From Steven.Tan-EXT at glpg.com Mon Feb 3 06:51:07 2020 From: Steven.Tan-EXT at glpg.com (Steven Tan-EXT) Date: Mon, 3 Feb 2020 14:51:07 +0000 Subject: [bioontology-support] Request: VMWare Virtual Appliance Message-ID: Dear, According to the wiki, I'd like to request to the 'VMWare Virtual Appliance'. Username: StevenTan Project Goals: Integrating use of ontologies in business processes Reason for preferring the local installation: Development/Testing Environment Kind regards, Steven Tan Business Analyst External Consultant contracted by Ordina [cid:image001.png at 01D5DAA9.BEDEFA70] Galapagos Generaal De Wittelaan L11 A3 2800 Mechelen Belgium T: +32 15 342 900 www.glpg.com -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 1587 bytes Desc: image001.png URL: From vendetti at stanford.edu Mon Feb 3 15:00:20 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 3 Feb 2020 23:00:20 +0000 Subject: [bioontology-support] Question about migrating ontologies from BioPortal to local VM In-Reply-To: References: Message-ID: <5719F11C-8E7A-4CAF-8578-6F7F9D609A63@stanford.edu> Hello Jahoon, On Jan 31, 2020, at 2:01 PM, Koo, Jahoon > wrote: I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided. It seems like some ontologies migrate with missing classes, and I don?t know what?s causing this error. I have migrated HIVO004, FB-CV, and CHEAR ontologies, but they are missing classes and have a comment saying ?No submissions available? on the web UI. For more information, I didn?t get any http errors while running the bioportal_ontologies_import.rb script with the ontologies mentioned above. Is there any way to fix this error? I?m wondering if you could tell us if your ontologies have fully parsed in your appliance? You can find instructions for how to do that on our wiki: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F It can take BioPortal a little bit of time to fully process all ontologies in the processing queue. If the ontologies are fully parsed and the ontology data is still not visible in the appliance user interface, could you try flushing the cache? Instructions are available on the wiki for this as well: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_can_I_clear_the_memcached-based_UI_cache.3F Another thing to look at if all of the above fails is to check the processing logs for each ontology for processing errors. The log files are located using the following pattern: /srv/ncbo/repository/{ontology acronym}/{submission id} For example, the log file for CHEAR would be located in the following directory: /srv/ncbo/repository/CHEAR/1 Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sina.Madani at vumc.org Tue Feb 4 05:43:06 2020 From: Sina.Madani at vumc.org (Madani, Sina) Date: Tue, 4 Feb 2020 13:43:06 +0000 Subject: [bioontology-support] Sorting object property values Message-ID: Hi, It seems the values of object properties are sorted randomly (not even by their URIs) in our local instance of OntoPortal (first screenshot below). Those values are sorted alphabetically in our ontology editing environment (second screenshot) Is there a way to enforce such sorting in OntoPortal? Thanks! Sina [cid:image001.png at 01D5DB2E.BC5BF7A0] [cid:image002.png at 01D5DB2E.BC5BF7A0] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 96059 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 44358 bytes Desc: image002.png URL: From mdorf at stanford.edu Tue Feb 4 11:32:15 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 4 Feb 2020 19:32:15 +0000 Subject: [bioontology-support] Sorting object property values In-Reply-To: References: Message-ID: <485C08E7-5F69-43AE-ADB7-3FDAC4421002@stanford.edu> Hi Sina, Thank you for your report. Yes indeed, it does seem a bit random, especially for classes with a huge number of properties, such as this one: http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F71388002 This may not be a trivial issue to resolve, as the rest service, which the UI uses to retrieve the values for properties only contains the URIs: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F71388002?display=all The UI then uses AJAX based calls to gradually resolve all corresponding labels for these terms. In any case, I?ve created an issue to be tracked here: https://github.com/ncbo/bioportal_web_ui/issues/123 Feel free to add any details there you deem relevant. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 4, 2020, at 5:43 AM, Madani, Sina > wrote: Hi, It seems the values of object properties are sorted randomly (not even by their URIs) in our local instance of OntoPortal (first screenshot below). Those values are sorted alphabetically in our ontology editing environment (second screenshot) Is there a way to enforce such sorting in OntoPortal? Thanks! Sina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Feb 3 21:42:13 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 03 Feb 2020 21:42:13 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Babak Kamkar Message-ID: <5e3904352663a_531222e0ffc24f2@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Feb 4 11:41:58 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 4 Feb 2020 19:41:58 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Babak Kamkar In-Reply-To: <5e3904352663a_531222e0ffc24f2@ncbo-prd-app-08.stanford.edu.mail> References: <5e3904352663a_531222e0ffc24f2@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Babak, Thank you for contacting us. I think this message from our mailing list archive may address your question: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Jaime-Parra-MD-phD-tp4655505p4655508.html If not, feel free to follow up again. Thanks, Michael On Feb 3, 2020, at 9:42 PM, support at bioontology.org wrote: Name: Babak Kamkar Email: DRBKAMKAR at GMAIL.COM Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D1014507 Feedback: What does the Inverse of SIB mean? _______________________________________________ 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 Gacquer.William at chu-amiens.fr Thu Feb 6 05:22:09 2020 From: Gacquer.William at chu-amiens.fr (Gacquer William) Date: Thu, 6 Feb 2020 13:22:09 +0000 Subject: [bioontology-support] Request for VM access Message-ID: Dear NCBO Virtual Appliance managers, We request the right to download your virtual appliance for in house installation. I do represent a public hospital in France and we would like to deploy your VM for research purpose. We cannot use the cloud based instance because the data we own must not get out of the hospital for patient privacy reasons. Our goal is to translate medical annotations, taken at the emergency ward, to tags for further deep learning analysis and predictions. May you please grant us access to the OntoPortal Virtual Appliance ? Please know that my BioPortal account username is WilliamGacquer. Best regards William GACQUER Data Scientist, Direction des Services Num?riques CHU Amiens?Picardie, 1 rond point du Pr Christian Cabrol, 80054 AMIENS cedex 1 ?[cid:image002.jpg at 01D5DCF8.D01D02E0]? 03 22 08 80 68 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3201 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 879 bytes Desc: image002.jpg URL: From support at bioontology.org Fri Feb 7 12:51:48 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 07 Feb 2020 12:51:48 -0800 Subject: [bioontology-support] [BioPortal] Feedback from kkochut Message-ID: <5e3dcde469be3_1a4f2363ee823568@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Trevor.Rempel at Point72.com Thu Feb 6 15:43:48 2020 From: Trevor.Rempel at Point72.com (Rempel, Trevor) Date: Thu, 6 Feb 2020 23:43:48 +0000 Subject: [bioontology-support] API Access Message-ID: <560665D4A4A38044B89A5EE99B2E724DA5BECE2C@SAC22E10CHM01.saccap.int> Hello, I was wondering if I could get access to your REST API? Thanks! Best, Trevor DISCLAIMER: This e-mail message and any attachments are intended solely for the use of the individual or entity to which it is addressed and may contain information that is confidential or legally privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately and permanently delete this message and any attachments. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri Feb 7 13:43:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 7 Feb 2020 21:43:59 +0000 Subject: [bioontology-support] API Access In-Reply-To: <560665D4A4A38044B89A5EE99B2E724DA5BECE2C@SAC22E10CHM01.saccap.int> References: <560665D4A4A38044B89A5EE99B2E724DA5BECE2C@SAC22E10CHM01.saccap.int> Message-ID: <468B0D61-3CCD-410C-A473-A864D1EF3CE1@stanford.edu> Hi Trevor, To access our REST API, you?ll need an API key. The instructions for getting an API key are found on the BioPortal wiki: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Our REST API documentation is located here: http://data.bioontology.org/documentation Thanks, Michael On Feb 6, 2020, at 3:43 PM, Rempel, Trevor > wrote: Hello, I was wondering if I could get access to your REST API? Thanks! Best, Trevor ________________________________ DISCLAIMER: This e-mail message and any attachments are intended solely for the use of the individual or entity to which it is addressed and may contain information that is confidential or legally privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately and permanently delete this message and any attachments. _______________________________________________ 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 Feb 7 13:58:00 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 7 Feb 2020 21:58:00 +0000 Subject: [bioontology-support] API Access In-Reply-To: <560665D4A4A38044B89A5EE99B2E724DA5BF00E8@SAC22E10CHM01.saccap.int> References: <560665D4A4A38044B89A5EE99B2E724DA5BECE2C@SAC22E10CHM01.saccap.int> <468B0D61-3CCD-410C-A473-A864D1EF3CE1@stanford.edu> <560665D4A4A38044B89A5EE99B2E724DA5BF00E8@SAC22E10CHM01.saccap.int> Message-ID: <752973C3-EF38-43DB-8F0E-A34934F81CAD@stanford.edu> Hi Trevor, I am assuming you mean iterate over classes for a given ontology (parsing an ontology is an internal process and isn?t available via the REST service). To iterate over an ontology, you can call the ?classes endpoint?, paging through the classes as you perform your custom logic on them. For example: http://data.bioontology.org/ontologies/CPT/classes?page=1 http://data.bioontology.org/ontologies/CPT/classes?page=2 etc?until you get to the last page. Hope this helps. Michael On Feb 7, 2020, at 1:46 PM, Rempel, Trevor > wrote: Hello Michael, Thanks for getting back to me. I have been able to get an API key and have been looking through the API documentation, although I am having a bit of trouble trying to parse through a given ontology. Suppose I wanted to parse out the CPT ontology, how would I approach that? Best, Trevor From: Michael Dorf > Sent: Friday, February 7, 2020 4:44 PM To: Rempel, Trevor > Cc: support at bioontology.org; Data Compliance > Subject: Re: [bioontology-support] API Access Hi Trevor, To access our REST API, you?ll need an API key. The instructions for getting an API key are found on the BioPortal wiki: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Our REST API documentation is located here: http://data.bioontology.org/documentation Thanks, Michael On Feb 6, 2020, at 3:43 PM, Rempel, Trevor > wrote: Hello, I was wondering if I could get access to your REST API? Thanks! Best, Trevor ________________________________ DISCLAIMER: This e-mail message and any attachments are intended solely for the use of the individual or entity to which it is addressed and may contain information that is confidential or legally privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately and permanently delete this message and any attachments. _______________________________________________ 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 JAHOON.KOO at UCDENVER.EDU Fri Feb 7 15:02:55 2020 From: JAHOON.KOO at UCDENVER.EDU (Koo, Jahoon) Date: Fri, 7 Feb 2020 23:02:55 +0000 Subject: [bioontology-support] Question about migrating ontologies from BioPortal to local VM Message-ID: Hi BioPortal, This is Jahoon, a student worker from Health Data Compass. I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided. It seems like many ontologies migrated have missing classes. On the UI, they have "no submission available". I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F I am currently using this URL: http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status. I have migrated FB-CV ontology, and the submission status of FB-CV ontology is "Uploaded" at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below. * errors": [ o "Ontology FB-CV submission not found." ], * "status": 404 I have cleared the memcached-based UI cache, but it wasn't helpful. I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says, "Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8" "Pull location found, but no file in the upload file path" What should I do to fix this migration issue? Respectfully, Jahoon -------------- next part -------------- An HTML attachment was scrubbed... URL: From JAHOON.KOO at UCDENVER.EDU Fri Feb 7 15:15:29 2020 From: JAHOON.KOO at UCDENVER.EDU (Koo, Jahoon) Date: Fri, 7 Feb 2020 23:15:29 +0000 Subject: [bioontology-support] Question about processing UMLS ontologies Message-ID: Hi BioPortal, This is Jahoon, a student worker from Health Data Compass. For my project, I have to migrate multiple UMLS ontologies from BioPortal into my virtual appliance. On your wiki, it says "UMLS ontologies can be processed to work with our system by converting them to RDF. There is no automated way to do this and you must have your own UMLS MySQL installation and an OSX/Linux/Unix machine with 8GB+ of RAM in order for the conversion process to work. Once you have converted UMLS to RDF, you will get Turtle (.ttl) files that can be uploaded using the BioPortal Web UI". I would like to double check if there is no automated way to convert UMLS ontologies to RDF. If not, I am wondering if there is an automated way to upload Turtle (.ttl) files to my virtual appliance without using the Web UI. Respectfully, Jahoon -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri Feb 7 15:36:45 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 7 Feb 2020 23:36:45 +0000 Subject: [bioontology-support] Question about processing UMLS ontologies In-Reply-To: References: Message-ID: <0CA331EF-1D22-44E6-86F4-21244116081E@stanford.edu> Hi Jahoon, We have a script that converts the relational database representation of UMLS ontologies to RDF: https://github.com/ncbo/umls2rdf Once you?ve succeeded creating the Turtle files, you can try loading them into your appliance. Unfortunately, I am not in a position to offer a more detailed help on this process. We have our own internal way of loading UMLS ontologies into our repository that isn?t publicly available at the moment. Aside from the above process, we don?t publicly accept individual UMLS ontologies. Sorry I couldn?t offer more help on this. Michael On Feb 7, 2020, at 3:15 PM, Koo, Jahoon > wrote: Hi BioPortal, This is Jahoon, a student worker from Health Data Compass. For my project, I have to migrate multiple UMLS ontologies from BioPortal into my virtual appliance. On your wiki, it says ?UMLS ontologies can be processed to work with our system by converting them to RDF. There is no automated way to do this and you must have your own UMLS MySQL installation and an OSX/Linux/Unix machine with 8GB+ of RAM in order for the conversion process to work. Once you have converted UMLS to RDF, you will get Turtle (.ttl) files that can be uploaded using the BioPortal Web UI?. I would like to double check if there is no automated way to convert UMLS ontologies to RDF. If not, I am wondering if there is an automated way to upload Turtle (.ttl) files to my virtual appliance without using the Web UI. Respectfully, Jahoon _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 7 15:48:50 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 7 Feb 2020 23:48:50 +0000 Subject: [bioontology-support] Question about migrating ontologies from BioPortal to local VM In-Reply-To: References: Message-ID: Hello Jahoon, I looked at the ontology you mentioned below (FB-CV). It appears that it's configured in our production system to pull new versions from this URL: http://purl.obolibrary.org/obo/fbcv/dpo.owl However, this URL is no longer valid (results in a 404 error). This is why you see an error message in the parsing log file about ?no file in the upload file path?. You could try contacting the ontology author to see if they have an updated URL for pulling new versions. Their contact information is available on the ontology summary page: http://bioportal.bioontology.org/ontologies/FB-CV. Alternatively, if you want to get this ontology into your appliance quickly, you could manually download the OWL file from our production site and upload it via your appliance UI. I also noticed a GitHub repository that appears to be related: https://github.com/FlyBase/flybase-controlled-vocabulary It?s unclear to me which of their ontology entries maps to the dpo.owl file they originally entered in BioPortal. If you can provide more specifics about the other ontologies you?re having trouble with, we can try to help further. Kind regards, Jennifer On Feb 7, 2020, at 3:02 PM, Koo, Jahoon > wrote: Hi BioPortal, This is Jahoon, a student worker from Health Data Compass. I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided. It seems like many ontologies migrated have missing classes. On the UI, they have ?no submission available?. I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F I am currently using this URL: http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status. I have migrated FB-CV ontology, and the submission status of FB-CV ontology is ?Uploaded? at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below. ? errors": [ o "Ontology FB-CV submission not found." ], ? "status": 404 I have cleared the memcached-based UI cache, but it wasn?t helpful. I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says, ?Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8? ?Pull location found, but no file in the upload file path? What should I do to fix this migration issue? Respectfully, Jahoon _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 7 16:01:05 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 8 Feb 2020 00:01:05 +0000 Subject: [bioontology-support] Question about migrating ontologies from BioPortal to local VM In-Reply-To: References: Message-ID: One more thing to note here - I went ahead and entered an issue in their GitHub tracker to see if they can give us an updated pull URL: https://github.com/FlyBase/flybase-controlled-vocabulary/issues/98 Jennifer On Feb 7, 2020, at 3:48 PM, Jennifer Leigh Vendetti > wrote: Hello Jahoon, I looked at the ontology you mentioned below (FB-CV). It appears that it's configured in our production system to pull new versions from this URL: http://purl.obolibrary.org/obo/fbcv/dpo.owl However, this URL is no longer valid (results in a 404 error). This is why you see an error message in the parsing log file about ?no file in the upload file path?. You could try contacting the ontology author to see if they have an updated URL for pulling new versions. Their contact information is available on the ontology summary page: http://bioportal.bioontology.org/ontologies/FB-CV. Alternatively, if you want to get this ontology into your appliance quickly, you could manually download the OWL file from our production site and upload it via your appliance UI. I also noticed a GitHub repository that appears to be related: https://github.com/FlyBase/flybase-controlled-vocabulary It?s unclear to me which of their ontology entries maps to the dpo.owl file they originally entered in BioPortal. If you can provide more specifics about the other ontologies you?re having trouble with, we can try to help further. Kind regards, Jennifer On Feb 7, 2020, at 3:02 PM, Koo, Jahoon > wrote: Hi BioPortal, This is Jahoon, a student worker from Health Data Compass. I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided. It seems like many ontologies migrated have missing classes. On the UI, they have ?no submission available?. I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F I am currently using this URL: http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status. I have migrated FB-CV ontology, and the submission status of FB-CV ontology is ?Uploaded? at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below. ? errors": [ o "Ontology FB-CV submission not found." ], ? "status": 404 I have cleared the memcached-based UI cache, but it wasn?t helpful. I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says, ?Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8? ?Pull location found, but no file in the upload file path? What should I do to fix this migration issue? Respectfully, Jahoon _______________________________________________ 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 Trevor.Rempel at Point72.com Fri Feb 7 13:46:24 2020 From: Trevor.Rempel at Point72.com (Rempel, Trevor) Date: Fri, 7 Feb 2020 21:46:24 +0000 Subject: [bioontology-support] API Access In-Reply-To: <468B0D61-3CCD-410C-A473-A864D1EF3CE1@stanford.edu> References: <560665D4A4A38044B89A5EE99B2E724DA5BECE2C@SAC22E10CHM01.saccap.int> <468B0D61-3CCD-410C-A473-A864D1EF3CE1@stanford.edu> Message-ID: <560665D4A4A38044B89A5EE99B2E724DA5BF00E8@SAC22E10CHM01.saccap.int> Hello Michael, Thanks for getting back to me. I have been able to get an API key and have been looking through the API documentation, although I am having a bit of trouble trying to parse through a given ontology. Suppose I wanted to parse out the CPT ontology, how would I approach that? Best, Trevor From: Michael Dorf Sent: Friday, February 7, 2020 4:44 PM To: Rempel, Trevor Cc: support at bioontology.org; Data Compliance Subject: Re: [bioontology-support] API Access Hi Trevor, To access our REST API, you?ll need an API key. The instructions for getting an API key are found on the BioPortal wiki: https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key Our REST API documentation is located here: http://data.bioontology.org/documentation Thanks, Michael On Feb 6, 2020, at 3:43 PM, Rempel, Trevor > wrote: Hello, I was wondering if I could get access to your REST API? Thanks! Best, Trevor ________________________________ DISCLAIMER: This e-mail message and any attachments are intended solely for the use of the individual or entity to which it is addressed and may contain information that is confidential or legally privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately and permanently delete this message and any attachments. _______________________________________________ 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 mah79 at cam.ac.uk Mon Feb 10 02:29:29 2020 From: mah79 at cam.ac.uk (Dr Midori A. Harris) Date: Mon, 10 Feb 2020 10:29:29 +0000 (GMT) Subject: [bioontology-support] [BioPortal] Load from URL failure for Fission Yeast Phenotype Ontology In-Reply-To: <5e3f6b137864e_36732afdc38c209441680@ncbo-prd-app-31.stanford.edu.mail> References: <5e3f6b137864e_36732afdc38c209441680@ncbo-prd-app-31.stanford.edu.mail> Message-ID: Hello, On Sat, 8 Feb 2020, admin at bioontology.org wrote: > BioPortal failed to load Fission Yeast Phenotype Ontology (FYPO) from URL: > https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl. This URL is correct, and is working for me now. Can you try the BioPortal load again? Thank you, Midori > Please verify the URL you provided for daily loading of your ontology: > 1. Make sure you are signed in to BioPortal. > 2. Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/FYPO. > 3. Click the "Edit submission information" link. > 4. In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area. > If you need further assistance, please contact us via the BioPortal support mailing list. > > Thank you, > The BioPortal Team > Midori A. Harris, PhD Database Curator, PomBase Department of Biochemistry University of Cambridge Cambridge, UK mah79 at cam.ac.uk From support at bioontology.org Sun Feb 9 15:36:01 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 09 Feb 2020 15:36:01 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Donna Message-ID: <5e4097617bbcb_77d91f8d60c64227@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Feb 9 15:39:07 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 09 Feb 2020 15:39:07 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Donna Message-ID: <5e40981b5674_73dd2703b20263f0@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Feb 9 15:40:06 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 09 Feb 2020 15:40:06 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Donna Message-ID: <5e4098564d8bc_77d91f8d60c64355@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Feb 9 15:41:16 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 09 Feb 2020 15:41:16 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Donna Message-ID: <5e40989cd30fb_77d91f8d60c644e8@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Feb 10 09:07:02 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 10 Feb 2020 17:07:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Donna In-Reply-To: <5e4098564d8bc_77d91f8d60c64355@ncbo-prd-app-08.stanford.edu.mail> References: <5e4098564d8bc_77d91f8d60c64355@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <5790C500-8A39-4779-9AF8-6C27D8A09589@stanford.edu> Hi Donna, Thank you for your reports. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2020AA and 2020AB. Their release schedule is usually May and November). CPT is one of the vocabularies contained in the UMLS distribution. We don't have any control over what goes into these distributions or whether each individual vocabulary is up-to-date with its latest version. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 9, 2020, at 3:40 PM, support at bioontology.org wrote: Name: Donna Email: prvbs327 at yahoo.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F35741 Feedback: Update - Code deleted http://purl.bioontology.org/ontology/CPT/35741 _______________________________________________ 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 Mon Feb 10 15:40:58 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 10 Feb 2020 23:40:58 +0000 Subject: [bioontology-support] [BioPortal] Feedback from kkochut In-Reply-To: <5e3dcde469be3_1a4f2363ee823568@ncbo-prd-app-09.stanford.edu.mail> References: <5e3dcde469be3_1a4f2363ee823568@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <07FBB318-6A53-432B-A8C9-79FD33735454@stanford.edu> hi Krys, As we discussed offline, we know we can't upload ontologies above a certain size (not yet quantified, but for sure above 2 GB). Let's continue to discuss a strategy for troubleshooting this off-line?I think a test with BiblioPortal may be useful. John On Feb 7, 2020, at 12:51 PM, support at bioontology.org wrote: Name: kkochut Email: kkochut at uga.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Hello, I created a summary page for a new ontology submission without any problems. It is a Protein Kinase Ontology (PROKINO). However, I am having problems uploading the OWL file. The ontology includes many individuals and the serialized OWL file is quite large (about 2.9 GB). After failing a couple of times while using the Web browser-based submission form, I tried a command line on a Linux system using the cURL command. It also failed with the following result: 413 Request Entity Too Large 413 Request Entity Too Large ________________________________ nginx/1.16.1 I was executing a POST request (using curl) on the resource /ontologies/PROKINO/submissions, using the -T option and I specified the "chunked" encoding. However, the upload failed after uploading nearly 37% of the file. Is there an alternative way to upload this ontology? Thank you. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Feb 11 14:33:11 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 11 Feb 2020 22:33:11 +0000 Subject: [bioontology-support] [BioPortal] Load from URL failure for Fission Yeast Phenotype Ontology In-Reply-To: References: <5e3f6b137864e_36732afdc38c209441680@ncbo-prd-app-31.stanford.edu.mail> Message-ID: Hello Midori, Thank you for this note. The system will retry automatically each night, and will only re-import the ontology if it has changed since the last successful import. The lack of an error email indicates the ontology was successfully acceseed by the system. So, unless the ontology has changed since the successful February 7 upload, everything is operating as it should be. Please let us know if you still see a concern. Thank you! John On Feb 10, 2020, at 2:29 AM, Dr Midori A. Harris > wrote: Hello, On Sat, 8 Feb 2020, admin at bioontology.org wrote: BioPortal failed to load Fission Yeast Phenotype Ontology (FYPO) from URL: https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl. This URL is correct, and is working for me now. Can you try the BioPortal load again? Thank you, Midori Please verify the URL you provided for daily loading of your ontology: 1. Make sure you are signed in to BioPortal. 2. Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/FYPO. 3. Click the "Edit submission information" link. 4. In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area. If you need further assistance, please contact us via the BioPortal support mailing list. Thank you, The BioPortal Team Midori A. Harris, PhD Database Curator, PomBase Department of Biochemistry University of Cambridge Cambridge, UK mah79 at cam.ac.uk _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Feb 11 04:12:20 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 11 Feb 2020 04:12:20 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Svetlana Message-ID: <5e429a244d70e_465f26430782094a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Feb 11 14:47:03 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 11 Feb 2020 22:47:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Svetlana In-Reply-To: <5e429a244d70e_465f26430782094a@ncbo-prd-app-09.stanford.edu.mail> References: <5e429a244d70e_465f26430782094a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <93F1160F-0727-4ECB-A274-5BBC3BD29282@stanford.edu> Hello Svetlana, Thank you for this input. Generally we are simply hosting these ontologies, which are owned by others and managed elsewhere. You can find the contact information for each ontology on the ontology's summary page. In this case, I forwarded your email to the contact for the FMA ontology, just to make sure BioPortal isn't introducing an error in some way. John On Feb 11, 2020, at 4:12 AM, support at bioontology.org wrote: Name: Svetlana Email: sv.koltsova at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFMA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.org%252Fsig%252Font%252Ffma%252Ffma0327741%26jump_to_nav%3Dtrue Feedback: Hello, It seems like you have a duplication of terms: http://purl.org/sig/ont/fma/fma322212 http://purl.org/sig/ont/fma/fma0327741 Kind regards, Svetlana _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sv.koltsova at gmail.com Wed Feb 12 00:46:13 2020 From: sv.koltsova at gmail.com (Svetlana Koltsova) Date: Wed, 12 Feb 2020 09:46:13 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Svetlana In-Reply-To: <93F1160F-0727-4ECB-A274-5BBC3BD29282@stanford.edu> References: <5e429a244d70e_465f26430782094a@ncbo-prd-app-09.stanford.edu.mail> <93F1160F-0727-4ECB-A274-5BBC3BD29282@stanford.edu> Message-ID: John, thank you! On Tue, Feb 11, 2020 at 11:47 PM John Graybeal wrote: > Hello Svetlana, > > Thank you for this input. Generally we are simply hosting these > ontologies, which are owned by others and managed elsewhere. You can find > the contact information for each ontology on the ontology's summary page. > > In this case, I forwarded your email to the contact for the FMA ontology, > just to make sure BioPortal isn't introducing an error in some way. > > John > > On Feb 11, 2020, at 4:12 AM, support at bioontology.org wrote: > > Name: Svetlana > > Email: sv.koltsova at gmail.com > > Location: https%3A%2F%2Fbioportal.bioontology.org > %2Fontologies%2FFMA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F% > 252Fpurl.org%252Fsig%252Font%252Ffma%252Ffma0327741%26jump_to_nav%3Dtrue > > > *Feedback:* > > Hello, > > It seems like you have a duplication of terms: > http://purl.org/sig/ont/fma/fma322212 > http://purl.org/sig/ont/fma/fma0327741 > > Kind regards, > Svetlana > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 | ORCID 0000-0001-6875-5360 > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.martinez1 at uniandes.edu.co Thu Feb 13 15:24:02 2020 From: d.martinez1 at uniandes.edu.co (Daniel Martinez) Date: Thu, 13 Feb 2020 23:24:02 +0000 Subject: [bioontology-support] Mapping queries Internal Error Message-ID: Hello, I have been trying to query through the mappings endpoint programmatically, and also at the endpoint of the website, but it constantly says Internal Error 500 on both sides. What can I do to solve this and be able to test the queries? This is for my master's thesis, so I would be glad to know if there is any way to solve this problem to be able to make the queries Thank you, Daniel Mart?nez -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Feb 13 18:14:57 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 14 Feb 2020 02:14:57 +0000 Subject: [bioontology-support] Mapping queries Internal Error In-Reply-To: References: Message-ID: <5E15BF91-7446-4E33-8D4D-F39E4F170307@stanford.edu> Daniel, When I just tried this, both worked for me. Can you try again, perhaps refreshing your browser cache and retrying if at first it doesn't work? To refresh your browser cache in Chrome: 1) Open the Chrome developer tools as described at http://anti-code.com/devtools-cheatsheet/. 2) In the top left of the page, right click or control-click on the refresh icon and choose ?Empty Cache and Hard Reload? 3) Close the developer tools with the small X at upper right, or by entering the developer tools key sequence again. John On Feb 13, 2020, at 3:24 PM, Daniel Martinez > wrote: Hello, I have been trying to query through the mappings endpoint programmatically, and also at the endpoint of the website, but it constantly says Internal Error 500 on both sides. What can I do to solve this and be able to test the queries? This is for my master's thesis, so I would be glad to know if there is any way to solve this problem to be able to make the queries Thank you, Daniel Mart?nez _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markampa at pennmedicine.upenn.edu Fri Feb 14 05:51:24 2020 From: markampa at pennmedicine.upenn.edu (Miller, Mark) Date: Fri, 14 Feb 2020 13:51:24 +0000 Subject: [bioontology-support] Virtual Appliance request Message-ID: Hello, BioPortal. Please provide me with access to the Virtual Appliance images. For the PennTURBO project, I routinely instantiate your excellent mappings into an RDF triplestore. Retrieving the mappings from LOINC to ChEMBL, the cell ontology, Uberon, etc. can take a while via the public API at bioontology.org. We also use the search and recommendation tools, but we can't guarantee that out input is scrubbed from personal health information. A prescription or lab order occasionally contains a patient name. thanks, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From markampa at pennmedicine.upenn.edu Mon Feb 17 10:28:28 2020 From: markampa at pennmedicine.upenn.edu (Miller, Mark) Date: Mon, 17 Feb 2020 18:28:28 +0000 Subject: [bioontology-support] Flexibility in term mapping (in virtual appliance) Message-ID: I have a 2.4 virtual BioPortal appliance running in my lab now. Thanks! How much configuration is possible with the term mapping? Or can manual mappings be added somewhere? I would like to assert (or discover) that http://purl.bioontology.org/ontology/LNC/LP14419-3 "Leukocytes" is the same as http://purl.obolibrary.org/obo/CL_0000738 "leukocyte" and that http://purl.bioontology.org/ontology/LNC/LP7057-5 "Bld" is the same as http://purl.obolibrary.org/obo/UBERON_0000178 "blood" thanks, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.fiorelli at gmail.com Mon Feb 17 08:40:09 2020 From: manuel.fiorelli at gmail.com (Manuel Fiorelli) Date: Mon, 17 Feb 2020 17:40:09 +0100 Subject: [bioontology-support] Problems with root concepts in a SKOS ontology Message-ID: Dear BioPortal Support team I've been doing some experiments with BioPortal using two private repositories, TESTONT (an OWL ontology) and TESTTES (a SKOS ontology). Yesterday I submitted the attached RDF data to TESTTES (please note that the description of the concept scheme is split between two tags). The file should conform to BioPortal constraints, such as the presence of a concept scheme and the use of skos:hasTopConcept. However, the page that should retrieve the concepts informs me that there was an unspecified problem retrieving classes. https://bioportal.bioontology.org/ontologies/TESTTES/?p=classes&conceptid=root [image: immagine.png] However, if I visit the URL corresponding to the detailed view of a concept, I can see the description of that concept together with the concept tree on the left side (note that the submission is a flat list of concepts). https://bioportal.bioontology.org/ontologies/TESTTES/?p=classes&conceptid=http%3A%2F%2Fexample.org%2Fc_48989b6a [image: immagine.png] PS I should have asked before; however, I took the opportunity to ask whether my use of private ontologies is good for experimentation, or whether there is a sandbox or other test system elsewhere. Indeed, I've just realized that there is no explicit delete button to remove the test ontologies. Best regards Manuel Fiorelli -- Manuel Fiorelli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: immagine.png Type: image/png Size: 17231 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: immagine.png Type: image/png Size: 30853 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: submission.rdf Type: application/rdf+xml Size: 3768 bytes Desc: not available URL: From Shelley.King at choa.org Tue Feb 18 08:40:35 2020 From: Shelley.King at choa.org (King, Shelley) Date: Tue, 18 Feb 2020 16:40:35 +0000 Subject: [bioontology-support] REDCap CPT updates Message-ID: <7cb84179249642dc8039388f6c76601b@choa.org> Hi Can you please put a space in the account name between CHOA and CHARGEMASTER? Also, who do I contact regarding our REDCap CPT updates for 2020? Shelley King| Charge Master Specialist| Children's Healthcare of Atlanta| 1455 Tullie Circle, Atlanta, GA, 30329 *: 404.785.3345 | *: shelley.king at choa.org [cid:image007.jpg at 01D5E650.3BA74DD0][cid:image008.png at 01D5E650.3BA74DD0][cid:image009.png at 01D5E650.3BA74DD0] Confidentiality Notice: The information contained in this message is confidential and may be legally privileged. It is intended only for the individual or entity named. If the reader of this message is not the intended recipient, you are hereby notified that any use, dissemination or copy of this electronic mail is strictly prohibited. If you have received this electronic mail in error, please immediately notify Shelley King 404) 785-3345. Thank you. As a not-for-profit organization, Children's benefits from the generous philanthropic and volunteer support of our community. To donate, call 404-785-GIVE or visit us online at www.choa.org/give. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image007.jpg Type: image/jpeg Size: 4625 bytes Desc: image007.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image008.png Type: image/png Size: 10948 bytes Desc: image008.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image009.png Type: image/png Size: 12313 bytes Desc: image009.png URL: From support at bioontology.org Mon Feb 17 08:29:53 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 17 Feb 2020 08:29:53 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler at Thermo Fisher Scientific Message-ID: <5e4abf818b113_356f2bd80c4877c7@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 18 11:01:45 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 18 Feb 2020 19:01:45 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler at Thermo Fisher Scientific In-Reply-To: <5e4abf818b113_356f2bd80c4877c7@ncbo-prd-app-09.stanford.edu.mail> References: <5e4abf818b113_356f2bd80c4877c7@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <7012DDB9-365C-4EB8-92E9-B56CC98A6FD7@stanford.edu> Apologies that you?re having issues with that page Mark. I looked at your account in our system and don?t see any issues. I also tested accessing the Account Settings page for a few accounts and I?m not seeing the 500 error. I went ahead and flushed our application caches in the event it?s a caching issue. Could you please try again? If it still doesn?t work, could you try clearing your browser cache for the BioPortal site? I can send instructions if you let me know which browser you?re using. Kind regards, Jennifer On Feb 17, 2020, at 8:29 AM, support at bioontology.org wrote: Name: Mark Ressler at Thermo Fisher Scientific Email: mark.ressler at thermofisher.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I have been trying to access my Account Settings for about a week now, but the site gives an error: "We're sorry but something has gone wrong. We have been notified of this error." Consequently, I cannot retrieve my API Key. _______________________________________________ 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 Tue Feb 18 07:38:25 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 18 Feb 2020 15:38:25 +0000 Subject: [bioontology-support] Flexibility in term mapping (in virtual appliance) In-Reply-To: References: Message-ID: <68869653-2484-47A6-864D-6A3F198243CE@stanford.edu> Hi Mark, You can assert mappings using our REST API: http://data.bioontology.org/documentation#Mapping We have example code for programmatically creating mappings in our GitHub sample code repository: https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java John On Feb 17, 2020, at 10:28 AM, Miller, Mark > wrote: I have a 2.4 virtual BioPortal appliance running in my lab now. Thanks! How much configuration is possible with the term mapping? Or can manual mappings be added somewhere? I would like to assert (or discover) that http://purl.bioontology.org/ontology/LNC/LP14419-3 "Leukocytes" is the same as http://purl.obolibrary.org/obo/CL_0000738 "leukocyte" and that http://purl.bioontology.org/ontology/LNC/LP7057-5 "Bld" is the same as http://purl.obolibrary.org/obo/UBERON_0000178 "blood" thanks, Mark _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 18 16:22:26 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 19 Feb 2020 00:22:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler at Thermo Fisher Scientific In-Reply-To: <7012DDB9-365C-4EB8-92E9-B56CC98A6FD7@stanford.edu> References: <5e4abf818b113_356f2bd80c4877c7@ncbo-prd-app-09.stanford.edu.mail> <7012DDB9-365C-4EB8-92E9-B56CC98A6FD7@stanford.edu> Message-ID: Hi Mark, Thanks for letting me know that you have two BioPortal accounts. In my initial response below, I was looking at your account where the account name is your email address. With regard to the other account, I was able to reproduce the 500 error you reported. It turns out there is a bug in our system that prevents users from being able to view the account settings page if the account name has space characters. I documented this in more detail in our issue tracker: https://github.com/ncbo/bioportal_web_ui/issues/126 I published a fix to our production system just now, so you should be able to log in using your secondary account that has spaces in the account name and see your API key, etc. Kind regards, Jennifer On Feb 18, 2020, at 11:01 AM, Jennifer Leigh Vendetti > wrote: Apologies that you?re having issues with that page Mark. I looked at your account in our system and don?t see any issues. I also tested accessing the Account Settings page for a few accounts and I?m not seeing the 500 error. I went ahead and flushed our application caches in the event it?s a caching issue. Could you please try again? If it still doesn?t work, could you try clearing your browser cache for the BioPortal site? I can send instructions if you let me know which browser you?re using. Kind regards, Jennifer On Feb 17, 2020, at 8:29 AM, support at bioontology.org wrote: Name: Mark Ressler at Thermo Fisher Scientific Email: mark.ressler at thermofisher.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I have been trying to access my Account Settings for about a week now, but the site gives an error: "We're sorry but something has gone wrong. We have been notified of this error." Consequently, I cannot retrieve my API Key. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 18 16:29:30 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 19 Feb 2020 00:29:30 +0000 Subject: [bioontology-support] REDCap CPT updates In-Reply-To: <7cb84179249642dc8039388f6c76601b@choa.org> References: <7cb84179249642dc8039388f6c76601b@choa.org> Message-ID: Hello Shelley, On Feb 18, 2020, at 8:40 AM, King, Shelley > wrote: Can you please put a space in the account name between CHOA and CHARGEMASTER? Apologies that we can?t change an account name once an account is created in our system. You?ll need to create a new account with your desired account name, which you can do via this form: https://bioportal.bioontology.org/accounts/new Also, who do I contact regarding our REDCap CPT updates for 2020? You?ve reached the support list for the Stanford-hosted instance of the BioPortal application. We aren?t associated with REDCap, so I?m afraid I can?t help with this question. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From erhard.eibl at rwth-aachen.de Wed Feb 19 05:30:24 2020 From: erhard.eibl at rwth-aachen.de (Erhard Eibl) Date: Wed, 19 Feb 2020 14:30:24 +0100 Subject: [bioontology-support] BioPortal mapping data Message-ID: Dear Sir or Madam, for a university project I would like to run a clustering algorithm on the BioPortal mapping data. As my internet ist fairly slow and unstable using the API to download all mappings is unfortunately not an option. Is there a way to directly download the mapping data (preferrably as JSON)? Thank you in advance Erhard Eibl From amassengale at rsna.org Thu Feb 20 08:14:49 2020 From: amassengale at rsna.org (Andrew Massengale) Date: Thu, 20 Feb 2020 16:14:49 +0000 Subject: [bioontology-support] Bio Portal API not working Message-ID: <92CE77DB-0C5C-4934-9551-80A6DE481736@hq.rsna.org> Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: From amassengale at rsna.org Thu Feb 20 08:16:27 2020 From: amassengale at rsna.org (Andrew Massengale) Date: Thu, 20 Feb 2020 16:16:27 +0000 Subject: [bioontology-support] Bio Portal API not working In-Reply-To: <92CE77DB-0C5C-4934-9551-80A6DE481736@hq.rsna.org> References: <92CE77DB-0C5C-4934-9551-80A6DE481736@hq.rsna.org> Message-ID: <291D2645-D097-4625-8BF7-FCB592C2F32C@hq.rsna.org> It looks like the issue is intermittent. It appears to be working now, but I was not getting a response after waiting for 5 minutes when testing around 15 minutes ago. From: Andrew Massengale Date: Thursday, February 20, 2020 at 10:14 AM To: "support at bioontology.org" Cc: Derrick Lottich Subject: Bio Portal API not working Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 20 11:11:09 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 20 Feb 2020 19:11:09 +0000 Subject: [bioontology-support] Bio Portal API not working In-Reply-To: <291D2645-D097-4625-8BF7-FCB592C2F32C@hq.rsna.org> References: <92CE77DB-0C5C-4934-9551-80A6DE481736@hq.rsna.org> <291D2645-D097-4625-8BF7-FCB592C2F32C@hq.rsna.org> Message-ID: <5A764609-19E1-4CF7-B2E4-FB3A474C1C37@stanford.edu> Hello Andrew, I?ve looked at our monitoring software & log files a bit. The site was indeed sluggish from roughly 8:10 to 8:15AM PST. It appears to have been bot traffic downloading large numbers of ontology source files. We?ve been working on mitigating this issue both in the code and on the IT side on an ongoing basis. Apologies for the inconvenience - the site should be back to normal now. Jennifer On Feb 20, 2020, at 8:16 AM, Andrew Massengale > wrote: It looks like the issue is intermittent. It appears to be working now, but I was not getting a response after waiting for 5 minutes when testing around 15 minutes ago. From: Andrew Massengale > Date: Thursday, February 20, 2020 at 10:14 AM To: "support at bioontology.org" > Cc: Derrick Lottich > Subject: Bio Portal API not working Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago _______________________________________________ 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 amassengale at rsna.org Thu Feb 20 11:49:52 2020 From: amassengale at rsna.org (Andrew Massengale) Date: Thu, 20 Feb 2020 19:49:52 +0000 Subject: [bioontology-support] Bio Portal API not working In-Reply-To: <5A764609-19E1-4CF7-B2E4-FB3A474C1C37@stanford.edu> References: <92CE77DB-0C5C-4934-9551-80A6DE481736@hq.rsna.org> <291D2645-D097-4625-8BF7-FCB592C2F32C@hq.rsna.org> <5A764609-19E1-4CF7-B2E4-FB3A474C1C37@stanford.edu> Message-ID: <8949F107-5580-4BCF-BE95-5235F0F22D90@hq.rsna.org> Thanks Jennifer! Confirmed that things look good on our end as well now. Thanks! From: Jennifer Leigh Vendetti Date: Thursday, February 20, 2020 at 1:11 PM To: Andrew Massengale Cc: "support at bioontology.org" , Derrick Lottich Subject: Re: [bioontology-support] Bio Portal API not working Hello Andrew, I?ve looked at our monitoring software & log files a bit. The site was indeed sluggish from roughly 8:10 to 8:15AM PST. It appears to have been bot traffic downloading large numbers of ontology source files. We?ve been working on mitigating this issue both in the code and on the IT side on an ongoing basis. Apologies for the inconvenience - the site should be back to normal now. Jennifer On Feb 20, 2020, at 8:16 AM, Andrew Massengale > wrote: It looks like the issue is intermittent. It appears to be working now, but I was not getting a response after waiting for 5 minutes when testing around 15 minutes ago. From: Andrew Massengale > Date: Thursday, February 20, 2020 at 10:14 AM To: "support at bioontology.org" > Cc: Derrick Lottich > Subject: Bio Portal API not working Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 20 18:12:38 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 21 Feb 2020 02:12:38 +0000 Subject: [bioontology-support] BioPortal mapping data In-Reply-To: References: Message-ID: <51C9F8A6-3167-4FA8-AB9E-9483AE9F602A@stanford.edu> Hello Erhard, Unfortunately, we don?t offer mappings as file downloads. The mapping data isn?t persisted in our back-end storage mechanism. Rather, the mappings are materialized on the fly in response to REST API calls. We?ve documented this as a feature request [1] in one of our GitHub repositories. As of yet, we haven?t been able to come up with the resources to have someone work on this. Apologies that I don?t have a better answer for you. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal-project/issues/84 On Feb 19, 2020, at 5:30 AM, Erhard Eibl > wrote: Dear Sir or Madam, for a university project I would like to run a clustering algorithm on the BioPortal mapping data. As my internet ist fairly slow and unstable using the API to download all mappings is unfortunately not an option. Is there a way to directly download the mapping data (preferrably as JSON)? Thank you in advance Erhard Eibl _______________________________________________ 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 murielbennett60 at yahoo.com Fri Feb 21 05:26:00 2020 From: murielbennett60 at yahoo.com (Muriel Bennett) Date: Fri, 21 Feb 2020 13:26:00 +0000 (UTC) Subject: [bioontology-support] bioontology-support Digest, Vol 142, Issue 26 In-Reply-To: References: Message-ID: <711989267.10654022.1582291560029@mail.yahoo.com> please take? On Thursday, 20 February 2020, 11:16:41 GMT-5, bioontology-support-request at lists.stanford.edu wrote: please take me off e-mail list. unsubscribe murielbennett60 at yahoo.com . thank you. Send bioontology-support mailing list submissions to ??? bioontology-support at lists.stanford.edu To subscribe or unsubscribe via the World Wide Web, visit .?? ??? https://mailman.stanford.edu/mailman/listinfo/bioontology-support or, via email, send a message with subject or body 'help' to ??? bioontology-support-request at lists.stanford.edu You can reach the person managing the list at ??? bioontology-support-owner at lists.stanford.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of bioontology-support digest..." Today's Topics: ? 1. Bio Portal API not working (Andrew Massengale) ? 2. Re: Bio Portal API not working (Andrew Massengale) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Feb 2020 16:14:49 +0000 From: Andrew Massengale To: "support at bioontology.org" Cc: Derrick Lottich Subject: [bioontology-support] Bio Portal API not working Message-ID: <92CE77DB-0C5C-4934-9551-80A6DE481736 at hq.rsna.org> Content-Type: text/plain; charset="utf-8" Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Thu, 20 Feb 2020 16:16:27 +0000 From: Andrew Massengale To: "support at bioontology.org" Cc: Derrick Lottich Subject: Re: [bioontology-support] Bio Portal API not working Message-ID: <291D2645-D097-4625-8BF7-FCB592C2F32C at hq.rsna.org> Content-Type: text/plain; charset="utf-8" It looks like the issue is intermittent. It appears to be working now, but I was not getting a response after waiting for 5 minutes when testing around 15 minutes ago. From: Andrew Massengale Date: Thursday, February 20, 2020 at 10:14 AM To: "support at bioontology.org" Cc: Derrick Lottich Subject: Bio Portal API not working Hello, The Bio Portal API has stopped working. Our API key worked yesterday, but is not working today. Did our API key get invalidated somehow, or is this a problem with the API? For example, we are trying to hit the following endpoint: https://data.bioontology.org/ontologies/RADLEX/classes/RID1385?apikey=XXXXX-XXX-XXXXX&include=prefLabel,properties,children Let me know if you need any more information. Thanks, Andrew M Andrew Massengale Senior Software Engineer (630) 481-1012 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2020 Annual Meeting November 29th - December 4th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ------------------------------ End of bioontology-support Digest, Vol 142, Issue 26 **************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Feb 26 12:44:50 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 26 Feb 2020 12:44:50 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Tracy Safran Message-ID: <5e56d8c2541f9_71ac2a39c0493379@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From xz485 at drexel.edu Thu Feb 27 11:00:05 2020 From: xz485 at drexel.edu (Zhao,Xintong) Date: Thu, 27 Feb 2020 19:00:05 +0000 Subject: [bioontology-support] NCIT Ontology csv Download Failed on BioPortal Message-ID: Good Afternoon, This is Xintong, a graduate student trying to download your NCIT (National Cancer Institute Thesaurus) ontology (CSV format) from BioPortal. However, when I tried to download the csv file (Version 20.02d), the webpage returned error message as follows: { * - "errors": [ * "Cannot read latest submission upload file: /srv/ncbo/repository/NCIT/88/NCIT.csv.gz" ], * "status": 500 } I contacted ncicbiit at mail.nih.gov and they redirected me here. Could you check on that csv file please? Its download links for other format (such as RDF, OWL) works fine. Thank you for your help, Xintong -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Feb 28 07:13:18 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 28 Feb 2020 07:13:18 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Francis Nguyen Message-ID: <5e592e0e2df8d_478f24b79c031378@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Feb 28 08:03:17 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 28 Feb 2020 08:03:17 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton Message-ID: <5e5939c5144f5_16ab243ddc832385@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Feb 28 02:55:30 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 28 Feb 2020 02:55:30 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Jorge Hernansanz Message-ID: <5e58f1a24b6c0_3a932e8a2e0192fe@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri Feb 28 09:59:45 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 17:59:45 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jorge Hernansanz In-Reply-To: <5e58f1a24b6c0_3a932e8a2e0192fe@ncbo-prd-app-09.stanford.edu.mail> References: <5e58f1a24b6c0_3a932e8a2e0192fe@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <88EBCDE4-3F84-4B7E-8655-18889A038BC0@stanford.edu> Hi Jorge, Thank you for contacting us. We?re unable to make NDFRT available for download via our website and/or REST API due to licensing restrictions. If you have a current UMLS license, please contact our technical program manager John Graybeal offline (cc?d) for more information about possible access to a source file. For info on obtaining a license, please follow the link below: https://uts.nlm.nih.gov/license.html Kind regards, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 28, 2020, at 2:55 AM, support at bioontology.org wrote: Name: Jorge Hernansanz Email: jorge.hernansanz at cpr.ku.dk Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNDFRT Feedback: Good morning I am trying to get a csv file of the ontology of NDFRT. The one I want is the latest one (From 2018), but there is no option of download. Moreover, when I try to access through the REST API, it says that its download is restricted. Is it possible to download it or is it a private file that I cannot have access to? Kind regards, Jorge _______________________________________________ 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 Feb 28 13:02:35 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 21:02:35 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Francis Nguyen In-Reply-To: <5e592e0e2df8d_478f24b79c031378@ncbo-prd-app-09.stanford.edu.mail> References: <5e592e0e2df8d_478f24b79c031378@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Francis, Thank you for contacting support. The /submissions endpoint is naturally a bit slower, as it retrieves roughly 1000 records without the benefit of pagination. That said, we?ve had some intermittent performance issues with our REST services around the time of your request. The endpoint is working fine on my end now. On a different note, this list is a public forum, and sharing your private API key with the entire community is never a good idea. I?ve invalidated the API key you shared and replaced it with a new one. There appears to be a different user attached to the API key you were using. Are the two of you part of the same organization? In any case, I?ll follow this up with a private email to the owner of the original API key (CCd), containing the new API key for the account. If you two are related, please ask him or her to share the new API key with you. Thanks, Michael On Feb 28, 2020, at 7:13 AM, support at bioontology.org wrote: Name: Francis Nguyen Email: fr.nguyen at mail.utoronto.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I'm trying to access the BioOntology API at: http://data.bioontology.org/submissions/?apikey=8ac0298d-99f4-4793-8c70-fb7d3400f279&display_context=false&display_links=false&include=acronym%2Cdescription%2Cname%2Contology%2Creleased%2Cstatus%2Cversion Unfortunately, I'm getting a blank page. This URL was working yesterday -- did something about the API change? Thank you for your time, Francis Nguyen _______________________________________________ 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 Feb 28 13:39:56 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 21:39:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Francis Nguyen In-Reply-To: References: <5e592e0e2df8d_478f24b79c031378@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <4ED9210A-AD93-4F0C-A5A4-8EA3B5F86398@stanford.edu> Super! Thanks a lot! Michael On Feb 28, 2020, at 1:18 PM, Francis Nguyen > wrote: Oh, my apologies, I wasn't aware this was a public forum -- I just used the "Contact Us" link at the bottom of the page. I just updated my API key on our end (And yes, Sergiu and I work together). Thank you for your help! -- Francis Nguyen On Fri, 28 Feb 2020 at 16:02, Michael Dorf > wrote: Hi Francis, Thank you for contacting support. The /submissions endpoint is naturally a bit slower, as it retrieves roughly 1000 records without the benefit of pagination. That said, we?ve had some intermittent performance issues with our REST services around the time of your request. The endpoint is working fine on my end now. On a different note, this list is a public forum, and sharing your private API key with the entire community is never a good idea. I?ve invalidated the API key you shared and replaced it with a new one. There appears to be a different user attached to the API key you were using. Are the two of you part of the same organization? In any case, I?ll follow this up with a private email to the owner of the original API key (CCd), containing the new API key for the account. If you two are related, please ask him or her to share the new API key with you. Thanks, Michael On Feb 28, 2020, at 7:13 AM, support at bioontology.org wrote: Name: Francis Nguyen Email: fr.nguyen at mail.utoronto.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I'm trying to access the BioOntology API at: http://data.bioontology.org/submissions/?apikey=8ac0298d-99f4-4793-8c70-fb7d3400f279&display_context=false&display_links=false&include=acronym%2Cdescription%2Cname%2Contology%2Creleased%2Cstatus%2Cversion Unfortunately, I'm getting a blank page. This URL was working yesterday -- did something about the API change? Thank you for your time, Francis Nguyen _______________________________________________ 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 Feb 28 14:09:12 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 22:09:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton In-Reply-To: <5e5939c5144f5_16ab243ddc832385@ncbo-prd-app-09.stanford.edu.mail> References: <5e5939c5144f5_16ab243ddc832385@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <40C2ABB6-84AE-45A2-B2D3-B1B1073962ED@stanford.edu> Hi Michele, Thank you for your email. The version of NCIT we host in BioPortal is provided to us directly by the NIH/NCI staff. I?ve CCd Gilberto Fragoso from NIH/NCI, who has been in charge of maintaining the BioPortal version of NCI Thesaurus. It looks like a new version (20.02d) of the ontology was uploaded to us recently (2/24/20). I hope Gilberto can offer some light on what changes have been introduced since the previous version (20.01d). Sorry, I couldn?t be more helpful, but Gilberto should be able to offer some assistance with your concerns. Thanks! Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 28, 2020, at 8:03 AM, support at bioontology.org wrote: Name: Michele LeNoue-Newton Email: michele.l.lenoue-newton at vumc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT Feedback: The latest version of the NCIT released in the BioPortal and used in applications like REDCap appears to be incomplete. It no longer contains many critical terms, including major disease classifications (Melanoma, Lung Adenocarcinoma) or single drug entities (carboplatin, cisplatin). _______________________________________________ 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 Feb 28 14:29:03 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 22:29:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton In-Reply-To: <40C2ABB6-84AE-45A2-B2D3-B1B1073962ED@stanford.edu> References: <5e5939c5144f5_16ab243ddc832385@ncbo-prd-app-09.stanford.edu.mail> <40C2ABB6-84AE-45A2-B2D3-B1B1073962ED@stanford.edu> Message-ID: Hi Michele, Upon further inspection, it looks like the latest version did process correctly, but the part that generates the index for searches had not fully completed. I?ll try to re-indexing it on my and and see if that addresses your issue. I?ll keep you posted. Thanks! Michael On Feb 28, 2020, at 2:09 PM, Michael Dorf > wrote: Hi Michele, Thank you for your email. The version of NCIT we host in BioPortal is provided to us directly by the NIH/NCI staff. I?ve CCd Gilberto Fragoso from NIH/NCI, who has been in charge of maintaining the BioPortal version of NCI Thesaurus. It looks like a new version (20.02d) of the ontology was uploaded to us recently (2/24/20). I hope Gilberto can offer some light on what changes have been introduced since the previous version (20.01d). Sorry, I couldn?t be more helpful, but Gilberto should be able to offer some assistance with your concerns. Thanks! Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 28, 2020, at 8:03 AM, support at bioontology.org wrote: Name: Michele LeNoue-Newton Email: michele.l.lenoue-newton at vumc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT Feedback: The latest version of the NCIT released in the BioPortal and used in applications like REDCap appears to be incomplete. It no longer contains many critical terms, including major disease classifications (Melanoma, Lung Adenocarcinoma) or single drug entities (carboplatin, cisplatin). _______________________________________________ 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 Feb 28 15:05:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 23:05:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton In-Reply-To: References: <5e5939c5144f5_16ab243ddc832385@ncbo-prd-app-09.stanford.edu.mail> <40C2ABB6-84AE-45A2-B2D3-B1B1073962ED@stanford.edu> Message-ID: Hi Michele, The reprocessing of NCIT has been completed. Looks like the search is now working properly. Let me know if any of the terms you are expecting to find are still missing. Thank you, Michael On Feb 28, 2020, at 2:31 PM, Lenoue-newton, Michele Laura > wrote: Hi Michael, Thanks for the update! -Michele From: Michael Dorf > Sent: Friday, February 28, 2020 4:29 PM To: support at bioontology.org Cc: Lenoue-newton, Michele Laura Subject: Re: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton Hi Michele, Upon further inspection, it looks like the latest version did process correctly, but the part that generates the index for searches had not fully completed. I?ll try to re-indexing it on my and and see if that addresses your issue. I?ll keep you posted. Thanks! Michael On Feb 28, 2020, at 2:09 PM, Michael Dorf > wrote: Hi Michele, Thank you for your email. The version of NCIT we host in BioPortal is provided to us directly by the NIH/NCI staff. I?ve CCd Gilberto Fragoso from NIH/NCI, who has been in charge of maintaining the BioPortal version of NCI Thesaurus. It looks like a new version (20.02d) of the ontology was uploaded to us recently (2/24/20). I hope Gilberto can offer some light on what changes have been introduced since the previous version (20.01d). Sorry, I couldn?t be more helpful, but Gilberto should be able to offer some assistance with your concerns. Thanks! Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 28, 2020, at 8:03 AM, support at bioontology.org wrote: Name: Michele LeNoue-Newton Email: michele.l.lenoue-newton at vumc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT Feedback: The latest version of the NCIT released in the BioPortal and used in applications like REDCap appears to be incomplete. It no longer contains many critical terms, including major disease classifications (Melanoma, Lung Adenocarcinoma) or single drug entities (carboplatin, cisplatin). _______________________________________________ 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 Feb 28 15:14:03 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 28 Feb 2020 23:14:03 +0000 Subject: [bioontology-support] NCIT Ontology csv Download Failed on BioPortal In-Reply-To: References: Message-ID: <3C06930E-D463-4307-A25E-D17A7D4C51F5@stanford.edu> Hi Xintong, The latest version of NCIT (20.02d) was uploaded on 2/24/20 and, for some reason, several parts of its processing workflow had not completed successfully. I?ve re-processed the ontology, and it?s now fully operational, including the availability of the CSV file. Let me know if you experience further issues. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 27, 2020, at 11:00 AM, Zhao,Xintong > wrote: Good Afternoon, This is Xintong, a graduate student trying to download your NCIT (National Cancer Institute Thesaurus) ontology (CSV format) from BioPortal. However, when I tried to download the csv file (Version 20.02d), the webpage returned error message as follows: { * - "errors": [ * "Cannot read latest submission upload file: /srv/ncbo/repository/NCIT/88/NCIT.csv.gz" ], * "status": 500 } I contacted ncicbiit at mail.nih.gov and they redirected me here. Could you check on that csv file please? Its download links for other format (such as RDF, OWL) works fine. Thank you for your help, Xintong _______________________________________________ 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 Feb 28 16:01:37 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Sat, 29 Feb 2020 00:01:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Tracy Safran In-Reply-To: <5e56d8c2541f9_71ac2a39c0493379@ncbo-prd-app-08.stanford.edu.mail> References: <5e56d8c2541f9_71ac2a39c0493379@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <57836EBC-FD3B-4FF8-B402-F5B0FC4A36AA@stanford.edu> Thank you for your report, Tracy. I?ve confirmed this behavior on my end. Indeed, it appears that our Mappings REST service does not always respect the ordering of the two target ontologies when returning results. I found other cases of this behavior. For example: http://bioportal.bioontology.org/mappings/show/SNOMEDCT?target=http://data.bioontology.org/ontologies/BRO I?ve created a bug report in our Github repository to track this issue: https://github.com/ncbo/ontologies_api/issues/63 We?ll try to keep you posted once we?ve had a chance to further look into this issue. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Feb 26, 2020, at 12:44 PM, support at bioontology.org wrote: Name: Tracy Safran Email: safrant at mail.nih.gov Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT%3Fp%3Dclasses Feedback: On the mappings page for NCI_Thesaurus http://bioportal.bioontology.org/ontologies/NCIT/?p=mappings you have a mapping to World Health Organization (WHO) Adverse Reaction Terminology. Within the mapping at http://bioportal.bioontology.org/mappings/show/NCIT?target=http://data.bioontology.org/ontologies/WHO-ART&height=600&width=800 the column names are reversed. The NCIt concepts are in the WHO column and vice versa. _______________________________________________ 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 fr.nguyen at mail.utoronto.ca Fri Feb 28 13:18:54 2020 From: fr.nguyen at mail.utoronto.ca (Francis Nguyen) Date: Fri, 28 Feb 2020 21:18:54 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Francis Nguyen In-Reply-To: References: <5e592e0e2df8d_478f24b79c031378@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Oh, my apologies, I wasn't aware this was a public forum -- I just used the "Contact Us" link at the bottom of the page. I just updated my API key on our end (And yes, Sergiu and I work together). Thank you for your help! -- Francis Nguyen On Fri, 28 Feb 2020 at 16:02, Michael Dorf > wrote: Hi Francis, Thank you for contacting support. The /submissions endpoint is naturally a bit slower, as it retrieves roughly 1000 records without the benefit of pagination. That said, we?ve had some intermittent performance issues with our REST services around the time of your request. The endpoint is working fine on my end now. On a different note, this list is a public forum, and sharing your private API key with the entire community is never a good idea. I?ve invalidated the API key you shared and replaced it with a new one. There appears to be a different user attached to the API key you were using. Are the two of you part of the same organization? In any case, I?ll follow this up with a private email to the owner of the original API key (CCd), containing the new API key for the account. If you two are related, please ask him or her to share the new API key with you. Thanks, Michael On Feb 28, 2020, at 7:13 AM, support at bioontology.org wrote: Name: Francis Nguyen Email: fr.nguyen at mail.utoronto.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I'm trying to access the BioOntology API at: http://data.bioontology.org/submissions/?apikey=8ac0298d-99f4-4793-8c70-fb7d3400f279&display_context=false&display_links=false&include=acronym%2Cdescription%2Cname%2Contology%2Creleased%2Cstatus%2Cversion Unfortunately, I'm getting a blank page. This URL was working yesterday -- did something about the API change? Thank you for your time, Francis Nguyen _______________________________________________ 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: