From support at bioontology.org Wed Feb 2 06:47:14 2022 From: support at bioontology.org (support at bioontology.org) Date: Wed, 02 Feb 2022 06:47:14 -0800 Subject: [bioontology-support] [BioPortal] Feedback from David.Linke Message-ID: <61fa9972293c6_742818861d879c6@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Feb 2 09:16:00 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 2 Feb 2022 17:16:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from David.Linke In-Reply-To: <61fa9972293c6_742818861d879c6@ncbo-prd-app-08.stanford.edu.mail> References: <61fa9972293c6_742818861d879c6@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <4F1D2D1F-57DF-4C13-91B4-1089758F3228@stanford.edu> Hello David, Apologies that you?re having issues installing on Win10. I?ve entered an issue in our tracker to start the investigation on our end: https://github.com/ncbo/virtual_appliance/issues/29 Kind regards, Jennifer On Feb 2, 2022, at 6:47 AM, support at bioontology.org wrote: Name: David.Linke Email: david.linke at catalysis.de Location: https%3A%2F%2Fbioportal.bioontology.org%2Fvirtual_appliance Feedback: I am currently using 3.0.5-ova. Today, I tried to set up 3.0.6 ova (https://www.bioontology.org/ontoportal-appliance/ontoportal_appliance-vmware-3.0.6.ova) Importing the appliance to Virtual Box 6.1.30 on Win10Pro-64bit was possible. However, starting the appliance failed with lots of warning lines: `dracut-initqueue[234]: Warning: dracut-initqueue timeout - starting timeout scripts` ending with a line `Entering emergency mode`. Finally a `dracut:/#` prompt is shown. The md5-hash of the downloaded appliance was AF033F46E2DD9D577B5788E66C689427 Best regards David Linke _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Feb 2 23:12:43 2022 From: support at bioontology.org (support at bioontology.org) Date: Wed, 02 Feb 2022 23:12:43 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Xing Song Message-ID: <61fb806b3b41_7723120270896524@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 3 08:51:56 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 3 Feb 2022 16:51:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Xing Song In-Reply-To: <61fb806b3b41_7723120270896524@ncbo-prd-app-09.stanford.edu.mail> References: <61fb806b3b41_7723120270896524@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Song, On Feb 2, 2022, at 11:12 PM, support at bioontology.org wrote: I wrote some python codes hitting API to get some ontology information about few rxnorm and icd codes. However, it seems that my account has somehow been disabled (due to hitting the API too frequently?). Is there a way to reactivate my account? Song We throttle API requests at 15 per second per IP address. We don?t disable accounts that exceed the limit, instead issuing a ?429 Too Many Requests? response code. Are you seeing this response code? If not and it?s some other issue, please provide more information and a stack trace if possible. If you are seeing this response code, you can add wait statements to you code to make sure you don?t exceed the limit. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From adrian.gomez at hospitalitaliano.org.ar Thu Feb 3 10:39:50 2022 From: adrian.gomez at hospitalitaliano.org.ar (ADRIAN RAUL GOMEZ) Date: Thu, 3 Feb 2022 15:39:50 -0300 Subject: [bioontology-support] Snomed clinical terms problems Message-ID: Good morning I work at the italian hospital in buenos aires, argentina and we use bioportal , the spanish version of snomed clinical terms has problems with the character set, it can be fixed. https://bioportal.bioontology.org/ontologies/SCTSPA/?p=classes&conceptid=root Thanks adrian gomez -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 3 09:26:49 2022 From: support at bioontology.org (support at bioontology.org) Date: Thu, 03 Feb 2022 09:26:49 -0800 Subject: [bioontology-support] [BioPortal] Feedback from sorceroinc Message-ID: <61fc10592816b_77a8219a5bc57673@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 3 17:22:50 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 4 Feb 2022 01:22:50 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sorceroinc In-Reply-To: <61fc10592816b_77a8219a5bc57673@ncbo-prd-app-09.stanford.edu.mail> References: <61fc10592816b_77a8219a5bc57673@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Tushar, On Feb 3, 2022, at 9:26 AM, support at bioontology.org wrote: When I log in to my OntoPortal appliance, under the Ontologies tab I only see 1 available ontology. I was under the assumption that I can access all the public ontologies available on https://bioportal.bioontology.org/ontologies on the OntoPortal appliance. Is this not the case? No, that?s not the case. OntoPortal provides the infrastructure to host ontologies, but doesn?t come pre-populated. The single ontology you refer to is there because it provides semantic types that are required by services such as the Annotator. We host an installation of the software here at Stanford that we call BioPortal because the content is specific to the biomedical domain. Over a number of years, end users have submitted their ontologies such that we now host in excess of 1200. There?s a script in our GitHub repository that enables you to specify a list of BioPortal ontology acronyms, and programmatically import them into an OntoPortal appliance instance: https://github.com/ncbo/virtual_appliance/blob/d576fbb2d2f50dd6101d5681f7255e22ea793f95/utils/bioportal_ontologies_import.rb Let us know if we can be of any further assistance. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 3 17:49:04 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 4 Feb 2022 01:49:04 +0000 Subject: [bioontology-support] Snomed clinical terms problems In-Reply-To: References: Message-ID: <4401CA3E-C0BC-4620-B009-47EEFBD5E48F@stanford.edu> Hello Adrian, Apologies for the inconvenience. I?ve entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/238 We?re a bit short-handed at the moment, so I don?t have an exact date to offer as to when this will get addressed. Kind regards, Jennifer On Feb 3, 2022, at 10:39 AM, ADRIAN RAUL GOMEZ > wrote: Good morning I work at the italian hospital in buenos aires, argentina and we use bioportal , the spanish version of snomed clinical terms has problems with the character set, it can be fixed. https://bioportal.bioontology.org/ontologies/SCTSPA/?p=classes&conceptid=root Thanks adrian gomez _______________________________________________ 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 tushar at sorcero.com Thu Feb 3 17:56:45 2022 From: tushar at sorcero.com (Tushar Hegde) Date: Fri, 4 Feb 2022 01:56:45 +0000 Subject: [bioontology-support] [BioPortal] Feedback from sorceroinc In-Reply-To: References: <61fc10592816b_77a8219a5bc57673@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Jennifer, Could you help me out with the question I have above? Thanks, Tushar Get Outlook for Android ________________________________ From: Jennifer Leigh Vendetti Sent: Thursday, February 3, 2022 5:22:50 PM To: NCBO User Support Cc: tushar at sorcero.com Subject: Re: [bioontology-support] [BioPortal] Feedback from sorceroinc Hello Tushar, On Feb 3, 2022, at 9:26 AM, support at bioontology.org wrote: When I log in to my OntoPortal appliance, under the Ontologies tab I only see 1 available ontology. I was under the assumption that I can access all the public ontologies available on https://bioportal.bioontology.org/ontologies on the OntoPortal appliance. Is this not the case? No, that?s not the case. OntoPortal provides the infrastructure to host ontologies, but doesn?t come pre-populated. The single ontology you refer to is there because it provides semantic types that are required by services such as the Annotator. We host an installation of the software here at Stanford that we call BioPortal because the content is specific to the biomedical domain. Over a number of years, end users have submitted their ontologies such that we now host in excess of 1200. There?s a script in our GitHub repository that enables you to specify a list of BioPortal ontology acronyms, and programmatically import them into an OntoPortal appliance instance: https://github.com/ncbo/virtual_appliance/blob/d576fbb2d2f50dd6101d5681f7255e22ea793f95/utils/bioportal_ontologies_import.rb Let us know if we can be of any further assistance. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at stanford.edu Sat Feb 5 06:50:08 2022 From: noreply at stanford.edu (noreply at stanford.edu) Date: Sat, 5 Feb 2022 06:50:08 -0800 Subject: [bioontology-support] Stanford Spam Policy Violation: [BioPortal] Feedback from RobertFow Message-ID: The following message was rejected by Stanford's Spam Policy: Sender: support at bioontology.org Recipients: an16 at 4ttmail.com, support at bioontology.org Subject: [BioPortal] Feedback from RobertFow If you feel this was in error or if you have any questions, please submit a ServiceNow ticket: http://services.stanford.edu From support at bioontology.org Wed Feb 9 02:59:50 2022 From: support at bioontology.org (support at bioontology.org) Date: Wed, 09 Feb 2022 02:59:50 -0800 Subject: [bioontology-support] [BioPortal] Feedback from maggiesun Message-ID: <62039ea6ae7f4_716b11ee24421717@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Feb 15 09:34:26 2022 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 15 Feb 2022 17:34:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from maggiesun In-Reply-To: <62039ea6ae7f4_716b11ee24421717@ncbo-prd-app-09.stanford.edu.mail> References: <62039ea6ae7f4_716b11ee24421717@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <3F17943D-FD0F-46B9-8E65-EEBB856B7A33@stanford.edu> Hi Maggie, Thank you for contacting us. Unfortunately, what you're running into is a know bug in our system. It's described in detail here: https://github.com/ncbo/ontologies_api/issues/52 CADSR-VS is a "private" ontology, which means that only its maintainers have access to it both via the user interface and the API. At the moment, the mappings endpoint ignores the "private" designation and still shows that mapping. We don't have the resources to address it at this point, but we are keeping track of it and plan to resolve it as soon as we have an opportunity to do so. Meanwhile, I would suggest just skipping over the links that return status 403 in your code. Thank you, 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 9, 2022, at 02:59, support at bioontology.org wrote: Name: maggiesun Email: sunrmin.ele at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCL%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000232%26jump_to_nav%3Dtrue Feedback: Hello, I am trying to use API to download the data from the mappings of the cell with ID: CL_0000232. The detailed steps are as below: 1) I start from the url including all mapping information of the cell (url: https://data.bioontology.org/ontologies/CL/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000232/mappings). 2) Then I select the 'self' url from the second item in each 'classes'. 3) The last step is to request the data from the 'self' url (https://data.bioontology.org/ontologies/CADSR-VS/classes/https%3A%2F%2Fcadsr.nci.nih.gov%2Fmetadata%2FCADSR-VS%2Fd29bc749e17176ca944a3f634c82fa6237e100d9). And the 403 error occurs in partial of the mapping urls. The error says: "{ - "errors": [ "Access denied for this resource" ], "status": 403 }" Here comes my questions: (1) Is this an account authorization problem? (2) If yes, why does my account suffer from the access limitation? If no, what's the exact reason? (3) I get the 403 error in only parts of mapping urls. What kind of databases do these urls link to? Is there any possibility that these database can be accessed in the future? Look forward to your response. Thanks and best regards, Maggie Sun _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Feb 18 06:01:32 2022 From: support at bioontology.org (support at bioontology.org) Date: Fri, 18 Feb 2022 06:01:32 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Vincent Message-ID: <620fa6bce0e5b_6f912e7a16040368@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 17 10:58:00 2022 From: support at bioontology.org (support at bioontology.org) Date: Thu, 17 Feb 2022 10:58:00 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Oshin Miranda Message-ID: <620e9ab81cae3_42181117ce49555d@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From diller17 at ufl.edu Mon Feb 21 08:25:49 2022 From: diller17 at ufl.edu (Diller,Matthew A) Date: Mon, 21 Feb 2022 16:25:49 +0000 Subject: [bioontology-support] Question about RDF/XML downloads Message-ID: <725B9605-19CC-4802-B83E-6FB1FC7C4EDA@ufl.edu> To whom it may concern, I understand that the RDF/XML download option for each ontology indexed in Bioportal is automatically generated by Bioportal?s web services, but if someone were to upload their ontology to Bioportal in RDF/XML would the download option for that file be distinct from the default RDF/XML download option? The reason I?m asking is because I am working on a scoping review and am trying to note what syntax an ontology is made available in by its developers. I?m assuming the answer to my question is ?yes? and that the uploaded file would be available for download under an OWL download option. Thanks, Matt Diller PhD Candidate Department of Health Outcomes and Biomedical Informatics College of Medicine | University of Florida 2004 Mowry Road, Gainesville, FL 32603 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 22 09:59:55 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Feb 2022 17:59:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Vincent In-Reply-To: <620fa6bce0e5b_6f912e7a16040368@ncbo-prd-app-08.stanford.edu.mail> References: <620fa6bce0e5b_6f912e7a16040368@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <27DAF32A-386C-44FF-A6B8-4848C162D479@stanford.edu> Hello Vincent, We offer a virtual appliance distribution of BioPortal (called OntoPortal) that you can install and use locally. More information is available here: https://ontoportal.github.io/administration/ Kind regards, Jennifer On Feb 18, 2022, at 6:01 AM, support at bioontology.org wrote: Name: Vincent Email: vincent-bouget at hotmail.fr Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotatorplus Feedback: Good Morning, I am a researcher and I would like to use the bioportal to annotate some free text. However, I am working on sensitive data (clinical notes) hence I would like to avoid to send this data through the REST API. Is it possible to make a local use of the Bioportal Annotator? Best regards, Vincent Bouget _______________________________________________ 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 22 10:37:58 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Feb 2022 18:37:58 +0000 Subject: [bioontology-support] Question about RDF/XML downloads In-Reply-To: <725B9605-19CC-4802-B83E-6FB1FC7C4EDA@ufl.edu> References: <725B9605-19CC-4802-B83E-6FB1FC7C4EDA@ufl.edu> Message-ID: <0CF7A7DF-478A-431B-B7B5-D8044FD9C890@stanford.edu> Hello Matt, On Feb 21, 2022, at 8:25 AM, Diller,Matthew A > wrote: I understand that the RDF/XML download option for each ontology indexed in Bioportal is automatically generated by Bioportal?s web services, but if someone were to upload their ontology to Bioportal in RDF/XML would the download option for that file be distinct from the default RDF/XML download option? Yes, the download option always points to the original source file that was submitted to us by the end user. The reason I?m asking is because I am working on a scoping review and am trying to note what syntax an ontology is made available in by its developers. I?m assuming the answer to my question is ?yes? and that the uploaded file would be available for download under an OWL download option. This is not exactly correct. When an end user creates a new submission of their ontology, we allow them to specify the ontology language (see screen shot below). The format listed for the download option is the format specified by the end user. Occasionally, I see entries in BioPortal where an end user has uploaded an ontology in a format that?s different from the option they chose in the format dropdown, e.g., they uploaded an OBO ontology and erroneously chose OWL format. I think this is rare, but we don?t have the resources to do detailed curation, so I can?t say exactly how many occurrences of this there may be in our system. Kind regards, Jennifer [cid:A99DE0D5-ECD1-4E7F-80C3-25A3EA351FB2] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-02-22 at 10.32.12 AM.png Type: image/png Size: 19172 bytes Desc: Screen Shot 2022-02-22 at 10.32.12 AM.png URL: From support at bioontology.org Tue Feb 22 10:28:25 2022 From: support at bioontology.org (support at bioontology.org) Date: Tue, 22 Feb 2022 10:28:25 -0800 Subject: [bioontology-support] [BioPortal] Feedback from benjaminc Message-ID: <62152b49c1061_4add261b1e04087b@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 22 15:37:10 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Feb 2022 23:37:10 +0000 Subject: [bioontology-support] [BioPortal] Feedback from benjaminc In-Reply-To: <62152b49c1061_4add261b1e04087b@ncbo-prd-app-08.stanford.edu.mail> References: <62152b49c1061_4add261b1e04087b@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9A66AED6-AE9D-4D3B-96A2-3EF2F18BA75C@stanford.edu> Hello Benjamin, I?ve investigated the error in BioPortal. Once you submit a new term request, we send the request to a 3rd-party API maintained by the University of Miami. We?re getting 500 error codes returned from their API: [{"error":"Problem creating a new term /RequestTerm: RestClient::SSLCertificateNotVerified - SSL_connect returned=1 errno=0 state=error: certificate verify failed (unspecified certificate verification error)"},500] I?ve contacted the API maintainers this afternoon, and will keep you informed when I hear something back. Kind regards, Jennifer On Feb 22, 2022, at 10:28 AM, support at bioontology.org wrote: Name: benjaminc Email: benjamin_chittick at vrtx.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBAO%3Fp%3Dclasses%26conceptid%3Droot Feedback: My email is benjamin_chittick at vrtx.com. I am trying to submit a New Term Request, but it is saying: "The following error has occured: Internal Server Error. Please try again." The URL is: https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0000179#request_term My term request is: Preferred Name: Uptake ratio Definitions: Ratio of cellular concentrations subClassOf: ratio Justification: This paper presents an assay for an OAT uptake ratio (cells over expressing OAT)/(cells with mock plasmid) https://pubmed.ncbi.nlm.nih.gov/19919292/. Given that there is an uptake endpoint in the percent response section, for parity there should be an uptake ratio. _______________________________________________ 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 jonquet.lirmm at gmail.com Wed Feb 23 00:41:09 2022 From: jonquet.lirmm at gmail.com (Clement Jonquet) Date: Wed, 23 Feb 2022 09:41:09 +0100 Subject: [bioontology-support] Question about RDF/XML downloads In-Reply-To: <0CF7A7DF-478A-431B-B7B5-D8044FD9C890@stanford.edu> References: <725B9605-19CC-4802-B83E-6FB1FC7C4EDA@ufl.edu> <0CF7A7DF-478A-431B-B7B5-D8044FD9C890@stanford.edu> Message-ID: Hi Matthew, all, A lite complement to Jennifer?s response (as we experience also the situation accessing all ontologies in a unique format in AgroPortal): => The RDF/XML outputs always generated by BioPortal will materialize the imports. For instance, this ontology in AgroPortal: http://agroportal.lirmm.fr/ontologies/DEMETER-AIM The original source file only contains owl:imports statements. Where as the ref/xml file contains al the statements of all the imported owl files. Regards Clement > Le 22 f?vr. 2022 ? 19:37, Jennifer Leigh Vendetti a ?crit : > > Hello Matt, > >> On Feb 21, 2022, at 8:25 AM, Diller,Matthew A > wrote: >> >> I understand that the RDF/XML download option for each ontology indexed in Bioportal is automatically generated by Bioportal?s web services, but if someone were to upload their ontology to Bioportal in RDF/XML would the download option for that file be distinct from the default RDF/XML download option? > > > Yes, the download option always points to the original source file that was submitted to us by the end user. > > >> The reason I?m asking is because I am working on a scoping review and am trying to note what syntax an ontology is made available in by its developers. I?m assuming the answer to my question is ?yes? and that the uploaded file would be available for download under an OWL download option. > > > This is not exactly correct. When an end user creates a new submission of their ontology, we allow them to specify the ontology language (see screen shot below). The format listed for the download option is the format specified by the end user. Occasionally, I see entries in BioPortal where an end user has uploaded an ontology in a format that?s different from the option they chose in the format dropdown, e.g., they uploaded an OBO ontology and erroneously chose OWL format. I think this is rare, but we don?t have the resources to do detailed curation, so I can?t say exactly how many occurrences of this there may be in our system. > > Kind regards, > Jennifer > > > > > _______________________________________________ > 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 Vincent-Bouget at hotmail.fr Wed Feb 23 00:28:03 2022 From: Vincent-Bouget at hotmail.fr (Vincent Bouget) Date: Wed, 23 Feb 2022 08:28:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Vincent In-Reply-To: <27DAF32A-386C-44FF-A6B8-4848C162D479@stanford.edu> References: <620fa6bce0e5b_6f912e7a16040368@ncbo-prd-app-08.stanford.edu.mail> <27DAF32A-386C-44FF-A6B8-4848C162D479@stanford.edu> Message-ID: Dear Jennifer, Thank you very much. Best regards, Vincent De : Jennifer Leigh Vendetti Envoy? : 22 February 2022 19:00 ? : NCBO User Support Cc : vincent-bouget at hotmail.fr Objet : Re: [bioontology-support] [BioPortal] Feedback from Vincent Hello Vincent, We offer a virtual appliance distribution of BioPortal (called OntoPortal) that you can install and use locally. More information is available here: https://ontoportal.github.io/administration/ Kind regards, Jennifer On Feb 18, 2022, at 6:01 AM, support at bioontology.org wrote: Name: Vincent Email: vincent-bouget at hotmail.fr Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotatorplus Feedback: Good Morning, I am a researcher and I would like to use the bioportal to annotate some free text. However, I am working on sensitive data (clinical notes) hence I would like to avoid to send this data through the REST API. Is it possible to make a local use of the Bioportal Annotator? Best regards, Vincent Bouget _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 24 05:50:04 2022 From: support at bioontology.org (support at bioontology.org) Date: Thu, 24 Feb 2022 05:50:04 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Rasmus Rosenberg Larsen Message-ID: <62178d0cd2e3e_d3d15edd2c1788f@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Ben.Chisum at imail.org Thu Feb 24 11:35:32 2022 From: Ben.Chisum at imail.org (Ben Chisum) Date: Thu, 24 Feb 2022 19:35:32 +0000 Subject: [bioontology-support] MEDDRA version Message-ID: Hi support, Sorry if this is an ignorant question, but can you tell me what version of MEDDRA is currently being utilized? We use REDCap to connect to BioPortal and subsequently the MEDDRA ontology. We need to know what MEDDRA version that connection is drawing from. Really appreciate the help. Ben Chisum Application Systems Manager Intermountain Healthcare 5121 S Cottonwood Street Salt Lake City, UT 84107 Office: 801-507-4584 | ben.chisum at imail.org NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 24 11:48:28 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 24 Feb 2022 19:48:28 +0000 Subject: [bioontology-support] MEDDRA version In-Reply-To: References: Message-ID: <978B823F-A2DD-4680-BB42-C42700B5F4C4@stanford.edu> Hello Ben, We import MedDRA from the UMLS Metathesaurus. The version they are currently distributing is MDR24_0, as shown on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html This is the version BioPortal is serving. Kind regards, Jennifer On Feb 24, 2022, at 11:35 AM, Ben Chisum > wrote: Hi support, Sorry if this is an ignorant question, but can you tell me what version of MEDDRA is currently being utilized? We use REDCap to connect to BioPortal and subsequently the MEDDRA ontology. We need to know what MEDDRA version that connection is drawing from. Really appreciate the help. Ben Chisum Application Systems Manager Intermountain Healthcare 5121 S Cottonwood Street Salt Lake City, UT 84107 Office: 801-507-4584 | ben.chisum at imail.org NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents. _______________________________________________ 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 Ben.Chisum at imail.org Thu Feb 24 11:54:12 2022 From: Ben.Chisum at imail.org (Ben Chisum) Date: Thu, 24 Feb 2022 19:54:12 +0000 Subject: [bioontology-support] MEDDRA version In-Reply-To: <978B823F-A2DD-4680-BB42-C42700B5F4C4@stanford.edu> References: <978B823F-A2DD-4680-BB42-C42700B5F4C4@stanford.edu> Message-ID: Perfect! Thanks so much for the super-fast response. Much appreciated/ Ben From: Jennifer Leigh Vendetti Sent: Thursday, February 24, 2022 12:48 PM To: Ben Chisum Cc: support at bioontology.org Subject: Re: [bioontology-support] MEDDRA version External Sender: Be aware! Read with care! Hello Ben, We import MedDRA from the UMLS Metathesaurus. The version they are currently distributing is MDR24_0, as shown on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html This is the version BioPortal is serving. Kind regards, Jennifer On Feb 24, 2022, at 11:35 AM, Ben Chisum > wrote: Hi support, Sorry if this is an ignorant question, but can you tell me what version of MEDDRA is currently being utilized? We use REDCap to connect to BioPortal and subsequently the MEDDRA ontology. We need to know what MEDDRA version that connection is drawing from. Really appreciate the help. Ben Chisum Application Systems Manager Intermountain Healthcare 5121 S Cottonwood Street Salt Lake City, UT 84107 Office: 801-507-4584 | ben.chisum at imail.org NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Feb 24 14:28:35 2022 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 24 Feb 2022 22:28:35 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Rasmus Rosenberg Larsen In-Reply-To: <62178d0cd2e3e_d3d15edd2c1788f@ncbo-prd-app-08.stanford.edu.mail> References: <62178d0cd2e3e_d3d15edd2c1788f@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <6F40CABB-3687-4C68-852E-13A939569832@stanford.edu> Congratulations on your submission! Can we please see a copy of the screenshot you will use, and have a tiny bit of the context for it? John On Feb 24, 2022, at 5:50 AM, support at bioontology.org wrote: Name: Rasmus Rosenberg Larsen Email: rosenberg.larsen at utoronto.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Dear Bioportal, I hope this finds you well. My group is working on a publication (appearing in The Lancet) where we are including a figure illustrating some user features in Bioportal. In this figure, we are using a screenshot of (parts of) the portal. My question is: do we have your approval to use such a screenshot? Looking forward to hearing from you. Best wishes, Rasmus Rosenberg Larsen Assistant Professor University of Toronto _______________________________________________ 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 Thu Feb 24 14:34:30 2022 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 24 Feb 2022 22:34:30 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Oshin Miranda In-Reply-To: <620e9ab81cae3_42181117ce49555d@ncbo-prd-app-08.stanford.edu.mail> References: <620e9ab81cae3_42181117ce49555d@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <56573B6F-2101-4762-BFA5-7F07C84238A5@stanford.edu> Oshin, I don't see any response to your question yet, but I'm not sure exactly what you are asking for. If you are asking for "the vocabulary" BioPortal uses to annotate terms in a corpus, it uses all the concepts from the entire collection of public ontologies in BioPortal. This is over 14,000,000 terms in over 950 ontologies. It seems like your best bet would be to change the software that does the conversion from concepts to numbers, so that the software logs all its found concepts into a document. Then you can easily work with that text. John On Feb 17, 2022, at 10:58 AM, support at bioontology.org wrote: Name: Oshin Miranda Email: osm7 at pitt.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hello, My name is Oshin Miranda, and I am a PhD student at University of Pittsburgh School of pharmacy. I am interested in using the biomedical annotator for my NLP project. I am annotating a large bunch of clinical notes of 39,000 patients. And, I am using an NLP algorithm called Convae to classify my patients into disease subtypes based on the annotations. In order to pass the annotations into the NLP algorithm I need a vocabulary or library which has all the terms annotated into a specific number. For example, if a clinical note has the word Alzheimer's disease, once passed through the annotator it is converted into a number such as 123, since the notes have multiple words, the notes will be converted into 123, 154, 167, 134 etc, for each clinical note for each patient, where each word meant a word. The vocabulary contains the words that were labeled into the respective numbers. I would like to know if you could direct me to where can i get the vocabulary since I can't find it in the soft code of the biomedical annotator or in the system for download. The paper I have linked down below had a vocabulary V composed by 57, 464 clinical concepts. The link to the paper for your reference is https://arxiv.org/pdf/2003.06516.pdf Thank you. With regards, Oshin Mirana. _______________________________________________ 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 Thu Feb 24 22:46:23 2022 From: support at bioontology.org (support at bioontology.org) Date: Thu, 24 Feb 2022 22:46:23 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das Message-ID: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 24 22:54:53 2022 From: support at bioontology.org (support at bioontology.org) Date: Thu, 24 Feb 2022 22:54:53 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Rakesh Malpure Message-ID: <62187d3d7a427_5a001cc6b804778f@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 25 09:10:14 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 25 Feb 2022 17:10:14 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> Hello Sougato, I spot checked a few classes in the CSV file and the Parents column contained correct data. Could you be more specific? For what classes do you see an empty Parents column where you think there should be data? Jennifer On Feb 24, 2022, at 10:46 PM, support at bioontology.org wrote: Name: Sougato Das Email: sougato_das at hotmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH Feedback: I downloaded MeSH ontology from Bioportal in CSV format. The Parent column is almost entirely empty. I assume this is an error? Thanks, Sougato _______________________________________________ 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 25 09:13:52 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 25 Feb 2022 17:13:52 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Rakesh Malpure In-Reply-To: <62187d3d7a427_5a001cc6b804778f@ncbo-prd-app-09.stanford.edu.mail> References: <62187d3d7a427_5a001cc6b804778f@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <8EA0F0AD-F25F-4476-A79C-2878783C2444@stanford.edu> Hello Rakesh, On Feb 24, 2022, at 10:54 PM, support at bioontology.org wrote: I am not able find coding for antidrug antibody. We need LLT of antidrug antibody in MedDRA You?ve reached technical support for the BioPortal software. We host ontologies from a variety of sources, but we are not the authors and/or maintainers of the ontology content. If you feel that MedDRA is missing a term that you need, please contact MedDRA support: mssohelp at meddra.org. Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From sougato_das at hotmail.com Fri Feb 25 13:40:02 2022 From: sougato_das at hotmail.com (Sougato Das) Date: Fri, 25 Feb 2022 21:40:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> Message-ID: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? Thanks, Sougato ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 25, 2022 12:10 PM To: NCBO User Support Cc: sougato_das at hotmail.com Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das Hello Sougato, I spot checked a few classes in the CSV file and the Parents column contained correct data. Could you be more specific? For what classes do you see an empty Parents column where you think there should be data? Jennifer On Feb 24, 2022, at 10:46 PM, support at bioontology.org wrote: Name: Sougato Das Email: sougato_das at hotmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH Feedback: I downloaded MeSH ontology from Bioportal in CSV format. The Parent column is almost entirely empty. I assume this is an error? Thanks, Sougato _______________________________________________ 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 25 14:29:47 2022 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 25 Feb 2022 22:29:47 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> Message-ID: <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> Hello Sougato, On Feb 25, 2022, at 1:40 PM, Sougato Das > wrote: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView We import MeSH from the UMLS Metathesaurus: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html The version of MeSH that was last distributed as part of the UMLS Metathesaurus is MSH2022_2021_07_20, as seen on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? I chose a few of the classes with no parents in the CSV file we generated and searched for them in the NLM?s UMLS Metathesaurus Browser: https://uts.nlm.nih.gov/uts/umls/home If you filter on MSH in their browser, I found the same classes there - for example, the class with a preferred label of "Acaulospora ignota? is listed as present in MeSH: [cid:2CD98139-37AF-4DFA-9ACF-5151C7453F1E] I also found this term using the search functionality in the MeSH Browser you linked to above. If you choose ?All Terms? and ?Exact Match? for the search parameters, I see the following: [cid:ABBFDF03-D14C-402A-A06C-AD1DB671C4A5] I hope this information is helpful. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-02-25 at 2.15.28 PM.png Type: image/png Size: 93320 bytes Desc: Screen Shot 2022-02-25 at 2.15.28 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-02-25 at 2.22.44 PM.png Type: image/png Size: 54858 bytes Desc: Screen Shot 2022-02-25 at 2.22.44 PM.png URL: From swt at stanford.edu Fri Feb 25 14:47:56 2022 From: swt at stanford.edu (Samson Tu) Date: Fri, 25 Feb 2022 22:47:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> Message-ID: <23934034-90A1-4C51-8CFC-AE085C1876BB@stanford.edu> Maybe entries in MeSH Supplementary Concept Data have no parent in the CSV file? "Acaulospora ignota? is mapped to Fungi, but it is not a child of Fungi in the MeSH hierarchy. With best regards, Samson On Feb 25, 2022, at 2:29 PM, Jennifer Leigh Vendetti > wrote: Hello Sougato, On Feb 25, 2022, at 1:40 PM, Sougato Das > wrote: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView We import MeSH from the UMLS Metathesaurus: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html The version of MeSH that was last distributed as part of the UMLS Metathesaurus is MSH2022_2021_07_20, as seen on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? I chose a few of the classes with no parents in the CSV file we generated and searched for them in the NLM?s UMLS Metathesaurus Browser: https://uts.nlm.nih.gov/uts/umls/home If you filter on MSH in their browser, I found the same classes there - for example, the class with a preferred label of "Acaulospora ignota? is listed as present in MeSH: I also found this term using the search functionality in the MeSH Browser you linked to above. If you choose ?All Terms? and ?Exact Match? for the search parameters, I see the following: I hope this information is helpful. Kind regards, Jennifer _______________________________________________ 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 sougato_das at hotmail.com Fri Feb 25 14:34:59 2022 From: sougato_das at hotmail.com (Sougato Das) Date: Fri, 25 Feb 2022 22:34:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> Message-ID: Thank you again Jennifer, that clears it up. I was searching only on the MeSH headings; I should have also looked in the supplementary concept data. Kind regards, Sougato ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 25, 2022 5:29 PM To: Sougato Das Cc: NCBO User Support Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das Hello Sougato, On Feb 25, 2022, at 1:40 PM, Sougato Das > wrote: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView We import MeSH from the UMLS Metathesaurus: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html The version of MeSH that was last distributed as part of the UMLS Metathesaurus is MSH2022_2021_07_20, as seen on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? I chose a few of the classes with no parents in the CSV file we generated and searched for them in the NLM?s UMLS Metathesaurus Browser: https://uts.nlm.nih.gov/uts/umls/home If you filter on MSH in their browser, I found the same classes there - for example, the class with a preferred label of "Acaulospora ignota? is listed as present in MeSH: [cid:2CD98139-37AF-4DFA-9ACF-5151C7453F1E] I also found this term using the search functionality in the MeSH Browser you linked to above. If you choose ?All Terms? and ?Exact Match? for the search parameters, I see the following: [cid:ABBFDF03-D14C-402A-A06C-AD1DB671C4A5] I hope this information is helpful. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-02-25 at 2.15.28 PM.png Type: image/png Size: 93320 bytes Desc: Screen Shot 2022-02-25 at 2.15.28 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-02-25 at 2.22.44 PM.png Type: image/png Size: 54858 bytes Desc: Screen Shot 2022-02-25 at 2.22.44 PM.png URL: From sougato_das at hotmail.com Fri Feb 25 14:50:13 2022 From: sougato_das at hotmail.com (Sougato Das) Date: Fri, 25 Feb 2022 22:50:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <23934034-90A1-4C51-8CFC-AE085C1876BB@stanford.edu> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> <23934034-90A1-4C51-8CFC-AE085C1876BB@stanford.edu> Message-ID: Hello Samson, thank you for your insight. It seems you are correct. Kind regards, Sougato ________________________________ From: Samson Tu Sent: Friday, February 25, 2022 5:47 PM To: Jennifer Leigh Vendetti Cc: Samson Tu ; Sougato Das ; NCBO User Support Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das Maybe entries in MeSH Supplementary Concept Data have no parent in the CSV file? "Acaulospora ignota? is mapped to Fungi, but it is not a child of Fungi in the MeSH hierarchy. With best regards, Samson On Feb 25, 2022, at 2:29 PM, Jennifer Leigh Vendetti > wrote: Hello Sougato, On Feb 25, 2022, at 1:40 PM, Sougato Das > wrote: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView We import MeSH from the UMLS Metathesaurus: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html The version of MeSH that was last distributed as part of the UMLS Metathesaurus is MSH2022_2021_07_20, as seen on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? I chose a few of the classes with no parents in the CSV file we generated and searched for them in the NLM?s UMLS Metathesaurus Browser: https://uts.nlm.nih.gov/uts/umls/home If you filter on MSH in their browser, I found the same classes there - for example, the class with a preferred label of "Acaulospora ignota? is listed as present in MeSH: I also found this term using the search functionality in the MeSH Browser you linked to above. If you choose ?All Terms? and ?Exact Match? for the search parameters, I see the following: I hope this information is helpful. Kind regards, Jennifer _______________________________________________ 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 sougato_das at hotmail.com Sun Feb 27 13:08:51 2022 From: sougato_das at hotmail.com (Sougato Das) Date: Sun, 27 Feb 2022 21:08:51 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das In-Reply-To: <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> References: <62187b3fbc41_49d31360884556dc@ncbo-prd-app-08.stanford.edu.mail> <1F097A6C-25C5-4E94-85B6-6BCB9591E1DB@stanford.edu> <77D0C94A-B052-4FE5-AC0A-72872435CA74@stanford.edu> Message-ID: Sorry, one more question: I have a MedDRA license. Is there a way I can download the MedDRA CSV from Bioportal? Your format is much better than MedDRA's. Thanks Sougato ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 25, 2022 5:29 PM To: Sougato Das Cc: NCBO User Support Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das Hello Sougato, On Feb 25, 2022, at 1:40 PM, Sougato Das > wrote: Thanks for your quick response Jennifer. I think perhaps I have a misunderstanding of what's presented in Bioportal. I thought it was the same ontology available here: https://meshb.nlm.nih.gov/treeView We import MeSH from the UMLS Metathesaurus: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html The version of MeSH that was last distributed as part of the UMLS Metathesaurus is MSH2022_2021_07_20, as seen on the metadata page: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH/metadata.html All the rows in Bioportal's MeSH CSV that have a value in the Parents column (about 10% of the total rows) seem to exist on the NLM's MeSH browser. However the rows that do not have a value in the Parents column do not exist in NLM's MeSH. I guess Bioportal's MeSH includes nodes from some other source? I chose a few of the classes with no parents in the CSV file we generated and searched for them in the NLM?s UMLS Metathesaurus Browser: https://uts.nlm.nih.gov/uts/umls/home If you filter on MSH in their browser, I found the same classes there - for example, the class with a preferred label of "Acaulospora ignota? is listed as present in MeSH: [cid:2CD98139-37AF-4DFA-9ACF-5151C7453F1E] I also found this term using the search functionality in the MeSH Browser you linked to above. If you choose ?All Terms? and ?Exact Match? for the search parameters, I see the following: [cid:ABBFDF03-D14C-402A-A06C-AD1DB671C4A5] I hope this information is helpful. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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