From vendetti at stanford.edu Thu May 2 16:43:52 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 2 May 2019 23:43:52 +0000 Subject: [bioontology-support] [External] [BioPortal] Feedback from fergusonch In-Reply-To: <5B767879-2D31-4C91-AFA7-87D1E7E1D068@bah.com> References: <697544E5-A874-4001-AEA4-F6EBC477E9F5@bah.com> <5B767879-2D31-4C91-AFA7-87D1E7E1D068@bah.com> Message-ID: <1800B114-4233-461E-AF81-85FFBBA7D5B6@stanford.edu> Hi Chris, On Apr 29, 2019, at 1:26 PM, Ferguson, Christopher [USA] > wrote: Hi Jennifer, Thank you again. I did try resubmitting an OWL file into another test and had it load fine. I?m not sure what the problem was with my earliest attempted submissions, but I?ll be sure to convert from TTL to OWL prior to submission in the future. One thing I did notice though is that the annotation properties are duplicated (PATEpiTest Ontology), is that because I provided the URIs for the respective properties during the submission process? (i.e. I entered http://www.w3.org/2000/01/rdf-schema#label for Preferred Label and now see ?Preferred Name? and ?Label? in the Class viewer) There?s a post in our mailing list archive that I believe answers your question: http://ncbo-support.2288202.n4.nabble.com/Re-bioontology-support-SNOMED-ttl-file-tp4656300.html If you still have questions after looking it over, feel free to follow up with us. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon May 6 16:54:21 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 6 May 2019 23:54:21 +0000 Subject: [bioontology-support] Help Loading my ontology to the In-Reply-To: <9DFB6B02-2E58-4B0C-97AF-34FD28155CF0@stanford.edu> References: <55ACAE58-864B-4D50-8DC3-2D074881F521@stanford.edu> <9DFB6B02-2E58-4B0C-97AF-34FD28155CF0@stanford.edu> Message-ID: <3012DC59-EE21-4C76-878B-E6113879475B@stanford.edu> Hi Dan, As requested, I?ve converted NEO from a view of SNOMEDCT into a standalone ontology. The ontology has been re-processed and is now available for viewing: http://bioportal.bioontology.org/ontologies/NEO Please let us know if you require further assistance. Thanks, Michael On May 3, 2019, at 4:46 PM, Jennifer Leigh Vendetti > wrote: Hello Dan, Apologies for the delayed response. We?ve been in the process of importing a large number of UMLS ontologies into our system, which has required us to hold off on making changes to existing ontologies. I?m out of the office next week, but my colleague Michael has kindly offered to make the modification you requested below. I?ve entered an issue in our tracker to that effect: https://github.com/ncbo/bioportal-project/issues/116 Best regards, Jennifer On Apr 30, 2019, at 3:52 PM, Daniel Hier > wrote: Thank you again. I pasted the definition into Web Protege. I am pretty far along in rebuilding my ontology. I feel I know more now and am using Protege correctly. My prior attempts were a mix of different IRIs. Now everything looks consistent and professional. Is there any way for me to change my NEO ontology from "ontology view" back to "ontology"? Thanks again for all of your expert help! I will try to get a descriptive paper published in NEUROINFORMATICS as a data project and I will cite the BIOPORTAL as the repository. Dan On Mon, Apr 29, 2019 at 6:20 PM Jennifer Leigh Vendetti > wrote: Hello Dan, On Apr 28, 2019, at 7:14 AM, Daniel Hier > wrote: Thank you for helping me with my ontology NEO (neurological examination ontology). I have decided to rebuild it from scratch in PROTEGE and my partial version with 400 classes and it will now load properly. I will finish it with 650 classes. I particularly like the download feature of CSV file--that is a very nice feature that I will use when I post-process my file. Thanks again for your help. There must have been subtle errors in my original ontology. I am about 60% done rebuilding it. OK - thanks for letting us know that you?ve made additional uploads. Nonetheless, I did want to track down why your previous submissions were failing. The problem occurred fairly deep in our stack in some code where we use a 3rd party library to load / parse ontologies. Normally this library produces helpful error messages, but in this particular case, we weren?t getting any indication of failure, so it took some digging around and testing before i was able to isolate the issue. It turns out there?s a syntax error on line 1033 of your ontology (shown in bold below): <apraxic gait><Bruns apraxia><magnetic gait><frontal gait>| |30767006| C1510417 gait apraxia ? where a skos:definition has an opening tag, but no closing tag. I added an end tag, i.e.: apraxia for walking, accompanied by inability to make skilled walking movements with the legs.gait apraxia; unexplained by weakness, sensory loss, or incoordination (n.d.) Farlex Partner Medical Dictionary. (2012). [Retrieved April 21 2016 from http://medical-dictionary.thefreedictionary.com/gait+apraxia] ... and tested uploading this fixed version of your ontology in our staging environment, and it succeeded. I?m wondering - did you hand edit your ontology file before you submitted it to BioPortal? Or, did you simply upload the file that you exported from WebProtege? If it?s the latter, I recommend notifying the Protege team that your ontology was exported without an end tag for that particular skos definition. Kind regards, Jennifer -- Daniel B Hier MD -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon May 6 20:09:31 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 7 May 2019 03:09:31 +0000 Subject: [bioontology-support] I've uploaded an ontology (Adherence and Integrated Care in Spanish) to Bioportal but I can't retrieve the classes to visualize them. In-Reply-To: <584AAA93-86B3-4AD9-9F66-96FF41003FC1@juntadeandalucia.es> References: <0B60ABDC-5519-46B9-B8EA-4D62BC460037@juntadeandalucia.es> <86DCB185-15E5-4179-9354-58D325A1B820@stanford.edu> <584AAA93-86B3-4AD9-9F66-96FF41003FC1@juntadeandalucia.es> Message-ID: <136EB984-365F-4D5E-B9B4-E902A2598B1E@stanford.edu> Hi Carlos, Your ontology has been re-processed and is now available at: http://bioportal.bioontology.org/ontologies/ADHER_INTCARE_SP?p=classes Let us know if you run into any other issues. Thanks, Michael On Apr 29, 2019, at 10:19 PM, Carlos Luis Parra Calder?n > wrote: Hi Jennifer. Ok. We wait for your solution. Thanks. Carlos. Carlos Luis Parra Calder?n Jefe de Secci?n de Innovaci?n Tecnol?gica Hospital Universitario Virgen del Roc?o Servicio Andaluz de Salud Consejer?a de Salud Avda. Manuel Siurot S/N - 41013 Sevilla Tel: +34 955 01 36 62 - (31 36 62) M?vil: +34 697 95 48 64 - (75 48 64) www.huvr.es carlos.parra.sspa at juntadeandalucia.es skype: carlos.luis.parra Director del Grupo de Investigaci?n e Innovaci?n en Inform?tica Biom?dica, Ingenier?a biom?dica y Econom?a de la Salud. Instituto de Biomedicina de Sevilla www.ibis-sevilla.es/ Asistente Honorario. Escuela T?cnica Superior de Ingenier?a Inform?tica. Universidad de Sevilla. _________________________________________________________________________________________________ Head of Technological Innovation Virgen del Roc?o University Hospital Head of Research and Innovation in Biomedical Informatics, Biomedical Engineering & Health Economy, Institute of Biomedicine of Seville Honorary assistant School Computer Science University of Seville ________________________________________ El 30 abr 2019, a las 1:33, Jennifer Leigh Vendetti > escribi?: Hello Carlos, Yes, you?re correct. We?re going to look at your ontology and try to figure out why it?s not loading in BioPortal. We should be able to start investigating tomorrow. Kind regards, Jennifer On Apr 29, 2019, at 3:20 PM, Carlos Luis Parra Calder?n > wrote: Dear Jennifer. Thank you very much for your support and commitment!! I understand that you are going to try to diagnose and try to solve the problem? All the best. Carlos. Carlos Luis Parra Calder?n Jefe de Secci?n de Innovaci?n Tecnol?gica Hospital Universitario Virgen del Roc?o Servicio Andaluz de Salud Consejer?a de Salud Avda. Manuel Siurot S/N - 41013 Sevilla Tel: +34 955 01 36 62 - (31 36 62) M?vil: +34 697 95 48 64 - (75 48 64) www.huvr.es carlos.parra.sspa at juntadeandalucia.es skype: carlos.luis.parra Director del Grupo de Investigaci?n e Innovaci?n en Inform?tica Biom?dica, Ingenier?a biom?dica y Econom?a de la Salud. Instituto de Biomedicina de Sevilla www.ibis-sevilla.es/ Asistente Honorario. Escuela T?cnica Superior de Ingenier?a Inform?tica. Universidad de Sevilla. _________________________________________________________________________________________________ Head of Technological Innovation Virgen del Roc?o University Hospital Head of Research and Innovation in Biomedical Informatics, Biomedical Engineering & Health Economy, Institute of Biomedicine of Seville Honorary assistant School Computer Science University of Seville ________________________________________ El 29 abr 2019, a las 17:55, Jennifer Leigh Vendetti > escribi?: Apologies that you?re having difficulty loading your ontology in BioPortal. I?ve entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/112 ? so that we can have a look. _______________________________________________ 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 shyamanm.jayasundara at student.montana.edu Tue May 7 06:21:18 2019 From: shyamanm.jayasundara at student.montana.edu (Jayasundara, Shyaman) Date: Tue, 7 May 2019 13:21:18 +0000 Subject: [bioontology-support] Requesting NCBO - VMWare Virtual Appliance Message-ID: Hello NCBO support, I am a research student at Montana State University and I'm trying to use NCBO ontology recommender scores for a project. Since I am retrieving scores for a large abstract database, it consumes a lot of time. Therefore I want to install this locally. The project is related to Research Domain Criteria (RDoC) and research articles classification according to RDoC construct categories. Therefore I hope to gain access to the VMWare Virtual Appliance. Sincerely, Shyaman -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 8 06:15:18 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 08 May 2019 06:15:18 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Vaibhav Message-ID: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From filipowj at tchpc.tcd.ie Thu May 9 04:29:01 2019 From: filipowj at tchpc.tcd.ie (filipowj at tchpc.tcd.ie) Date: Thu, 09 May 2019 11:29:01 +0000 Subject: [bioontology-support] OWL Ontology Message-ID: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie> Hi there, I work for Trinity College Dublin and looking to submit new ontology to the BioPortal. I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal. I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value. So I add them as annotation to the class in protege. Once .owl file is submitted to BioPortal I can see them as new properties on Details Section but when I use API Get call they're not visible like they were never parsed. Here is the call: http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey (http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=ce36656e-7615-400a-ac5c-2f1ea4b39908) cui and notation are included but there are not showing up. My ontology is created with Protege, please find attached the screenshots. I'd appreciate your suggestions. Best Regards, Juliusz Filipowski -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-05-09 at 12.26.40 (2).png Type: image/png Size: 340785 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-05-09 at 12.26.33 (2).png Type: image/png Size: 243371 bytes Desc: not available URL: From mdorf at stanford.edu Thu May 9 13:48:08 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 9 May 2019 20:48:08 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Vaibhav In-Reply-To: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail> References: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9366E929-182C-4072-9178-01ADCFDB6D5B@stanford.edu> Hi Vaibhav, Thank you for contacting us. I?ve tried the links you sent, and they all resolve fine on my end. Does the problem still exist on yours? We?ve been working on a fresh import of UMLS ontologies from the National Library of Medicine over the last few days. Our work may have caused a brief downtime that you?ve experienced. Please let us know if this is still an issue. Thanks, Michael On May 8, 2019, at 6:15 AM, support at bioontology.org wrote: Name: Vaibhav Email: vaibhav.joy at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F175050003%26jump_to_nav%3Dtrue Feedback: This API is return error message "The input class id '175050003' is not a valid IRI". http://data.bioontology.org/ontologies/SNOMEDCT/classes/175050003/children Also, it is not showing on the website for the following URL http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=175050003 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu May 9 14:00:49 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 9 May 2019 21:00:49 +0000 Subject: [bioontology-support] OWL Ontology In-Reply-To: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie> References: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie> Message-ID: Hi Juliusz, Thank you for contacting us. The ontology TESTJF that your call below is referring to isn?t the same as the one you are referring to in your screenshots. TESTJF contains only two classes and none of the annotations that you mentioned (see screenshots). Is it possible that you uploaded a wrong ontology? Michael [cid:DD280B99-1FA4-42F9-BA65-EEF63DEFBC4D at stanford.edu] [cid:4B80A9F1-3790-422E-81DD-F3486F24A077 at stanford.edu] On May 9, 2019, at 4:29 AM, filipowj at tchpc.tcd.ie wrote: Hi there, I work for Trinity College Dublin and looking to submit new ontology to the BioPortal. I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal. I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value. So I add them as annotation to the class in protege. Once .owl file is submitted to BioPortal I can see them as new properties on Details Section but when I use API Get call they're not visible like they were never parsed. Here is the call: http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey cui and notation are included but there are not showing up. My ontology is created with Protege, please find attached the screenshots. I'd appreciate your suggestions. Best Regards, Juliusz Filipowski _______________________________________________ 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: PastedGraphic-1.png Type: image/png Size: 239755 bytes Desc: PastedGraphic-1.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-2.png Type: image/png Size: 123466 bytes Desc: PastedGraphic-2.png URL: From hpan at rti.org Thu May 9 14:29:13 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Thu, 9 May 2019 21:29:13 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> , <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> Message-ID: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf Cc: Jennifer Leigh Vendetti ; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu May 9 16:52:13 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 9 May 2019 23:52:13 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> Message-ID: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Thu May 9 17:29:37 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 10 May 2019 00:29:37 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Thank you, Michael! I apologize for mixing up the formats. Yes, it makes sense. Best regards, Helen From: Michael Dorf Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti ; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Fri May 10 04:25:19 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 10 May 2019 11:25:19 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti ; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri May 10 11:50:54 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 10 May 2019 18:50:54 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Fri May 10 11:54:38 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 10 May 2019 18:54:38 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: It works on my end as well! I appreciate your help, Michael! Have a great weekend! Helen From: Michael Dorf Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti ; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From hpan at rti.org Fri May 10 13:41:42 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 10 May 2019 20:41:42 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Hi Michael, Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing? I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload? Thank you for your help! Helen From: Michael Dorf Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti ; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri May 10 13:59:44 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 10 May 2019 20:59:44 +0000 Subject: [bioontology-support] OWL Ontology In-Reply-To: <5dafd28c86c39aa8523d807b8820e2c8@tchpc.tcd.ie> References: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie> <5dafd28c86c39aa8523d807b8820e2c8@tchpc.tcd.ie> Message-ID: <3BD73393-5010-4CE1-B431-4CD0EA154516@stanford.edu> Hi Juliusz, Thanks for getting back to us. Before I proceed with my specific comments on your ontology, please note that the BioPortal support is mainly focused on issues related to using the BioPortal system as well as the BioPortal REST APIs. For questions related to ontology development, I would suggest posting your query on the Protege support list [1], which tends to be monitored by a larger community of ontology experts. My background is in software development, so I?m not very good at recommending ways of defining your ontology structure. That said, I?ve compared the class in your ontology that you were referring to, ?Maxillary sinus?, with a couple of classes from other UMLS ontologies that define the properties ?notation? and ?cui?. The difference appears to be in the namespace that is used for the ?notation?: Your class: http://data.bioontology.org/ontologies/ICD-O-3-T/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCDN-O-3-T%2FC31.0?display=all http://purl.bioontology.org/ontology/CDN-O-3-T/notation": [ * "C001" ] SNOMEDCT: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006?display=all http://www.w3.org/2004/02/skos/core#notation": [ * "410607006" ] ICD10: http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FK70-K77.9?display=all http://www.w3.org/2004/02/skos/core#notation": [ * "K70-K77.9? ] Try using the namespace http://www.w3.org/2004/02/skos/core for your ?notation? property. Once in place, we should be able to recognize it and process it correctly for our search index. As far as the property ?cui?, it doesn?t appear to exist in any of the classes that you referred to in your ontology, so I can?t comment on whether it?s defined properly. Thanks, Michael [1] https://protege.stanford.edu/support.php On May 10, 2019, at 1:26 AM, filipowj at tchpc.tcd.ie wrote: Hi Michael, Many thanks for your email. I'm sorry for confusion there I used TESTJF for testing and tried uploading different versions. Please take a look at my correct ontology: ICD-O-3-T and screenshots attached I've added notation through the annotations to class Lip and it's visible in the description but via API call it is attached to properties and not to an actual attribute? In an essence I'm not sure how to add attributes: notation and cui. I appreciate your help. Juliusz Filipowski May 9, 2019 10:45 PM, "Michael Dorf" > wrote: Hi Juliusz, Thank you for contacting us. The ontology TESTJF that your call below is referring to isn?t the same as the one you are referring to in your screenshots. TESTJF contains only two classes and none of the annotations that you mentioned (see screenshots). Is it possible that you uploaded a wrong ontology? Michael On May 9, 2019, at 4:29 AM, filipowj at tchpc.tcd.ie wrote: Hi there, I work for Trinity College Dublin and looking to submit new ontology to the BioPortal. I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal. I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value. So I add them as annotation to the class in protege. Once .owl file is submitted to BioPortal I can see them as new properties on Details Section but when I use API Get call they're not visible like they were never parsed. Here is the call: http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey cui and notation are included but there are not showing up. My ontology is created with Protege, please find attached the screenshots. I'd appreciate your suggestions. Best Regards, Juliusz Filipowski _______________________________________________ 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 May 10 14:59:51 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Fri, 10 May 2019 21:59:51 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes Thanks, Helen From: Pan, Huaqin (Helen) Sent: Friday, May 10, 2019 4:42 PM To: Michael Dorf Cc: Jennifer Leigh Vendetti ; support at bioontology.org; Pan, Huaqin (Helen) Subject: RE: [bioontology-support] metadata treeview error message Hi Michael, Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing? I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload? Thank you for your help! Helen From: Michael Dorf > Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri May 10 16:53:55 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 10 May 2019 23:53:55 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Helen, I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing? It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?). However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache. John On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) > wrote: Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes Thanks, Helen From: Pan, Huaqin (Helen) > Sent: Friday, May 10, 2019 4:42 PM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Michael, Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing? I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload? Thank you for your help! Helen From: Michael Dorf > Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ 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 mdorf at stanford.edu Fri May 10 17:20:12 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Sat, 11 May 2019 00:20:12 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Hi Helen, Both ontologies appear properly on my end as well. The LungMap ontology now has a single root class, ?respiratory system?, hope that?s as intended. As John said, it does take a bit of time for the results of the processing to propagate through our various architecture layers. Feel free to contact us if the issue still persists. Thanks, Michael On May 10, 2019, at 4:53 PM, John Graybeal > wrote: Helen, I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing? It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?). However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache. John On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) > wrote: Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes Thanks, Helen From: Pan, Huaqin (Helen) > Sent: Friday, May 10, 2019 4:42 PM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Michael, Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing? I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload? Thank you for your help! Helen From: Michael Dorf > Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ 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 hpan at rti.org Sat May 11 05:46:47 2019 From: hpan at rti.org (Pan, Huaqin (Helen)) Date: Sat, 11 May 2019 12:46:47 +0000 Subject: [bioontology-support] metadata treeview error message In-Reply-To: References: <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu> <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu> <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu> Message-ID: Hi John and Michael, I just did another upload of mouse obo file, and indeed it was able to reload successfully. I will try clear cache if I run into any errors. Yes, the single root class is what I wanted. Thanks again for your help! Best regards, Helen From: Michael Dorf Sent: Friday, May 10, 2019 8:20 PM To: Pan, Huaqin (Helen) Cc: support at bioontology.org; John Graybeal Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Both ontologies appear properly on my end as well. The LungMap ontology now has a single root class, ?respiratory system?, hope that?s as intended. As John said, it does take a bit of time for the results of the processing to propagate through our various architecture layers. Feel free to contact us if the issue still persists. Thanks, Michael On May 10, 2019, at 4:53 PM, John Graybeal > wrote: Helen, I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing? It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?). However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache. John On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) > wrote: Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes Thanks, Helen From: Pan, Huaqin (Helen) > Sent: Friday, May 10, 2019 4:42 PM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Michael, Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing? I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload? Thank you for your help! Helen From: Michael Dorf > Sent: Friday, May 10, 2019 2:51 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you. Thanks, Michael On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) > wrote: Hi Michael, The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Thursday, May 9, 2019 7:52 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results: http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at: https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes Thanks, Michael On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look? Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine. Many thanks, Helen From: Pan, Huaqin (Helen) > Sent: Saturday, April 27, 2019 1:59 AM To: Michael Dorf > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Michael, It?s working now! Thank you! Helen Get Outlook for iOS ________________________________ From: Michael Dorf > Sent: Friday, April 26, 2019 11:00 PM To: Pan, Huaqin (Helen) Cc: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end? Thanks! Michael On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) > wrote: Hi Michael, Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thank you! Helen From: Michael Dorf > Sent: Wednesday, April 10, 2019 6:14 PM To: Pan, Huaqin (Helen) > Cc: Jennifer Leigh Vendetti >; support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal. https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes Let us know if you run into further issues. Thanks! Michael On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ? https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2 Thanks a lot! Helen From: Pan, Huaqin (Helen) > Sent: Monday, March 18, 2019 8:24 AM To: Jennifer Leigh Vendetti > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: RE: [bioontology-support] metadata treeview error message Hi Jennifer, Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution. I appreciate your help! Helen From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 6:31 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, OK - thank you for the clarification. The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language: 1). For OWL ontologies we use ?subClassOf". 2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?. 3). For SKOS ontologies we use ?broader?. There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies. As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2]. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php#desktop-protege [2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) > wrote: Hi Jennifer, I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view. I am available for a phone call or web conference if that?s helpful. I appreciate your help! Helen 919-434-4665 From: Jennifer Leigh Vendetti > Sent: Friday, March 15, 2019 2:56 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] metadata treeview error message Hi Helen, Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree? I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me. Kind regards, Jennifer On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) > wrote: Hi John, I think this question is for your team ? I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both ?subclass? and ?part_of?. http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary Thank you! Helen From: John Graybeal > Sent: Thursday, March 14, 2019 12:59 PM To: Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message Just the ontologies ones. Everything about your BioPortal experience still comes to us! Best wishes. john On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) > wrote: Thanks, John! I will send questions to protege-user at lists.stanford.edu moving forward. Best regards, Helen From: John Graybeal > Sent: Thursday, March 14, 2019 2:10 AM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org; Pan, Huaqin (Helen) > Subject: Re: [bioontology-support] metadata treeview error message EXTERNAL: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Helen, This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu. The people on that list should be able to help you. John ________________________________ From: Pan, Huaqin (Helen) > Sent: Wednesday, March 13, 2019 20:40 To: John Graybeal Cc: support at bioontology.org; Pan, Huaqin (Helen) Subject: [bioontology-support] metadata treeview error message Hi John, I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue? Thank you for your help! Helen From: John Graybeal > Sent: Saturday, March 24, 2018 5:51 PM To: Pan, Huaqin (Helen) > Cc: support at bioontology.org Subject: Re: [bioontology-support] problem with ontology submission - please help! Helen, I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages. Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology. I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts. When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues. Thanks, John [1] Results of submission: Thank you for submitting your ontology to BioPortal. We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology. When your ontology is ready for viewing, it will be available here: http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1 If you have any questions or problems, please email the BioPortal support team at support at bioontology.org On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) > wrote: Hello, Hello, I tried several times to submit an ontology: initial submission always got Another try always got It repeats that when I tried different name/acronyms on different web browsers. Would you please help me create the ontology? Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung Acronym: LUNGMAP-HUMAN Public Anatomy Owl is attached. Thanks! Helen _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ 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 support at bioontology.org Fri May 10 11:10:41 2019 From: support at bioontology.org (support at bioontology.org) Date: Fri, 10 May 2019 11:10:41 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Joab Message-ID: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From c.cruschi at elif.it Mon May 13 03:16:20 2019 From: c.cruschi at elif.it (Claudio Cruschi) Date: Mon, 13 May 2019 12:16:20 +0200 Subject: [bioontology-support] technical support for bioportal_web_UI Message-ID: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it> Hi, I'm writing because I have some problems with the web ui bioportal rails application (the latest github version of the master branch) in the virtual appliance. I copied the web app to the rails/releases/ directory, I created the "current" symbolic link to this folder, I created all the other symbolic links to the shared folder and restarted all services with the bprestart command. But when I open the browser to the IP address of the appliance, the following error is returned to me: "We're sorry, but something went wrong. Web application could not be started by the Phusion Passenger application server." Could you give me a step by step procedures to deploy and run bioportal web ui in the virtual machine? Regards Claudio C. --- Questa e-mail ? stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.skrenchuk at stanford.edu Mon May 13 12:26:31 2019 From: alex.skrenchuk at stanford.edu (Alex Skrenchuk) Date: Mon, 13 May 2019 19:26:31 +0000 Subject: [bioontology-support] technical support for bioportal_web_UI In-Reply-To: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it> References: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it> Message-ID: Hi Claudio Ontoportal Virtual Appliance v2.5 is not configured appropriately to run latest version of bioportal web ui. We will be releasing a new version of the appliance that runs latest version of Bioportal stack in the next few weeks. -Alex From: bioontology-support on behalf of Claudio Cruschi Date: Monday, May 13, 2019 at 9:21 AM To: "support at bioontology.org" Subject: [bioontology-support] technical support for bioportal_web_UI Hi, I'm writing because I have some problems with the web ui bioportal rails application (the latest github version of the master branch) in the virtual appliance. I copied the web app to the rails/releases/ directory, I created the "current" symbolic link to this folder, I created all the other symbolic links to the shared folder and restarted all services with the bprestart command. But when I open the browser to the IP address of the appliance, the following error is returned to me: "We're sorry, but something went wrong. Web application could not be started by the Phusion Passenger application server." Could you give me a step by step procedures to deploy and run bioportal web ui in the virtual machine? Regards Claudio C. [Image removed by sender.] Mail priva di virus. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonquet at lirmm.fr Mon May 13 14:39:00 2019 From: jonquet at lirmm.fr (Clement Jonquet) Date: Mon, 13 May 2019 14:39:00 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Joab In-Reply-To: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail> References: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Dear Chen, Could you specify your question a bit more? 1. Are you interested in ontologies in other languages in BioPortal? 2. Somewhere else? 3. Interested in ontologies that have been explicitly translated or in multilingual ontologies (providing labels in different languages)? 4. Are you interested in mappings btw ontologies in different languages? 5. Other ;) Best Clement Jonquet > Le 10 mai 2019 ? 11:10, support at bioontology.org a ?crit : > > Name: Joab > > Email: chen.joab at gmail.com > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Fmappings > > > Feedback: > > Hi, > > Are there ontologies that are translated and not in english? ie. French, German etc. > > > _______________________________________________ > 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 Thu May 16 06:31:20 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 16 May 2019 06:31:20 -0700 Subject: [bioontology-support] [BioPortal] Feedback from William Van Woensel Message-ID: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu May 16 08:09:41 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 16 May 2019 15:09:41 +0000 Subject: [bioontology-support] [BioPortal] Feedback from William Van Woensel In-Reply-To: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail> References: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi William, Could you please include a URL for one of the pages where you see this error? The BioPortal application does use some older 3rd party JavaScript plug-ins that we haven?t had the resources to look into replacing yet. It?s unclear to me if you?re referring to one of those pages. Kind regards, Jennifer On May 16, 2019, at 6:31 AM, support at bioontology.org wrote: Name: William Van Woensel Email: william.van.woensel at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDOID%3Fp%3Dclasses%26conceptid%3Droot Feedback: Hi, It looks like there's an issue with loading JavaScript on the webpages - I'm seeing a lot of errors such as : "Blocked loading mixed active content ?http://code.jquery.com/.." This is due to the fact that you're website is hosted on HTTPS but it's trying to load resources from HTTP. It should be easy to fix this. Thanks, William _______________________________________________ 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 Thu May 16 13:37:12 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 16 May 2019 13:37:12 -0700 Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero Message-ID: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu May 16 16:21:25 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 16 May 2019 23:21:25 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero In-Reply-To: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu> Hi Sean, Due to CPT licensing restrictions, we?re not able to offer downloads of the ontology data in any format. I?m not sure I followed exactly what you?d like to do. We have a REST API that could help with efficiently retrieving preferred names, e.g.: [cid:B5292DF1-A834-4A8D-83EE-38F34574A6C4 at stanford.edu] The API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer On May 16, 2019, at 1:37 PM, support at bioontology.org wrote: Name: sean.guerrero Email: sean.guerrero at hoag.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F11056%26jump_to_nav%3Dtrue Feedback: Hello, I'm looking at the Current Procedural Terminology section under the "Classes" tab. I'm looking for a way to pull the Preferred Name of the CPT codes I am searching for. Is there an excel file that I can use to reference? -Sean _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-05-16 16.20.22.png Type: image/png Size: 125763 bytes Desc: Screenshot 2019-05-16 16.20.22.png URL: From Sean.Guerrero at Hoag.org Thu May 16 17:31:37 2019 From: Sean.Guerrero at Hoag.org (Guerrero, Sean) Date: Fri, 17 May 2019 00:31:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero In-Reply-To: <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu> References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu> Message-ID: Hi Jennifer, Thanks for the quick response! I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below: It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names? [cid:image001.png at 01D50C0D.35029ED0] 24546 24565 24566 24575 24579 24586 Sean A. Guerrero, MHA Manager of Business Intelligence, Strategic Analytics and Reporting Hoag Orthopedic Institute 949/727-5066 Sean.Guerrero at hoag.org | www.HoagOrthopedicInstitute.com [cid:image001.png at 01D27580.6E6F5760] From: Jennifer Leigh Vendetti Sent: Thursday, May 16, 2019 4:21 PM To: support at bioontology.org Cc: Guerrero, Sean Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from sean.guerrero Hi Sean, Due to CPT licensing restrictions, we?re not able to offer downloads of the ontology data in any format. I?m not sure I followed exactly what you?d like to do. We have a REST API that could help with efficiently retrieving preferred names, e.g.: [cid:image003.png at 01D50C0D.35029ED0] The API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer On May 16, 2019, at 1:37 PM, support at bioontology.org wrote: Name: sean.guerrero Email: sean.guerrero at hoag.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F11056%26jump_to_nav%3Dtrue Feedback: Hello, I'm looking at the Current Procedural Terminology section under the "Classes" tab. I'm looking for a way to pull the Preferred Name of the CPT codes I am searching for. Is there an excel file that I can use to reference? -Sean _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ---------------------------------------------------------------------- #NOTICE TO RECIPIENT: If you are not the intended recipient of this email, you are prohibited from sharing, copying, using or disclosing its contents. If you have received this email in error, please notify the sender immediately by reply email and permanently delete this email and any attachments without reading, forwarding or saving. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 69129 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 11155 bytes Desc: image002.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.png Type: image/png Size: 125763 bytes Desc: image003.png URL: From vendetti at stanford.edu Fri May 17 17:13:23 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 18 May 2019 00:13:23 +0000 Subject: [bioontology-support] [BioPortal] Feedback from William Van Woensel In-Reply-To: <004501d50cba$a3e630c0$ebb29240$@gmail.com> References: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail> <004501d50cba$a3e630c0$ebb29240$@gmail.com> Message-ID: <6296F66A-10E6-420B-AB0B-3EC6E3857DFE@stanford.edu> Hi William, On May 17, 2019, at 7:13 AM, William Van Woensel > wrote: See for instance: https://bioportal.bioontology.org/ontologies/DOID/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_4#visualization Thanks for the link. We?re aware of this occurrence. The mixed content errors are originating from biomixer [1] - a 3rd party application for visualizing ontologies that was developed by the University of Victoria and contributed to BioPortal. They no longer maintain the application, and as I mentioned below, we?ve so far lacked the resources to take over the code base. There are several issues with the software, which we track in the GitHub repository [2]. For the moment, if you want to use the software, you can change the protocol in the address bar of your browser to http and you?ll be able to see the visualizations. Apologies for the inconvenience. Kind regards, Jennifer [1] https://github.com/ncbo/biomixer [2] https://github.com/ncbo/biomixer/issues -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri May 17 17:39:38 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 18 May 2019 00:39:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero In-Reply-To: References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu> Message-ID: <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu> Hi Sean, The web-based BioPortal application doesn?t have a table that lists CPT codes and preferred names. We just display the ontology classes as a navigable tree structure. I?m not sure if using the REST API is a possibility for you. You can pass multiple terms to the search endpoint, e.g., the following URL uses all the CPT codes you listed below (see the q={?} portion): http://data.bioontology.org/search?q={24546%2024565%2024566%2024575%2024579%2024586}&ontologies=CPT&include=prefLabel&display_links=false&display_context=false If you enter that URL in a browser window, you can see a list of the preferred names for those codes. Screen shot below. FYI - you need an API key to use the REST API (instructions for getting one are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key). We also provide examples in a GitHub repository for using the API programmatically: https://github.com/ncbo/ncbo_rest_sample_code. It?s possible to write a short script that would retrieve this data. Hope that information helps. Kind regards, Jennifer [cid:A72B13FE-2EB4-4BAD-8159-77088307DAAA at stanford.edu] On May 16, 2019, at 5:31 PM, Guerrero, Sean > wrote: Hi Jennifer, Thanks for the quick response! I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below: It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names? 24546 24565 24566 24575 24579 24586 Sean A. Guerrero, MHA Manager of Business Intelligence, Strategic Analytics and Reporting Hoag Orthopedic Institute 949/727-5066 Sean.Guerrero at hoag.org | www.HoagOrthopedicInstitute.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-05-17 17.25.55.png Type: image/png Size: 280099 bytes Desc: Screenshot 2019-05-17 17.25.55.png URL: From Sean.Guerrero at Hoag.org Mon May 20 09:57:17 2019 From: Sean.Guerrero at Hoag.org (Guerrero, Sean) Date: Mon, 20 May 2019 16:57:17 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero In-Reply-To: <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu> References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail> <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu> <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu> Message-ID: This is perfect, Jennifer. Thank you so much! Sean A. Guerrero, MHA Manager of Business Intelligence, Strategic Analytics and Reporting Hoag Orthopedic Institute 949/727-5066 Sean.Guerrero at hoag.org | www.HoagOrthopedicInstitute.com [cid:image001.png at 01D27580.6E6F5760] From: Jennifer Leigh Vendetti Sent: Friday, May 17, 2019 5:40 PM To: Guerrero, Sean Cc: support at bioontology.org Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from sean.guerrero Hi Sean, The web-based BioPortal application doesn?t have a table that lists CPT codes and preferred names. We just display the ontology classes as a navigable tree structure. I?m not sure if using the REST API is a possibility for you. You can pass multiple terms to the search endpoint, e.g., the following URL uses all the CPT codes you listed below (see the q={?} portion): http://data.bioontology.org/search?q={24546%2024565%2024566%2024575%2024579%2024586}&ontologies=CPT&include=prefLabel&display_links=false&display_context=false If you enter that URL in a browser window, you can see a list of the preferred names for those codes. Screen shot below. FYI - you need an API key to use the REST API (instructions for getting one are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key). We also provide examples in a GitHub repository for using the API programmatically: https://github.com/ncbo/ncbo_rest_sample_code. It?s possible to write a short script that would retrieve this data. Hope that information helps. Kind regards, Jennifer [cid:image002.png at 01D50EF2.676A4570] On May 16, 2019, at 5:31 PM, Guerrero, Sean > wrote: Hi Jennifer, Thanks for the quick response! I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below: It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names? 24546 24565 24566 24575 24579 24586 Sean A. Guerrero, MHA Manager of Business Intelligence, Strategic Analytics and Reporting Hoag Orthopedic Institute 949/727-5066 Sean.Guerrero at hoag.org | www.HoagOrthopedicInstitute.com ---------------------------------------------------------------------- #NOTICE TO RECIPIENT: If you are not the intended recipient of this email, you are prohibited from sharing, copying, using or disclosing its contents. If you have received this email in error, please notify the sender immediately by reply email and permanently delete this email and any attachments without reading, forwarding or saving. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 11155 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 280099 bytes Desc: image002.png URL: From support at bioontology.org Thu May 23 08:51:03 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 23 May 2019 08:51:03 -0700 Subject: [bioontology-support] [BioPortal] Feedback from John Nguyen Message-ID: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From ias41 at cam.ac.uk Wed May 22 07:21:24 2019 From: ias41 at cam.ac.uk (Ines Smit) Date: Wed, 22 May 2019 15:21:24 +0100 Subject: [bioontology-support] getting 'classified as' information via API Message-ID: Hello BioPortal team, On the page of the MedDRA term 'Blood pressure Lowered' on the interface (https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10024982), there is the information 'Classified as: Blood pressure decreased'. This redirects to the term 'Blood pressure decreased'. This latter concept is the Preferred Term (PT) and the former is the Lower Level Term (LLT) in MedDRA. The PT has the ID 10005734. How can I get that relationship via the API? When I search the LLT (10024982) I get the concept but it doesn't include the ID or name of the PT (10005734). I'm using 'http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA' I would like to find the PT (Blood pressure decreased - 10005734) upon submitting the LLT (Blood pressure lowered - 10024982). I also tried the Annotate service with the hierarchy parameter but it loosk like the LLT>PT is not included as a level in the hierarchy, as it jumps straight from the LLT to the higher level terms. Thank you, Ines From jgraybeal at stanford.edu Thu May 23 19:59:15 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 May 2019 02:59:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from John Nguyen In-Reply-To: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail> References: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello John, With apologies, our widgets have an issue right now that we have not had time to troubleshoot. This is documented in the ticket https://github.com/ncbo/bioportal_web_ui/issues/79; I am adding your detailed information to that ticket. We have just a few urgent priorities which we need to complete, and we will have a look at this as soon as we can thereafter. John On May 23, 2019, at 8:51 AM, support at bioontology.org wrote: Name: John Nguyen Email: jnguyen at ipro.us Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dwidgets Feedback: Hi, I'm trying to implement the NCBO web widget form autocomplete for a company's project. I follow the directions on the wiki but ran this error in the javascript console. jQuery(...).bioportal_autocomplete is not a function. I went on the form_complete.js code and found on line 273 that it seems I have to include a script that I assumed you guys had called public/javascripts/JqueryPlugins/autocomplete/crossdomain_autocomplete.js I was wondering if this script was suppose to be included with the form_complete.js and if so I was wondering how I can access it? _______________________________________________ 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 Thu May 23 20:11:29 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 May 2019 03:11:29 +0000 Subject: [bioontology-support] getting 'classified as' information via API In-Reply-To: References: Message-ID: Hello Ines, I believe you can get what you want by adding "include=properties" to your query, as in http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA&include=properties This will include all the annotation properties, one of which is 'classified_as'. (You may wish to append ',notation' to the above so that you can see the concept for which the properties apply, when there is more than one concept returned by the search.) John On May 22, 2019, at 7:21 AM, Ines Smit > wrote: Hello BioPortal team, On the page of the MedDRA term 'Blood pressure Lowered' on the interface (https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10024982), there is the information 'Classified as: Blood pressure decreased'. This redirects to the term 'Blood pressure decreased'. This latter concept is the Preferred Term (PT) and the former is the Lower Level Term (LLT) in MedDRA. The PT has the ID 10005734. How can I get that relationship via the API? When I search the LLT (10024982) I get the concept but it doesn't include the ID or name of the PT (10005734). I'm using 'http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA' I would like to find the PT (Blood pressure decreased - 10005734) upon submitting the LLT (Blood pressure lowered - 10024982). I also tried the Annotate service with the hierarchy parameter but it loosk like the LLT>PT is not included as a level in the hierarchy, as it jumps straight from the LLT to the higher level terms. Thank you, Ines _______________________________________________ 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 support at bioontology.org Thu May 23 12:37:13 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 23 May 2019 12:37:13 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples Message-ID: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Sat May 25 04:45:36 2019 From: support at bioontology.org (support at bioontology.org) Date: Sat, 25 May 2019 04:45:36 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf Message-ID: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 27 21:52:59 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 28 May 2019 04:52:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples In-Reply-To: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail> References: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Jeff, Thank you for this report. We have not assessed this deeply enough to find out what is causing this problem, though I believe you are correct that the link for the property should go to p=properties. I created ticket https://github.com/ncbo/bioportal-project/issues/118 to track this problem; not sure how quickly we'll be able to address it. Please let us know if it will be impacting you significantly in the near term. John On May 23, 2019, at 12:37 PM, support at bioontology.org wrote: Name: Jeffrey Staples Email: jeffrey.staples at regeneron.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F Feedback: I am encountering an IRI issue that may because by improper URL forwarding for ontology properties. For example, LOINC property "member_of" as the IRI "http://purl.bioontology.org/ontology/LNC/member_of", which forwards to "http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=member_of". This page says "The page you are looking for wasn't found. Please try again." However, if I change the forwarded URL to "http://bioportal.bioontology.org/ontologies/LOINC?p=properties&conceptid=member_of" then I get what I believe to be the correct page. I don't if correcting the URL forwarding will fix IRI problem, but I thought you would want to know in the case that it does cause a problem for others. Best, Jeff _______________________________________________ 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 Mon May 27 22:22:09 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 28 May 2019 05:22:09 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf In-Reply-To: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail> References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu> Manuel, Thank you for this report. We have entered it as https://github.com/ncbo/bioportal-project/issues/119, and will be examining it in more detail soon. I note that all of the top-level classes in FMA have been defined as owl#Thing in BioPortal, so I believe this is a design decision made by the original developers of the ontology representation (that is, not a bug). If you would like to be more explicit about why you see it as wrong, that may help us assess the situation more clearly. Thank you for your time to share this with us. John On May 25, 2019, at 4:45 AM, support at bioontology.org wrote: Name: Manuel T. Schrempf Email: e0920136 at student.tuwien.ac.at Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFMA Feedback: Hello Bioporal, in your FMA 5.0.0 CSV file the following entry is wrong: http://purl.org/sig/ont/fma/fma85802,FMA attribute entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, since the parent "http://www.w3.org/2002/07/owl#Thing" does not contain a valid FMA id. I guess some other errors are in other anatomy datasets too, since my automatic parsing threw some errors. I will just exclude this anatomy from my parsing and hope future releases will have the errors fixed. Best, Manuel T. Schrempf _______________________________________________ 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 e0920136 at student.tuwien.ac.at Mon May 27 23:08:13 2019 From: e0920136 at student.tuwien.ac.at (Manuel T. Schrempf) Date: Tue, 28 May 2019 08:08:13 +0200 Subject: [bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf In-Reply-To: <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu> References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail> <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu> Message-ID: Hello John, just that owl#Thing has no ID as (FMAxxxxxx), I parse the FMA CSV with a bash script and remove reduntant information, meaning everything except the pure integer number, since the rest is not needed for a unique identifacion by an ID on a database. "http://www.w3.org/2002/07/owl#Thing" has no FMA ID, that is why I reported the issue. Best, Manuel On 28.05.19 07:22, John Graybeal wrote: > Manuel, > > Thank you for this report. We have entered it as > https://github.com/ncbo/bioportal-project/issues/119, and will be > examining it in more detail soon. > > I note that all of the top-level classes in FMA have been defined as > owl#Thing in BioPortal, so I believe this is a design decision made by > the original developers of the ontology representation (that is, not a > bug). If you would like to be more explicit about why you see it as > wrong, that may help us assess the situation more clearly. > > Thank you for your time to share this with us. > > John > >> On May 25, 2019, at 4:45 AM, support at bioontology.org >> wrote: >> >> Name: Manuel T. Schrempf >> >> Email: e0920136 at student.tuwien.ac.at >> >> >> Location: http%3A%2F%2Fbioportal.bioontology.org >> %2Fontologies%2FFMA >> >> >> *Feedback:* >> >> Hello Bioporal, >> in your FMA 5.0.0 CSV file the following entry is wrong: >> >> http://purl.org/sig/ont/fma/fma85802,FMA attribute >> entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >> >> since the parent "http://www.w3.org/2002/07/owl#Thing" does not >> contain a valid FMA id. I guess some other errors are in other >> anatomy datasets too, since my automatic parsing threw some errors. I >> will just exclude this anatomy from my parsing and hope future >> releases will have the errors fixed. >> >> Best, >> Manuel T. Schrempf >> >> >> _______________________________________________ >> 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 Tue May 28 10:32:23 2019 From: swt at stanford.edu (Samson Tu) Date: Tue, 28 May 2019 17:32:23 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf In-Reply-To: References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail> <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu> Message-ID: <99B7E352-06AE-4CA9-B108-A19D9D929DED@stanford.edu> Hi, By definition, every top-level entity in an OWL ontology has owl#Thing as a parent. It?s not a design decision on the part of FMA developers. It?s a design decision on the part of Bioportal CSV-output developers whether to generate an entry for this definitional parent-child relationship. Given that decision, users of the CSV output have to live with the consequences either way. With best regards, Samson > On May 27, 2019, at 11:08 PM, Manuel T. Schrempf wrote: > > Hello John, > > just that owl#Thing has no ID as (FMAxxxxxx), I parse the FMA CSV with a bash script and remove reduntant information, meaning everything except the pure integer number, since the rest is not needed for a unique identifacion by an ID on a database. "http://www.w3.org/2002/07/owl#Thing" has no FMA ID, that is why I reported the issue. > > Best, > Manuel > > On 28.05.19 07:22, John Graybeal wrote: >> Manuel, >> >> Thank you for this report. We have entered it as https://github.com/ncbo/bioportal-project/issues/119 , and will be examining it in more detail soon. >> >> I note that all of the top-level classes in FMA have been defined as owl#Thing in BioPortal, so I believe this is a design decision made by the original developers of the ontology representation (that is, not a bug). If you would like to be more explicit about why you see it as wrong, that may help us assess the situation more clearly. >> >> Thank you for your time to share this with us. >> >> John >> >>> On May 25, 2019, at 4:45 AM, support at bioontology.org wrote: >>> >>> Name: Manuel T. Schrempf >>> >>> Email: e0920136 at student.tuwien.ac.at >>> Location: http%3A%2F%2Fbioportal.bioontology.org %2Fontologies%2FFMA >>> >>> >>> Feedback: >>> >>> Hello Bioporal, >>> in your FMA 5.0.0 CSV file the following entry is wrong: >>> >>> http://purl.org/sig/ont/fma/fma85802,FMA attribute entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, >>> >>> since the parent "http://www.w3.org/2002/07/owl#Thing " does not contain a valid FMA id. I guess some other errors are in other anatomy datasets too, since my automatic parsing threw some errors. I will just exclude this anatomy from my parsing and hope future releases will have the errors fixed. >>> >>> Best, >>> Manuel T. Schrempf >>> >>> >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> ======================== >> John Graybeal >> Technical Program Manager >> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal >> Stanford Center for Biomedical Informatics Research >> 650-736-1632 >> >> > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1364 bytes Desc: not available URL: From julius.pasion at corteva.com Tue May 28 11:26:02 2019 From: julius.pasion at corteva.com (Pasion, Julius) Date: Tue, 28 May 2019 18:26:02 +0000 Subject: [bioontology-support] Homepage not working? Message-ID: Dear NCBO, I have set up an EC2 instance using AWS, and set up an Application Load Balancer to redirect HTTP80 to HTTPS443, and forward to the instance. However, my homepage is always returning an invalid response. When I try to access the homepage, the url is the same except ":80" is added to the end of the url. Even weirder is that if I type in other parts of the website like "domain.com/help" or "domain.com/search", I am able to see the website (although in some of those pages, I get errors from the website itself). Would you be able to help with this issue? I get a 500: internal server error whenever I try to access the homepage. My current pipeline is: * Route53 url is input by client * redirect to ALB * redirects 80 to 443 (w/SSL) * forwards to target group on port 80 * EC2 instance Any help is appreciated thank you! Sincerely, Julius * This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail,in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue May 28 19:23:07 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 29 May 2019 02:23:07 +0000 Subject: [bioontology-support] Homepage not working? In-Reply-To: References: Message-ID: Hi Julius, I'm sorry, but I think your question is simply about handling redirects, and is outside the scope of this list, which is specifically about BioPortal and OntoPortal software and virtual appliance issues. You may want to look in or post to a more general-purpose site like StackExchange or Quora? I will touch base with you offline to discuss possible Virtual Appliance related topics. John On May 28, 2019, at 11:26 AM, Pasion, Julius > wrote: Dear NCBO, I have set up an EC2 instance using AWS, and set up an Application Load Balancer to redirect HTTP80 to HTTPS443, and forward to the instance. However, my homepage is always returning an invalid response. When I try to access the homepage, the url is the same except ":80" is added to the end of the url. Even weirder is that if I type in other parts of the website like "domain.com/help" or "domain.com/search", I am able to see the website (although in some of those pages, I get errors from the website itself). Would you be able to help with this issue? I get a 500: internal server error whenever I try to access the homepage. My current pipeline is: ? Route53 url is input by client ? redirect to ALB ? redirects 80 to 443 (w/SSL) ? forwards to target group on port 80 ? EC2 instance Any help is appreciated thank you! Sincerely, Julius ? This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail,in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html_______________________________________________ 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 May 29 10:06:17 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 29 May 2019 17:06:17 +0000 Subject: [bioontology-support] commercial use license In-Reply-To: <6cc2617a-c86d-4bfc-98cc-5faf6f730e33@Spark> References: <0d8970a2-284d-4a0f-8a35-34aa7e540147@Spark> <6cc2617a-c86d-4bfc-98cc-5faf6f730e33@Spark> Message-ID: Hi Tom, Thanks for your question, I hope you don't mind my using it as an opportunity for a general answer. The majority of the ontologies in the BioPortal resource can be downloaded directly, either via the UI or API. Their license terms, if any, are specified in the metadata field shown in the summary page for the ontology. (There is even a tool to support populating your own OntoPortal instance with these ontologies, but I think that isn't your use case.) Some licenses?mostly for UMLS ontologies but also some others?do not allow us to make the download directly available. In those few cases where the UMLS license or a private agreement allows it, we will make an individual ontology available in response to a direct request, under the circumstances you describe. We recommend to users who want to work with UMLS content, and who have licenses to do so, build the necessary pipeline to convert the UMLS content to ontology form. Many users use the umls2rdf pipeline available in the NCBO repository (https://github.com/ncbo/umls2rdf); there are other similar software repositories in GitHub but I am not familiar with them. If you do not want to do that development itself, I expect you could contract with us to set up the software on your behalf. (Please note, I haven't thought that all the way through; contact me offline if you want to discuss it further.) I hope this synopsis helps you consider how you would like to proceed. Please don't hesitate to contact me if you wish to ask any other questions. John On May 29, 2019, at 4:41 AM, Tom Nygren > wrote: Hi there, We are a Cambridge (UK) based health insurance analytics company. We would be interested in incorporating some of your data for use in our analytics. If we meet the licensing requirements with the original providers of the ontology, do you offer any kind of commercial license that would allow us to use the ontologies themselves? Thanks and regards Tom --- Tom Nygren COO Kirontech +44 7771 268 566 ======================== 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 mdorf at stanford.edu Wed May 29 14:50:28 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 29 May 2019 21:50:28 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples In-Reply-To: References: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Jeff, Unfortunately, BioPortal UI doesn?t offer the same support for individual property URLs, as it does for ontology classes. You can access the entire property tree via the http://bioportal.bioontology.org/ontologies/LOINC?p=properties link, but the same link cannot be used to access individual properties. If you do require access to individual properties, your best bet is to use our REST services. Here are a couple of links that may be of note: http://data.bioontology.org/ontologies/LOINC/properties http://data.bioontology.org/ontologies/LOINC/properties/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2Fanalyzes?include=all Hope this helps! Michael On May 27, 2019, at 9:52 PM, John Graybeal > wrote: Jeff, Thank you for this report. We have not assessed this deeply enough to find out what is causing this problem, though I believe you are correct that the link for the property should go to p=properties. I created ticket https://github.com/ncbo/bioportal-project/issues/118 to track this problem; not sure how quickly we'll be able to address it. Please let us know if it will be impacting you significantly in the near term. John On May 23, 2019, at 12:37 PM, support at bioontology.org wrote: Name: Jeffrey Staples Email: jeffrey.staples at regeneron.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F Feedback: I am encountering an IRI issue that may because by improper URL forwarding for ontology properties. For example, LOINC property "member_of" as the IRI "http://purl.bioontology.org/ontology/LNC/member_of", which forwards to "http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=member_of". This page says "The page you are looking for wasn't found. Please try again." However, if I change the forwarded URL to "http://bioportal.bioontology.org/ontologies/LOINC?p=properties&conceptid=member_of" then I get what I believe to be the correct page. I don't if correcting the URL forwarding will fix IRI problem, but I thought you would want to know in the case that it does cause a problem for others. Best, Jeff _______________________________________________ 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... 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