From mdorf at stanford.edu Tue Aug 1 13:18:38 2017 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 1 Aug 2017 20:18:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens In-Reply-To: References: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <456641F6-555A-4E8C-90A5-80CA9F858E6F@stanford.edu> Done. Thanks! On Jul 31, 2017, at 11:46 AM, Terry Chamberlin > wrote: Would you please unsubscribe my email address from these notifications: terry.chamberlin at genelux.com Thank You, Terry ------------------------------------------------- Ms. Terry A. Chamberlin, CCRA Director, Clinical Trial Operations Genelux Corporation Ph: +1.858.210.6808 Fax: +1.858.483.0025 Email: terry.chamberlin at genelux.com From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of support at bioontology.org Sent: Monday, July 31, 2017 5:54 AM To: support at bioontology.org; marvin.martens at maastrichtuniversity.nl Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens Name: Marvin Martens Email: marvin.martens at maastrichtuniversity.nl Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPW%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPW_0000001 Feedback: Dear BioPortal group, I am working on pathways on WikiPathways, which uses your Pathway ontology. However, I work on a type of pathways that is not in there, and is different: Adverse Outcome Pathways. They are pathways that cover multiple cell types, multiple processes, and often multiple biological levels. I think it would be a great addition if we could work on an ontology for this kind of patway, as it is a growing concept and soon many more of these pathways will be made in wikipathways. Could you tell me what is the best thing to do? What are the possibilities? Kind regards, Marvin _______________________________________________ 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 Wed Aug 2 04:31:33 2017 From: support at bioontology.org (support at bioontology.org) Date: Wed, 02 Aug 2017 04:31:33 -0700 Subject: [bioontology-support] [BioPortal] Feedback from ligusd Message-ID: <5981b815dae97_23f13f849357661818869@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Aug 2 06:44:51 2017 From: support at bioontology.org (support at bioontology.org) Date: Wed, 02 Aug 2017 06:44:51 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung Message-ID: <5981d7531c331_5bc43fa458a313bc516ec@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From David.Ligus at uzis.cz Wed Aug 2 04:33:06 2017 From: David.Ligus at uzis.cz (=?iso-8859-2?Q?Ligu=B9_David?=) Date: Wed, 2 Aug 2017 11:33:06 +0000 Subject: [bioontology-support] [BioPortal] Feedback from ligusd In-Reply-To: <5981b815dae97_23f13f849357661818869@ncbo-prd-app-09.stanford.edu.mail> References: <5981b815dae97_23f13f849357661818869@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <6fca7f489c7f4bc59f9a365a5067df89@MZSEXC12.mzcr.cz> Oh sorry and my email is this one. Mgr. David Ligu? Datov? Centrum ?stav zdravotnick?ch informac? a statistiky ?R Palack?ho n?m. 4, 128 01, Praha 2 tel.: +420 22497 2238 e-mail: David.ligus at uzis.cz http://www.uzis.cz/ Od: support at bioontology.org Odesl?no:st?eda 2. srpna 2017 13:32 Komu: support at bioontology.org; Ligu? David P?edm?t: [BioPortal] Feedback from ligusd Name: ligusd Email: david.ligus at uzis.cz Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMKN_10_TEST%3Fp%3Dsummary Feedback: Dear Sir/Madam I am experiencing a problem with ontology. On our institution UZIS (www.uzis.cz) we are looking for method of questionnaire, which would be used to get health and medical information from Hospitals, etc. In order to do it we are using system called REDCap. It's possible to use an ontology (for example like ICD-10) in this system in various questions. Sadly on bioportal site is only the English language ones and we need to have ontology in Czech language. So and the problem is: We created an ontology of ICD-10 in Czech, uploaded it and tried to use, but there are no whisperer, which is in English version. So I am asking for a help in this topic, because i can see the ontology, it's possible even to use it, but when i type something in the field in REDCap questionnaire, there is nothing. So do I need to set up something correctly in ontology or how is it possible to get our ontology into the system? Here on bioportal it is under the name MKN_10_test. Out ontology is basically a 1 CSV or excel file, so I am asking for a help. Thank you Sincerely David Ligu? -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 2 13:11:37 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 2 Aug 2017 20:11:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung In-Reply-To: <5981d7531c331_5bc43fa458a313bc516ec@ncbo-prd-app-09.stanford.edu.mail> References: <5981d7531c331_5bc43fa458a313bc516ec@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <9A85208B-1FFF-4876-A85F-95C4D282B8F8@stanford.edu> Hi Caty, Apologies for the delay in responding to you. The latest submission of DTO is now fully parsed and available in BioPortal. Kind regards, Jennifer On Aug 2, 2017, at 6:44 AM, support at bioontology.org wrote: Name: Caty Chung Email: c.chung at miami.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDTO Feedback: Mon 7/31, 1:43 PM support at bioontology.org Hello, On the BioPortal site, we changed from private to public and release the Ontology, it has been parsing since 07/20/2017 Can you guide us to the issue, why BioPortal does not finish the parsing, indexing, metrics and annotations for: http://bioportal.bioontology.org/ontologies/DTO Caty _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 2 13:23:59 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 2 Aug 2017 20:23:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from ligusd In-Reply-To: <5981b815dae97_23f13f849357661818869@ncbo-prd-app-09.stanford.edu.mail> References: <5981b815dae97_23f13f849357661818869@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <716621F1-5252-427B-B583-5E9A058B584E@stanford.edu> Hello David, On Aug 2, 2017, at 4:31 AM, support at bioontology.org wrote: Name: ligusd Email: david.ligus at uzis.cz Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMKN_10_TEST%3Fp%3Dsummary Feedback: Dear Sir/Madam I am experiencing a problem with ontology. On our institution UZIS (www.uzis.cz) we are looking for method of questionnaire, which would be used to get health and medical information from Hospitals, etc. In order to do it we are using system called REDCap. It's possible to use an ontology (for example like ICD-10) in this system in various questions. Sadly on bioportal site is only the English language ones and we need to have ontology in Czech language. So and the problem is: We created an ontology of ICD-10 in Czech, uploaded it and tried to use, but there are no whisperer, which is in English version. So I am asking for a help in this topic, because i can see the ontology, it's possible even to use it, but when i type something in the field in REDCap questionnaire, there is nothing. So do I need to set up something correctly in ontology or how is it possible to get our ontology into the system? Here on bioportal it is under the name MKN_10_test. Out ontology is basically a 1 CSV or excel file, so I am asking for a help. In our BioPortal application, I see this ontology entry: http://bioportal.bioontology.org/ontologies/MKN However, it has no ontology file submission associated with it. I also found this ontology entry: http://bioportal.bioontology.org/ontologies/MKN10 The ontology file that was uploaded here is a small text file. BioPortal is an online repository for ontologies in OWL, OBO, or SKOS format. We?re unable to handle CSV or Excel files. You might consider looking at the WebProtege or Protege ontology editing environments, which I believe have some kind of facility for importing Excel spreadsheets, and converting to other ontology formats. For help with getting more information on that, I suggest contacting the developers via their support list [1]. Kind regards, Jennifer [1] http://protege.stanford.edu/support.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.chung at med.miami.edu Wed Aug 2 16:48:22 2017 From: c.chung at med.miami.edu (Chung, Caty Elizabeth) Date: Wed, 2 Aug 2017 23:48:22 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung In-Reply-To: <9A85208B-1FFF-4876-A85F-95C4D282B8F8@stanford.edu> References: <5981d7531c331_5bc43fa458a313bc516ec@ncbo-prd-app-09.stanford.edu.mail>, <9A85208B-1FFF-4876-A85F-95C4D282B8F8@stanford.edu> Message-ID: Thank you! ________________________________ From: Jennifer Leigh Vendetti Sent: Wednesday, August 2, 2017 4:11:37 PM To: support at bioontology.org Cc: Chung, Caty Elizabeth Subject: Re: [bioontology-support] [BioPortal] Feedback from Caty Chung Hi Caty, Apologies for the delay in responding to you. The latest submission of DTO is now fully parsed and available in BioPortal. Kind regards, Jennifer On Aug 2, 2017, at 6:44 AM, support at bioontology.org wrote: Name: Caty Chung Email: c.chung at miami.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDTO Feedback: Mon 7/31, 1:43 PM support at bioontology.org Hello, On the BioPortal site, we changed from private to public and release the Ontology, it has been parsing since 07/20/2017 Can you guide us to the issue, why BioPortal does not finish the parsing, indexing, metrics and annotations for: http://bioportal.bioontology.org/ontologies/DTO Caty _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 2 17:40:23 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 3 Aug 2017 00:40:23 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Marvin Martens In-Reply-To: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail> References: <597f287b613ed_7eb43f9427c87044502ce@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <69AA18FE-4AF8-47F0-ABA1-A2DE873CA24F@stanford.edu> Hi Marvin, On Jul 31, 2017, at 5:54 AM, support at bioontology.org wrote: Name: Marvin Martens Email: marvin.martens at maastrichtuniversity.nl Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPW%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPW_0000001 Feedback: Dear BioPortal group, I am working on pathways on WikiPathways, which uses your Pathway ontology. However, I work on a type of pathways that is not in there, and is different: Adverse Outcome Pathways. They are pathways that cover multiple cell types, multiple processes, and often multiple biological levels. I think it would be a great addition if we could work on an ontology for this kind of patway, as it is a growing concept and soon many more of these pathways will be made in wikipathways. Could you tell me what is the best thing to do? What are the possibilities? I?m not sure I can offer you much in the way of assistance. This support list is focused around addressing questions / issues with the BioPortal software, and/or parsing issues that arise when ontologies are submitted. You might want to consider contacting the authors of the PW ontology (their contact information is listed on the ontology summary page [1]), as they may have ideas about how to extend their ontology, or create a related one. Alternatively, if you?re looking for assistance with how to model the concepts in your domain, you could try posting a message on the support list for the Protege ontology editing environment [2]. Their list has a large number of subscribers, many of whom are familiar with best practices when building ontologies. Kind regards, Jennifer [1] http://bioportal.bioontology.org/ontologies/PW [2] http://protege.stanford.edu/support.php -------------- next part -------------- An HTML attachment was scrubbed... URL: From dko at coh.org Thu Aug 3 17:22:37 2017 From: dko at coh.org (Ko, Dave) Date: Fri, 4 Aug 2017 00:22:37 +0000 Subject: [bioontology-support] NCBO Widgets - issues getting definitions Message-ID: <4DC56B51183B7841907C484D28B0F2B259F94ABC@PPWEXCH2KX13.coh.org> Hi, I'm trying to incorporate these widgets for project, and I'm using this attribute: data-bp_include_definitions="true" When I attempt to render the control, Chrome throws a series of errors: Refused to execute script from 'https://bioportal.bioontology.org/ajax/json_class?callback=jQuery2240390514...p%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD034402&_=1501805987867' because its MIME type ('application/json') is not executable, and strict MIME type checking is enabled. Do you know of any way around this? Also, any word as to when these widgets would be compatible with any version of jQuery higher than 2.2.4? Thanks in advance! ++++++++++ Dave Ko dko at coh.org City of Hope National Medical Center Human Islet Research Network --------------------------------------------------------------------- -SECURITY/CONFIDENTIALITY WARNING- This message (and any attachments) are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) --------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Aug 4 13:30:52 2017 From: support at bioontology.org (support at bioontology.org) Date: Fri, 04 Aug 2017 13:30:52 -0700 Subject: [bioontology-support] [BioPortal] Feedback from tomc Message-ID: <5984d97c65234_66243ff06a4ee93c97834@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From laia.subirats at gmail.com Sat Aug 5 21:52:59 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Sun, 6 Aug 2017 06:52:59 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology Message-ID: Dear Sir/Madam, I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD , I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem. Yours faithfully, -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sun Aug 6 16:31:29 2017 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 6 Aug 2017 23:31:29 +0000 Subject: [bioontology-support] [BioPortal] Feedback from tomc In-Reply-To: <5984d97c65234_66243ff06a4ee93c97834@ncbo-prd-app-09.stanford.edu.mail> References: <5984d97c65234_66243ff06a4ee93c97834@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <7D1280DD-E9BE-4556-8A4A-DF6A24B9E139@stanford.edu> Tom, Thank you for your input, appreciate your taking the time. 1) Yes!. It is a good point that we should make the site exclusively https, and I see there are indeed places that really need it. We'll take care of this, thanks for pointing it out. (I know in one or two cases we came across a library that isn't compatible, but we need to see if we can carve out an exception for those cases, if any remain.) 2) Where are you seeing the recapture that breaks? I was just able to successfully submit feedback with and without https protocol, at least from Chrome. 3) We agree, and BioPortal is working correctly in this particular case. Under normal operations, the portal reports "page not found" to a URL like http://bioportal.bioontology.org/ontologies/BUNNYFOOFOO. When you are seeing a 500 error, that is an actual server error, for example because too many requests are pending. Often performing a reload (sometimes after clearing your cache) will fix this. While we have seen other cases where we are returning 500 errors inappropriately, I believe we have fixed all that we've seen. We'll continue to watch for those specific situations. John On Aug 4, 2017, at 1:30 PM, support at bioontology.org wrote: Name: tomc Email: Tom.Conlin at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fmappings Feedback: Hi First impressions 1) You are not using httpS even where you really need to. see letsencrypt/certbot 2) The recaptcha is broken in secure browsers so one can't create account or feedback (possibly related to #1) I had to create this account with a browser I never use 3) in http "page not found" is a 400 level error not a 500 (server error) i.e http://bioportal.bioontology.org/ontologies/BUNNYFOOFOO thanks and sorry to be terse, must keep moving _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sun Aug 6 16:40:00 2017 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 6 Aug 2017 23:40:00 +0000 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: Message-ID: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> Hi Laia, Sorry for the trouble you are having. Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step. In this case, a quick look at the error log indicated two issues: * "OWL_IMPORT_MISSING: http://who.int/icf" * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations. If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks. John On Aug 5, 2017, at 9:52 PM, Laia Subirats > wrote: Dear Sir/Madam, I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD, I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem. Yours faithfully, -- Laia Subirats _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From laia.subirats at gmail.com Sun Aug 6 22:21:23 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Mon, 7 Aug 2017 07:21:23 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> Message-ID: Hi John, I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear. Cheers, Laia Subirats On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal wrote: > Hi Laia, > > Sorry for the trouble you are having. Usually that message indicates > there has been a problem parsing the ontology, and you can try verifying > the ontology parses with Protege or WebProtege as a next step. > > In this case, a quick look at the error log indicated two issues: > * "OWL_IMPORT_MISSING: http://who.int/icf" > * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" > > A quick suggestion (sorry, no time today to verify myself) is to check to > confirm that those two ontologies are indeed at those locations, and if > they are not, change the references in the source ontology to point to > correct locations. > > If you are still having trouble after that, please send another note > indicating your latest understanding, and our team will try to help. Thanks. > > John > > > On Aug 5, 2017, at 9:52 PM, Laia Subirats wrote: > > Dear Sir/Madam, > > I would like to see the metrics of my ontology in > http://bioportal.bioontology.org/ontologies/HORD > , I do not know if there > is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do > not see the problem. > > Yours faithfully, > -- > Laia Subirats > _______________________________________________ > 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 > -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomc at cs.uoregon.edu Sun Aug 6 17:28:29 2017 From: tomc at cs.uoregon.edu (tomc) Date: Sun, 6 Aug 2017 17:28:29 -0700 Subject: [bioontology-support] [BioPortal] Feedback from tomc In-Reply-To: <7D1280DD-E9BE-4556-8A4A-DF6A24B9E139@stanford.edu> References: <5984d97c65234_66243ff06a4ee93c97834@ncbo-prd-app-09.stanford.edu.mail> <7D1280DD-E9BE-4556-8A4A-DF6A24B9E139@stanford.edu> Message-ID: <43d8ee0e-01af-f934-f613-68ebd263effa@cs.uoregon.edu> 1) sounds good 2) the 'create an account' page and the 'provide feedback' page from Firefox on linux with only whitelisted 3rd party js https_everwhere privacy_badger 2.5) I needed to use Croinum to create an account then feedback did not present a recaptcha if I was logged in. 3) You are right, must have been unfortunate timings on my part but no browser caches were involved just http HEAD from a script. 3.5) Is your server often overloaded? If so could we explore another mechanism to determine if a namespace/prefix is registered/taken in your system. ... nice weather eh? tomc at cs.uoregon.edu On 08/06/2017 04:31 PM, John Graybeal wrote: > Tom, > > Thank you for your input, appreciate your taking the time. > > 1) Yes!. It is a good point that we should make the site exclusively > https, and I see there are indeed places that really need it. We'll take > care of this, thanks for pointing it out. (I know in one or two cases we > came across a library that isn't compatible, but we need to see if we > can carve out an exception for those cases, if any remain.) > > 2) Where are you seeing the recapture that breaks? I was just able to > successfully submit feedback with and without https protocol, at least > from Chrome. > > 3) We agree, and BioPortal is working correctly in this particular case. > Under normal operations, the portal reports "page not found" to a URL > like http://bioportal.bioontology.org/ontologies/BUNNYFOOFOO. When you > are seeing a 500 error, that is an actual server error, for example > because too many requests are pending. Often performing a reload > (sometimes after clearing your cache) will fix this. While we have seen > other cases where we are returning 500 errors inappropriately, I believe > we have fixed all that we've seen. We'll continue to watch for those > specific situations. > > John > > >> On Aug 4, 2017, at 1:30 PM, support at bioontology.org >> wrote: >> >> Name: tomc >> >> Email: Tom.Conlin at gmail.com >> >> Location: http%3A%2F%2Fbioportal.bioontology.org >> %2Fmappings >> >> >> *Feedback:* >> >> Hi >> First impressions >> >> 1) You are not using httpS even where you really need to. >> see letsencrypt/certbot >> >> 2) The recaptcha is broken in secure browsers so one >> can't create account or feedback (possibly related to #1) >> I had to create this account with a browser I never use >> >> 3) in http "page not found" is a 400 level error not a 500 (server error) >> i.e >> http://bioportal.bioontology.org/ontologies/BUNNYFOOFOO >> >> thanks and sorry to be terse, must keep moving >> >> >> _______________________________________________ >> 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 From vendetti at stanford.edu Mon Aug 7 09:46:53 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Aug 2017 16:46:53 +0000 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> Message-ID: <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> Hello Laia, I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl). There are still a number of problems with the import statements. 1). It?s not valid to use a BioPortal REST API call as a download URL for the location of an ontology that you?d like to import. The import statements on lines 21 and 23 in your ontology file will result in not found errors: ? ? which has a URL that doesn?t resolve to anything. Kind regards, Jennifer [1] http://protege.stanford.edu/products.php On Aug 6, 2017, at 10:21 PM, Laia Subirats > wrote: Hi John, I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear. Cheers, Laia Subirats On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal > wrote: Hi Laia, Sorry for the trouble you are having. Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step. In this case, a quick look at the error log indicated two issues: * "OWL_IMPORT_MISSING: http://who.int/icf" * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations. If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks. John On Aug 5, 2017, at 9:52 PM, Laia Subirats > wrote: Dear Sir/Madam, I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD, I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem. Yours faithfully, -- Laia Subirats _______________________________________________ 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 -- Laia Subirats _______________________________________________ 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 2017-08-07 09.20.54.png Type: image/png Size: 37932 bytes Desc: Screenshot 2017-08-07 09.20.54.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-07 09.21.22.png Type: image/png Size: 39093 bytes Desc: Screenshot 2017-08-07 09.21.22.png URL: From laia.subirats at gmail.com Tue Aug 8 04:00:48 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Tue, 8 Aug 2017 13:00:48 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> Message-ID: Hello Jennifer, I change the imports. I uploaded the external ontologies in my Github webpage and pointed my ontology to them. I also changed the unamed.owl import. However, now I have this error: "(Uploaded, Error Rdf)". I have uploaded to webprotege and it works properly, and in my local Prot?g? as well. Sorry for making you spend time helping me. Best, Laia On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti < vendetti at stanford.edu> wrote: > Hello Laia, > > I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl). > There are still a number of problems with the import statements. > > 1). It?s not valid to use a BioPortal REST API call as a download URL for > the location of an ontology that you?d like to import. The import > statements on lines 21 and 23 in your ontology file will result in not > found errors: > > > ? > > > ? which has a URL that doesn?t resolve to anything. > > Kind regards, > Jennifer > > [1] http://protege.stanford.edu/products.php > > > > On Aug 6, 2017, at 10:21 PM, Laia Subirats > wrote: > > Hi John, > > I changed the references and now there is not a parsing problem anymore. > However, the metrics do not appear. > > Cheers, > > Laia Subirats > On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal > wrote: > >> Hi Laia, >> >> Sorry for the trouble you are having. Usually that message indicates >> there has been a problem parsing the ontology, and you can try verifying >> the ontology parses with Protege or WebProtege as a next step. >> >> In this case, a quick look at the error log indicated two issues: >> * "OWL_IMPORT_MISSING: http://who.int/icf" >> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" >> >> A quick suggestion (sorry, no time today to verify myself) is to check to >> confirm that those two ontologies are indeed at those locations, and if >> they are not, change the references in the source ontology to point to >> correct locations. >> >> If you are still having trouble after that, please send another note >> indicating your latest understanding, and our team will try to help. Thanks. >> >> John >> >> >> On Aug 5, 2017, at 9:52 PM, Laia Subirats >> wrote: >> >> Dear Sir/Madam, >> >> I would like to see the metrics of my ontology in http://bioportal. >> bioontology.org/ontologies/HORD >> , I do not know if >> there is any problem. I see that there is a "(Uploaded, Error Rdf)" but >> I do not see the problem. >> >> Yours faithfully, >> -- >> Laia Subirats >> _______________________________________________ >> 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 >> > > > > -- > Laia Subirats > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-07 09.21.22.png Type: image/png Size: 39093 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-07 09.20.54.png Type: image/png Size: 37932 bytes Desc: not available URL: From support at bioontology.org Wed Aug 9 01:45:01 2017 From: support at bioontology.org (support at bioontology.org) Date: Wed, 09 Aug 2017 01:45:01 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Ben Griffin Message-ID: <598acb8d3f016_777c3fabae7a10a46683a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 9 16:48:36 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 9 Aug 2017 23:48:36 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Ben Griffin In-Reply-To: <598acb8d3f016_777c3fabae7a10a46683a@ncbo-prd-app-09.stanford.edu.mail> References: <598acb8d3f016_777c3fabae7a10a46683a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <7F085FD8-FF31-4768-A7FB-EAA8E93C8C3C@stanford.edu> Hi Ben, On Aug 9, 2017, at 1:45 AM, support at bioontology.org wrote: Name: Ben Griffin Email: ben at redsnapper.net Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCTO Feedback: am grateful to you for the provision of the CT Ontology as found at http://bioportal.bioontology.org/ontologies/CTO/?p=summary I am wondering if there are further classes available, When end users submit an ontology file to BIoPortal, all classes in the ontology are parsed and made available in the user interface (assuming no parsing issues occur). I?m not aware of any additional classes in CTO that aren?t displayed in our UI. or being considered for the roles being played by those who participate in a CT: - such as clinicians, healthcare providers, GPs, additional carers, and so on? This support list is mainly for questions or issue reports with regard to the BioPortal software. If you?re interested in extending CTO, I suggest you try contacting the ontology author - it appears that his contact information is available on the summary page for CTO. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From dschober at ipb-halle.de Thu Aug 10 06:07:13 2017 From: dschober at ipb-halle.de (Schober, Daniel) Date: Thu, 10 Aug 2017 15:07:13 +0200 Subject: [bioontology-support] Keywords to describe ontologies on Bioportal Message-ID: Dear Bioportal Folks, I have tried to annotate my the new NMR CV submission at http://bioportal.bioontology.org/ontologies/NMR with appropriate keyword descriptors and was not really able to find the ones needed in the dropdown list. I would therefore request the following new keywords to be added: *assaying technology * (e.g. Mass Spec, NMR, imaging, ...) *metabolomics* ( a domain as is genomics and transcriptomics) I would remove the '*other*' Descriptor as it tempts users to be shallow in their annotation... Cheers, Daniel Schober. -- Dr. Daniel Schober Senior Ontologist, Data manager Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry Weinberg 3 Tel. +49 (0) 345 5582 - 1476 06120 Halle -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Aug 10 21:26:45 2017 From: support at bioontology.org (support at bioontology.org) Date: Thu, 10 Aug 2017 21:26:45 -0700 Subject: [bioontology-support] [BioPortal] Feedback from saucap Message-ID: <598d32054a01a_168b3fd95afb3920998bd@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Aug 11 17:15:37 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 12 Aug 2017 00:15:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from saucap In-Reply-To: <598d32054a01a_168b3fd95afb3920998bd@ncbo-prd-app-09.stanford.edu.mail> References: <598d32054a01a_168b3fd95afb3920998bd@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <10B5972F-CFB4-48C9-A7E1-1F2208B15CED@stanford.edu> Hi Neilson, On Aug 10, 2017, at 9:26 PM, support at bioontology.org wrote: Name: saucap Email: gr.nhppd at health.wa.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Hi, I signed up but made an error in the email address so have not received a confirmation email. I have now created a new account with the correct email address but still haven't received a confirmation email. The details of the two accounts are: One to be kept: saucap, email address gr.nhppd at health.wa.gov.au One to delete: Sau_redcap, email address originally gr.nhppd.health.gov.wa.au but changed to gr.nhppd at health.wa.gov.au OK - I deleted Sau_redcap from our system. Do I take it that the API key will not work until I've responded to the confirmation email? I did some investigation into this and it turns out that there's a bug in our software with regard to subscription to the BioPortal announcements email list (bioportal-announce at lists.stanford.edu). Your account was successfully created and you shouldn?t have any trouble using your API key. (I tested the account creation process, as well as using a newly created API key). The part that isn?t working is the process that initiates a subscription of your email address to the BioPortal announcements email list. I?ve entered an issue for this in our tracker [1]. If you?d like to subscribe to either our announcement list or our support list, you?ll need to do so manually via these URLs: https://mailman.stanford.edu/mailman/listinfo/bioportal-announce https://mailman.stanford.edu/mailman/listinfo/bioontology-support Apologies for the inconvenience. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal_web_ui/issues/60 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Aug 11 17:22:30 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 12 Aug 2017 00:22:30 +0000 Subject: [bioontology-support] Keywords to describe ontologies on Bioportal In-Reply-To: References: Message-ID: Hi Daniel, Are you referring to the ability to associate your ontology entry with categories, as in this screen shot: [cid:BFA735CB-9281-4FBF-AFE6-B18BCE30FDB5 at stanford.edu] ? Kind regards, Jennifer On Aug 10, 2017, at 6:07 AM, Schober, Daniel > wrote: Dear Bioportal Folks, I have tried to annotate my the new NMR CV submission at http://bioportal.bioontology.org/ontologies/NMR with appropriate keyword descriptors and was not really able to find the ones needed in the dropdown list. I would therefore request the following new keywords to be added: assaying technology (e.g. Mass Spec, NMR, imaging, ...) metabolomics ( a domain as is genomics and transcriptomics) I would remove the 'other' Descriptor as it tempts users to be shallow in their annotation... Cheers, Daniel Schober. -- Dr. Daniel Schober Senior Ontologist, Data manager Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry Weinberg 3 Tel. +49 (0) 345 5582 - 1476 06120 Halle _______________________________________________ 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 2017-08-11 17.20.11.png Type: image/png Size: 46761 bytes Desc: Screenshot 2017-08-11 17.20.11.png URL: From als371 at yahoo.com Tue Aug 15 22:44:30 2017 From: als371 at yahoo.com (Al Shapiro) Date: Wed, 16 Aug 2017 05:44:30 +0000 (UTC) Subject: [bioontology-support] No annotations found... References: <406527539.2638857.1502862270643.ref@mail.yahoo.com> Message-ID: <406527539.2638857.1502862270643@mail.yahoo.com> Hi Guys, The Bioportal Annotator appears to be down for last 2 to 3 hours or possibly longer... I have tried accessing via our in-house application, and directly within Bioportal itself... Please have a look and advise... Thank you, The Future is Now! Al Shapiro -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Aug 15 22:58:08 2017 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 16 Aug 2017 05:58:08 +0000 Subject: [bioontology-support] No annotations found... In-Reply-To: <406527539.2638857.1502862270643@mail.yahoo.com> References: <406527539.2638857.1502862270643.ref@mail.yahoo.com> <406527539.2638857.1502862270643@mail.yahoo.com> Message-ID: <65BAB810-2F76-4B4C-BB05-2B4B0D6BB033@stanford.edu> Thank you Al. It appears we may have a misconfiguration -- the developers probably will have to have a look in the morning. Apologies for the inconvenience. John On Aug 15, 2017, at 10:44 PM, Al Shapiro > wrote: Hi Guys, The Bioportal Annotator appears to be down for last 2 to 3 hours or possibly longer... I have tried accessing via our in-house application, and directly within Bioportal itself... Please have a look and advise... Thank you, The Future is Now! Al Shapiro _______________________________________________ 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 skype: graybealski -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcia.bowen at duke.edu Tue Aug 15 14:47:51 2017 From: marcia.bowen at duke.edu (Marci Bowen) Date: Tue, 15 Aug 2017 21:47:51 +0000 Subject: [bioontology-support] BioPortal Message-ID: <530CC913-50C0-4C07-8AA7-BFCF9DFE950B@duke.edu> I would like to obtain the VMWare Virtual Appliance for my research. Would you please contact me as soon as possible? Thank you, Marci Bowen From support at bioontology.org Wed Aug 16 11:37:37 2017 From: support at bioontology.org (support at bioontology.org) Date: Wed, 16 Aug 2017 11:37:37 -0700 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen Message-ID: <599490f1b14f0_2efa3ffbefb476b8918df@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Aug 16 13:09:27 2017 From: support at bioontology.org (support at bioontology.org) Date: Wed, 16 Aug 2017 13:09:27 -0700 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen Message-ID: <5994a6779799c_428f3ffbb66e469090e5@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 16 13:18:33 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 16 Aug 2017 20:18:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen In-Reply-To: <5994a6779799c_428f3ffbb66e469090e5@ncbo-prd-app-08.stanford.edu.mail> References: <5994a6779799c_428f3ffbb66e469090e5@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Marcia, Could you give me an example of the term you?re searching for? Are you using any of the advanced search options? Which browser are you using? Also, do you mean that search is only working for you when you?re logged out? Kind regards, Jennifer On Aug 16, 2017, at 1:09 PM, support at bioontology.org wrote: Name: marcibowen Email: marcia.bowen at duke.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I desperately need your help. I keep getting : We're sorry but something has gone wrong. We have been notified of this error. When I try to search after I log in. What do I need to do? _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 16 12:26:56 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 16 Aug 2017 19:26:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen In-Reply-To: <599490f1b14f0_2efa3ffbefb476b8918df@ncbo-prd-app-08.stanford.edu.mail> References: <599490f1b14f0_2efa3ffbefb476b8918df@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9AB4171B-57D3-4E9E-A125-8F3B04FD2DAD@stanford.edu> Hi Marci, Our REST API with examples of URLs for retrieving particular types of data is available here: http://data.bioontology.org/documentation Here?s a specific example of retrieving the class data for a class in the SNOMED ontology: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F123037004 Notice that the class ID has to be URL encoded. I don?t know which property you?re referring to when you say ?code?. You may want to use the ?include=all? parameter when making the above call to see which part of the result is of interest to you, e.g.: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F123037004?include=all If you want to make these calls via curl, simply prepend the URL with ?curl?, e.g.: curl https://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F123037004 You need an API key to use our REST API. Instructions for getting an API key are here: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer On Aug 16, 2017, at 11:37 AM, support at bioontology.org wrote: Name: marcibowen Email: marcia.bowen at duke.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F500%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F91175000 Feedback: Would you please send me the link to the documentation for a query using CURL? I need to be able to search for a term in SNOMED CT, download a report of those codes, but I do not know how to do it. Thanks, Marci Bowen _______________________________________________ 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 Wed Aug 16 15:52:03 2017 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 16 Aug 2017 22:52:03 +0000 Subject: [bioontology-support] No annotations found... In-Reply-To: <65BAB810-2F76-4B4C-BB05-2B4B0D6BB033@stanford.edu> References: <406527539.2638857.1502862270643.ref@mail.yahoo.com> <406527539.2638857.1502862270643@mail.yahoo.com> <65BAB810-2F76-4B4C-BB05-2B4B0D6BB033@stanford.edu> Message-ID: Hi Al, Thank you again for brining this issue to our attention. The problem has been identified and resolved, and the Annotator is now working properly. Let us know if you encounter any others issues. Thanks! Michael On Aug 15, 2017, at 10:58 PM, John Graybeal > wrote: Thank you Al. It appears we may have a misconfiguration -- the developers probably will have to have a look in the morning. Apologies for the inconvenience. John On Aug 15, 2017, at 10:44 PM, Al Shapiro > wrote: Hi Guys, The Bioportal Annotator appears to be down for last 2 to 3 hours or possibly longer... I have tried accessing via our in-house application, and directly within Bioportal itself... Please have a look and advise... Thank you, The Future is Now! Al Shapiro _______________________________________________ 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 skype: graybealski _______________________________________________ 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 laia.subirats at gmail.com Thu Aug 17 03:32:07 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Thu, 17 Aug 2017 12:32:07 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> Message-ID: Dear Jennifer, I would like to ask you help about this issue. I am still lost about how can I solve this error. Best, Laia On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats wrote: > Hello Jennifer, > > I change the imports. I uploaded the external ontologies in my Github > webpage and pointed my ontology to them. I also changed the unamed.owl > import. > > However, now I have this error: "(Uploaded, Error Rdf)". > > I have uploaded to webprotege and it works properly, and in my local > Prot?g? as well. > > Sorry for making you spend time helping me. > > Best, > > Laia > On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti < > vendetti at stanford.edu> wrote: > >> Hello Laia, >> >> I looked at your latest ontology source file >> (HORD_all_2017_08_07_scenarios.owl). There are still a number of >> problems with the import statements. >> >> 1). It?s not valid to use a BioPortal REST API call as a download URL for >> the location of an ontology that you?d like to import. The import >> statements on lines 21 and 23 in your ontology file will result in not >> found errors: >> >> >> ? >> >> >> ? which has a URL that doesn?t resolve to anything. >> >> Kind regards, >> Jennifer >> >> [1] http://protege.stanford.edu/products.php >> >> >> >> On Aug 6, 2017, at 10:21 PM, Laia Subirats >> wrote: >> >> Hi John, >> >> I changed the references and now there is not a parsing problem anymore. >> However, the metrics do not appear. >> >> Cheers, >> >> Laia Subirats >> On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal >> wrote: >> >>> Hi Laia, >>> >>> Sorry for the trouble you are having. Usually that message indicates >>> there has been a problem parsing the ontology, and you can try verifying >>> the ontology parses with Protege or WebProtege as a next step. >>> >>> In this case, a quick look at the error log indicated two issues: >>> * "OWL_IMPORT_MISSING: http://who.int/icf" >>> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" >>> >>> A quick suggestion (sorry, no time today to verify myself) is to check >>> to confirm that those two ontologies are indeed at those locations, and if >>> they are not, change the references in the source ontology to point to >>> correct locations. >>> >>> If you are still having trouble after that, please send another note >>> indicating your latest understanding, and our team will try to help. Thanks. >>> >>> John >>> >>> >>> On Aug 5, 2017, at 9:52 PM, Laia Subirats >>> wrote: >>> >>> Dear Sir/Madam, >>> >>> I would like to see the metrics of my ontology in >>> http://bioportal.bioontology.org/ontologies/HORD >>> , I do not know if >>> there is any problem. I see that there is a "(Uploaded, Error Rdf)" but >>> I do not see the problem. >>> >>> Yours faithfully, >>> -- >>> Laia Subirats >>> _______________________________________________ >>> 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 >>> >> >> >> >> -- >> Laia Subirats >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> >> > > > -- > Laia Subirats > -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-07 09.21.22.png Type: image/png Size: 39093 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-07 09.20.54.png Type: image/png Size: 37932 bytes Desc: not available URL: From vendetti at stanford.edu Thu Aug 17 11:28:01 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 17 Aug 2017 18:28:01 +0000 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen In-Reply-To: References: <5994a6779799c_428f3ffbb66e469090e5@ncbo-prd-app-08.stanford.edu.mail> <14770E37-0036-4850-B0EA-A2A1F0A25C94@duke.edu> <1629B870-006A-4104-B8C7-67AFE1D4CA79@stanford.edu> Message-ID: Hello Marci, On Aug 16, 2017, at 4:12 PM, Marci Bowen > wrote: I use Firefox. I cleared the cache and that corrected the problem. Now, how I can I download the SNOMED code and description of all the decedents that result from searching. Due to licensing restrictions, we?re unable to provide the SNOMED ontology as a file download. You can however, access SNOMED data via our REST API. For example, to retrieve the descendants of the ?Seizure? term, you can use this call: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/descendants I don?t know what property you?re referring to when you say ?code?. You can use the BioPortal user interface to look at the properties and their associated values for any class: [cid:4B1C4D28-57CB-49BD-87DC-713F36DFCF9A at stanford.edu] I don?t see any properties on the right-hand side that are called code or definition. If you can?t find what you?re looking for in BioPortal, you might consider getting a UMLS license (free and easy), and try out the web-based browser that they offer for the set of UMLS ontologies (SNOMEDCT is one of them). [cid:CA44E871-4794-4B2B-9549-178F9086A91F at stanford.edu] Can I also download the hierarchy? In this case, I searched seizure. Yes, this is possible from the REST endpoint. You may want to look at the tree and/or paths_to_root calls: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/tree http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/paths_to_root The REST API documentation is here: http://data.bioontology.org/documentation#nav_home Kind regards, Jennifer Thanks, Marci On Aug 16, 2017, at 19:01, Jennifer Leigh Vendetti > wrote: Hi Marci, I?m wondering if you could try clearing your browser cache? I?m not sure what browser you?re using. To clear the cache in Chrome, you?d select the menu item ?Chrome? -> ?Clear Browsing Data?? and follow the instructions in the resulting dialog. Kind regards, Jennifer On Aug 16, 2017, at 1:27 PM, Marci Bowen > wrote: This is what I am doing: after I log in, under tools, I select "Ontology Browser?. then I select blue highlighted "SNOMED CT?, I get this error: We're sorry but something has gone wrong. We have been notified of this error. So I then have to go back and select classes. I type in Seziure in the jump to: box. Then I get : We're sorry but something has gone wrong. We have been notified of this error. I just want to get a report of all the SNOMED codes and descriptions that a search for seizure gets. Thanks, Marci PS My phone number is 828.408.2434 if you would prefer to call. Hi Marcia, Could you give me an example of the term you?re searching for? Are you using any of the advanced search options? Which browser are you using? Also, do you mean that search is only working for you when you?re logged out? Kind regards, Jennifer On Aug 16, 2017, at 1:09 PM, support at bioontology.org wrote: Name: marcibowen Email: marcia.bowen at duke.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I desperately need your help. I keep getting : We're sorry but something has gone wrong. We have been notified of this error. When I try to search after I log in. What do I need to do? _______________________________________________ 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 2017-08-17 11.15.50.png Type: image/png Size: 174320 bytes Desc: Screenshot 2017-08-17 11.15.50.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-17 11.20.08.png Type: image/png Size: 344600 bytes Desc: Screenshot 2017-08-17 11.20.08.png URL: From vendetti at stanford.edu Thu Aug 17 14:47:58 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 17 Aug 2017 21:47:58 +0000 Subject: [bioontology-support] [BioPortal] Feedback from marcibowen In-Reply-To: References: <5994a6779799c_428f3ffbb66e469090e5@ncbo-prd-app-08.stanford.edu.mail> <14770E37-0036-4850-B0EA-A2A1F0A25C94@duke.edu> <1629B870-006A-4104-B8C7-67AFE1D4CA79@stanford.edu> Message-ID: Hi Marci, On Aug 17, 2017, at 11:32 AM, Marci Bowen > wrote: Thank you. I am so confused. How do I get access to the REST API? The BioPortal REST API is freely available. The only step required for use is to create an account on the BioPortal website, which will generate an API key for you. Instructions for creating an account, and accessing your resulting API key are available on our wiki: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Once you have your API key, you include it as a parameter every time you issue a REST API call. For example, you could enter the following URL in a browser to see a list of all the ontologies available in BioPortal: http://data.bioontology.org/ontologies?apikey=your_api_key_here Kind regards, Jennifer Thanks, Marci Bowen On Aug 17, 2017, at 2:28 PM, Jennifer Leigh Vendetti > wrote: Hello Marci, On Aug 16, 2017, at 4:12 PM, Marci Bowen > wrote: I use Firefox. I cleared the cache and that corrected the problem. Now, how I can I download the SNOMED code and description of all the decedents that result from searching. Due to licensing restrictions, we?re unable to provide the SNOMED ontology as a file download. You can however, access SNOMED data via our REST API. For example, to retrieve the descendants of the ?Seizure? term, you can use this call: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/descendants I don?t know what property you?re referring to when you say ?code?. You can use the BioPortal user interface to look at the properties and their associated values for any class: I don?t see any properties on the right-hand side that are called code or definition. If you can?t find what you?re looking for in BioPortal, you might consider getting a UMLS license (free and easy), and try out the web-based browser that they offer for the set of UMLS ontologies (SNOMEDCT is one of them). Can I also download the hierarchy? In this case, I searched seizure. Yes, this is possible from the REST endpoint. You may want to look at the tree and/or paths_to_root calls: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/tree http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000/paths_to_root The REST API documentation is here: http://data.bioontology.org/documentation#nav_home Kind regards, Jennifer Thanks, Marci On Aug 16, 2017, at 19:01, Jennifer Leigh Vendetti > wrote: Hi Marci, I?m wondering if you could try clearing your browser cache? I?m not sure what browser you?re using. To clear the cache in Chrome, you?d select the menu item ?Chrome? -> ?Clear Browsing Data?? and follow the instructions in the resulting dialog. Kind regards, Jennifer On Aug 16, 2017, at 1:27 PM, Marci Bowen > wrote: This is what I am doing: after I log in, under tools, I select "Ontology Browser?. then I select blue highlighted "SNOMED CT?, I get this error: We're sorry but something has gone wrong. We have been notified of this error. So I then have to go back and select classes. I type in Seziure in the jump to: box. Then I get : We're sorry but something has gone wrong. We have been notified of this error. I just want to get a report of all the SNOMED codes and descriptions that a search for seizure gets. Thanks, Marci PS My phone number is 828.408.2434 if you would prefer to call. Hi Marcia, Could you give me an example of the term you?re searching for? Are you using any of the advanced search options? Which browser are you using? Also, do you mean that search is only working for you when you?re logged out? Kind regards, Jennifer On Aug 16, 2017, at 1:09 PM, support at bioontology.org wrote: Name: marcibowen Email: marcia.bowen at duke.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I desperately need your help. I keep getting : We're sorry but something has gone wrong. We have been notified of this error. When I try to search after I log in. What do I need to do? _______________________________________________ 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 Thu Aug 17 18:06:41 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 18 Aug 2017 01:06:41 +0000 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> Message-ID: <90FD1246-BAE1-42B0-8A04-D213E457130B@stanford.edu> Hi Laia, You?re including the ORDO ontology, which doesn?t parse in BioPortal at the moment. Unfortunately, the problem is a bug in the OWL API, which is 3rd party software that we use to load / parse ontologies. I?ve been corresponding with the developer of the OWL API and he has released a bug fix version that may address the problem with ORDO. I plan to integrate this new version of the OWL API into BioPortal, but haven?t been able to get to it yet due to some other work that is higher priority at the moment. I apologize that I don?t have an exact date for you when the problem with ORDO will be resolved, but it should be in the near future. Kind regards, Jennifer On Aug 17, 2017, at 3:32 AM, Laia Subirats > wrote: Dear Jennifer, I would like to ask you help about this issue. I am still lost about how can I solve this error. Best, Laia On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats > wrote: Hello Jennifer, I change the imports. I uploaded the external ontologies in my Github webpage and pointed my ontology to them. I also changed the unamed.owl import. However, now I have this error: "(Uploaded, Error Rdf)". I have uploaded to webprotege and it works properly, and in my local Prot?g? as well. Sorry for making you spend time helping me. Best, Laia On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti > wrote: Hello Laia, I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl). There are still a number of problems with the import statements. 1). It?s not valid to use a BioPortal REST API call as a download URL for the location of an ontology that you?d like to import. The import statements on lines 21 and 23 in your ontology file will result in not found errors: ? ? which has a URL that doesn?t resolve to anything. Kind regards, Jennifer [1] http://protege.stanford.edu/products.php On Aug 6, 2017, at 10:21 PM, Laia Subirats > wrote: Hi John, I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear. Cheers, Laia Subirats On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal > wrote: Hi Laia, Sorry for the trouble you are having. Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step. In this case, a quick look at the error log indicated two issues: * "OWL_IMPORT_MISSING: http://who.int/icf" * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations. If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks. John On Aug 5, 2017, at 9:52 PM, Laia Subirats > wrote: Dear Sir/Madam, I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD, I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem. Yours faithfully, -- Laia Subirats _______________________________________________ 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 -- Laia Subirats _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -- Laia Subirats -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From laia.subirats at gmail.com Thu Aug 17 22:59:47 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Fri, 18 Aug 2017 07:59:47 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: <90FD1246-BAE1-42B0-8A04-D213E457130B@stanford.edu> References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> <90FD1246-BAE1-42B0-8A04-D213E457130B@stanford.edu> Message-ID: Hi Jennifer, Thank you for your answer. Kind regards, Laia On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti < vendetti at stanford.edu> wrote: > Hi Laia, > > You?re including the ORDO ontology, which doesn?t parse in BioPortal at > the moment. Unfortunately, the problem is a bug in the OWL API, which is > 3rd party software that we use to load / parse ontologies. I?ve been > corresponding with the developer of the OWL API and he has released a bug > fix version that may address the problem with ORDO. I plan to integrate > this new version of the OWL API into BioPortal, but haven?t been able to > get to it yet due to some other work that is higher priority at the moment. > > I apologize that I don?t have an exact date for you when the problem with > ORDO will be resolved, but it should be in the near future. > > Kind regards, > Jennifer > > > > On Aug 17, 2017, at 3:32 AM, Laia Subirats > wrote: > > Dear Jennifer, > > I would like to ask you help about this issue. I am still lost about how > can I solve this error. > > Best, > > Laia > > On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats > wrote: > >> Hello Jennifer, >> >> I change the imports. I uploaded the external ontologies in my Github >> webpage and pointed my ontology to them. I also changed the unamed.owl >> import. >> >> However, now I have this error: "(Uploaded, Error Rdf)". >> >> I have uploaded to webprotege and it works properly, and in my local >> Prot?g? as well. >> >> Sorry for making you spend time helping me. >> >> Best, >> >> Laia >> On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti < >> vendetti at stanford.edu> wrote: >> >>> Hello Laia, >>> >>> I looked at your latest ontology source file >>> (HORD_all_2017_08_07_scenarios.owl). There are still a number of >>> problems with the import statements. >>> >>> 1). It?s not valid to use a BioPortal REST API call as a download URL >>> for the location of an ontology that you?d like to import. The import >>> statements on lines 21 and 23 in your ontology file will result in not >>> found errors: >>> >>> >>> ? >>> >>> >>> ? which has a URL that doesn?t resolve to anything. >>> >>> Kind regards, >>> Jennifer >>> >>> [1] http://protege.stanford.edu/products.php >>> >>> >>> >>> On Aug 6, 2017, at 10:21 PM, Laia Subirats >>> wrote: >>> >>> Hi John, >>> >>> I changed the references and now there is not a parsing problem anymore. >>> However, the metrics do not appear. >>> >>> Cheers, >>> >>> Laia Subirats >>> On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal >>> wrote: >>> >>>> Hi Laia, >>>> >>>> Sorry for the trouble you are having. Usually that message indicates >>>> there has been a problem parsing the ontology, and you can try verifying >>>> the ontology parses with Protege or WebProtege as a next step. >>>> >>>> In this case, a quick look at the error log indicated two issues: >>>> * "OWL_IMPORT_MISSING: http://who.int/icf" >>>> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" >>>> >>>> A quick suggestion (sorry, no time today to verify myself) is to check >>>> to confirm that those two ontologies are indeed at those locations, and if >>>> they are not, change the references in the source ontology to point to >>>> correct locations. >>>> >>>> If you are still having trouble after that, please send another note >>>> indicating your latest understanding, and our team will try to help. Thanks. >>>> >>>> John >>>> >>>> >>>> On Aug 5, 2017, at 9:52 PM, Laia Subirats >>>> wrote: >>>> >>>> Dear Sir/Madam, >>>> >>>> I would like to see the metrics of my ontology in >>>> http://bioportal.bioontology.org/ontologies/HORD >>>> , I do not know if >>>> there is any problem. I see that there is a "(Uploaded, Error Rdf)" >>>> but I do not see the problem. >>>> >>>> Yours faithfully, >>>> -- >>>> Laia Subirats >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> >>> -- >>> Laia Subirats >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> >> >> >> -- >> Laia Subirats >> > > > > -- > Laia Subirats > > > -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From brant.chee at jhuapl.edu Wed Aug 23 05:43:56 2017 From: brant.chee at jhuapl.edu (Brant Chee) Date: Wed, 23 Aug 2017 08:43:56 -0400 Subject: [bioontology-support] NCBO VIRTUAL APPLIANCE Message-ID: <9f75bb3a-b69a-309a-588a-8efcfb9b4a10@jhuapl.edu> My name is Brant Chee. I am a research at Johns Hopkins University APL and we are interested in obtaining a copy of the NCBO virtual appliance. We are interested in evaluating the NCBO annotator on clinical notes to support our existing NLP work (IRB NA_00045103). However due to PHI contained within notes we would like deploy it locally on our network. Thank you, Brant From vendetti at stanford.edu Wed Aug 23 16:28:51 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 23 Aug 2017 23:28:51 +0000 Subject: [bioontology-support] [ORDO] bioportal issue In-Reply-To: <426ea122-5b25-8056-63c5-4747701190cd@inserm.fr> References: <53721CEC.4010600@inserm.fr> <56CDC203.5070001@inserm.fr> <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu> <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu> <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu> <426ea122-5b25-8056-63c5-4747701190cd@inserm.fr> Message-ID: <665ED8EC-1BBC-4C9B-805E-1B7BE3B76093@stanford.edu> Hello Marc, Apologies that it took me some time to sort this one out. I had to correspond with the developers of the OWL API. They confirmed that there was a bug in their API that generated invalid blank node identifiers when saving ontologies in RDF/XML format. They released a new version of their API, which I have incorporated into BioPortal. I reprocessed ORDO, which is now fully parsed and available. On Jul 27, 2017, at 8:49 AM, Marc Hanauer > wrote: Hello Jennifer, The structure was exactly the same in ORDO V2.3 (especially for this exemple of annotation embeded). Yes, I had noticed that. I think the issue stemmed from the fact that we were using a newer version of the OWL API (v4.3.1) when you submitted ORDO 2.4. The issue didn?t appear to be present in the version of the OWL API that we were using (v4.2.5) when you submitted ORDO 2.3 in December of last year. The OWL file is code generated and then checked with Protegee. Thanks for that information. We have try to reproduce your issue using OWL API but we never succeed to have this kind of axiom. My correspondence with the OWL API developers included example code for how this problem arose in BioPortal. If anyone is interested in the particulars, the conversation is still available in their public list archive: https://sourceforge.net/p/owlapi/mailman/owlapi-developer/?viewmonth=201707 Kind regards, Jennifer Please feel free to contact our developper Samuel Demarest (in cc) who's in charge of the generating code if you have any other question. I'll be back in september. Best regards, www.orpha.net | Twitter @Orphanet Marc HANAUER Directeur Adjoint / Deputy Director Directeur technique / Chief technology officer Strat?gie et Innovation marc.hanauer at inserm.fr ORPHANET - INSERM US14 Plateforme Maladies Rares / Rare Disease Platform 96 rue Didot 75014 PARIS FRANCE Le 14/07/2017 ? 18:41, Jennifer Leigh Vendetti a ?crit : Hello Marc, I don?t have a solution yet for parsing ORDO 2.4 in BioPortal, but I?ll provide a summary below of what I?ve discovered so far. The system is having difficulty handling classes in your ontology that have annotations nested 3 levels deep. Here?s a screenshot of your ontology in the Protege ontology editor with class ?48,XXYY syndrome? highlighted: Note the second occurrence of hasDbXref in the screenshot where there?s an annotation on an annotation on an annotation. I think I mentioned in a previous correspondence that we use the OWL API internally for parsing. When the OWL API loads this ontology, it inserts a blank node for these nested annotations with a blank node identifier in the form of ?_:genid?. Using the example in the screen shot above, this is a snippet of the ontology source, as loaded by the OWL API: ICD-10:Q98.8 Attributed Attributed NTBT (narrower term maps to a broader term) Although we can load the ontology without errors, the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store: Illegal rdf:nodeID value '_:genid25' rapper: Failed to parse file I went looking for a specification for what is considered valid syntax for blank node identifiers, but so far I haven?t been able to find anything. It?s unclear to me if the OWL API is generating invalid RDF, or if the Raptor RDF parser isn?t handling blank nodes that it should be. I will likely need to correspond with the developers of one or both projects. Apologies that it hasn?t been straightforward so far to track this down. On another note, I?m wondering if you could give me some basic information about how your OWL file is generated. Is it done programmatically? Or, do you use an ontology editing environment to maintain the ontology? Kind regards, Jennifer On Jul 10, 2017, at 6:26 PM, Jennifer Leigh Vendetti > wrote: Hello Marc, I?ve entered an issue in our tracker [1], and will have a look. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal-project/issues/31 On Jul 10, 2017, at 2:11 PM, marc.hanauer at inserm.fr wrote: Hello Jennifer, Sorry about that, but once again the new version of ORDO (2.4) seems to have issues : 2.3 (Uploaded, Error Rdf) 07/05/2017 07/05/2017 https://bioportal.bioontology.org/ontologies/ORDO This version was produced the same way than the previous one. Any ideas ? Best regards, --- Marc HANAUER Directeur Adjoint / Deputy Director Directeur technique / Chief technology officer Strat?gie et Innovation marc.hanauer at inserm.fr ORPHANET - INSERM US14 Plateforme Maladies Rares / Rare Disease Platform 96 rue Didot 75014 PARIS FRANCE Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit : Hello Marc, We've addressed the issue I mentioned below. Version 2.2 of ORDO is parsed and available in BioPortal: http://bioportal.bioontology.org/ontologies/ORDO Apologies again that this one took us some time to address. Best, Jennifer On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti > wrote: Hi Marc, I am writing with a status report regarding BioPortal's failure to handle ORDO 2.2. As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing. I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly. The parsing succeeds, which indicates to me that your ontology file is valid. When the OWL API parses your ontology file, it emits a very large number of "unparsed triple" messages (roughly 15.5K of them), e.g.: [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty -> http://purl.obolibrary.org/obo/ECO_0000218 [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource -> _:genid120261 The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal's source code. I am currently working toward fixing the issue, and hope to have something available soon. Apologies that this one is taking some time for us to track down / fix. Best, Jennifer [1] http://owlcs.github.io/owlapi/ On Jun 27, 2016, at 3:18 AM, Marc Hanauer > wrote: Hello Jennifer, I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error. The version in our own server is now "2.2" but it appears with this line on bioportal: 2.1 (Uploaded, Error Rdf) 06/22/2016 06/22/2016 OWL | Diff Any idea ? Best regards, Marc HANAUER Directeur Adjoint / Deputy Director Directeur technique / Chief technology officer Strat?gie et Innovation marc.hanauer at inserm.fr ORPHANET - INSERM US14 Plateforme Maladies Rares / Rare Disease Platform 96 rue Didot 75014 PARIS FRANCE Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit : Hello Marc, On Feb 24, 2016, at 6:45 AM, Marc Hanauer > wrote: Dear support, We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago). Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ) and then the bioportal website automatically upload it. It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1) Do we need to perform any manual action in order to update it on bioportal ? You don't need to do anything manual. We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies. The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight. By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this) Sorry you're having difficulties. I tried reproducing this behavior here and so far haven't had any luck. I've viewed your ontology in BioPortal, both when logged in and logged out (screen shot below). I also verified that your user account of "ORDO_Orphanet" is valid, and I don't see any issues there. Are you still seeing this behavior? Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Aug 23 16:44:55 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 23 Aug 2017 23:44:55 +0000 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> <90FD1246-BAE1-42B0-8A04-D213E457130B@stanford.edu> Message-ID: Hello Laia, The issue that was preventing ORDO from parsing/loading in BioPortal has been fixed. I reprocessed your HORD ontology, which is now fully parsed and available. Kind regards, Jennifer On Aug 17, 2017, at 10:59 PM, Laia Subirats > wrote: Hi Jennifer, Thank you for your answer. Kind regards, Laia On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti > wrote: Hi Laia, You?re including the ORDO ontology, which doesn?t parse in BioPortal at the moment. Unfortunately, the problem is a bug in the OWL API, which is 3rd party software that we use to load / parse ontologies. I?ve been corresponding with the developer of the OWL API and he has released a bug fix version that may address the problem with ORDO. I plan to integrate this new version of the OWL API into BioPortal, but haven?t been able to get to it yet due to some other work that is higher priority at the moment. I apologize that I don?t have an exact date for you when the problem with ORDO will be resolved, but it should be in the near future. Kind regards, Jennifer On Aug 17, 2017, at 3:32 AM, Laia Subirats > wrote: Dear Jennifer, I would like to ask you help about this issue. I am still lost about how can I solve this error. Best, Laia On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats > wrote: Hello Jennifer, I change the imports. I uploaded the external ontologies in my Github webpage and pointed my ontology to them. I also changed the unamed.owl import. However, now I have this error: "(Uploaded, Error Rdf)". I have uploaded to webprotege and it works properly, and in my local Prot?g? as well. Sorry for making you spend time helping me. Best, Laia On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti > wrote: Hello Laia, I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl). There are still a number of problems with the import statements. 1). It?s not valid to use a BioPortal REST API call as a download URL for the location of an ontology that you?d like to import. The import statements on lines 21 and 23 in your ontology file will result in not found errors: ? ? which has a URL that doesn?t resolve to anything. Kind regards, Jennifer [1] http://protege.stanford.edu/products.php On Aug 6, 2017, at 10:21 PM, Laia Subirats > wrote: Hi John, I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear. Cheers, Laia Subirats On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal > wrote: Hi Laia, Sorry for the trouble you are having. Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step. In this case, a quick look at the error log indicated two issues: * "OWL_IMPORT_MISSING: http://who.int/icf" * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations. If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks. John On Aug 5, 2017, at 9:52 PM, Laia Subirats > wrote: Dear Sir/Madam, I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD, I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem. Yours faithfully, -- Laia Subirats _______________________________________________ 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 -- Laia Subirats _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -- Laia Subirats -- Laia Subirats -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From laia.subirats at gmail.com Wed Aug 23 23:11:22 2017 From: laia.subirats at gmail.com (Laia Subirats) Date: Thu, 24 Aug 2017 08:11:22 +0200 Subject: [bioontology-support] Missing metrics in HORD ontology In-Reply-To: References: <8A58DDB0-FBF5-40A1-9657-25931E8A796C@stanford.edu> <9F37273B-2328-435E-8BE4-1E90FA2A16EE@stanford.edu> <90FD1246-BAE1-42B0-8A04-D213E457130B@stanford.edu> Message-ID: Thank you Jennifer, We want to submit this ontology in a journal on the 1st October so it has been just in time. Kind regards, Laia On Thu, Aug 24, 2017 at 1:44 AM, Jennifer Leigh Vendetti < vendetti at stanford.edu> wrote: > Hello Laia, > > The issue that was preventing ORDO from parsing/loading in BioPortal has > been fixed. I reprocessed your HORD ontology, which is now fully parsed and > available. > > Kind regards, > Jennifer > > > > > On Aug 17, 2017, at 10:59 PM, Laia Subirats > wrote: > > Hi Jennifer, > > Thank you for your answer. > > Kind regards, > > Laia > On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti < > vendetti at stanford.edu> wrote: > >> Hi Laia, >> >> You?re including the ORDO ontology, which doesn?t parse in BioPortal at >> the moment. Unfortunately, the problem is a bug in the OWL API, which is >> 3rd party software that we use to load / parse ontologies. I?ve been >> corresponding with the developer of the OWL API and he has released a bug >> fix version that may address the problem with ORDO. I plan to integrate >> this new version of the OWL API into BioPortal, but haven?t been able to >> get to it yet due to some other work that is higher priority at the moment. >> >> I apologize that I don?t have an exact date for you when the problem with >> ORDO will be resolved, but it should be in the near future. >> >> Kind regards, >> Jennifer >> >> >> >> On Aug 17, 2017, at 3:32 AM, Laia Subirats >> wrote: >> >> Dear Jennifer, >> >> I would like to ask you help about this issue. I am still lost about how >> can I solve this error. >> >> Best, >> >> Laia >> >> On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats >> wrote: >> >>> Hello Jennifer, >>> >>> I change the imports. I uploaded the external ontologies in my Github >>> webpage and pointed my ontology to them. I also changed the unamed.owl >>> import. >>> >>> However, now I have this error: "(Uploaded, Error Rdf)". >>> >>> I have uploaded to webprotege and it works properly, and in my local >>> Prot?g? as well. >>> >>> Sorry for making you spend time helping me. >>> >>> Best, >>> >>> Laia >>> On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti < >>> vendetti at stanford.edu> wrote: >>> >>>> Hello Laia, >>>> >>>> I looked at your latest ontology source file >>>> (HORD_all_2017_08_07_scenarios.owl). There are still a number of >>>> problems with the import statements. >>>> >>>> 1). It?s not valid to use a BioPortal REST API call as a download URL >>>> for the location of an ontology that you?d like to import. The import >>>> statements on lines 21 and 23 in your ontology file will result in not >>>> found errors: >>>> >>>> >>>> ? >>>> >>>> >>>> ? which has a URL that doesn?t resolve to anything. >>>> >>>> Kind regards, >>>> Jennifer >>>> >>>> [1] http://protege.stanford.edu/products.php >>>> >>>> >>>> >>>> On Aug 6, 2017, at 10:21 PM, Laia Subirats >>>> wrote: >>>> >>>> Hi John, >>>> >>>> I changed the references and now there is not a parsing problem >>>> anymore. However, the metrics do not appear. >>>> >>>> Cheers, >>>> >>>> Laia Subirats >>>> On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal >>>> wrote: >>>> >>>>> Hi Laia, >>>>> >>>>> Sorry for the trouble you are having. Usually that message indicates >>>>> there has been a problem parsing the ontology, and you can try verifying >>>>> the ontology parses with Protege or WebProtege as a next step. >>>>> >>>>> In this case, a quick look at the error log indicated two issues: >>>>> * "OWL_IMPORT_MISSING: http://who.int/icf" >>>>> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4" >>>>> >>>>> A quick suggestion (sorry, no time today to verify myself) is to check >>>>> to confirm that those two ontologies are indeed at those locations, and if >>>>> they are not, change the references in the source ontology to point to >>>>> correct locations. >>>>> >>>>> If you are still having trouble after that, please send another note >>>>> indicating your latest understanding, and our team will try to help. Thanks. >>>>> >>>>> John >>>>> >>>>> >>>>> On Aug 5, 2017, at 9:52 PM, Laia Subirats >>>>> wrote: >>>>> >>>>> Dear Sir/Madam, >>>>> >>>>> I would like to see the metrics of my ontology in >>>>> http://bioportal.bioontology.org/ontologies/HORD >>>>> , I do not know if >>>>> there is any problem. I see that there is a "(Uploaded, Error Rdf)" >>>>> but I do not see the problem. >>>>> >>>>> Yours faithfully, >>>>> -- >>>>> Laia Subirats >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> Laia Subirats >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>>> >>> >>> >>> -- >>> Laia Subirats >>> >> >> >> >> -- >> Laia Subirats >> >> >> > > > -- > Laia Subirats > > > -- Laia Subirats -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Aug 25 12:46:11 2017 From: support at bioontology.org (support at bioontology.org) Date: Fri, 25 Aug 2017 12:46:11 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Marisa Hughes Message-ID: <59a07e83863e_7dd93f8bde0f71f8558c1@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From marc.hanauer at inserm.fr Mon Aug 28 03:00:04 2017 From: marc.hanauer at inserm.fr (marc.hanauer at inserm.fr) Date: Mon, 28 Aug 2017 12:00:04 +0200 Subject: [bioontology-support] [ORDO] bioportal issue In-Reply-To: <665ED8EC-1BBC-4C9B-805E-1B7BE3B76093@stanford.edu> References: <53721CEC.4010600@inserm.fr> <56CDC203.5070001@inserm.fr> <848E2F34-E02F-4DA3-987D-7A836EBB874B@stanford.edu> <876518B6-C6F6-465C-A1B2-AB055368F899@stanford.edu> <1D5A5F16-E85A-42EF-AFB0-8C7DDA72DC04@stanford.edu> <426ea122-5b25-8056-63c5-4747701190cd@inserm.fr> <665ED8EC-1BBC-4C9B-805E-1B7BE3B76093@stanford.edu> Message-ID: <49234715a8c395da90ad29d37af2972d@inserm.fr> Hello, Good news, everything seems fine now. Thanks! Best regards, --- Marc HANAUER Directeur Adjoint / Deputy Director Directeur technique / Chief technology officer Strat?gie et Innovation marc.hanauer at inserm.fr ORPHANET - INSERM US14 Plateforme Maladies Rares / Rare Disease Platform 96 rue Didot 75014 PARIS FRANCE Le 24-08-2017 01:28, Jennifer Leigh Vendetti a ?crit : > Hello Marc, > > Apologies that it took me some time to sort this one out. I had to correspond with the developers of the OWL API. They confirmed that there was a bug in their API that generated invalid blank node identifiers when saving ontologies in RDF/XML format. They released a new version of their API, which I have incorporated into BioPortal. I reprocessed ORDO, which is now fully parsed and available. > >> On Jul 27, 2017, at 8:49 AM, Marc Hanauer wrote: >> >> Hello Jennifer, >> >> The structure was exactly the same in ORDO V2.3 (especially for this exemple of annotation embeded). > > Yes, I had noticed that. I think the issue stemmed from the fact that we were using a newer version of the OWL API (v4.3.1) when you submitted ORDO 2.4. The issue didn't appear to be present in the version of the OWL API that we were using (v4.2.5) when you submitted ORDO 2.3 in December of last year. > >> The OWL file is code generated and then checked with Protegee. > > Thanks for that information. > >> We have try to reproduce your issue using OWL API but we never succeed to have this kind of axiom. > > My correspondence with the OWL API developers included example code for how this problem arose in BioPortal. If anyone is interested in the particulars, the conversation is still available in their public list archive: > > https://sourceforge.net/p/owlapi/mailman/owlapi-developer/?viewmonth=201707 > > Kind regards, > Jennifer > > Please feel free to contact our developper Samuel Demarest (in cc) who's in charge of the generating code if you have any other question. I'll be back in september. > > Best regards, > > www.orpha.net [1] | Twitter @Orphanet [2] > MARC HANAUER > Directeur Adjoint / Deputy Director > Directeur technique / Chief technology officer > Strat?gie et Innovation > marc.hanauer at inserm.fr > > ORPHANET - INSERM US14 > Plateforme Maladies Rares / Rare Disease Platform > 96 rue Didot > 75014 PARIS > FRANCE > Le 14/07/2017 ? 18:41, Jennifer Leigh Vendetti a ?crit : Hello Marc, > > I don't have a solution yet for parsing ORDO 2.4 in BioPortal, but I'll provide a summary below of what I've discovered so far. > > The system is having difficulty handling classes in your ontology that have annotations nested 3 levels deep. Here's a screenshot of your ontology in the Protege ontology editor with class "48,XXYY syndrome" highlighted: > > > > Note the second occurrence of hasDbXref in the screenshot where there's an annotation on an annotation on an annotation. > > I think I mentioned in a previous correspondence that we use the OWL API internally for parsing. When the OWL API loads this ontology, it inserts a blank node for these nested annotations with a blank node identifier in the form of "_:genid". Using the example in the screen shot above, this is a snippet of the ontology source, as loaded by the OWL API: > > > > > > > ICD-10:Q98.8 > Attributed > > > > Attributed > NTBT (narrower term maps to a broader term) > > > Although we can load the ontology without errors, the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store: > > _Illegal rdf:nodeID value '_:genid25' rapper: Failed to parse file_ > > I went looking for a specification for what is considered valid syntax for blank node identifiers, but so far I haven't been able to find anything. It's unclear to me if the OWL API is generating invalid RDF, or if the Raptor RDF parser isn't handling blank nodes that it should be. I will likely need to correspond with the developers of one or both projects. > > Apologies that it hasn't been straightforward so far to track this down. > > On another note, I'm wondering if you could give me some basic information about how your OWL file is generated. Is it done programmatically? Or, do you use an ontology editing environment to maintain the ontology? > > Kind regards, > Jennifer > > On Jul 10, 2017, at 6:26 PM, Jennifer Leigh Vendetti wrote: > > Hello Marc, > > I've entered an issue in our tracker [1], and will have a look. > > Kind regards, > Jennifer > > [1] https://github.com/ncbo/bioportal-project/issues/31 > > On Jul 10, 2017, at 2:11 PM, marc.hanauer at inserm.fr wrote: > > Hello Jennifer, > > Sorry about that, but once again the new version of ORDO (2.4) seems to have issues : 2.3 (Uploaded, Error Rdf) 07/05/2017 07/05/2017 > https://bioportal.bioontology.org/ontologies/ORDO > > This version was produced the same way than the previous one. > > Any ideas ? > > Best regards, > > --- > > Marc HANAUER > Directeur Adjoint / Deputy Director > Directeur technique / Chief technology officer > Strat?gie et Innovation > marc.hanauer at inserm.fr > > ORPHANET - INSERM US14 > Plateforme Maladies Rares / Rare Disease Platform > 96 rue Didot > 75014 PARIS > FRANCE > > Le 11-08-2016 19:22, Jennifer Leigh Vendetti a ?crit : Hello Marc, > > We've addressed the issue I mentioned below. Version 2.2 of ORDO is parsed and available in BioPortal: > > http://bioportal.bioontology.org/ontologies/ORDO > > Apologies again that this one took us some time to address. > > Best, > Jennifer > > On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti wrote: > > Hi Marc, > > I am writing with a status report regarding BioPortal's failure to handle ORDO 2.2. > > As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing. I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly. The parsing succeeds, which indicates to me that your ontology file is valid. When the OWL API parses your ontology file, it emits a very large number of "unparsed triple" messages (roughly 15.5K of them), e.g.: > > [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty [3] -> http://purl.obolibrary.org/obo/ECO_0000218 [4] > [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource [5] -> _:genid120261 > > The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal's source code. I am currently working toward fixing the issue, and hope to have something available soon. > > Apologies that this one is taking some time for us to track down / fix. > > Best, > Jennifer > > [1] http://owlcs.github.io/owlapi/ > > On Jun 27, 2016, at 3:18 AM, Marc Hanauer wrote: > > Hello Jennifer, > > I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error. > > The version in our own server is now "2.2" but it appears with this line on bioportal: > > 2.1 (Uploaded, Error Rdf) > 06/22/2016 > 06/22/2016 > OWL [6] | Diff [7] > > Any idea ? > > Best regards, > > Marc HANAUER > Directeur Adjoint / Deputy Director > Directeur technique / Chief technology officer > Strat?gie et Innovation > marc.hanauer at inserm.fr > > ORPHANET - INSERM US14 > Plateforme Maladies Rares / Rare Disease Platform > 96 rue Didot > 75014 PARIS > FRANCE > Le 25/02/2016 ? 00:41, Jennifer Leigh Vendetti a ?crit : > Hello Marc, > > On Feb 24, 2016, at 6:45 AM, Marc Hanauer wrote: > > Dear support, > We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago). > Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl [8] ) and then the bioportal website automatically upload it. > > It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1) > > Do we need to perform any manual action in order to update it on bioportal ? > > You don't need to do anything manual. We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies. The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight. > > By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this) > > Sorry you're having difficulties. I tried reproducing this behavior here and so far haven't had any luck. I've viewed your ontology in BioPortal, both when logged in and logged out (screen shot below). I also verified that your user account of "ORDO_Orphanet" is valid, and I don't see any issues there. Are you still seeing this behavior? > > Jennifer > > _______________________________________________ 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 Links: ------ [1] https://www.orpha.net/ [2] https://twitter.com/Orphanet [3] http://www.w3.org/2002/07/owl#annotatedProperty [4] http://purl.obolibrary.org/obo/ECO_0000218 [5] http://www.w3.org/2002/07/owl#annotatedSource [6] http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb [7] http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb [8] http://www.orphadata.org/data/ORDO/ordo_orphanet.owl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Aug 28 09:09:45 2017 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 28 Aug 2017 16:09:45 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Marisa Hughes In-Reply-To: <59a07e83863e_7dd93f8bde0f71f8558c1@ncbo-prd-app-09.stanford.edu.mail> References: <59a07e83863e_7dd93f8bde0f71f8558c1@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <510C6EE1-34B8-48A5-AB93-66BF6169133B@stanford.edu> Hi Marisa, I'll contact you off-line to discuss this further. john On Aug 25, 2017, at 12:46 PM, support at bioontology.org wrote: Name: Marisa Hughes Email: MHughes at apa.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAPAONTO%3Fp%3Dclasses%26conceptid%3Droot Feedback: Hi -- I'm the taxonomist at the American Psychological Association, and I'm interested in receiving further data and metrics on the site visits to our ontology (APAONTO) on your site. Thank you - Marisa R. Hughes MHughes at apa.org _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nlorimer at stanford.edu Mon Aug 28 14:55:49 2017 From: nlorimer at stanford.edu (Nancy Lorimer) Date: Mon, 28 Aug 2017 14:55:49 -0700 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> Hi Jennifer, I went on hiatus with this again, and tried once more to load and got nowhere. Obviously, I'm doing something wrong. My ontology is in Protege and it is in GitHub. Perhaps if you could direct me to what URL I am supposed to use? I feel like I've tried them all, but clearly haven't hit the right one or am trying to load it the wrong way. thanks Nancy On 6/16/2017 1:27 PM, Jennifer Leigh Vendetti wrote: > Hi Nancy, > > >> On Jun 16, 2017, at 1:05 PM, support at bioontology.org >> wrote: >> >> Name: nlorimer >> >> Email: nlorimer at stanford.edu >> >> Location: http%3A%2F%2Fbioportal.bioontology.org >> %2Fontologies%2FPMO >> >> >> *Feedback:* >> >> Hi, I tried way to early on to load the Performed Music Ontology >> (part of the LD4P project in the libraries). It never did load properly. >> > > I looked at the PMO ontology in BioPortal. The ontology never loaded > because the URL specified in the ?Load from URL? section resolves to a > 404 error. If you?d like BioPortal to load your ontology from a URL, > the URL must point to the exact location of the file (with the file > name included). I noticed that PMO has a viewing restriction of > private. You?re welcome to send us the correct URL via private email > (vendetti at stanford.edu ). We could enter it on > your behalf and reprocess the ontology. Alternatively, you could > navigate to your ontology summary page and click the ?Edit submission > information? link to show the form that would allow you to enter a > valid file location. > >> I'd like to get rid of it and start again in the Biblio slice. Could >> you just delte this for me? >> > > We can add ontologies to a slice retroactively after they?ve been > created in BioPortal. Would you like us to assist you in resolving the > loading issue and add PMO to the Biblio slice? I think we can repair > the current entry without needing to do a deletion. > > Kind regards, > Jennifer > -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Aug 28 18:35:41 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 01:35:41 +0000 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> Message-ID: Hi Nancy, The latest version of the PMO ontology shows as successfully parsed in BioPortal. I looked at the submission information though, and the last submission appears to have been a file upload. If you want to have it pulled from GitHub, could you send the URL of the ontology in GitHub? You can send it to me privately if that?s sensitive information (vendetti at stanford.edu). Also, did you still want to have this ontology in the Biblio slice as you mentioned previously below? Kind regards, Jennifer On Aug 28, 2017, at 2:55 PM, Nancy Lorimer > wrote: Hi Jennifer, I went on hiatus with this again, and tried once more to load and got nowhere. Obviously, I'm doing something wrong. My ontology is in Protege and it is in GitHub. Perhaps if you could direct me to what URL I am supposed to use? I feel like I've tried them all, but clearly haven't hit the right one or am trying to load it the wrong way. thanks Nancy On 6/16/2017 1:27 PM, Jennifer Leigh Vendetti wrote: Hi Nancy, On Jun 16, 2017, at 1:05 PM, support at bioontology.org wrote: Name: nlorimer Email: nlorimer at stanford.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FPMO Feedback: Hi, I tried way to early on to load the Performed Music Ontology (part of the LD4P project in the libraries). It never did load properly. I looked at the PMO ontology in BioPortal. The ontology never loaded because the URL specified in the ?Load from URL? section resolves to a 404 error. If you?d like BioPortal to load your ontology from a URL, the URL must point to the exact location of the file (with the file name included). I noticed that PMO has a viewing restriction of private. You?re welcome to send us the correct URL via private email (vendetti at stanford.edu). We could enter it on your behalf and reprocess the ontology. Alternatively, you could navigate to your ontology summary page and click the ?Edit submission information? link to show the form that would allow you to enter a valid file location. I'd like to get rid of it and start again in the Biblio slice. Could you just delte this for me? We can add ontologies to a slice retroactively after they?ve been created in BioPortal. Would you like us to assist you in resolving the loading issue and add PMO to the Biblio slice? I think we can repair the current entry without needing to do a deletion. Kind regards, Jennifer -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nlorimer at stanford.edu Mon Aug 28 21:40:14 2017 From: nlorimer at stanford.edu (Nancy Lorimer) Date: Mon, 28 Aug 2017 21:40:14 -0700 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> Message-ID: <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> Huh, it just took a really long time, and I seem to have pulled in the BF base as well, which I didn't quite want. Comes from using the Protege file, I guess. I do manage to find something wrong to do! On Github, it is at https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. Would I use that URL? thanks and sorry for being so dumb about this Nancy On 8/28/2017 6:35 PM, Jennifer Leigh Vendetti wrote: > Hi Nancy, > > The latest version of the PMO ontology shows as successfully parsed in > BioPortal. I looked at the submission information though, and the last > submission appears to have been a file upload. If you want to have it > pulled from GitHub, could you send the URL of the ontology in GitHub? > You can send it to me privately if that?s sensitive information > (vendetti at stanford.edu ). > > Also, did you still want to have this ontology in the Biblio slice as > you mentioned previously below? > > Kind regards, > Jennifer > > >> On Aug 28, 2017, at 2:55 PM, Nancy Lorimer > > wrote: >> >> Hi Jennifer, >> >> I went on hiatus with this again, and tried once more to load and got >> nowhere. Obviously, I'm doing something wrong. My ontology is in >> Protege and it is in GitHub. Perhaps if you could direct me to what >> URL I am supposed to use? I feel like I've tried them all, but >> clearly haven't hit the right one or am trying to load it the wrong way. >> >> thanks >> Nancy >> >> On 6/16/2017 1:27 PM, Jennifer Leigh Vendetti wrote: >>> Hi Nancy, >>> >>> >>>> On Jun 16, 2017, at 1:05 PM, support at bioontology.org >>>> wrote: >>>> >>>> Name: nlorimer >>>> >>>> Email: nlorimer at stanford.edu >>>> >>>> Location: http%3A%2F%2Fbioportal.bioontology.org >>>> %2Fontologies%2FPMO >>>> >>>> >>>> *Feedback:* >>>> >>>> Hi, I tried way to early on to load the Performed Music Ontology >>>> (part of the LD4P project in the libraries). It never did load >>>> properly. >>>> >>> >>> I looked at the PMO ontology in BioPortal. The ontology never loaded >>> because the URL specified in the ?Load from URL? section resolves to >>> a 404 error. If you?d like BioPortal to load your ontology from a >>> URL, the URL must point to the exact location of the file (with the >>> file name included). I noticed that PMO has a viewing restriction of >>> private. You?re welcome to send us the correct URL via private email >>> (vendetti at stanford.edu ). We could enter it >>> on your behalf and reprocess the ontology. Alternatively, you could >>> navigate to your ontology summary page and click the ?Edit >>> submission information? link to show the form that would allow you >>> to enter a valid file location. >>> >>>> I'd like to get rid of it and start again in the Biblio slice. >>>> Could you just delte this for me? >>>> >>> >>> We can add ontologies to a slice retroactively after they?ve been >>> created in BioPortal. Would you like us to assist you in resolving >>> the loading issue and add PMO to the Biblio slice? I think we can >>> repair the current entry without needing to do a deletion. >>> >>> Kind regards, >>> Jennifer >>> >> >> >> -- >> Nancy Lorimer >> Head, Metadata Dept >> Stanford University Libraries >> nlorimer at stanford.edu >> 650-725-8819 > -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Aug 29 09:02:53 2017 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Aug 2017 09:02:53 -0700 Subject: [bioontology-support] [BioPortal] Feedback from michelle Message-ID: <59a5902da88d6_63343fbf3d0901c81968e@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From csongor.nyulas at stanford.edu Tue Aug 29 10:07:09 2017 From: csongor.nyulas at stanford.edu (Csongor Nyulas) Date: Tue, 29 Aug 2017 10:07:09 -0700 Subject: [bioontology-support] Fwd: [protege-announce] Early bird deadline approaching: Register today to the Protege Short Course at Stanford University, Oct 9 - 11, 2017! In-Reply-To: <6431a91e-62f6-4cf8-7498-abffd80341eb@stanford.edu> References: <6431a91e-62f6-4cf8-7498-abffd80341eb@stanford.edu> Message-ID: In case anyone is interested in participating at the Prot?g? Short Course please read below... Csongor -------- Forwarded Message -------- Dear all, Don't miss the chance to register at reduced rate to the next Prot?g? Short Course, to be held at Stanford University, California between Oct 9 - 11, 2017. *There are less than two weeks left until the "early bird" deadline!* Register here: https://protege.stanford.edu/shortcourse/201710/registration.html The Prot?g? Short Course offers a 3-day intensive training in use of the Prot?g? toolset, ontology development, and OWL. We cover best practices in ontology building and the latest Semantic Web technologies, including OWL 2, RDF, and SPARQL. We also cover topics such as real-world applications with ontologies, and data access and import from different data sources. The course is hands-on and is taught by the members of the Prot?g? team. Read more about it at: https://protege.stanford.edu/shortcourse/201710/ If you have any questions about the Prot?g? Short Course, please email: protege-shortcourse at lists.stanford.edu Please feel free to forward this announcement to anyone who might be interested in the course. Thank you! We look forward to seeing you in October! Best regards, The Prot?g? Team -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ protege-announce mailing list protege-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/protege-announce To unsubscribe, use this Web form: http://mailman.stanford.edu/mailman/listinfo/protege-announce From support at bioontology.org Tue Aug 29 09:32:41 2017 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Aug 2017 09:32:41 -0700 Subject: [bioontology-support] [BioPortal] Feedback from michelle Message-ID: <59a597291d3ec_658d3f8d91bf2c2497913@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From zkrodel at iupui.edu Tue Aug 29 09:53:22 2017 From: zkrodel at iupui.edu (Krodel, Zachary) Date: Tue, 29 Aug 2017 16:53:22 +0000 Subject: [bioontology-support] NCBO Virtual Appliance Download Request Message-ID: <15d7b7fd7eaf413f882df2e99cdaa1a1@bl-cci-exch0g.ads.iu.edu> Hello, My name is Zachary Krodel. I am a tech support staff member at Indiana University-Purdue University Indianapolis. We have received a request from a faculty member and graduate student in our Informatics program to install the NCBO Virtual Appliance via Virtual Box on their computers. They require a local installation. As such, if possible, I would like to initiate a download request for the OVF file. I made a BioPortal account under "zkrodel" if that is needed. Thank you, Zachary Krodel Desktop Support Technician Indiana University-Purdue University Indianapolis School of Informatics and Computing Informatics & Communications Technology Complex (IT) 472 535 W. Michigan Street Indianapolis, IN 46202 zkrodel at iupui.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 2135 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 5697 bytes Desc: not available URL: From vendetti at stanford.edu Tue Aug 29 10:25:54 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 17:25:54 +0000 Subject: [bioontology-support] [BioPortal] Feedback from michelle In-Reply-To: <59a5902da88d6_63343fbf3d0901c81968e@ncbo-prd-app-09.stanford.edu.mail> References: <59a5902da88d6_63343fbf3d0901c81968e@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Michelle, The W-A ontology has been deleted. Kind regards, Jennifer On Aug 29, 2017, at 9:02 AM, support at bioontology.org wrote: Name: michelle Email: futo at stanford.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCTERMS%2Fsubmissions%2F1%2Fedit Feedback: please delete W-A ontology submission (I thought the OA ontology wasn't working properly so W-A was an attempt to load it differently but now OA seems fine.) Thanks! _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Aug 29 10:42:12 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 17:42:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> Message-ID: <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> Hi Nancy, On Aug 28, 2017, at 9:40 PM, Nancy Lorimer > wrote: Huh, it just took a really long time, and I seem to have pulled in the BF base as well, which I didn't quite want. Comes from using the Protege file, I guess. BIBFRAME is pulled in due to the import statement on line 22 of your ontology source file. Here?s a link to the exact line in the version in GitHub: https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl#L22 On Github, it is at https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. Would I use that URL? There is one additional step you need to take to get the correct URL. On the page that you reference above, click the ?Raw? button to navigate to the raw ontology source file. The resulting URL in the browser window is the one you use, i.e.: https://raw.githubusercontent.com/LD4P/PerformedMusicOntology/master/PerformedMusicOntology.owl Notice that the URL begins with ?raw.githubusercontent.com?. I created a new submission on your behalf and entered this URL as the pull location. The new submission is fully parsed and available to view in BioPortal. Your pull URL will be checked nightly for new versions. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From nlorimer at stanford.edu Tue Aug 29 10:55:07 2017 From: nlorimer at stanford.edu (Nancy Lorimer) Date: Tue, 29 Aug 2017 10:55:07 -0700 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> Message-ID: Thanks very much! So to get rid of the Bibframe, I would need to remove that connection in Protege... Nancy On 8/29/2017 10:42 AM, Jennifer Leigh Vendetti wrote: > Hi Nancy, > > >> On Aug 28, 2017, at 9:40 PM, Nancy Lorimer > > wrote: >> >> Huh, it just took a really long time, and I seem to have pulled in >> the BF base as well, which I didn't quite want. Comes from using the >> Protege file, I guess. > > > BIBFRAME is pulled in due to the import statement on line 22 of your > ontology source file. Here?s a link to the exact line in the version > in GitHub: > > https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl#L22 > > > >> >> On Github, it is at >> https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. >> Would I use that URL? > > > There is one additional step you need to take to get the correct URL. > On the page that you reference above, click the ?Raw? button to > navigate to the raw ontology source file. The resulting URL in the > browser window is the one you use, i.e.: > > https://raw.githubusercontent.com/LD4P/PerformedMusicOntology/master/PerformedMusicOntology.owl > > Notice that the URL begins with ?raw.githubusercontent.com > ?. > > I created a new submission on your behalf and entered this URL as the > pull location. The new submission is fully parsed and available to > view in BioPortal. Your pull URL will be checked nightly for new versions. > > Kind regards, > Jennifer > > -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Aug 29 11:20:32 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 18:20:32 +0000 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> Message-ID: Yes - on the Active Ontology tab in Protege you can see the list of imports that your ontology uses. You can also add and remove the imports from this tab. Once doing so, you?d need to upload your new version to GitHub so that BioPortal can access as part of the nightly pull. Kind regards, Jennifer [cid:E2308338-FC9C-4D4F-9635-D0F1F174B9C9 at stanford.edu] On Aug 29, 2017, at 10:55 AM, Nancy Lorimer > wrote: Thanks very much! So to get rid of the Bibframe, I would need to remove that connection in Protege... Nancy On 8/29/2017 10:42 AM, Jennifer Leigh Vendetti wrote: Hi Nancy, On Aug 28, 2017, at 9:40 PM, Nancy Lorimer > wrote: Huh, it just took a really long time, and I seem to have pulled in the BF base as well, which I didn't quite want. Comes from using the Protege file, I guess. BIBFRAME is pulled in due to the import statement on line 22 of your ontology source file. Here?s a link to the exact line in the version in GitHub: https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl#L22 On Github, it is at https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. Would I use that URL? There is one additional step you need to take to get the correct URL. On the page that you reference above, click the ?Raw? button to navigate to the raw ontology source file. The resulting URL in the browser window is the one you use, i.e.: https://raw.githubusercontent.com/LD4P/PerformedMusicOntology/master/PerformedMusicOntology.owl Notice that the URL begins with ?raw.githubusercontent.com?. I created a new submission on your behalf and entered this URL as the pull location. The new submission is fully parsed and available to view in BioPortal. Your pull URL will be checked nightly for new versions. Kind regards, Jennifer -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2017-08-29 11.18.39.png Type: image/png Size: 98778 bytes Desc: Screenshot 2017-08-29 11.18.39.png URL: From support at bioontology.org Tue Aug 29 14:44:58 2017 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Aug 2017 14:44:58 -0700 Subject: [bioontology-support] [BioPortal] Feedback from michelle Message-ID: <59a5e05ac6f7c_58f43fc05cee475415750@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Sina.Madani at vumc.org Tue Aug 29 12:26:41 2017 From: Sina.Madani at vumc.org (Madani, Sina) Date: Tue, 29 Aug 2017 19:26:41 +0000 Subject: [bioontology-support] search by id in a subtree Message-ID: Hi, Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children? Thanks! Sina -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Aug 29 16:12:40 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 23:12:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from michelle In-Reply-To: <59a597291d3ec_658d3f8d91bf2c2497913@ncbo-prd-app-08.stanford.edu.mail> References: <59a597291d3ec_658d3f8d91bf2c2497913@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Michelle, I entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/40 You can view the issue for more detailed comments and/or to follow our progress. Kind regards, Jennifer On Aug 29, 2017, at 9:32 AM, support at bioontology.org wrote: Name: michelle Email: futo at stanford.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCTERMS Feedback: when I try to view Classes in this ontology https://bioportal.bioontology.org/ontologies/DCTERMS/ I get "problem retrieving classes" but Metrics say there are 25 classes Properties tab works ok _______________________________________________ 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 nlorimer at stanford.edu Tue Aug 29 16:15:45 2017 From: nlorimer at stanford.edu (Nancy Lorimer) Date: Tue, 29 Aug 2017 16:15:45 -0700 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> Message-ID: Thanks. Two final things. 1. I removed it from being "Private" to be "Public". I take it that could take some time to take effect? I can't see it in CEDAR yet. 2. Could you move this into the BiblioPortal slice for me? thanks again for all your patient help. Nancy On 8/29/2017 11:20 AM, Jennifer Leigh Vendetti wrote: > Yes - on the Active Ontology tab in Protege you can see the list of > imports that your ontology uses. You can also add and remove the > imports from this tab. Once doing so, you?d need to upload your new > version to GitHub so that BioPortal can access as part of the nightly > pull. > > Kind regards, > Jennifer > > > > > > >> On Aug 29, 2017, at 10:55 AM, Nancy Lorimer > > wrote: >> >> Thanks very much! So to get rid of the Bibframe, I would need to >> remove that connection in Protege... >> >> Nancy >> >> On 8/29/2017 10:42 AM, Jennifer Leigh Vendetti wrote: >>> Hi Nancy, >>> >>> >>>> On Aug 28, 2017, at 9:40 PM, Nancy Lorimer >>> > wrote: >>>> >>>> Huh, it just took a really long time, and I seem to have pulled in >>>> the BF base as well, which I didn't quite want. Comes from using >>>> the Protege file, I guess. >>> >>> >>> BIBFRAME is pulled in due to the import statement on line 22 of your >>> ontology source file. Here?s a link to the exact line in the version >>> in GitHub: >>> >>> https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl#L22 >>> >>> >>> >>>> >>>> On Github, it is at >>>> https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. >>>> Would I use that URL? >>> >>> >>> There is one additional step you need to take to get the correct >>> URL. On the page that you reference above, click the ?Raw? button to >>> navigate to the raw ontology source file. The resulting URL in the >>> browser window is the one you use, i.e.: >>> >>> https://raw.githubusercontent.com/LD4P/PerformedMusicOntology/master/PerformedMusicOntology.owl >>> >>> Notice that the URL begins with ?raw.githubusercontent.com >>> ?. >>> >>> I created a new submission on your behalf and entered this URL as >>> the pull location. The new submission is fully parsed and available >>> to view in BioPortal. Your pull URL will be checked nightly for new >>> versions. >>> >>> Kind regards, >>> Jennifer >>> >>> >> >> >> -- >> Nancy Lorimer >> Head, Metadata Dept >> Stanford University Libraries >> nlorimer at stanford.edu >> 650-725-8819 > -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 98778 bytes Desc: not available URL: From vendetti at stanford.edu Tue Aug 29 16:39:12 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 23:39:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from michelle In-Reply-To: <59a5e05ac6f7c_58f43fc05cee475415750@ncbo-prd-app-08.stanford.edu.mail> References: <59a5e05ac6f7c_58f43fc05cee475415750@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <0F7EDF0F-477A-42EB-9357-DE31B27D98FF@stanford.edu> Hi Michelle, On Aug 29, 2017, at 2:44 PM, support at bioontology.org wrote: Name: michelle Email: futo at stanford.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFAST-EVENT%3Fp%3Dclasses Feedback: I submitted this ontology today https://bioportal.bioontology.org/ontologies/FAST-EVENT/ and I left the default as OWL. Maybe it should have been SKOS. My question is: does that setting (OWL vs SKOS vs OBO etc) change anything about how BioPortal handles the ontology? Wanted to ask this before going to the trouble of submitting it again with SKOS option, and comparing the two. The formats that BioPortal accepts are OWL, OBO, SKOS, and UMLS. The FAST-EVENT ontology is RDF. The BioPortal user interface doesn?t offer you the option to select RDF as a format since it?s not one of the ones we officially support. I would say it?s not necessary to change the format since the list of available ones doesn?t contain the value that truly reflects the format of the ontology. All ontologies that are submitted via the UI or the REST endpoint are parsed internally using the same software, regardless of the format specified. The reason that a number of RDF ontologies submitted to BioPortal do end up parsing successfully has to do with how parsing is handled internally. We use 3rd party software to handle the parsing of ontologies called the OWL API [1]. When the OWL API consumes an ontology, it has a number of different parsers it attempts to use to parse the ontology sources. This group of parsers has expanded over the years to include ones that handle RDF. In some cases, RDF ontologies submitted to us will parse, and in other cases, there are difficulties (as you reported with the DCTERMS ontology showing no classes). The class tree for this ontology appears the same in BioPortal as in the Protege ontology editor, so it appeared to me that this is one case of an RDF ontology that our system handled properly. Unless there was something out of the ordinary you noticed? Kind regards, Jennier [1] https://github.com/owlcs/owlapi/wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Aug 29 16:49:11 2017 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Aug 2017 23:49:11 +0000 Subject: [bioontology-support] [BioPortal] Feedback from michelle In-Reply-To: References: <59a597291d3ec_658d3f8d91bf2c2497913@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Michelle, On Aug 29, 2017, at 4:26 PM, Michelle Futornick > wrote: Thanks Jennifer. Re "It's worth noting that this submission is an RDF file, which is not one of the formats we officially support." Is there a list somewhere of what models BioPortal supports for submission and in what serializations/formats? We accept OWL, OBO, and SKOS ontologies via our UI or our REST endpoint. Roughly twice per year, we also execute a separate process to import a set of UMLS ontologies from the National Library of Medicine. Internally we use the OWL API for loading / parsing ontologies. The OWL API supports a variety of serializations - the complete list is available on their introductory documentation page: https://github.com/owlcs/owlapi/wiki It seems like BioPortal does accept OWL ontologies expressed in RDF/XML. Yes, definitely. This is probably the most commonly used format for OWL submissions. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Aug 31 11:59:40 2017 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 31 Aug 2017 18:59:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from nlorimer In-Reply-To: References: <59443a013583f_55e63f8e349e86c43262@ncbo-prd-app-09.stanford.edu.mail> <76cbea46-20d9-3f50-01c5-29707db1f6b3@stanford.edu> <6332b191-7b22-9d6e-4a06-7c623bb32034@stanford.edu> <343A3C2C-96FC-4225-AFCB-9AF0F4FD6531@stanford.edu> Message-ID: <9EA8FB7C-D66B-4C3D-A511-8EE44AA39808@stanford.edu> Hi Nancy, Jennifer is out for the rest of the week. I?ve added PMO to the BIBLIO slice. The ?Public? status of the ontology has taken effect. Let me know if you have additional questions. Thanks! Michael On Aug 29, 2017, at 4:15 PM, Nancy Lorimer > wrote: Thanks. Two final things. 1. I removed it from being "Private" to be "Public". I take it that could take some time to take effect? I can't see it in CEDAR yet. 2. Could you move this into the BiblioPortal slice for me? thanks again for all your patient help. Nancy On 8/29/2017 11:20 AM, Jennifer Leigh Vendetti wrote: Yes - on the Active Ontology tab in Protege you can see the list of imports that your ontology uses. You can also add and remove the imports from this tab. Once doing so, you?d need to upload your new version to GitHub so that BioPortal can access as part of the nightly pull. Kind regards, Jennifer On Aug 29, 2017, at 10:55 AM, Nancy Lorimer > wrote: Thanks very much! So to get rid of the Bibframe, I would need to remove that connection in Protege... Nancy On 8/29/2017 10:42 AM, Jennifer Leigh Vendetti wrote: Hi Nancy, On Aug 28, 2017, at 9:40 PM, Nancy Lorimer > wrote: Huh, it just took a really long time, and I seem to have pulled in the BF base as well, which I didn't quite want. Comes from using the Protege file, I guess. BIBFRAME is pulled in due to the import statement on line 22 of your ontology source file. Here?s a link to the exact line in the version in GitHub: https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl#L22 On Github, it is at https://github.com/LD4P/PerformedMusicOntology/blob/master/PerformedMusicOntology.owl. Would I use that URL? There is one additional step you need to take to get the correct URL. On the page that you reference above, click the ?Raw? button to navigate to the raw ontology source file. The resulting URL in the browser window is the one you use, i.e.: https://raw.githubusercontent.com/LD4P/PerformedMusicOntology/master/PerformedMusicOntology.owl Notice that the URL begins with ?raw.githubusercontent.com?. I created a new submission on your behalf and entered this URL as the pull location. The new submission is fully parsed and available to view in BioPortal. Your pull URL will be checked nightly for new versions. Kind regards, Jennifer -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 -- Nancy Lorimer Head, Metadata Dept Stanford University Libraries nlorimer at stanford.edu 650-725-8819 _______________________________________________ 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 Aug 31 14:38:30 2017 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 31 Aug 2017 21:38:30 +0000 Subject: [bioontology-support] search by id in a subtree In-Reply-To: References: Message-ID: <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu> Hi Sina, I am not sure which one of the two interpretations you are asking about: 1. Determine whether a term with a given id is located within a specific subtree. If that?s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002 in a subtree of the term ?Asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001 OR 2. Get ALL the descendants (direct/indirect) of a given term (?Asthma?). In this case, the call would be: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree Let me know if this helps. Thank you for keeping in touch with us! Michael On Aug 29, 2017, at 12:26 PM, Madani, Sina > wrote: Hi, Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children? Thanks! Sina _______________________________________________ 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 Aug 31 14:42:20 2017 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 31 Aug 2017 21:42:20 +0000 Subject: [bioontology-support] search by id in a subtree In-Reply-To: <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu> References: <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu> Message-ID: <4A1D84A2-3CE5-417C-8641-388DBFA54D58@stanford.edu> One clarification on the answer number 2. The tree endpoint will give you an expanded tree for the term ?Asthma?. If you are simply looking for the descendants, the call below would be more apt: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/descendants Thanks! Michael On Aug 31, 2017, at 2:38 PM, Michael Dorf > wrote: Hi Sina, I am not sure which one of the two interpretations you are asking about: 1. Determine whether a term with a given id is located within a specific subtree. If that?s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002 in a subtree of the term ?Asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001 OR 2. Get ALL the descendants (direct/indirect) of a given term (?Asthma?). In this case, the call would be: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree Let me know if this helps. Thank you for keeping in touch with us! Michael On Aug 29, 2017, at 12:26 PM, Madani, Sina > wrote: Hi, Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children? Thanks! Sina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From 1431288072 at qq.com Thu Aug 31 04:58:16 2017 From: 1431288072 at qq.com (=?gb18030?B?18++ow==?=) Date: Thu, 31 Aug 2017 19:58:16 +0800 Subject: [bioontology-support] question on ontology Message-ID: I have a question about the LOINC ontology document. Why it has so much individuals,that is ,why not using classes only like other ontologies such as HPO. And if I want to build a chinese loinc based the translation, what should I do? what format should I use? Looking forward any suggestions.Thanks so much. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nbpumphr at iupui.edu Wed Aug 30 09:51:18 2017 From: nbpumphr at iupui.edu (Pumphrey, Noah Bailey) Date: Wed, 30 Aug 2017 16:51:18 +0000 Subject: [bioontology-support] VMWare Virtual Appliance Request Message-ID: <1504111877984.49802@iupui.edu> Hello! I'm with the technology staff for Indiana University and we have a research team looking to use your product. They provided us this wiki leak and I've asked them to provide the information required. Username: vidhurds Organization goals: To build and sustain strategic research clusters of excellence that leverage existing university strengths, match well with future directions of the university, offer good career opportunities for university graduates that are of strategic importance to Indiana and the nation Reason: retrieve and process information from ncbo annotator faster. If you need any other information, please let me know. Thank you, Noah Pumphrey Desktop Support Technician for the School of Informatics and Computing Indiana University Purdue University Indianapolis 535 W. Michigan Street IT472 Indianapolis, IN 46202 nbpumphr at iupui.edu -------------- next part -------------- An HTML attachment was scrubbed... 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