRA. Kind regards, Jennifer _______________________________________________ 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 Aug 27 13:28:08 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 27 Aug 2021 20:28:08 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zach Smith In-Reply-To: <8BC7ECCC-1B2B-4D34-BBC6-B53190467150@stanford.edu> References: <61291726305b4_33de281ee9c63925@ncbo-prd-app-08.stanford.edu.mail> <8BC7ECCC-1B2B-4D34-BBC6-B53190467150@stanford.edu> Message-ID: <9F3E4A34-1C19-492D-8513-E081B3C1151A@stanford.edu> Zach, I happen to have previously checked, they do have a 6-month update cycle for MedDRA, releasing about 4-6 weeks before UMLS releases it's biannual update. You can find this information on the official MedDRA web site. Unfortunately UMLS pulls in *MedDRA* updates only once a year, so for 6-7 months UMLS lags the latest MedDRA release by 6 months. There is nothing we can do to get around this discrepancy in release dates, and currently we are in the lag period, thereby missing most of the interesting COVID terms (and some others). John On Aug 27, 2021, at 10:15 AM, Jennifer Leigh Vendetti > wrote: Hello Zach, On Aug 27, 2021, at 9:47 AM, support at bioontology.org wrote: Hello Sir or Madam, I am currently utilizing the bioontology API for MedDRA through RedCAP. There is a question around the update cycle and current version for reporting. A few questions: 1) How often is the MedDRA version updated? We import MedDRA into BioPortal from the National Library of Medicine?s UMLS. The UMLS is updated twice per year in May (the ?AA? release) and November (the ?AB? release), e.g., this year will be 2021AA and 2021AB. Although we host MedDRA, we?re not the authors and/or maintainers of the vocabulary. I don?t know whether each UMLS release contains a new version of MedDRA. The UMLS provides a vocabulary documentation page where you can find information about when each vocabulary was last updated: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html In particular, this page shows the metadata for MedDRA: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/index.html 2) Confirming the current version, is it 23.1? Yes 3) Is there a regular cycle for MedDRA updates? You may want to check with the authors / maintainers of MedDRA directly to get an answer to this question: https://www.meddra.org/contact Kind regards, Jennifer _______________________________________________ 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 Fri Aug 27 17:03:06 2021 From: support at bioontology.org (support at bioontology.org) Date: Fri, 27 Aug 2021 17:03:06 -0700 Subject: [bioontology-support] [BioPortal] Feedback from mdiller Message-ID: <61297d3a73eeb_67b2297d75c93869@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From amy.dang at deakin.edu.au Sun Aug 29 16:42:29 2021 From: amy.dang at deakin.edu.au (Amy Dang) Date: Sun, 29 Aug 2021 23:42:29 +0000 Subject: [bioontology-support] Can I please find out what version of MedDRA are we using in REDCap? In-Reply-To: References:

Message-ID: Hi John & Jennifer, Thank you for the response below, that is really helpful. Many thanks, Amy From: John Graybeal Sent: Saturday, 28 August 2021 6:24 AM To: Amy Dang ; JESSICA CATHERINE COSTA-PINTO Cc: support at bioontology.org; Jennifer Leigh Vendetti Subject: Re: [bioontology-support] Can I please find out what version of MedDRA are we using in REDCap? Amy, Jessica, If I may add to this excellent summary, we know that MedDRA itself (at the MedDRA site) has been updated to version 24. We do not know why MedDRA is not updated every 6 months in UMLS, but because it is not updated in UMLS, and we get MedDRA only through UMLS, we are unable to provide version 24 of MedDRA in BioPortal. We have not been able to find any other ontological source for MedDRA that can legally be put on BioPortal, so we do not anticipate the latest version of MedDRA itself being on BioPortal until late this year, likely late November. John On Aug 27, 2021, at 10:01 AM, Jennifer Leigh Vendetti > wrote: Hi Amy, On Aug 26, 2021, at 11:29 PM, Amy Dang > wrote: H Bio Ontology team, Can I please find out what version of MedDRA are we using? We import MedDRA into BioPortal from the National Library of Medicine?s UMLS: https://www.nlm.nih.gov/research/umls/quickstart.html We used the MedDRA coding in the RECap provided and when I went to the link it said version 2021AA, 2021AA refers to the UMLS release version, not the MedDRA version. If you want to know what version of MedDRA is included in the 2021AA UMLS release, you can look at this page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html It?s MedDRA version 23.1. is the updated version in REDCap? Do you automatically update the latest versions in REDCap and is this the correct place to find that detail? https://bioportal.bioontology.org/ontologies/MEDDRA?p=summary We?re the developers and maintainers of the BioPortal application, not REDCap. What I can say is that BioPortal only serves the most recent version of any given ontology. I assume that REDCap uses the BioPortal REST API to retrieve ontology data, so I?d guess they are also serving the most recent version of MedDRA. Kind regards, Jennifer _______________________________________________ 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 Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Aug 30 10:08:26 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 30 Aug 2021 17:08:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from mdiller In-Reply-To: <61297d3a73eeb_67b2297d75c93869@ncbo-prd-app-08.stanford.edu.mail> References: <61297d3a73eeb_67b2297d75c93869@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello, Could you please be more specific with your problem report? It would be helpful to see the specific REST calls you issued, along with examples of specific terms where you see this behavior. Kind regards, Jennifer On Aug 27, 2021, at 5:03 PM, support at bioontology.org wrote: Name: mdiller Email: diller17 at ufl.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Email: diller17 at ufl.edu RESTful API for Term Search returns more than just exact matches even if require_exact_matches is set to 'true'. _______________________________________________ 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: