From support at bioontology.org Sat Nov 2 15:50:26 2019 From: support at bioontology.org (support at bioontology.org) Date: Sat, 02 Nov 2019 15:50:26 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Michal Iglewski Message-ID: <5dbe083269f84_4f8326c862441433@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Nov 5 09:44:25 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 05 Nov 2019 09:44:25 -0800 Subject: [bioontology-support] [BioPortal] Feedback from sschurer Message-ID: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Nov 5 11:07:33 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 5 Nov 2019 19:07:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Michal Iglewski In-Reply-To: <5dbe083269f84_4f8326c862441433@ncbo-prd-app-09.stanford.edu.mail> References: <5dbe083269f84_4f8326c862441433@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <8E0BDCCE-E1E7-414B-8080-DA32A059B62C@stanford.edu> Hello Michal, BioPortal is currently configured to check the following URL nightly for new versions of OBOREL: http://purl.obolibrary.org/obo/ro.owl The above PURL resolves to: https://raw.githubusercontent.com/oborel/obo-relations/master/ro.owl I looked at the commit history for ro.owl in GitHub: https://github.com/oborel/obo-relations/commits/master/ro.owl The last time this file changed was on Sept. 25th. BioPortal pulled and processed that version of OBOREL. As far as I can tell, our system is up to date. Can you be more specific about what you mean when you say that we don?t match the GitHub version? Kind regards, Jennifer On Nov 2, 2019, at 3:50 PM, support at bioontology.org wrote: Name: Michal Iglewski Email: iglewski at uqo.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FOBOREL Feedback: The Relations Ontology (https://bioportal.bioontology.org/ontologies/OBOREL) does not match the github version (https://github.com/oborel/obo-relations/pull/324). It applies to the browser and download buttons. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Nov 5 11:14:40 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 5 Nov 2019 19:14:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.chung at med.miami.edu Tue Nov 5 12:34:49 2019 From: c.chung at med.miami.edu (Chung, Caty Elizabeth) Date: Tue, 5 Nov 2019 20:34:49 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail>, Message-ID: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org Cc: Stephan Sch?rer, PhD ; Chung, Caty Elizabeth Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephan.schurer at gmail.com Tue Nov 5 13:27:46 2019 From: stephan.schurer at gmail.com (=?UTF-8?Q?Stephan_Sch=C3=BCrer=2C_PhD?=) Date: Tue, 5 Nov 2019 16:27:46 -0500 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> Message-ID: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti < vendetti at stanford.edu> wrote: > Hello Caty, > > That change is now in effect in our production system: > > https://bioportal.bioontology.org/ontologies/BAO > > Kind regards, > Jennifer > > > > On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: > > Dear Jennifer, please replace CC by 3 to CC by SA4 ( > https://creativecommons.org/licenses/by-sa/4.0/) > Thank you, > Caty > > > > ------------------------------ > *From:* Jennifer Leigh Vendetti > *Sent:* Tuesday, November 5, 2019 2:14 PM > *To:* support at bioontology.org > *Cc:* Stephan Sch?rer, PhD ; Chung, Caty > Elizabeth > *Subject:* Re: [bioontology-support] [BioPortal] Feedback from sschurer > > Hello Stephan, > > > On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: > The license information in BioPortal shows CC by 3. The edit does not > allow to update the license. > > > Yes, apologies that this is a shortcoming in the current system. > > How can we update the license information for: > https://bioportal.bioontology.org/ontologies/BAO > > to reflect: > > > You can send us the desired license text and we can update it on your > behalf. > > Please reply to: c.chung at miami.edu > > > cc?ed > > > Kind regards, > Jennifer > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Nov 5 13:25:52 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 5 Nov 2019 21:25:52 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.chung at med.miami.edu Tue Nov 5 14:23:04 2019 From: c.chung at med.miami.edu (Chung, Caty Elizabeth) Date: Tue, 5 Nov 2019 22:23:04 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu>, Message-ID: <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu> Jennifer, the URL link should be only the license acronym ?CC by SA4? Caty [image1.jpeg] Caty On Nov 5, 2019, at 4:28 PM, Stephan Sch?rer, PhD > wrote: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti > wrote: Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image1.jpeg Type: image/jpeg Size: 45786 bytes Desc: image1.jpeg URL: From vendetti at stanford.edu Tue Nov 5 14:54:04 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 5 Nov 2019 22:54:04 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu> References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu> Message-ID: <7F70A032-06AC-4E0A-9885-974CAF16E323@stanford.edu> So - to clarify - you want the text to look exactly as follows: This ontology is made available under the Creative Commons Attribution-ShareAlike 4.0 International (CC by SA4) license. ? Jennifer On Nov 5, 2019, at 2:23 PM, Chung, Caty Elizabeth > wrote: Jennifer, the URL link should be only the license acronym ?CC by SA4? Caty Caty On Nov 5, 2019, at 4:28 PM, Stephan Sch?rer, PhD > wrote: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti > wrote: Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.chung at med.miami.edu Tue Nov 5 15:44:10 2019 From: c.chung at med.miami.edu (Chung, Caty Elizabeth) Date: Tue, 5 Nov 2019 23:44:10 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: <7F70A032-06AC-4E0A-9885-974CAF16E323@stanford.edu> References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu>, <7F70A032-06AC-4E0A-9885-974CAF16E323@stanford.edu> Message-ID: <7C5C132D-BE6F-4E78-B751-2373E4010C5D@med.miami.edu> If it is not too much trouble, yes, please Caty On Nov 5, 2019, at 5:54 PM, Jennifer Leigh Vendetti > wrote: So - to clarify - you want the text to look exactly as follows: This ontology is made available under the Creative Commons Attribution-ShareAlike 4.0 International (CC by SA4) license. ? Jennifer On Nov 5, 2019, at 2:23 PM, Chung, Caty Elizabeth > wrote: Jennifer, the URL link should be only the license acronym ?CC by SA4? Caty Caty On Nov 5, 2019, at 4:28 PM, Stephan Sch?rer, PhD > wrote: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti > wrote: Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Nov 5 17:41:06 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 6 Nov 2019 01:41:06 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: <7C5C132D-BE6F-4E78-B751-2373E4010C5D@med.miami.edu> References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu> <7F70A032-06AC-4E0A-9885-974CAF16E323@stanford.edu> <7C5C132D-BE6F-4E78-B751-2373E4010C5D@med.miami.edu> Message-ID: Sure, no problem. That change is now reflected in our production system. Jennifer On Nov 5, 2019, at 3:44 PM, Chung, Caty Elizabeth > wrote: If it is not too much trouble, yes, please Caty On Nov 5, 2019, at 5:54 PM, Jennifer Leigh Vendetti > wrote: So - to clarify - you want the text to look exactly as follows: This ontology is made available under the Creative Commons Attribution-ShareAlike 4.0 International (CC by SA4) license. ? Jennifer On Nov 5, 2019, at 2:23 PM, Chung, Caty Elizabeth > wrote: Jennifer, the URL link should be only the license acronym ?CC by SA4? Caty Caty On Nov 5, 2019, at 4:28 PM, Stephan Sch?rer, PhD > wrote: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti > wrote: Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.chung at med.miami.edu Wed Nov 6 03:34:12 2019 From: c.chung at med.miami.edu (Chung, Caty Elizabeth) Date: Wed, 6 Nov 2019 11:34:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sschurer In-Reply-To: References: <5dc1b4f98328a_793628e8a949267@ncbo-prd-app-09.stanford.edu.mail> <06BAF4FC-201C-49E9-89F3-B64D9ADFA8DE@stanford.edu> <8775623D-5FEA-4BE5-AFD1-0AB7483934E5@med.miami.edu> <7F70A032-06AC-4E0A-9885-974CAF16E323@stanford.edu> <7C5C132D-BE6F-4E78-B751-2373E4010C5D@med.miami.edu>, Message-ID: Thank you! Caty On Nov 5, 2019, at 8:41 PM, Jennifer Leigh Vendetti > wrote: Sure, no problem. That change is now reflected in our production system. Jennifer On Nov 5, 2019, at 3:44 PM, Chung, Caty Elizabeth > wrote: If it is not too much trouble, yes, please Caty On Nov 5, 2019, at 5:54 PM, Jennifer Leigh Vendetti > wrote: So - to clarify - you want the text to look exactly as follows: This ontology is made available under the Creative Commons Attribution-ShareAlike 4.0 International (CC by SA4) license. ? Jennifer On Nov 5, 2019, at 2:23 PM, Chung, Caty Elizabeth > wrote: Jennifer, the URL link should be only the license acronym ?CC by SA4? Caty Caty On Nov 5, 2019, at 4:28 PM, Stephan Sch?rer, PhD > wrote: Thank you for your help! Stephan On Tue, Nov 5, 2019 at 4:25 PM Jennifer Leigh Vendetti > wrote: Hello Caty, That change is now in effect in our production system: https://bioportal.bioontology.org/ontologies/BAO Kind regards, Jennifer On Nov 5, 2019, at 12:34 PM, Chung, Caty Elizabeth > wrote: Dear Jennifer, please replace CC by 3 to CC by SA4 (https://creativecommons.org/licenses/by-sa/4.0/) Thank you, Caty ________________________________ From: Jennifer Leigh Vendetti > Sent: Tuesday, November 5, 2019 2:14 PM To: support at bioontology.org > Cc: Stephan Sch?rer, PhD >; Chung, Caty Elizabeth > Subject: Re: [bioontology-support] [BioPortal] Feedback from sschurer Hello Stephan, On Nov 5, 2019, at 9:44 AM, support at bioontology.org wrote: The license information in BioPortal shows CC by 3. The edit does not allow to update the license. Yes, apologies that this is a shortcoming in the current system. How can we update the license information for: https://bioportal.bioontology.org/ontologies/BAO to reflect: You can send us the desired license text and we can update it on your behalf. Please reply to: c.chung at miami.edu cc?ed Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.mozejko at databiology.com Tue Nov 5 19:51:33 2019 From: alex.mozejko at databiology.com (Alex Mozejko) Date: Wed, 6 Nov 2019 03:51:33 +0000 Subject: [bioontology-support] VMWare Virtual Appliance - Databiology Message-ID: Hi, We are interested in the bioontology virtual appliance. We have set up an in instance in our AWS account but would also like to test in our other virtualised environments. Can we please have access to the virtual appliance ova? Our Bioontology account is 'Databiology' and website is www.databiology.com. Thanks, Alex. -------------- next part -------------- An HTML attachment was scrubbed... URL: From samira.babalou at uni-jena.de Sun Nov 10 07:11:55 2019 From: samira.babalou at uni-jena.de (Samira Babalou) Date: Sun, 10 Nov 2019 16:11:55 +0100 Subject: [bioontology-support] mapping of classes- json output question Message-ID: Dear Sir or Madam, I have one question and would be very thankful, if you could help me on that. I used your API to get the existing mapping for my_class(e.g.410607006) in one ontology (e.g. SNOMEDCT). The result is a JSON file. From this JSON output, e.g. this page , *which elements should I read?* From the output, i am retrieving : _jsonOutput.get("classes").get(0).get("links").get("self")_ is mapped to _jsonOutput.get("classes").get(1).get("links").get("self")_ But I have doubt, that this is correct. Could you tell me which entities from this json output should I read? Actually, I want to have a list that give me, for instance * my_class is mapped to A. * my_class is mapped to B. * etc. I would really appreciate your help, Thanks & Regards, Samira Babalou -- Heinz-Nixdorf Chair for Distributed Information Systems Friedrich Schiller University of Jena Institute of Computer Science Leutragraben 1, Jentower, R17N01 07743 Jena, Germany Email: Samira.babalou at uni-jena.de Web: http://fusion.cs.uni-jena.de/fusion/ http://fusion.cs.uni-jena.de/fusion/members/samira-babalou/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pEpkey.asc Type: application/pgp-keys Size: 1774 bytes Desc: not available URL: From vk396 at njit.edu Mon Nov 11 09:57:29 2019 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 11 Nov 2019 12:57:29 -0500 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: Hi Michael, Thank you for the detailed response. I tried to resolve the first issue that you mentioned - not properly defining the synonyms. Now for the concept with id 56265001 (Heart disease) we