From mah79 at cam.ac.uk Wed Jan 3 04:22:53 2018 From: mah79 at cam.ac.uk (Dr Midori A. Harris) Date: Wed, 3 Jan 2018 12:22:53 +0000 (GMT) Subject: [bioontology-support] FYPO metadata - download link update Message-ID: Hello, I noticed (embarrassingly recently) that we need to update the link for BioPortal to retrieve the Fission Yeast Phenotype Ontology (FYPO). It should be downloaded from either the OBO Foundry PURL (http://purl.obolibrary.org/obo/fypo.owl) or the PomBase GitHub respository (https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl). There's also a typo in the PomBase URL in the Description field - it should be www.pombase.org. How can I make these corrections/updates? Many thanks, Midori Midori A. Harris, PhD Database Curator, PomBase Department of Biochemistry University of Cambridge Cambridge, UK mah79 at cam.ac.uk From thiamang at deloitte.com Tue Jan 2 11:38:05 2018 From: thiamang at deloitte.com (Hiamang, Tokunbo (US - New York)) Date: Tue, 2 Jan 2018 19:38:05 +0000 Subject: [bioontology-support] Local Copy of Medra & RXNorm For Semantic Project Message-ID: Hello BioPortal Team - Hope all is well. We are trying to build an internal semantic application to do graph based inferencing. I have an API Key to access the NCBO API REST services, but I need a local copy of these files (MEDRA & RXNORM) for our application to work optimally. Without a local copy, we will have to make hundreds or more API calls. Would it be possible to please let me know what it would take to get a local copy of these files? If needed, I can set up a quick call between you and me to discuss. Thank you, Tokunbo M. Hiamang Senior Consultant | Analytics + Information Management Deloitte Consulting LLP 30 ROCKEFELLER PLAZA NEW YORK, NY 10112-0015 United States Tel: +1 212-436-2948 Mobile: +1 732-272-2363 thiamang at deloitte.com | www.deloitte.com Please consider the environment before printing. This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and any disclosure, copying, or distribution of this message, or the taking of any action based on it, by you is strictly prohibited. v.E.1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Adam.Hansen at bcm.edu Tue Jan 2 11:22:02 2018 From: Adam.Hansen at bcm.edu (Hansen, Adam Wesley) Date: Tue, 2 Jan 2018 19:22:02 +0000 Subject: [bioontology-support] Request for VMWare Virtual Appliance Message-ID: <1C1E3F1A-D71E-4168-AF89-243BFCD925CC@contoso.com> Hello, I am interested in having a local copy of the NCBO virtual appliance. As part of our sample intake pipeline, we would like to ?map? phenotypic strings to HPO terms. We process thousands of samples and feel that a local installation would be more convenient than relying on and constantly hitting the web API. My BioPortal username is: awhansen Please let me know if you have any questions. Happy new year, Adam W. Hansen Laboratory of Dr. Richard Gibbs Human Genome Sequencing Center Department of Molecular and Human Genetics Adam.Hansen at bcm.edu 713-798-5372 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 3 10:45:24 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 3 Jan 2018 18:45:24 +0000 Subject: [bioontology-support] FYPO metadata - download link update In-Reply-To: References: Message-ID: Hello Midori, I appreciate your contacting us. I will give a general answer for the email list, and will also contact you directly about managing this ontology. Generally, if you are a BioPortal administrator of the ontology, you can edit the ontology information (including its Name, Administrators, Viewing Restriction, Categories, and whether the ontology is a view of another ontology), at http://bioportal.bioontology.org/ontologies/NAME/edit where NAME is replaced by the acronym (e.g., FYPO) of the ontology. You can also edit the specific submission information by clicking on the "Edit submission information" link at the ontology summary page. This will let you update (for the current submission) Description, Format, Version, Status, Release Date, Contact Name and Email, Home Page, Documentation Page, and Publications Page. The submission metadata also lets you update the Location from which the ontology is obtained, and any Load from URL location will be checked each night for an updated version of the ontology, which will be uploaded automatically if it is found. I have made the changes you mention, and if I have done so successfully, we should see the new ontology has been ingested tomorrow. John On Jan 3, 2018, at 4:22 AM, Dr Midori A. Harris > wrote: Hello, I noticed (embarrassingly recently) that we need to update the link for BioPortal to retrieve the Fission Yeast Phenotype Ontology (FYPO). It should be downloaded from either the OBO Foundry PURL (http://purl.obolibrary.org/obo/fypo.owl) or the PomBase GitHub respository (https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl). There's also a typo in the PomBase URL in the Description field - it should be www.pombase.org. How can I make these corrections/updates? Many thanks, Midori Midori A. Harris, PhD Database Curator, PomBase Department of Biochemistry University of Cambridge Cambridge, UK mah79 at cam.ac.uk _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 3 11:12:09 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 3 Jan 2018 19:12:09 +0000 Subject: [bioontology-support] Local Copy of Medra & RXNorm For Semantic Project In-Reply-To: References: Message-ID: <482694DA-E0DC-4C56-8DE1-734FA1BF9C48@stanford.edu> Hello, Thank you for your interest. First, two important notes: (A) We have not yet imported the 2017 releases of the UMLS ontologies, We hope to do so in January. (B) Ontology license information is provided at the summary page for the ontology, and these license terms must be followed. (I note particularly the requirement that use of MEDDRA for commercial purposes requires a license fee, in case that applies.) That covered, the RXNORM ontology is available as a file download from the summary page, under the Submissions section (as RDF/TTL). We will contact you offline about MEDDRA availability once we are back in the office next Monday. In the meantime, you may wish to explore the MEDDRA site, and the UMLS registration process, if you have not done so already?there has been quite a bit of development in recent years, and there may even be a more straightforward access mechanism that we have not integrated into BioPortal. (If so, please let us know.) In any case, from past experience I expect UMLS registration would be a part of the licensing terms to be able to access and use MEDDRA. John On Jan 2, 2018, at 11:38 AM, Hiamang, Tokunbo (US - New York) > wrote: Hello BioPortal Team ? Hope all is well. We are trying to build an internal semantic application to do graph based inferencing. I have an API Key to access the NCBO API REST services, but I need a local copy of these files (MEDRA & RXNORM) for our application to work optimally. Without a local copy, we will have to make hundreds or more API calls. Would it be possible to please let me know what it would take to get a local copy of these files? If needed, I can set up a quick call between you and me to discuss. Thank you, Tokunbo M. Hiamang Senior Consultant | Analytics + Information Management Deloitte Consulting LLP 30 ROCKEFELLER PLAZA NEW YORK, NY 10112-0015 United States Tel: +1 212-436-2948 Mobile: +1 732-272-2363 thiamang at deloitte.com | www.deloitte.com Please consider the environment before printing. This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and any disclosure, copying, or distribution of this message, or the taking of any action based on it, by you is strictly prohibited. v.E.1 _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mah79 at cam.ac.uk Thu Jan 4 02:35:30 2018 From: mah79 at cam.ac.uk (Dr Midori A. Harris) Date: Thu, 4 Jan 2018 10:35:30 +0000 (GMT) Subject: [bioontology-support] FYPO metadata - download link update In-Reply-To: References: Message-ID: Hi John, Thanks very much for the useful info. I too will send additional responses off-list. Best regards, Midori On Wed, 3 Jan 2018, John Graybeal wrote: > Hello Midori, > > I appreciate your contacting us. I will give a general answer for the email list, and will also contact you directly about managing this ontology. > > Generally, if you are a BioPortal administrator of the ontology, you can edit the ontology information (including its Name, Administrators, Viewing Restriction, Categories, and whether the ontology is a view of another ontology), at > http://bioportal.bioontology.org/ontologies/NAME/edit > where NAME is replaced by the acronym (e.g., FYPO) of the ontology. > > You can also edit the specific submission information by clicking on the "Edit submission information" link at the ontology summary page. This will let you update (for the current submission) Description, Format, Version, Status, Release Date, Contact Name and Email, Home Page, Documentation Page, and Publications Page. The submission metadata also lets you update the Location from which the ontology is obtained, and any Load from URL location will be checked each night for an updated version of the ontology, which will be uploaded automatically if it is found. > > I have made the changes you mention, and if I have done so successfully, we should see the new ontology has been ingested tomorrow. > > John > > > On Jan 3, 2018, at 4:22 AM, Dr Midori A. Harris > wrote: > > Hello, > > I noticed (embarrassingly recently) that we need to update the link for BioPortal to retrieve the Fission Yeast Phenotype Ontology (FYPO). It should be downloaded from either the OBO Foundry PURL (http://purl.obolibrary.org/obo/fypo.owl) or the PomBase GitHub respository (https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl). > > There's also a typo in the PomBase URL in the Description field - it should be www.pombase.org. > > How can I make these corrections/updates? > > Many thanks, > Midori > > > Midori A. Harris, PhD > Database Curator, PomBase > Department of Biochemistry > University of Cambridge > Cambridge, UK > mah79 at cam.ac.uk > > _______________________________________________ > 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 > > > From support at bioontology.org Fri Jan 5 09:37:26 2018 From: support at bioontology.org (support at bioontology.org) Date: Fri, 05 Jan 2018 09:37:26 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Andrej Kastrin Message-ID: <5a4fb7d693472_62f43f8abadf71c099422@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sat Jan 6 11:22:25 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 6 Jan 2018 19:22:25 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Andrej Kastrin In-Reply-To: <5a4fb7d693472_62f43f8abadf71c099422@ncbo-prd-app-08.stanford.edu.mail> References: <5a4fb7d693472_62f43f8abadf71c099422@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <99D6BDD2-7F92-4135-8858-8D932E031BBD@stanford.edu> Hello Andrej, thank you for your email. I suspect the service has gone offline, and can be easily restarted once the team is back in the office sometime Monday. As you likely know, the SPARQL data is now quite old, as we have not had time to refresh this beta service. You may be interested to know (breaking news!), we are investigating the possibility of replacing this service with an Allegrograph-based solution from Franz, Inc. We hope to have more information on this investigation in the next month. And if anyone wants to contribute to expediting this replacement effort, please feel contact me!) John ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 On Jan 5, 2018, at 9:37 AM, support at bioontology.org wrote: Name: Andrej Kastrin Email: andrej.kastrin at gmail.com Location: http://sparql.bioontology.org/ Feedback: Dear Sir/Madam, I found your portal, especially SPARQL interface very useful for my current research. However, it seems that SPARQL service does not work anymore. I cannot access data even programmatically through an API. Could you please check what's wrong? With kind regards, Andrej Kastrin _______________________________________________ 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 jb.escudie at gmail.com Tue Jan 9 11:07:34 2018 From: jb.escudie at gmail.com (=?UTF-8?Q?Jean-Baptiste_Escudi=c3=a9?=) Date: Tue, 9 Jan 2018 20:07:34 +0100 Subject: [bioontology-support] NCBO virtual appliance access request Message-ID: <8b89cf7c-ccc1-4301-5108-ac0bfe121b94@gmail.com> Dear bioontology support team, I'd like to get access to the NCBO virtual appliance. My goal is to annotate large copora of clinical documents starting with the MIMIC III database, then clinical data warehouse of the public parisian hospitals which documents can be annotated with the REST API for confidentiality reasons. Best regards, Jean-Baptiste INFO: Bioportal account login is jb.escudie https://www.linkedin.com/in/jbescudie/ http://www.eq22.fr/people/jbescudie/ From jonquet at lirmm.fr Thu Jan 11 11:52:22 2018 From: jonquet at lirmm.fr (Clement Jonquet) Date: Thu, 11 Jan 2018 11:52:22 -0800 Subject: [bioontology-support] NCBO virtual appliance access request In-Reply-To: <8b89cf7c-ccc1-4301-5108-ac0bfe121b94@gmail.com> References: <8b89cf7c-ccc1-4301-5108-ac0bfe121b94@gmail.com> Message-ID: Hello Jean-Baptiste, For the data in English (MIMIC) indeed, you might have to use the NCBO Virtual Appliance or if the data is public directly the NCBO Annotator. For data in French, you might be aware of our SIFR BioPortal project which goal is to build a French Annotator: http://bioportal.lirmm.fr/annotator We have also now a Docker compose installation that allow to install locally the services. We actually deployed it already within HEGP?s server for the ANR PractikPharma project. (I shall detail this in another message) Cordialement Clement Jonquet > Le 9 janv. 2018 ? 11:07, Jean-Baptiste Escudi? a ?crit : > > Dear bioontology support team, > > I'd like to get access to the NCBO virtual appliance. My goal is to annotate large copora of clinical documents starting with the MIMIC III database, then clinical data warehouse of the public parisian hospitals which documents can be annotated with the REST API for confidentiality reasons. > > Best regards, > > Jean-Baptiste > > INFO: > > Bioportal account login is jb.escudie > > https://www.linkedin.com/in/jbescudie/ > > http://www.eq22.fr/people/jbescudie/ > > _______________________________________________ > 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 alexgarciac at gmail.com Tue Jan 16 01:45:51 2018 From: alexgarciac at gmail.com (Alexander Garcia Castro) Date: Tue, 16 Jan 2018 10:45:51 +0100 Subject: [bioontology-support] sparql Message-ID: Hi, the sparql endpoint is down, it is unresponsive since yesterday. any chance it is back online anytime soon? -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 16 10:58:15 2018 From: support at bioontology.org (support at bioontology.org) Date: Tue, 16 Jan 2018 10:58:15 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Matthew Diller Message-ID: <5a5e4b4721cc0_2ef43fa5a1b1953c4543c@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 16 12:38:08 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 16 Jan 2018 20:38:08 +0000 Subject: [bioontology-support] EDAM update - same problem again - please help In-Reply-To: <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> References: <9580125B-AFC1-48AA-9BF7-C9AC1F7837B9@stanford.edu> <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> Message-ID: <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> Hi Matus, It would be helpful if you could send your comments to the support list so that my colleagues are able to remain in the loop on correspondences regarding BioPortal issues. > On Jan 15, 2018, at 3:15 PM, Matus Kalas wrote: > > When I open http://bioportal.bioontology.org/ontologies/EDAM/?p=classes without being loggen in, in a private browser window, it works fine. > > When I'm logged in, http://bioportal.bioontology.org/ontologies/EDAM/?p=classes shows "We're sorry but something has gone wrong. We have been notified of this error.", and clicking "Classes" at http://bioportal.bioontology.org/ontologies/EDAM shows "Problem retrieving classes?. Are you still seeing a 500 error for EDAM classes page? I?m logged in and can?t reproduce this at the moment. > > Another instance of the same kind of problem: > > I uploaded a new version of http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING about an hour ago, and it still shows it as not parsed at the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING, whether I'm looged in, or not logged in a private browser window. I was able to reproduce this behavior here (I?ve cleared BioPortal?s caches, so your ontology is accessible now). BioPortal has 3 distinct caching layers in the stack. Based on the information provided in your last two messages, we think we?ve narrowed the problem to the client side in-memory cache. > > One more question, or rather two: > > Is the CSV version for download generated by some internal BioPortal machinery, or is it using some available libraries? The CSV is generated internally, using Ruby?s standard CSV library: https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/utils/ontology_csv_writer.rb > > Related to that, if the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING doesn't show the new version as parsed, and thus doesn't provide it CSV, is there another URL I could use to download the newly generated CSV? No, not that I?m aware of. > > This looks like quite a mess. Could you guys please somehow prioritize fixing these issues? It's causing us and our users some serious trouble. We take all problem reports seriously and care a great deal about providing end users with the best experience possible. Having said that, we?re a very small team supporting a relatively large user community. We?re doing the best we can with the resources we have and will continue to look into / address this issue as time permits. Kind regards, Jennifer From vendetti at stanford.edu Tue Jan 16 13:38:31 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 16 Jan 2018 21:38:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Matthew Diller In-Reply-To: <5a5e4b4721cc0_2ef43fa5a1b1953c4543c@ncbo-prd-app-08.stanford.edu.mail> References: <5a5e4b4721cc0_2ef43fa5a1b1953c4543c@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Matthew, Thanks for reporting that. We?ve removed the spam project entries. Kind regards, Jennifer On Jan 16, 2018, at 10:58 AM, support at bioontology.org wrote: Name: Matthew Diller Email: diller17 at ufl.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDRON Feedback: I noticed that for multiple ontologies there is a strange entry listed under "Projects" that definitely shouldn't be there. Two ontologies, in particular, that I noticed this in were Apollo-SV and CPT. The entry seems to provide a link to some sample WordPress page in German. _______________________________________________ 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 Jan 16 15:45:16 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 16 Jan 2018 23:45:16 +0000 Subject: [bioontology-support] sparql In-Reply-To: References: Message-ID: Apologies Alexander. It?s back online now. Kind regards, Jennifer On Jan 16, 2018, at 1:45 AM, Alexander Garcia Castro > wrote: Hi, the sparql endpoint is down, it is unresponsive since yesterday. any chance it is back online anytime soon? -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac _______________________________________________ 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 Matus.Kalas at uib.no Tue Jan 16 18:36:36 2018 From: Matus.Kalas at uib.no (Matus Kalas) Date: Wed, 17 Jan 2018 03:36:36 +0100 Subject: [bioontology-support] EDAM update - same problem again - please help In-Reply-To: <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> References: <9580125B-AFC1-48AA-9BF7-C9AC1F7837B9@stanford.edu> <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> Message-ID: Hi Jennifer and others, Thank you so much for looking into this, and narrowing down the problem! The current status with both EDAM and EDAM-BIOIMAGING is that when I'm logged out, everything is up to date, and when I'm logged in, the "Classes" browsing doesn't work, showing "We're sorry but something has gone wrong. We have been notified of this error." A million thanks again for all your detailed answers & all best luck with finding and solving the problem, Matus On 2018-01-16 21:38, Jennifer Leigh Vendetti wrote: > Hi Matus, > > It would be helpful if you could send your comments to the support > list so that my colleagues are able to remain in the loop on > correspondences regarding BioPortal issues. > > >> On Jan 15, 2018, at 3:15 PM, Matus Kalas wrote: >> >> When I open >> http://bioportal.bioontology.org/ontologies/EDAM/?p=classes without >> being loggen in, in a private browser window, it works fine. >> >> When I'm logged in, >> http://bioportal.bioontology.org/ontologies/EDAM/?p=classes shows >> "We're sorry but something has gone wrong. We have been notified of >> this error.", and clicking "Classes" at >> http://bioportal.bioontology.org/ontologies/EDAM shows "Problem >> retrieving classes?. > > > Are you still seeing a 500 error for EDAM classes page? I?m logged in > and can?t reproduce this at the moment. > > >> >> Another instance of the same kind of problem: >> >> I uploaded a new version of >> http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING about an >> hour ago, and it still shows it as not parsed at the summary page at >> http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING, whether >> I'm looged in, or not logged in a private browser window. > > > I was able to reproduce this behavior here (I?ve cleared BioPortal?s > caches, so your ontology is accessible now). BioPortal has 3 distinct > caching layers in the stack. Based on the information provided in your > last two messages, we think we?ve narrowed the problem to the client > side in-memory cache. > > >> >> One more question, or rather two: >> >> Is the CSV version for download generated by some internal BioPortal >> machinery, or is it using some available libraries? > > > The CSV is generated internally, using Ruby?s standard CSV library: > > https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/utils/ontology_csv_writer.rb > > >> >> Related to that, if the summary page at >> http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING doesn't >> show the new version as parsed, and thus doesn't provide it CSV, is >> there another URL I could use to download the newly generated CSV? > > > No, not that I?m aware of. > > >> >> This looks like quite a mess. Could you guys please somehow prioritize >> fixing these issues? It's causing us and our users some serious >> trouble. > > > We take all problem reports seriously and care a great deal about > providing end users with the best experience possible. Having said > that, we?re a very small team supporting a relatively large user > community. We?re doing the best we can with the resources we have and > will continue to look into / address this issue as time permits. > > Kind regards, > Jennifer From TIFFANY.CALLAHAN at UCDENVER.EDU Wed Jan 17 07:07:54 2018 From: TIFFANY.CALLAHAN at UCDENVER.EDU (Callahan, Tiffany) Date: Wed, 17 Jan 2018 15:07:54 +0000 Subject: [bioontology-support] Account Request Message-ID: <70670CF8-5C79-4EB5-B922-1555D92ECC22@ucdenver.edu> Hello- My name is Tiffany Callahan and I am a PhD Student in Computational Biology at the University of Colorado Denver. I recently requested an account in order to use the API. I have not received confirmation that my request was received or is being processed. Can you please confirm that I have provided the need information? If there is any further information needed to process this request, please don?t hesitate to let me know. Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 17 11:02:23 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 17 Jan 2018 19:02:23 +0000 Subject: [bioontology-support] EDAM update - same problem again - please help In-Reply-To: <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> References: <9580125B-AFC1-48AA-9BF7-C9AC1F7837B9@stanford.edu> <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> Message-ID: <1E087D7D-7886-4987-9694-645DE6879FE6@stanford.edu> Hi Matus, I am also replying in more detail separately, to understand the exact needs to address this request: This looks like quite a mess. Could you guys please somehow prioritize fixing these issues? It's causing us and our users some serious trouble. But I mainly wanted to note that I think there may be a way to download CSVs before the link is available. I haven't tested this, but I see the CSV link looks like this: http://data.bioontology.org/ontologies/EDAM-BIOIMAGING/download?apikey=&download_format=csv Unless I am mistaken, this will always download the most recent CSV which has been created. So as soon as we've created a CSV, even if your UI is not showing it is available yet, this call may work just fine. John On Jan 16, 2018, at 12:38 PM, Jennifer Leigh Vendetti > wrote: Hi Matus, It would be helpful if you could send your comments to the support list so that my colleagues are able to remain in the loop on correspondences regarding BioPortal issues. On Jan 15, 2018, at 3:15 PM, Matus Kalas > wrote: When I open http://bioportal.bioontology.org/ontologies/EDAM/?p=classes without being loggen in, in a private browser window, it works fine. When I'm logged in, http://bioportal.bioontology.org/ontologies/EDAM/?p=classes shows "We're sorry but something has gone wrong. We have been notified of this error.", and clicking "Classes" at http://bioportal.bioontology.org/ontologies/EDAM shows "Problem retrieving classes?. Are you still seeing a 500 error for EDAM classes page? I?m logged in and can?t reproduce this at the moment. Another instance of the same kind of problem: I uploaded a new version of http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING about an hour ago, and it still shows it as not parsed at the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING, whether I'm looged in, or not logged in a private browser window. I was able to reproduce this behavior here (I?ve cleared BioPortal?s caches, so your ontology is accessible now). BioPortal has 3 distinct caching layers in the stack. Based on the information provided in your last two messages, we think we?ve narrowed the problem to the client side in-memory cache. One more question, or rather two: Is the CSV version for download generated by some internal BioPortal machinery, or is it using some available libraries? The CSV is generated internally, using Ruby?s standard CSV library: https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/utils/ontology_csv_writer.rb Related to that, if the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING doesn't show the new version as parsed, and thus doesn't provide it CSV, is there another URL I could use to download the newly generated CSV? No, not that I?m aware of. This looks like quite a mess. Could you guys please somehow prioritize fixing these issues? It's causing us and our users some serious trouble. We take all problem reports seriously and care a great deal about providing end users with the best experience possible. Having said that, we?re a very small team supporting a relatively large user community. We?re doing the best we can with the resources we have and will continue to look into / address this issue as time permits. Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 17 11:08:47 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 17 Jan 2018 19:08:47 +0000 Subject: [bioontology-support] EDAM update - same problem again - please help In-Reply-To: References: <9580125B-AFC1-48AA-9BF7-C9AC1F7837B9@stanford.edu> <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> Message-ID: Hi Matus, > On Jan 16, 2018, at 6:36 PM, Matus Kalas wrote: > > Hi Jennifer and others, > > Thank you so much for looking into this, and narrowing down the problem! > > The current status with both EDAM and EDAM-BIOIMAGING is that when I'm logged out, everything is up to date, and when I'm logged in, the "Classes" browsing doesn't work, showing "We're sorry but something has gone wrong. We have been notified of this error.? As a logged in user, I?m able to view the classes for EDAM and EDAM-BIOIMAGING in Chrome (Version 63.0.3239.132), Firefox (57.0.4), and Safari (Version 11.0.2 (13604.4.7.1.6)). I?ve seen a problem like this reported on the support list before, and it was solved by clearing the browser cache, e.g., in Chrome doing something like Preferences? | Clear Browsing Data? Have you tried this? Kind regards, Jennifer From vendetti at stanford.edu Wed Jan 17 11:15:47 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 17 Jan 2018 19:15:47 +0000 Subject: [bioontology-support] Account Request In-Reply-To: <70670CF8-5C79-4EB5-B922-1555D92ECC22@ucdenver.edu> References: <70670CF8-5C79-4EB5-B922-1555D92ECC22@ucdenver.edu> Message-ID: Hi Tiffany, I queried our system for a user account with your email address, but found nothing. Did you use the following page on the BioPortal website to sign up for an account: https://bioportal.bioontology.org/accounts/new ? If you did, you should be able to click the ?Login? menu item at the top right of the application, and enter your account name and password to access your Account Setting page. This is the page where your API key is listed. If you?re still having issues, please let us know what your account name is so that we can find you in our system and confirm that an account was created. Kind regards, Jennifer On Jan 17, 2018, at 7:07 AM, Callahan, Tiffany > wrote: Hello- My name is Tiffany Callahan and I am a PhD Student in Computational Biology at the University of Colorado Denver. I recently requested an account in order to use the API. I have not received confirmation that my request was received or is being processed. Can you please confirm that I have provided the need information? If there is any further information needed to process this request, please don?t hesitate to let me know. Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 _______________________________________________ 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 TIFFANY.CALLAHAN at UCDENVER.EDU Wed Jan 17 11:49:04 2018 From: TIFFANY.CALLAHAN at UCDENVER.EDU (Callahan, Tiffany) Date: Wed, 17 Jan 2018 19:49:04 +0000 Subject: [bioontology-support] Account Request In-Reply-To: References: <70670CF8-5C79-4EB5-B922-1555D92ECC22@ucdenver.edu> Message-ID: Hi Jennifer- Thank you so much for your quick response. I thought I had used this email to make the request, but there is a chance that the request was made under callahantiff at gmail.com. Do you by chance have a request under that email? I was requesting the username ?callahantiff?, not sure if that is a field you can search for as well. Thank you again for your help! Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 On Jan 17, 2018, at 12:15 PM, Jennifer Leigh Vendetti > wrote: Hi Tiffany, I queried our system for a user account with your email address, but found nothing. Did you use the following page on the BioPortal website to sign up for an account: https://bioportal.bioontology.org/accounts/new ? If you did, you should be able to click the ?Login? menu item at the top right of the application, and enter your account name and password to access your Account Setting page. This is the page where your API key is listed. If you?re still having issues, please let us know what your account name is so that we can find you in our system and confirm that an account was created. Kind regards, Jennifer On Jan 17, 2018, at 7:07 AM, Callahan, Tiffany > wrote: Hello- My name is Tiffany Callahan and I am a PhD Student in Computational Biology at the University of Colorado Denver. I recently requested an account in order to use the API. I have not received confirmation that my request was received or is being processed. Can you please confirm that I have provided the need information? If there is any further information needed to process this request, please don?t hesitate to let me know. Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 _______________________________________________ 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 Jan 17 14:19:09 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 17 Jan 2018 22:19:09 +0000 Subject: [bioontology-support] Account Request In-Reply-To: References: <70670CF8-5C79-4EB5-B922-1555D92ECC22@ucdenver.edu> Message-ID: Hi Tiffany, On Jan 17, 2018, at 11:49 AM, Callahan, Tiffany > wrote: I thought I had used this email to make the request, but there is a chance that the request was made under callahantiff at gmail.com. Do you by chance have a request under that email? I was requesting the username ?callahantiff?, not sure if that is a field you can search for as well. I didn?t find any user accounts with your Gmail address, or the username you list above. On a related note, we don?t require you to confirm account creation via email. When you fill out this form on the website: https://bioportal.bioontology.org/accounts/new ? and click the Create button, you should be navigated to the Ontology Browse page, and notice that the ?Login? link in the top right has changed to your username. The text blurb on the new user account page that mentions email confirmation refers to signing up for the BioPortal announcements mailing list. Perhaps you could try creating an account again at the page above and let us know what you see? Do you get an error message? Kind regards, Jennifer Thank you again for your help! Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 On Jan 17, 2018, at 12:15 PM, Jennifer Leigh Vendetti > wrote: Hi Tiffany, I queried our system for a user account with your email address, but found nothing. Did you use the following page on the BioPortal website to sign up for an account: https://bioportal.bioontology.org/accounts/new ? If you did, you should be able to click the ?Login? menu item at the top right of the application, and enter your account name and password to access your Account Setting page. This is the page where your API key is listed. If you?re still having issues, please let us know what your account name is so that we can find you in our system and confirm that an account was created. Kind regards, Jennifer On Jan 17, 2018, at 7:07 AM, Callahan, Tiffany > wrote: Hello- My name is Tiffany Callahan and I am a PhD Student in Computational Biology at the University of Colorado Denver. I recently requested an account in order to use the API. I have not received confirmation that my request was received or is being processed. Can you please confirm that I have provided the need information? If there is any further information needed to process this request, please don?t hesitate to let me know. Best- Tiffany J. Callahan, MPH PhD Student Computational Bioscience University of Colorado Denver Anschutz Medical Campus E: tiffany.callahan at ucdenver.edu P: 505-917-0197 _______________________________________________ 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 Jan 17 16:11:23 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 18 Jan 2018 00:11:23 +0000 Subject: [bioontology-support] EDAM update - same problem again - please help In-Reply-To: <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> References: <9580125B-AFC1-48AA-9BF7-C9AC1F7837B9@stanford.edu> <2a213f41dd932b469fdc9e8b3ce8047b@webmail.uib.no> <83461676-90A6-4EB8-B438-62AA7FF39446@stanford.edu> Message-ID: Hi Matus, Another instance of the same kind of problem: I uploaded a new version of http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING about an hour ago, and it still shows it as not parsed at the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING, whether I'm looged in, or not logged in a private browser window. I was able to reproduce this behavior here (I?ve cleared BioPortal?s caches, so your ontology is accessible now). BioPortal has 3 distinct caching layers in the stack. Based on the information provided in your last two messages, we think we?ve narrowed the problem to the client side in-memory cache. I?ve entered an issue in our tracker against the code base that contains the front end caching code: https://github.com/ncbo/ontologies_api_ruby_client/issues/2 This is where we?ll post progress updates on this issue. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 18 18:11:40 2018 From: support at bioontology.org (support at bioontology.org) Date: Thu, 18 Jan 2018 18:11:40 -0800 Subject: [bioontology-support] [BioPortal] Feedback from VIJAYAYERUVA Message-ID: <5a6153dc1f7ea_54953fee23f775f0930bf@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 18 21:19:35 2018 From: support at bioontology.org (support at bioontology.org) Date: Thu, 18 Jan 2018 21:19:35 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Rakshya Message-ID: <5a617fe7783f7_23273fc373359b7c4967d@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Jan 19 10:29:33 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 19 Jan 2018 18:29:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Rakshya In-Reply-To: <5a617fe7783f7_23273fc373359b7c4967d@ncbo-prd-app-09.stanford.edu.mail> References: <5a617fe7783f7_23273fc373359b7c4967d@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <252A7051-D787-4E30-854B-93ECB2680F0A@stanford.edu> Hello Rakshya, I queried our system and found no user accounts associated with your email address. Do you remember your account name? Or, if you signed up under a different email address? Also, is this the page you used to register for an account with us: https://bioportal.bioontology.org/accounts/new ? Kind regards, Jennifer On Jan 18, 2018, at 9:19 PM, support at bioontology.org wrote: Name: Rakshya Email: rakshya.khadka at telethonkids.org.au Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I have been trying to login to my account but I get error. I also tried to use the forgot password but even that is not working/ Could you please help me out here. _______________________________________________ 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 Abigail_Ward at DFCI.HARVARD.EDU Fri Jan 19 11:23:06 2018 From: Abigail_Ward at DFCI.HARVARD.EDU (Ward, Abigail) Date: Fri, 19 Jan 2018 19:23:06 +0000 Subject: [bioontology-support] Ontology Set Up Message-ID: Hello! My name is Abbie Ward and I am one of the research coordinators at Dana-Farber. For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here: http://bioportal.bioontology.org/ontologies/ICD-O-3_1 It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon? Also, as this is a very well established ontology, is there somewhere else that it is located? Thanks! Abbie Abigail Ward Clinical Research Coordinator Pediatric Oncology, Solid Tumor Program Dana-Farber/Boston Children's Cancer and Blood Disorders Center 450 Brookline Ave. Shield's Warren 439 Boston, MA 02215 Tel: 617.632.2606 Fax: 617.582.8861 DFCI Pager: 40290 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Jan 19 11:39:55 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 19 Jan 2018 19:39:55 +0000 Subject: [bioontology-support] Ontology Set Up In-Reply-To: References: Message-ID: Hello Abbie, On Jan 19, 2018, at 11:23 AM, Ward, Abigail > wrote: Hello! My name is Abbie Ward and I am one of the research coordinators at Dana-Farber. For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here: http://bioportal.bioontology.org/ontologies/ICD-O-3_1 It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon? I looked at the ontology submission you created in BioPortal. It appears that you specified the ontology should be loaded by our system from the following URL: http://codes.iarc.fr/codegroup/2 This URL points to an HTML page, rather than an ontology source file. We handle ontologies in OWL, OBO, and SKOS formats. A typical URL for loading an ontology includes the exact path to the ontology source file, including the file name itself, e.g.: http://www.example.com/my_ontology.owl It?s unclear to me from looking at their site if they provide their ontology in any of the formats BioPortal is able to load. If you?re able to locate something in one of the above mentioned formats, we could further assist you in trying to get it into BioPortal. Also, as this is a very well established ontology, is there somewhere else that it is located? I don?t know of anything offhand, but perhaps other subscribed to this support list know more? Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Mon Jan 22 13:59:27 2018 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Mon, 22 Jan 2018 21:59:27 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. Best regards, Helen From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Tuesday, March 29, 2016 3:17 PM To: Pan, Huaqin (Helen) Cc: Qin, Ying ; NCBO User Support Subject: Re: [bioontology-support] Help with Submission Hi Helen, I uploaded the new version of the ontology that you attached. It?s now available in BioPortal: http://bioportal.bioontology.org/ontologies/PHENX Best, Jennifer On Mar 29, 2016, at 6:55 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I reviewed the current version at bioportal and found a handful of classes missing subclass relation. I attached an updated owl. Would you please help loading this version to replace the existing one? Many thanks! Helen From: Pan, Huaqin (Helen) Sent: Tuesday, March 29, 2016 9:31 AM To: Jennifer Leigh Vendetti > Cc: Qin, Ying > Subject: RE: [bioontology-support] Help with Submission Hi Jennifer, I replied too soon ? As I read through the end of email, I realized that you have already fixed the syntax errors and uploaded the file for us. I appreciate your help! Best regards, Helen From: Pan, Huaqin (Helen) Sent: Tuesday, March 29, 2016 9:01 AM To: Jennifer Leigh Vendetti > Cc: Qin, Ying >; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] Help with Submission Hi Jennifer, I will look into the error messages you summarized, update and test in Prot?g?, and upload. Thank you for your help! Best, Helen From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Monday, March 28, 2016 7:57 PM To: Qin, Ying >; Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] Help with Submission Hello Ying Qin, I?ve had a chance to look at your ontology in detail and have some information for you about why it didn?t load in BioPortal. There were a number of syntax errors in your ontology, i.e.: 1). Unescaped embedded HTML. If you want to embed HTML in your ontology, you need to either escape the HTML, or use the XML Literal parse type. For example, the following is valid because the parse type is Literal: Body Composition Guidance ? and the following is also valid because the parse type is string, but the HTML is properly escaped: <a href="http://www.phenxtoolkit.org/toolkit_content/supplemental_info/anthropometrics/additional_info/Body_Composition_Guidance.doc">Body Composition Guidance</a> 2). The ® and — entities were undeclared. 3). There were unescaped ampersands. I took the liberty of fixing these errors and re-submitted your ontology to BioPortal, which uploaded and parsed successfully: http://bioportal.bioontology.org/ontologies/PHENX If you want to see the exact edits I made to the OWL file, I?ve attached a diff (generated by the git version control system). For future submissions of your ontology to be successful, you?ll need to incorporate these fixes. On a related note, I?m wondering how you are generating your ontology file? These sorts of syntax errors generally aren?t present if you?re using one of the popular ontology editing tools like Protege to maintain your ontology. Best, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 24 17:18:39 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 25 Jan 2018 01:18:39 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Wed Jan 24 18:05:51 2018 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Thu, 25 Jan 2018 02:05:51 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: OK. Thank you for your advice. Jennifer! Best regards, Helen From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Wednesday, January 24, 2018 8:19 PM To: Pan, Huaqin (Helen) Cc: NCBO User Support Subject: Re: [bioontology-support] Help with Submission Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 24 19:58:36 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 25 Jan 2018 03:58:36 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: I might add a few thoughts to Jennifer's summary. My bias in such things is to make the ontology correct (i.e., do not misrepresent partOf relationships as subclasses, because it messes up any inferencing that people may want to do (and maybe quite important research, too). It's better to 'force' the tools to improve than to create improper data artifacts, even if it is painful. Re the visualization, I understand the Protege team may be working on an improved visual presentation of tree hierarchies, partly to address this issue?I just saw a note to that effect in another list, but haven't asked the team. If that's the case, we would definitely see if leveraging that code for BioPortal could be possible, though it wouldn't happen quickly. Regarding the proposed idea to publish them privately at first?since you don't know which one you'll make public, you won't know which one to give the correct acronym. I'd give them both 'fake' acronyms, then republish the one you like publicly under the correct acronym. (We could delete the private ones afterwards, that would be best for BioPortal.) And finally, a really bad suggestion given my bias above: if you basically _added_ a subclass relation for each partOf relation, if the ontology parsed (not sure if it could), you'd have both worlds?a hierarchical view and still being able to see the partOf relations. But I really hope you don't do that. John On Jan 24, 2018, at 5:18 PM, Jennifer Leigh Vendetti > wrote: Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From viansabeeh at oakland.edu Thu Jan 25 07:38:13 2018 From: viansabeeh at oakland.edu (Vian Sabeeh) Date: Thu, 25 Jan 2018 07:38:13 -0800 Subject: [bioontology-support] bioportal problem Message-ID: Dear Sir: Today I tried to access Bioportal restfull service but it does not work, I used it yesterday and it was working perfectly. can you help me with this problem? username: viansabeeh email: viansabeeh at oakland.edu Regards Vian Sabeeh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: problem.jpg Type: image/jpeg Size: 110501 bytes Desc: not available URL: From Abigail_Ward at DFCI.HARVARD.EDU Wed Jan 24 13:48:52 2018 From: Abigail_Ward at DFCI.HARVARD.EDU (Ward, Abigail) Date: Wed, 24 Jan 2018 21:48:52 +0000 Subject: [bioontology-support] Ontology Set Up In-Reply-To: References: Message-ID: Hi Jennifer, Thank you for your response. At this time I have been unable to locate a source file for this ontology, however if I find one in the future I will update the submission. Thanks! Abbie From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Friday, January 19, 2018 2:40 PM To: Ward, Abigail Cc: support at bioontology.org Subject: Re: [bioontology-support] Ontology Set Up Hello Abbie, On Jan 19, 2018, at 11:23 AM, Ward, Abigail > wrote: Hello! My name is Abbie Ward and I am one of the research coordinators at Dana-Farber. For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here: http://bioportal.bioontology.org/ontologies/ICD-O-3_1 It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon? I looked at the ontology submission you created in BioPortal. It appears that you specified the ontology should be loaded by our system from the following URL: http://codes.iarc.fr/codegroup/2 This URL points to an HTML page, rather than an ontology source file. We handle ontologies in OWL, OBO, and SKOS formats. A typical URL for loading an ontology includes the exact path to the ontology source file, including the file name itself, e.g.: http://www.example.com/my_ontology.owl It?s unclear to me from looking at their site if they provide their ontology in any of the formats BioPortal is able to load. If you?re able to locate something in one of the above mentioned formats, we could further assist you in trying to get it into BioPortal. Also, as this is a very well established ontology, is there somewhere else that it is located? I don?t know of anything offhand, but perhaps other subscribed to this support list know more? Kind regards, Jennifer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Jan 25 09:30:36 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 25 Jan 2018 17:30:36 +0000 Subject: [bioontology-support] NCBO virtual appliance In-Reply-To: References: Message-ID: <017BE204-69FE-418C-A83E-B8E381C5A736@stanford.edu> Hello Chad, I believe I previously responded directly to this request, within an hour of your sending it. Can you please see if you received that email from you? I will resend it shortly if I don't hear from you. John On Jan 23, 2018, at 8:44 PM, Shaw, Chad A. > wrote: Hello I am a faculty member at Baylor College of Medicine Genetics, and I work with our exome diagnostic group. I write to request a copy of the NCBO virtual appliance for the purpose of applying NLP methods to the conversion of clinical notes to HPO terms to assist in diagnostic variant prioritization. I am interested in the virtual appliance for NCBO HPO translation of clinical notes. Please let me know Thank you Chad Shaw _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cashaw at bcm.edu Tue Jan 23 20:44:30 2018 From: cashaw at bcm.edu (Shaw, Chad A.) Date: Wed, 24 Jan 2018 04:44:30 +0000 Subject: [bioontology-support] NCBO virtual appliance Message-ID: Hello I am a faculty member at Baylor College of Medicine Genetics, and I work with our exome diagnostic group. I write to request a copy of the NCBO virtual appliance for the purpose of applying NLP methods to the conversion of clinical notes to HPO terms to assist in diagnostic variant prioritization. I am interested in the virtual appliance for NCBO HPO translation of clinical notes. Please let me know Thank you Chad Shaw -------------- next part -------------- An HTML attachment was scrubbed... URL: From ancarrol at med.umich.edu Thu Jan 25 08:30:19 2018 From: ancarrol at med.umich.edu (Carroll, Andrew) Date: Thu, 25 Jan 2018 16:30:19 +0000 Subject: [bioontology-support] API, Login, & Password Reset Issues Message-ID: <0ca05628fe5847a5bb1d8aadd3e32188@med.umich.edu> Hello, We are a institution that uses the Biomedical Ontology API for the REDCap application and had user report issues searching the RxNorm ontology as of this morning. I was able to reproduce this issue, and attempting to log in using our account 'michr_redcap' gives a 'Sorry, unrecognized username or password' message. Attempting to request a new password gives a similar 'not recognized' message. * If I select 'Create new account', I receive the message (screenshot below) * * warning: include(./sites/all/themes/bioontology/user-register.tpl.php): failed to open stream: No such file or directory in /srv/www/vhosts/www.bioontology.org/drupal-6.38/includes/theme.inc on line 1079. * warning: include(): Failed opening './sites/all/themes/bioontology/user-register.tpl.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /srv/www/vhosts/www.bioontology.org/drupal-6.38/includes/theme.inc on line 1079.' [cid:image002.jpg at 01D395CF.E0A36590] This was reported as working without issue yesterday - can you confirm if there is an outage or known issues with your API service? Andrew Carroll Application System Analyst / Programmer Michigan Institute for Clinical & Health Research (MICHR) 1600 Huron Parkway (street) 2800 Plymouth Road (mail) Building 400 Ann Arbor, MI 48109-2800 734.998.6797 p www.michr.umich.edu www.UMHealthResearch.org [cid:image001.png at 01CF2EF5.0EDA0C70] CITE IT: Please help us continue our support for clinical and translational research by citing our grant numbers in relevant publications: UL1TR000433 and UL1TR002240. Thank you. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 23236 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 15506 bytes Desc: image002.jpg URL: From vendetti at stanford.edu Thu Jan 25 08:49:04 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 25 Jan 2018 16:49:04 +0000 Subject: [bioontology-support] bioportal problem In-Reply-To: References: Message-ID: <5979D149-AE2C-4E56-9AAE-CF0470B8866C@stanford.edu> Hello Vian, We had a BioPortal outage for roughly 3 hours this morning. The system is back up and showing results for the query you were trying to execute. Apologies for the inconvenience. Kind regards, Jennifer [cid:D9966753-E3F7-4540-AD4E-257B648270AE] On Jan 25, 2018, at 7:38 AM, Vian Sabeeh > wrote: Dear Sir: Today I tried to access Bioportal restfull service but it does not work, I used it yesterday and it was working perfectly. can you help me with this problem? username: viansabeeh email: viansabeeh at oakland.edu Regards Vian Sabeeh _______________________________________________ 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 2018-01-25 08.43.01.png Type: image/png Size: 278469 bytes Desc: Screenshot 2018-01-25 08.43.01.png URL: From vendetti at stanford.edu Thu Jan 25 08:49:17 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 25 Jan 2018 16:49:17 +0000 Subject: [bioontology-support] API, Login, & Password Reset Issues In-Reply-To: <0ca05628fe5847a5bb1d8aadd3e32188@med.umich.edu> References: <0ca05628fe5847a5bb1d8aadd3e32188@med.umich.edu> Message-ID: Hello Andrew, There was a BioPortal outage this morning for roughly 3 hours between 5:30 - 8:30AM PST. The system is back up now. Apologies for the inconvenience. Kind regards, Jennifer On Jan 25, 2018, at 8:30 AM, Carroll, Andrew > wrote: Hello, We are a institution that uses the Biomedical Ontology API for the REDCap application and had user report issues searching the RxNorm ontology as of this morning. I was able to reproduce this issue, and attempting to log in using our account ?michr_redcap? gives a ?Sorry, unrecognized username or password? message. Attempting to request a new password gives a similar ?not recognized? message. ? If I select ?Create new account?, I receive the message (screenshot below) ? ? warning: include(./sites/all/themes/bioontology/user-register.tpl.php): failed to open stream: No such file or directory in /srv/www/vhosts/www.bioontology.org/drupal-6.38/includes/theme.inc on line 1079. ? warning: include(): Failed opening './sites/all/themes/bioontology/user-register.tpl.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /srv/www/vhosts/www.bioontology.org/drupal-6.38/includes/theme.inc on line 1079.? This was reported as working without issue yesterday ? can you confirm if there is an outage or known issues with your API service? Andrew Carroll Application System Analyst / Programmer Michigan Institute for Clinical & Health Research (MICHR) 1600 Huron Parkway (street) 2800 Plymouth Road (mail) Building 400 Ann Arbor, MI 48109-2800 734.998.6797 p www.michr.umich.edu www.UMHealthResearch.org CITE IT: Please help us continue our support for clinical and translational research by citing our grant numbers in relevant publications: UL1TR000433 and UL1TR002240. Thank you. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Thu Jan 25 15:12:22 2018 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Thu, 25 Jan 2018 23:12:22 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: Hi Jennifer and John, Thank you both for your advice! I will submit both versions as private first, and choose the ?correct? one to make public. John, I appreciate your suggestion in the last paragraph. Yes, I didn?t do that (have both ?part-of? AND ?subclass?). In version 1, I don?t have ?part-of?. In version 2 where I have ?part-of?, it?s either ?part-of? or ?subclass_of?, not BOTH. Best regards, Helen From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Wednesday, January 24, 2018 10:59 PM To: Jennifer Leigh Vendetti Cc: Pan, Huaqin (Helen) ; NCBO User Support Subject: Re: [bioontology-support] Help with Submission I might add a few thoughts to Jennifer's summary. My bias in such things is to make the ontology correct (i.e., do not misrepresent partOf relationships as subclasses, because it messes up any inferencing that people may want to do (and maybe quite important research, too). It's better to 'force' the tools to improve than to create improper data artifacts, even if it is painful. Re the visualization, I understand the Protege team may be working on an improved visual presentation of tree hierarchies, partly to address this issue?I just saw a note to that effect in another list, but haven't asked the team. If that's the case, we would definitely see if leveraging that code for BioPortal could be possible, though it wouldn't happen quickly. Regarding the proposed idea to publish them privately at first?since you don't know which one you'll make public, you won't know which one to give the correct acronym. I'd give them both 'fake' acronyms, then republish the one you like publicly under the correct acronym. (We could delete the private ones afterwards, that would be best for BioPortal.) And finally, a really bad suggestion given my bias above: if you basically _added_ a subclass relation for each partOf relation, if the ontology parsed (not sure if it could), you'd have both worlds?a hierarchical view and still being able to see the partOf relations. But I really hope you don't do that. John On Jan 24, 2018, at 5:18 PM, Jennifer Leigh Vendetti > wrote: Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From swt at stanford.edu Thu Jan 25 20:03:50 2018 From: swt at stanford.edu (Samson Tu) Date: Fri, 26 Jan 2018 04:03:50 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: Hi, I?d endorse John?s advocacy of ?mak[ing] the ontology correct (i.e., do not misrepresent partOf relationships as subclasses.)." Where you have ?part-of? relation in your domain, don?t modeled it as ?subclass_of.? Perhaps you want to create a third version where ?part-of? is never modeled as ?subclass_of?. The next version of Protege (which may become available in February) will display relationships other than subclass-of. In the current version of Protege, there is an Individual Hierarchy plugin that you can install that can display object-property assertions as hierarchies at the individual level. It may not be what you need, but I am mentioning it just in case. With best regards, Samson On Jan 25, 2018, at 3:12 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer and John, Thank you both for your advice! I will submit both versions as private first, and choose the ?correct? one to make public. John, I appreciate your suggestion in the last paragraph. Yes, I didn?t do that (have both ?part-of? AND ?subclass?). In version 1, I don?t have ?part-of?. In version 2 where I have ?part-of?, it?s either ?part-of? or ?subclass_of?, not BOTH. Best regards, Helen From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Wednesday, January 24, 2018 10:59 PM To: Jennifer Leigh Vendetti > Cc: Pan, Huaqin (Helen) >; NCBO User Support > Subject: Re: [bioontology-support] Help with Submission I might add a few thoughts to Jennifer's summary. My bias in such things is to make the ontology correct (i.e., do not misrepresent partOf relationships as subclasses, because it messes up any inferencing that people may want to do (and maybe quite important research, too). It's better to 'force' the tools to improve than to create improper data artifacts, even if it is painful. Re the visualization, I understand the Protege team may be working on an improved visual presentation of tree hierarchies, partly to address this issue?I just saw a note to that effect in another list, but haven't asked the team. If that's the case, we would definitely see if leveraging that code for BioPortal could be possible, though it wouldn't happen quickly. Regarding the proposed idea to publish them privately at first?since you don't know which one you'll make public, you won't know which one to give the correct acronym. I'd give them both 'fake' acronyms, then republish the one you like publicly under the correct acronym. (We could delete the private ones afterwards, that would be best for BioPortal.) And finally, a really bad suggestion given my bias above: if you basically _added_ a subclass relation for each partOf relation, if the ontology parsed (not sure if it could), you'd have both worlds?a hierarchical view and still being able to see the partOf relations. But I really hope you don't do that. John On Jan 24, 2018, at 5:18 PM, Jennifer Leigh Vendetti > wrote: Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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 hpan at rti.org Fri Jan 26 06:58:00 2018 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 26 Jan 2018 14:58:00 +0000 Subject: [bioontology-support] Help with Submission In-Reply-To: References: <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu> Message-ID: Thank you, Samson! I will look into the hierarchy plugin, and wait for the new version of Prot?g? ? Best regards, Helen From: Samson Tu [mailto:swt at stanford.edu] Sent: Thursday, January 25, 2018 11:04 PM To: Pan, Huaqin (Helen) Cc: Samson Tu ; John Graybeal ; Jennifer Leigh Vendetti ; NCBO User Support Subject: Re: [bioontology-support] Help with Submission Hi, I?d endorse John?s advocacy of ?mak[ing] the ontology correct (i.e., do not misrepresent partOf relationships as subclasses.)." Where you have ?part-of? relation in your domain, don?t modeled it as ?subclass_of.? Perhaps you want to create a third version where ?part-of? is never modeled as ?subclass_of?. The next version of Protege (which may become available in February) will display relationships other than subclass-of. In the current version of Protege, there is an Individual Hierarchy plugin that you can install that can display object-property assertions as hierarchies at the individual level. It may not be what you need, but I am mentioning it just in case. With best regards, Samson On Jan 25, 2018, at 3:12 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer and John, Thank you both for your advice! I will submit both versions as private first, and choose the ?correct? one to make public. John, I appreciate your suggestion in the last paragraph. Yes, I didn?t do that (have both ?part-of? AND ?subclass?). In version 1, I don?t have ?part-of?. In version 2 where I have ?part-of?, it?s either ?part-of? or ?subclass_of?, not BOTH. Best regards, Helen From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Wednesday, January 24, 2018 10:59 PM To: Jennifer Leigh Vendetti > Cc: Pan, Huaqin (Helen) >; NCBO User Support > Subject: Re: [bioontology-support] Help with Submission I might add a few thoughts to Jennifer's summary. My bias in such things is to make the ontology correct (i.e., do not misrepresent partOf relationships as subclasses, because it messes up any inferencing that people may want to do (and maybe quite important research, too). It's better to 'force' the tools to improve than to create improper data artifacts, even if it is painful. Re the visualization, I understand the Protege team may be working on an improved visual presentation of tree hierarchies, partly to address this issue?I just saw a note to that effect in another list, but haven't asked the team. If that's the case, we would definitely see if leveraging that code for BioPortal could be possible, though it wouldn't happen quickly. Regarding the proposed idea to publish them privately at first?since you don't know which one you'll make public, you won't know which one to give the correct acronym. I'd give them both 'fake' acronyms, then republish the one you like publicly under the correct acronym. (We could delete the private ones afterwards, that would be best for BioPortal.) And finally, a really bad suggestion given my bias above: if you basically _added_ a subclass relation for each partOf relation, if the ontology parsed (not sure if it could), you'd have both worlds?a hierarchical view and still being able to see the partOf relations. But I really hope you don't do that. John On Jan 24, 2018, at 5:18 PM, Jennifer Leigh Vendetti > wrote: Hi Helen, On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/. Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal. My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful. * Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of? * Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of? We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?. One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?. Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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 Fri Jan 26 01:33:41 2018 From: support at bioontology.org (support at bioontology.org) Date: Fri, 26 Jan 2018 01:33:41 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Elspeth Bruford Message-ID: <5a6af5f5c10ac_31e03f97d78abf845169e@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 29 05:16:42 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 29 Jan 2018 13:16:42 +0000 Subject: [bioontology-support] Ontology Set Up In-Reply-To: References: Message-ID: <59BA1DA6-2DDF-4978-ADC1-D27EF8A98166@stanford.edu> Hi Abbie, Thanks for letting us know. I disabled the download URL, but left your ontology metadata in place in BioPortal. Feel free to modify it in the future if you do find a source file. Kind regards, Jennifer On Jan 24, 2018, at 4:48 PM, Ward, Abigail > wrote: Hi Jennifer, Thank you for your response. At this time I have been unable to locate a source file for this ontology, however if I find one in the future I will update the submission. Thanks! Abbie From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Friday, January 19, 2018 2:40 PM To: Ward, Abigail > Cc: support at bioontology.org Subject: Re: [bioontology-support] Ontology Set Up Hello Abbie, On Jan 19, 2018, at 11:23 AM, Ward, Abigail > wrote: Hello! My name is Abbie Ward and I am one of the research coordinators at Dana-Farber. For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here: http://bioportal.bioontology.org/ontologies/ICD-O-3_1 It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon? I looked at the ontology submission you created in BioPortal. It appears that you specified the ontology should be loaded by our system from the following URL: http://codes.iarc.fr/codegroup/2 This URL points to an HTML page, rather than an ontology source file. We handle ontologies in OWL, OBO, and SKOS formats. A typical URL for loading an ontology includes the exact path to the ontology source file, including the file name itself, e.g.: http://www.example.com/my_ontology.owl It?s unclear to me from looking at their site if they provide their ontology in any of the formats BioPortal is able to load. If you?re able to locate something in one of the above mentioned formats, we could further assist you in trying to get it into BioPortal. Also, as this is a very well established ontology, is there somewhere else that it is located? I don?t know of anything offhand, but perhaps other subscribed to this support list know more? Kind regards, Jennifer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mihai.Virtosu at hsc.utah.edu Mon Jan 29 09:21:17 2018 From: Mihai.Virtosu at hsc.utah.edu (Mihai Virtosu) Date: Mon, 29 Jan 2018 17:21:17 +0000 Subject: [bioontology-support] New API key Message-ID: <1FC5A6557F16EA4AB81820F32AB05856CFFE0F1F@X-MB1.xds.umail.utah.edu> Hello, I am trying to create a new account to get a new API key but the following website does not work: http://bioportal.bioontology.org/accounts/new Could you please look into it? Thank you, Mihai Virtosu University of Utah -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 29 12:23:12 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 29 Jan 2018 20:23:12 +0000 Subject: [bioontology-support] New API key In-Reply-To: <1FC5A6557F16EA4AB81820F32AB05856CFFE0F1F@X-MB1.xds.umail.utah.edu> References: <1FC5A6557F16EA4AB81820F32AB05856CFFE0F1F@X-MB1.xds.umail.utah.edu> Message-ID: <4AD0670E-AF68-464E-A55A-64904AAEFE0F@stanford.edu> Hello Mihai, Apologies - we had a brief outage today. The page you refer to below is up. Are you still experiencing issues? Kind regards, Jennifer On Jan 29, 2018, at 12:21 PM, Mihai Virtosu > wrote: Hello, I am trying to create a new account to get a new API key but the following website does not work: http://bioportal.bioontology.org/accounts/new Could you please look into it? Thank you, Mihai Virtosu University of Utah _______________________________________________ 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 Jan 31 01:26:54 2018 From: support at bioontology.org (support at bioontology.org) Date: Wed, 31 Jan 2018 01:26:54 -0800 Subject: [bioontology-support] [BioPortal] Feedback from martin bailey Message-ID: <5a718bdecb250_1c673fe3bf3af6b4363e2@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 31 03:15:33 2018 From: support at bioontology.org (support at bioontology.org) Date: Wed, 31 Jan 2018 03:15:33 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Joao Sequeira Message-ID: <5a71a5555d688_1a423f86dde6b588576b5@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From N.Hardiker at hud.ac.uk Wed Jan 31 02:27:34 2018 From: N.Hardiker at hud.ac.uk (Nick Hardiker) Date: Wed, 31 Jan 2018 10:27:34 +0000 Subject: [bioontology-support] ICNP Message-ID: <16ACE35CE120B3469929F208DE8FC80579CE0F@VIGILANTE.AD.HUD.AC.UK> I am writing on behalf of the International Council of Nurses who issued a new release of ICNP last year. What is the easiest way of making a new submission? Is this something that you manage centrally or is it something we can do via the portal? With best wishes Nick Professor Nick Hardiker Associate Dean (Research & Enterprise), School of Human and Health Sciences [Description: Description: Description: ico-3]01484 473461 [Description: Description: Description: ico-1]n.hardiker at hud.ac.uk [Description: Description: Description: ico-4]www.hud.ac.uk School of Human and Health Sciences University of Huddersfield | HW2/9, Harold Wilson Building | Queensgate | Huddersfield | HD1 3DH University of Huddersfield inspiring tomorrow's professionals. [http://marketing.hud.ac.uk/_HOSTED/EmailSig2014/EmailSigFooter.jpg] This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 765 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 857 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 878 bytes Desc: image003.jpg URL: From vendetti at stanford.edu Wed Jan 31 05:38:44 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 31 Jan 2018 13:38:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from martin bailey In-Reply-To: <5a718bdecb250_1c673fe3bf3af6b4363e2@ncbo-prd-app-09.stanford.edu.mail> References: <5a718bdecb250_1c673fe3bf3af6b4363e2@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Martin, I refreshed our application caches and the tree for EDDA now appears to be accessible without issues. Are you still experiencing difficulties on your end? Kind regards, Jennifer [cid:AD1BF6B2-9FB6-4CF7-99F9-BCAC07CDCB4C at Belkin] On Jan 31, 2018, at 4:26 AM, support at bioontology.org wrote: Name: martin bailey Email: martin.bailey at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FEDDA Feedback: Hi http://bioportal.bioontology.org/ontologies/EDDA?p=classes&conceptid=root can't open tree, I get 'Error please try again' Kind regards Martin _______________________________________________ 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 2018-01-31 08.36.23.png Type: image/png Size: 260223 bytes Desc: Screenshot 2018-01-31 08.36.23.png URL: From vendetti at stanford.edu Wed Jan 31 05:48:37 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 31 Jan 2018 13:48:37 +0000 Subject: [bioontology-support] ICNP In-Reply-To: <16ACE35CE120B3469929F208DE8FC80579CE0F@VIGILANTE.AD.HUD.AC.UK> References: <16ACE35CE120B3469929F208DE8FC80579CE0F@VIGILANTE.AD.HUD.AC.UK> Message-ID: <35CE4629-9B10-4B73-A412-6144BFADD833@stanford.edu> Hi Nick, We can either create one for you (if you send us the ontology source file), or anyone with write permissions for this ontology could create a new submission themselves. I looked at the list of administrators for this ontology - there is only one account with username ?coenena?. It?s up to you how to proceed. If you wanted to do it yourself, you would need to create an account in BioPortal and let us know the username so that we can add you as an administrator for the ontology. Or, like I said above, send us the OWL file and we can upload it on your behalf. On a related note, BioPortal has the ability to check a download URL nightly for new versions of an ontology. So - you have the option of creating a new submission that points to a download URL - which means that new versions of your ontology would get pulled automatically by our system. Not required - just thought you might want to know about that. Kind regards, Jennifer On Jan 31, 2018, at 5:27 AM, Nick Hardiker > wrote: I am writing on behalf of the International Council of Nurses who issued a new release of ICNP last year. What is the easiest way of making a new submission? Is this something that you manage centrally or is it something we can do via the portal? With best wishes Nick Professor Nick Hardiker Associate Dean (Research & Enterprise), School of Human and Health Sciences 01484 473461 n.hardiker at hud.ac.uk www.hud.ac.uk School of Human and Health Sciences University of Huddersfield | HW2/9, Harold Wilson Building | Queensgate | Huddersfield | HD1 3DH University of Huddersfield inspiring tomorrow's professionals. [http://marketing.hud.ac.uk/_HOSTED/EmailSig2014/EmailSigFooter.jpg] This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability. _______________________________________________ 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 Jan 31 08:36:36 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 31 Jan 2018 16:36:36 +0000 Subject: [bioontology-support] ICNP In-Reply-To: <16ACE35CE120B3469929F208DE8FC80579D5EE@VIGILANTE.AD.HUD.AC.UK> References: <16ACE35CE120B3469929F208DE8FC80579CE0F@VIGILANTE.AD.HUD.AC.UK> <35CE4629-9B10-4B73-A412-6144BFADD833@stanford.edu> <16ACE35CE120B3469929F208DE8FC80579D5EE@VIGILANTE.AD.HUD.AC.UK> Message-ID: <96451F55-7142-4880-B382-DFDD340B6F11@stanford.edu> Hi Nick, I added your account as an administrator for the ontology. You should now be able to go to the ontology summary page (http://bioportal.bioontology.org/ontologies/ICNP), and click the ?Add submission? link to submit your new version. Let us know if you run into any issues. Kind regards, Jennifer On Jan 31, 2018, at 8:58 AM, Nick Hardiker > wrote: Hi Jennifer My colleague Amy Coenen has now retired and I have assumed responsibility for ICNP within Bioportal. Could you please replace the administrator with me: nrhardiker. I will endeavour to upload the new version and will get back to you if I get unstuck. Thank you for the information about automatic upload. We will bear this in mind. With best wishes Nick Professor Nick Hardiker Associate Dean (Research & Enterprise), School of Human and Health Sciences 01484 473461 n.hardiker at hud.ac.uk www.hud.ac.uk School of Human and Health Sciences University of Huddersfield | HW2/9, Harold Wilson Building | Queensgate | Huddersfield | HD1 3DH From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: 31 January 2018 13:49 To: Nick Hardiker > Cc: support at bioontology.org Subject: Re: [bioontology-support] ICNP Hi Nick, We can either create one for you (if you send us the ontology source file), or anyone with write permissions for this ontology could create a new submission themselves. I looked at the list of administrators for this ontology - there is only one account with username ?coenena?. It?s up to you how to proceed. If you wanted to do it yourself, you would need to create an account in BioPortal and let us know the username so that we can add you as an administrator for the ontology. Or, like I said above, send us the OWL file and we can upload it on your behalf. On a related note, BioPortal has the ability to check a download URL nightly for new versions of an ontology. So - you have the option of creating a new submission that points to a download URL - which means that new versions of your ontology would get pulled automatically by our system. Not required - just thought you might want to know about that. Kind regards, Jennifer On Jan 31, 2018, at 5:27 AM, Nick Hardiker > wrote: I am writing on behalf of the International Council of Nurses who issued a new release of ICNP last year. What is the easiest way of making a new submission? Is this something that you manage centrally or is it something we can do via the portal? With best wishes Nick Professor Nick Hardiker Associate Dean (Research & Enterprise), School of Human and Health Sciences 01484 473461 n.hardiker at hud.ac.uk www.hud.ac.uk School of Human and Health Sciences University of Huddersfield | HW2/9, Harold Wilson Building | Queensgate | Huddersfield | HD1 3DH University of Huddersfield inspiring tomorrow's professionals. [http://marketing.hud.ac.uk/_HOSTED/EmailSig2014/EmailSigFooter.jpg] This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support University of Huddersfield inspiring tomorrow's professionals. [http://marketing.hud.ac.uk/_HOSTED/EmailSig2014/EmailSigFooter.jpg] This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mihai.Virtosu at hsc.utah.edu Wed Jan 31 08:27:25 2018 From: Mihai.Virtosu at hsc.utah.edu (Mihai Virtosu) Date: Wed, 31 Jan 2018 16:27:25 +0000 Subject: [bioontology-support] New API key In-Reply-To: <4AD0670E-AF68-464E-A55A-64904AAEFE0F@stanford.edu> References: <1FC5A6557F16EA4AB81820F32AB05856CFFE0F1F@X-MB1.xds.umail.utah.edu> <4AD0670E-AF68-464E-A55A-64904AAEFE0F@stanford.edu> Message-ID: <1FC5A6557F16EA4AB81820F32AB05856CFFE3DF0@X-MB1.xds.umail.utah.edu> Hello, I was able to create the account and get the API key. Thank you, Mihai Virtosu From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Monday, January 29, 2018 1:23 PM To: Mihai Virtosu Cc: support at bioontology.org Subject: Re: [bioontology-support] New API key Hello Mihai, Apologies - we had a brief outage today. The page you refer to below is up. Are you still experiencing issues? Kind regards, Jennifer On Jan 29, 2018, at 12:21 PM, Mihai Virtosu > wrote: Hello, I am trying to create a new account to get a new API key but the following website does not work: http://bioportal.bioontology.org/accounts/new Could you please look into it? Thank you, Mihai Virtosu University of Utah _______________________________________________ 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 Jan 31 12:11:11 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 31 Jan 2018 20:11:11 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Joao Sequeira In-Reply-To: <5a71a5555d688_1a423f86dde6b588576b5@ncbo-prd-app-08.stanford.edu.mail> References: <5a71a5555d688_1a423f86dde6b588576b5@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <55DC11A6-27A6-44B2-B7D5-8F0E115BDC30@stanford.edu> Hello Joao, On Jan 31, 2018, at 6:15 AM, support at bioontology.org wrote: We are interested in using your API to access MedDRA dictionary and I would like to confirm, since this tool will be provided to our clients, if we can distribute it with a single API Key, in the certainty that each client has his own MedDRA MSSO commercial license. BioPortal throttles (and, if necessary, restricts access) based on API keys. If any of your clients, or all of them together, end up exceeding the access limits or violating BioPortal policies, all of the clients will be affected by any restrictions that result. Please feel free to contact our Technical Program Manager John Graybeal (cc?ed) directly about the best way to proceed to make sure the system continues to work as expected. Also, we could not find a way to check the current version of the dictionary via API (current version is 20.1 from September 2017), could you give us a hint? We import MedDRA into BioPortal roughly twice per year from UMLS distributions. We currently have the 2016AB distribution of UMLS ontologies imported. According to the UMLS documentation, their 2016AB release contained version MDR18_0 of MedDRA: Last year we got behind in doing these imports, though we?re actively trying to catch up at the moment. There are a couple of issues in our tracker for getting the 2017 AA and AB releases into the BioPortal: https://github.com/ncbo/bioportal-project/issues/60 https://github.com/ncbo/bioportal-project/issues/28 You could look there to follow our progress, or check in with us directly via the support list. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 31 15:05:44 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 31 Jan 2018 23:05:44 +0000 Subject: [bioontology-support] Fwd: search by id in a subtree References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu> Message-ID: <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu> Hi, I am using a local version of Appliance 2.5 RC3 as well as UMLS2RDF script against UMLS2017AB database to generate and load SNOMED.ttl file (1.29Gb). However, upon submitting a new ontology and after few seconds I get this error message in the web UI: ?something went wrong?. Also, http://ontotoportal.admin report under issues section shows ?ontology has no submission?. Under /srv/ncbo/repository path no directory was created for SNOMED. Seems manually creating ?1? submission directory and copying SNOMED ttl into that directory doesn?t have any effect even with manual parsing per instruction. Is it possible to manually load large ttl files and create submissions? Scheduler.log or appliance.log doesn?t show any error either. I re-tried the submission with a compressed tar file (72 Mb) too. This time, http://ontotoportal.admin showed ERROR_RDF under Error Status field. Also, on admin page, the log link under URL field shows below messages. It seems manually unzipping the file and/or reprocessing it doesn?t have any effect either Is there a workaround for loading/parsing SNOMED (or similar large ontologies) into OntoPortal? Also, is it possible to access 4store directly in our local instance from a sparql endpoint similar to Bioportal website? Thanks! Sina I, [2018-01-28T11:19:17.181176 #3910] INFO -- : ["Starting to process http://data.bioontology.org/ontologies/SNOMED/submissions/1"] I, [2018-01-28T11:19:17.219473 #3910] INFO -- : ["Starting to process SNOMED/submissions/1"] I, [2018-01-28T11:19:17.338663 #3910] INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"] E, [2018-01-28T11:19:17.338923 #3910] ERROR -- : ["ArgumentError: invalid byte sequence in UTF-8\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:398:in `block in generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `foreach'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:414:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:903:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:228:in `block (3 levels) in
'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in trigger_job'"] -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Jan 31 16:50:03 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 1 Feb 2018 00:50:03 +0000 Subject: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal In-Reply-To: <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu> References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu> <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu> Message-ID: <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu> Sina, (Changing the topic line to focus on the SPARQL question that I'm addressing here.) The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site". On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org. There are a few complexities before the queries get to the backend service, which is a separate 4store service from the one used to serve BioPortal itself. (Which is why the backend data is not the same.) We could tell you about all those details and provide code to make it all work, but you may not need things to be configured that way on your system. It is certainly possible to configure the primary backend store (4store) that your Virtual Appliance uses, so that it can accept queries from anywhere. If you are running a public service, you might not want to do that, because it is difficult to protect your back end from queries that can take the system down. (That's why we don't do it that way on BioPortal.) I think that Clement Jonquet may have found a way to do it that doesn't have many problems, for his AgroPortal installation. He reads this list and will likely weigh in, but if not we can make sure he gets this question too. I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers! John On Jan 31, 2018, at 3:05 PM, Michael Dorf > wrote: Hi, I am using a local version of Appliance 2.5 RC3 as well as UMLS2RDF script against UMLS2017AB database to generate and load SNOMED.ttl file (1.29Gb). However, upon submitting a new ontology and after few seconds I get this error message in the web UI: ?something went wrong?. Also, http://ontotoportal.admin report under issues section shows ?ontology has no submission?. Under /srv/ncbo/repository path no directory was created for SNOMED. Seems manually creating ?1? submission directory and copying SNOMED ttl into that directory doesn?t have any effect even with manual parsing per instruction. Is it possible to manually load large ttl files and create submissions? Scheduler.log or appliance.log doesn?t show any error either. I re-tried the submission with a compressed tar file (72 Mb) too. This time, http://ontotoportal.admin showed ERROR_RDF under Error Status field. Also, on admin page, the log link under URL field shows below messages. It seems manually unzipping the file and/or reprocessing it doesn?t have any effect either Is there a workaround for loading/parsing SNOMED (or similar large ontologies) into OntoPortal? Also, is it possible to access 4store directly in our local instance from a sparql endpoint similar to Bioportal website? Thanks! Sina I, [2018-01-28T11:19:17.181176 #3910] INFO -- : ["Starting to process http://data.bioontology.org/ontologies/SNOMED/submissions/1"] I, [2018-01-28T11:19:17.219473 #3910] INFO -- : ["Starting to process SNOMED/submissions/1"] I, [2018-01-28T11:19:17.338663 #3910] INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"] E, [2018-01-28T11:19:17.338923 #3910] ERROR -- : ["ArgumentError: invalid byte sequence in UTF-8\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:398:in `block in generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `foreach'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:414:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:903:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:228:in `block (3 levels) in
'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in trigger_job'"] _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: