From jgraybeal at stanford.edu Wed Apr 1 13:35:43 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 1 Apr 2020 20:35:43 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan In-Reply-To: References: <5e8372cbc1b50_305c1e682a456779@ncbo-prd-app-09.stanford.edu.mail> Message-ID: For the list, Rob Taylor from REDCap provided this information, and said I could relay it. John To answer the question, in REDCap v8.4.0 (released two years ago) and higher, REDCap should *always* make calls to data.bioontology.org over SSL. If your REDCap installation doesn?t do this (or if you?re not sure), have your REDCap database person execute the SQL below in the REDCap database to fix it. Note: This will not hurt anything at all either way. Also, if this is not working, then you may need to have your IT folks who manage your REDCap server ensure that the server can make outbound HTTP requests to https://data.bioontology.org, in case that is being prevented by a firewall or something. You shouldn?t have to worry about certificates or anything. Hope that helps. update redcap_config set value = 'https://data.bioontology.org/' where field_name ='bioportal_api_url' and value = 'http://data.bioontology.org/'; Rob Taylor REDCap Team Manager and Lead Developer (https://projectredcap.org) Vanderbilt Institute for Clinical and Translational Research (VICTR) On Apr 1, 2020, at 9:12 AM, Vaughan, Eoin > wrote: Hi John, Yes that is exactly what I was trying to ask. I believe that REDCap by default has the cert validation for HTTPS requests option turned off maybe to to prevent errors and loss of functionality, can happen easily from a certificate swap. I have contacted our IT service and they're looking into it. Thanks again for this information I can at least tell them the actions from your side now. Thanks, Eoin. ________________________________ From: John Graybeal > Sent: March 31, 2020 10:43:21 PM To: support at bioontology.org Cc: Vaughan, Eoin Subject: Re: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan Eoin, I'm going to restate your request a little bit to make sure we're talking about the same thing. You want to be sure that when REDCap is configured to get data from BioPortal, it is able to do so on a connection secured by SSL, so that the content going back and forth is not in plain text and not capable of being intercepted/rewritten. Correct? The typical scenario for SSL encryption is that the client?your REDCap service?makes the request using https, and the HTTP server on our end provides a certificate to show it can securely manage the encrypted communication. BioPortal doesn't really know anything about that process, but the web server ensures your end-to-end encryption requirement is met, if your client uses the https protocol. For this to work, however, I believe your IT service will have to ensure that REDCap makes it requests using the https protocol. You will need to contact the REDCap team if REDCap does not support this option. I will provide some REDCap contacts offline to facilitate this for you. (I should mention for the record that the service endpoint URLs provided by BioPortal in its API responses are prefixed with http, not https. This does not affect clients' ability to make the same requests using https, but I'm pretty sure it doesn't matter for the REDCap use case.) John On Mar 31, 2020, at 9:41 AM, support at bioontology.org wrote: Name: Eoin Vaughan Email: eoin.vaughan at ubc.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: I'm just looking into utilising the "Bioportal Ontology Service" within our departments REDCap instance and I'm in the process of writing up the PIA for this request to our IT service, I was hoping to find out whether the Bioportal Service checks/verifies the SSL certificate like curl does in our API calls for R,Python scripts. I know they will be wary of the 'man in middle' attack that we may be subject to if not, don't want to assume anything. Thanks, Eoin. _______________________________________________ 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 ======================== 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 eoin.vaughan at ubc.ca Wed Apr 1 09:12:04 2020 From: eoin.vaughan at ubc.ca (Vaughan, Eoin) Date: Wed, 1 Apr 2020 16:12:04 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan In-Reply-To: References: <5e8372cbc1b50_305c1e682a456779@ncbo-prd-app-09.stanford.edu.mail>, Message-ID: Hi John, Yes that is exactly what I was trying to ask. I believe that REDCap by default has the cert validation for HTTPS requests option turned off maybe to to prevent errors and loss of functionality, can happen easily from a certificate swap. I have contacted our IT service and they're looking into it. Thanks again for this information I can at least tell them the actions from your side now. Thanks, Eoin. ________________________________ From: John Graybeal Sent: March 31, 2020 10:43:21 PM To: support at bioontology.org Cc: Vaughan, Eoin Subject: Re: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan Eoin, I'm going to restate your request a little bit to make sure we're talking about the same thing. You want to be sure that when REDCap is configured to get data from BioPortal, it is able to do so on a connection secured by SSL, so that the content going back and forth is not in plain text and not capable of being intercepted/rewritten. Correct? The typical scenario for SSL encryption is that the client?your REDCap service?makes the request using https, and the HTTP server on our end provides a certificate to show it can securely manage the encrypted communication. BioPortal doesn't really know anything about that process, but the web server ensures your end-to-end encryption requirement is met, if your client uses the https protocol. For this to work, however, I believe your IT service will have to ensure that REDCap makes it requests using the https protocol. You will need to contact the REDCap team if REDCap does not support this option. I will provide some REDCap contacts offline to facilitate this for you. (I should mention for the record that the service endpoint URLs provided by BioPortal in its API responses are prefixed with http, not https. This does not affect clients' ability to make the same requests using https, but I'm pretty sure it doesn't matter for the REDCap use case.) John On Mar 31, 2020, at 9:41 AM, support at bioontology.org wrote: Name: Eoin Vaughan Email: eoin.vaughan at ubc.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: I'm just looking into utilising the "Bioportal Ontology Service" within our departments REDCap instance and I'm in the process of writing up the PIA for this request to our IT service, I was hoping to find out whether the Bioportal Service checks/verifies the SSL certificate like curl does in our API calls for R,Python scripts. I know they will be wary of the 'man in middle' attack that we may be subject to if not, don't want to assume anything. Thanks, Eoin. _______________________________________________ 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 Wed Apr 1 10:06:12 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 01 Apr 2020 10:06:12 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Joseph Greschner Message-ID: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Apr 1 14:51:51 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 1 Apr 2020 21:51:51 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Joseph Greschner In-Reply-To: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail> References: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <97077F79-C862-41FD-8B91-315B809744EC@stanford.edu> Joseph, You would have to ask the contact person for that ontology. Unfortunately, you don't mention which ontology you found the term in, but the contact informationis provided on the summary page of each ontology. For the SNOMEDCT ontology, for example, the summary page is http://bioportal.bioontology.org/ontologies/SNOMEDCT John On Apr 1, 2020, at 10:06 AM, support at bioontology.org wrote: Name: Joseph Greschner Email: joseph.greschner at ohiohealth.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F Feedback: In your ontology of trimalleolar fracture, what do the "specialty" percentages next to 'orthopedic surgery' and 'podiatry' indicate? _______________________________________________ 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 mrbarnes at uw.edu Thu Apr 2 12:31:41 2020 From: mrbarnes at uw.edu (Megan R Barnes) Date: Thu, 2 Apr 2020 19:31:41 +0000 Subject: [bioontology-support] NCBO Annotator VM Question Message-ID: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running at http://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Apr 2 03:13:45 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 02 Apr 2020 03:13:45 -0700 Subject: [bioontology-support] [BioPortal] Feedback from emicholt Message-ID: <5e85bad981800_50362002f10276bb@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Apr 3 04:42:05 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 03 Apr 2020 04:42:05 -0700 Subject: [bioontology-support] [BioPortal] Feedback from nrhardiker Message-ID: <5e87210d109e6_70642545cd487023@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Apr 3 09:31:30 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 03 Apr 2020 09:31:30 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Jonathan Gardner Message-ID: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Apr 3 11:31:36 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 3 Apr 2020 18:31:36 +0000 Subject: [bioontology-support] NCBO Annotator VM Question In-Reply-To: References: Message-ID: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu> Megan, Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame. Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.) It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies. If you send us the example of your two responses, we can look closely at them and give you more specific feedback. John On Apr 2, 2020, at 12:31 PM, Megan R Barnes > wrote: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington _______________________________________________ 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 Fri Apr 3 11:35:13 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 3 Apr 2020 18:35:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jonathan Gardner In-Reply-To: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail> References: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <601F47B8-25F5-4E19-BF7B-1E5985BD3EC1@stanford.edu> Jonathan, Our apologies, you are correct that these scripts are not functioning. We have an outstanding ticket on this (https://github.com/ncbo/bioportal_web_ui/issues/79), and expected to fix it before now. We'll prioritize the task to document/handle the issue on the site soon. John On Apr 3, 2020, at 9:31 AM, support at bioontology.org wrote: Name: Jonathan Gardner Email: jgardner at qualityhealthnd.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT Feedback: The "Form Autocomplete" scripts do not appear to be functioning. I would really like to use this widget on our own web application, but even the demo page doesn't appear to work (nothing happens). Is there something I might be doing wrong? The page URL I'm trying to use is: http://bioportal.bioontology.org/ontologies/CPT/?p=widgets _______________________________________________ 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 Fri Apr 3 13:06:09 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 3 Apr 2020 20:06:09 +0000 Subject: [bioontology-support] Posting large amounts of text into Annotator In-Reply-To: References: Message-ID: <59963F56-CC54-4366-9E28-120BCCB5A069@stanford.edu> Vivian, The Annotator API is what we mean when we say Annotator Web Service. The HTTP 414 error is a function of HTTP limits on URL size enforced by various services. (See for example http://ncbo-support.2288202.n4.nabble.com/bioontology-support-JAVA-IOException-code-414-URL-too-long-with-get-call-td4652615.html.) Try using a POST instead of a GET URI. (Reference this previous support message: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Annotating-large-texts-tp4652649p4652661.html). I'm sorry, I don't think we have explicit examples, but this is a common way of communicating over HTTP, so lots of web documentation. You reach a practical limit of 60 seconds before a timeout occurs on your request, so especially during busy times you will haeve to keep your request sizes lower. (Limiting the number of ontologies that you request annotation against is another way to minimize the computation time.) If you have a lot of large pieces of text, you will need to install the virtual appliance (free), or ask us to set up a dedicated server (contact us). John On Apr 3, 2020, at 12:05 PM, Vivian Zhu > wrote: Dear Mr. Graybeal, I was wondering how I could annotate large amounts of text (500 words or more) with the Annotator. The Annotator website tells me that I can use the Annotator Web Service to annotate large pieces of text. However, when I click the link to the web service, I am redirected to the Annotator API. The API says that I can post text using "/annotator?text={input text}", but this only works if I input small pieces of text. When I input large pieces of text, I get an HTTP 414 error saying that my URI request is too large. How can I solve this issue? Thank you! Vivian ======================== 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 vivianzhu88 at gmail.com Fri Apr 3 12:05:53 2020 From: vivianzhu88 at gmail.com (Vivian Zhu) Date: Fri, 3 Apr 2020 12:05:53 -0700 Subject: [bioontology-support] Posting large amounts of text into Annotator Message-ID: Dear Mr. Graybeal, I was wondering how I could annotate large amounts of text (500 words or more) with the Annotator. The Annotator website tells me that I can use the Annotator Web Service to annotate large pieces of text. However, when I click the link to the web service, I am redirected to the Annotator API. The API says that I can post text using "/annotator?text={input text}", but this only works if I input small pieces of text. When I input large pieces of text, I get an HTTP 414 error saying that my URI request is too large. How can I solve this issue? Thank you! Vivian -------------- next part -------------- An HTML attachment was scrubbed... URL: From rakesh at pieriandx.com Tue Apr 7 13:26:15 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Tue, 7 Apr 2020 15:26:15 -0500 Subject: [bioontology-support] Issue Message-ID: Hello, For the following URLs: http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children I get the following error: { -"errors": [ "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in ontology DOID submission 598" ], "status": 404 } Can you please fix this? Thanks, Rakesh -- *Rakesh Nagarajan* Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Apr 7 16:56:19 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 7 Apr 2020 23:56:19 +0000 Subject: [bioontology-support] Issue In-Reply-To: References: Message-ID: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> Rakesh, I'm sorry, I'm unable to duplicate this problem. When I click on the first URL I get the actual content I'd expect from the API. [1] When I click on the second URL I get a simple response that suggests there are no children, which matches what BioPortal and OntoBee say. My only thought is that perhaps there was a brief outage and your browser or application cached the results. Perhaps you can try another browser to see if it has the same behavior? If you are still having this problem in another browser, please let us know with any additional details you can provide, and we can brainstorm ideas about what might be happening. John [1] Content from API for http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 { ? "prefLabel": "Warburg micro syndrome 3", ? -"synonym": [ ? "Micro Syndrome 3", ? "WARBM3" ], ? -"definition": [ ? "A Warburg micro syndrome that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the RAB18 gene on chromosome 10p12." ], ? "cui": [ ], ? "semanticType": [ ], ? "obsolete": false, ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718", ? "@type": "http://www.w3.org/2002/07/owl#Class", ? -"links": { ? "self": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718", ? "ontology": "http://data.bioontology.org/ontologies/DOID", ? "children": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children", On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan > wrote: Hello, For the following URLs: http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children I get the following error: { -"errors": [ "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in ontology DOID submission 598" ], "status": 404 } Can you please fix this? Thanks, Rakesh -- Rakesh Nagarajan Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. _______________________________________________ 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 rakesh at pieriandx.com Wed Apr 8 06:17:45 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Wed, 8 Apr 2020 08:17:45 -0500 Subject: [bioontology-support] Issue In-Reply-To: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> References: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> Message-ID: Thanks John. I agree it is intermittent but somewhat frequent. I got errors for the following overnight: Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children When I get such an error I wait 60 seconds and then try again but then exit when it fails 30 times. So these errors do occur for >30 minutes or so. I also noticed that this specific ontology has long response times per call. Any ideas how this can be more robust? Thanks, Rakesh On Tue, Apr 7, 2020 at 6:56 PM John Graybeal wrote: > Rakesh, > > I'm sorry, I'm unable to duplicate this problem. > > When I click on the first URL I get the actual content I'd expect from the > API. [1] > > When I click on the second URL I get a simple response that suggests there > are no children, which matches what BioPortal and OntoBee say. > > My only thought is that perhaps there was a brief outage and your browser > or application cached the results. Perhaps you can try another browser to > see if it has the same behavior? > > If you are still having this problem in another browser, please let us > know with any additional details you can provide, and we can brainstorm > ideas about what might be happening. > > John > > > > [1] Content from API for > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 > > > { > ? "prefLabel": "Warburg micro syndrome 3", > ? -"synonym": [ > ? "Micro Syndrome 3", > ? "WARBM3" > ], > ? -"definition": [ > ? "A Warburg micro syndrome that has_material_basis_in autosomal recessive > inheritance of homozygous or compound heterozygous mutation in the RAB18 > gene on chromosome 10p12." > ], > ? "cui": [ ], > ? "semanticType": [ ], > ? "obsolete": false, > ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718", > ? "@type": "http://www.w3.org/2002/07/owl#Class", > ? -"links": { > ? "self": " > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 > ", > ? "ontology": "http://data.bioontology.org/ontologies/DOID", > ? "children": " > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children > ", > > On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan wrote: > > Hello, > For the following URLs: > > > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 > > > > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children > > I get the following error: > > { > -"errors": [ > "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in > ontology DOID submission 598" > ], > "status": 404 > } > > > Can you please fix this? > > Thanks, > Rakesh > -- > > *Rakesh Nagarajan* > > Founder and Executive Chairman > > m: 314-504-5620 > e: rakesh at pieriandx.com > > [image: pierian-logo-trans-light-background] > [image: linkedin_circle-512] > [image: twitter_circle-512] > > > Wisdom in Every Report? > > CONFIDENTIALITY NOTICE: This message and any attachments are solely for > the use of the intended recipient and may contain privileged, confidential > or other legally protected information. If you are not the intended > recipient, please destroy all copies without reading or disclosing their > contents and notify the sender of the error by reply email. > > > > _______________________________________________ > 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 > > > > -- *Rakesh Nagarajan* Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rakesh at pieriandx.com Wed Apr 8 06:50:02 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Wed, 8 Apr 2020 08:50:02 -0500 Subject: [bioontology-support] Issue In-Reply-To: References: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> Message-ID: John, May I also request access to the virtual appliance as I can cache some ontologies (e.g. HPO, NCIT, SNOMED-CT, MeSH, and Disease Ontology) that we frequently refresh and perhaps wouldn't run into these errors where we're hitting your instance? Thanks, Rakesh On Wed, Apr 8, 2020 at 8:17 AM Rakesh Nagarajan wrote: > Thanks John. I agree it is intermittent but somewhat frequent. I got > errors for the following overnight: > > Error in > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children > Error in > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children > > When I get such an error I wait 60 seconds and then try again but then > exit when it fails 30 times. So these errors do occur for >30 minutes or > so. I also noticed that this specific ontology has long response times per > call. Any ideas how this can be more robust? > > Thanks, > Rakesh > > > > On Tue, Apr 7, 2020 at 6:56 PM John Graybeal > wrote: > >> Rakesh, >> >> I'm sorry, I'm unable to duplicate this problem. >> >> When I click on the first URL I get the actual content I'd expect from >> the API. [1] >> >> When I click on the second URL I get a simple response that suggests >> there are no children, which matches what BioPortal and OntoBee say. >> >> My only thought is that perhaps there was a brief outage and your browser >> or application cached the results. Perhaps you can try another browser to >> see if it has the same behavior? >> >> If you are still having this problem in another browser, please let us >> know with any additional details you can provide, and we can brainstorm >> ideas about what might be happening. >> >> John >> >> >> >> [1] Content from API for >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> >> >> { >> ? "prefLabel": "Warburg micro syndrome 3", >> ? -"synonym": [ >> ? "Micro Syndrome 3", >> ? "WARBM3" >> ], >> ? -"definition": [ >> ? "A Warburg micro syndrome that has_material_basis_in autosomal >> recessive inheritance of homozygous or compound heterozygous mutation in >> the RAB18 gene on chromosome 10p12." >> ], >> ? "cui": [ ], >> ? "semanticType": [ ], >> ? "obsolete": false, >> ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718", >> ? "@type": "http://www.w3.org/2002/07/owl#Class", >> ? -"links": { >> ? "self": " >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> ", >> ? "ontology": "http://data.bioontology.org/ontologies/DOID", >> ? "children": " >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children >> ", >> >> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan >> wrote: >> >> Hello, >> For the following URLs: >> >> >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> >> >> >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children >> >> I get the following error: >> >> { >> -"errors": [ >> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in >> ontology DOID submission 598" >> ], >> "status": 404 >> } >> >> >> Can you please fix this? >> >> Thanks, >> Rakesh >> -- >> >> *Rakesh Nagarajan* >> >> Founder and Executive Chairman >> >> m: 314-504-5620 >> e: rakesh at pieriandx.com >> >> [image: pierian-logo-trans-light-background] >> [image: linkedin_circle-512] >> [image: >> twitter_circle-512] >> >> Wisdom in Every Report? >> >> CONFIDENTIALITY NOTICE: This message and any attachments are solely for >> the use of the intended recipient and may contain privileged, confidential >> or other legally protected information. If you are not the intended >> recipient, please destroy all copies without reading or disclosing their >> contents and notify the sender of the error by reply email. >> >> >> >> _______________________________________________ >> 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 >> >> >> >> > > -- > > *Rakesh Nagarajan* > > Founder and Executive Chairman > > m: 314-504-5620 > e: rakesh at pieriandx.com > > [image: pierian-logo-trans-light-background] > [image: linkedin_circle-512] > [image: twitter_circle-512] > > > Wisdom in Every Report? > > CONFIDENTIALITY NOTICE: This message and any attachments are solely for > the use of the intended recipient and may contain privileged, confidential > or other legally protected information. If you are not the intended > recipient, please destroy all copies without reading or disclosing their > contents and notify the sender of the error by reply email. > > > > -- *Rakesh Nagarajan* Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mrbarnes at uw.edu Wed Apr 8 07:16:45 2020 From: mrbarnes at uw.edu (Megan R Barnes) Date: Wed, 8 Apr 2020 14:16:45 +0000 Subject: [bioontology-support] FW: NCBO Annotator VM Question In-Reply-To: <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu> References: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu> <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu> Message-ID: <81156C25-4423-401A-A712-0B3E2D773404@uw.edu> Forwarding this message to the support channel, as I realize I forgot to include it in my reply. Megan Barnes PhD Student in Computational Linguistics University of Washington From: Megan R Barnes Date: Friday, April 3, 2020 at 2:04 PM To: John Graybeal Subject: Re: [bioontology-support] NCBO Annotator VM Question Hi John, Thanks for your help. As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request: http://data.bioontology.org/annotator?text=surrounding+end+of+life+care with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"} The annotations we get back that come from NCIT are: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] I will attach full responses from each, as well. Let me know if there?s more info I can provide. Thanks, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal Date: Friday, April 3, 2020 at 11:32 AM To: Megan R Barnes Cc: "support at bioontology.org" Subject: Re: [bioontology-support] NCBO Annotator VM Question Megan, Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame. Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.) It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies. If you send us the example of your two responses, we can look closely at them and give you more specific feedback. John On Apr 2, 2020, at 12:31 PM, Megan R Barnes > wrote: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: local_response.json Type: application/json Size: 4115 bytes Desc: local_response.json URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bioportal_response.json Type: application/json Size: 22488 bytes Desc: bioportal_response.json URL: From Philip.Whalen at RoswellPark.org Wed Apr 8 08:52:13 2020 From: Philip.Whalen at RoswellPark.org (Whalen, Philip) Date: Wed, 8 Apr 2020 15:52:13 +0000 Subject: [bioontology-support] NCIT API key Message-ID: Hello, I?ve been working with the NCIT for some time now and was just looking into utilizing the API that is provided. However, I don?t see anywhere to request an API key for this service. Would you be able to point me to where I may request one? Thank you! Philip Whalen, MA Business Systems Analyst, Biomedical Data Science Shared Resource Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263 Ext. 7197 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Apr 8 10:55:49 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 8 Apr 2020 17:55:49 +0000 Subject: [bioontology-support] NCIT API key In-Reply-To: References: Message-ID: <942A2A88-1D50-4A0A-8468-E18AB7ABABDA@stanford.edu> Philip, Information on how to get and see your API key is at https://bioportal.bioontology.org/help#Getting_an_API_key. John On Apr 8, 2020, at 8:52 AM, Whalen, Philip > wrote: Hello, I?ve been working with the NCIT for some time now and was just looking into utilizing the API that is provided. However, I don?t see anywhere to request an API key for this service. Would you be able to point me to where I may request one? Thank you! Philip Whalen, MA Business Systems Analyst, Biomedical Data Science Shared Resource Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263 Ext. 7197 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Apr 8 11:13:01 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 8 Apr 2020 18:13:01 +0000 Subject: [bioontology-support] NCBO Annotator VM Question In-Reply-To: <81156C25-4423-401A-A712-0B3E2D773404@uw.edu> References: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu> <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu> <81156C25-4423-401A-A712-0B3E2D773404@uw.edu> Message-ID: <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu> Thanks Megan. I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing. The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent. When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings. If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included. John On Apr 8, 2020, at 7:16 AM, Megan R Barnes > wrote: Forwarding this message to the support channel, as I realize I forgot to include it in my reply. Megan Barnes PhD Student in Computational Linguistics University of Washington From: Megan R Barnes > Date: Friday, April 3, 2020 at 2:04 PM To: John Graybeal > Subject: Re: [bioontology-support] NCBO Annotator VM Question Hi John, Thanks for your help. As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request: http://data.bioontology.org/annotator?text=surrounding+end+of+life+care with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"} The annotations we get back that come from NCIT are: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] I will attach full responses from each, as well. Let me know if there?s more info I can provide. Thanks, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal > Date: Friday, April 3, 2020 at 11:32 AM To: Megan R Barnes > Cc: "support at bioontology.org" > Subject: Re: [bioontology-support] NCBO Annotator VM Question Megan, Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame. Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.) It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies. If you send us the example of your two responses, we can look closely at them and give you more specific feedback. John On Apr 2, 2020, at 12:31 PM, Megan R Barnes > wrote: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington _______________________________________________ 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 _______________________________________________ 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 p.vandamme at amsterdamumc.nl Thu Apr 9 02:35:46 2020 From: p.vandamme at amsterdamumc.nl (Damme, P. van (Philip)) Date: Thu, 9 Apr 2020 09:35:46 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme In-Reply-To: References: <5e6910a5ebd82_2b0221a26cc130b6@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl> Dear Michael, others, Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances. I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results. For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389 = http://purl.bioontology.org/ontology/SNOMEDCT/56717001. I can use the API calling http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings I noticed the following: * The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001 and SNOMEDCT. * The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings, however, using different URI (http://snomed.info/id/56717001) and referring to ontology SNO_COPY which is not accessible. * The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT. I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY, which is returning an empty set. I was hoping that you could help me to clarify this. Thank you in advance! Please know that you have my full understanding if it?s not possible to answer my email due to the coronavirus. Best, Philip On 12 Mar 2020, at 20:17, Michael Vladimir Dorf > wrote: Hi Philip, Thank you for alerting us to this issue. We?ve had an operational outage yesterday that triggered a full rebuild of our Annotator/Recommender database. The services have now been fully restored. Please try your API calls again and let us know if you run into any further issues. Thank you so much for your patience. Sincerely, ---------------------------------------------------- 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 Mar 11, 2020, at 9:24 AM, support at bioontology.org wrote: Name: Philip van Damme Email: p.vandamme at amsterdamumc.nl Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Both the annotator and the recommender don't return any results. A few hours ago the website had some brief downtime and did not accept API-calls. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Apr 10 08:53:12 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 10 Apr 2020 08:53:12 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Jean Message-ID: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Apr 10 16:00:08 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 10 Apr 2020 23:00:08 +0000 Subject: [bioontology-support] BioPortal maintenance this weekend; minimal impact planned Message-ID: <1450E9EE-141B-4334-AA3E-41EE3EE31A3D@stanford.edu> Hello everyone, This Saturday evening at 21:00 (GMT-7), we'll begin a maintenance upgrade activity on BioPortal which we hope will be almost transparent, with perhaps a brief interrupt in service. If there are problems, which we think highly unlikely, we need to reserve the next day for possible corrections. On Tuesday evening we'll be performing another maintenance upgrade, which is not expected to require any downtime or service interruptions. For more about why we're performing these barely-visible upgrades, visit https://www.bioontology.org/non-breaking-news-changes-coming-to-bioportal/. Some interesting things are coming to BioPortal. We look forward to sharing more about those soon. John ======================== 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 Fri Apr 10 16:08:48 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 10 Apr 2020 23:08:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jean In-Reply-To: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail> References: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <5B2E23F3-61C1-465C-BE99-3BAEE1D63D2C@stanford.edu> Jean, I confess I am uncertain about what might is causing this, but I can ask some useful questions that will help our team troubleshoot more next week. The clearest picture would be to see the logs corresponding to those requests, ideally from the Apache or similar logs. The requests from your NiFi flow almost certainly will look different in some way. Is it possible there are two ontologies that look almost the same, and the flow is asking for the second ontology which only has one submission? Or alternatively, there are two Bioportal instances and the Apache flow is accessing an instance with only one submission for that ontology? The more concrete details you can provide, the better our chance of coming up with useful suggestions. John On Apr 10, 2020, at 8:53 AM, support at bioontology.org wrote: Name: Jean Email: jean.travassos-ext at glpg.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I'm facing a problem while using BioPortal API and was wondering if you can get me some clarification. I have BP installed in one server for dev purposes and while I use the URL to GET all children of the master node of our Ontology, it works well (testing in Postman or Firefox or curl). However, our Ontology has 3 submissions. When another application (an Apache NiFi flow) makes the http GET request with exactly the same URL, in returns only data from the FIRST submission. It should return the data of the latest submission, of course. Can you get any direction? Is there any parameter or something like that I should configure to prevent this to happen? Thank you for your attention. Best regards _______________________________________________ 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 Fri Apr 10 16:10:35 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 10 Apr 2020 23:10:35 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme In-Reply-To: <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl> References: <5e6910a5ebd82_2b0221a26cc130b6@ncbo-prd-app-09.stanford.edu.mail> <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl> Message-ID: <8F031C33-78D2-4849-92F9-567D04E752D7@stanford.edu> Philip, Thanks for your understanding, and your detailed query! I know we will not be able to dig into it this week, as it is not a trivial situation. We should have a chance to revisit this next week?please ping me if you haven't heard anything by late in the week. John On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) > wrote: Dear Michael, others, Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances. I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results. For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389 = http://purl.bioontology.org/ontology/SNOMEDCT/56717001. I can use the API calling http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings I noticed the following: * The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001 and SNOMEDCT. * The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings, however, using different URI (http://snomed.info/id/56717001) and referring to ontology SNO_COPY which is not accessible. * The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT. I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY, which is returning an empty set. I was hoping that you could help me to clarify this. Thank you in advance! Please know that you have my full understanding if it?s not possible to answer my email due to the coronavirus. Best, Philip On 12 Mar 2020, at 20:17, Michael Vladimir Dorf > wrote: Hi Philip, Thank you for alerting us to this issue. We?ve had an operational outage yesterday that triggered a full rebuild of our Annotator/Recommender database. The services have now been fully restored. Please try your API calls again and let us know if you run into any further issues. Thank you so much for your patience. Sincerely, ---------------------------------------------------- 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 Mar 11, 2020, at 9:24 AM, support at bioontology.org wrote: Name: Philip van Damme Email: p.vandamme at amsterdamumc.nl Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Both the annotator and the recommender don't return any results. A few hours ago the website had some brief downtime and did not accept API-calls. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer _______________________________________________ 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 Fri Apr 10 16:17:20 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 10 Apr 2020 23:17:20 +0000 Subject: [bioontology-support] Issue In-Reply-To: References: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> Message-ID: <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu> Rakesh, Belatedly, we've thought about these behaviors and none of us could put our finger on what is causing your problem. It is the case that there is a timeout on API requests, I believe it is 60 seconds. So if a request is making a complex query, it might be taking too long during period of heavy use. The longer response times for this ontology suggest complexity that might be slowing things down. Sometimes when BioPortal gets a bad response from the backend store, it can get cached for an extended period. If you're able to check in real time when an error occurs, you could see if the browser gets the same error; and if other calls are getting the same error. Unfortunately our browser caches for as long as 2 hours, so that is not totally satisfying to know that. (Perhaps you could try making a different query that asks for more than just children, so that any cached results wouldn't affect the variant query.) We would be happy to take this offline if it remains a significant issue for you. John On Apr 8, 2020, at 6:17 AM, Rakesh Nagarajan > wrote: Thanks John. I agree it is intermittent but somewhat frequent. I got errors for the following overnight: Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children When I get such an error I wait 60 seconds and then try again but then exit when it fails 30 times. So these errors do occur for >30 minutes or so. I also noticed that this specific ontology has long response times per call. Any ideas how this can be more robust? Thanks, Rakesh On Tue, Apr 7, 2020 at 6:56 PM John Graybeal > wrote: Rakesh, I'm sorry, I'm unable to duplicate this problem. When I click on the first URL I get the actual content I'd expect from the API. [1] When I click on the second URL I get a simple response that suggests there are no children, which matches what BioPortal and OntoBee say. My only thought is that perhaps there was a brief outage and your browser or application cached the results. Perhaps you can try another browser to see if it has the same behavior? If you are still having this problem in another browser, please let us know with any additional details you can provide, and we can brainstorm ideas about what might be happening. John [1] Content from API for http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 { ? "prefLabel": "Warburg micro syndrome 3", ? -"synonym": [ ? "Micro Syndrome 3", ? "WARBM3" ], ? -"definition": [ ? "A Warburg micro syndrome that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the RAB18 gene on chromosome 10p12." ], ? "cui": [ ], ? "semanticType": [ ], ? "obsolete": false, ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718", ? "@type": "http://www.w3.org/2002/07/owl#Class", ? -"links": { ? "self": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718", ? "ontology": "http://data.bioontology.org/ontologies/DOID", ? "children": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children", On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan > wrote: Hello, For the following URLs: http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children I get the following error: { -"errors": [ "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in ontology DOID submission 598" ], "status": 404 } Can you please fix this? Thanks, Rakesh -- Rakesh Nagarajan Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. _______________________________________________ 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 -- Rakesh Nagarajan Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. ======================== 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 chinghua at us.ibm.com Sun Apr 12 13:41:08 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Sun, 12 Apr 2020 20:41:08 +0000 Subject: [bioontology-support] API key on Virtual Appliance Message-ID: An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sun Apr 12 18:43:46 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 13 Apr 2020 01:43:46 +0000 Subject: [bioontology-support] API key on Virtual Appliance In-Reply-To: References: Message-ID: Ching-Hua Chen, Thanks for this question. No, your APIkey for your Virtual Appliance installation is not supposed to be the same one you use to access the BIoPortal. To access your Virtual Appliance via the API, you will need to get an account on *that* Virtual Appliance. This will create a unique API key for you for that Appliance. Whoever installed the Virtual Appliance for you should be able to give you the address at which you can access the Virtual Appliance. Once logged in, you can visit the Drop-down menu with your user name on it to see Account Settings, or visit the URL https://{ip_address_of_application/account. You will see your API key on that page. John On Apr 12, 2020, at 1:41 PM, Ching-Hua Chen > wrote: Hi, Is the APIkey on the virtual appliance supposed to be the same one used in the bioportal? One of my admins installed the virtual appliance for me, and didn't give me a key... Wondering if I should be asking my admin for it? I tried going to http://{ip_address_of_appliance}/account in my browser but this doesn't seem to work. Thanks, Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson _______________________________________________ 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 rakesh at pieriandx.com Mon Apr 13 14:03:31 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Mon, 13 Apr 2020 16:03:31 -0500 Subject: [bioontology-support] Issue In-Reply-To: <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu> References: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu> <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu> Message-ID: John, Let's discuss offline if you can, say by phone. I am simply trying to get information about a node and then recursing through children to leaf to get their information. To determine children for a part (one root node only- e.g. "Drug, Food, Chemical, or Biomedical Material") of an ontology like NCIT using the API is now taking more than 5 days when it used to complete in about 1 day. Did something materially change to reduce the performance of the API? Thanks, Rakesh On Fri, Apr 10, 2020 at 6:17 PM John Graybeal wrote: > Rakesh, > > Belatedly, we've thought about these behaviors and none of us could put > our finger on what is causing your problem. > > It is the case that there is a timeout on API requests, I believe it is 60 > seconds. So if a request is making a complex query, it might be taking too > long during period of heavy use. The longer response times for this > ontology suggest complexity that might be slowing things down. > > Sometimes when BioPortal gets a bad response from the backend store, it > can get cached for an extended period. If you're able to check in real time > when an error occurs, you could see if the browser gets the same error; and > if other calls are getting the same error. Unfortunately our browser caches > for as long as 2 hours, so that is not totally satisfying to know that. > (Perhaps you could try making a different query that asks for more than > just children, so that any cached results wouldn't affect the variant > query.) > > We would be happy to take this offline if it remains a significant issue > for you. > > John > > On Apr 8, 2020, at 6:17 AM, Rakesh Nagarajan wrote: > > Thanks John. I agree it is intermittent but somewhat frequent. I got > errors for the following overnight: > > Error in > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children > Error in > http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children > > When I get such an error I wait 60 seconds and then try again but then > exit when it fails 30 times. So these errors do occur for >30 minutes or > so. I also noticed that this specific ontology has long response times per > call. Any ideas how this can be more robust? > > Thanks, > Rakesh > > > > On Tue, Apr 7, 2020 at 6:56 PM John Graybeal > wrote: > >> Rakesh, >> >> I'm sorry, I'm unable to duplicate this problem. >> >> When I click on the first URL I get the actual content I'd expect from >> the API. [1] >> >> When I click on the second URL I get a simple response that suggests >> there are no children, which matches what BioPortal and OntoBee say. >> >> My only thought is that perhaps there was a brief outage and your browser >> or application cached the results. Perhaps you can try another browser to >> see if it has the same behavior? >> >> If you are still having this problem in another browser, please let us >> know with any additional details you can provide, and we can brainstorm >> ideas about what might be happening. >> >> John >> >> >> >> [1] Content from API for >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> >> >> { >> ? "prefLabel": "Warburg micro syndrome 3", >> ? -"synonym": [ >> ? "Micro Syndrome 3", >> ? "WARBM3" >> ], >> ? -"definition": [ >> ? "A Warburg micro syndrome that has_material_basis_in autosomal >> recessive inheritance of homozygous or compound heterozygous mutation in >> the RAB18 gene on chromosome 10p12." >> ], >> ? "cui": [ ], >> ? "semanticType": [ ], >> ? "obsolete": false, >> ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718", >> ? "@type": "http://www.w3.org/2002/07/owl#Class", >> ? -"links": { >> ? "self": " >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> ", >> ? "ontology": "http://data.bioontology.org/ontologies/DOID", >> ? "children": " >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children >> ", >> >> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan >> wrote: >> >> Hello, >> For the following URLs: >> >> >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718 >> >> >> >> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children >> >> I get the following error: >> >> { >> -"errors": [ >> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in >> ontology DOID submission 598" >> ], >> "status": 404 >> } >> >> >> Can you please fix this? >> >> Thanks, >> Rakesh >> -- >> >> *Rakesh Nagarajan* >> >> Founder and Executive Chairman >> >> m: 314-504-5620 >> e: rakesh at pieriandx.com >> >> [image: pierian-logo-trans-light-background] >> [image: linkedin_circle-512] >> [image: >> twitter_circle-512] >> >> Wisdom in Every Report? >> >> CONFIDENTIALITY NOTICE: This message and any attachments are solely for >> the use of the intended recipient and may contain privileged, confidential >> or other legally protected information. If you are not the intended >> recipient, please destroy all copies without reading or disclosing their >> contents and notify the sender of the error by reply email. >> >> >> >> _______________________________________________ >> 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 >> >> >> >> > > -- > > *Rakesh Nagarajan* > > Founder and Executive Chairman > > m: 314-504-5620 > e: rakesh at pieriandx.com > > [image: pierian-logo-trans-light-background] > [image: linkedin_circle-512] > [image: twitter_circle-512] > > > Wisdom in Every Report? > > CONFIDENTIALITY NOTICE: This message and any attachments are solely for > the use of the intended recipient and may contain privileged, confidential > or other legally protected information. If you are not the intended > recipient, please destroy all copies without reading or disclosing their > contents and notify the sender of the error by reply email. > > > > > ======================== > 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 > > > > -- *Rakesh Nagarajan* Founder and Executive Chairman m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mrbarnes at uw.edu Tue Apr 14 14:28:05 2020 From: mrbarnes at uw.edu (Megan R Barnes) Date: Tue, 14 Apr 2020 21:28:05 +0000 Subject: [bioontology-support] NCBO Annotator VM Question In-Reply-To: <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu> References: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu> <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu> <81156C25-4423-401A-A712-0B3E2D773404@uw.edu> <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu> Message-ID: Thanks John, It?s true that adding ?&exclude_synonyms=true" to the API string removes synonyms from the BioPortal mappings (despite the curious fact that I had been including that parameter setting in the data POSTed already). We would actually like for the synonyms to be included in the response from our VM, however. I tried adding ?&exclude_synonyms=false" to the API string we send to our VM and synonyms are still not included. Best, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal Date: Wednesday, April 8, 2020 at 11:17 AM To: Megan R Barnes Cc: "support at bioontology.org" Subject: Re: [bioontology-support] NCBO Annotator VM Question Thanks Megan. I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing. The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent. When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings. If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included. John On Apr 8, 2020, at 7:16 AM, Megan R Barnes > wrote: Forwarding this message to the support channel, as I realize I forgot to include it in my reply. Megan Barnes PhD Student in Computational Linguistics University of Washington From: Megan R Barnes > Date: Friday, April 3, 2020 at 2:04 PM To: John Graybeal > Subject: Re: [bioontology-support] NCBO Annotator VM Question Hi John, Thanks for your help. As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request: http://data.bioontology.org/annotator?text=surrounding+end+of+life+care with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"} The annotations we get back that come from NCIT are: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] I will attach full responses from each, as well. Let me know if there?s more info I can provide. Thanks, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal > Date: Friday, April 3, 2020 at 11:32 AM To: Megan R Barnes > Cc: "support at bioontology.org" > Subject: Re: [bioontology-support] NCBO Annotator VM Question Megan, Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame. Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.) It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies. If you send us the example of your two responses, we can look closely at them and give you more specific feedback. John On Apr 2, 2020, at 12:31 PM, Megan R Barnes > wrote: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington _______________________________________________ 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 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Apr 14 17:03:12 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 15 Apr 2020 00:03:12 +0000 Subject: [bioontology-support] NCBO Annotator VM Question In-Reply-To: References: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu> <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu> <81156C25-4423-401A-A712-0B3E2D773404@uw.edu> <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu> Message-ID: Megan, Please send me your exact API request that you are sending, so we can attempt to duplicate the issue here. Thank you. John On Apr 14, 2020, at 2:28 PM, Megan R Barnes > wrote: Thanks John, It?s true that adding ?&exclude_synonyms=true" to the API string removes synonyms from the BioPortal mappings (despite the curious fact that I had been including that parameter setting in the data POSTed already). We would actually like for the synonyms to be included in the response from our VM, however. I tried adding ?&exclude_synonyms=false" to the API string we send to our VM and synonyms are still not included. Best, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal > Date: Wednesday, April 8, 2020 at 11:17 AM To: Megan R Barnes > Cc: "support at bioontology.org" > Subject: Re: [bioontology-support] NCBO Annotator VM Question Thanks Megan. I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing. The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent. When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings. If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included. John On Apr 8, 2020, at 7:16 AM, Megan R Barnes > wrote: Forwarding this message to the support channel, as I realize I forgot to include it in my reply. Megan Barnes PhD Student in Computational Linguistics University of Washington From: Megan R Barnes > Date: Friday, April 3, 2020 at 2:04 PM To: John Graybeal > Subject: Re: [bioontology-support] NCBO Annotator VM Question Hi John, Thanks for your help. As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request: http://data.bioontology.org/annotator?text=surrounding+end+of+life+care with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"} The annotations we get back that come from NCIT are: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get: [ [{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}], [{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}], [{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}], [{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}] ] I will attach full responses from each, as well. Let me know if there?s more info I can provide. Thanks, Megan Barnes PhD Student in Computational Linguistics University of Washington From: John Graybeal > Date: Friday, April 3, 2020 at 11:32 AM To: Megan R Barnes > Cc: "support at bioontology.org" > Subject: Re: [bioontology-support] NCBO Annotator VM Question Megan, Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame. Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.) It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies. If you send us the example of your two responses, we can look closely at them and give you more specific feedback. John On Apr 2, 2020, at 12:31 PM, Megan R Barnes > wrote: Hello BioPortal Support, I?m writing with a question about the VMWare Virtual Appliance. We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API. I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions. This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/. Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API? Thanks for your help, Megan Barnes PhD Student in Computational Linguistics University of Washington _______________________________________________ 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 _______________________________________________ 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 ======================== 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 Wed Apr 15 09:53:25 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 15 Apr 2020 16:53:25 +0000 Subject: [bioontology-support] Fwd: [BioPortal] Feedback from Jean References: <3d94eb1b28004a6ebc26ac521102dea1@glpg.com> Message-ID: Reforwarding to list after deleting API key information... Begin forwarded message: From: Jean Travassos-EXT > Subject: RE: [bioontology-support] [BioPortal] Feedback from Jean Date: April 15, 2020 at 6:11:46 AM PDT To: John Graybeal >, "support at bioontology.org" > Hello John, Thank you for replying me. I don?t actually know why but I could get this working in NiFi by passing parameters twice: http://10.10.3.79:8080/ontologies/GAAT38/classes/http%3A%2F%2Fwebprotege.stanford.edu%2FR8T0KZCbVZAr6ly04QxKhXU?apikey=&include=all&include=all&display_context=false&display_context=false Params include=all and display_context=false was only read after duplicate them. But it is working. I checked with our infrastructure team and we only have one instance of BP. Another strange behaviour is exclusive of BP: We have this Ontology with 3 submissions. When we open the Ontology, its tree is outdated. After we click in any node, the tree updates itself for the latest and correct version. Do you know if this may be caused by the lack of any property when submitting a new version? There?s nothing to do with we trying to consume data, it?s something exclusive from BioPortal? In attachment there?s examples: - AAT38 is our Ontology, contains 3 submissions. - Submission3-WhenEnters is the tree in the moment when we first see the Ontology. There?s ?Reference Compound UoM? node, which is outdated. - Submission3-AfterSelection show the reloaded tree after we select any valid node. - Submission3-SelectingUnexisting is the error page if we select the node that shouldn?t be shown anymore, since it existed only in the first submission. Thank you very much for your attention and time. If you prefer, I can arrange a quick call. Best Regards, Jean Travassos From: John Graybeal > Sent: 11 April 2020 01:09 To: support at bioontology.org Cc: Jean Travassos-EXT > Subject: Re: [bioontology-support] [BioPortal] Feedback from Jean *** CAUTION : External e-mail *** Jean, I confess I am uncertain about what might is causing this, but I can ask some useful questions that will help our team troubleshoot more next week. The clearest picture would be to see the logs corresponding to those requests, ideally from the Apache or similar logs. The requests from your NiFi flow almost certainly will look different in some way. Is it possible there are two ontologies that look almost the same, and the flow is asking for the second ontology which only has one submission? Or alternatively, there are two Bioportal instances and the Apache flow is accessing an instance with only one submission for that ontology? The more concrete details you can provide, the better our chance of coming up with useful suggestions. John On Apr 10, 2020, at 8:53 AM, support at bioontology.org wrote: Name: Jean Email: jean.travassos-ext at glpg.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hello, I'm facing a problem while using BioPortal API and was wondering if you can get me some clarification. I have BP installed in one server for dev purposes and while I use the URL to GET all children of the master node of our Ontology, it works well (testing in Postman or Firefox or curl). However, our Ontology has 3 submissions. When another application (an Apache NiFi flow) makes the http GET request with exactly the same URL, in returns only data from the FIRST submission. It should return the data of the latest submission, of course. Can you get any direction? Is there any parameter or something like that I should configure to prevent this to happen? Thank you for your attention. Best regards _______________________________________________ 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 ________________________________ This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. [cid:93703B8E-A924-4420-A65E-E6DBFFD5322B at attlocal.net][cid:3C427FC3-8F0E-4BCE-9D77-0C0E68CCD0FB at attlocal.net][cid:380AAF4C-35CB-49B2-88BA-583150E3D42B at attlocal.net][cid:2F6B6989-0599-478B-9A9A-EA026352AD3A at attlocal.net] ======================== 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: BP-AAT38.png Type: image/png Size: 193027 bytes Desc: BP-AAT38.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BP-AAT38-Submission3-WhenEnters.png Type: image/png Size: 146639 bytes Desc: BP-AAT38-Submission3-WhenEnters.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BP-AAT38-Submission3-AfterSelection.png Type: image/png Size: 231004 bytes Desc: BP-AAT38-Submission3-AfterSelection.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BP-AAT38-Submission3-SelectingUnexisting.png Type: image/png Size: 79102 bytes Desc: BP-AAT38-Submission3-SelectingUnexisting.png URL: From chinghua at us.ibm.com Thu Apr 16 03:58:02 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Thu, 16 Apr 2020 10:58:02 +0000 Subject: [bioontology-support] API key on Virtual Appliance In-Reply-To: References: , Message-ID: An HTML attachment was scrubbed... URL: From chinghua at us.ibm.com Thu Apr 16 04:06:25 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Thu, 16 Apr 2020 11:06:25 +0000 Subject: [bioontology-support] Trying to troubleshoot annotate_text output Message-ID: An HTML attachment was scrubbed... URL: From chinghua at us.ibm.com Thu Apr 16 07:48:13 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Thu, 16 Apr 2020 14:48:13 +0000 Subject: [bioontology-support] Trying to troubleshoot annotate_text output In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Apr 16 09:06:01 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 16 Apr 2020 16:06:01 +0000 Subject: [bioontology-support] Trying to troubleshoot annotate_text output In-Reply-To: References: Message-ID: <6878BDA4-B9E1-435E-A8B0-4C626A7B4854@stanford.edu> I'm glad the issue is resolved. One thing you can check if it comes back is whether the same annotation request from the UI works. If it does, then the delay may be coming from your application. (You can also try running the request from a browser, or from curl, to see how fast it comes back, and to make sure your API command is working as you expect.) If the UI request doesn't work, then there may be a problem with processing the ontology. If the UI works but the API doesn't, there is likely a problem with the API request format, and you could send it to the support list (along with the behaviors that result) if you can't figure out what it should be. John On Apr 16, 2020, at 7:48 AM, Ching-Hua Chen > wrote: This issue is resolved. Not sure why... but I am getting outputs. I think there was a really long lag in print to screen for some reason. Thanks. Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson ----- Original message ----- From: Ching-Hua Chen/Watson/IBM To: bioontology-support at lists.stanford.edu Cc: Subject: Trying to troubleshoot annotate_text output Date: Thu, Apr 16, 2020 7:06 AM Hi, I have used the ruby script (bioportal_ontologies_import.rb) provided to import the OCHV ontology to my virtual appliance. When I run "list_ontologies.py" I see that it is listed, after the ontology "STY". I only have these two ontologies on my appliance at the moment. When I ran "annotate_text.py", as is, using the data.bioontology.org URL, the script returned results from OCHV (I only have OCHV in my bioportal account). However, when I edited "annotate_text.py" to reference my virtual appliance URL (I didn't not edit anything else in the script), the script returned nothing. It ran to completion without error. I'm wondering why I'm not getting any results when I run "annotate_text" on my virtual appliance, compared to when I ran the same thing on the bioontology.org. Best, Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson _______________________________________________ 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 s1anbenn at uni-bayreuth.de Thu Apr 16 10:41:21 2020 From: s1anbenn at uni-bayreuth.de (Andreas Benndorf) Date: Thu, 16 Apr 2020 19:41:21 +0200 Subject: [bioontology-support] Usage of Semantic Types via BioPortal REST-API Message-ID: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de> Dear Sir or Madam, in my master's thesis I am developing a Named Entity Recognition system that can retrieve, inter alia, health care activities and diseases in text documents. For the recognition I will use the BioPortal REST-API as follows: 1. Send the document text to the annotator endpoint using the MEDDRA ontology. 2. For every found term in the text, look up the semantic type in the returned JSON file and distinguish with the aid of several semantic types whether the term is a health care activity or a disease. For this, some constants are used in my program for several semantic types like "Sign or Symptom (T184)". 3. Then the term is saved as an annotation without the semantic type information. I don't have a UMLS license and I live in a non-member territory. Is the described procedure compliant to the Terms of Use of BioPortal? In particular, I am referring to the following passage of the Terms of Use: "The sub-licensee is only permitted to access SNOMED CTR using this software (or service) for the purpose of exploring and evaluating the terminology. 2, The sub-licensee is not permitted the use of this software as part of a system that constitutes a SNOMED CT "Data Creation System" or "Data Analysis System", as defined in the IHTSDO Affiliate License. This means that the sub-licensee must not use NCBO BioPortal to add or copy SNOMED CT identifiers into any type of record system, database or document." MEDDRA allows the usage without a license for a research project. So, this shouldn't be a problem. But is the extraction and the distinction of the semantic type from the response of MEDDRA adding or copying "SNOMED CT identifiers into any type of record system, database or document" - especially regarding the fact that I am not saving the semantic type anywhere permanently? Thank you very much in advance for your response. Kind regards, Andreas Benndorf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Apr 17 09:57:14 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 17 Apr 2020 16:57:14 +0000 Subject: [bioontology-support] Usage of Semantic Types via BioPortal REST-API In-Reply-To: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de> References: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de> Message-ID: <2D52FB1F-7A91-4165-B8F1-FC6BDB1A589A@stanford.edu> Hello Andreas, I think this question is ideally asked of the SNOMED CT organization. We are not lawyers, and our users need to resolve legal and licensing questions directly with the providers who have specified the license. (Also, we have no idea what the legal system says in your non-member territory.) I would just note, as a lay person, that a literal reading of the cited language would mean that Google could never put up a web page (which relies on record systems, databases, *and* documents) that contain a SNOMED CT identifier. So, no public resource could ever put up a web page with such an identifier. So, there could never be any posted discussion of SNOMED CT identifiers. Which would fairly clearly violate fair use legal standards in the United States, but your situation in a non-member territory would be different. That may or may not have any implications for your application. As a practical matter, it would inform how I would interpret this kind of narrow use of a secondary provision of the identifier. (If I had to. Which I don't, because, see first paragraph.) Hope this helps your process. Best wishes for your thesis. John On Apr 16, 2020, at 10:41 AM, Andreas Benndorf > wrote: Dear Sir or Madam, in my master?s thesis I am developing a Named Entity Recognition system that can retrieve, inter alia, health care activities and diseases in text documents. For the recognition I will use the BioPortal REST-API as follows: 1. Send the document text to the annotator endpoint using the MEDDRA ontology. 2. For every found term in the text, look up the semantic type in the returned JSON file and distinguish with the aid of several semantic types whether the term is a health care activity or a disease. For this, some constants are used in my program for several semantic types like ?Sign or Symptom (T184)?. 3. Then the term is saved as an annotation without the semantic type information. I don?t have a UMLS license and I live in a non-member territory. Is the described procedure compliant to the Terms of Use of BioPortal? In particular, I am referring to the following passage of the Terms of Use: ?The sub-licensee is only permitted to access SNOMED CT? using this software (or service) for the purpose of exploring and evaluating the terminology. 2, The sub-licensee is not permitted the use of this software as part of a system that constitutes a SNOMED CT ?Data Creation System? or ?Data Analysis System?, as defined in the IHTSDO Affiliate License. This means that the sub-licensee must not use NCBO BioPortal to add or copy SNOMED CT identifiers into any type of record system, database or document.? MEDDRA allows the usage without a license for a research project. So, this shouldn?t be a problem. But is the extraction and the distinction of the semantic type from the response of MEDDRA adding or copying ?SNOMED CT identifiers into any type of record system, database or document? ? especially regarding the fact that I am not saving the semantic type anywhere permanently? Thank you very much in advance for your response. Kind regards, Andreas Benndorf _______________________________________________ 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 Sat Apr 18 06:25:36 2020 From: support at bioontology.org (support at bioontology.org) Date: Sat, 18 Apr 2020 06:25:36 -0700 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry Message-ID: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sun Apr 19 13:41:56 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 19 Apr 2020 20:41:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry In-Reply-To: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> Hi Vincent, Here are some quick replies for now, please respond with whatever issues remain. - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) If you are asking to have this deleted, we can do that. Please confirm that is what you want. - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list). - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues. Hope this helps! John On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote: Name: VJHenry Email: vincent643 at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBIPOM-CC-INF Feedback: Hi, I'm wondering if its possible to change some mistakes I made: - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? Thank you very much for all, Best regards, Vincent (VJHenry; vincent643 at gmail.com) _______________________________________________ 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 alexgarciac at gmail.com Mon Apr 20 05:59:27 2020 From: alexgarciac at gmail.com (Alexander Garcia Castro) Date: Mon, 20 Apr 2020 14:59:27 +0200 Subject: [bioontology-support] icd10 Message-ID: hi, I need the latest version of ICD10 in a format that is not a pdf. a CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where can I get it? I have only been able to find pdfs for the latest version of ICD10. Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what world is the WHO living? am I missing something, I hope so. Best. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Sun Apr 19 21:50:21 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 19 Apr 2020 21:50:21 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Chai Message-ID: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Apr 20 10:33:10 2020 From: mdorf at stanford.edu (Michael Vladimir Dorf) Date: Mon, 20 Apr 2020 17:33:10 +0000 Subject: [bioontology-support] icd10 In-Reply-To: References: Message-ID: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu> Hi Alexander, Thanks for contacting us. Our version of ICD10 comes from the UMLS distribution that we import into BioPortal roughly twice per year. Due to licensing restrictions, we can?t post a download link on our site. If you have a UMLS license, please send us the license number (exclude the NCBO support list when replying) and we can provide you with a TTL file privately. If you don?t already have a license, they are free and you can sign up for one here: https://www.nlm.nih.gov/databases/umls.html#license_request Thanks, Michael On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro > wrote: hi, I need the latest version of ICD10 in a format that is not a pdf. a CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where can I get it? I have only been able to find pdfs for the latest version of ICD10. Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what world is the WHO living? am I missing something, I hope so. Best. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexgarciac at gmail.com Mon Apr 20 12:50:03 2020 From: alexgarciac at gmail.com (Alexander Garcia Castro) Date: Mon, 20 Apr 2020 21:50:03 +0200 Subject: [bioontology-support] icd10 In-Reply-To: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu> References: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu> Message-ID: thanks for the quick response. does it mean that if I want to use the 2020 OWL version of ICD10 then I have to have a umls licence? doesnt icd releases something that is not a PDF? thanks a lot in advance. On Mon, Apr 20, 2020 at 7:33 PM Michael Vladimir Dorf wrote: > Hi Alexander, > > Thanks for contacting us. Our version of ICD10 comes from the UMLS > distribution that we import into BioPortal roughly twice per year. Due to > licensing restrictions, we can?t post a download link on our site. If you > have a UMLS license, please send us the license number (exclude the NCBO > support list when replying) and we can provide you with a TTL file > privately. If you don?t already have a license, they are free and you can > sign up for one here: > > https://www.nlm.nih.gov/databases/umls.html#license_request > > Thanks, > > Michael > > > > > On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro < > alexgarciac at gmail.com> wrote: > > hi, I need the latest version of ICD10 in a format that is not a pdf. a > CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where > can I get it? I have only been able to find pdfs for the latest version of > ICD10. > > Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in > what world is the WHO living? am I missing something, I hope so. > > > Best. > > -- > Alexander Garcia > https://www.researchgate.net/profile/Alexander_Garcia > http://www.usefilm.com/photographer/75943.html > http://www.linkedin.com/in/alexgarciac > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -- 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 jgraybeal at stanford.edu Mon Apr 20 13:21:31 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 20 Apr 2020 20:21:31 +0000 Subject: [bioontology-support] icd10 In-Reply-To: References: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu> Message-ID: I would have said "yes", although a quick Google search found https://dkm.fbk.eu/technologies/icd-10-ontology. John On Apr 20, 2020, at 12:50 PM, Alexander Garcia Castro > wrote: thanks for the quick response. does it mean that if I want to use the 2020 OWL version of ICD10 then I have to have a umls licence? doesnt icd releases something that is not a PDF? thanks a lot in advance. On Mon, Apr 20, 2020 at 7:33 PM Michael Vladimir Dorf > wrote: Hi Alexander, Thanks for contacting us. Our version of ICD10 comes from the UMLS distribution that we import into BioPortal roughly twice per year. Due to licensing restrictions, we can?t post a download link on our site. If you have a UMLS license, please send us the license number (exclude the NCBO support list when replying) and we can provide you with a TTL file privately. If you don?t already have a license, they are free and you can sign up for one here: https://www.nlm.nih.gov/databases/umls.html#license_request Thanks, Michael On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro > wrote: hi, I need the latest version of ICD10 in a format that is not a pdf. a CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where can I get it? I have only been able to find pdfs for the latest version of ICD10. Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what world is the WHO living? am I missing something, I hope so. Best. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac ======================== 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 mdorf at stanford.edu Mon Apr 20 16:31:44 2020 From: mdorf at stanford.edu (Michael Vladimir Dorf) Date: Mon, 20 Apr 2020 23:31:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry In-Reply-To: <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> Message-ID: <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu> Hi Vincent, I?ve done some further troubleshooting of your ontologies, and some flags were raised by our tools in regards to their source: Although we can load the ontologies without errors (including in Protege), the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store: ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples rapper: Parsing URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser ntriples rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column 2531 - Junk after terminating "." rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column 2561 - Junk after terminating ?." Both of these errors refer to a comment that appears inside ALL of your ontology source files. The NTriples file refers to this section of code: BiPOm> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA. \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO) (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO) (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr . Below is the original source code corresponding to this triple: BiPOm 1. Copyright of ontology The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France and by the D?partement MMIP AgroParisTech of the INRA, France. ***************** SNIP ***************** 4. Contact For questions and remarks concerning BiPOm: Anne Goelzer Anne.Goelzer I am not an ontology development expert to point to the exact issue with this code, but both my colleague and I think that the language definition is incorrect: The expectation is to see something like xml:lang="en" or xml:lang=?fr" I?d recommend correcting this entry and adding a new submission of your ontology(ies). Also, please let us know which ontologies need to be deleted so as to address the incorrect acronym issue. 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 Apr 19, 2020, at 1:41 PM, John Graybeal > wrote: Hi Vincent, Here are some quick replies for now, please respond with whatever issues remain. - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) If you are asking to have this deleted, we can do that. Please confirm that is what you want. - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list). - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues. Hope this helps! John On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote: Name: VJHenry Email: vincent643 at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBIPOM-CC-INF Feedback: Hi, I'm wondering if its possible to change some mistakes I made: - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? Thank you very much for all, Best regards, Vincent (VJHenry; vincent643 at gmail.com) _______________________________________________ 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 _______________________________________________ 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 Mon Apr 20 18:21:43 2020 From: mdorf at stanford.edu (Michael Vladimir Dorf) Date: Tue, 21 Apr 2020 01:21:43 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Chai In-Reply-To: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail> References: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <35C902F9-2F7C-4B43-BF7D-161AED7FF399@stanford.edu> Hi Chai, Thank you for contacting us. I am not exactly sure how I can help except to point out that we display the hierarchy of the classes based on the subClassOf relationship. The details of each class presented in our user interface display ALL available properties of the class. You can view the same data using our REST API, and you can see, the two views are identical. For example: https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882 AND http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882?no_links=true&no_context=true&display=prefLabel,synonym,definition,properties,submission You?ll need to append your BioPortal API key to the latter example for it to display properly. You can also try using the FMA Visualization tool to see if that presentation gives you a better idea of the relationships between FMA classes: http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882#visualization Just note that there?s currently a known issue in BioPortal where the visualizations don?t work over HTTPS, so please make sure to use ?http://? instead of ?https://? when viewing that tab. Do you have specific examples of classes in FMA, whose relationships are missing from BioPortal? Thanks, Michael On Apr 19, 2020, at 9:50 PM, support at bioontology.org wrote: Name: Chai Email: humanitiesclinic at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Dear Person-in-Charge My question pertains to the Foundational Model of Anatomy. As from the original website for the FMA, there are (1) spatial (2) part-of/contains relationship data available between classes in the FMA. However, I cannot seem to find these on your website. Can you advise where I can access such data? Regards, Chai _______________________________________________ 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 Tue Apr 21 12:56:49 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 21 Apr 2020 19:56:49 +0000 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry In-Reply-To: References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu> Message-ID: <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu> Hi Vincent, I?ve deleted BIPOM-INST ontology from our system. As far the error, I think the culprit is the language designation, not the contact email. That last fragment should end with: nAnne Goelzer\nAnne.Goelzer?@en instead of: nAnne Goelzer\nAnne.Goelzer"@inra.fr The @en indicates the language from this field: This should instead read: Hope this clarifies it. Michael On Apr 21, 2020, at 9:26 AM, Vincent Henry > wrote: Hi Michael, Thank you very much for your return. You're right, it is a contact email address with "@" that was misinterpreted. I'll never find it by myself. I'll upload new files. Best regards, Vincent On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf > wrote: Hi Vincent, I?ve done some further troubleshooting of your ontologies, and some flags were raised by our tools in regards to their source: Although we can load the ontologies without errors (including in Protege), the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store: ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples rapper: Parsing URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser ntriples rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column 2531 - Junk after terminating "." rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column 2561 - Junk after terminating ?." Both of these errors refer to a comment that appears inside ALL of your ontology source files. The NTriples file refers to this section of code: BiPOm> 2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA. \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO) (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO) (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr . Below is the original source code corresponding to this triple: BiPOm 1. Copyright of ontology The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France and by the D?partement MMIP AgroParisTech of the INRA, France. ***************** SNIP ***************** 4. Contact For questions and remarks concerning BiPOm: Anne Goelzer Anne.Goelzer I am not an ontology development expert to point to the exact issue with this code, but both my colleague and I think that the language definition is incorrect: The expectation is to see something like xml:lang="en" or xml:lang=?fr" I?d recommend correcting this entry and adding a new submission of your ontology(ies). Also, please let us know which ontologies need to be deleted so as to address the incorrect acronym issue. 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 Apr 19, 2020, at 1:41 PM, John Graybeal > wrote: Hi Vincent, Here are some quick replies for now, please respond with whatever issues remain. - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) If you are asking to have this deleted, we can do that. Please confirm that is what you want. - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list). - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues. Hope this helps! John On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote: Name: VJHenry Email: vincent643 at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBIPOM-CC-INF Feedback: Hi, I'm wondering if its possible to change some mistakes I made: - the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST) - the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following - the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? Thank you very much for all, Best regards, Vincent (VJHenry; vincent643 at gmail.com) _______________________________________________ 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 _______________________________________________ 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 vincent643 at gmail.com Tue Apr 21 09:26:31 2020 From: vincent643 at gmail.com (Vincent Henry) Date: Tue, 21 Apr 2020 18:26:31 +0200 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry In-Reply-To: <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu> References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu> Message-ID: Hi Michael, Thank you very much for your return. You're right, it is a contact email address with "@" that was misinterpreted. I'll never find it by myself. I'll upload new files. Best regards, Vincent On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf wrote: > Hi Vincent, > > I?ve done some further troubleshooting of your ontologies, and some flags > were raised by our tools in regards to their source: > > Although we can load the ontologies without errors (including in Protege), > the second step in the parsing process fails when we attempt to serialize > the data to ntriples format to load it into our RDF store: > > ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples > rapper: Parsing URI > file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser > ntriples > rapper: Error - URI > file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column > 2531 - Junk after terminating "." > rapper: Error - URI > file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column > 2561 - Junk after terminating ?." > > Both of these errors refer to a comment that appears inside ALL of your > ontology source files. The NTriples file refers to this section of code: > > "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA. \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO) (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO) (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr . > > Below is the original source code corresponding to this triple: > > > BiPOm > > 1. Copyright of ontology > > The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science > from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France and by the D?partement MMIP AgroParisTech of the INRA, France. > > ***************** SNIP ***************** > > 4. Contact > For questions and remarks concerning BiPOm: > Anne Goelzer > Anne.Goelzer > > > I am not an ontology development expert to point to the exact issue with > this code, but both my colleague and I think that the language definition > is incorrect: > > > > > The expectation is to see something like xml:lang="en" or xml:lang=?fr" > > I?d recommend correcting this entry and adding a new submission of your > ontology(ies). Also, please let us know which ontologies need to be deleted > so as to address the incorrect acronym issue. > > 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 Apr 19, 2020, at 1:41 PM, John Graybeal wrote: > > Hi Vincent, > > Here are some quick replies for now, please respond with whatever issues > remain. > > - the creation of "BiPOm-RPCC-instanciated" ( > https://bioportal.bioontology.org/ontologies/BIPOM-INST) > > If you are asking to have this deleted, we can do that. Please confirm > that is what you want. > > - the description of "BiPOm inferences for Calvin cycle" ( > https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed > instead of following > > Descriptions can be modified by you; click on the pencil icon to edit the > ontology metadata (at upper right) or the submission metadata (above the > submission list). > > - the acronym of "BiPOm E-Coli metabolism instantiation" ( > https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) > BIPOM-ECMET-INST instead of BIPOM-ECMET-INF > and the the acronym of "BiPOm inferences for E-Coli metabolism" ( > https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) > BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. > > Acronyms can not be changed they are the index for everything in the > system. To make this happen, you will need to re-submit your ontology(ies) > under the new acronym you want to use, then tell us to delete the original > ontology(ies). Unfortunately the history will be lost. > > Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? > > I don't have time to look at the details at this moment, but the best way > to figure this out is to try loading the ontology in Protege. If it is not > parseable in BioPortal (which is what this indicates), it is almost always > not parseable in Protege, for the same reasons because they use the same > parser. And Protege actually shows you the errors, which makes it a much > better tool for finding and fixing issues. > > Hope this helps! > > John > > > On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote: > > Name: VJHenry > > Email: vincent643 at gmail.com > > Location: https%3A%2F%2Fbioportal.bioontology.org > %2Fontologies%2FBIPOM-CC-INF > > > *Feedback:* > > Hi, > I'm wondering if its possible to change some mistakes I made: > - the creation of "BiPOm-RPCC-instanciated" ( > https://bioportal.bioontology.org/ontologies/BIPOM-INST) > - the description of "BiPOm inferences for Calvin cycle" ( > https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed > instead of following > - the acronym of "BiPOm E-Coli metabolism instantiation" ( > https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) > BIPOM-ECMET-INST instead of BIPOM-ECMET-INF > and the the acronym of "BiPOm inferences for E-Coli metabolism" ( > https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) > BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. > > Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? > > Thank you very much for all, > Best regards, > Vincent (VJHenry; vincent643 at gmail.com) > > _______________________________________________ > 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 > > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Apr 20 23:56:41 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 20 Apr 2020 23:56:41 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Serenella Ferro Rojas Message-ID: <5e9e9929eb6c0_6d24292ade0910cc@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vincent643 at gmail.com Wed Apr 22 01:00:08 2020 From: vincent643 at gmail.com (Vincent Henry) Date: Wed, 22 Apr 2020 10:00:08 +0200 Subject: [bioontology-support] [BioPortal] Feedback from VJHenry In-Reply-To: <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu> References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail> <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu> <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu> <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu> Message-ID: Hi Micheal, Thank you very much for your the deletion (all my apologies for my mistake) and for your help. I modified the files and it were well integrate in BioPortal. Thanks again, Best regards, Vincent On Tue, Apr 21, 2020 at 9:57 PM Michael Dorf wrote: > Hi Vincent, > > I?ve deleted BIPOM-INST ontology from our system. As far the error, I > think the culprit is the language designation, not the contact email. That > last fragment should end with: > > nAnne Goelzer\nAnne.Goelzer?@en >> >> instead of: > > nAnne Goelzer\nAnne.Goelzer"@inra.fr >> >> > The @en indicates the language from this field: > > >> >> > This should instead read: > > >> >> > Hope this clarifies it. > > Michael > > > On Apr 21, 2020, at 9:26 AM, Vincent Henry wrote: > > Hi Michael, > > Thank you very much for your return. > You're right, it is a contact email address with "@" that was > misinterpreted. > I'll never find it by myself. I'll upload new files. > > Best regards, > Vincent > > On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf > wrote: > >> Hi Vincent, >> >> I?ve done some further troubleshooting of your ontologies, and some flags >> were raised by our tools in regards to their source: >> >> Although we can load the ontologies without errors (including in >> Protege), the second step in the parsing process fails when we attempt to >> serialize the data to ntriples format to load it into our RDF store: >> >> ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples >> rapper: Parsing URI >> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser >> ntriples >> rapper: Error - URI >> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column >> 2531 - Junk after terminating "." >> rapper: Error - URI >> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column >> 2561 - Junk after terminating ?." >> >> Both of these errors refer to a comment that appears inside ALL of your >> ontology source files. The NTriples file refers to this section of code: >> >> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA. \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO) (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO) (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr . >> >> Below is the original source code corresponding to this triple: >> >> >> BiPOm >> >> 1. Copyright of ontology >> >> The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science >> from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France and by the D?partement MMIP AgroParisTech of the INRA, France. >> >> ***************** SNIP ***************** >> >> 4. Contact >> For questions and remarks concerning BiPOm: >> Anne Goelzer >> Anne.Goelzer >> >> >> I am not an ontology development expert to point to the exact issue with >> this code, but both my colleague and I think that the language definition >> is incorrect: >> >> >> >> >> The expectation is to see something like xml:lang="en" or xml:lang=?fr" >> >> I?d recommend correcting this entry and adding a new submission of your >> ontology(ies). Also, please let us know which ontologies need to be deleted >> so as to address the incorrect acronym issue. >> >> 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 Apr 19, 2020, at 1:41 PM, John Graybeal >> wrote: >> >> Hi Vincent, >> >> Here are some quick replies for now, please respond with whatever issues >> remain. >> >> - the creation of "BiPOm-RPCC-instanciated" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-INST) >> >> If you are asking to have this deleted, we can do that. Please confirm >> that is what you want. >> >> - the description of "BiPOm inferences for Calvin cycle" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed >> instead of following >> >> Descriptions can be modified by you; click on the pencil icon to edit the >> ontology metadata (at upper right) or the submission metadata (above the >> submission list). >> >> - the acronym of "BiPOm E-Coli metabolism instantiation" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) >> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF >> and the the acronym of "BiPOm inferences for E-Coli metabolism" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) >> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. >> >> Acronyms can not be changed they are the index for everything in the >> system. To make this happen, you will need to re-submit your ontology(ies) >> under the new acronym you want to use, then tell us to delete the original >> ontology(ies). Unfortunately the history will be lost. >> >> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? >> >> I don't have time to look at the details at this moment, but the best way >> to figure this out is to try loading the ontology in Protege. If it is not >> parseable in BioPortal (which is what this indicates), it is almost always >> not parseable in Protege, for the same reasons because they use the same >> parser. And Protege actually shows you the errors, which makes it a much >> better tool for finding and fixing issues. >> >> Hope this helps! >> >> John >> >> >> On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote: >> >> Name: VJHenry >> >> Email: vincent643 at gmail.com >> >> Location: https%3A%2F%2Fbioportal.bioontology.org >> %2Fontologies%2FBIPOM-CC-INF >> >> >> *Feedback:* >> >> Hi, >> I'm wondering if its possible to change some mistakes I made: >> - the creation of "BiPOm-RPCC-instanciated" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-INST) >> - the description of "BiPOm inferences for Calvin cycle" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed >> instead of following >> - the acronym of "BiPOm E-Coli metabolism instantiation" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) >> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF >> and the the acronym of "BiPOm inferences for E-Coli metabolism" ( >> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) >> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF. >> >> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ? >> >> Thank you very much for all, >> Best regards, >> Vincent (VJHenry; vincent643 at gmail.com) >> >> _______________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 Apr 22 05:26:11 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 22 Apr 2020 05:26:11 -0700 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be Message-ID: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Apr 22 12:13:33 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 22 Apr 2020 19:13:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be In-Reply-To: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail> References: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Chen, Thank you for contacting us. The description for ontology is attached to the submission record, meaning if you submit a new version of the ontology (new submission), its description may be different from the previous one. To modify the description, click on the blue edit icon next to Submissions header (see image below). Hope this helps! Michael [cid:66072A4E-44BA-417B-8B18-B75665EA0D44 at stanford.edu] On Apr 22, 2020, at 5:26 AM, support at bioontology.org wrote: Name: chen.yang at ugent.be Email: chen.yang at ugent.be Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FONE%252Fstandards%2523caseStudies Feedback: Dear, I am the developer of the ontology for nutritional epidemiology (https://bioportal.bioontology.org/ontologies/ONE). I was going to edit the "Description" of the ontology on the page. However, I did not find where I can do the change. Could you please help me? Thanks in advance, Chen _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: edit_description.png Type: image/png Size: 356119 bytes Desc: edit_description.png URL: From support at bioontology.org Fri Apr 24 12:47:36 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 24 Apr 2020 12:47:36 -0700 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari Message-ID: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Apr 24 15:09:25 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 Apr 2020 22:09:25 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Shruthi, I am happy to help you, and just want to clarify the situation. I can see a public ontology called SCO that fits your description, with you as the contact, and it seems to be publicly visible. So if you are still having trouble seeing this ontology, can you please provide further details about what you are doing? It appears the owner of the ontology may have been mis-assigned (possibly an operator error on our side); I have re-assigned you as the owner. My apologies for this issue. Please try to access it and let me know if you have any difficulty. john On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: Name: shruthichari Email: charis at rpi.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Hi Sir/Madam, I had an ontology on Bioportal under the name, Study Cohort Ontology and acronym, SCO. Not only can I not find it anymore but I can't resubmit as somebody else has made a submission. I attest that I am the author of this ontology and we even have a paper in the International Semantic Web Conference (ISWC) last year: https://arxiv.org/abs/1907.04358. Can you please help me resubmit my ontology? Feel free to reach out to me at charis at rpi.edu -Thanks, Shruthi _______________________________________________ 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 Fri Apr 24 16:06:34 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 Apr 2020 23:06:34 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> Message-ID: <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> Ah, that explains it, thank you. I have changed the setting to not be View, and saved that. (It would have showed up previously, if you enabled the Views checkbox. But if it isn't a view that isn't what you want!) There may be some additional processing required as a result; I'll ask our expert on such things when she is back on Monday. I notice there are no classes being displayed, due to an RDF parsing error; do you understand why that is? Let us know if you need help figuring that out?my basic rule of thumb is to try opening it in Protege to see if that reports any errors, and fix all those first. If it works there but not in BioPortal, let us know and we'll try to hep. John On Apr 24, 2020, at 3:50 PM, Shruthi Chari > wrote: Hi John, Thanks so much for reassigning ownership to me, with this, I am able to upload a new version. I have a problem in that my ontology doesn't show up on Bioportal's main page as an ontology page as I accidentally made it an ontology view. Can you help revert this option and instead set it as an ontology? -Thanks, Shruthi On 2020-04-24 18:09, John Graybeal wrote: Hi Shruthi, I am happy to help you, and just want to clarify the situation. I can see a public ontology called SCO that fits your description, with you as the contact, and it seems to be publicly visible. So if you are still having trouble seeing this ontology, can you please provide further details about what you are doing? It appears the owner of the ontology may have been mis-assigned (possibly an operator error on our side); I have re-assigned you as the owner. My apologies for this issue. Please try to access it and let me know if you have any difficulty. john On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: Name: shruthichari Email: charis at rpi.edu Location: https%3A%2F%2Fbioportal.bioontology.org [1]%2Fontologies FEEDBACK: Hi Sir/Madam, I had an ontology on Bioportal under the name, Study Cohort Ontology and acronym, SCO. Not only can I not find it anymore but I can't resubmit as somebody else has made a submission. I attest that I am the author of this ontology and we even have a paper in the International Semantic Web Conference (ISWC) last year: https://arxiv.org/abs/1907.04358 [2]. Can you please help me resubmit my ontology? Feel free to reach out to me at charis at rpi.edu -Thanks, Shruthi _______________________________________________ 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 Links: ------ [1] http://2Fbioportal.bioontology.org [2] https://arxiv.org/abs/1907.04358 ======================== 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 Fri Apr 24 16:48:35 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 24 Apr 2020 23:48:35 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: <30a7355d5a089c13602f7139326bb4eb@rpi.edu> References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> Message-ID: Hi Shruthi, I had a look at the logs. There appear to be two locations in the file that say "rdf:resoure" (instead of rdf:resource). Just a warning in the OWLAPI parser, but our Rapper software (http://librdf.org/raptor/rapper.html) didn't like it. See if fixing those makes it better, yes? John On Apr 24, 2020, at 4:23 PM, Shruthi Chari > wrote: Hi John, I don't want it to be a view yes. Thanks for making the change. As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference. However, I want to make some import clean up changes so I will work on that and hopefully it should render better? Not sure why it doesn't render on Bioportal though. -Thanks, Shruthi On 2020-04-24 19:06, John Graybeal wrote: Ah, that explains it, thank you. I have changed the setting to not be View, and saved that. (It would have showed up previously, if you enabled the Views checkbox. But if it isn't a view that isn't what you want!) There may be some additional processing required as a result; I'll ask our expert on such things when she is back on Monday. I notice there are no classes being displayed, due to an RDF parsing error; do you understand why that is? Let us know if you need help figuring that out?my basic rule of thumb is to try opening it in Protege to see if that reports any errors, and fix all those first. If it works there but not in BioPortal, let us know and we'll try to hep. John On Apr 24, 2020, at 3:50 PM, Shruthi Chari > wrote: Hi John, Thanks so much for reassigning ownership to me, with this, I am able to upload a new version. I have a problem in that my ontology doesn't show up on Bioportal's main page as an ontology page as I accidentally made it an ontology view. Can you help revert this option and instead set it as an ontology? -Thanks, Shruthi On 2020-04-24 18:09, John Graybeal wrote: Hi Shruthi, I am happy to help you, and just want to clarify the situation. I can see a public ontology called SCO that fits your description, with you as the contact, and it seems to be publicly visible. So if you are still having trouble seeing this ontology, can you please provide further details about what you are doing? It appears the owner of the ontology may have been mis-assigned (possibly an operator error on our side); I have re-assigned you as the owner. My apologies for this issue. Please try to access it and let me know if you have any difficulty. john On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: Name: shruthichari Email: charis at rpi.edu Location: https%3A%2F%2Fbioportal.bioontology.org [1] [1]%2Fontologies FEEDBACK: Hi Sir/Madam, I had an ontology on Bioportal under the name, Study Cohort Ontology and acronym, SCO. Not only can I not find it anymore but I can't resubmit as somebody else has made a submission. I attest that I am the author of this ontology and we even have a paper in the International Semantic Web Conference (ISWC) last year: https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me resubmit my ontology? Feel free to reach out to me at charis at rpi.edu -Thanks, Shruthi _______________________________________________ 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 Links: ------ [1] http://2Fbioportal.bioontology.org [1] [2] https://arxiv.org/abs/1907.04358 [2] ======================== 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 Links: ------ [1] http://2fbioportal.bioontology.org/ [2] https://arxiv.org/abs/1907.04358 ======================== 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 charis at rpi.edu Fri Apr 24 15:50:10 2020 From: charis at rpi.edu (Shruthi Chari) Date: Fri, 24 Apr 2020 18:50:10 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> Hi John, Thanks so much for reassigning ownership to me, with this, I am able to upload a new version. I have a problem in that my ontology doesn't show up on Bioportal's main page as an ontology page as I accidentally made it an ontology view. Can you help revert this option and instead set it as an ontology? -Thanks, Shruthi On 2020-04-24 18:09, John Graybeal wrote: > Hi Shruthi, > > I am happy to help you, and just want to clarify the situation. > > I can see a public ontology called SCO that fits your description, > with you as the contact, and it seems to be publicly visible. So if > you are still having trouble seeing this ontology, can you please > provide further details about what you are doing? > > It appears the owner of the ontology may have been mis-assigned > (possibly an operator error on our side); I have re-assigned you as > the owner. > > My apologies for this issue. Please try to access it and let me know > if you have any difficulty. > > john > >> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >> >> Name: shruthichari >> >> Email: charis at rpi.edu >> >> Location: https%3A%2F%2Fbioportal.bioontology.org [1]%2Fontologies >> >> FEEDBACK: >> >> Hi Sir/Madam, >> >> I had an ontology on Bioportal under the name, Study Cohort Ontology >> and acronym, SCO. Not only can I not find it anymore but I can't >> resubmit as somebody else has made a submission. I attest that I am >> the author of this ontology and we even have a paper in the >> International Semantic Web Conference (ISWC) last year: >> https://arxiv.org/abs/1907.04358 [2]. Can you please help me >> resubmit my ontology? >> >> Feel free to reach out to me at charis at rpi.edu >> >> -Thanks, >> Shruthi >> >> _______________________________________________ >> 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 > > > > Links: > ------ > [1] http://2Fbioportal.bioontology.org > [2] https://arxiv.org/abs/1907.04358 From support at bioontology.org Mon Apr 27 00:13:55 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 27 Apr 2020 00:13:55 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger Message-ID: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From charis at rpi.edu Fri Apr 24 16:23:03 2020 From: charis at rpi.edu (Shruthi Chari) Date: Fri, 24 Apr 2020 19:23:03 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> Message-ID: <30a7355d5a089c13602f7139326bb4eb@rpi.edu> Hi John, I don't want it to be a view yes. Thanks for making the change. As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference. However, I want to make some import clean up changes so I will work on that and hopefully it should render better? Not sure why it doesn't render on Bioportal though. -Thanks, Shruthi On 2020-04-24 19:06, John Graybeal wrote: > Ah, that explains it, thank you. > > I have changed the setting to not be View, and saved that. (It would > have showed up previously, if you enabled the Views checkbox. But if > it isn't a view that isn't what you want!) > > There may be some additional processing required as a result; I'll ask > our expert on such things when she is back on Monday. > > I notice there are no classes being displayed, due to an RDF parsing > error; do you understand why that is? Let us know if you need help > figuring that out?my basic rule of thumb is to try opening it in > Protege to see if that reports any errors, and fix all those first. If > it works there but not in BioPortal, let us know and we'll try to hep. > > > John > >> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >> >> Hi John, >> >> Thanks so much for reassigning ownership to me, with this, I am >> able to upload a new version. I have a problem in that my ontology >> doesn't show up on Bioportal's main page as an ontology page as I >> accidentally made it an ontology view. Can you help revert this >> option and instead set it as an ontology? >> >> -Thanks, >> Shruthi >> >> On 2020-04-24 18:09, John Graybeal wrote: >> Hi Shruthi, >> I am happy to help you, and just want to clarify the situation. >> I can see a public ontology called SCO that fits your description, >> with you as the contact, and it seems to be publicly visible. So if >> you are still having trouble seeing this ontology, can you please >> provide further details about what you are doing? >> It appears the owner of the ontology may have been mis-assigned >> (possibly an operator error on our side); I have re-assigned you as >> the owner. >> My apologies for this issue. Please try to access it and let me >> know >> if you have any difficulty. >> john >> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >> Name: shruthichari >> Email: charis at rpi.edu >> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >> [1]%2Fontologies >> FEEDBACK: >> Hi Sir/Madam, >> I had an ontology on Bioportal under the name, Study Cohort >> Ontology >> and acronym, SCO. Not only can I not find it anymore but I can't >> resubmit as somebody else has made a submission. I attest that I am >> the author of this ontology and we even have a paper in the >> International Semantic Web Conference (ISWC) last year: >> https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me >> resubmit my ontology? >> Feel free to reach out to me at charis at rpi.edu >> -Thanks, >> Shruthi >> _______________________________________________ >> 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 >> Links: >> ------ >> [1] http://2Fbioportal.bioontology.org [1] >> [2] https://arxiv.org/abs/1907.04358 [2] > > ======================== > 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 > > > > Links: > ------ > [1] http://2fbioportal.bioontology.org/ > [2] https://arxiv.org/abs/1907.04358 -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-24 at 7.15.07 PM.png Type: image/png Size: 546532 bytes Desc: not available URL: From charis at rpi.edu Fri Apr 24 19:02:23 2020 From: charis at rpi.edu (Shruthi Chari) Date: Fri, 24 Apr 2020 22:02:23 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: Message-ID: <9BC3F099-3A8C-4426-BE69-8A85D158C38E@rpi.edu> Hi John, Great thanks I will fix those issues. Thanks for the tool reference I will use it to test. So just to confirm if I run my ontology through this tool, is Bioportal guaranteed to render it? -Thanks, Shruthi Sent from my iPhone > On Apr 24, 2020, at 7:48 PM, John Graybeal wrote: > > ? Hi Shruthi, > > I had a look at the logs. There appear to be two locations in the file that say "rdf:resoure" (instead of rdf:resource). Just a warning in the OWLAPI parser, but our Rapper software (http://librdf.org/raptor/rapper.html) didn't like it. See if fixing those makes it better, yes? > > John > > > >> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >> >> Hi John, >> >> I don't want it to be a view yes. Thanks for making the change. >> >> As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference. >> >> However, I want to make some import clean up changes so I will work on that and hopefully it should render better? >> >> Not sure why it doesn't render on Bioportal though. >> >> -Thanks, >> Shruthi >> >>> On 2020-04-24 19:06, John Graybeal wrote: >>> Ah, that explains it, thank you. >>> I have changed the setting to not be View, and saved that. (It would >>> have showed up previously, if you enabled the Views checkbox. But if >>> it isn't a view that isn't what you want!) >>> There may be some additional processing required as a result; I'll ask >>> our expert on such things when she is back on Monday. >>> I notice there are no classes being displayed, due to an RDF parsing >>> error; do you understand why that is? Let us know if you need help >>> figuring that out?my basic rule of thumb is to try opening it in >>> Protege to see if that reports any errors, and fix all those first. If >>> it works there but not in BioPortal, let us know and we'll try to hep. >>> John >>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >>>> Hi John, >>>> Thanks so much for reassigning ownership to me, with this, I am >>>> able to upload a new version. I have a problem in that my ontology >>>> doesn't show up on Bioportal's main page as an ontology page as I >>>> accidentally made it an ontology view. Can you help revert this >>>> option and instead set it as an ontology? >>>> -Thanks, >>>> Shruthi >>>> On 2020-04-24 18:09, John Graybeal wrote: >>>> Hi Shruthi, >>>> I am happy to help you, and just want to clarify the situation. >>>> I can see a public ontology called SCO that fits your description, >>>> with you as the contact, and it seems to be publicly visible. So if >>>> you are still having trouble seeing this ontology, can you please >>>> provide further details about what you are doing? >>>> It appears the owner of the ontology may have been mis-assigned >>>> (possibly an operator error on our side); I have re-assigned you as >>>> the owner. >>>> My apologies for this issue. Please try to access it and let me >>>> know >>>> if you have any difficulty. >>>> john >>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >>>> Name: shruthichari >>>> Email: charis at rpi.edu >>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >>>> [1]%2Fontologies >>>> FEEDBACK: >>>> Hi Sir/Madam, >>>> I had an ontology on Bioportal under the name, Study Cohort >>>> Ontology >>>> and acronym, SCO. Not only can I not find it anymore but I can't >>>> resubmit as somebody else has made a submission. I attest that I am >>>> the author of this ontology and we even have a paper in the >>>> International Semantic Web Conference (ISWC) last year: >>>> https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me >>>> resubmit my ontology? >>>> Feel free to reach out to me at charis at rpi.edu >>>> -Thanks, >>>> Shruthi >>>> _______________________________________________ >>>> 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 >>>> Links: >>>> ------ >>>> [1] http://2Fbioportal.bioontology.org [1] >>>> [2] https://arxiv.org/abs/1907.04358 [2] >>> ======================== >>> 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 >>> Links: >>> ------ >>> [1] http://2fbioportal.bioontology.org/ >>> [2] https://arxiv.org/abs/1907.04358 >> > > ======================== > 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 charis at rpi.edu Sat Apr 25 13:38:44 2020 From: charis at rpi.edu (Shruthi Chari) Date: Sat, 25 Apr 2020 16:38:44 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> Message-ID: <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> Hi John, Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late. I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator. Thanks for your assistance and looking forward to getting this last issue resolved. -Thanks, Shruthi On 2020-04-24 19:48, John Graybeal wrote: > Hi Shruthi, > > I had a look at the logs. There appear to be two locations in the file > that say "rdf:resoure" (instead of rdf:resource). Just a warning in > the OWLAPI parser, but our Rapper software > (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if > fixing those makes it better, yes? > > John > >> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >> >> Hi John, >> >> I don't want it to be a view yes. Thanks for making the change. >> >> As for the RDF parsing error, I am not sure what is happening. Can >> you send me the log as I don't see to it on my end. I don't see >> errors on Protege per se it opens there. I am attaching a screenshot >> for your reference. >> >> However, I want to make some import clean up changes so I will work >> on that and hopefully it should render better? >> >> Not sure why it doesn't render on Bioportal though. >> >> -Thanks, >> Shruthi >> >> On 2020-04-24 19:06, John Graybeal wrote: >> Ah, that explains it, thank you. >> I have changed the setting to not be View, and saved that. (It >> would >> have showed up previously, if you enabled the Views checkbox. But >> if >> it isn't a view that isn't what you want!) >> There may be some additional processing required as a result; I'll >> ask >> our expert on such things when she is back on Monday. >> I notice there are no classes being displayed, due to an RDF >> parsing >> error; do you understand why that is? Let us know if you need help >> figuring that out?my basic rule of thumb is to try opening it in >> Protege to see if that reports any errors, and fix all those first. >> If >> it works there but not in BioPortal, let us know and we'll try to >> hep. >> John >> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >> Hi John, >> Thanks so much for reassigning ownership to me, with this, I am >> able to upload a new version. I have a problem in that my ontology >> doesn't show up on Bioportal's main page as an ontology page as I >> accidentally made it an ontology view. Can you help revert this >> option and instead set it as an ontology? >> -Thanks, >> Shruthi >> On 2020-04-24 18:09, John Graybeal wrote: >> Hi Shruthi, >> I am happy to help you, and just want to clarify the situation. >> I can see a public ontology called SCO that fits your description, >> with you as the contact, and it seems to be publicly visible. So if >> you are still having trouble seeing this ontology, can you please >> provide further details about what you are doing? >> It appears the owner of the ontology may have been mis-assigned >> (possibly an operator error on our side); I have re-assigned you as >> the owner. >> My apologies for this issue. Please try to access it and let me >> know >> if you have any difficulty. >> john >> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >> Name: shruthichari >> Email: charis at rpi.edu >> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >> [1]%2Fontologies >> FEEDBACK: >> Hi Sir/Madam, >> I had an ontology on Bioportal under the name, Study Cohort >> Ontology >> and acronym, SCO. Not only can I not find it anymore but I can't >> resubmit as somebody else has made a submission. I attest that I am >> the author of this ontology and we even have a paper in the >> International Semantic Web Conference (ISWC) last year: >> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help >> me >> resubmit my ontology? >> Feel free to reach out to me at charis at rpi.edu >> -Thanks, >> Shruthi >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> [2] >> ======================== >> 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 >> Links: >> ------ >> [1] http://2Fbioportal.bioontology.org [3] [1] >> [2] https://arxiv.org/abs/1907.04358 [1] [2] >> ======================== >> 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 >> Links: >> ------ >> [1] http://2fbioportal.bioontology.org/ [3] >> [2] https://arxiv.org/abs/1907.04358 [1] > > > ======================== > 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 > > > > Links: > ------ > [1] https://arxiv.org/abs/1907.04358 > [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support > [3] http://2fbioportal.bioontology.org/ > [4] http://librdf.org/raptor/rapper.html From support at bioontology.org Sat Apr 25 14:19:32 2020 From: support at bioontology.org (support at bioontology.org) Date: Sat, 25 Apr 2020 14:19:32 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin Message-ID: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Apr 27 10:10:46 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 17:10:46 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger In-Reply-To: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail> References: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <0CFC2970-5C49-49C2-B2E4-E87922E982ED@stanford.edu> Hi Thomas, Apologies that I?m not following your question. When end users upload an ontology to BioPortal, we generate the CSV from the original ontology source file. Could you give me an example of a term from the ontology where you feel there is a discrepancy between the OWL file content and the CSV? It would be helpful if I could have a starting point to look into this in more detail. Kind regards, Jennifer On Apr 27, 2020, at 12:13 AM, support at bioontology.org wrote: Name: Thomas Lemberger Email: thomas.lemberger at embo.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBAO Feedback: Dear Helpdesk, I am trying to download the BAO ontology http://bioportal.bioontology.org/ontologies/BAO as an .owl file from http://data.bioontology.org/ontologies/BAO/submissions/36/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb Unfortunately, this owl file seems incomplete and does not include any description of the terms, definitions etc. This information is present in the .csv file http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv but not in the owl. Is there a way to regenerate the .owl files so that they contain the complete ontology? Man thanks! Thomas _______________________________________________ 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 Mon Apr 27 10:26:24 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 17:26:24 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin In-Reply-To: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail> References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Jay, I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/164 ? and am looking into the parsing errors. Kind regards. Jennifer On Apr 25, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Jay Franklin Email: frankj7 at rpi.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hi, It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004". Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this. Thanks, Jay Franklin Rensselaer Polytechnic Institute _______________________________________________ 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 Mon Apr 27 11:11:59 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 18:11:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin In-Reply-To: References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi again Jay, I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3 If I don?t get a response shortly, I?ll attempt to fix it on our end and reprocess. Jennifer On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti > wrote: Hi Jay, I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/164 ? and am looking into the parsing errors. Kind regards. Jennifer On Apr 25, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Jay Franklin Email: frankj7 at rpi.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hi, It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004". Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this. Thanks, Jay Franklin Rensselaer Polytechnic Institute _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Apr 27 11:52:59 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 18:52:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> Message-ID: Hello Shruthi Your ontology has been fully converted to standalone vs. a view. I?ve also reprocessed your ontology so that you can use it with the Annotator functionality. Kind regards, Jennifer > On Apr 25, 2020, at 1:38 PM, Shruthi Chari wrote: > > Hi John, > > Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late. > > I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator. > > Thanks for your assistance and looking forward to getting this last issue resolved. > > -Thanks, > Shruthi > > On 2020-04-24 19:48, John Graybeal wrote: >> Hi Shruthi, >> I had a look at the logs. There appear to be two locations in the file >> that say "rdf:resoure" (instead of rdf:resource). Just a warning in >> the OWLAPI parser, but our Rapper software >> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if >> fixing those makes it better, yes? >> John >>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >>> Hi John, >>> I don't want it to be a view yes. Thanks for making the change. >>> As for the RDF parsing error, I am not sure what is happening. Can >>> you send me the log as I don't see to it on my end. I don't see >>> errors on Protege per se it opens there. I am attaching a screenshot >>> for your reference. >>> However, I want to make some import clean up changes so I will work >>> on that and hopefully it should render better? >>> Not sure why it doesn't render on Bioportal though. >>> -Thanks, >>> Shruthi >>> On 2020-04-24 19:06, John Graybeal wrote: >>> Ah, that explains it, thank you. >>> I have changed the setting to not be View, and saved that. (It >>> would >>> have showed up previously, if you enabled the Views checkbox. But >>> if >>> it isn't a view that isn't what you want!) >>> There may be some additional processing required as a result; I'll >>> ask >>> our expert on such things when she is back on Monday. >>> I notice there are no classes being displayed, due to an RDF >>> parsing >>> error; do you understand why that is? Let us know if you need help >>> figuring that out?my basic rule of thumb is to try opening it in >>> Protege to see if that reports any errors, and fix all those first. >>> If >>> it works there but not in BioPortal, let us know and we'll try to >>> hep. >>> John >>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >>> Hi John, >>> Thanks so much for reassigning ownership to me, with this, I am >>> able to upload a new version. I have a problem in that my ontology >>> doesn't show up on Bioportal's main page as an ontology page as I >>> accidentally made it an ontology view. Can you help revert this >>> option and instead set it as an ontology? >>> -Thanks, >>> Shruthi >>> On 2020-04-24 18:09, John Graybeal wrote: >>> Hi Shruthi, >>> I am happy to help you, and just want to clarify the situation. >>> I can see a public ontology called SCO that fits your description, >>> with you as the contact, and it seems to be publicly visible. So if >>> you are still having trouble seeing this ontology, can you please >>> provide further details about what you are doing? >>> It appears the owner of the ontology may have been mis-assigned >>> (possibly an operator error on our side); I have re-assigned you as >>> the owner. >>> My apologies for this issue. Please try to access it and let me >>> know >>> if you have any difficulty. >>> john >>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >>> Name: shruthichari >>> Email: charis at rpi.edu >>> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >>> [1]%2Fontologies >>> FEEDBACK: >>> Hi Sir/Madam, >>> I had an ontology on Bioportal under the name, Study Cohort >>> Ontology >>> and acronym, SCO. Not only can I not find it anymore but I can't >>> resubmit as somebody else has made a submission. I attest that I am >>> the author of this ontology and we even have a paper in the >>> International Semantic Web Conference (ISWC) last year: >>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help >>> me >>> resubmit my ontology? >>> Feel free to reach out to me at charis at rpi.edu >>> -Thanks, >>> Shruthi >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> [2] >>> ======================== >>> 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 >>> Links: >>> ------ >>> [1] http://2Fbioportal.bioontology.org [3] [1] >>> [2] https://arxiv.org/abs/1907.04358 [1] [2] >>> ======================== >>> 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 >>> Links: >>> ------ >>> [1] http://2fbioportal.bioontology.org/ [3] >>> [2] https://arxiv.org/abs/1907.04358 [1] >> >> ======================== >> 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 >> Links: >> ------ >> [1] https://arxiv.org/abs/1907.04358 >> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> [3] http://2fbioportal.bioontology.org/ >> [4] http://librdf.org/raptor/rapper.html > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From charis at rpi.edu Mon Apr 27 12:28:30 2020 From: charis at rpi.edu (Shruthi Chari) Date: Mon, 27 Apr 2020 15:28:30 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> Message-ID: Hi Jennifer, Thanks so much for this update. I have a quick question if we resubmit a version of the ontology - do we need to take extra steps to ensure that it is usable via the Annotator functionality? -Thanks, Shruthi On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote: > Hello Shruthi > > Your ontology has been fully converted to standalone vs. a view. I?ve > also reprocessed your ontology so that you can use it with the > Annotator functionality. > > Kind regards, > Jennifer > > > >> On Apr 25, 2020, at 1:38 PM, Shruthi Chari wrote: >> >> Hi John, >> >> Thanks a bunch the logs you sent me were a lifesaver. I was able to >> reupload our ontology and now the classes show up. I should have >> reached out to support a year earlier, but never too late. >> >> I am still waiting on the ontology view fix as in to revert this to be >> a stand-alone ontology and not a view. This would then allow our >> ontology to be queryable by the BioAnnotator. >> >> Thanks for your assistance and looking forward to getting this last >> issue resolved. >> >> -Thanks, >> Shruthi >> >> On 2020-04-24 19:48, John Graybeal wrote: >>> Hi Shruthi, >>> I had a look at the logs. There appear to be two locations in the >>> file >>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in >>> the OWLAPI parser, but our Rapper software >>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if >>> fixing those makes it better, yes? >>> John >>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >>>> Hi John, >>>> I don't want it to be a view yes. Thanks for making the change. >>>> As for the RDF parsing error, I am not sure what is happening. Can >>>> you send me the log as I don't see to it on my end. I don't see >>>> errors on Protege per se it opens there. I am attaching a screenshot >>>> for your reference. >>>> However, I want to make some import clean up changes so I will work >>>> on that and hopefully it should render better? >>>> Not sure why it doesn't render on Bioportal though. >>>> -Thanks, >>>> Shruthi >>>> On 2020-04-24 19:06, John Graybeal wrote: >>>> Ah, that explains it, thank you. >>>> I have changed the setting to not be View, and saved that. (It >>>> would >>>> have showed up previously, if you enabled the Views checkbox. But >>>> if >>>> it isn't a view that isn't what you want!) >>>> There may be some additional processing required as a result; I'll >>>> ask >>>> our expert on such things when she is back on Monday. >>>> I notice there are no classes being displayed, due to an RDF >>>> parsing >>>> error; do you understand why that is? Let us know if you need help >>>> figuring that out?my basic rule of thumb is to try opening it in >>>> Protege to see if that reports any errors, and fix all those first. >>>> If >>>> it works there but not in BioPortal, let us know and we'll try to >>>> hep. >>>> John >>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >>>> Hi John, >>>> Thanks so much for reassigning ownership to me, with this, I am >>>> able to upload a new version. I have a problem in that my ontology >>>> doesn't show up on Bioportal's main page as an ontology page as I >>>> accidentally made it an ontology view. Can you help revert this >>>> option and instead set it as an ontology? >>>> -Thanks, >>>> Shruthi >>>> On 2020-04-24 18:09, John Graybeal wrote: >>>> Hi Shruthi, >>>> I am happy to help you, and just want to clarify the situation. >>>> I can see a public ontology called SCO that fits your description, >>>> with you as the contact, and it seems to be publicly visible. So if >>>> you are still having trouble seeing this ontology, can you please >>>> provide further details about what you are doing? >>>> It appears the owner of the ontology may have been mis-assigned >>>> (possibly an operator error on our side); I have re-assigned you as >>>> the owner. >>>> My apologies for this issue. Please try to access it and let me >>>> know >>>> if you have any difficulty. >>>> john >>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >>>> Name: shruthichari >>>> Email: charis at rpi.edu >>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >>>> [1]%2Fontologies >>>> FEEDBACK: >>>> Hi Sir/Madam, >>>> I had an ontology on Bioportal under the name, Study Cohort >>>> Ontology >>>> and acronym, SCO. Not only can I not find it anymore but I can't >>>> resubmit as somebody else has made a submission. I attest that I am >>>> the author of this ontology and we even have a paper in the >>>> International Semantic Web Conference (ISWC) last year: >>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help >>>> me >>>> resubmit my ontology? >>>> Feel free to reach out to me at charis at rpi.edu >>>> -Thanks, >>>> Shruthi >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> [2] >>>> ======================== >>>> 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 >>>> Links: >>>> ------ >>>> [1] http://2Fbioportal.bioontology.org [3] [1] >>>> [2] https://arxiv.org/abs/1907.04358 [1] [2] >>>> ======================== >>>> 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 >>>> Links: >>>> ------ >>>> [1] http://2fbioportal.bioontology.org/ [3] >>>> [2] https://arxiv.org/abs/1907.04358 [1] >>> >>> ======================== >>> 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 >>> Links: >>> ------ >>> [1] https://arxiv.org/abs/1907.04358 >>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> [3] http://2fbioportal.bioontology.org/ >>> [4] http://librdf.org/raptor/rapper.html >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support From vendetti at stanford.edu Mon Apr 27 12:36:06 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 19:36:06 +0000 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> Message-ID: Hello Shruthi, No, you don?t need to take extra steps. BioPortal only serves data from the most recent version of an ontology. Please note though - when you submit a new version of your ontology it goes into the queue for ontology processing, and there may be a time delay of an hour or two before the new version is fully processed and available in our system. If you notice any irregularities, feel free to contact us again via this support list. Kind regards, Jennifer > On Apr 27, 2020, at 12:28 PM, Shruthi Chari wrote: > > Hi Jennifer, > > Thanks so much for this update. I have a quick question if we resubmit a version of the ontology - do we need to take extra steps to ensure that it is usable via the Annotator functionality? > > -Thanks, > Shruthi > > On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote: >> Hello Shruthi >> Your ontology has been fully converted to standalone vs. a view. I?ve >> also reprocessed your ontology so that you can use it with the >> Annotator functionality. >> Kind regards, >> Jennifer >>> On Apr 25, 2020, at 1:38 PM, Shruthi Chari wrote: >>> Hi John, >>> Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late. >>> I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator. >>> Thanks for your assistance and looking forward to getting this last issue resolved. >>> -Thanks, >>> Shruthi >>> On 2020-04-24 19:48, John Graybeal wrote: >>>> Hi Shruthi, >>>> I had a look at the logs. There appear to be two locations in the file >>>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in >>>> the OWLAPI parser, but our Rapper software >>>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if >>>> fixing those makes it better, yes? >>>> John >>>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >>>>> Hi John, >>>>> I don't want it to be a view yes. Thanks for making the change. >>>>> As for the RDF parsing error, I am not sure what is happening. Can >>>>> you send me the log as I don't see to it on my end. I don't see >>>>> errors on Protege per se it opens there. I am attaching a screenshot >>>>> for your reference. >>>>> However, I want to make some import clean up changes so I will work >>>>> on that and hopefully it should render better? >>>>> Not sure why it doesn't render on Bioportal though. >>>>> -Thanks, >>>>> Shruthi >>>>> On 2020-04-24 19:06, John Graybeal wrote: >>>>> Ah, that explains it, thank you. >>>>> I have changed the setting to not be View, and saved that. (It >>>>> would >>>>> have showed up previously, if you enabled the Views checkbox. But >>>>> if >>>>> it isn't a view that isn't what you want!) >>>>> There may be some additional processing required as a result; I'll >>>>> ask >>>>> our expert on such things when she is back on Monday. >>>>> I notice there are no classes being displayed, due to an RDF >>>>> parsing >>>>> error; do you understand why that is? Let us know if you need help >>>>> figuring that out?my basic rule of thumb is to try opening it in >>>>> Protege to see if that reports any errors, and fix all those first. >>>>> If >>>>> it works there but not in BioPortal, let us know and we'll try to >>>>> hep. >>>>> John >>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >>>>> Hi John, >>>>> Thanks so much for reassigning ownership to me, with this, I am >>>>> able to upload a new version. I have a problem in that my ontology >>>>> doesn't show up on Bioportal's main page as an ontology page as I >>>>> accidentally made it an ontology view. Can you help revert this >>>>> option and instead set it as an ontology? >>>>> -Thanks, >>>>> Shruthi >>>>> On 2020-04-24 18:09, John Graybeal wrote: >>>>> Hi Shruthi, >>>>> I am happy to help you, and just want to clarify the situation. >>>>> I can see a public ontology called SCO that fits your description, >>>>> with you as the contact, and it seems to be publicly visible. So if >>>>> you are still having trouble seeing this ontology, can you please >>>>> provide further details about what you are doing? >>>>> It appears the owner of the ontology may have been mis-assigned >>>>> (possibly an operator error on our side); I have re-assigned you as >>>>> the owner. >>>>> My apologies for this issue. Please try to access it and let me >>>>> know >>>>> if you have any difficulty. >>>>> john >>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >>>>> Name: shruthichari >>>>> Email: charis at rpi.edu >>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >>>>> [1]%2Fontologies >>>>> FEEDBACK: >>>>> Hi Sir/Madam, >>>>> I had an ontology on Bioportal under the name, Study Cohort >>>>> Ontology >>>>> and acronym, SCO. Not only can I not find it anymore but I can't >>>>> resubmit as somebody else has made a submission. I attest that I am >>>>> the author of this ontology and we even have a paper in the >>>>> International Semantic Web Conference (ISWC) last year: >>>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help >>>>> me >>>>> resubmit my ontology? >>>>> Feel free to reach out to me at charis at rpi.edu >>>>> -Thanks, >>>>> Shruthi >>>>> _______________________________________________ >>>>> bioontology-support mailing list >>>>> bioontology-support at lists.stanford.edu >>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>> [2] >>>>> ======================== >>>>> 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 >>>>> Links: >>>>> ------ >>>>> [1] http://2Fbioportal.bioontology.org [3] [1] >>>>> [2] https://arxiv.org/abs/1907.04358 [1] [2] >>>>> ======================== >>>>> 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 >>>>> Links: >>>>> ------ >>>>> [1] http://2fbioportal.bioontology.org/ [3] >>>>> [2] https://arxiv.org/abs/1907.04358 [1] >>>> >>>> ======================== >>>> 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 >>>> Links: >>>> ------ >>>> [1] https://arxiv.org/abs/1907.04358 >>>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> [3] http://2fbioportal.bioontology.org/ >>>> [4] http://librdf.org/raptor/rapper.html >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support From charis at rpi.edu Mon Apr 27 12:42:00 2020 From: charis at rpi.edu (Shruthi Chari) Date: Mon, 27 Apr 2020 15:42:00 -0400 Subject: [bioontology-support] [BioPortal] Feedback from shruthichari In-Reply-To: References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail> <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu> <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu> <30a7355d5a089c13602f7139326bb4eb@rpi.edu> <92d937d82850397ea6d36aab9f7bc85a@rpi.edu> Message-ID: <2549f3ec30dded55bdbd6b8c70557899@rpi.edu> Hi Jennifer, Thanks for your response, it helps clear my doubts and it is really good to know that there is an active support team out there. Stay safe and healthy. Looking forward to continuing to use Bioportal. Thanks for helping with our issues and to get our ontology up and running on the site. -Thanks, Shruthi On 2020-04-27 15:36, Jennifer Leigh Vendetti wrote: > Hello Shruthi, > > No, you don?t need to take extra steps. BioPortal only serves data > from the most recent version of an ontology. > > Please note though - when you submit a new version of your ontology it > goes into the queue for ontology processing, and there may be a time > delay of an hour or two before the new version is fully processed and > available in our system. If you notice any irregularities, feel free > to contact us again via this support list. > > Kind regards, > Jennifer > > > >> On Apr 27, 2020, at 12:28 PM, Shruthi Chari wrote: >> >> Hi Jennifer, >> >> Thanks so much for this update. I have a quick question if we resubmit >> a version of the ontology - do we need to take extra steps to ensure >> that it is usable via the Annotator functionality? >> >> -Thanks, >> Shruthi >> >> On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote: >>> Hello Shruthi >>> Your ontology has been fully converted to standalone vs. a view. I?ve >>> also reprocessed your ontology so that you can use it with the >>> Annotator functionality. >>> Kind regards, >>> Jennifer >>>> On Apr 25, 2020, at 1:38 PM, Shruthi Chari wrote: >>>> Hi John, >>>> Thanks a bunch the logs you sent me were a lifesaver. I was able to >>>> reupload our ontology and now the classes show up. I should have >>>> reached out to support a year earlier, but never too late. >>>> I am still waiting on the ontology view fix as in to revert this to >>>> be a stand-alone ontology and not a view. This would then allow our >>>> ontology to be queryable by the BioAnnotator. >>>> Thanks for your assistance and looking forward to getting this last >>>> issue resolved. >>>> -Thanks, >>>> Shruthi >>>> On 2020-04-24 19:48, John Graybeal wrote: >>>>> Hi Shruthi, >>>>> I had a look at the logs. There appear to be two locations in the >>>>> file >>>>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in >>>>> the OWLAPI parser, but our Rapper software >>>>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if >>>>> fixing those makes it better, yes? >>>>> John >>>>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari wrote: >>>>>> Hi John, >>>>>> I don't want it to be a view yes. Thanks for making the change. >>>>>> As for the RDF parsing error, I am not sure what is happening. Can >>>>>> you send me the log as I don't see to it on my end. I don't see >>>>>> errors on Protege per se it opens there. I am attaching a >>>>>> screenshot >>>>>> for your reference. >>>>>> However, I want to make some import clean up changes so I will >>>>>> work >>>>>> on that and hopefully it should render better? >>>>>> Not sure why it doesn't render on Bioportal though. >>>>>> -Thanks, >>>>>> Shruthi >>>>>> On 2020-04-24 19:06, John Graybeal wrote: >>>>>> Ah, that explains it, thank you. >>>>>> I have changed the setting to not be View, and saved that. (It >>>>>> would >>>>>> have showed up previously, if you enabled the Views checkbox. But >>>>>> if >>>>>> it isn't a view that isn't what you want!) >>>>>> There may be some additional processing required as a result; I'll >>>>>> ask >>>>>> our expert on such things when she is back on Monday. >>>>>> I notice there are no classes being displayed, due to an RDF >>>>>> parsing >>>>>> error; do you understand why that is? Let us know if you need help >>>>>> figuring that out?my basic rule of thumb is to try opening it in >>>>>> Protege to see if that reports any errors, and fix all those >>>>>> first. >>>>>> If >>>>>> it works there but not in BioPortal, let us know and we'll try to >>>>>> hep. >>>>>> John >>>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari wrote: >>>>>> Hi John, >>>>>> Thanks so much for reassigning ownership to me, with this, I am >>>>>> able to upload a new version. I have a problem in that my ontology >>>>>> doesn't show up on Bioportal's main page as an ontology page as I >>>>>> accidentally made it an ontology view. Can you help revert this >>>>>> option and instead set it as an ontology? >>>>>> -Thanks, >>>>>> Shruthi >>>>>> On 2020-04-24 18:09, John Graybeal wrote: >>>>>> Hi Shruthi, >>>>>> I am happy to help you, and just want to clarify the situation. >>>>>> I can see a public ontology called SCO that fits your description, >>>>>> with you as the contact, and it seems to be publicly visible. So >>>>>> if >>>>>> you are still having trouble seeing this ontology, can you please >>>>>> provide further details about what you are doing? >>>>>> It appears the owner of the ontology may have been mis-assigned >>>>>> (possibly an operator error on our side); I have re-assigned you >>>>>> as >>>>>> the owner. >>>>>> My apologies for this issue. Please try to access it and let me >>>>>> know >>>>>> if you have any difficulty. >>>>>> john >>>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote: >>>>>> Name: shruthichari >>>>>> Email: charis at rpi.edu >>>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1] >>>>>> [1]%2Fontologies >>>>>> FEEDBACK: >>>>>> Hi Sir/Madam, >>>>>> I had an ontology on Bioportal under the name, Study Cohort >>>>>> Ontology >>>>>> and acronym, SCO. Not only can I not find it anymore but I can't >>>>>> resubmit as somebody else has made a submission. I attest that I >>>>>> am >>>>>> the author of this ontology and we even have a paper in the >>>>>> International Semantic Web Conference (ISWC) last year: >>>>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help >>>>>> me >>>>>> resubmit my ontology? >>>>>> Feel free to reach out to me at charis at rpi.edu >>>>>> -Thanks, >>>>>> Shruthi >>>>>> _______________________________________________ >>>>>> bioontology-support mailing list >>>>>> bioontology-support at lists.stanford.edu >>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>>> [2] >>>>>> ======================== >>>>>> 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 >>>>>> Links: >>>>>> ------ >>>>>> [1] http://2Fbioportal.bioontology.org [3] [1] >>>>>> [2] https://arxiv.org/abs/1907.04358 [1] [2] >>>>>> ======================== >>>>>> 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 >>>>>> Links: >>>>>> ------ >>>>>> [1] http://2fbioportal.bioontology.org/ [3] >>>>>> [2] https://arxiv.org/abs/1907.04358 [1] >>>>> >>>>> ======================== >>>>> 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 >>>>> Links: >>>>> ------ >>>>> [1] https://arxiv.org/abs/1907.04358 >>>>> [2] >>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>> [3] http://2fbioportal.bioontology.org/ >>>>> [4] http://librdf.org/raptor/rapper.html >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support From vendetti at stanford.edu Mon Apr 27 15:59:21 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 27 Apr 2020 22:59:21 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger In-Reply-To: <74258F94-CB04-4A2D-A226-DCBECB66919F@embo.org> References: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail> <0CFC2970-5C49-49C2-B2E4-E87922E982ED@stanford.edu> <74258F94-CB04-4A2D-A226-DCBECB66919F@embo.org> Message-ID: Hi Thomas, Thank you for providing additional detail. Please see my answers inline below. On Apr 27, 2020, at 1:18 PM, Thomas Lemberger > wrote: Dear Jennifer, Many thanks for getting back to me and apologies if my description was confusing. Maybe it is just my misunderstanding. Let?s take the example of the term bao:BAO_0002424 for the assay ?western blot?. In the CSV file (http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv), ?western blot? is described in row 172 Class ID Preferred Label Synonyms Definitions Obsolete CUI Semantic Types Parents alternative term alternative_term axiom_lost_from_external_ontology based on normalization bearer of catalyzed by connected to contains process contributor curator notes database_cross_reference definition definition definition source derives from derives into detects detects phenotype development_notes editor note editor preferred term~editor preferred label encodes example of usage external_definition external_ontology_notes fma_set_term function_notes has absorbance wavelength value has activity threshold value has alternate assay conditions has alternate assay format has alternate assay type has alternate cell line assay has alternate confirmatory assay has alternate organism assay has alternate target assay has anti-sense strand sequence has antibody source has artificial regulatory region copy number has assay control has assay deposition date has assay design method has assay footprint has assay format has assay kit has assay kit component has assay medium has assay method has assay phase characteristic has assay pressure value has assay protocol has assay readout content has assay readout content parametricity has assay readout type has assay serum has assay source has assay stage has assay supporting method has assay temperature value has assay title has associated disease has binding site has bioassay type has biosafety level has cDNA copy number has cell count has cell line has cell modification temperature value has cell modification time value has compound aggregation assay has compound fluorescence assay has compound redox-activity assay has compound toxicity assay has concentration has concentration throughput has concentration unit has confirmatory assay has copy number has counter assay has coupled substrate incubation temperature value has coupled substrate incubation time value has curation status has curve fit specification has detected entity has detection method has DNA sequence has emission wavelength value has endpoint has endpoint modifier has enzyme reaction temperature value has enzyme reaction time value has excitation wavelength value has form has function has function in has gene symbol has id value has identical assay has incubation time value has indicator has inducer has lead optimization assay has ligand incubation time value has manufacturer has marker has measure group has measured entity has mode of action has molecular phenotype has morphological phenotype has negative control has nucleic acid sequence has organism has orthogonal assay design has orthogonal assay technology has parental cell line assay has part has participant has passage number has percent response has percent response value has perturbagen has perturbagen incubation temperature value has perturbagen incubation time value has phenotype has physicochemical profiling assay has positive control has preparation method has primary assay has protein sequence has purity unit has quality has recommended name has repetition point-number has repetition throughput has response unit has response value has RNA sequence has role has selectivity assay has sense strand sequence has sequence has sequence position has shRNA probe sense sequence position has shRNA sense sequence has signal direction has siRNA probe sense sequence position has specification has substrate has substrate incubation temperature value has substrate incubation time value has summary assay has target has temperature unit has temperature value has time unit has transcription factor has unit has value has variant construct assay has wavelength value has_alternative_id has_broad_synonym has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_relational_adjective homology_notes http://data.bioontology.org/metadata/prefixIRI http://purl.obolibrary.org/obo/hasDbXref http://purl.obolibrary.org/obo/hasOBONamespace http://purl.obolibrary.org/obo/IAO_0000231 http://purl.obolibrary.org/obo/id http://purl.obolibrary.org/obo/is_metadata_tag http://purl.obolibrary.org/obo/RO_0002161 http://purl.obolibrary.org/obo/RO_0002174 http://purl.obolibrary.org/obo/shorthand http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation http://purl.org/dc/elements/1.1/source http://www.ebi.ac.uk/cellline/definition http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance http://www.ebi.ac.uk/efo/definition_citation http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation http://www.ebi.ac.uk/efo/FBdv_definition_citation http://www.ebi.ac.uk/efo/MAT_definition_citation http://www.ebi.ac.uk/efo/MSH_definition_citation http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation http://www.ebi.ac.uk/efo/NIFSTD_definition_citation http://www.ebi.ac.uk/efo/obsoleted_in_version http://www.ebi.ac.uk/efo/organizational_class http://www.ebi.ac.uk/efo/reason_for_obsolescence http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation http://www.ebi.ac.uk/efo/WBls_definition_citation http://www.ebi.ac.uk/efo/XAO_definition_citation http://www.ebi.ac.uk/efo/ZFS_definition_citation http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date http://www.geneontology.org/formats/oboInOwl#hasDefinition http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level http://www.geneontology.org/formats/oboInOwl#is_metadata_tag http://www.w3.org/2000/01/rdf-schema#comment http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://www.w3.org/2000/01/rdf-schema#seeAlso http://www.w3.org/2002/07/owl#deprecated http://www.w3.org/2002/07/owl#topDataProperty http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation http://xmlns.com/foaf/0.1/depicted_by imported from in_subset inheres in involves biological process involves molecular function is alternate assay conditions of is alternate assay format of is alternate assay type of is alternate cell line assay of is alternate confirmatory assay of is alternate organism assay of is alternate target assay of is assay format of is assay method of is assay protocol of is associated disease of is binding site of is bioassay type of is cell line of is compound aggregation assay of is compound fluorescence assay of is compound redox-activity assay of is compound toxicity assay of is confirmatory assay of is counter assay of is derived from is described by is detected by is detection method of is endpoint of is grown in is identical assay of is indicator of is input data value of is lead optimization assay of is localized in is marker of is measure group of is measured entity of is opposite_of is orthogonal assay design of is orthogonal assay technology of is parental cell line assay of is perturbagen of is phenotype of is physicochemical profiling assay of is primary assay of is regulated by is regulator of is related assay to is role of is selectivity assay of is specification of is substrate of is summary assay of is target of is transfected into is unit of is variant construct assay of label LINCS ID occurs in part of participates in phenotype of PubChem AID quantifies recombinantly expressed in reports reports assay measurment value shorthand silences stains structure_notes taxon_notes term editor term replaced by uses as substrate uses assay kit uses detection instrument http://www.bioassayontology.org/bao#BAO_0002424 western blot The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein. FALSE http://www.bioassayontology.org/bao#BAO_0002422 The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein. bao:BAO_0002424 western blot I think this term is absent from the owl file (http://data.bioontology.org/ontologies/BAO/submissions/36/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb). The ontology source file for BAO (bao_complete.owl) has two import statements near the top of the file: At processing time, BioPortal reads those import statements and dynamically pulls in the content from the imported ontologies. So, yes - you are correct that the ?western blot? term doesn?t appear in the root ontology (bao_complete.owl). However, it does appear in one of the ontologies that BAO imports, which is why you see that data in BioPortal. The BAO ontology has a fairy complicated import structure. I opened it in the Protege ontology editor (https://protege.stanford.edu/) where you can see a graphical representations of the imports: [cid:F2D14877-A216-4A61-901D-300DB8CACA4E at stanford.edu] Furthermore, other terms that are in the owl file, for example bao:BAO_0000978 ?NP-40? seem to include only the class/sub class hierarchy but no other information (no definition, no label etc?) The equivalent term in the CSV (row 1640) is: Class ID Preferred Label Synonyms Definitions Obsolete CUI Semantic Types Parents alternative term alternative_term axiom_lost_from_external_ontology based on normalization bearer of catalyzed by connected to contains process contributor curator notes database_cross_reference definition definition definition source derives from derives into detects detects phenotype development_notes editor note editor preferred term~editor preferred label encodes example of usage external_definition external_ontology_notes fma_set_term function_notes has absorbance wavelength value has activity threshold value has alternate assay conditions has alternate assay format has alternate assay type has alternate cell line assay has alternate confirmatory assay has alternate organism assay has alternate target assay has anti-sense strand sequence has antibody source has artificial regulatory region copy number has assay control has assay deposition date has assay design method has assay footprint has assay format has assay kit has assay kit component has assay medium has assay method has assay phase characteristic has assay pressure value has assay protocol has assay readout content has assay readout content parametricity has assay readout type has assay serum has assay source has assay stage has assay supporting method has assay temperature value has assay title has associated disease has binding site has bioassay type has biosafety level has cDNA copy number has cell count has cell line has cell modification temperature value has cell modification time value has compound aggregation assay has compound fluorescence assay has compound redox-activity assay has compound toxicity assay has concentration has concentration throughput has concentration unit has confirmatory assay has copy number has counter assay has coupled substrate incubation temperature value has coupled substrate incubation time value has curation status has curve fit specification has detected entity has detection method has DNA sequence has emission wavelength value has endpoint has endpoint modifier has enzyme reaction temperature value has enzyme reaction time value has excitation wavelength value has form has function has function in has gene symbol has id value has identical assay has incubation time value has indicator has inducer has lead optimization assay has ligand incubation time value has manufacturer has marker has measure group has measured entity has mode of action has molecular phenotype has morphological phenotype has negative control has nucleic acid sequence has organism has orthogonal assay design has orthogonal assay technology has parental cell line assay has part has participant has passage number has percent response has percent response value has perturbagen has perturbagen incubation temperature value has perturbagen incubation time value has phenotype has physicochemical profiling assay has positive control has preparation method has primary assay has protein sequence has purity unit has quality has recommended name has repetition point-number has repetition throughput has response unit has response value has RNA sequence has role has selectivity assay has sense strand sequence has sequence has sequence position has shRNA probe sense sequence position has shRNA sense sequence has signal direction has siRNA probe sense sequence position has specification has substrate has substrate incubation temperature value has substrate incubation time value has summary assay has target has temperature unit has temperature value has time unit has transcription factor has unit has value has variant construct assay has wavelength value has_alternative_id has_broad_synonym has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_relational_adjective homology_notes http://data.bioontology.org/metadata/prefixIRI http://purl.obolibrary.org/obo/hasDbXref http://purl.obolibrary.org/obo/hasOBONamespace http://purl.obolibrary.org/obo/IAO_0000231 http://purl.obolibrary.org/obo/id http://purl.obolibrary.org/obo/is_metadata_tag http://purl.obolibrary.org/obo/RO_0002161 http://purl.obolibrary.org/obo/RO_0002174 http://purl.obolibrary.org/obo/shorthand http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation http://purl.org/dc/elements/1.1/source http://www.ebi.ac.uk/cellline/definition http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance http://www.ebi.ac.uk/efo/definition_citation http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation http://www.ebi.ac.uk/efo/FBdv_definition_citation http://www.ebi.ac.uk/efo/MAT_definition_citation http://www.ebi.ac.uk/efo/MSH_definition_citation http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation http://www.ebi.ac.uk/efo/NIFSTD_definition_citation http://www.ebi.ac.uk/efo/obsoleted_in_version http://www.ebi.ac.uk/efo/organizational_class http://www.ebi.ac.uk/efo/reason_for_obsolescence http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation http://www.ebi.ac.uk/efo/WBls_definition_citation http://www.ebi.ac.uk/efo/XAO_definition_citation http://www.ebi.ac.uk/efo/ZFS_definition_citation http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date http://www.geneontology.org/formats/oboInOwl#hasDefinition http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level http://www.geneontology.org/formats/oboInOwl#is_metadata_tag http://www.w3.org/2000/01/rdf-schema#comment http://www.w3.org/2000/01/rdf-schema#isDefinedBy http://www.w3.org/2000/01/rdf-schema#seeAlso http://www.w3.org/2002/07/owl#deprecated http://www.w3.org/2002/07/owl#topDataProperty http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation http://xmlns.com/foaf/0.1/depicted_by imported from in_subset inheres in involves biological process involves molecular function is alternate assay conditions of is alternate assay format of is alternate assay type of is alternate cell line assay of is alternate confirmatory assay of is alternate organism assay of is alternate target assay of is assay format of is assay method of is assay protocol of is associated disease of is binding site of is bioassay type of is cell line of is compound aggregation assay of is compound fluorescence assay of is compound redox-activity assay of is compound toxicity assay of is confirmatory assay of is counter assay of is derived from is described by is detected by is detection method of is endpoint of is grown in is identical assay of is indicator of is input data value of is lead optimization assay of is localized in is marker of is measure group of is measured entity of is opposite_of is orthogonal assay design of is orthogonal assay technology of is parental cell line assay of is perturbagen of is phenotype of is physicochemical profiling assay of is primary assay of is regulated by is regulator of is related assay to is role of is selectivity assay of is specification of is substrate of is summary assay of is target of is transfected into is unit of is variant construct assay of label LINCS ID occurs in part of participates in phenotype of PubChem AID quantifies recombinantly expressed in reports reports assay measurment value shorthand silences stains structure_notes taxon_notes term editor term replaced by uses as substrate uses assay kit uses detection instrument http://www.bioassayontology.org/bao#BAO_0000978 NP-40 NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol. FALSE http://www.bioassayontology.org/bao#BAO_0003043 bao:BAO_0000978 NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol. NP-40 This is the same situation where the definition is formally declared not in the root ontology, but in one of the ontologies that BAO imports. The BioPortal user interface doesn?t present any information that would help you track down which import the declaration lives in - for that, you would need to use a different tool. If you?re familiar with the Protege application that I mentioned above, you could use the following steps: 1). Open bao_complete.owl 2). Click the Search? button in the top right corner and enter NP-40 in the resulting Search dialog 3). Double click the first match in the result list: [cid:EC6287D3-3CBC-4901-9D73-784E9E973719 at stanford.edu] This will navigate to NP-40 in the classes tree where you can view all of the properties attached to the class. If you hover your mouse over the rdfs:comment on the right-hand side in the Class Annotations pane, you?ll see a tooltip pop up that will tell you where the comment was declared. In this case, I see tooltip content of ?Asserted in: http://www.bioassayontology.org/bao/bao_vocabulary_materialentity.owl?. In the meantime, I found that the RDF/XML file http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf includes the entire ontology, so I am not sure what is the role of the .owl file in the case of BAO. This seems to be different with other ontologies I downloaded. Maybe I am just misunderstanding something. The OWL file is the canonical source file that was submitted to BioPortal by the ontology maintainer. The RDF/XML file is generated by BioPortal at processing time and includes everything from the original ontology source file, as well as data from imported ontologies. BioPortal is backed by an RDF store, so we need to have this intermediate step of generating an RDF/XML representation from the various ontology formats that end users are allowed to submit (OWL, OBO, and SKOS). In the case of other ontologies, for example OBI https://bioportal.bioontology.org/ontologies/OBI, the .owl file (http://data.bioontology.org/ontologies/OBI/submissions/42/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb) does include the whole ontology and not only the class/subclass hierarchy. I checked OBI and it doesn?t have any imports, which is why the entirety of the ontology content is visible in the original source OWL file. Hope this information is helpful. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... 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My Username: rsingh552 Thanks & Regards, *Radhey Shyam Singh* DevOps Lead P: office: 314-628-0035/ cell: 412-298-5345 E: rsingh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential, or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Apr 28 09:51:19 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 28 Apr 2020 16:51:19 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin In-Reply-To: References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail> Message-ID: I haven?t received a response from the ontology maintainers, so I fixed the small error in the ontology source file that was causing parsing issues and reprocessed it in our system. CMO is fully available in BioPortal now, including the ability to use with the Annotator. Jennifer On Apr 27, 2020, at 11:11 AM, Jennifer Leigh Vendetti > wrote: Hi again Jay, I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3 If I don?t get a response shortly, I?ll attempt to fix it on our end and reprocess. Jennifer On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti > wrote: Hi Jay, I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker: https://github.com/ncbo/bioportal-project/issues/164 ? and am looking into the parsing errors. Kind regards. Jennifer On Apr 25, 2020, at 2:19 PM, support at bioontology.org wrote: Name: Jay Franklin Email: frankj7 at rpi.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hi, It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004". Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this. Thanks, Jay Franklin Rensselaer Polytechnic Institute _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Apr 28 11:56:44 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 28 Apr 2020 18:56:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme In-Reply-To: <5FCF14AD-B0A3-42D7-9FE2-BEC284FF3C4B@stanford.edu> References: <5FCF14AD-B0A3-42D7-9FE2-BEC284FF3C4B@stanford.edu> Message-ID: Hello Philip, On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) > wrote: Dear Michael, others, Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances. I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results. For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389 = http://purl.bioontology.org/ontology/SNOMEDCT/56717001. I can use the API calling http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings I noticed the following: * The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001 and SNOMEDCT. Yes, I confirm that I see the same. * The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings, however, using different URI (http://snomed.info/id/56717001) and referring to ontology SNO_COPY which is not accessible. I don?t see the same here. I issued the REST call that you list above, and the mapping between the Tuberculosis terms in ORDO and SNOMEDCT does exist in the result set. Here?s a screen shot showing the LOOM mapping: [cid:CAB488B4-906C-417D-8302-942F2DB18543 at stanford.edu] I also see the other mapping you referred to, i.e., the LOOM mapping between the Tuberculosis terms in ORDO and SNO_COPY: [cid:7854C9AF-8DD7-4B34-A1D3-FB605FC4FE02 at stanford.edu] With regard to this latter case, I see two issues: 1). There's a known issue with the BioPortal REST API where the mappings endpoint returns results that include terms from private ontologies (documented here: https://github.com/ncbo/ontologies_api/issues/52). SNO_COPY is a private ontology, which is why it?s not accessible to you. 2). There appears to be a duplicate of the same LOOM mapping from Tuberculosis in ORDO to Tuberculosis in SNO_COPY. It?s not immediately clear to me why the duplicate exists. I?ve entered a new issue in our tracker: https://github.com/ncbo/ontologies_api/issues/67. * The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT. Yes, I confirm that I see the same. There?s a known issue with the BioPortal REST API where occasional irregularities exist between result sets from the /mappings and /classes/:cls/mappings endpoints. That issue is documented in our GitHub repository, and I?ve added your observations just now: https://github.com/ncbo/ontologies_api/issues/50#issuecomment-620784355. I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY, which is returning an empty set. No, you?re not missing something. As I mentioned above, you?ve run into a known issue with the API. Hope these explanations were helpful. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-28 10.46.10.png Type: image/png Size: 191265 bytes Desc: Screenshot 2020-04-28 10.46.10.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-28 10.53.30.png Type: image/png Size: 202130 bytes Desc: Screenshot 2020-04-28 10.53.30.png URL: From chinghua at us.ibm.com Wed Apr 29 15:37:27 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Wed, 29 Apr 2020 22:37:27 +0000 Subject: [bioontology-support] Annotation GET results Message-ID: An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Apr 29 16:24:53 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 29 Apr 2020 23:24:53 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: References: Message-ID: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Hello Ching-Hua, On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen > wrote: I am running the sample code "annotate_txt.py" and experiencing results that I can't understand. I modified the API call to the following, in order to specifically use the ICD10 ontology: get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate)) When I reference the public bioportal, I get non-zero results for the text_to_annotate provided. I?m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used: http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye. ? and I see an empty result set: [cid:67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu] However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance. This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening? If you?re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include ?Parsed, Indexed, Metrics, Annotator?: [cid:9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu] Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-29 16.14.04.png Type: image/png Size: 71529 bytes Desc: Screenshot 2020-04-29 16.14.04.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-29 16.20.21.png Type: image/png Size: 108163 bytes Desc: Screenshot 2020-04-29 16.20.21.png URL: From chinghua at us.ibm.com Thu Apr 30 07:59:33 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Thu, 30 Apr 2020 14:59:33 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> References: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>, Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu.png Type: image/png Size: 71529 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu.png Type: image/png Size: 108163 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: Image.9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu.png Type: image/png Size: 108163 bytes Desc: not available URL: From vendetti at stanford.edu Thu Apr 30 09:02:40 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 30 Apr 2020 16:02:40 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: References: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Message-ID: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu> Hi Ching-Hua, You could use an API call like the following to examine the latest submission of a given ontology: http://data.bioontology.org/ontologies/ICD10/latest_submission?include=all In the JSON results, there should be a ?submissionStatus? name/value pair with an array of statuses, e.g.: [cid:AAB79AAB-3DE6-4EC3-9430-1DDF539B5A07 at stanford.edu] If any of the processing steps failed, there would be status values with an ?ERROR? string, e.g.: [cid:098F4D4C-6B11-4CCA-81C8-11AFFE790663 at stanford.edu] Alternatively, you could issue API calls to get the root classes of an ontology, or all of the classes for an ontology. If the ontology failed to process correctly, you would likely see failures or empty sets when trying to access the ontology content: http://data.bioontology.org/ontologies/ICD10/classes/roots http://data.bioontology.org/ontologies/ICD10/classes Finally, you could look at the log file for a given ontology to see if there were any error during processing. Information about log file location is here: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#Is_there_a_log_file_for_parsing.3F We also have some public documentation of the REST API that you may find helpful: http://data.bioontology.org/documentation Kind regards, Jennifer On Apr 30, 2020, at 7:59 AM, Ching-Hua Chen > wrote: Thanks, Jennifer! My apologies, the text I was actually annotating is: text_to_annotate = "Relationship among genotype, biochemical phenotype, and cognitive performance in females with phenylalanine hydroxylase deficiency: report from the Maternal Phenylketonuria Collaborative Study. OBJECTIVE To examine the relationship of phenylalanine hydroxylase ( PAH ) genotypes to biochemical phenotype and cognitive development in maternal phenylketonuria ( PKU ) . METHODOLOGY PAH gene mutations were examined in 222 hyperphenylalaninemic females enrolled in the Maternal PKU Collaborative Study ( MPKUCS ) . A total of 84 different mutations were detected , and complete genotype was obtained in 199 individuals . Based on previous knowledge about mutation-phenotype associations , 78 of the mutations could be assigned to one of four classes of severity ( severe PKU , moderate PKU , mild PKU , and mild hyperphenylalaninemia [ MHP ] ) . Then , 189 MPKUCS subjects were grouped according to the various combinations of mutation classifications . The sample sizes were large enough for statistical testing in four groups with at least one mutation that completely abolishes enzyme activity . These patients are considered functionally hemizygous . RESULTS The biochemical phenotype predicted from the genotype in functionally hemizygous patients was related significantly to the assigned phenylalanine level . Cognitive performance ( IQ ) was also significantly related to genotype . The IQ of PAH-deficient mothers with a severe PKU mutation in combination with a MHP mutation or a mild PKU mutation was 99 and 96 , respectively , whereas the IQ of PKU mothers with two severe PKU mutations or with one severe and one moderate PKU mutation was 83 and 84 , respectively . Of the patients with PKU , 92 % had been treated during childhood . Those who were untreated or treated late had lower than average IQ scores for their group of mutation combinations . Females with moderate or mild PKU who were treated early and treated for > 6 years showed IQ scores 10 points above average for their group . CONCLUSIONS The reproductive outcome in maternal phenylketonuria is dependent on prenatal metabolic control and postnatal environmental circumstances . Both factors depend on the intellectual resources of the mother with PKU . The significant relationship among genotype , biochemical phenotype , and cognitive performance observed in the present study is of importance for the development of an optimal strategy for future treatment of females with PKU who plan pregnancy" Is there a way to check the status of submitted ontologies without using the UI? (My appliance is not very responsive when I try to access it using the UI. However, when I make API calls it seems to be quite responsive. Maybe the reason I am getting empty results for some ontologies is that the request is timing out....) Should I be examining the ontology submission status? I'm not very familiar with the API yet, if you are able to provide an example API call that can return the status would be much appreciated! Best, Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson ----- Original message ----- From: Jennifer Leigh Vendetti > To: Ching-Hua Chen > Cc: "bioontology-support at lists.stanford.edu" > Subject: [EXTERNAL] Re: [bioontology-support] Annotation GET results Date: Wed, Apr 29, 2020 7:25 PM Hello Ching-Hua, On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen > wrote: I am running the sample code "annotate_txt.py" and experiencing results that I can't understand. I modified the API call to the following, in order to specifically use the ICD10 ontology: get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate)) When I reference the public bioportal, I get non-zero results for the text_to_annotate provided. I?m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used: http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye. ? and I see an empty result set: However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance. This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening? If you?re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include ?Parsed, Indexed, Metrics, Annotator?: Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-30 08.47.08.png Type: image/png Size: 111523 bytes Desc: Screenshot 2020-04-30 08.47.08.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-04-30 08.51.44.png Type: image/png Size: 110173 bytes Desc: Screenshot 2020-04-30 08.51.44.png URL: From hoyle at buffalo.edu Thu Apr 30 13:50:48 2020 From: hoyle at buffalo.edu (Hoyle, Patrick) Date: Thu, 30 Apr 2020 20:50:48 +0000 Subject: [bioontology-support] Question regarding OntoPortal Virtual Appliance 3.0 Message-ID: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu> Hi-- I currently support a couple of instances of the OntoPortal Virtual Appliance for a professor at the University at Buffalo. One is version 2.4, and the other is 2.5. I plan to upgrade both of these to version 3.0 as soon as it is released, since both 2.4 and 2.5 are based on CentOS 6, which reaches end of life on 30 November. Could you tell me which Linux distro version 3.0 will be based on?? Thanks in advance, -- ________________________________________________________________________ Patrick Hoyle Instructional Support Specialist, CASet College of Arts and Sciences University at Buffalo (716) 645-5638 From vendetti at stanford.edu Thu Apr 30 16:32:42 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 30 Apr 2020 23:32:42 +0000 Subject: [bioontology-support] Question regarding OntoPortal Virtual Appliance 3.0 In-Reply-To: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu> References: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu> Message-ID: <42ED7782-BA48-4B72-8A09-78DC758A8309@stanford.edu> Hi Patrick, OntoPortal 3.0 is based on CentOS 7. Kind regards, Jennifer > On Apr 30, 2020, at 1:50 PM, Hoyle, Patrick wrote: > > Hi-- > > I currently support a couple of instances of the OntoPortal Virtual Appliance for a professor at the University at Buffalo. One is version 2.4, and the other is 2.5. I plan to upgrade both of these to version 3.0 as soon as it is released, since both 2.4 and 2.5 are based on CentOS 6, which reaches end of life on 30 November. Could you tell me which Linux distro version 3.0 will be based on?? > > Thanks in advance, > > -- > ________________________________________________________________________ > Patrick Hoyle > Instructional Support Specialist, CASet > College of Arts and Sciences > University at Buffalo > (716) 645-5638 > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From chinghua at us.ibm.com Thu Apr 30 16:39:20 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Thu, 30 Apr 2020 23:39:20 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu> References: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>, <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.AAB79AAB-3DE6-4EC3-9430-1DDF539B5A07 at stanford.edu.png Type: image/png Size: 111523 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.098F4D4C-6B11-4CCA-81C8-11AFFE790663 at stanford.edu.png Type: image/png Size: 110173 bytes Desc: not available URL: From chinghua at us.ibm.com Thu Apr 30 19:23:52 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Fri, 1 May 2020 02:23:52 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: References: , <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>, <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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