discussed previously the attached figure shows the modified details. I have used http://www.w3.org/2004/02/skos/core#altLabel to define synonyms and below is the term definition now. Heart disease Morbus cordis Cardiopathy Disorder of heart Cardiac disorder Heart disease (disorder) Is it not possible to give multiple values to altLabel? I need to have more than one synonyms. What should I do to achieve this? In the attached figure Synonyms property shows only Cardiopathy and not the other values like Morbus Cordis, Disorder of heart, etc. So I guess Synonyms is taking only the first value of altLabel. Thank you. Vipina On Wed, Oct 23, 2019 at 3:05 PM Michael Dorf wrote: > Hi Vipina, > > There are two issues at play here. The first is that the ontology does not > properly define synonyms. The second is the earlier mentioned issue that > prevents regular Annotator refreshes ( > https://github.com/ncbo/ncbo_annotator/issues/8). > > The term ?Cardiac disorder? contains multiple entries of " > http://www.w3.org/2000/01/rdf-schema#label?, which does not translate > into synonyms. By default, BioPortal uses these properties to define its > own reserved property called ?synonym?. A custom synonym property is > allowed, but the ontology submitter must specify it on the metadata form > when uploading the ontology. > > http://www.w3.org/2004/02/skos/core#altLabel > http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym > http://purl.obolibrary.org/obo/synonym > http://www.geneontology.org/formats/oboInOwl#hasExactSynonym > http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym > http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym > > The default ?prefLabel" property is set using one these properties (unless > the user specified a custom one): > > http://www.w3.org/2004/02/skos/core#prefLabel > http://www.w3.org/2000/01/rdf-schema#label > http://data.bioontology.org/metadata/def/prefLabel > > As you can see, the "http://www.w3.org/2000/01/rdf-schema#label? property > is used to determine a prefLabel for the term. When there are multiple > entries, BioPortal either picks the English one (if multiple languages are > used), or the very first one as the de-facto prefLabel. > > In your older version of the ontology (v6), the term ?Cardiac disorder? is > defined as: > > > > > Heart > disease > > > In the latest version, the same term is defined as: > > > > > Cardiac > disorder > Cardiopathy > Cardiopathy, > NOS > Disorder > of heart > Heart > disease > Heart > disease (disorder) > Heart > disease, NOS > Morbus > cordis > Morbus > cordis, NOS > > > Because of the Annotator refresh issue, both, the original prefLabel, > "Heart disease? and the new prefLabel, ?Cardiac disorder? are being stored > in the Annotator, that?s why you're seeing two annotations in your results. > However, there are NO matches on synonyms, since none are defined. Note the > result of this API call: > > > http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F56265001?display=all > > > As you can see, the ?synonym? property contains an empty array. > > I am going to try to refresh our Annotator repository in the upcoming > days, so that at least for the time being it is synchronized with the > latest version of CC_SNOMED. > > Thanks again for your inquiry. > > 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 Oct 23, 2019, at 9:40 AM, Kuttichikeloth, Vipina > wrote: > > I am sorry about not explaining it properly. > I am talking about "Cardiac disorder" and sorry that "24 hour ....." was > highlighted. > From the synonyms of Cardiac disorder in the attached figure, you can see > that "Morbus cordis" and "Cardiopathy" and "Heart disease" are synonyms. > Now when I give the text "*Cardiac disorder, Heart disease, Morbus > cordis, Cardiopathy*" to the Annotator, Cardiac disorder and Heart > disease are annotated to "Cardiac disorder" (preferred label in this case) > as you can see in the second screenshot I attached while "Morbus cordis > and Cardiopathy" are not annotated. > > On Wed, Oct 23, 2019 at 12:28 PM Michael Dorf wrote: > >> Hi Vipina, >> >> Thank you for reaching out. I?ve looked at the term you are referring to, >> but I am seeing a different picture on my end. None of the synonyms from >> your screenshot are listed under the term ?24 hour diastolic blood pressure >> (observable entity)?: >> >> >> >> These synonyms ARE, however, listed under the term ?Cardiac disorder? >> (see below), so your Annotator results appear to be consistent. I?ve >> flushed our caches, but it hasn?t changed the structure of the ?24 hour?.? >> term. >> >> >> >> >> The REST endpoint results are also consistent with my screenshot above: >> >> >> http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all >> >> >> Is it possible that that page is somehow browser-cached on your end? >> >> Thanks, >> >> Michael >> >> >> >> >> On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina >> wrote: >> >> Hi, >> >> I am having an issue trying to annotate synonyms. Some synonyms are >> getting annotated while some others are not. >> For example, for the concept "Cardiac disorder" the first image attached >> shows all the alternate labels for the concept in CC_SNOMED. >> The second image is the result of the Annotator. >> I read about sort of a similar issue here >> https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned >> that it has something to do with the way the ontology is designed. >> >> Is this also an issue with the design of the ontology? But then why are >> some synonyms getting annotated. >> >> Thank you, >> Vipina >> >> On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina >> wrote: >> >>> Thank you so much for your help and explanation. >>> >>> ~Vipina >>> >>> >>> >>> On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf wrote: >>> >>>> Hi Vipina, >>>> >>>> I was finally able to identify the issue that was causing the behavior >>>> you reported. The culprit is an earlier version of CC_SNOMED ontology, in >>>> which the terms in question contained different labels: >>>> >>>> Earlier version (cc_v6.owl): >>>> >>>> >>>> >>>> >>>> >>>> Left >>>> >>>> >>>> Latest version: >>>> >>>> >>>> >>>> >>>> >>>> Left (non-mitral) >>>> atrioventricular valve structure >>>> Left (non-mitral) >>>> atrioventricular valve structure (body structure) >>>> >>>> >>>> The same applies to the other false match, the term with the id " >>>> http://snomed.info/id/312524003?: >>>> >>>> Earlier version (cc_v6.owl): >>>> >>>> >>>> >>>> >>>> >>>> Right >>>> >>>> >>>> Latest version: >>>> >>>> >>>> >>>> >>>> >>>> Right (non-tricuspid) >>>> atrioventricular valve structure >>>> Right (non-tricuspid) >>>> atrioventricular valve structure (body structure) >>>> >>>> >>>> We currently have a limitation in the Annotator that prevents us from >>>> removing older records on ontology re-processing. So when the pref labels >>>> got changed, both the old and the new values ended up being stored in the >>>> Annotator. As a workaround for this specific case, I have removed the old >>>> values from the Annotator datastore. Your text "left right left? no longer >>>> returns annotations. I?ve logged this issue in our Github repository: >>>> >>>> https://github.com/ncbo/ncbo_annotator/issues/8 >>>> >>>> Thank you again 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 Oct 15, 2019, at 2:01 PM, Michael Dorf wrote: >>>> >>>> Hi Vipina, >>>> >>>> Thanks for your report. I need a bit of time to investigate this. >>>> Indeed, this does not appear to be an expected behavior. I?ll keep you >>>> posted as soon as I get to the bottom of it. >>>> >>>> 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina >>>> wrote: >>>> >>>> Thank you for the response. I played a little bit more with the >>>> ontology to add multiple labels to each concept (synonyms) and then >>>> annotating some text. >>>> I noticed that every mention of "left" or "right" in the text is >>>> getting annotated with a concept as shown in the attached image. >>>> I gave the text to be annotated as "left right left". >>>> I thought I understood what you said in your response, but in that case >>>> (and if I understood it correctly), it shouldn't be matching "left" which >>>> is a part of the entire label >>>> "Left (non-mitral) atrioventricular valve structure". Am I missing >>>> something else here? >>>> >>>> Thank you. >>>> Vipina >>>> >>>> On Sat, Oct 5, 2019 at 9:37 PM John Graybeal >>>> wrote: >>>> >>>>> Hi Vipina, >>>>> >>>>> Our team discussed your experience Friday and I am offering our latest >>>>> thoughts for the list, and some of my own observations. (I have the >>>>> specific example you sent Jennifer but have not copied it here.) >>>>> >>>>> When I remove '(finding)' from Jennifer's example, I still see an >>>>> annotation for CC-SNOMED. It does not matter what boxes are or are not >>>>> checked, this still works. >>>>> >>>>> Now, I see that your class ( >>>>> https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006 >>>>> ) is >>>>> currently called simply 'abdominal aortic bruit', and so it seems likely >>>>> that you have removed the parenthetical expressions from your latest >>>>> submission. Based on some further examples (using 'abdominal' and >>>>> 'abdominal aortic'), here is the likely explanation. >>>>> >>>>> When Annotator is looking for matches, it is only looking for class >>>>> names that exactly match a string in the source text. (If Annotator matched >>>>> any class that *contained* a string in your text, there would be an >>>>> impossibly large number of matches for any significant text, and the vast >>>>> majority of them would be incorrect.) >>>>> >>>>> So for example, Annotator will not match 'abdominal' to the class >>>>> 'abdominal aortic bruit', because text describing 'abdominal pain' should >>>>> not result in a match to that detailed class. >>>>> >>>>> So if we reconsider your class name that contains '(finding)', if you >>>>> remove that from the text that you are trying to annotate, the Annotator >>>>> will no longer consider it a match (because Annotator will not want to >>>>> assume the more general phrase 'abdominal aortic bruit' matches the more >>>>> specific phrase 'abdominal aortic bruit (finding)'). This seems >>>>> appropriately conservative, considering the above example of matching >>>>> 'abdominal' to the longer phrase. >>>>> >>>>> Checking 'Match partial words' does not have any impact on this >>>>> behavior; it is simply used to enable a short word to match a longer word, >>>>> for example, to match suffixed words. >>>>> >>>>> On another point, if you compare your results with the matches found >>>>> in SNOMED-CT, there you will find matches to the shorter strings?but only >>>>> because SNOMED-CT has those exact shorter strings as classes. >>>>> >>>>> This matching behavior is different than searching, which will match >>>>> any appearance of the string in a class name, but will prioritize more >>>>> complete matches. This is appropriate also, to let people find classes that >>>>> may have only some of the entered search string. >>>>> >>>>> I hope this explains your experience so far. Pleae feel free to follow >>>>> up with further questions or concerns. >>>>> >>>>> John >>>>> >>>>> >>>>> On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti < >>>>> vendetti at stanford.edu> wrote: >>>>> >>>>>> Hello Vipina, >>>>>> >>>>>> Could you give me a specific example of the text you are entering >>>>>> where you don?t see results that you think should be present? I looked at >>>>>> your ontology with the Annotator just now. I entered the text of one of >>>>>> your class names in the Annotator and selected CC_SNOMED under advanced >>>>>> options. The Annotator returned results as I would have expected: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Kind regards, >>>>>> Jennifer >>>>>> >>>>>> >>>>>> >>>>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>>>>> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> Recently I uploaded an ontology named Cardiology Component of SNOMED >>>>>> CT (CC_SNOMED). The visibility is set to private. I can see and browse the >>>>>> classes on BioPortal. >>>>>> >>>>>> I want to annotate some medical text using this ontology that I >>>>>> created. In the advanced options under "select ontologies", I am able to >>>>>> select CC_SNOMED but when I click "Get annotations" no results appear. I >>>>>> have tried putting the concepts that exist in CC_SNOMED in the medical text >>>>>> still no results. Also, if I select SNOMED CT then the text gets annotated >>>>>> and all these concepts are shown. Is there anything I am missing and please >>>>>> let me know why this is not working? >>>>>> >>>>>> Thank you. >>>>>> Vipina >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> bioontology-support mailing list >>>>>> bioontology-support at lists.stanford.edu >>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>>> >>>>>> >>>>> On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti < >>>>> vendetti at stanford.edu> wrote: >>>>> >>>>> Hello Vipina, >>>>> >>>>> Could you give me a specific example of the text you are entering >>>>> where you don?t see results that you think should be present? I looked at >>>>> your ontology with the Annotator just now. I entered the text of one of >>>>> your class names in the Annotator and selected CC_SNOMED under advanced >>>>> options. The Annotator returned results as I would have expected: >>>>> >>>>> >>>>> >>>>> >>>>> Kind regards, >>>>> Jennifer >>>>> >>>>> >>>>> >>>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Recently I uploaded an ontology named Cardiology Component of SNOMED >>>>> CT (CC_SNOMED). The visibility is set to private. I can see and browse the >>>>> classes on BioPortal. >>>>> >>>>> I want to annotate some medical text using this ontology that I >>>>> created. In the advanced options under "select ontologies", I am able to >>>>> select CC_SNOMED but when I click "Get annotations" no results appear. I >>>>> have tried putting the concepts that exist in CC_SNOMED in the medical text >>>>> still no results. Also, if I select SNOMED CT then the text gets annotated >>>>> and all these concepts are shown. Is there anything I am missing and please >>>>> let me know why this is not working? >>>>> >>>>> Thank you. >>>>> Vipina >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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: heart_disease.png Type: image/png Size: 35056 bytes Desc: not available URL: From jgraybeal at stanford.edu Mon Nov 11 17:40:07 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 12 Nov 2019 01:40:07 +0000 Subject: [bioontology-support] mapping of classes- json output question In-Reply-To: References: Message-ID: <674F9D8D-30E8-4082-9395-68269C7476CC@stanford.edu> Samira, I am not a programmer, but I think this will tell you what you need to know. If this does not help you please reply and one of our programmers may be able to help. In English, the mapping output is organized as follows: - an array of all the mappings; for each mapping: - the id of the mapping (null in most of these cases) - the source of the mapping - an array containing the two classes that are mapped to each other; for each class: - the identifier (@id) for the class - the type (type) for the class - an array of links that will let you learn more about that class (including the link to the class itself, which you were following) The key entity you care about is 'the identifier (@id) for the class', for each of the two classes in each mapping. Because for your request the array of all the mappings always shows mappings from your class to something else, you will see that the the first class in the array will always be your class (@id = "http://purl.bioontology.org/ontology/SNOMEDCT/410607006"). Thus it is the list of @id values, from the second class of every pair, that you want to have. I *think* this would be something like jsonOutput.get("classes").get(1).get("@id") but I am not 100% sure what get("classes") returns ,and this may just return the first pair of classes, or the second entry from a very long array of matching classes. See if something like that works for you. John On Nov 10, 2019, at 7:11 AM, Samira Babalou > wrote: Dear Sir or Madam, I have one question and would be very thankful, if you could help me on that. I used your API to get the existing mapping for my_class(e.g.410607006) in one ontology (e.g. SNOMEDCT). The result is a JSON file. From this JSON output, e.g. this page, which elements should I read? >From the output, i am retrieving : jsonOutput.get("classes").get(0).get("links").get("self") is mapped to jsonOutput.get("classes").get(1).get("links").get("self") But I have doubt, that this is correct. Could you tell me which entities from this json output should I read? Actually, I want to have a list that give me, for instance * my_class is mapped to A. * my_class is mapped to B. * etc. I would really appreciate your help, Thanks & Regards, Samira Babalou -- Heinz-Nixdorf Chair for Distributed Information Systems Friedrich Schiller University of Jena Institute of Computer Science Leutragraben 1, Jentower, R17N01 07743 Jena, Germany Email: Samira.babalou at uni-jena.de Web: http://fusion.cs.uni-jena.de/fusion/ http://fusion.cs.uni-jena.de/fusion/members/samira-babalou/ _______________________________________________ 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 Tue Nov 12 11:34:16 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 12 Nov 2019 19:34:16 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: <9E756B51-B23F-445D-AAB8-895DC883D1D0@stanford.edu> Hi Vipina, Thank you for this report and for giving me the opportunity to investigate it. Indeed, what you are describing appears contrary to my expectations of this functionality. BioPortal uses http://www.w3.org/2004/02/skos/core#altLabel as its default synonym property, so I expected this to work correctly. Yet, after looking at a number of terms defined across different ontologies, it is clear that BioPortal does not handle this property properly. Here are some additional examples from several prominent ontologies that demonstrate the issue: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F272379006?display=all http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD009422?display=all http://data.bioontology.org/ontologies/NCBITAXON/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%2F2157?display=all In all these cases, BioPortal has chosen the very first defined value as the synonym. Sadly, as with some of your other excellent reports, there is no immediate fix. I?ve logged the issue below and hope to attend to it in the near future: https://github.com/ncbo/ontologies_linked_data/issues/97 There IS a workaround, if you are OK with making additional modifications to your ontology. It appears that when defining synonyms using either of the properties below, BioPortal correctly handles the multiple values: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym Examples: http://data.bioontology.org/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_33250?display=all http://data.bioontology.org/ontologies/ENVO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0007033?display=all If you are able to revise your synonym definitions using one of the above properties, the multiple values should be be recognized property. Hope this helps! Thanks again! 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 Nov 11, 2019, at 9:57 AM, Kuttichi Keloth, Vipina > wrote: Hi Michael, Thank you for the detailed response. I tried to resolve the first issue that you mentioned - not properly defining the synonyms. Now for the concept with id 56265001 (Heart disease) we discussed previously the attached figure shows the modified details. I have used http://www.w3.org/2004/02/skos/core#altLabel to define synonyms and below is the term definition now. Heart disease Morbus cordis Cardiopathy Disorder of heart Cardiac disorder Heart disease (disorder) Is it not possible to give multiple values to altLabel? I need to have more than one synonyms. What should I do to achieve this? In the attached figure Synonyms property shows only Cardiopathy and not the other values like Morbus Cordis, Disorder of heart, etc. So I guess Synonyms is taking only the first value of altLabel. Thank you. Vipina On Wed, Oct 23, 2019 at 3:05 PM Michael Dorf > wrote: Hi Vipina, There are two issues at play here. The first is that the ontology does not properly define synonyms. The second is the earlier mentioned issue that prevents regular Annotator refreshes (https://github.com/ncbo/ncbo_annotator/issues/8). The term ?Cardiac disorder? contains multiple entries of "http://www.w3.org/2000/01/rdf-schema#label?, which does not translate into synonyms. By default, BioPortal uses these properties to define its own reserved property called ?synonym?. A custom synonym property is allowed, but the ontology submitter must specify it on the metadata form when uploading the ontology. http://www.w3.org/2004/02/skos/core#altLabel http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym http://purl.obolibrary.org/obo/synonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym The default ?prefLabel" property is set using one these properties (unless the user specified a custom one): http://www.w3.org/2004/02/skos/core#prefLabel http://www.w3.org/2000/01/rdf-schema#label http://data.bioontology.org/metadata/def/prefLabel As you can see, the "http://www.w3.org/2000/01/rdf-schema#label? property is used to determine a prefLabel for the term. When there are multiple entries, BioPortal either picks the English one (if multiple languages are used), or the very first one as the de-facto prefLabel. In your older version of the ontology (v6), the term ?Cardiac disorder? is defined as: Heart disease In the latest version, the same term is defined as: Cardiac disorder Cardiopathy Cardiopathy, NOS Disorder of heart Heart disease Heart disease (disorder) Heart disease, NOS Morbus cordis Morbus cordis, NOS Because of the Annotator refresh issue, both, the original prefLabel, "Heart disease? and the new prefLabel, ?Cardiac disorder? are being stored in the Annotator, that?s why you're seeing two annotations in your results. However, there are NO matches on synonyms, since none are defined. Note the result of this API call: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F56265001?display=all As you can see, the ?synonym? property contains an empty array. I am going to try to refresh our Annotator repository in the upcoming days, so that at least for the time being it is synchronized with the latest version of CC_SNOMED. Thanks again for your inquiry. 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 Oct 23, 2019, at 9:40 AM, Kuttichikeloth, Vipina > wrote: I am sorry about not explaining it properly. I am talking about "Cardiac disorder" and sorry that "24 hour ....." was highlighted. From the synonyms of Cardiac disorder in the attached figure, you can see that "Morbus cordis" and "Cardiopathy" and "Heart disease" are synonyms. Now when I give the text "Cardiac disorder, Heart disease, Morbus cordis, Cardiopathy" to the Annotator, Cardiac disorder and Heart disease are annotated to "Cardiac disorder" (preferred label in this case) as you can see in the second screenshot I attached while "Morbus cordis and Cardiopathy" are not annotated. On Wed, Oct 23, 2019 at 12:28 PM Michael Dorf > wrote: Hi Vipina, Thank you for reaching out. I?ve looked at the term you are referring to, but I am seeing a different picture on my end. None of the synonyms from your screenshot are listed under the term ?24 hour diastolic blood pressure (observable entity)?: These synonyms ARE, however, listed under the term ?Cardiac disorder? (see below), so your Annotator results appear to be consistent. I?ve flushed our caches, but it hasn?t changed the structure of the ?24 hour?.? term. The REST endpoint results are also consistent with my screenshot above: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all Is it possible that that page is somehow browser-cached on your end? Thanks, Michael On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina > wrote: Hi, I am having an issue trying to annotate synonyms. Some synonyms are getting annotated while some others are not. For example, for the concept "Cardiac disorder" the first image attached shows all the alternate labels for the concept in CC_SNOMED. The second image is the result of the Annotator. I read about sort of a similar issue here https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that it has something to do with the way the ontology is designed. Is this also an issue with the design of the ontology? But then why are some synonyms getting annotated. Thank you, Vipina On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina > wrote: Thank you so much for your help and explanation. ~Vipina On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf > wrote: Hi Vipina, I was finally able to identify the issue that was causing the behavior you reported. The culprit is an earlier version of CC_SNOMED ontology, in which the terms in question contained different labels: Earlier version (cc_v6.owl): Left Latest version: Left (non-mitral) atrioventricular valve structure Left (non-mitral) atrioventricular valve structure (body structure) The same applies to the other false match, the term with the id "http://snomed.info/id/312524003?: Earlier version (cc_v6.owl): Right Latest version: Right (non-tricuspid) atrioventricular valve structure Right (non-tricuspid) atrioventricular valve structure (body structure) We currently have a limitation in the Annotator that prevents us from removing older records on ontology re-processing. So when the pref labels got changed, both the old and the new values ended up being stored in the Annotator. As a workaround for this specific case, I have removed the old values from the Annotator datastore. Your text "left right left? no longer returns annotations. I?ve logged this issue in our Github repository: https://github.com/ncbo/ncbo_annotator/issues/8 Thank you again 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 Oct 15, 2019, at 2:01 PM, Michael Dorf > wrote: Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ 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 _______________________________________________ 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 Nov 12 07:42:48 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 12 Nov 2019 07:42:48 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Krys Kochut Message-ID: <5dcad2f8b28f9_2e4127f78b0343b9@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Nov 12 14:39:25 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 12 Nov 2019 22:39:25 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Krys Kochut In-Reply-To: <5dcad2f8b28f9_2e4127f78b0343b9@ncbo-prd-app-09.stanford.edu.mail> References: <5dcad2f8b28f9_2e4127f78b0343b9@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Krys, Thank you for your question. Yes, we have had some cases where it appears an ontology exceeded a limit in our system, though that was an experiment and we have not finished identifying the bottleneck. It would be helpful if you submitted the ontology, and assuming it also has this problem, we will create a ticket describing the specific issue your ontology is having. As your submission is not experimental, we will look at it as quickly as we can (given available staff) to try to work out any submission issues. I should note that BioPortal recognizes the individuals and can display them via the API, but does not have a user interface for examining individuals. (This has come up as an issue/feature request very rarely in BioPortal's history, to my understanding.) If you would be willing, I would appreciate the chance to work with you offline to understand to what extent this is a concern, and what features for individuals you think would be important for your primary BioPortal use cases. I'll send you a separate email on that topic. John On Nov 12, 2019, at 7:42 AM, support at bioontology.org wrote: Name: Krys Kochut Email: kkochut at uga.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, Our bioinformatics team is planning to submit to BioPortal an ontology on protein kinases. Is there a limit on the size of ontologies that can be submitted? Our ontology has many instances (individuals) and it's approximately 3GB when serialized in OWL. Thanks, Krys _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Nov 14 11:02:41 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 14 Nov 2019 11:02:41 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Isaac Message-ID: <5dcda4d148624_531e254f270655d0@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Nov 18 06:39:20 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 18 Nov 2019 06:39:20 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Philadelphia Message-ID: <5dd2ad186fd38_2d01fda8bc63879@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Nov 18 13:53:00 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 18 Nov 2019 21:53:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Philadelphia In-Reply-To: <5dd2ad186fd38_2d01fda8bc63879@ncbo-prd-app-08.stanford.edu.mail> References: <5dd2ad186fd38_2d01fda8bc63879@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <0C9F5E76-4B17-487F-BFE4-1090072F684B@stanford.edu> Hi Melissa, Thank you for contacting us. Our team consists of software engineers who build and maintain BioPortal. As such, we are not necessarily experts in each individual ontology that we host, CPT included. That said, I did some basic Google search for ?cpt codes?, which, yielded this page: https://coder.aapc.com/search/ Searching there for ?lung scan? revealed the following CPT code: https://coder.aapc.com/cpt-codes/78580 I then found the same code in BioPortal: http://bioportal.bioontology.org/ontologies/CPT?p=classes&conceptid=78580 I?m hoping that that?s the code you were looking for. If this isn?t, I?d recommend emailing the person listed as the ?Contact? for CPT on the ontology summary page here: https://bioportal.bioontology.org/ontologies/CPT?p=summary Hope this helps. Thanks! 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 Nov 18, 2019, at 6:39 AM, support at bioontology.org wrote: Name: Melissa Philadelphia Email: mphiladelphia at tryonmed.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D78580 Feedback: Greetings, I'm trying to located CPT code for NM, lung scan, ventilation/perfusion. Can you please assist? Thank you!! Melissa Philadelphia _______________________________________________ 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 Nov 19 03:52:52 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 19 Nov 2019 03:52:52 -0800 Subject: [bioontology-support] [BioPortal] Feedback from smileyk11 Message-ID: <5dd3d79471da3_5c862c05f4c996a@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Nov 19 11:25:21 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 19 Nov 2019 19:25:21 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Isaac In-Reply-To: <5dcda4d148624_531e254f270655d0@ncbo-prd-app-09.stanford.edu.mail> References: <5dcda4d148624_531e254f270655d0@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Isaac, Thank you for contacting us. There?s a known issue in BioPortal where the visualizations don?t work over HTTPS [1]. If you change the protocol identifier in the address bar of your browser from ?https? to ?http?, the visualizations work. We?re using a 3rd party tool for these visualizations, and have not had the resources to address this issue as of yet. Thank you, Michael [1] https://github.com/ncbo/biomixer/issues/2 On Nov 14, 2019, at 11:02 AM, support at bioontology.org wrote: Name: Isaac Email: Isaac.kunz at hci.utah.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: I was interested in the visualization tab. How can i get that to display correctly? I tried in a couple different browsers. Is it java? Thanks, Isaac _______________________________________________ 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 Tue Nov 19 11:34:02 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 19 Nov 2019 19:34:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from smileyk11 In-Reply-To: <5dd3d79471da3_5c862c05f4c996a@ncbo-prd-app-08.stanford.edu.mail> References: <5dd3d79471da3_5c862c05f4c996a@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <7FD7C2C2-CFAD-4D30-8F17-5593C0A84F62@stanford.edu> Hi Smiley, Thank you for contacting us. I?ve clicked on the link below, but I am not able to reproduce the issue you are describing. The mappings do appear on my end. I?ve also checked the REST service, and that, too, appears to work correctly: http://data.bioontology.org/mappings?ontologies=NDDF,SNOMEDCT Can you please try accessing the mappings again and let me know if the problem persists? Thank you, Michael On Nov 19, 2019, at 3:52 AM, support at bioontology.org wrote: Name: smileyk11 Email: smileyk at pku.edu.cn Location: https%3A%2F%2Fbioportal.bioontology.org%2Fmappings Feedback: The mappings from "National Drug Data File" to "SNOMED CT" is not available. The location of mappings is :https://bioportal.bioontology.org/mappings/show/NDDF?target=http://data.bioontology.org/ontologies/SNOMEDCT&height=600&width=800 It shows "No mappings found". I will be very appreciated if you can fix it. _______________________________________________ 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 rakesh at pieriandx.com Sat Nov 23 09:22:37 2019 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Sat, 23 Nov 2019 11:22:37 -0600 Subject: [bioontology-support] HTTP 404 error Message-ID: Hello, The following API call ( http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628/children) throws an HTTP 404 error: { -"errors": [ "Resource 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C152628' not found in ontology NCIT submission 84" ], "status": 404 } Can you please fix? Thanks, Rakesh -- *Rakesh Nagarajan* Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sat Nov 23 12:29:50 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 23 Nov 2019 20:29:50 +0000 Subject: [bioontology-support] HTTP 404 error In-Reply-To: References: Message-ID: <4EC2D6B7-0E6B-4051-984C-03D16BF448D9@stanford.edu> Rakesh, Thanks for this report. We've just ingested UMLS 2019AB, I'm guessing something went awry with the indexing. We'll take a look at this Monday. John On Nov 23, 2019, at 9:22 AM, Rakesh Nagarajan > wrote: Hello, The following API call (http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628/children) throws an HTTP 404 error: { -"errors": [ "Resource 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C152628' not found in ontology NCIT submission 84" ], "status": 404 } Can you please fix? Thanks, Rakesh -- Rakesh Nagarajan Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Nov 25 08:27:17 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 25 Nov 2019 16:27:17 +0000 Subject: [bioontology-support] HTTP 404 error In-Reply-To: References: Message-ID: <9D0DB05F-5BEA-4060-8B30-D3305EC1C714@stanford.edu> Hello Rakesh, The REST call to retrieve the ?Tilidine? class no longer returns a 404: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628 The call to retrieve children of this class (that you listed below), returns an empty collection. I double checked the class in BioPortal, and this appears to be correct as the class has no children in the latest version of NCIT. Kind regards, Jennifer [cid:91D6AA7D-E5BD-49C4-B72C-456306D1ED3B at stanford.edu] On Nov 23, 2019, at 9:22 AM, Rakesh Nagarajan > wrote: Hello, The following API call (http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628/children) throws an HTTP 404 error: { -"errors": [ "Resource 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C152628' not found in ontology NCIT submission 84" ], "status": 404 } Can you please fix? Thanks, Rakesh -- Rakesh Nagarajan Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. _______________________________________________ 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: Screenshot 2019-11-25 08.25.50.png Type: image/png Size: 155102 bytes Desc: Screenshot 2019-11-25 08.25.50.png URL: From rakesh at pieriandx.com Mon Nov 25 15:26:27 2019 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Mon, 25 Nov 2019 17:26:27 -0600 Subject: [bioontology-support] HTTP 404 error In-Reply-To: <9D0DB05F-5BEA-4060-8B30-D3305EC1C714@stanford.edu> References: <9D0DB05F-5BEA-4060-8B30-D3305EC1C714@stanford.edu> Message-ID: Thanks Jennifer! I?ll confirm later tonight. > On Nov 25, 2019, at 10:27 AM, Jennifer Leigh Vendetti wrote: > > ? Hello Rakesh, > > The REST call to retrieve the ?Tilidine? class no longer returns a 404: > > http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628 > > The call to retrieve children of this class (that you listed below), returns an empty collection. I double checked the class in BioPortal, and this appears to be correct as the class has no children in the latest version of NCIT. > > Kind regards, > Jennifer > > > > > > > >> On Nov 23, 2019, at 9:22 AM, Rakesh Nagarajan wrote: >> >> Hello, >> The following API call (http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C152628/children) throws an HTTP 404 error: >> >> >> { >> -"errors": [ >> "Resource 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C152628' not found in ontology NCIT submission 84" >> ], >> "status": 404 >> } >> >> Can you please fix? >> >> Thanks, >> Rakesh >> >> -- >> Rakesh Nagarajan >> >> Founder and Executive Chairman >> >> m: 314-504-5620 >> e: rakesh at pieriandx.com >> >> >> >> Wisdom in Every Report? >> >> CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. >> >> >> >> >> >> _______________________________________________ >> 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: