From gcheng at health.ucsd.edu Thu Oct 1 07:29:21 2020 From: gcheng at health.ucsd.edu (Cheng, George) Date: Thu, 1 Oct 2020 14:29:21 +0000 Subject: [bioontology-support] question Message-ID: Hi how do I access CPT code search from bioontology? it helps me build my practice and I?d appreciate your help in this matter. thank you, gc George Cheng MD PhD Director of Interventional Pulmonology, Bronchoscopy, and Pleural Disease University of California San Diego 9300 Campus Point Drive MC 7381 San Diego, CA 92103 From RushikeshKulkarni at mednet.ucla.edu Thu Oct 1 14:54:37 2020 From: RushikeshKulkarni at mednet.ucla.edu (Kulkarni, Rushikesh) Date: Thu, 1 Oct 2020 21:54:37 +0000 Subject: [bioontology-support] NCBO Virtual Appliance configuration with RadLex In-Reply-To: <066CC123-F9CF-4241-85DC-1150D12D779A@stanford.edu> References: <262BCEE0-FA2E-44C7-BC96-71CF3B3E899C@stanford.edu> <615B7359-80BA-4083-8983-357D69FF83C3@stanford.edu> <066CC123-F9CF-4241-85DC-1150D12D779A@stanford.edu> Message-ID: Thanks Michael for all you help! I was able to login with admin credentials. Regards, Rushi From: Michael Dorf Sent: Wednesday, September 30, 2020 4:57 PM To: Kulkarni, Rushikesh Cc: John Graybeal ; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Please see my responses embedded below. Thanks, Michael On Sep 30, 2020, at 3:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, Thank you for your prompt reply! I followed your steps and able to set RadLex?s preferred name and other properties. I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it? Here are my questions, 1. How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing but, it took me to login page. That?s the correct URL. Just login with your default admin credentials and you should see your Appliance ID there: * Username: admin * Password: changemeNOW I encourage you to review our Virtual Appliance documentation. All of these answers can be found there: https://ontoportal.github.io/administration/steps/initial_installation/ https://ontoportal.github.io/administration/steps/registration/ 2. Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account? Answered above Once again, Thank you for all you help. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 1:29 PM To: John Graybeal > Cc: Kulkarni, Rushikesh >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Try setting the Preferred Name, Synonym, and Definition properties under ?advanced OWL options? via the ?Edit Submission Information? page to these: Once you hit ?Save Submission?, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn?t try re-processing the ontology manually after you?ve set the advanced OWL options. Let me know if this helps. Thank you, Michael On Sep 30, 2020, at 1:18 PM, John Graybeal > wrote: Rushi, Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away. John On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh > wrote: Hello, I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI. But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference) For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'. Can you please help me with this issue? I tried following things to debug the issue, 1. Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script. 2. Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"] 3. Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine. Thanks in advance. Regards, Rushi Kulkarni UCLA Health ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Oct 1 15:04:15 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 1 Oct 2020 22:04:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail> References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. [cid:1CD8F7AF-59E3-40D0-902C-3E10F6C02872] Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ 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 2020-10-01 at 2.59.28 PM.png Type: image/png Size: 74037 bytes Desc: Screen Shot 2020-10-01 at 2.59.28 PM.png URL: From RScheuermann at jcvi.org Thu Oct 1 15:12:21 2020 From: RScheuermann at jcvi.org (Scheuermann, Richard) Date: Thu, 1 Oct 2020 22:12:21 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail> Message-ID: How do we change that? -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf Date: Thursday, October 1, 2020 at 3:05 PM To: "support at bioontology.org" Cc: "Richard H. Scheuermann" Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. [cid:image001.png at 01D69805.40790620] Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ 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: image001.png Type: image/png Size: 74038 bytes Desc: image001.png URL: From jgraybeal at stanford.edu Thu Oct 1 16:18:26 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 1 Oct 2020 23:18:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail>

Message-ID: <24E9FAE4-F78D-42A0-A169-C753003B457F@stanford.edu> Richard, Thanks for your question. We can talk offline about the exact form of the change that would suit you?for example, it is straightforward to search for it on the ontologies page, but if it's important do so so from the main page also, we could add a checkbox to offer the option of including views in the search. Possibly another option would appeal more to you. Because at the moment we are excruciatingly limited in our available development resources, we don't have anyone who can do this change. If you can identify a funding source, I believe we could use it to acquire additional resources for the time needed to make the change. Please contact me directly if this interests you. John On Oct 1, 2020, at 3:12 PM, Scheuermann, Richard > wrote: How do we change that? -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf > Date: Thursday, October 1, 2020 at 3:05 PM To: "support at bioontology.org" > Cc: "Richard H. Scheuermann" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From RScheuermann at jcvi.org Thu Oct 1 16:24:42 2020 From: RScheuermann at jcvi.org (Scheuermann, Richard) Date: Thu, 1 Oct 2020 23:24:42 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: <24E9FAE4-F78D-42A0-A169-C753003B457F@stanford.edu> References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail>

<24E9FAE4-F78D-42A0-A169-C753003B457F@stanford.edu> Message-ID: <10A139BB-47CB-4658-A3F3-9DF41C622AA2@jcvi.org> John, Thanks for getting back to me. I think we figured it out. We can now find PCL through the search function! Best, Richard -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: John Graybeal Date: Thursday, October 1, 2020 at 4:22 PM To: "Richard H. Scheuermann" Cc: Michael Dorf , "support at bioontology.org" Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Richard, Thanks for your question. We can talk offline about the exact form of the change that would suit you?for example, it is straightforward to search for it on the ontologies page, but if it's important do so so from the main page also, we could add a checkbox to offer the option of including views in the search. Possibly another option would appeal more to you. Because at the moment we are excruciatingly limited in our available development resources, we don't have anyone who can do this change. If you can identify a funding source, I believe we could use it to acquire additional resources for the time needed to make the change. Please contact me directly if this interests you. John On Oct 1, 2020, at 3:12 PM, Scheuermann, Richard > wrote: How do we change that? -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf > Date: Thursday, October 1, 2020 at 3:05 PM To: "support at bioontology.org" > Cc: "Richard H. Scheuermann" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Oct 1 16:30:23 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 1 Oct 2020 23:30:23 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: <10A139BB-47CB-4658-A3F3-9DF41C622AA2@jcvi.org> References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail>

<24E9FAE4-F78D-42A0-A169-C753003B457F@stanford.edu> <10A139BB-47CB-4658-A3F3-9DF41C622AA2@jcvi.org> Message-ID: <69C30BC4-EC04-4438-8493-BEF570A3203D@stanford.edu> Hi Richard, You are able to find PCL because I?ve removed the ?view? relationship between PCL and CL. The ontology is still being re-processed in order for all the relevant ontology-only services to get enabled. It should be fully processed as a standalone ontology in the next hour. Thanks, Michael On Oct 1, 2020, at 4:24 PM, Scheuermann, Richard > wrote: John, Thanks for getting back to me. I think we figured it out. We can now find PCL through the search function! Best, Richard -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: John Graybeal > Date: Thursday, October 1, 2020 at 4:22 PM To: "Richard H. Scheuermann" > Cc: Michael Dorf >, "support at bioontology.org" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Richard, Thanks for your question. We can talk offline about the exact form of the change that would suit you?for example, it is straightforward to search for it on the ontologies page, but if it's important do so so from the main page also, we could add a checkbox to offer the option of including views in the search. Possibly another option would appeal more to you. Because at the moment we are excruciatingly limited in our available development resources, we don't have anyone who can do this change. If you can identify a funding source, I believe we could use it to acquire additional resources for the time needed to make the change. Please contact me directly if this interests you. John On Oct 1, 2020, at 3:12 PM, Scheuermann, Richard > wrote: How do we change that? -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf > Date: Thursday, October 1, 2020 at 3:05 PM To: "support at bioontology.org" > Cc: "Richard H. Scheuermann" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From RScheuermann at jcvi.org Thu Oct 1 16:42:57 2020 From: RScheuermann at jcvi.org (Scheuermann, Richard) Date: Thu, 1 Oct 2020 23:42:57 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann In-Reply-To: <69C30BC4-EC04-4438-8493-BEF570A3203D@stanford.edu> References: <5f74f6542b4ab_6d0c1ea73c8656e@ncbo-prd-app-08.stanford.edu.mail>

<24E9FAE4-F78D-42A0-A169-C753003B457F@stanford.edu> <10A139BB-47CB-4658-A3F3-9DF41C622AA2@jcvi.org> <69C30BC4-EC04-4438-8493-BEF570A3203D@stanford.edu> Message-ID: <7078B51C-3F3D-4C4A-A4EA-C2166499840F@jcvi.org> Thanks so much Michael! -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf Date: Thursday, October 1, 2020 at 4:30 PM To: "Richard H. Scheuermann" Cc: John Graybeal , "support at bioontology.org" Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, You are able to find PCL because I?ve removed the ?view? relationship between PCL and CL. The ontology is still being re-processed in order for all the relevant ontology-only services to get enabled. It should be fully processed as a standalone ontology in the next hour. Thanks, Michael On Oct 1, 2020, at 4:24 PM, Scheuermann, Richard > wrote: John, Thanks for getting back to me. I think we figured it out. We can now find PCL through the search function! Best, Richard -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: John Graybeal > Date: Thursday, October 1, 2020 at 4:22 PM To: "Richard H. Scheuermann" > Cc: Michael Dorf >, "support at bioontology.org" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Richard, Thanks for your question. We can talk offline about the exact form of the change that would suit you?for example, it is straightforward to search for it on the ontologies page, but if it's important do so so from the main page also, we could add a checkbox to offer the option of including views in the search. Possibly another option would appeal more to you. Because at the moment we are excruciatingly limited in our available development resources, we don't have anyone who can do this change. If you can identify a funding source, I believe we could use it to acquire additional resources for the time needed to make the change. Please contact me directly if this interests you. John On Oct 1, 2020, at 3:12 PM, Scheuermann, Richard > wrote: How do we change that? -------------------------------------------- Richard H. Scheuermann, Ph.D. Director, La Jolla Campus J. Craig Venter Institute 4120 Capricorn Ln. La Jolla, CA 92037 www.jcvi.org rscheuermann at jcvi.org 858-200-1876 From: Michael Dorf > Date: Thursday, October 1, 2020 at 3:05 PM To: "support at bioontology.org" > Cc: "Richard H. Scheuermann" > Subject: Re: [bioontology-support] [BioPortal] Feedback from Richard Scheuermann Hi Richard, Thank you for contacting us. The PCL ontology appears to be configured as a ?View? of Cell Line ontology (CL) rather than a standalone ontology. A view usually means a ?subset? of the main ontology. By design, views do not appear in the main ontology selector, although the terms from views are searchable via the main BioPortal search. Thanks, Michael On Sep 30, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Richard Scheuermann Email: rscheuermann at jcvi.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: The Provisional Cell Ontology (https://bioportal.bioontology.org/ontologies/PCL ) does not appear to be discoverable from the Find an ontology search function on the BioPortal home page. Why is that? _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yongqunh at med.umich.edu Sun Oct 4 19:56:11 2020 From: yongqunh at med.umich.edu (He, Oliver) Date: Mon, 5 Oct 2020 02:56:11 +0000 Subject: [bioontology-support] CIDO new version uploading error in BioPortal Message-ID: As shown on the CIDO BioPortal site: http://bioportal.bioontology.org/ontologies/CIDO the version there is 1.0.146 on 9/3/2020. However, the newest version should be 1.0.159 on 9/25/2020: http://purl.obolibrary.org/obo/cido.owl or: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl I was trying to add the newest version manually. Then I got this error: Errors On Form ? [:error, #>] I am not sure what the error message means. Thanks, Oliver ********************************************************** 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 support at bioontology.org Fri Oct 2 12:09:26 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 02 Oct 2020 12:09:26 -0700 Subject: [bioontology-support] [BioPortal] Feedback from jlai Message-ID: <5f777ae6edc2f_10e220ab8b855584@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Oct 5 14:45:43 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 5 Oct 2020 21:45:43 +0000 Subject: [bioontology-support] [BioPortal] Feedback from jlai In-Reply-To: <5f777ae6edc2f_10e220ab8b855584@ncbo-prd-app-08.stanford.edu.mail> References: <5f777ae6edc2f_10e220ab8b855584@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Jasmine, Instructions for getting an API key are available on our wiki: http://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Thanks! John > On Oct 2, 2020, at 12:09 PM, support at bioontology.org wrote: > > Name: jlai > > Email: jasminelai at nceas.ucsb.edu > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount > > > Feedback: > > Hello, > > I have accidentally exposed my API key at BioPortal. Is it possible to generate a new API key for my account jlai? > > Thank you, > > Jasmine > > > _______________________________________________ > 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 From jgraybeal at stanford.edu Tue Oct 6 15:17:12 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 6 Oct 2020 22:17:12 +0000 Subject: [bioontology-support] CIDO new version uploading error in BioPortal In-Reply-To: References: Message-ID: <621394B6-5E09-4D6B-9EF3-5CF08C890814@stanford.edu> Oliver, We are short of resources through today, but will be looking at this tomorrow. Sorry for the delay. John On Oct 4, 2020, at 7:56 PM, He, Oliver > wrote: As shown on the CIDO BioPortal site: http://bioportal.bioontology.org/ontologies/CIDO the version there is 1.0.146 on 9/3/2020. However, the newest version should be 1.0.159 on 9/25/2020: http://purl.obolibrary.org/obo/cido.owl or: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl I was trying to add the newest version manually. Then I got this error: Errors On Form ? [:error, #>] I am not sure what the error message means. Thanks, Oliver ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ 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 mdorf at stanford.edu Wed Oct 7 10:37:23 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 7 Oct 2020 17:37:23 +0000 Subject: [bioontology-support] CIDO new version uploading error in BioPortal In-Reply-To: <621394B6-5E09-4D6B-9EF3-5CF08C890814@stanford.edu> References: <621394B6-5E09-4D6B-9EF3-5CF08C890814@stanford.edu> Message-ID: Hi Oliver, There was an orphan record in our database that prevented a new version of CIDO from being submitted. Not sure how it ended up there, but I?ve removed it and cleared our internal caches. You should be able to submit your new version of CIDO now. Let us know if you run into further issues. Thank you for your patience. Michael On Oct 6, 2020, at 3:17 PM, John Graybeal > wrote: Oliver, We are short of resources through today, but will be looking at this tomorrow. Sorry for the delay. John On Oct 4, 2020, at 7:56 PM, He, Oliver > wrote: As shown on the CIDO BioPortal site: http://bioportal.bioontology.org/ontologies/CIDO the version there is 1.0.146 on 9/3/2020. However, the newest version should be 1.0.159 on 9/25/2020: http://purl.obolibrary.org/obo/cido.owl or: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl I was trying to add the newest version manually. Then I got this error: Errors On Form ? [:error, #>] I am not sure what the error message means. Thanks, Oliver ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From yongqunh at med.umich.edu Wed Oct 7 10:39:53 2020 From: yongqunh at med.umich.edu (He, Oliver) Date: Wed, 7 Oct 2020 17:39:53 +0000 Subject: [bioontology-support] CIDO new version uploading error in BioPortal In-Reply-To: References: <621394B6-5E09-4D6B-9EF3-5CF08C890814@stanford.edu> Message-ID: <6dfecf6b05cd4a42abe7ba30bc1a5ca7@med.umich.edu> Thanks, Michael, for your taking the time to work on it! I will submit a new version soon. Oliver From: Michael Dorf Sent: Wednesday, October 7, 2020 1:37 PM To: He, Oliver Cc: support at bioontology.org; John Graybeal Subject: Re: [bioontology-support] CIDO new version uploading error in BioPortal External Email - Use Caution Hi Oliver, There was an orphan record in our database that prevented a new version of CIDO from being submitted. Not sure how it ended up there, but I?ve removed it and cleared our internal caches. You should be able to submit your new version of CIDO now. Let us know if you run into further issues. Thank you for your patience. Michael On Oct 6, 2020, at 3:17 PM, John Graybeal > wrote: Oliver, We are short of resources through today, but will be looking at this tomorrow. Sorry for the delay. John On Oct 4, 2020, at 7:56 PM, He, Oliver > wrote: As shown on the CIDO BioPortal site: http://bioportal.bioontology.org/ontologies/CIDO the version there is 1.0.146 on 9/3/2020. However, the newest version should be 1.0.159 on 9/25/2020: http://purl.obolibrary.org/obo/cido.owl or: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl I was trying to add the newest version manually. Then I got this error: Errors On Form ? [:error, #>] I am not sure what the error message means. Thanks, Oliver ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ********************************************************** 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 hanfeib at gmail.com Thu Oct 8 19:57:59 2020 From: hanfeib at gmail.com (=?UTF-8?B?5YyF5ZCr6aOe?=) Date: Thu, 8 Oct 2020 22:57:59 -0400 Subject: [bioontology-support] From Hanfei Bao Message-ID: Dear colleagues, I have some problem for my ontologies: When I open the ontology about the mutations of HIV-1 at the site: http://bioportal.bioontology.org/ontologies/HIVMT it shows like Pic-1.png(see the attachment), which is done normally. But at my computer, it shows normally like Pic-2.png (see the attachment) . It seems the problem happens because of a mistake of importing ontology : The ontology imported should be: *https://bioportal.bioontology.org/ontologies/HIVO004* but actually it has imported .../HIVO0004(with three zeros) Unfortunately I finally failed to correct that mistake. Thank you! Hanfei Bao -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Pic-1.png Type: image/png Size: 141495 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Pic-2.png Type: image/png Size: 81755 bytes Desc: not available URL: From support at bioontology.org Thu Oct 8 15:44:49 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 08 Oct 2020 15:44:49 -0700 Subject: [bioontology-support] [BioPortal] Feedback from arash-sh Message-ID: <5f7f96617576a_dd21fc0bd864739@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri Oct 9 10:39:46 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 9 Oct 2020 17:39:46 +0000 Subject: [bioontology-support] From Hanfei Bao In-Reply-To: References: Message-ID: <48A6E222-59FC-47DB-B6C8-6CF8258301ED@stanford.edu> Hi Hanfei, Thanks for contacting us. Perhaps I don?t fully comprehend the problem, but looking at the source file for HIVMT, I see this statement: The source file for HIVO004 has these statements: > wrote: Dear colleagues, I have some problem for my ontologies: When I open the ontology about the mutations of HIV-1 at the site: http://bioportal.bioontology.org/ontologies/HIVMT it shows like Pic-1.png(see the attachment), which is done normally. But at my computer, it shows normally like Pic-2.png (see the attachment) . It seems the problem happens because of a mistake of importing ontology : The ontology imported should be: https://bioportal.bioontology.org/ontologies/HIVO004 but actually it has imported .../HIVO0004(with three zeros) Unfortunately I finally failed to correct that mistake. Thank you! Hanfei Bao

_______________________________________________ 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 RushikeshKulkarni at mednet.ucla.edu Fri Oct 9 12:07:06 2020 From: RushikeshKulkarni at mednet.ucla.edu (Kulkarni, Rushikesh) Date: Fri, 9 Oct 2020 19:07:06 +0000 Subject: [bioontology-support] NCBO Virtual Appliance configuration with RadLex References: <262BCEE0-FA2E-44C7-BC96-71CF3B3E899C@stanford.edu> <615B7359-80BA-4083-8983-357D69FF83C3@stanford.edu> <066CC123-F9CF-4241-85DC-1150D12D779A@stanford.edu> Message-ID: Hi Michael, I hope you are doing well! I am trying to configure NCIT (National Cancer Institute Thesaurus) into locally running bioportal. Do I have to setup any ?advanced OWL options? to configure Synonyms? So far I have imported latest NCIT OWL and successfully parsed/indexed. There is ?FULL_SYN? property in class structure which represents synonyms. But, I don?t see actual ?Synonyms? property. Thanks in advance! Regards, Rushi Kulkarni UCLA Health From: Kulkarni, Rushikesh Sent: Thursday, October 1, 2020 2:55 PM To: 'Michael Dorf' Cc: John Graybeal ; support at bioontology.org Subject: RE: [bioontology-support] NCBO Virtual Appliance configuration with RadLex Thanks Michael for all you help! I was able to login with admin credentials. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 4:57 PM To: Kulkarni, Rushikesh > Cc: John Graybeal >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Please see my responses embedded below. Thanks, Michael On Sep 30, 2020, at 3:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, Thank you for your prompt reply! I followed your steps and able to set RadLex?s preferred name and other properties. I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it? Here are my questions, 1. How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing but, it took me to login page. That?s the correct URL. Just login with your default admin credentials and you should see your Appliance ID there: * Username: admin * Password: changemeNOW I encourage you to review our Virtual Appliance documentation. All of these answers can be found there: https://ontoportal.github.io/administration/steps/initial_installation/ https://ontoportal.github.io/administration/steps/registration/ 2. Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account? Answered above Once again, Thank you for all you help. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 1:29 PM To: John Graybeal > Cc: Kulkarni, Rushikesh >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Try setting the Preferred Name, Synonym, and Definition properties under ?advanced OWL options? via the ?Edit Submission Information? page to these: Once you hit ?Save Submission?, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn?t try re-processing the ontology manually after you?ve set the advanced OWL options. Let me know if this helps. Thank you, Michael On Sep 30, 2020, at 1:18 PM, John Graybeal > wrote: Rushi, Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away. John On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh > wrote: Hello, I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI. But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference) For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'. Can you please help me with this issue? I tried following things to debug the issue, 1. Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script. 2. Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"] 3. Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine. Thanks in advance. Regards, Rushi Kulkarni UCLA Health ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Oct 12 10:01:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 12 Oct 2020 17:01:59 +0000 Subject: [bioontology-support] NCBO Virtual Appliance configuration with RadLex In-Reply-To: References: <262BCEE0-FA2E-44C7-BC96-71CF3B3E899C@stanford.edu> <615B7359-80BA-4083-8983-357D69FF83C3@stanford.edu> <066CC123-F9CF-4241-85DC-1150D12D779A@stanford.edu> Message-ID: Hi Rushi, This is what we have set in our own version of NCIT: Preferred Name: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108 Synonym: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 Definition: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 Let us know if that works. Thanks! Michael [cid:654D7620-D6CC-42AE-86D7-CA930F13FA77] On Oct 9, 2020, at 12:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, I hope you are doing well! I am trying to configure NCIT (National Cancer Institute Thesaurus) into locally running bioportal. Do I have to setup any ?advanced OWL options? to configure Synonyms? So far I have imported latest NCIT OWL and successfully parsed/indexed. There is ?FULL_SYN? property in class structure which represents synonyms. But, I don?t see actual ?Synonyms? property. Thanks in advance! Regards, Rushi Kulkarni UCLA Health From: Kulkarni, Rushikesh Sent: Thursday, October 1, 2020 2:55 PM To: 'Michael Dorf' > Cc: John Graybeal >; support at bioontology.org Subject: RE: [bioontology-support] NCBO Virtual Appliance configuration with RadLex Thanks Michael for all you help! I was able to login with admin credentials. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 4:57 PM To: Kulkarni, Rushikesh > Cc: John Graybeal >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Please see my responses embedded below. Thanks, Michael On Sep 30, 2020, at 3:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, Thank you for your prompt reply! I followed your steps and able to set RadLex?s preferred name and other properties. I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it? Here are my questions, 1. How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing but, it took me to login page. That?s the correct URL. Just login with your default admin credentials and you should see your Appliance ID there: * Username: admin * Password: changemeNOW I encourage you to review our Virtual Appliance documentation. All of these answers can be found there: https://ontoportal.github.io/administration/steps/initial_installation/ https://ontoportal.github.io/administration/steps/registration/ 2. Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account? Answered above Once again, Thank you for all you help. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 1:29 PM To: John Graybeal > Cc: Kulkarni, Rushikesh >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Try setting the Preferred Name, Synonym, and Definition properties under ?advanced OWL options? via the ?Edit Submission Information? page to these: Once you hit ?Save Submission?, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn?t try re-processing the ontology manually after you?ve set the advanced OWL options. Let me know if this helps. Thank you, Michael On Sep 30, 2020, at 1:18 PM, John Graybeal > wrote: Rushi, Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away. John On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh > wrote: Hello, I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI. But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference) For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'. Can you please help me with this issue? I tried following things to debug the issue, 1. Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script. 2. Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"] 3. Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine. Thanks in advance. Regards, Rushi Kulkarni UCLA Health ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-10-12 at 10.01.07 AM.png Type: image/png Size: 241438 bytes Desc: Screen Shot 2020-10-12 at 10.01.07 AM.png URL: From mdorf at stanford.edu Mon Oct 12 10:38:36 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 12 Oct 2020 17:38:36 +0000 Subject: [bioontology-support] [BioPortal] Feedback from arash-sh In-Reply-To: <5f7f96617576a_dd21fc0bd864739@ncbo-prd-app-08.stanford.edu.mail> References: <5f7f96617576a_dd21fc0bd864739@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Arash, Thanks for contacting us. I?ve tried loading your OWL file into my local Protege client and got the error below. You need to fix the existing errors in your ontology and make sure you can open it in Protege without issues before submitting a new version to BioPortal. We don?t have the bandwidth to investigate exactly what the issue (or issues) is, but, hopefully, the Protege errors should point you in the right direction. Thanks, Michael [cid:5DB52A65-1DD4-46C1-8B66-A1172F7C74CD] On Oct 8, 2020, at 3:44 PM, support at bioontology.org wrote: Name: arash-sh Email: ashabann at uthsc.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello Madam/Sir, We uploaded the owl files for the ACES Ontology (ACESO) https://bioportal.bioontology.org/ontologies/ACESO but we are unable to see the class and property hierarchies of the ontology. The error message we got is "Problem retrieving classes". Your help would be highly appreciated. Thank You! _______________________________________________ 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 2020-10-12 at 10.31.38 AM.png Type: image/png Size: 374695 bytes Desc: Screen Shot 2020-10-12 at 10.31.38 AM.png URL: From RushikeshKulkarni at mednet.ucla.edu Mon Oct 12 14:08:08 2020 From: RushikeshKulkarni at mednet.ucla.edu (Kulkarni, Rushikesh) Date: Mon, 12 Oct 2020 21:08:08 +0000 Subject: [bioontology-support] NCBO Virtual Appliance configuration with RadLex In-Reply-To: References: <262BCEE0-FA2E-44C7-BC96-71CF3B3E899C@stanford.edu> <615B7359-80BA-4083-8983-357D69FF83C3@stanford.edu> <066CC123-F9CF-4241-85DC-1150D12D779A@stanford.edu>

Message-ID: Thanks Michael! It worked. Regards, Rushi From: Michael Dorf Sent: Monday, October 12, 2020 10:02 AM To: Kulkarni, Rushikesh Cc: John Graybeal ; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, This is what we have set in our own version of NCIT: Preferred Name: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108 Synonym: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 Definition: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 Let us know if that works. Thanks! Michael [cid:image001.png at 01D6A0A1.1ACD0170] On Oct 9, 2020, at 12:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, I hope you are doing well! I am trying to configure NCIT (National Cancer Institute Thesaurus) into locally running bioportal. Do I have to setup any ?advanced OWL options? to configure Synonyms? So far I have imported latest NCIT OWL and successfully parsed/indexed. There is ?FULL_SYN? property in class structure which represents synonyms. But, I don?t see actual ?Synonyms? property. Thanks in advance! Regards, Rushi Kulkarni UCLA Health From: Kulkarni, Rushikesh Sent: Thursday, October 1, 2020 2:55 PM To: 'Michael Dorf' > Cc: John Graybeal >; support at bioontology.org Subject: RE: [bioontology-support] NCBO Virtual Appliance configuration with RadLex Thanks Michael for all you help! I was able to login with admin credentials. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 4:57 PM To: Kulkarni, Rushikesh > Cc: John Graybeal >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Please see my responses embedded below. Thanks, Michael On Sep 30, 2020, at 3:07 PM, Kulkarni, Rushikesh > wrote: Hi Michael, Thank you for your prompt reply! I followed your steps and able to set RadLex?s preferred name and other properties. I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it? Here are my questions, 1. How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing but, it took me to login page. That?s the correct URL. Just login with your default admin credentials and you should see your Appliance ID there: * Username: admin * Password: changemeNOW I encourage you to review our Virtual Appliance documentation. All of these answers can be found there: https://ontoportal.github.io/administration/steps/initial_installation/ https://ontoportal.github.io/administration/steps/registration/ 2. Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account? Answered above Once again, Thank you for all you help. Regards, Rushi From: Michael Dorf > Sent: Wednesday, September 30, 2020 1:29 PM To: John Graybeal > Cc: Kulkarni, Rushikesh >; support at bioontology.org Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender. Hi Rushi, Try setting the Preferred Name, Synonym, and Definition properties under ?advanced OWL options? via the ?Edit Submission Information? page to these: Once you hit ?Save Submission?, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn?t try re-processing the ontology manually after you?ve set the advanced OWL options. Let me know if this helps. Thank you, Michael On Sep 30, 2020, at 1:18 PM, John Graybeal > wrote: Rushi, Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away. John On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh > wrote: Hello, I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI. But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference) For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'. Can you please help me with this issue? I tried following things to debug the issue, 1. Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script. 2. Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"] 3. Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine. Thanks in advance. Regards, Rushi Kulkarni UCLA Health ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 81683 bytes Desc: image001.png URL: From samanthacsik at gmail.com Tue Oct 13 09:56:59 2020 From: samanthacsik at gmail.com (Samantha Csik) Date: Tue, 13 Oct 2020 09:56:59 -0700 Subject: [bioontology-support] api key request In-Reply-To: <32fca949-546e-4fb1-aa5c-37066174228a@Spark> References: <32fca949-546e-4fb1-aa5c-37066174228a@Spark> Message-ID: <51aabc3d-e2f0-4c1d-a91c-f1a77e927732@Spark> Hi there, I?m a Data Fellow with the Arctic Data Center at the National Center for Ecological Analysis & Synthesis. I was hoping to get access to an api key for some semantics work I?m doing. Please let me know if you might need any other information from me. Thanks so much, Samantha Csik -------------- next part -------------- An HTML attachment was scrubbed... URL: From samuel.roze at birdie.care Wed Oct 14 14:44:42 2020 From: samuel.roze at birdie.care (=?UTF-8?B?U2FtdWVsIFJvesOp?=) Date: Wed, 14 Oct 2020 22:44:42 +0100 Subject: [bioontology-support] SPARQL endpoint & federation Message-ID: Hi there, First, thank you for exposing many APIs around health-care concepts & tools, this is a great contribution to the ecosystem. I have been trying to use your SPARQL endpoint in some prototype but I keep getting 403s from the endpoint: {"requestId":"e4ba9488-62bd-8696-ecb6-422668b079e1","code":"BadRequestException","detailedMessage":"The SERVICE call returned an unexpected HTTP result: 403, endpoint: http://sparql.bioontology.org/mappings/sparql/?apikey=0fc6a637-14ef-4d31-8691-ec13dc026d05 "} This `apikey` is the one that I can find in my `sroze` account unfortunately. Would you be able to guide me towards a reason? Are they different kind of API keys for this SPARQL endpoint? Thank you very much, Samuel. -- *Samuel Roz?* VP of Engineering +447789932317 40 Islington High St N1 8XB London Birdie.care - Birdie, your digital care companion -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri Oct 16 10:18:45 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 16 Oct 2020 17:18:45 +0000 Subject: [bioontology-support] api key request In-Reply-To: <51aabc3d-e2f0-4c1d-a91c-f1a77e927732@Spark> References: <32fca949-546e-4fb1-aa5c-37066174228a@Spark> <51aabc3d-e2f0-4c1d-a91c-f1a77e927732@Spark> Message-ID: <5E769120-6331-45D8-BA7E-A58996FEDB3C@stanford.edu> Hi Samantha, There are instructions for getting an API key on the BioPortal wiki: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Kind regards, Michael On Oct 13, 2020, at 9:56 AM, Samantha Csik > wrote: Hi there, I?m a Data Fellow with the Arctic Data Center at the National Center for Ecological Analysis & Synthesis. I was hoping to get access to an api key for some semantics work I?m doing. Please let me know if you might need any other information from me. Thanks so much, Samantha Csik _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Oct 16 11:57:40 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 16 Oct 2020 18:57:40 +0000 Subject: [bioontology-support] SPARQL endpoint & federation In-Reply-To: References: Message-ID: Samuel, Our apologies, the current SPARQL endpoint is a beta service, and it appears the mappings endpoint is down. We will try to bring it back up when we can, but I can't guarantee when that will be. John On Oct 14, 2020, at 2:44 PM, Samuel Roz? > wrote: Hi there, First, thank you for exposing many APIs around health-care concepts & tools, this is a great contribution to the ecosystem. I have been trying to use your SPARQL endpoint in some prototype but I keep getting 403s from the endpoint: {"requestId":"e4ba9488-62bd-8696-ecb6-422668b079e1","code":"BadRequestException","detailedMessage":"The SERVICE call returned an unexpected HTTP result: 403, endpoint: http://sparql.bioontology.org/mappings/sparql/?apikey=0fc6a637-14ef-4d31-8691-ec13dc026d05"} This `apikey` is the one that I can find in my `sroze` account unfortunately. Would you be able to guide me towards a reason? Are they different kind of API keys for this SPARQL endpoint? Thank you very much, Samuel. -- [https://drive.google.com/a/kametventures.com/uc?id=0ByatJtfiS-ANZ3hwQkRacm1sUlk&export=download] Samuel Roz? VP of Engineering +447789932317 40 Islington High St N1 8XB London Birdie.care - Birdie, your digital care companion _______________________________________________ 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 Oct 16 16:18:31 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 16 Oct 2020 23:18:31 +0000 Subject: [bioontology-support] SPARQL endpoint & federation In-Reply-To: References:

Message-ID: Samuel, This is done through our umls2rdf software. You can find other references to it in our mailing list archives, e.g., http://ncbo-support.2288202.n4.nabble.com/bioontology-support-CPT-Ontology-td4658098.html#a4658099. John On Oct 16, 2020, at 2:43 PM, Samuel Roz? > wrote: Hi John, That's fair enough, thank you for your reply. Would you mind guiding me towards how you have done the Snomed -> RDF conversion and whether this is open-source or not? Thank you very much, Samuel. On Fri, 16 Oct 2020 at 19:57, John Graybeal > wrote: Samuel, Our apologies, the current SPARQL endpoint is a beta service, and it appears the mappings endpoint is down. We will try to bring it back up when we can, but I can't guarantee when that will be. John On Oct 14, 2020, at 2:44 PM, Samuel Roz? > wrote: Hi there, First, thank you for exposing many APIs around health-care concepts & tools, this is a great contribution to the ecosystem. I have been trying to use your SPARQL endpoint in some prototype but I keep getting 403s from the endpoint: {"requestId":"e4ba9488-62bd-8696-ecb6-422668b079e1","code":"BadRequestException","detailedMessage":"The SERVICE call returned an unexpected HTTP result: 403, endpoint: http://sparql.bioontology.org/mappings/sparql/?apikey=0fc6a637-14ef-4d31-8691-ec13dc026d05"} This `apikey` is the one that I can find in my `sroze` account unfortunately. Would you be able to guide me towards a reason? Are they different kind of API keys for this SPARQL endpoint? Thank you very much, Samuel. -- [https://drive.google.com/a/kametventures.com/uc?id=0ByatJtfiS-ANZ3hwQkRacm1sUlk&export=download] Samuel Roz? VP of Engineering +447789932317 40 Islington High St N1 8XB London Birdie.care - Birdie, your digital care companion _______________________________________________ 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 -- [https://drive.google.com/a/kametventures.com/uc?id=0ByatJtfiS-ANZ3hwQkRacm1sUlk&export=download] Samuel Roz? VP of Engineering +447789932317 40 Islington High St N1 8XB London Birdie.care - Birdie, your digital care companion ======================== 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 samuel.roze at birdie.care Fri Oct 16 14:43:53 2020 From: samuel.roze at birdie.care (=?UTF-8?B?U2FtdWVsIFJvesOp?=) Date: Fri, 16 Oct 2020 22:43:53 +0100 Subject: [bioontology-support] SPARQL endpoint & federation In-Reply-To: References:

Message-ID: Hi John, That's fair enough, thank you for your reply. Would you mind guiding me towards how you have done the Snomed -> RDF conversion and whether this is open-source or not? Thank you very much, Samuel. On Fri, 16 Oct 2020 at 19:57, John Graybeal wrote: > Samuel, > > Our apologies, the current SPARQL endpoint is a beta service, and it > appears the mappings endpoint is down. We will try to bring it back up when > we can, but I can't guarantee when that will be. > > John > > On Oct 14, 2020, at 2:44 PM, Samuel Roz? wrote: > > Hi there, > > First, thank you for exposing many APIs around health-care concepts & > tools, this is a great contribution to the ecosystem. I have been trying to > use your SPARQL endpoint > in some prototype but > I keep getting 403s from the endpoint: > > {"requestId":"e4ba9488-62bd-8696-ecb6-422668b079e1","code":"BadRequestException","detailedMessage":"The > SERVICE call returned an unexpected HTTP result: 403, endpoint: > http://sparql.bioontology.org/mappings/sparql/?apikey=0fc6a637-14ef-4d31-8691-ec13dc026d05 > "} > > This `apikey` is the one that I can find in my `sroze` account > unfortunately. Would > you be able to guide me towards a reason? Are they different kind of API > keys for this SPARQL endpoint? > > Thank you very much, > Samuel. > > -- > > > *Samuel Roz?* > > VP of Engineering > +447789932317 > 40 Islington High St > > N1 8XB London > > > Birdie.care - Birdie, your digital care companion > _______________________________________________ > 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 > > > > -- *Samuel Roz?* VP of Engineering +447789932317 40 Islington High St N1 8XB London Birdie.care - Birdie, your digital care companion -------------- next part -------------- An HTML attachment was scrubbed... URL: From samanthacsik at gmail.com Fri Oct 16 15:46:43 2020 From: samanthacsik at gmail.com (Samantha Csik) Date: Fri, 16 Oct 2020 15:46:43 -0700 Subject: [bioontology-support] api key request In-Reply-To: <5E769120-6331-45D8-BA7E-A58996FEDB3C@stanford.edu> References: <32fca949-546e-4fb1-aa5c-37066174228a@Spark> <51aabc3d-e2f0-4c1d-a91c-f1a77e927732@Spark> <5E769120-6331-45D8-BA7E-A58996FEDB3C@stanford.edu> Message-ID: <03406107-764a-49b3-96df-c3b3ad39536c@Spark> Hi Michael, So sorry to spam you and the support team?I happened upon these instructions some time after reaching out. Thanks for your help, and enjoy your weekend! Sam On Oct 16, 2020, 10:18 AM -0700, Michael Dorf , wrote: > Hi Samantha, > > There are instructions for getting an API key on the BioPortal wiki: > > https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key > > Kind regards, > > Michael > > > > On Oct 13, 2020, at 9:56 AM, Samantha Csik wrote: > > > > Hi there, > > > > I?m a Data Fellow with the Arctic Data Center at the National Center for Ecological Analysis & Synthesis. I was hoping to get access to an api key for some semantics work I?m doing. Please let me know if you might need any other information from me. > > > > Thanks so much, > > Samantha Csik > > _______________________________________________ > > 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 Mon Oct 26 15:44:39 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 26 Oct 2020 15:44:39 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Suzanne Message-ID: <5f975157cdd23_28772981e88366c1@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Oct 27 08:40:25 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 27 Oct 2020 15:40:25 +0000 Subject: [bioontology-support] From Hanfei Bao In-Reply-To: References: Message-ID: <27BC1DAA-88E0-49BE-8550-B51F68F8DE80@stanford.edu> Hi Hanfei, First, I?d like to ask you to send all your questions or issues related to BioPortal to support at bioontology.org instead of my personal email. We have a number of people who monitor this list and can offer assistance. As far as your ontology, I am not seeing any issues. There are several recursive relationships in your ontology, which BioPortal does not display. For example, the term ?Location? is both a superclass and a subclass of the term ?ConceptRelatingToGeneralizedSpace?. BioPortal shows that term only once in the tree as a subclass of the term ?NaturalObject?. Since I am not an ontology design expert, I wouldn?t speculate on whether such recursive relationships are a standard practice, but, obviously, Protege has no issues with them. Michael [cid:76776297-83D3-4726-A359-7ABC97FE0451][cid:4A9BB0BD-813C-44F9-8231-80A75F415B99] On Oct 27, 2020, at 7:50 AM, ??? > wrote: Hi Mike, I tried to take the first step to update the main HIV ontology at https://bioportal.bioontology.org/ontologies/HIVO004. But there was some thing wrong existing: After up loading the new version of the ontology, some information was changed as expected, but the classes of it was keeping unchanged(See Fig.2), rather than the picture it should be (see Fig. 1) . Do you think I should rebuild a new ontology instead of the old one? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-10-27 at 8.32.47 AM.png Type: image/png Size: 449901 bytes Desc: Screen Shot 2020-10-27 at 8.32.47 AM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-10-27 at 8.33.15 AM.png Type: image/png Size: 395236 bytes Desc: Screen Shot 2020-10-27 at 8.33.15 AM.png URL: From jonquet at lirmm.fr Wed Oct 28 08:37:24 2020 From: jonquet at lirmm.fr (Clement Jonquet) Date: Wed, 28 Oct 2020 16:37:24 +0100 Subject: [bioontology-support] =?utf-8?q?AgroPortal_2=2E0_released_?= =?utf-8?q?=E2=80=93_synchronization_with_OntoPortal=2C_tons_of_new_conten?= =?utf-8?q?t_and_much_more?= Message-ID: <868C855C-B5BE-444D-AA18-200C831DD084@lirmm.fr> Dear all, We are pleased to announce the 2.0 release of the AgroPortal vocabulary and ontology repository: http://agroportal.lirmm.fr/ From a technical perspective: AgroPortal is now based on OntoPortal 3.0 . The OntoPortal Alliance is the community effort of organizations reusing the original NCBO BioPortal software. AgroPortal specific features (mappings, metadata model and visualization, cf. previous notes, etc.) have been merged in OntoPortal 3.0 code in our own LIRMM?s branches. Code developed at LIRMM for AgroPortal and the SIFR BioPortal is now hosted at: https://github.com/ontoportal-lirmm Side projects, community feedback, issues is still on AgroPortal?s GitHub: https://github.com/agroportal This release includes significantly changed user interfaces, more responsive and user friendly. We also fixed the BioMixer plugin and the graph visualization tabs are now working when browsing a class. For other fixes and features, you can also check BioPortal release notes . We congrat and acknowledge our collaborators at Stanford BMIR for all this work! AgroPortal Annotator now includes the latest version of the FastContext algorithm used to contextualize textual annotation. This feature has been mainly developed for biomedicine, but could be relevant for other contexts too. From a community/content perspective: AgroPortal now hosts 128 semantic resources. Many new ontologies, thesauri and other semantic resources have been uploaded in the last 3 years, either by us or directly by external users. Around half of these resources are exclusively hosted on AgroPortal. Fixed ontology metrics for all the semantic resources: the portal now counts 2,627,105 classes (mostly owl:Classes, not distinct) and 2,170,609 individuals (mostly skos:Concept). We have generated, extracted and analyzed more than 400,000 mappings between concepts based on term reuse, term overlap and declared mappings in AgroPortal ontologies (EKAW 2020 paper ). Eventually such analysis will be automatically done in AgroPortal. We have investigated one million XRefs in 30 ontologies from the OBO world stored in AgroPortal and provided recommendations to mitigate issues (ICBO 2020 paper ). Semantic resources include: 23 ontologies selected from the OBO Foundry registry, 30 semantic resources provided by INRAE (for which AgroPortal plays role of reference server), all the ontologies/trait dictionaries from the Crop Ontology project, and much more. AGROVOC is now back, sorry for the inconvenience! Feel free to contact us for information, feedback or to upload/access agronomy related semantic resources. Documentation: https://github.com/agroportal/documentation/wiki Support at: agroportal-support at lirmm.fr Report issues to: https://github.com/agroportal/documentation/issues Acknowledgments: AgroPortal is currently being developed within French ANR D2KAB project (ANR-18-CE23-0017 ). It also receives or received support from ANR SIFR project (ANR-12-JS02-0010 ), European Union H2020-MSCA SIFRm project (No 701771 ), the NUMEV Labex (ANR-10-LABX-0020 ), the IBC of Montpellier project (ANR-11-BINF0002 ), the Agro Labex (ANR-10-LABX-0001 ) as well as from University of Montpellier, CNRS and INRAE. ------------------------------------------------------------------------------------------- Dr. Clement JONQUET ? PhD in Informatics Associate Research Scientist ? INRAE (MISTEA) Associate Professor ? University of Montpellier (LIRMM) Coordinator of the SIFR , AgroPortal and D2KAB projects jonquet at lirmm.fr or clement.jonquet at inrae.fr http://www.lirmm.fr/~jonquet @MISTEA (L,M,M,J): +33/0 4 99 61 22 77 @LIRMM (V): +33/0 4 67 14 97 43 ------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Oct 28 23:57:30 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 28 Oct 2020 23:57:30 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Dongmin Sun Message-ID: <5f9a67da35f2f_55a42cbbbd09669@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From neha.gupta at indegene.com Thu Oct 29 02:04:07 2020 From: neha.gupta at indegene.com (Neha Gupta) Date: Thu, 29 Oct 2020 09:04:07 +0000 Subject: [bioontology-support] Help for mapping MedRA and SNOMED Adverse events Message-ID: