From JAHOON.KOO at UCDENVER.EDU Wed Jan 8 12:49:22 2020 From: JAHOON.KOO at UCDENVER.EDU (Koo, Jahoon) Date: Wed, 8 Jan 2020 20:49:22 +0000 Subject: [bioontology-support] Request for the VMWare Virtual Appliance Message-ID: Hi, This is a student worker from Health Data Compass on CU Anschutz campus. I would like to obtain the VMWare Virtual Appliance for a project that my team is currently working on. My BioPortal username is jahoon1998. The primary goal of our project is to figure out a NLP tool used in health data field that is appropriate for our domain's purpose. Currently, we are exploring Google's NLP tools and academic and open source NLP tools. For Google's NLP tools, we are looking into Cloud Healthcare API, Google Cloud AutoML Natural Language, Cloud Natural Language API, and Cloud Data Loss Prevention. Also, we are studying various academic and open source NLP tools used in health data, such as BioPortal, MetaMap, and CLAMP. For each tool, the notes, measures, and topics we will explore are: organization responsible for the tool, maintenance license (academic, commercial, open source), computer language, pre-trained algorithms availability, programmable/editable/extensible, difficulty to setup and use the tool, OS compatibility, standalone and/or web, time to process and complete an NLP task, number of items (term, section, negation, temporality, etc.) found, terminologies/Vocabularies used Permit term/vocabulary customization, corpora/Lexicon used, text processing, Bag of Words (BOW) and N-Grams Document, distance or similarity metric, Topic Models, Sections/Headers/Paragraphs/Sentences, Negation, Temporality (past, current and future events), Topic Modeling, Named Entity Recognition, Sentiment Analysis, Regular Expression, Acronyms and abbreviations, Measures/Quantities, HIPAA De-Identifying Elements. We will use MIMIC-III Clinical Database 1.4 to test different NLP tools, and our health data experts will evaluate the accuracy of results and compare results from different NLP tools. I have used the BioPortal REST API to run MIMIC dataset, but I have experienced the HTTP 414 error - URI Too Long and latency issue when annotating long texts from MIMIC dataset. Also, we will eventually run the tool with actual patient's' data and transmitting private data through REST API is not acceptable. Therefore, we prefer the local installation. Thank you. Jahoon -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Jan 8 15:31:20 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 8 Jan 2020 23:31:20 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Proteins In-Reply-To: <5e00d5e3b6e98_6e2e23f4858700a6@ncbo-prd-app-08.stanford.edu.mail> References: <5e00d5e3b6e98_6e2e23f4858700a6@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <147406EC-FD4E-4160-AE91-5E2B7EE813BD@stanford.edu> Hello Daniel, Apologies for a late reply. We are catching up with a backlog of tasks after Stanford?s 2 week winter closure. On Dec 23, 2019, at 6:57 AM, support at bioontology.org wrote: using the 'Term Search' endpoint in your REST API, I would like to receive the 'properties' field alongside the 'matchType' field. Right now it is only possible to receive the 'matchType' if I don't add the 'include' parameter. Using 'include=properties' removes the 'matchType' and the 'include' does not accept 'matchType'. Also, 'include=all' does not work. Is it possible to receive both fields in one response? Yes, you should be able to use matchType with the include parameter. However, as you reported above, the API is returning a 400 status code with message: "The `include` query string parameter cannot accept matchType, please use only prefLabel, synonym, definition, notation, cui, semanticType, properties" I?ve entered an issue in our tracker so that we can get this fixed: https://github.com/ncbo/ontologies_api/issues/62 Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 9 03:51:02 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 09 Jan 2020 03:51:02 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Dr. Karen Schomburg Message-ID: <5e1713a6bb0fe_2e072711e3c654ed@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From e13cook at gmail.com Thu Jan 9 08:38:08 2020 From: e13cook at gmail.com (Elizabeth Anderson) Date: Thu, 9 Jan 2020 09:38:08 -0700 Subject: [bioontology-support] Can't Download NCIT database Message-ID: <5e1756f2.1c69fb81.882ef.46c8@mx.google.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NCIT error message.JPG Type: image/jpeg Size: 16004 bytes Desc: not available URL: From vk396 at njit.edu Thu Jan 9 13:46:53 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Thu, 9 Jan 2020 16:46:53 -0500 Subject: [bioontology-support] Not able to use the ontology with the Annotator Message-ID: Hi, I had uploaded a new ontology (CIO_FirstEdition_Anchoring) on January 5th to BioPortal. I can view the classes but in the summary page next to the submission version it shows only Parsed and the metrics are not calculated (usually it shows - Parsed, Indexed, Metrics, Annotator). Is this the reason why I am not able to use this ontology in the Annotator for annotating the text? I am able to select this ontology from the list of ontologies but annotation is not giving any results. Could you please look into this? Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: From fragosog at mail.nih.gov Thu Jan 9 13:53:44 2020 From: fragosog at mail.nih.gov (Fragoso, Gilberto (NIH/NCI) [E]) Date: Thu, 9 Jan 2020 21:53:44 +0000 Subject: [bioontology-support] Can't Download NCIT database In-Reply-To: <5e1756f2.1c69fb81.882ef.46c8@mx.google.com> References: <5e1756f2.1c69fb81.882ef.46c8@mx.google.com> Message-ID: Hello Elizabeth, This seems to be an issue at the BioPortal. I'm cc'ing them as they'll probably need to jump in and examine the ncit.csv.gz file. I examined the available OWL and RDF/XML files in the BioPortal's NCIT download area and the files look good. However, although I was able to download the gzipped CSV file, I couldn't extract it from the archive. The archiver also reports that the decompressed file is 4 GB in size, which seems somewhat high to me. Depending on what the group at BioPortal finds out we might need to reprocess our file and resubmit it. For other options in the meantime, and if you don't need the CSV format, you could download the NCIt OWL or RDF/XML files from BioPortal, or the RDF/XML from our FTP site (ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/), or the OBO edition of the NCIt from http://obofoundry.org/ontology/ncit.html. We also have a flat file version in our FTP site, but I don't know how it compares to the CSV distribution. Regards, Gilberto Fragoso ________________________________ From: Elizabeth Anderson Sent: Thursday, January 9, 2020 11:38 AM To: NCI CBIIT Subject: [bioontology-support] Can't Download NCIT database To whom it may be concerned, My name is Elizabeth Anderson and I?m developing a web tool that programmatically accesses information from BioPortal for analyses, and I?ve been using the NCIT database for about nine months (https://bioportal.bioontology.org/ontologies/NCIT). Within the last few days, I?ve been trying to access it and I get a server 500 error that says ?Cannot read the latest submission upload file: /srv/ncbo/repository/NCIT/86/NCIT.csv.gz.? I?ve attached an image of the error I receive. It seems like there was an update to the database on December 30 and I was wondering if this might have caused the error. The NCIT database has been an essential and wonderful asset in the development of my web tool and I am hoping that the error can be fixed so my tool can be used to its full potential. Thank you for all the work you?ve put into it! Sincerely, Elizabeth Elizabeth Cook Anderson e13cook at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Jan 9 14:16:26 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 9 Jan 2020 22:16:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Dr. Karen Schomburg In-Reply-To: <5e1713a6bb0fe_2e072711e3c654ed@ncbo-prd-app-08.stanford.edu.mail> References: <5e1713a6bb0fe_2e072711e3c654ed@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <3789317C-FF06-4F79-9791-32FBDDC9655A@stanford.edu> Hello Karen, Yes, it?s correct that we limit the results to 25. We do this for performance reasons, as running the recommender can be an expensive operation - particularly if users are submitting long text, and/or asking for ontology groups in the results (pick 3 or 4 best). I?m not aware of any way that you could work around this, short of downloading our virtual appliance and customizing the code (BioPortal is open source). Kind regards, Jennifer On Jan 9, 2020, at 3:51 AM, support at bioontology.org wrote: Name: Dr. Karen Schomburg Email: karen.schomburg at osthus.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Frecommender Feedback: Dear Sir or Madam, I am figuring out how to use the "Recommender" best, and found that when I submit keywords, the returned list of matching ontologies is at most 25. Is that correct? Is there a parameter to the REST-API how I can change that maximum to e.g. 50? Best, Karen Schomburg _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Jan 9 14:35:27 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 9 Jan 2020 22:35:27 +0000 Subject: [bioontology-support] Can't Download NCIT database In-Reply-To: References: <5e1756f2.1c69fb81.882ef.46c8@mx.google.com> Message-ID: Hello Elizabeth, Gilberto is correct - the issue was on our end. An error occurred in our system on the first attempt to process this latest version of NCIT. I?ve reprocessed the ontology, which is now fully available in BioPortal (including the CSV file). Apologies for the inconvenience. Kind regards, Jennifer GitHub issue for reference: https://github.com/ncbo/bioportal-project/issues/143 On Jan 9, 2020, at 1:53 PM, Fragoso, Gilberto (NIH/NCI) [E] > wrote: Hello Elizabeth, This seems to be an issue at the BioPortal. I'm cc'ing them as they'll probably need to jump in and examine the ncit.csv.gz file. I examined the available OWL and RDF/XML files in the BioPortal's NCIT download area and the files look good. However, although I was able to download the gzipped CSV file, I couldn't extract it from the archive. The archiver also reports that the decompressed file is 4 GB in size, which seems somewhat high to me. Depending on what the group at BioPortal finds out we might need to reprocess our file and resubmit it. For other options in the meantime, and if you don't need the CSV format, you could download the NCIt OWL or RDF/XML files from BioPortal, or the RDF/XML from our FTP site (ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/), or the OBO edition of the NCIt from http://obofoundry.org/ontology/ncit.html. We also have a flat file version in our FTP site, but I don't know how it compares to the CSV distribution. Regards, Gilberto Fragoso ________________________________ From: Elizabeth Anderson > Sent: Thursday, January 9, 2020 11:38 AM To: NCI CBIIT > Subject: [bioontology-support] Can't Download NCIT database To whom it may be concerned, My name is Elizabeth Anderson and I?m developing a web tool that programmatically accesses information from BioPortal for analyses, and I?ve been using the NCIT database for about nine months (https://bioportal.bioontology.org/ontologies/NCIT). Within the last few days, I?ve been trying to access it and I get a server 500 error that says ?Cannot read the latest submission upload file: /srv/ncbo/repository/NCIT/86/NCIT.csv.gz.? I?ve attached an image of the error I receive. It seems like there was an update to the database on December 30 and I was wondering if this might have caused the error. The NCIT database has been an essential and wonderful asset in the development of my web tool and I am hoping that the error can be fixed so my tool can be used to its full potential. Thank you for all the work you?ve put into it! Sincerely, Elizabeth Elizabeth Cook Anderson e13cook at gmail.com _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Jan 9 14:56:59 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 9 Jan 2020 22:56:59 +0000 Subject: [bioontology-support] Not able to use the ontology with the Annotator In-Reply-To: References: Message-ID: Hello Vipina, Apologies for the inconvenience. An error occurred in our system on the initial attempt to process your ontology. I?ve reprocessed your submission, which is now fully available in BioPortal. I also confirmed that the Annotator includes your ontology in result sets. Kind regards, Jennifer > On Jan 9, 2020, at 1:46 PM, Kuttichi Keloth, Vipina wrote: > > Hi, > > I had uploaded a new ontology (CIO_FirstEdition_Anchoring) on January 5th to BioPortal. I can view the classes but in the summary page next to the submission version it shows only Parsed and the metrics are not calculated (usually it shows - Parsed, Indexed, Metrics, Annotator). > > Is this the reason why I am not able to use this ontology in the Annotator for annotating the text? > I am able to select this ontology from the list of ontologies but annotation is not giving any results. > > Could you please look into this? > > Thank you. > Vipina > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From support at bioontology.org Fri Jan 10 04:31:15 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 10 Jan 2020 04:31:15 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Roman Baum Message-ID: <5e186e93eadf2_9361da6fa058311@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Jan 10 11:15:26 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 10 Jan 2020 19:15:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Roman Baum In-Reply-To: <5e186e93eadf2_9361da6fa058311@ncbo-prd-app-08.stanford.edu.mail> References: <5e186e93eadf2_9361da6fa058311@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Roman, On Jan 10, 2020, at 4:31 AM, support at bioontology.org wrote: Name: Roman Baum Email: baum at zbmed.de Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FICD10 Feedback: Hi, I have a question about the ICD10 ontology. There seems to be an error with the ontology. I can not browse it Could you be more specific about what you mean when you say you can?t browse it? Are you seeing some kind of error in the browser window? I looked at ICD10 this morning, and I?m not able to reproduce any kind of errors on my end (see screen shot below of the class tree). and I can also not download it. https://bioportal.bioontology.org/ontologies/ICD10 Is there a specific reason for that or is this just a bug? We are unable to offer downloads of the ICD10 ontology source file due to licensing restrictions. Kind regards, Jennifer [cid:6C224E0B-BC3C-4683-B883-5FF74051AB2F at stanford.edu] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-01-10 11.11.29.png Type: image/png Size: 235628 bytes Desc: Screenshot 2020-01-10 11.11.29.png URL: From vk396 at njit.edu Mon Jan 13 08:33:15 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 13 Jan 2020 11:33:15 -0500 Subject: [bioontology-support] Error RDF labels - CC_SNOMED Message-ID: Hi, I recently submitted a new version of CC_SNOMED on BioPortal. But the submission shows "Error RDF labels". I have changed the labels of the concepts (with respect to the previous version). I loaded the ontology on Protege and it works fine. So I am wondering whether it is because of this issue ( https://github.com/ncbo/ncbo_annotator/issues/8) which previously Mr. Dorf informed me of that prevents regular Annotator refreshes. If so could you please refresh it and archive previous versions. Or else please let me know what the problem is. Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 13 09:33:50 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 13 Jan 2020 17:33:50 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Roman Baum In-Reply-To: <30d6c70b-d7d3-2781-ff07-90189fd0d1bf@zbmed.de> References: <5e186e93eadf2_9361da6fa058311@ncbo-prd-app-08.stanford.edu.mail> <30d6c70b-d7d3-2781-ff07-90189fd0d1bf@zbmed.de> Message-ID: Hello Roman, Yes - as I mentioned in my previous reply - we are unable to offer downloads of the ICD10 ontology source file due to licensing restrictions. Kind regards, Jennifer On Jan 13, 2020, at 1:33 AM, Roman Baum > wrote: Hi Jennifer, thanks for your answer. Last Week it got an error message when i click on the tab 'Classes' for ICD10. That works for me today. Is there also a possibility to download the current Ontology from BioPortal? Probably there are some license issues? Thanks again for your reply, Roman Am 10.01.20 um 20:15 schrieb Jennifer Leigh Vendetti: Hello Roman, On Jan 10, 2020, at 4:31 AM, support at bioontology.org wrote: Name: Roman Baum Email: baum at zbmed.de Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FICD10 Feedback: Hi, I have a question about the ICD10 ontology. There seems to be an error with the ontology. I can not browse it Could you be more specific about what you mean when you say you can?t browse it? Are you seeing some kind of error in the browser window? I looked at ICD10 this morning, and I?m not able to reproduce any kind of errors on my end (see screen shot below of the class tree). and I can also not download it. https://bioportal.bioontology.org/ontologies/ICD10 Is there a specific reason for that or is this just a bug? We are unable to offer downloads of the ICD10 ontology source file due to licensing restrictions. Kind regards, Jennifer -- Roman Baum Softwareentwickler Wissensmanagement|ZB MED Informationszentrum Lebenswissenschaften Ag Informationsmanagement|Institut f?r Geod?sie und Geoinformation|Universit?t Bonn Katzenburgweg 1a|53115 Bonn|Email: baum at zbmed.de|Tel. 0228 73 5215 https://www.openstreetmap.org/?mlat=50.72501&mlon=7.08991#map=17/50.72501/7.08991 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jan 13 17:19:34 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 14 Jan 2020 01:19:34 +0000 Subject: [bioontology-support] Error RDF labels - CC_SNOMED In-Reply-To: References: Message-ID: <9B7F8FB6-DB23-4503-BE76-F7AE25FC4580@stanford.edu> Hi Vipina, Thank you for your email. There doesn?t appear to be anything wrong with your ontology. I?ve checked the parsing logs, and it looks like there was an error while processing the latest version of CC_SNOMED on its initial submission. The cause isn?t totally clear, but is most likely just incidental. I?ve reprocessed the ontology, and the process completed fully this time with no issues. The ontology is now fully usable/browsable. Let me know if you run into any further issues. Thanks! Michael On Jan 13, 2020, at 8:33 AM, Kuttichi Keloth, Vipina > wrote: Hi, I recently submitted a new version of CC_SNOMED on BioPortal. But the submission shows "Error RDF labels". I have changed the labels of the concepts (with respect to the previous version). I loaded the ontology on Protege and it works fine. So I am wondering whether it is because of this issue (https://github.com/ncbo/ncbo_annotator/issues/8) which previously Mr. Dorf informed me of that prevents regular Annotator refreshes. If so could you please refresh it and archive previous versions. Or else please let me know what the problem is. Thank you. Vipina _______________________________________________ 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 Wed Jan 15 08:34:25 2020 From: JAHOON.KOO at UCDENVER.EDU (Koo, Jahoon) Date: Wed, 15 Jan 2020 16:34:25 +0000 Subject: [bioontology-support] Question about the VMWare Virtual Appliance Message-ID: Hi, This is Jahoon, a student worker from Health Data Compass on CU Anschutz campus. I got a permission for the installation last Wednesday, but I was on a vacation and just got back. It seems like I get the 500 Internal Server Error from the link for the installation provided in the email. My BioPortal username is jahoon1998. Could you please double check it? Thank you. Jahoon -------------- next part -------------- An HTML attachment was scrubbed... URL: From kh.kim at mediex.co.kr Tue Jan 14 23:26:29 2020 From: kh.kim at mediex.co.kr (=?UTF-8?B?6rmA6rK97ZiE?=) Date: Wed, 15 Jan 2020 16:26:29 +0900 Subject: [bioontology-support] About "Anatomical Therapeutic Chemical" Classification version Message-ID: Hello~ I am Kyunghyun Kim and working as a Clinical Data Manager. I would like to ask you a question. In REDCap system(https://projectredcap.org/), I set up to use Anatomical Therapeutic Chemical Classification (Last uploaded: November 18, 2019) [image: image.png] [image: image.png] and I wanted to look up "mosapride(A03FA09)" in the ATC but there was no matching result. so, I searched the "mosapride" at WHOCC(https://www.whocc.no/atc_ddd_index/ ) [image: image.png] In other words, BioPotal's ATC code version(2019-11-18) and WHOCC's version (2019-12-16) are different. Do you have update cycle? when can I expect to find "mosapride(A03FA09)" in BioPotal's ATC? I am looking forward to hearing from you soon. thank you in advance. *????????????????????????????**??????????????**??**??* [image: MedicalExcellence] *??? ?? ??? ??? ???? **???? ??? ???? ??? ???? ?????.* *??? (Kyunghyun Kim) DBP/CDM* *Clinical Data Management Team**?** MedicalExcellence Inc.* 06591) 222 Banpo Road, Seocho-Gu, Seoul, KOREA T. 02-2258-7869 ? F. 02-6209-7800 ? E. *kh.kim at mediex.co.kr * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 85359 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82034 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 85484 bytes Desc: not available URL: From support at bioontology.org Wed Jan 15 08:07:34 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 15 Jan 2020 08:07:34 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Ning "Sunny" Shang Message-ID: <5e1f38c67181d_17782ca189877613@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jan 15 08:45:06 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 15 Jan 2020 08:45:06 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Mark A Miller Message-ID: <5e1f41923da9f_1581248616827259@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 15 11:21:24 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 15 Jan 2020 19:21:24 +0000 Subject: [bioontology-support] Question about the VMWare Virtual Appliance In-Reply-To: References: Message-ID: Hi Jahoon, Thanks for your email. We?ve experienced an unscheduled outage this morning around the time of your email. The download page should be back up now. Please try downloading the file again and let me know if you continue experiencing issues. Thanks, Michael On Jan 15, 2020, at 8:34 AM, Koo, Jahoon > wrote: Hi, This is Jahoon, a student worker from Health Data Compass on CU Anschutz campus. I got a permission for the installation last Wednesday, but I was on a vacation and just got back. It seems like I get the 500 Internal Server Error from the link for the installation provided in the email. My BioPortal username is jahoon1998. Could you please double check it? Thank you. 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 mdorf at stanford.edu Wed Jan 15 11:25:47 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 15 Jan 2020 19:25:47 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark A Miller In-Reply-To: <5e1f41923da9f_1581248616827259@ncbo-prd-app-08.stanford.edu.mail> References: <5e1f41923da9f_1581248616827259@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Mark, Thank you for bringing this to our attention. We?ve had a BioPortal outage this morning, which has now been resolved. Apologies for the interruption. Please let us know if you experience any further issues. Thanks, Michael On Jan 15, 2020, at 8:45 AM, support at bioontology.org wrote: Name: Mark A Miller Email: markampa at pennmedicine.upenn.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: BioPortal web site is offline as of 11:45 EST 2020-01-15 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 15 11:27:31 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 15 Jan 2020 19:27:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Ning "Sunny" Shang In-Reply-To: <5e1f38c67181d_17782ca189877613@ncbo-prd-app-09.stanford.edu.mail> References: <5e1f38c67181d_17782ca189877613@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <40E8D406-01B6-436C-81A0-ECFB80A8A083@stanford.edu> Hi Sunny, Thank you for your email. We?ve had a BioPortal outage this morning, which has now been resolved. Apologies for the interruption. I?ve checked your search query, and it appears to work properly at this point. Please let us know if you experience any further issues. Thanks, Michael On Jan 15, 2020, at 8:07 AM, support at bioontology.org wrote: Name: Ning "Sunny" Shang Email: sunnyshang001 at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I am using BioPortal REST API to query bioPortal, but I got Server returned HTTP request 401 error for URL http://data.bioontology.org/search?q=asthma. Please advise if there is any problem with account (e.g. API key). My user name is sunnyshang001. Thank you so much. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Jan 15 11:52:14 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 15 Jan 2020 19:52:14 +0000 Subject: [bioontology-support] About "Anatomical Therapeutic Chemical" Classification version In-Reply-To: References: Message-ID: <7B3A0815-7BE7-439C-B092-AA615F5281FB@stanford.edu> Hi Kyunghyun, Thank you for contacting support. 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). ATC is one of the vocabularies contained in the UMLS distribution. So, the version numbers for ATC that you see in BioPortal correspond to UMLS releases, e.g., 2019AA, 2019AB, etc. Their current released version is 2019AB, which is what we have in BioPortal [2]. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies included in the UMLS distribution. Looking at the UMLS details page for ATC [3], it appears to be updated annually. Hopefully, the May UMLS release (2020AA) will contain the up-to-date version of ATC. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ [2] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html [3] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC/index.html On Jan 14, 2020, at 11:26 PM, ??? > wrote: Hello~ I am Kyunghyun Kim and working as a Clinical Data Manager. I would like to ask you a question. In REDCap system(https://projectredcap.org/), I set up to use Anatomical Therapeutic Chemical Classification (Last uploaded: November 18, 2019) and I wanted to look up "mosapride(A03FA09)" in the ATC but there was no matching result. so, I searched the "mosapride" at WHOCC(https://www.whocc.no/atc_ddd_index/) In other words, BioPotal's ATC code version(2019-11-18) and WHOCC's version (2019-12-16) are different. Do you have update cycle? when can I expect to find "mosapride(A03FA09)" in BioPotal's ATC? I am looking forward to hearing from you soon. thank you in advance. ?????????????????????????????????????????????? [MedicalExcellence] ??? ?? ??? ??? ???? ???? ??? ???? ??? ???? ?????. ??? (Kyunghyun Kim) DBP/CDM Clinical Data Management Team? MedicalExcellence Inc. 06591) 222 Banpo Road, Seocho-Gu, Seoul, KOREA T. 02-2258-7869 ? F. 02-6209-7800 ? E. kh.kim at mediex.co.kr _______________________________________________ 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 rossella.troia at emnitaly.org Thu Jan 16 05:59:15 2020 From: rossella.troia at emnitaly.org (Rossella Troia) Date: Thu, 16 Jan 2020 14:59:15 +0100 Subject: [bioontology-support] Current Meddra Version Message-ID: Dear Bioontology team, could you please clarify to which Meddra version correspond the 2019AB version of Bioportal? Thank you for your support. Rossella -- Fondazione EMN Italy Onlus Sede operativa: *Via Nizza 52 - 10126 TorinoPhone+39 011 0243236** Fax +39 011 0133182* Sede legale: *Via Saluzzo, 1/A - 10125 Torino* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Jan 16 11:34:31 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 16 Jan 2020 19:34:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Ning "Sunny" Shang In-Reply-To: References: <5e1f38c67181d_17782ca189877613@ncbo-prd-app-09.stanford.edu.mail> <40E8D406-01B6-436C-81A0-ECFB80A8A083@stanford.edu> Message-ID: <7F8B34D5-8263-4508-AE98-122A5B15027C@stanford.edu> Hi Sunny, You can pass a parameter ?download_format=rdf? to download the RDF version of an ontology. http://data.bioontology.org/ontologies/ECO/download?apikey=your_api_key&download_format=rdf Our REST services documentation [1] contains a list of common parameters available in the bulk of our endpoints. When replying, please use the ?Reply All? feature of your email client so that it?s routed to our support list, which is actively monitored by our entire team. Thanks again for contacting us. Michael [1] http://data.bioontology.org/documentation On Jan 16, 2020, at 8:20 AM, Sunny Shang > wrote: Hello Michael, Thank you so much for your quick response and fix. I use BioPortal api to search relevant ontologies and to download them programmatically. However, I only know how to download it as owl file through http://data.bioontology.org/ontologies/mesh/download as an example. Can you advise if there is a way to download corresponding rdf file? Best regards, Sunny On Wed, Jan 15, 2020 at 2:27 PM Michael Dorf > wrote: Hi Sunny, Thank you for your email. We?ve had a BioPortal outage this morning, which has now been resolved. Apologies for the interruption. I?ve checked your search query, and it appears to work properly at this point. Please let us know if you experience any further issues. Thanks, Michael On Jan 15, 2020, at 8:07 AM, support at bioontology.org wrote: Name: Ning "Sunny" Shang Email: sunnyshang001 at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: I am using BioPortal REST API to query bioPortal, but I got Server returned HTTP request 401 error for URL http://data.bioontology.org/search?q=asthma. Please advise if there is any problem with account (e.g. API key). My user name is sunnyshang001. Thank you so much. _______________________________________________ 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 Jan 17 12:37:27 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 17 Jan 2020 20:37:27 +0000 Subject: [bioontology-support] Current Meddra Version In-Reply-To: References: Message-ID: Hi Rossella, Thank you for your email. 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). MEDDRA is one of the vocabularies contained in the UMLS distribution. The UMLS metadata page for MEDDRA [3] shows the version to be MDR22_0 (Version 22.0). Hope this is what you were looking for. Let us know if you require further assistance. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html On Jan 16, 2020, at 5:59 AM, Rossella Troia > wrote: Dear Bioontology team, could you please clarify to which Meddra version correspond the 2019AB version of Bioportal? Thank you for your support. Rossella -- [http://fonesa.it/assets/logo.png] Fondazione EMN Italy Onlus Sede operativa: Via Nizza 52 - 10126 Torino Phone+39 011 0243236 Fax +39 011 0133182 Sede legale: Via Saluzzo, 1/A - 10125 Torino _______________________________________________ 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 sunnyshang001 at gmail.com Fri Jan 17 08:37:29 2020 From: sunnyshang001 at gmail.com (Sunny Shang) Date: Fri, 17 Jan 2020 11:37:29 -0500 Subject: [bioontology-support] [BioPortal] Feedback from Ning "Sunny" Shang In-Reply-To: <7F8B34D5-8263-4508-AE98-122A5B15027C@stanford.edu> References: <5e1f38c67181d_17782ca189877613@ncbo-prd-app-09.stanford.edu.mail> <40E8D406-01B6-436C-81A0-ECFB80A8A083@stanford.edu> <7F8B34D5-8263-4508-AE98-122A5B15027C@stanford.edu> Message-ID: Thank you very much, Michael! Yes, I will reply-all for the communications. Best regards, Sunny On Thu, Jan 16, 2020 at 2:34 PM Michael Dorf wrote: > Hi Sunny, > > You can pass a parameter ?download_format=rdf? to download the RDF version > of an ontology. > > > http://data.bioontology.org/ontologies/ECO/download?apikey=your_api_key&download_format=rdf > > Our REST services documentation [1] contains a list of common parameters > available in the bulk of our endpoints. > > When replying, please use the ?Reply All? feature of your email client so > that it?s routed to our support list, which is actively monitored by our > entire team. > > Thanks again for contacting us. > > Michael > > [1] http://data.bioontology.org/documentation > > > On Jan 16, 2020, at 8:20 AM, Sunny Shang wrote: > > Hello Michael, > Thank you so much for your quick response and fix. > I use BioPortal api to search relevant ontologies and to download them > programmatically. However, I only know how to download it as owl file > through http://data.bioontology.org/ontologies/mesh/download as an > example. Can you advise if there is a way to download corresponding rdf > file? > Best regards, > Sunny > > On Wed, Jan 15, 2020 at 2:27 PM Michael Dorf wrote: > >> Hi Sunny, >> >> Thank you for your email. We?ve had a BioPortal outage this morning, >> which has now been resolved. Apologies for the interruption. I?ve checked >> your search query, and it appears to work properly at this point. >> >> Please let us know if you experience any further issues. >> >> Thanks, >> >> Michael >> >> >> On Jan 15, 2020, at 8:07 AM, support at bioontology.org wrote: >> >> Name: Ning "Sunny" Shang >> >> Email: sunnyshang001 at gmail.com >> >> Location: http%3A%2F%2Fbioportal.bioontology.org >> %2F500 >> >> >> *Feedback:* >> >> I am using BioPortal REST API to query bioPortal, but I got Server >> returned HTTP request 401 error for URL >> http://data.bioontology.org/search?q=asthma. Please advise if there is >> any problem with account (e.g. API key). >> My user name is sunnyshang001. >> Thank you so much. >> >> _______________________________________________ >> 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 rossella.troia at emnitaly.org Mon Jan 20 00:40:29 2020 From: rossella.troia at emnitaly.org (Rossella Troia) Date: Mon, 20 Jan 2020 09:40:29 +0100 Subject: [bioontology-support] Current Meddra Version In-Reply-To: References: Message-ID: Dear Michael, thank you for your clarification. This is exactly what I was looking for. BR, Rossella -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 23 05:41:49 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 23 Jan 2020 05:41:49 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Steven Paul Emrick Message-ID: <5e29a29db757a_5b7d24696bc26468@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 23 05:40:05 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 23 Jan 2020 05:40:05 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Allyson Lister Message-ID: <5e29a23594e16_7b0b233881033743@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Jan 23 15:15:59 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 23 Jan 2020 23:15:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Steven Paul Emrick In-Reply-To: <5e29a29db757a_5b7d24696bc26468@ncbo-prd-app-08.stanford.edu.mail> References: <5e29a29db757a_5b7d24696bc26468@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <1AC5C83A-F2C8-4D0D-90D8-9377AA0C036F@stanford.edu> Hi Steven, Allyson, and others inconvenienced this morning, With apologies for the belated notice: The system was in fact down this morning, and some services were intermittently offline in the hours preceding its outage. We had a sudden surge of requests that led to the outage, and brought it back online by about 9:45 AM PT (1645 GMT). We are investigating the original cause and will look to address that problem as well. Thank you for your reports. John On Jan 23, 2020, at 5:41 AM, support at bioontology.org wrote: Name: Steven Paul Emrick Email: spe at usp.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hello - I am trying to access the Allotrope Foundational Ontology at this URL: https://bioportal.bioontology.org/ontologies/AFO I'm getting an error message - is the site functioning properly? Thank you. From: support at bioontology.org Subject: [bioontology-support] [BioPortal] Feedback from Allyson Lister Date: January 23, 2020 at 5:40:05 AM PST To: support at bioontology.org, contact at fairsharing.org Name: Allyson Lister Email: contact at fairsharing.org Location: http%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Trying to view any ontology in BioPortal, e.g. http://bioportal.bioontology.org/ontologies/PTO, is resulting in what I believe is a 500 error, and a message stating "We're sorry but something has gone wrong. We have been notified of this error." Is there something wrong with the site, or is it just me? thanks :) Allyson ======================== 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 alexgarciac at gmail.com Fri Jan 24 04:10:02 2020 From: alexgarciac at gmail.com (Alexander Garcia Castro) Date: Fri, 24 Jan 2020 13:10:02 +0100 Subject: [bioontology-support] bioportal down? Message-ID: hi, is bioportal alive? I am getting a very very long waiting time until I get a non response error. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac -------------- next part -------------- An HTML attachment was scrubbed... URL: From amassengale at rsna.org Fri Jan 24 05:58:00 2020 From: amassengale at rsna.org (Andrew Massengale) Date: Fri, 24 Jan 2020 13:58:00 +0000 Subject: [bioontology-support] Bio Portal API not working Message-ID: 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 jgraybeal at stanford.edu Fri Jan 24 13:53:27 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 Jan 2020 21:53:27 +0000 Subject: [bioontology-support] bioportal down? In-Reply-To: References: Message-ID: <553229FA-7DDE-4EC1-943C-5717F224E774@stanford.edu> Apologies again to the list, for the problem and the noise on the list. We are seeing an intermittent problem that is proving difficult to track down. It does not take the system down entirely but causes persistent issues for a significant percentage of users. I appreciate the details that you have provided in your emails, and we are digging more deeply into the root causes of this issue. Because the latest issues have always happened at night local time (twice at 1200 GMT, once at 0900 GMT), the issues have lasted longer than we like in each case. We are evaluating how we can improve monitoring and remediation for issues like this, and we are open to your suggestions. John On Jan 24, 2020, at 4:10 AM, Alexander Garcia Castro > wrote: hi, is bioportal alive? I am getting a very very long waiting time until I get a non response error. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac On Jan 24, 2020, at 5:58 AM, Andrew Massengale > wrote: 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 ======================== 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 SPE at USP.org Thu Jan 23 17:19:26 2020 From: SPE at USP.org (Steven P. Emrick) Date: Fri, 24 Jan 2020 01:19:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Steven Paul Emrick In-Reply-To: <1AC5C83A-F2C8-4D0D-90D8-9377AA0C036F@stanford.edu> References: <5e29a29db757a_5b7d24696bc26468@ncbo-prd-app-08.stanford.edu.mail>, <1AC5C83A-F2C8-4D0D-90D8-9377AA0C036F@stanford.edu> Message-ID: Thank you John for the prompt response. Best Steve Get Outlook for Android ________________________________ From: John Graybeal Sent: Thursday, January 23, 2020 6:15:59 PM To: NCBO User Support Cc: Steven P. Emrick ; FAIRsharing Team Subject: Re: [bioontology-support] [BioPortal] Feedback from Steven Paul Emrick Hi Steven, Allyson, and others inconvenienced this morning, With apologies for the belated notice: The system was in fact down this morning, and some services were intermittently offline in the hours preceding its outage. We had a sudden surge of requests that led to the outage, and brought it back online by about 9:45 AM PT (1645 GMT). We are investigating the original cause and will look to address that problem as well. Thank you for your reports. John On Jan 23, 2020, at 5:41 AM, support at bioontology.org wrote: Name: Steven Paul Emrick Email: spe at usp.org Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hello - I am trying to access the Allotrope Foundational Ontology at this URL: https://bioportal.bioontology.org/ontologies/AFO I'm getting an error message - is the site functioning properly? Thank you. From: support at bioontology.org Subject: [bioontology-support] [BioPortal] Feedback from Allyson Lister Date: January 23, 2020 at 5:40:05 AM PST To: support at bioontology.org, contact at fairsharing.org Name: Allyson Lister Email: contact at fairsharing.org Location: http%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Trying to view any ontology in BioPortal, e.g. http://bioportal.bioontology.org/ontologies/PTO, is resulting in what I believe is a 500 error, and a message stating "We're sorry but something has gone wrong. We have been notified of this error." Is there something wrong with the site, or is it just me? thanks :) Allyson ======================== 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 Fri Jan 24 09:33:38 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 24 Jan 2020 09:33:38 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Victoria Young Message-ID: <5e2b2a72b8063_1f931ea28501132b@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Jan 24 00:27:29 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 24 Jan 2020 00:27:29 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Aritz Bilbao Message-ID: <5e2aaa71775f3_25702fa7f887334d@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 28 08:37:54 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 28 Jan 2020 08:37:54 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Mark McDowall Message-ID: <5e3063627e4c9_19b32a1f9943947a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 28 12:03:01 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 28 Jan 2020 20:03:01 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark McDowall In-Reply-To: <5e3063627e4c9_19b32a1f9943947a@ncbo-prd-app-09.stanford.edu.mail> References: <5e3063627e4c9_19b32a1f9943947a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <7432026F-5F3E-40B4-8ED0-03E8D913E684@stanford.edu> Apologies Mark. The latest submission from Jan. 15th didn?t fully process in our system. I reprocessed manually and the CSV is available now. Kind regards, Jennifer On Jan 28, 2020, at 8:37 AM, support at bioontology.org wrote: Name: Mark McDowall Email: mark at scibite.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FEFO Feedback: Hi, Was trying to download the EFO csv file and I am getting an HTTP 500 error. Cheers, Mark _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 28 15:27:07 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 28 Jan 2020 15:27:07 -0800 Subject: [bioontology-support] [BioPortal] Feedback from ubcarc_admin Message-ID: <5e30c34be2d83_7d8d2372268125cb@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 28 15:50:40 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 28 Jan 2020 23:50:40 +0000 Subject: [bioontology-support] [BioPortal] Feedback from ubcarc_admin In-Reply-To: <5e30c34be2d83_7d8d2372268125cb@ncbo-prd-app-09.stanford.edu.mail> References: <5e30c34be2d83_7d8d2372268125cb@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <995D4A7C-9B9A-4E7F-8986-6D34880AFAF4@stanford.edu> Hello Michael, Apologies that you?re having trouble logging in. I double-checked the site and your account and don?t see any issues at the moment. We had to clear our application caches a couple of times today as part of troubleshooting an ontology processing issue. I?m wondering if you?d be willing to do a hard refresh of the BioPortal home page (http://bioportal.bioontology.org/), then try logging in again. You can perform a hard refresh of the page with Cmd + Shift + R on the Mac, or Ctrl + Shift + R on Windows. If that doesn?t work, I?d like to try clearing your browser cache for BioPortal altogether. If you let us know what browser you?re working with, we could help you with instructions. Kind regards, Jennifer On Jan 28, 2020, at 3:27 PM, support at bioontology.org wrote: Name: ubcarc_admin Email: arc.admin at ubc.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hello, When I tried to login to our account, ubcarc_admin, today at https://bioportal.bioontology.org/, I got the following error message "We're sorry but something has gone wrong. We have been notified of this error.". We are wondering what the error means? Also how can we go about fixing the issue. We appreciate all of your help. You can contact me at arc.admin at ubc.ca or michael.tang at ubc.ca Many thanks, Michael Michael Tang Scientific Analyst Advanced Research Computing | Office of the Vice-President, Research & Innovation The University of British Columbia | Vancouver Campus | x?m??k??y??m (Musqueam) Traditional Territory Room 112A 2386 East Mall | Vancouver BC | V6T 1Z3 Canada Phone 604 827 3727 michael.tang at ubc.ca https://arc.ubc.ca/ _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 28 22:06:52 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 28 Jan 2020 22:06:52 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Balambal Narayanan Message-ID: <5e3120fcd546d_a71219641c5678e@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Jan 30 16:09:39 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 31 Jan 2020 00:09:39 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Balambal Narayanan In-Reply-To: <5e3120fcd546d_a71219641c5678e@ncbo-prd-app-09.stanford.edu.mail> References: <5e3120fcd546d_a71219641c5678e@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Balambal, On Jan 28, 2020, at 10:06 PM, support at bioontology.org wrote: Name: Balambal Narayanan Email: BALAMBAL.NARAYAN at Pfizer.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FMEDDRA%252F10051118%26jump_to_nav%3Dtrue Feedback: 1) Please help to elaborate the term "Member of ". Example: Unexpected beneficial therapeutic response, drug resistance and Drug ineffective for unapproved indication listed as member of "Lack of efficacy (LOE)". Wherein, there are not because of lack of effect. You?ve reached the support list for questions regarding the BioPortal software. Although we host ontologies, we are generally not the ontology content developers. If you have questions about the ?Member of? property, I suggest you contact the ontology authors directly. You can find contact information on the ontology summary page in BioPortal, e.g., for MEDDRA it would be here: http://bioportal.bioontology.org/ontologies/MEDDRA. Their contact email address appears to be mssohelp at meddra.org. 2) Please help to provide the path on how to look for definitions: Unexpected beneficial therapeutic response, drug resistance and Drug ineffective for unapproved indication It doesn?t seem that MEDDRA has a definition property attached to terms, at least in the version we are serving (which is downloaded from the UMLS Metathesaurus). Perhaps the ontology authors could shed some light here. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From JAHOON.KOO at UCDENVER.EDU Fri Jan 31 14:01:11 2020 From: JAHOON.KOO at UCDENVER.EDU (Koo, Jahoon) Date: Fri, 31 Jan 2020 22:01:11 +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 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? Thank you. 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