From jgraybeal at stanford.edu Mon Jan 4 11:41:50 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 4 Jan 2021 19:41:50 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Tiffanie Markus In-Reply-To: <5fd8b53c3ac21_42c325c83dc59b8@ncbo-prd-app-09.stanford.edu.mail> References: <5fd8b53c3ac21_42c325c83dc59b8@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Tiffanie, Yes, we tried to make that update before the end of the year, but we ran into some technical difficulties. We will give this a high priority, but continue to have very limited staff time, so I'm sorry to say that I can't promise a delivery date. John On Dec 15, 2020, at 5:08 AM, support at bioontology.org wrote: Name: Tiffanie Markus Email: tiffanie.m.markus at vumc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: 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, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update? Thank you, Tiffanie _______________________________________________ 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 tiffanie.m.markus at vumc.org Mon Jan 4 11:44:23 2021 From: tiffanie.m.markus at vumc.org (Markus, Tiffanie M) Date: Mon, 4 Jan 2021 19:44:23 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Tiffanie Markus In-Reply-To: References: <5fd8b53c3ac21_42c325c83dc59b8@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Great to hear. Thanks for the update. Tiffanie M. Markus, PhD, CCRP Research Assistant Professor Project Director, Emerging Infections Program Department of Health Policy Village at Vanderbilt, Suite 2600 Nashville, Tennessee 37212 Phone: 615-875-8695; Fax: 615-343-3914 tiffanie.m.markus at vumc.org From: John Graybeal Sent: Monday, January 4, 2021 1:42 PM To: support at bioontology.org Cc: Markus, Tiffanie M Subject: Re: [bioontology-support] [BioPortal] Feedback from Tiffanie Markus Tiffanie, Yes, we tried to make that update before the end of the year, but we ran into some technical difficulties. We will give this a high priority, but continue to have very limited staff time, so I'm sorry to say that I can't promise a delivery date. John On Dec 15, 2020, at 5:08 AM, support at bioontology.org wrote: Name: Tiffanie Markus Email: tiffanie.m.markus at vumc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: 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, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update? Thank you, Tiffanie _______________________________________________ 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 [ WARNING : This email came from an external source. Please treat this message with additional caution.] -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 4 12:37:06 2021 From: support at bioontology.org (support at bioontology.org) Date: Mon, 04 Jan 2021 12:37:06 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Keenan Caddell Message-ID: <5ff37c72ce87a_5e281fbe9f03632@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 5 02:04:59 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 05 Jan 2021 02:04:59 -0800 Subject: [bioontology-support] [BioPortal] Feedback from dammh Message-ID: <5ff439cb35c78_2a6c1e376cc667e9@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 5 02:08:48 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 05 Jan 2021 02:08:48 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Anna Jaeger Message-ID: <5ff43ab0394c2_3640276d1d88006c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 5 10:40:40 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 5 Jan 2021 18:40:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from hemien In-Reply-To: <5fdaf07ff0630_29772c8d3c096487@ncbo-prd-app-09.stanford.edu.mail> References: <5fdaf07ff0630_29772c8d3c096487@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <8FA52A7D-8886-4C66-85CE-2146C53F29C7@stanford.edu> Hello Meng Wu, We have deleted the requested ontology with acronym PMO-IMICAMS. Kind regards, Jennifer On Dec 16, 2020, at 9:45 PM, support at bioontology.org wrote: Name: hemien Email: wu.meng at imicams.ac.cn Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPMO-IMICAMS%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fwww.phoc.org.cn%252Fpmo%252Fclass%252FPMO_00000001 Feedback: Hello, We have submited the ontology of PMO-IMICAMS, but we want to have another acronym for it, so we resubmited it as a new ontology whose acronym is PMAPP-PMO as you mentioned in the Help document. Would you please help us to delete the previous ontology PMO-IMICAMS? Thank you very much. Meng Wu _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 6 10:08:49 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 6 Jan 2021 18:08:49 +0000 Subject: [bioontology-support] [BioPortal] Feedback concerning UMLS upgrade (note no changes until upgrade complete) In-Reply-To: <5ff43ab0394c2_3640276d1d88006c@ncbo-prd-app-09.stanford.edu.mail> References: <5ff43ab0394c2_3640276d1d88006c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <9BADA71D-8929-4D3A-9792-F7125B8D1800@stanford.edu> Anna, Hendrik, Keenan, and everyone, As you may have noticed upon visiting BioPortal this week, we intend to upload version 2020AB of the UMLS ontologies later this week. We trust this will address issues with missing codes, including for COVID, in MedDRA, ICD10CM, and the other UMLS ontologies. Please note that we are performing this upgrade process during the work week, and it will not be possible to process new submissions or perform other metadata changes until the upgrade is completed. The targeted upgrade completion time is Friday afternoon, and we'll update the banner on the site when it is fully operational. We will also correct the "Released" date for the 2020AA MedDRA ontology, which I am confident is incorrect even as the ontology is in fact the 2020AA release. (This date in our metadata must be manually updated for each ontology during the release process, and we apparently failed to update it in this case.) Thanks Anna for calling that to our attention. John On Jan 5, 2021, at 2:08 AM, support at bioontology.org wrote: Name: Anna Jaeger Email: anna.jaeger at bnitm.de Location: http%3A%2F%2Fbioportal.bioontology.org%2Ffeedback%3Flocation%3Dhttp%25253A%25252F%25252Fbioportal.bioontology.org%25252Fontologies%25252FMEDDRA%25253Fp%25253Dsummary Feedback: Dear Ladies and Gentlemen, I am wondering about the current version of MedDRA submission (from September 2020). Are you currently really uploaded the version 2020AA which was released in 2018 (05/04/2018)? If so, what is the rationale behind? Many thanks in advance for any reply. Best regards Anna Jaeger Name: dammh Email: dammh at uni-muenster.de Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, we are using the Medical Dictionary for Regulatory Activities Terminology (MedDRA) for a Clinical Study. unfortunately the current Version doesnt have COVID as a Term. Is it possible to get the Ontology updated or who would I have to ask about that? Many thanks and best Regards Hendrik Name: Keenan Caddell Email: keenan.caddell at duke.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FICD10CM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FICD10CM%252FN18%26jump_to_nav%3Dtrue Feedback: Hello, we are currently using the Bioportal API supported by our REDCap team here at Duke. I noticed that for ICD10CM, there was an update that became effective on October 1, 2020, however, some of the new codes from that update are not populating. For instance, N18.31. Can you please let me know if the ontology is fully updated or if there are updates coming soon? Thanks! ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 6 14:53:30 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 06 Jan 2021 14:53:30 -0800 Subject: [bioontology-support] [BioPortal] Feedback from George Oikonomoulas Message-ID: <5ff63f6a93aaf_42511e14af0297dd@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Mohammed.Amin at fda.hhs.gov Fri Jan 8 13:41:37 2021 From: Mohammed.Amin at fda.hhs.gov (Amin, Mohammed *) Date: Fri, 8 Jan 2021 21:41:37 +0000 Subject: [bioontology-support] Latest MedDRA ttl for FDA Message-ID: To whomever this may concern, Happy New Year! My name is Harris and I work on the FDA Search 360 which is a intra FDA search engine. A couple years ago, my colleagues reached out for a MedDRA turtle RDF file based on UMLS. Previously the DB was converted into RDF OWL/TTL file via the umls2rdf Github repo and given to us. If possible, can you please provide the latest TTL file up to and including terms in MedDRA 23.1 release? Best regards, M. Harris Amin Mercado FDA | Center for Drug Evaluation & Research Tel/Direct: +1 202 510 2126 mohammed.amin at fda.hhs.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Jan 11 11:03:07 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 Jan 2021 19:03:07 +0000 Subject: [bioontology-support] [BioPortal] Feedback from George Oikonomoulas In-Reply-To: <5ff63f6a93aaf_42511e14af0297dd@ncbo-prd-app-08.stanford.edu.mail> References: <5ff63f6a93aaf_42511e14af0297dd@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <541545BE-998C-47EF-A078-E5DBC714754A@stanford.edu> Yorgos, Thanks for this query. I'll contact you offline about a conversation! John On Jan 6, 2021, at 2:53 PM, support at bioontology.org wrote: Name: George Oikonomoulas Email: yorgos.oikonomoulas at insel.ch Location: http%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Dear Sir/Madame, I am a pediatric radiologist in the Children's University Hospital of Bern (Switzerland) and also a member in the scientific board of a radiology software company based in Switzerland. We are creating a new RIS/PACS with a few innovations and in this setting i would like to canvass your intentions about a future collaboration between RadLex and our RIS/PACS. Please let me know if you are interested too. I am waiting to your reply. Kind regards Yorgos Oikonomoulas _______________________________________________ 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 Jan 11 11:40:28 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 Jan 2021 19:40:28 +0000 Subject: [bioontology-support] UMLS upgrade complete In-Reply-To: <9BADA71D-8929-4D3A-9792-F7125B8D1800@stanford.edu> References: <5ff43ab0394c2_3640276d1d88006c@ncbo-prd-app-09.stanford.edu.mail> <9BADA71D-8929-4D3A-9792-F7125B8D1800@stanford.edu> Message-ID: <3B10FADE-3CE6-4041-B5DB-58F62C5E1365@stanford.edu> Hello everyone, We have completed the UMLS upgrade to 2020AB, and the BioPortal system is back to full operations. This should incorporate all COVID terms which were a part of UMLS ontology updates prior to November 2020. (Issues briefly observed with downloading ontologies have also gone away.) My thanks to the BioPortal team for putting extra effort into bringing the upgrade on-line right after the holiday break, and cleaning up many of our inactive ontologies. Please email the list with any issues. 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: From vendetti at stanford.edu Mon Jan 11 16:16:31 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 12 Jan 2021 00:16:31 +0000 Subject: [bioontology-support] Issues uploading ontology to bioportal In-Reply-To: References: Message-ID: <7DA494D9-E824-4048-BDD2-806E9BD9D27F@stanford.edu> Hello Inigo, Apologies for the delayed response. On Dec 15, 2020, at 7:02 AM, Inigo Bermejo > wrote: Yesterday I uploaded a new ontology to bioportal (http://bioportal.bioontology.org/ontologies/EMIF-AD), but it seems bioportal was not able to import it properly. For example, the names of classes are not shown (even if the class structure seems to have loaded). If I try to navigate to one of the classes, it never ends loading it. I can see in the Submissions section of the Summary tab that there were ?Error Rdf labels? but I don?t know which ones are wrong. Is there any way I could see the log of the upload/import or some way I can get any insight on what went wrong and where? We don?t currently offer a way for end users to view our ontology processing logs. The owl file (which I have attached) was created in webprotege and subsequently saved with Prot?g? 5.5.0. I?ve worked on reprocessing your ontology in BioPortal and it?s fully available now. I?ve kept track of the details in an issue report in our GitHub repository: https://github.com/ncbo/bioportal-project/issues/200 Feel free to refer to this ticket and contact us via the support list if you experience any other issues. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 11 16:24:57 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 12 Jan 2021 00:24:57 +0000 Subject: [bioontology-support] [BioPortal] Feedback from dammh In-Reply-To: <5ff439cb35c78_2a6c1e376cc667e9@ncbo-prd-app-09.stanford.edu.mail> References: <5ff439cb35c78_2a6c1e376cc667e9@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Hendrik, On Jan 5, 2021, at 2:04 AM, support at bioontology.org wrote: Hello, we are using the Medical Dictionary for Regulatory Activities Terminology (MedDRA) for a Clinical Study. unfortunately the current Version doesnt have COVID as a Term. Is it possible to get the Ontology updated or who would I have to ask about that? We import MedDRA from the National Library of Medicine?s UMLS Metathesaurus [1]. As of today, we've completed importing release 2020AB of the UMLS, which contains version MDR23_0 of MedDRA [2]. This particular version of MedDRA contains two COVID terms: ?Coronavirus infection? ?Coronavirus test positive? Kind regards, Jennifer [1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/sourcerepresentation.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Jan 15 08:40:21 2021 From: support at bioontology.org (support at bioontology.org) Date: Fri, 15 Jan 2021 08:40:21 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Wendy Chao Message-ID: <6001c57575c88_7eb12c5c69427d@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Jan 15 13:18:01 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 15 Jan 2021 21:18:01 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Wendy Chao In-Reply-To: <6001c57575c88_7eb12c5c69427d@ncbo-prd-app-08.stanford.edu.mail> References: <6001c57575c88_7eb12c5c69427d@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Wendy, Thanks for contacting us. We serve ontology data, but aren?t the ontology authors or maintainers. I suggest you contact the ontology authors directly if you feel that something is incorrectly represented. You can find contact information on the summary page for NDDF: http://bioportal.bioontology.org/ontologies/NDDF?p=summary Kind regards, Jennifer On Jan 15, 2021, at 8:40 AM, support at bioontology.org wrote: Name: Wendy Chao Email: oahcydnew at hotmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNDDF%3Fp%3Dclasses%26conceptid%3D004440 Feedback: http://bioportal.bioontology.org/ontologies/NDDF?p=classes&conceptid=004440# For sodium thiosalicylate 50 mg/mL injection ampul (CUI C0246203 C0980312; notation 004440), it has a synonym/altLabel of fluvastatin sodium. These two medications are very different and therefore I think there are some incorrect mappings are happening here. Thanks!! Wendy Chao RPh. _______________________________________________ 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 Tue Jan 19 03:59:36 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 19 Jan 2021 03:59:36 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Eigil Samset Message-ID: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 19 09:03:40 2021 From: support at bioontology.org (support at bioontology.org) Date: Tue, 19 Jan 2021 09:03:40 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Fabio Saccona Message-ID: <600710ece3b34_3bb829ee13c3937f@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 20 20:44:25 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 21 Jan 2021 04:44:25 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Fabio Saccona In-Reply-To: <600710ece3b34_3bb829ee13c3937f@ncbo-prd-app-08.stanford.edu.mail> References: <600710ece3b34_3bb829ee13c3937f@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Thank you for your report, Fabio. We?ve recently updated our UMLS distribution to its latest version, 2020AB, which included a new version of MEDDRA ontology. Unfortunately, it appears that we?re no longer able to retrieve the ontology roots, which is why the classes page is failing. I?ll keep you posted as soon as this issue is resolved. Thank you for your patience. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 9:03 AM, support at bioontology.org wrote: Name: Fabio Saccona Email: fabio.saccona at cpo.it Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA Feedback: Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root). Many thanks in advance, regards Fabio Saccona _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Jan 21 10:01:32 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 21 Jan 2021 18:01:32 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eigil Samset In-Reply-To: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> References: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <8ED85FDB-3D82-449F-A1B0-0EC5DE8D4821@stanford.edu> Hi Eigil, Thank you so much for your report. I was able to reproduce it on our end, and we are currently working on a solution. I?ll keep you posted once the SNOMED code search is fully functional. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 3:59 AM, support at bioontology.org wrote: Name: Eigil Samset Email: eigil.samset at ge.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F698871007 Feedback: It seems that searching for SNOMED CT codes is not working at the moment. It was not working yesterday (first time I noticed the problem) and not today. All queries give "No results found", e.g. : 698871007 _______________________________________________ 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 Yelena.Fridgant at health.nsw.gov.au Wed Jan 20 17:59:24 2021 From: Yelena.Fridgant at health.nsw.gov.au (Yelena Fridgant (Sydney LHD)) Date: Thu, 21 Jan 2021 01:59:24 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Yelena Fridgant In-Reply-To: <6008c744409eb_7b6e1edbd6c6948f@ncbo-prd-app-09.stanford.edu.mail> References: <6008c744409eb_7b6e1edbd6c6948f@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <07A7421E-63B6-426C-9780-9E5E1D0F8F12@health.nsw.gov.au> Is this a copy of my request with no actual answer ?? Confused now v Sent from my iPhone On 21 Jan 2021, at 11:15 am, support at bioontology.org wrote: ? Name: Yelena Fridgant Email: yelena.fridgant at health.nsw.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hi, I've forgotten what I've used for our account and it is linked to our REDCap installation. Could you please provide the account name or a way for me to reset ? I have used either my own email yelena.fridgant at health.nsw.gov.au, slhd-redcap at health.nsw.gov.au or slhd-research at health.nsw.gov.au for the account. thanks !! Yelena This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of NSW Health or any of its entities. -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 20 16:13:56 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 20 Jan 2021 16:13:56 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Yelena Fridgant Message-ID: <6008c744409eb_7b6e1edbd6c6948f@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 21 08:22:04 2021 From: support at bioontology.org (support at bioontology.org) Date: Thu, 21 Jan 2021 08:22:04 -0800 Subject: [bioontology-support] [BioPortal] Feedback from sdmiller Message-ID: <6009aa2cb96e6_49d32bec52463733@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From DVining at mdanderson.org Sat Jan 23 07:49:42 2021 From: DVining at mdanderson.org (Vining,David) Date: Sat, 23 Jan 2021 15:49:42 +0000 Subject: [bioontology-support] Incorrect SNOMED references Message-ID: <9b14310e2a7d4f13891cd25ad7e50fab@mdanderson.org> I was working with your copy of the SNOMED ontology, and I noticed some incorrect references as illustrated below. David David J. Vining, MD Professor, Department of Abdominal Imaging MD Anderson Cancer Center Disclosures as required by 2019 MDACC COI Management Plan: VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging [cid:image001.png at 01D6F16D.11D79A40] [cid:image002.png at 01D6F16D.11D79A40] The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 365537 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 362541 bytes Desc: image002.png URL: From jgraybeal at stanford.edu Sat Jan 23 11:49:20 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 23 Jan 2021 19:49:20 +0000 Subject: [bioontology-support] Incorrect SNOMED references In-Reply-To: <9b14310e2a7d4f13891cd25ad7e50fab@mdanderson.org> References: <9b14310e2a7d4f13891cd25ad7e50fab@mdanderson.org> Message-ID: <35A9F5E3-02BE-4CFA-993E-FF7A760FFDCD@stanford.edu> David, Thank you for this report. I was unable to reproduce this behavior?can you try again, perhaps in a new browser, and tell us if this is still happening for you, especially after your browser cache is refreshed? Any additional examples would be welcome?I assume many of the entries were working as expected? We have been working recently to re-index SNOMED and it may be we created a temporary inconsistency somehow, though I confess I am at a loss to imagine how! In any case, we look forward to sorting it out. John On Jan 23, 2021, at 7:49 AM, Vining,David > wrote: I was working with your copy of the SNOMED ontology, and I noticed some incorrect references as illustrated below. David David J. Vining, MD Professor, Department of Abdominal Imaging MD Anderson Cancer Center Disclosures as required by 2019 MDACC COI Management Plan: VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems. _______________________________________________ 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 Sat Jan 23 12:04:02 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 23 Jan 2021 20:04:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sdmiller In-Reply-To: <6009aa2cb96e6_49d32bec52463733@ncbo-prd-app-08.stanford.edu.mail> References: <6009aa2cb96e6_49d32bec52463733@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <540BCCC8-561B-4D4F-9A54-8239DA357F01@stanford.edu> Hello Sierra, Thank you for your report. I haven't been able to duplicate this behavior. Is the screenshot below the location that you are seeing the issue? Can you duplicate the issue after clearing your cache, or in a separate browser? Similar to another case today, it is hard for me to imagine what might be going on, so additional information would be helpful. John [cid:0B896F9E-3F7F-4A97-9CB9-C5266C0D1EFD] On Jan 21, 2021, at 8:22 AM, support at bioontology.org wrote: Name: sdmiller Email: sierra.miller at nist.gov Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNIST_GEL Feedback: Email: sierra.miller at nist.gov, I have an uploaded ontology where it is showing as Genome Editing Concepts/off-target but the dash disappears in the Classes tree on the left of the display. I have verified that the term contains this dash between "off" and "target" and it seems to have the dash in the labels to the right (can provide screen shot) but it isn't maintaining it on the left. Other terms below this do contain the dash so I'm not sure why it isn't for this term. _______________________________________________ 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 2021-01-23 at 11.53.13 AM.png Type: image/png Size: 112624 bytes Desc: Screen Shot 2021-01-23 at 11.53.13 AM.png URL: From jgraybeal at stanford.edu Sat Jan 23 12:09:30 2021 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 23 Jan 2021 20:09:30 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Yelena Fridgant In-Reply-To: <6008c744409eb_7b6e1edbd6c6948f@ncbo-prd-app-09.stanford.edu.mail> References: <6008c744409eb_7b6e1edbd6c6948f@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Yelena, I will reply offline to this request. John On Jan 20, 2021, at 4:13 PM, support at bioontology.org wrote: Name: Yelena Fridgant Email: yelena.fridgant at health.nsw.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hi, I've forgotten what I've used for our account and it is linked to our REDCap installation. Could you please provide the account name or a way for me to reset ? I have used either my own email yelena.fridgant at health.nsw.gov.au, slhd-redcap at health.nsw.gov.au or slhd-research at health.nsw.gov.au for the account. thanks !! Yelena _______________________________________________ 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 DVining at mdanderson.org Sat Jan 23 12:13:51 2021 From: DVining at mdanderson.org (Vining,David) Date: Sat, 23 Jan 2021 20:13:51 +0000 Subject: [bioontology-support] Incorrect SNOMED references In-Reply-To: <35A9F5E3-02BE-4CFA-993E-FF7A760FFDCD@stanford.edu> References: <9b14310e2a7d4f13891cd25ad7e50fab@mdanderson.org> <35A9F5E3-02BE-4CFA-993E-FF7A760FFDCD@stanford.edu> Message-ID: I refreshed my Chrome browser cache and that fixed the problem. I?ve had similar caching problems in the past with my own software development ? it just didn?t occur to me to refresh the cache. It?s so perplexing when that happens. Thanks, Daivd David J. Vining, MD Professor, Department of Abdominal Imaging MD Anderson Cancer Center Disclosures as required by 2019 MDACC COI Management Plan: VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging From: John Graybeal Sent: Saturday, January 23, 2021 1:49 PM To: Vining,David Cc: support at bioontology.org Subject: [EXT] Re: [bioontology-support] Incorrect SNOMED references WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe. David, Thank you for this report. I was unable to reproduce this behavior?can you try again, perhaps in a new browser, and tell us if this is still happening for you, especially after your browser cache is refreshed? Any additional examples would be welcome?I assume many of the entries were working as expected? We have been working recently to re-index SNOMED and it may be we created a temporary inconsistency somehow, though I confess I am at a loss to imagine how! In any case, we look forward to sorting it out. John On Jan 23, 2021, at 7:49 AM, Vining,David > wrote: I was working with your copy of the SNOMED ontology, and I noticed some incorrect references as illustrated below. David David J. Vining, MD Professor, Department of Abdominal Imaging MD Anderson Cancer Center Disclosures as required by 2019 MDACC COI Management Plan: VisionSR, Majority owner and CEO, multimedia structured reporting for use in advancing medical research Bracco Diagnostics, Inventor, virtual colonoscopy-related products for colorectal cancer imaging The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems. _______________________________________________ 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 The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Sat Jan 23 14:57:07 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Sat, 23 Jan 2021 22:57:07 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Fabio Saccona In-Reply-To: References: <600710ece3b34_3bb829ee13c3937f@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <3B529C2C-0AD4-4013-A4F1-5F51B8C03853@stanford.edu> Hi Fabio, Just wanted to give you an update on our MEDDRA investigation. We?ve discovered a number of significant differences between the latest (UMLS 2020AB) and the previous versions (UMLS 2020AA) of MEDDRA ontology. Most notably, some of the subclass declarations that appear in the older version are missing from the latest one. If you?re interested in the nitty gritty details, they are all documented in this Github issue: https://github.com/ncbo/bioportal-project/issues/202 We don?t have a concrete solution at this point other than switching the ontology to a ?flat? hierarchical mode, which allows browsing via the ?Jump to? box. https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes At the moment browsing the class tree no longer results in a ?Page not found? error, but a more permanent fix that would allow browsing the tree structure is yet to be implemented. As before, I?ll keep you posted once we fully resolve this issue. Thank you again for your patience. Michael On Jan 20, 2021, at 8:44 PM, Michael Dorf > wrote: Thank you for your report, Fabio. We?ve recently updated our UMLS distribution to its latest version, 2020AB, which included a new version of MEDDRA ontology. Unfortunately, it appears that we?re no longer able to retrieve the ontology roots, which is why the classes page is failing. I?ll keep you posted as soon as this issue is resolved. Thank you for your patience. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 9:03 AM, support at bioontology.org wrote: Name: Fabio Saccona Email: fabio.saccona at cpo.it Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA Feedback: Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root). Many thanks in advance, regards Fabio Saccona _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Jan 24 23:39:50 2021 From: support at bioontology.org (support at bioontology.org) Date: Sun, 24 Jan 2021 23:39:50 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Marjorie Medina Message-ID: <600e75c647f1e_9ff2bd462c660b@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Eigil.Samset at ge.com Thu Jan 21 23:42:58 2021 From: Eigil.Samset at ge.com (Samset, Eigil (GE Healthcare)) Date: Fri, 22 Jan 2021 07:42:58 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eigil Samset In-Reply-To: <8ED85FDB-3D82-449F-A1B0-0EC5DE8D4821@stanford.edu> References: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> <8ED85FDB-3D82-449F-A1B0-0EC5DE8D4821@stanford.edu> Message-ID: Thanks, Michael. The bioportal is great, so hope you?ll get the functionality back to normal soon. Eigil --- Eigil Samset, PhD Chief Technology Scientist Cardiology Solutions, GE Healthcare e-mail: eigil.samset at ge.com cell: +47 92831484 From: Michael Dorf Sent: Thursday, January 21, 2021 7:02 PM To: support at bioontology.org Cc: Samset, Eigil (GE Healthcare) Subject: EXT: Re: [bioontology-support] [BioPortal] Feedback from Eigil Samset Hi Eigil, Thank you so much for your report. I was able to reproduce it on our end, and we are currently working on a solution. I?ll keep you posted once the SNOMED code search is fully functional. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 3:59 AM, support at bioontology.org wrote: Name: Eigil Samset Email: eigil.samset at ge.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F698871007 Feedback: It seems that searching for SNOMED CT codes is not working at the moment. It was not working yesterday (first time I noticed the problem) and not today. All queries give "No results found", e.g. : 698871007 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jan 25 11:32:12 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 25 Jan 2021 19:32:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eigil Samset In-Reply-To: References: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> <8ED85FDB-3D82-449F-A1B0-0EC5DE8D4821@stanford.edu> Message-ID: Hi Eigil, Thank you for your patience with this issue. We have re-processed SNOMEDCT on our end, and the problem should now be resolved. Please let us know if you still notice anything abnormal. Michael On Jan 21, 2021, at 11:42 PM, Samset, Eigil (GE Healthcare) > wrote: Thanks, Michael. The bioportal is great, so hope you?ll get the functionality back to normal soon. Eigil --- Eigil Samset, PhD Chief Technology Scientist Cardiology Solutions, GE Healthcare e-mail: eigil.samset at ge.com cell: +47 92831484 From: Michael Dorf > Sent: Thursday, January 21, 2021 7:02 PM To: support at bioontology.org Cc: Samset, Eigil (GE Healthcare) Subject: EXT: Re: [bioontology-support] [BioPortal] Feedback from Eigil Samset Hi Eigil, Thank you so much for your report. I was able to reproduce it on our end, and we are currently working on a solution. I?ll keep you posted once the SNOMED code search is fully functional. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 3:59 AM, support at bioontology.org wrote: Name: Eigil Samset Email: eigil.samset at ge.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F698871007 Feedback: It seems that searching for SNOMED CT codes is not working at the moment. It was not working yesterday (first time I noticed the problem) and not today. All queries give "No results found", e.g. : 698871007 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jan 25 13:41:02 2021 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 25 Jan 2021 21:41:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Marjorie Medina In-Reply-To: <600e75c647f1e_9ff2bd462c660b@ncbo-prd-app-09.stanford.edu.mail> References: <600e75c647f1e_9ff2bd462c660b@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <1151015A-1670-4531-BD05-C03D6166FC41@stanford.edu> Hi Marjorie, Thank you for this report. Can you please give us a few specific examples of terms that are missing? We?ve noticed a number of significant changes in MEDDRA version 23.0 we?ve recently brought in as part of the UMLS 2020AB upgrade. One of these changes is preventing the class hierarchical tree from being displayed properly in BioPortal. At the moment, the only recourse is to use the ?Jump to? box to navigate to a specific term in MEDDRA. We are still exploring potential solutions to this issue. I wanted to see if your problem is related to the one we?re currently investigating. Thank you for your input and patience. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 24, 2021, at 11:39 PM, support at bioontology.org wrote: Name: Marjorie Medina Email: marjorie.medina at mims.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FMEDDRA%252F10012378%26jump_to_nav%3Dtrue Feedback: Hi. I have an issue with the organ classification in MedDRA. Currently, the organ classes are missing when I try to check on a specific term. _______________________________________________ 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 Eigil.Samset at ge.com Mon Jan 25 23:16:40 2021 From: Eigil.Samset at ge.com (Samset, Eigil (GE Healthcare)) Date: Tue, 26 Jan 2021 07:16:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eigil Samset In-Reply-To: References: <6006c9a86a579_6af728a2ff8340e0@ncbo-prd-app-09.stanford.edu.mail> <8ED85FDB-3D82-449F-A1B0-0EC5DE8D4821@stanford.edu>

Message-ID: Hi Michael, Everything is back up. Thanks for attending to this issue. Eigil From: Michael Dorf Sent: Monday, January 25, 2021 8:32 PM To: Samset, Eigil (GE Healthcare) Cc: support at bioontology.org Subject: EXT: Re: [bioontology-support] [BioPortal] Feedback from Eigil Samset Hi Eigil, Thank you for your patience with this issue. We have re-processed SNOMEDCT on our end, and the problem should now be resolved. Please let us know if you still notice anything abnormal. Michael On Jan 21, 2021, at 11:42 PM, Samset, Eigil (GE Healthcare) > wrote: Thanks, Michael. The bioportal is great, so hope you?ll get the functionality back to normal soon. Eigil --- Eigil Samset, PhD Chief Technology Scientist Cardiology Solutions, GE Healthcare e-mail: eigil.samset at ge.com cell: +47 92831484 From: Michael Dorf > Sent: Thursday, January 21, 2021 7:02 PM To: support at bioontology.org Cc: Samset, Eigil (GE Healthcare) > Subject: EXT: Re: [bioontology-support] [BioPortal] Feedback from Eigil Samset Hi Eigil, Thank you so much for your report. I was able to reproduce it on our end, and we are currently working on a solution. I?ll keep you posted once the SNOMED code search is fully functional. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 19, 2021, at 3:59 AM, support at bioontology.org wrote: Name: Eigil Samset Email: eigil.samset at ge.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F698871007 Feedback: It seems that searching for SNOMED CT codes is not working at the moment. It was not working yesterday (first time I noticed the problem) and not today. All queries give "No results found", e.g. : 698871007 _______________________________________________ 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 vasilis.promponas at gmail.com Wed Jan 27 01:00:30 2021 From: vasilis.promponas at gmail.com (Vasilis Promponas) Date: Wed, 27 Jan 2021 11:00:30 +0200 Subject: [bioontology-support] API related query Message-ID: Dear Sir/Madam, First thank you for providing these great resources. I have a problem with a perl script for programmatically accessing the Recommender functionality. My code (see below) is adapted from the example https://github.com/ncbo/ncbo_rest_sample_code/blob/master/perl/annotate_text.pl ### My code ### my $recommender_link = $resources->{'links'}->{'recommender'}; my $uri = $recommender_link . "?text=" . $text_to_annotate . "&include=prefLabel&apikey=" . $api_key; print $uri, "\n"; my $recommender_json = get( $uri ); die "Could not get $recommender_link!" unless defined $recommender_json; ############# The script terminates as follows: 'Could not get http://data.bioontology.org/recommender!' Importantly, when using the 'recommender_v1' resource the script does not terminate, however the json object returned is empty. For your information, I can get valid results when accessing the annotator resource. I would appreciate any advice on the above. Many thanks and best regards, Vasilis Promponas -------------------------------------------------- Vasilis Promponas, PhD Associate Professor in Bioinformatics Head, Bioinformatics Research Laboratory Department of Biological Sciences New Campus, Office B161 University of Cyprus P.O. Box 20537 CY 1678, NICOSIA CYPRUS tel: 00357-22892879 (office) 00357-22893972 (lab) fax: 00357-22895095 (departmental) email: vprobon at ucy.ac.cy, vprobon at biol.uoa.gr, vasilis.promponas at gmail.com web: http://troodos.biol.ucy.ac.cy Virus-free. www.avg.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 27 11:16:50 2021 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 27 Jan 2021 19:16:50 +0000 Subject: [bioontology-support] API related query In-Reply-To: References: Message-ID: <164B1379-4D1C-4741-AE09-804A126A681A@stanford.edu> Hello Vasilis, On Jan 27, 2021, at 1:00 AM, Vasilis Promponas > wrote: I have a problem with a perl script for programmatically accessing the Recommender functionality. My code (see below) is adapted from the example https://github.com/ncbo/ncbo_rest_sample_code/blob/master/perl/annotate_text.pl ### My code ### my $recommender_link = $resources->{'links'}->{'recommender'}; my $uri = $recommender_link . "?text=" . $text_to_annotate . "&include=prefLabel&apikey=" . $api_key; You?re using a parameter here called ?text?, which is incorrect for the /recommender endpoint - it should be ?input? instead. Also, you don't need the include parameter of ?prefLabel?. Full documentation for what the /recommender endpoint accepts is available here: http://data.bioontology.org/documentation#nav_recommender print $uri, "\n"; my $recommender_json = get( $uri ); die "Could not get $recommender_link!" unless defined $recommender_json; ############# The script terminates as follows: 'Could not get http://data.bioontology.org/recommender!' Importantly, when using the 'recommender_v1' resource the script does not terminate, however the json object returned is empty. Apologies if it isn?t clear, but the /recommender_v1 endpoint is an older version - you should use the /recommender endpoint. I created a gist in GitHub that you should be able to use to get the Perl example code working in your environment. You?ll need to modify it to enter your API key: https://gist.github.com/jvendetti/d98ec5d7423edc87b37dfddbf784161e Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 27 18:46:13 2021 From: support at bioontology.org (support at bioontology.org) Date: Wed, 27 Jan 2021 18:46:13 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Mark Miller Message-ID: <60122575cf588_1e5726c080c842ba@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vasilis.promponas at gmail.com Wed Jan 27 17:30:54 2021 From: vasilis.promponas at gmail.com (Vasilis Promponas) Date: Thu, 28 Jan 2021 03:30:54 +0200 Subject: [bioontology-support] API related query In-Reply-To: <164B1379-4D1C-4741-AE09-804A126A681A@stanford.edu> References: <164B1379-4D1C-4741-AE09-804A126A681A@stanford.edu> Message-ID: Dear Jennifer, Thank you very much for the prompt reply. Your help is very much appreciated!! Kind regards, Vasilis -------------------------------------------------- Vasilis Promponas, PhD Associate Professor in Bioinformatics Head, Bioinformatics Research Laboratory Department of Biological Sciences New Campus, Office B161 University of Cyprus P.O. Box 20537 CY 1678, NICOSIA CYPRUS tel: 00357-22892879 (office) 00357-22893972 (lab) fax: 00357-22895095 (departmental) email: vprobon at ucy.ac.cy, vprobon at biol.uoa.gr, vasilis.promponas at gmail.com web: http://troodos.biol.ucy.ac.cy On Wed, Jan 27, 2021 at 9:16 PM Jennifer Leigh Vendetti < vendetti at stanford.edu> wrote: > Hello Vasilis, > > > On Jan 27, 2021, at 1:00 AM, Vasilis Promponas < > vasilis.promponas at gmail.com> wrote: > > I have a problem with a perl script for programmatically accessing the > Recommender functionality. My code (see below) is adapted from the example > > > https://github.com/ncbo/ncbo_rest_sample_code/blob/master/perl/annotate_text.pl > > ### My code ### > my $recommender_link = $resources->{'links'}->{'recommender'}; > my $uri = $recommender_link . "?text=" . $text_to_annotate . > "&include=prefLabel&apikey=" . $api_key; > > > > You?re using a parameter here called ?text?, which is incorrect for the > /recommender endpoint - it should be ?input? instead. Also, you don't need > the include parameter of ?prefLabel?. Full documentation for what the > /recommender endpoint accepts is available here: > > http://data.bioontology.org/documentation#nav_recommender > > > print $uri, "\n"; > my $recommender_json = get( $uri ); > die "Could not get $recommender_link!" unless defined $recommender_json; > ############# > > The script terminates as follows: > > 'Could not get http://data.bioontology.org/recommender!' > > Importantly, when using the 'recommender_v1' resource the script does not > terminate, however the json object returned is empty. > > > > Apologies if it isn?t clear, but the /recommender_v1 endpoint is an older > version - you should use the /recommender endpoint. > > I created a gist in GitHub that you should be able to use to get the Perl > example code working in your environment. You?ll need to modify it to enter > your API key: > > https://gist.github.com/jvendetti/d98ec5d7423edc87b37dfddbf784161e > > Kind regards, > Jennifer > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mason.edmison at abbvie.com Thu Jan 28 11:39:43 2021 From: mason.edmison at abbvie.com (Edmison, Mason) Date: Thu, 28 Jan 2021 19:39:43 +0000 Subject: [bioontology-support] Download DRON as OWL? Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Jan 29 04:50:55 2021 From: support at bioontology.org (support at bioontology.org) Date: Fri, 29 Jan 2021 04:50:55 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Maarten Boers Message-ID: <601404aff1b42_6eae20215b4495c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From fabio.saccona at cpo.it Fri Jan 29 07:22:34 2021 From: fabio.saccona at cpo.it (Fabio Saccona) Date: Fri, 29 Jan 2021 16:22:34 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Fabio Saccona In-Reply-To: <3B529C2C-0AD4-4013-A4F1-5F51B8C03853@stanford.edu> References: <600710ece3b34_3bb829ee13c3937f@ncbo-prd-app-08.stanford.edu.mail> <3B529C2C-0AD4-4013-A4F1-5F51B8C03853@stanford.edu> Message-ID: Many thanks for your explanation, Micheal! For my development team, a complete solution is not urgent, because we use your "Form autocomplete" widget in one of our applications (great job!). Thanks for keeping me updated anyway, I need to report to an organization that usually uses your site and is very interested in solving the problem. Best regards, Fabio Il giorno sab 23 gen 2021 alle ore 23:57 Michael Dorf ha scritto: > Hi Fabio, > > Just wanted to give you an update on our MEDDRA investigation. We?ve > discovered a number of significant differences between the latest (UMLS > 2020AB) and the previous versions (UMLS 2020AA) of MEDDRA ontology. Most > notably, some of the subclass declarations that appear in the older version > are missing from the latest one. If you?re interested in the nitty gritty > details, they are all documented in this Github issue: > > https://github.com/ncbo/bioportal-project/issues/202 > > We don?t have a concrete solution at this point other than switching the > ontology to a ?flat? hierarchical mode, which allows browsing via the ?Jump > to? box. > > https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes > > At the moment browsing the class tree no longer results in a ?Page not > found? error, but a more permanent fix that would allow browsing the tree > structure is yet to be implemented. > > As before, I?ll keep you posted once we fully resolve this issue. > > Thank you again for your patience. > > Michael > > > > > On Jan 20, 2021, at 8:44 PM, Michael Dorf wrote: > > Thank you for your report, Fabio. We?ve recently updated our UMLS > distribution to its latest version, 2020AB, which included a new version of > MEDDRA ontology. Unfortunately, it appears that we?re no longer able to > retrieve the ontology roots, which is why the classes page is failing. I?ll > keep you posted as soon as this issue is resolved. > > Thank you for your patience. > > Michael > > > ---------------------------------------------------- > Michael Dorf > Chief Software Architect > The National Center for Biomedical Ontology > Stanford Biomedical Informatics Research > mdorf at stanford.edu > O: 650-723-0357 > M: 650-995-4374 > ---------------------------------------------------- > > On Jan 19, 2021, at 9:03 AM, support at bioontology.org wrote: > > Name: Fabio Saccona > > Email: fabio.saccona at cpo.it > > Location: http%3A%2F%2Fbioportal.bioontology.org > %2Fontologies%2FMEDDRA > > > *Feedback:* > > Please, verify MedDRA classes page, because is notifying problem > retrieving SOC (see: > http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root > ). > > Many thanks in advance, regards > Fabio Saccona > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -- Fabio SACCONA SSD Epidemiologia Clinica e Valutativa - CRPT SC Epidemiologia dei Tumori - CRPT U AOU Citt? della Salute e della Scienza di Torino Via Santena 7, 10126 Torino TO Tel.: +39 0116336854, Fax: +39 0116334571 fsaccona at cittadellasalute.to.it, fabio.saccona at cpo.it, fabio.saccona at unito.it -------------- next part -------------- An HTML attachment was scrubbed... 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