From support at bioontology.org Tue Oct 1 04:55:25 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 01 Oct 2019 04:55:25 -0700 Subject: [bioontology-support] [BioPortal] Feedback from jlomax Message-ID: <5d933ead5b79c_259d2ad877e71f4c6597b@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Oct 1 08:00:43 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 01 Oct 2019 08:00:43 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler Message-ID: <5d936a1b65f4d_1b522b0fdebe890813796@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Oct 1 08:02:39 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 01 Oct 2019 08:02:39 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler Message-ID: <5d936a8f7422b_1b992b0fdebe895813714@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Oct 1 08:05:07 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 01 Oct 2019 08:05:07 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler Message-ID: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Oct 1 10:41:18 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 1 Oct 2019 17:41:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <5d936a8f7422b_1b992b0fdebe895813714@ncbo-prd-app-09.stanford.edu.mail> References: <5d936a8f7422b_1b992b0fdebe895813714@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Mark, Thank you for your detailed report. What you?re describing is a known issue: https://github.com/ncbo/ontologies_linked_data/issues/88. Background: At some point in the past, we?ve implemented a system that prevents expensive COUNT queries going live against our 4store backend. These queries used to really bog down our servers, often resulting in downtime. The COUNT queries used to be executed on paged REST services, like the one that retrieves all mappings for a given ontology. So, in order to determine the correct number of pages for a given call, our system used to first execute a COUNT query, storing the result in the output. The new system would pre-cache these counts, so when a paged service call is made, the count would be retrieved from a static repository. Unfortunately, there appears to be a bug in this process that triggers the behavior you are seeing. For your specific example, it?s best to simply use an iterator to go through ALL pages of available mappings until you hit an empty collection instead of relying on the reported totalCount (as you probably are already doing). Hope this workaround works for you. Michael On Oct 1, 2019, at 8:02 AM, support at bioontology.org wrote: Name: Mark Ressler Email: mark at markressler.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT Feedback: I am using the REST API to retrieve all the mappings for a particular ontology, in this case the OGMS. - Start with this REST call: http://data.bioontology.org/ontologies/OGMS/mappings?display_context=false&display_links=false - The response shows 251 pageCount, with 12536 totalCount, which I assume is the total number of mappings, which would be about right for 251 pages with 50 mappings per page - I continue to follow the nextPage links, but starting with page 190 [http://data.bioontology.org/ontologies/OGMS/mappings?display_context=false&display_links=false&page=190], the collection list is empty. Subsequent pages through 251 likewise show the collection list empty - In the end, 9434 mappings were retrieved, not 12536. - On the other hand, from the counts on the OGMS ontology page [https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings], it seems that I should retrieve only 4196 mappings. So I am not sure exactly how many mappings for this ontology I should expect, but there seems to be a problem with the paging if some pages are returning no mappings at all. I will submit one more message for the results retrieved for mappings via the REST API. _______________________________________________ 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 Oct 1 11:55:52 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 1 Oct 2019 18:55:52 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> References: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Mark, To retrieve the mappings between just two ontologies, you can use the pattern of "/mappings?ontologies=ONT1,ONT2", e.g.: http://data.bioontology.org/mappings?ontologies=SNOMEDCT,OGMS Hope that helps. Kind regards, Jennifer On Oct 1, 2019, at 8:05 AM, support at bioontology.org wrote: Name: Mark Ressler Email: mark at markressler.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT Feedback: As with a prior message, I am using the REST API to retrieve all the mappings for a particular ontology, in this case the OGMS. - I see from the OGMS ontology page [https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings] that mappings associated with particular ontologies are identified, e.g. between OGMS and the APA Treatment Cluster. - However, when I retrieve the mapping results via the REST API [http://data.bioontology.org/ontologies/OGMS/mappings], I do not see any identifier within the entries in the classes list to indicate to which ontology the class belongs. Presumably the first entry in the list is the OGMS, but I would need to figure out in which ontology the second entry appeared on the basis of the base URI. - When the mapping source is SAME_URI, for example, both classes are the same, e.g. http://purl.obolibrary.org/obo/OGMS_0000096. I understand that the class URI appeared in the OGMS, but I have no way to identify the other ontology in which the URI appeared. - What I really would like is to be able to retrieve mappings between just two ontologies, rather than retrieve all mappings for an ontology, for instance, if there were an API endpoint like: /ontologies/:ontology1/mappings/:ontology2 - Not only would such an endpoint be convenient, but it would also reduce the load on your server. Eventually, I would like to retrieve the mappings for SNOMED-CT and one other ontology. If I needed to retrieve all mappings for SNOMED-CT, I see that would require 36133 REST calls. I hope your server would allow me to make all of those calls. _______________________________________________ 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 Oct 1 12:23:13 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 1 Oct 2019 19:23:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from fathalla In-Reply-To: <2039425837.1195255.1569911219988@mail.yahoo.com> References: <5d91fa0cf0a7e_155e2b222f37b924557fe@ncbo-prd-app-08.stanford.edu.mail> <2039425837.1195255.1569911219988@mail.yahoo.com> Message-ID: <1059291E-16C1-4C51-A79F-757E4776F7AD@stanford.edu> Hi Said, I?m not sure if something went wrong with the upload of the new version. I retrieved it from our server, but I still see those errors when I open in Protege. Could you send me a copy of the latest version of your ontology source file privately (vendetti at stanford.edu)? Thank you, Jennifer On Sep 30, 2019, at 11:26 PM, said fathalla > wrote: Hello Jennifer, I checked the ontology and I fixed these errors and uploaded the new version after opening it with Protege and checked the syntax using W3C RDF Validation Results but the problem still exist. W3C RDF Validation Results Mit freundlichen Gr??en, Said Fathalla On Tuesday, October 1, 2019, 01:30:50 AM GMT+2, Jennifer Leigh Vendetti > wrote: Hello, I?ve been attempting to load / examine your ontology outside of the BioPortal system. I used a programmatic approach with the OWL API [1], and also tried manually opening the ontology file in the Protege ontology editing application [2]. In both cases, there are a number of errors. If you happen to use Protege, you can see them via Window | Show log? menu: Here is the complete text of one of the errors: ERROR 16:16:32 Attempt to transform an axiom to correct misuse of properties failed. Property replacement: {=, =, =, =, =}, axiom: AnnotationAssertion( "A top level concept in the concept scheme."@en), error: uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplPlain cannot be cast to org.semanticweb.owlapi.model.IRI We can more readily help with getting an ontology uploaded / displaying properly in BioPortal when parsing errors like this aren?t present. Kind regards, Jennifer [1] http://owlcs.github.io/owlapi/ [2] https://protege.stanford.edu/ On Sep 30, 2019, at 5:50 AM, support at bioontology.org wrote: Name: fathalla Email: sm_fathalla at yahoo.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMODSCI%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fwww.w3.org%252F2003%252F01%252Fgeo%252Fwgs84_pos%2523SpatialThing Feedback: class names for my ontology do not appear well : http://bioportal.bioontology.org/ontologies/MODSCI/ _______________________________________________ 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 Oct 1 17:35:55 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 2 Oct 2019 00:35:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from jlomax In-Reply-To: <5d933ead5b79c_259d2ad877e71f4c6597b@ncbo-prd-app-09.stanford.edu.mail> References: <5d933ead5b79c_259d2ad877e71f4c6597b@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <1C4B4E34-E9BD-42AA-9581-C19AAD7F442A@stanford.edu> Hello Jane, Apologies - we?ve run into some difficulty with getting the latest version of NCBITAXON fully processed in BioPortal, which is why the CSV is unavailable. We?re still looking into it. Kind regards, Jennifer On Oct 1, 2019, at 4:55 AM, support at bioontology.org wrote: Name: jlomax Email: jane at scibite.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCBITAXON Feedback: Hi - the csv download for: https://bioportal.bioontology.org/ontologies/NCBITAXON is throwing an error. Please could you regenerate? thanks Jane Lomax (jane at scibite.com) _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Oct 1 22:29:31 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 2 Oct 2019 05:29:31 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> References: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <49FA8B53-1801-4BE3-BC38-BA69722AFA4A@stanford.edu> Mark, With respect to these issues: - However, when I retrieve the mapping results via the REST API [http://data.bioontology.org/ontologies/OGMS/mappings], I do not see any identifier within the entries in the classes list to indicate to which ontology the class belongs. Presumably the first entry in the list is the OGMS, but I would need to figure out in which ontology the second entry appeared on the basis of the base URI. - When the mapping source is SAME_URI, for example, both classes are the same, e.g. http://purl.obolibrary.org/obo/OGMS_0000096. I understand that the class URI appeared in the OGMS, but I have no way to identify the other ontology in which the URI appeared. The ontology that is the source of the mappings is listed in the links section for each term. { "@id": "http://purl.obolibrary.org/obo/OGMS_0000096", "@type": "http://www.w3.org/2002/07/owl#Class", -"links": { "self": "http://data.bioontology.org/ontologies/OGMS/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000096", "ontology": "http://data.bioontology.org/ontologies/OGMS", compare to { "@id": "http://purl.obolibrary.org/obo/OGMS_0000096", "@type": "http://www.w3.org/2002/07/owl#Class", -"links": { "self": "http://data.bioontology.org/ontologies/FLU/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000096", "ontology": "http://data.bioontology.org/ontologies/FLU", John On Oct 1, 2019, at 5:05 PM, support at bioontology.org wrote: Name: Mark Ressler Email: mark at markressler.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT Feedback: As with a prior message, I am using the REST API to retrieve all the mappings for a particular ontology, in this case the OGMS. - I see from the OGMS ontology page [https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings] that mappings associated with particular ontologies are identified, e.g. between OGMS and the APA Treatment Cluster. - However, when I retrieve the mapping results via the REST API [http://data.bioontology.org/ontologies/OGMS/mappings], I do not see any identifier within the entries in the classes list to indicate to which ontology the class belongs. Presumably the first entry in the list is the OGMS, but I would need to figure out in which ontology the second entry appeared on the basis of the base URI. - When the mapping source is SAME_URI, for example, both classes are the same, e.g. http://purl.obolibrary.org/obo/OGMS_0000096. I understand that the class URI appeared in the OGMS, but I have no way to identify the other ontology in which the URI appeared. - What I really would like is to be able to retrieve mappings between just two ontologies, rather than retrieve all mappings for an ontology, for instance, if there were an API endpoint like: /ontologies/:ontology1/mappings/:ontology2 - Not only would such an endpoint be convenient, but it would also reduce the load on your server. Eventually, I would like to retrieve the mappings for SNOMED-CT and one other ontology. If I needed to retrieve all mappings for SNOMED-CT, I see that would require 36133 REST calls. I hope your server would allow me to make all of those calls. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Wed Oct 2 08:57:40 2019 From: vk396 at njit.edu (Kuttichikeloth, Vipina) Date: Wed, 2 Oct 2019 11:57:40 -0400 Subject: [bioontology-support] Annotator issues Message-ID: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark at markressler.com Wed Oct 2 08:25:44 2019 From: mark at markressler.com (Mark Ressler) Date: Wed, 2 Oct 2019 09:25:44 -0600 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <49FA8B53-1801-4BE3-BC38-BA69722AFA4A@stanford.edu> References: <5d936b231e5f5_1ee92b0fdebe89081377d@ncbo-prd-app-09.stanford.edu.mail> <49FA8B53-1801-4BE3-BC38-BA69722AFA4A@stanford.edu> Message-ID: Thank you and your colleagues for your assistance on my recent messages. > On Oct 1, 2019, at 11:29 PM, John Graybeal wrote: > > Mark, > > With respect to these issues: > >> - However, when I retrieve the mapping results via the REST API [http://data.bioontology.org/ontologies/OGMS/mappings ], I do not see any identifier within the entries in the classes list to indicate to which ontology the class belongs. Presumably the first entry in the list is the OGMS, but I would need to figure out in which ontology the second entry appeared on the basis of the base URI. >> >> - When the mapping source is SAME_URI, for example, both classes are the same, e.g. http://purl.obolibrary.org/obo/OGMS_0000096 . I understand that the class URI appeared in the OGMS, but I have no way to identify the other ontology in which the URI appeared. >> > The ontology that is the source of the mappings is listed in the links section for each term. > > { > "@id": "http://purl.obolibrary.org/obo/OGMS_0000096 ", > "@type": "http://www.w3.org/2002/07/owl#Class ", > -"links": { > "self": "http://data.bioontology.org/ontologies/OGMS/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000096 ", > "ontology": "http://data.bioontology.org/ontologies/OGMS ", > > compare to > > { > "@id": "http://purl.obolibrary.org/obo/OGMS_0000096 ", > "@type": "http://www.w3.org/2002/07/owl#Class ", > -"links": { > "self": "http://data.bioontology.org/ontologies/FLU/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000096 ", > "ontology": "http://data.bioontology.org/ontologies/FLU ", > > John > >> On Oct 1, 2019, at 5:05 PM, support at bioontology.org wrote: >> >> Name: Mark Ressler >> >> Email: mark at markressler.com >> Location: https%3A%2F%2Fbioportal.bioontology.org %2Fontologies%2FSNOMEDCT >> >> >> Feedback: >> >> As with a prior message, I am using the REST API to retrieve all the mappings for a particular ontology, in this case the OGMS. >> >> - I see from the OGMS ontology page [https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings ] that mappings associated with particular ontologies are identified, e.g. between OGMS and the APA Treatment Cluster. >> >> - However, when I retrieve the mapping results via the REST API [http://data.bioontology.org/ontologies/OGMS/mappings ], I do not see any identifier within the entries in the classes list to indicate to which ontology the class belongs. Presumably the first entry in the list is the OGMS, but I would need to figure out in which ontology the second entry appeared on the basis of the base URI. >> >> - When the mapping source is SAME_URI, for example, both classes are the same, e.g. http://purl.obolibrary.org/obo/OGMS_0000096 . I understand that the class URI appeared in the OGMS, but I have no way to identify the other ontology in which the URI appeared. >> >> - What I really would like is to be able to retrieve mappings between just two ontologies, rather than retrieve all mappings for an ontology, for instance, if there were an API endpoint like: /ontologies/:ontology1/mappings/:ontology2 >> >> - Not only would such an endpoint be convenient, but it would also reduce the load on your server. Eventually, I would like to retrieve the mappings for SNOMED-CT and one other ontology. If I needed to retrieve all mappings for SNOMED-CT, I see that would require 36133 REST calls. I hope your server would allow me to make all of those calls. >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Oct 2 11:31:34 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 2 Oct 2019 18:31:34 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: Message-ID: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: [cid:55C1D3A2-B0E4-4DFF-9198-661335B3799B at stanford.edu] Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-10-02 11.27.49.png Type: image/png Size: 220584 bytes Desc: Screenshot 2019-10-02 11.27.49.png URL: From vendetti at stanford.edu Wed Oct 2 18:23:28 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 3 Oct 2019 01:23:28 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <5d936a1b65f4d_1b522b0fdebe890813796@ncbo-prd-app-09.stanford.edu.mail> References: <5d936a1b65f4d_1b522b0fdebe890813796@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <10326C26-77C4-4D3A-8768-93EE1D5F7293@stanford.edu> Hi Mark, On Oct 1, 2019, at 8:00 AM, support at bioontology.org wrote: - I am looking at the OGMS Mappings page: https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings - I see that the Amphibian Gross Anatomy Ontology is listed with 1 mapping - However, when I click the link for Amphibian Gross Anatomy Ontology, a message appears saying "No mappings found" (twice) It appears that the Amphibian Gross Anatomy ontology is defunct and was only partially removed from BioPortal. I?ve entered an issue in our tracker [1] and we?re working on cleaning up the data. - The APA Treatment Cluster Ontology is listed with 3 mappings - When I click the link for APA Treatment Cluster, a pop-up appears with two separate tables with the three mappings duplicated. Looks like two problems: (1) Some mappings are listed on the summary page, but the details are missing, and (2) Mapping details are listed twice in two tables on the pop-up. The two tables in the pop-up is reproducible on our end. I?ve entered an issue in our tracker [2] and am working on a fix. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal-project/issues/137 [2] https://github.com/ncbo/bioportal_web_ui/issues/103 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maria at ebi.ac.uk Thu Oct 3 06:08:20 2019 From: maria at ebi.ac.uk (Maria Herrero) Date: Thu, 3 Oct 2019 14:08:20 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> Hi Jennifer, Thanks a lot for having a look into this so quickly. I?m afraid this has been an error. We made a mistake and ?has substrate? is not empty. I have updated the list of empty fields below and I provide two examples: * The DDI with preferredLabel"naloxone/morphine DDI" should have two relationships has participantwith the classes with preferredLabel"naloxone" and "morphine". * The DDI with preferredLabel"propafenone/mirtazapine DDI" should have a relationship has DDI effect with the class with preferredLabel"bradycardia AE". Sorry for the misunderstanding, Kind regards, Maria adsorbs alters *_carries_* decreases describes determines *_facilitates_* has agent *_has DDI effect_* has metabolite has object has parameter *_has participant_* has precipitant has product has quality has study entity has study subject *_impaires_* increases is adsorbed by is agent in is altered by *_is carried by_* *_is DDI effect of_* is decreased by is described in is determined by is effect of *_is facilitated by_* *_is impaired by_* is increased by is metabolite of is object in is parameter of *_is participant in_* is precipitant in is product of is quality of is regulated by is role of is undergone by precedes regulates undergoes On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: > Hi Maria, > > I looked at one example in BioPortal from the list of fields that you > gave below. I chose the "alpha-1-acid glycoprotein 1? class from your > DINTO ontology: > > http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true > > > ? that uses ?has substrate?. The ?has substrate? field is populated > with 14 values in the BioPortal user interface: > > > > I double checked this against the contents of the CSV file that we > generated. To follow is a screen shot from Excel where the line for > the above class is shown. The column for has_substrate does contain > all 14 values (separated by the pipe character) of class IDs that were > used to populate this field: > > > > > It appears in this case the the CSV content matches what BioPortal > serves, both in the user interface and via our REST API [1]. Could you > provide us with a specific example of a class where you?ve detected > empty fields that you think are incorrect? > > Kind regards, > Jennifer > > [1] > http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false > > > >> On Sep 30, 2019, at 7:13 AM, support at bioontology.org >> wrote: >> >> Name: Maria Herrero >> >> Email: maria at ebi.ac.uk >> >> Location: https%3A%2F%2Fbioportal.bioontology.org >> %2Fontologies%2FDINTO >> >> >> *Feedback:* >> >> Dear colleagues, >> >> Thank you very much for publishing our ontology DINTO on your website >> and making it available for the public. >> We have been recently using the CSV file that you published in >> BioPortal for our latest version DINTO 1.3. to load a graph database, >> in which we have also implemented some rules for the inference of new >> relationships (unknown DDIs) between entities. >> This CSV version of the ontology is very useful, however, during the >> process we observed that some fields in the CSV are empty. They are >> very important for our project and we would like to know if it would >> be possible for you to look into the reason for these fields to be >> missing. In particular, we really need the following fields: >> >> carries >> facilitates >> has DDI effect >> has participant >> has substrate >> impairs >> is carried by >> is DDI effect of >> is facilitated by >> is impaired by >> is participant in >> >> We would really appreciate if you could help us with this by creating >> a new CSV from DINTO 1.3 with values for these fields. >> >> Kind regards, >> Maria Herrero >> maria at ebi.ac.uk >> maria.herrero at kcl.ac.uk >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-09-30 11.39.04.png Type: image/png Size: 140469 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-09-30 11.55.14.png Type: image/png Size: 70735 bytes Desc: not available URL: From support at bioontology.org Thu Oct 3 08:04:11 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 03 Oct 2019 08:04:11 -0700 Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_Jo?= =?utf-8?q?=C3=A3o_Ferreira?= Message-ID: <5d960deb13a7d_75192acf6a11a1e896020@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Oct 4 11:58:44 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 4 Oct 2019 18:58:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mark Ressler In-Reply-To: <10326C26-77C4-4D3A-8768-93EE1D5F7293@stanford.edu> References: <5d936a1b65f4d_1b522b0fdebe890813796@ncbo-prd-app-09.stanford.edu.mail> <10326C26-77C4-4D3A-8768-93EE1D5F7293@stanford.edu> Message-ID: <112B3C03-6CD8-4040-B867-75A5703E042F@stanford.edu> Hi Mark, Following up on the issues you reported: 1). AAO has been fully removed from BioPortal such that the mapping irregularity you saw with OGMS is gone. 2). I performed a production release this morning that fixed the issue with duplicate mapping tables in mapping dialogs. Kind regards, Jennifer On Oct 2, 2019, at 6:23 PM, Jennifer Leigh Vendetti > wrote: Hi Mark, On Oct 1, 2019, at 8:00 AM, support at bioontology.org wrote: - I am looking at the OGMS Mappings page: https://bioportal.bioontology.org/ontologies/OGMS/?p=mappings - I see that the Amphibian Gross Anatomy Ontology is listed with 1 mapping - However, when I click the link for Amphibian Gross Anatomy Ontology, a message appears saying "No mappings found" (twice) It appears that the Amphibian Gross Anatomy ontology is defunct and was only partially removed from BioPortal. I?ve entered an issue in our tracker [1] and we?re working on cleaning up the data. - The APA Treatment Cluster Ontology is listed with 3 mappings - When I click the link for APA Treatment Cluster, a pop-up appears with two separate tables with the three mappings duplicated. Looks like two problems: (1) Some mappings are listed on the summary page, but the details are missing, and (2) Mapping details are listed twice in two tables on the pop-up. The two tables in the pop-up is reproducible on our end. I?ve entered an issue in our tracker [2] and am working on a fix. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal-project/issues/137 [2] https://github.com/ncbo/bioportal_web_ui/issues/103 _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sat Oct 5 17:52:58 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 6 Oct 2019 00:52:58 +0000 Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_Jo?= =?utf-8?q?=C3=A3o_Ferreira?= In-Reply-To: <5d960deb13a7d_75192acf6a11a1e896020@ncbo-prd-app-09.stanford.edu.mail> References: <5d960deb13a7d_75192acf6a11a1e896020@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <1119552B-E2EE-4536-927C-9C637C4CB50B@stanford.edu> Hello Jo?o, Popularity is based on ontology visits in the User Interface. This is the value used on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies). These statistics change monthly based on Google metrics for page visits. I refer you to the following thread, which provides greater detail on this question. http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Melissa-Haendel-td4657259.html John On Oct 3, 2019, at 8:04 AM, support at bioontology.org wrote: Name: Jo?o Ferreira Email: jdferreira at fc.ul.pt Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Hi, I'm wondering what you mean by "Popularity" in your "Browse" page. What makes an ontology more popular than another, is it number of downloads? Number of unique views? I don't actually want to know the formula, just the more relevant criteria that are used. Thank you very much. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sat Oct 5 18:37:06 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 6 Oct 2019 01:37:06 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> Message-ID: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: [cid:16d8dfcd7f218f866181] Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-10-02 11.27.49.png Type: image/png Size: 220584 bytes Desc: Screenshot 2019-10-02 11.27.49.png URL: From jgraybeal at stanford.edu Sat Oct 5 22:31:44 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 6 Oct 2019 05:31:44 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel In-Reply-To: References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail> <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu> Message-ID: <0A525B2A-29A8-4F0B-99B4-C1067B1775D7@stanford.edu> Hi Melissa, Finally had a chance to check out these examples and think about this a bit more. I also had a nice discussion of Pier Luigi Buttigieg about 6 months ago that was very much along these lines. There are a lot of issues at different levels we could discuss, but I'll just hit a few key points. It was interesting to look at all those results in retrospect. The graphs for those two 'odd' ontologies are dead flat for all the other months we have records, except for the 1-2 months you checked them. I think each ontology had big events, though one might have been artificially pumped up. But there are a number of other clues we could be using: they're both beta, they have no projects using them, and the long-term visit count are obvious reasons they don't deserve high visibility. (And the number of classes is another huge clue!) So, good point. HPO (HP in BioPortal) and Mondo are both up and down but have a high average level, and 3 you cited are all a bit lower for May but on average much higher. I think you might be a bit harsh on OGMS, based on the number of updates and projects (4) using it. I know FOODON is very well known though, it might be nice if projects using FOODON register that in BioPortal just so people have that context. But here again, I think your fundamental point is spot on. The number of visits?which I think includes all visits on all the ontology's terms in the UI, not just in the visits to the home page?is (in my opinion) way too limited a metric for the purposes we apply it to. We are definitely up for working with the community to brainstorm all the factors that are important, there are one or two dozen candidates I'm aware of, not least the REST usage. (it's a "simple matter of programming" and all that, of course. ;->) One final note: The first thing found in a google search for an ontology is beyond our ability to influence. It is going to be driven by how many web sites point to the ontology, and how many users click on the different links Google offers. Searches may get driven to BioPortal because BioPortal has really high site rank, but I am pretty sure that won't affect which ontologies are shown first in a Google search. (A syntactic match is probably a very important factor for the Google search.) Let's continue the discussion offline about where and with whom we might get together to come up with appropriate criteria, yes? I think that would be a really rewarding discussion, and of course people on the list can add their thoughts to this thread. Thanks for your thoughts! John [cid:7DF4292F-5B20-41B9-8FD7-7C34629A6312 at attlocal.net][cid:C2CA8407-4367-481E-B849-E45D76CA5C73 at attlocal.net] [cid:B815BFB2-AEA1-464A-8C94-54912E2943D1 at attlocal.net][cid:9759E8F9-8232-44D1-B7D0-0F500C3F7B3C at attlocal.net][cid:083931DF-61D8-406F-9DEB-4C1217C6797A at attlocal.net] On Jun 24, 2019, at 7:42 PM, Melissa Haendel > wrote: Hi John, Well check on the following ones, just for grins and giggles: HPO (the popular one we care about) Mondo (the new not so popular one we care about) Some examples of surprising results: "Body in numbers project terminology? and ?growth medium ontology? are higher on the list than EFO or Uberon or GO FoodOn is pretty low down, lower than OGMS (which as far as I know, no one actually uses). FoodOn is quite popular in agriculture and diet domains these days. I know that ?use? is different than ?visited? or ?searched on Google and found? but I wonder if there is not some combined measure that would actually help understand usage? Another example is the Symptom ontology- no one uses this except the Disease ontology developers, but its a common search string. Do you see what I mean? Mind you I am not complaining whatsoever, this is just a really hard problem! Its more of a philosophical request than an actual one ;-) On Jun 24, 2019, at 7:32 PM, John Graybeal > wrote: Hi Melissa, Concrete examples will be helpful for me to appreciate your perspective. (For example, sometimes outdated ontologies actually get heavy usage for particular reasons, depending on the ontology. But the never-used case seems very strange.) Yes, I think these rankings are significantly driven by people landing from Google. We have thought about other ways to monitor traffic/value, like downloads, time-on-page, tree view clicks, API calls (weighted for ontology size, since we require people to page through an entire ontology it makes for more calls), and so on. I think it would be a really interesting exercise to brainstorm all the options with you, and perhaps others to review as well. We may have historical statistics, I will see what we can put together. I'd like to get a better idea what causes the variation if we can. Possibly we can change the algorithm to use a longer period of time, but no point if the variability has a long cycle. We'll see if anyone else chimes in on the list on this topic, and I'll let you know offline if/when I get more data. I should say, we are likely stretched too thin to make any immediate changes unless they are super-easy. But maybe we can get some data you can use for your purposes. John On Jun 24, 2019, at 7:09 PM, Melissa Haendel > wrote: Hi John, Nice to see you in my inbox. We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google? This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file? For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot. Anyway, there may well be nothing wrong, its just less useful for this purpose then? Let me know if you want to brainstorm. Cheers, Melissa On Jun 23, 2019, at 5:39 PM, John Graybeal > wrote: Hi Melissa, Can you help us with more precise details about your concern? Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies). These statistics change monthly based on Google metrics for page visits. The Recommender (https://bioportal.bioontology.org/recommender) makes recommendations based on a number of factors, one of which is the visit-based popularity. Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric? I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages. John On Jun 22, 2019, at 4:29 PM, support at bioontology.org wrote: Name: Melissa Haendel Email: melissa at tislab.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much? _______________________________________________ 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 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-05 at 9.54.48 PM.png Type: image/png Size: 58256 bytes Desc: Screen Shot 2019-10-05 at 9.54.48 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-05 at 9.54.27 PM.png Type: image/png Size: 54821 bytes Desc: Screen Shot 2019-10-05 at 9.54.27 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-05 at 9.58.43 PM.png Type: image/png Size: 65458 bytes Desc: Screen Shot 2019-10-05 at 9.58.43 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-05 at 10.07.00 PM.png Type: image/png Size: 68798 bytes Desc: Screen Shot 2019-10-05 at 10.07.00 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-05 at 10.03.18 PM.png Type: image/png Size: 62968 bytes Desc: Screen Shot 2019-10-05 at 10.03.18 PM.png URL: From melissa at tislab.org Mon Oct 7 06:15:51 2019 From: melissa at tislab.org (Melissa Haendel) Date: Mon, 7 Oct 2019 06:15:51 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Haendel In-Reply-To: <0A525B2A-29A8-4F0B-99B4-C1067B1775D7@stanford.edu> References: <5d0eb9f1e3c13_5ae12b00240657e42829a@ncbo-prd-app-08.stanford.edu.mail> <202A6C4C-B7FA-43F8-BDF7-F81912237409@stanford.edu> <0A525B2A-29A8-4F0B-99B4-C1067B1775D7@stanford.edu> Message-ID: Dear John, This is very cool, thank you for the deep dive! I will do some more poking so its more fresh in my mind. Perhaps its worth writing a little best practice guide or blog somewhere together? Could be a community thing too. Cheers, Melissa > On Oct 5, 2019, at 10:31 PM, John Graybeal wrote: > > Hi Melissa, > > Finally had a chance to check out these examples and think about this a bit more. > > I also had a nice discussion of Pier Luigi Buttigieg about 6 months ago that was very much along these lines. There are a lot of issues at different levels we could discuss, but I'll just hit a few key points. > > It was interesting to look at all those results in retrospect. The graphs for those two 'odd' ontologies are dead flat for all the other months we have records, except for the 1-2 months you checked them. I think each ontology had big events, though one might have been artificially pumped up. But there are a number of other clues we could be using: they're both beta, they have no projects using them, and the long-term visit count are obvious reasons they don't deserve high visibility. (And the number of classes is another huge clue!) So, good point. > > HPO (HP in BioPortal) and Mondo are both up and down but have a high average level, and 3 you cited are all a bit lower for May but on average much higher. > > I think you might be a bit harsh on OGMS, based on the number of updates and projects (4) using it. I know FOODON is very well known though, it might be nice if projects using FOODON register that in BioPortal just so people have that context. > > But here again, I think your fundamental point is spot on. The number of visits?which I think includes all visits on all the ontology's terms in the UI, not just in the visits to the home page?is (in my opinion) way too limited a metric for the purposes we apply it to. We are definitely up for working with the community to brainstorm all the factors that are important, there are one or two dozen candidates I'm aware of, not least the REST usage. (it's a "simple matter of programming" and all that, of course. ;->) > > One final note: The first thing found in a google search for an ontology is beyond our ability to influence. It is going to be driven by how many web sites point to the ontology, and how many users click on the different links Google offers. Searches may get driven to BioPortal because BioPortal has really high site rank, but I am pretty sure that won't affect which ontologies are shown first in a Google search. (A syntactic match is probably a very important factor for the Google search.) > > Let's continue the discussion offline about where and with whom we might get together to come up with appropriate criteria, yes? I think that would be a really rewarding discussion, and of course people on the list can add their thoughts to this thread. > > Thanks for your thoughts! > > John > > > > > > > > > > >> On Jun 24, 2019, at 7:42 PM, Melissa Haendel > wrote: >> >> Hi John, >> Well check on the following ones, just for grins and giggles: >> >> HPO (the popular one we care about) >> Mondo (the new not so popular one we care about) >> >> Some examples of surprising results: >> "Body in numbers project terminology? and ?growth medium ontology? are higher on the list than EFO or Uberon or GO >> >> FoodOn is pretty low down, lower than OGMS (which as far as I know, no one actually uses). FoodOn is quite popular in agriculture and diet domains these days. >> >> I know that ?use? is different than ?visited? or ?searched on Google and found? but I wonder if there is not some combined measure that would actually help understand usage? >> >> Another example is the Symptom ontology- no one uses this except the Disease ontology developers, but its a common search string. >> >> Do you see what I mean? Mind you I am not complaining whatsoever, this is just a really hard problem! >> Its more of a philosophical request than an actual one ;-) >> >> >> >> >> >> >>> On Jun 24, 2019, at 7:32 PM, John Graybeal > wrote: >>> >>> Hi Melissa, >>> >>> Concrete examples will be helpful for me to appreciate your perspective. (For example, sometimes outdated ontologies actually get heavy usage for particular reasons, depending on the ontology. But the never-used case seems very strange.) >>> >>> Yes, I think these rankings are significantly driven by people landing from Google. We have thought about other ways to monitor traffic/value, like downloads, time-on-page, tree view clicks, API calls (weighted for ontology size, since we require people to page through an entire ontology it makes for more calls), and so on. I think it would be a really interesting exercise to brainstorm all the options with you, and perhaps others to review as well. >>> >>> We may have historical statistics, I will see what we can put together. I'd like to get a better idea what causes the variation if we can. Possibly we can change the algorithm to use a longer period of time, but no point if the variability has a long cycle. >>> >>> We'll see if anyone else chimes in on the list on this topic, and I'll let you know offline if/when I get more data. >>> >>> I should say, we are likely stretched too thin to make any immediate changes unless they are super-easy. But maybe we can get some data you can use for your purposes. >>> >>> John >>> >>> >>> >>>> On Jun 24, 2019, at 7:09 PM, Melissa Haendel > wrote: >>>> >>>> Hi John, >>>> >>>> Nice to see you in my inbox. >>>> >>>> We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google? >>>> >>>> This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file? >>>> >>>> For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot. >>>> >>>> Anyway, there may well be nothing wrong, its just less useful for this purpose then? >>>> >>>> Let me know if you want to brainstorm. >>>> >>>> Cheers, >>>> Melissa >>>> >>>>> On Jun 23, 2019, at 5:39 PM, John Graybeal > wrote: >>>>> >>>>> Hi Melissa, >>>>> >>>>> Can you help us with more precise details about your concern? >>>>> >>>>> Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies ). These statistics change monthly based on Google metrics for page visits. >>>>> >>>>> The Recommender (https://bioportal.bioontology.org/recommender ) makes recommendations based on a number of factors, one of which is the visit-based popularity. >>>>> >>>>> Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric? I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages. >>>>> >>>>> John >>>>> >>>>>> On Jun 22, 2019, at 4:29 PM, support at bioontology.org wrote: >>>>>> >>>>>> Name: Melissa Haendel >>>>>> >>>>>> Email: melissa at tislab.org >>>>>> Location: https%3A%2F%2Fbioportal.bioontology.org %2Fontologies >>>>>> >>>>>> >>>>>> Feedback: >>>>>> >>>>>> popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much? >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> >>> >>> ======================== >>> John Graybeal >>> Technical Program Manager >>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal >>> Stanford Center for Biomedical Informatics Research >>> 650-736-1632 >>> >>> >> > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdferreira at fc.ul.pt Sun Oct 6 01:45:21 2019 From: jdferreira at fc.ul.pt (=?UTF-8?Q?Jo=C3=A3o_Ferreira?=) Date: Sun, 6 Oct 2019 09:45:21 +0100 Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_Jo?= =?utf-8?q?=C3=A3o_Ferreira?= In-Reply-To: <1119552B-E2EE-4536-927C-9C637C4CB50B@stanford.edu> References: <5d960deb13a7d_75192acf6a11a1e896020@ncbo-prd-app-09.stanford.edu.mail> <1119552B-E2EE-4536-927C-9C637C4CB50B@stanford.edu> Message-ID: Many thanks for the information. Cheers, Jo?o D Ferreira On Sun, 6 Oct 2019 at 01:53, John Graybeal wrote: > Hello Jo?o, > > Popularity is based on ontology visits in the User Interface. This is the > value used on the front page and the ontology browse page ( > https://bioportal.bioontology.org/ontologies). These statistics change > monthly based on Google metrics for page visits. > > I refer you to the following thread, which provides greater detail on this > question. > > > http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Melissa-Haendel-td4657259.html > > John > > On Oct 3, 2019, at 8:04 AM, support at bioontology.org wrote: > > Name: Jo?o Ferreira > > Email: jdferreira at fc.ul.pt > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies > > > *Feedback:* > > Hi, > > I'm wondering what you mean by "Popularity" in your "Browse" page. > What makes an ontology more popular than another, is it number of > downloads? Number of unique views? I don't actually want to know the > formula, just the more relevant criteria that are used. > > Thank you very much. > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Oct 7 11:59:16 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Oct 2019 18:59:16 +0000 Subject: [bioontology-support] [BioPortal] Feedback from jlomax In-Reply-To: <1C4B4E34-E9BD-42AA-9581-C19AAD7F442A@stanford.edu> References: <5d933ead5b79c_259d2ad877e71f4c6597b@ncbo-prd-app-09.stanford.edu.mail> <1C4B4E34-E9BD-42AA-9581-C19AAD7F442A@stanford.edu> Message-ID: <35135763-B0D3-40EA-9D77-B6E32F4E1E9F@stanford.edu> Hello Jane, The CSV representation of NCBITAXON is now available for download again in BioPortal. Apologies for the inconvenience. Kind regards, Jennifer On Oct 1, 2019, at 5:35 PM, Jennifer Leigh Vendetti > wrote: Hello Jane, Apologies - we?ve run into some difficulty with getting the latest version of NCBITAXON fully processed in BioPortal, which is why the CSV is unavailable. We?re still looking into it. Kind regards, Jennifer On Oct 1, 2019, at 4:55 AM, support at bioontology.org wrote: Name: jlomax Email: jane at scibite.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCBITAXON Feedback: Hi - the csv download for: https://bioportal.bioontology.org/ontologies/NCBITAXON is throwing an error. Please could you regenerate? thanks Jane Lomax (jane at scibite.com) _______________________________________________ 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 Oct 7 16:57:08 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Oct 2019 23:57:08 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> Message-ID: Hi Maria, I have a question for you (below) before I proceed further with troubleshooting the CSV content. I searched DINTO in BioPortal for both "naloxone/morphine DDI? and "propafenone/mirtazapine DDI? and couldn?t find any classes with those labels. I downloaded your ontology source file and opened it outside of the BioPortal system using the Protege ontology editing tool. I performed searches using that tool as well, and couldn?t find any matches. I noticed the last time DINTO was uploaded to our system was February 11, 2016. Is it possible you?re referring to a newer version of the ontology than what is hosted in our BioPortal system? Kind regards, Jennifer On Oct 3, 2019, at 6:08 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for having a look into this so quickly. I?m afraid this has been an error. We made a mistake and ?has substrate? is not empty. I have updated the list of empty fields below and I provide two examples: * The DDI with preferredLabel "naloxone/morphine DDI" should have two relationships has participant with the classes with preferredLabel "naloxone" and "morphine". * The DDI with preferredLabel "propafenone/mirtazapine DDI" should have a relationship has DDI effect with the class with preferredLabel "bradycardia AE". Sorry for the misunderstanding, Kind regards, Maria adsorbs alters carries decreases describes determines facilitates has agent has DDI effect has metabolite has object has parameter has participant has precipitant has product has quality has study entity has study subject impaires increases is adsorbed by is agent in is altered by is carried by is DDI effect of is decreased by is described in is determined by is effect of is facilitated by is impaired by is increased by is metabolite of is object in is parameter of is participant in is precipitant in is product of is quality of is regulated by is role of is undergone by precedes regulates undergoes On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: Hi Maria, I looked at one example in BioPortal from the list of fields that you gave below. I chose the "alpha-1-acid glycoprotein 1? class from your DINTO ontology: http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true ? that uses ?has substrate?. The ?has substrate? field is populated with 14 values in the BioPortal user interface: I double checked this against the contents of the CSV file that we generated. To follow is a screen shot from Excel where the line for the above class is shown. The column for has_substrate does contain all 14 values (separated by the pipe character) of class IDs that were used to populate this field: It appears in this case the the CSV content matches what BioPortal serves, both in the user interface and via our REST API [1]. Could you provide us with a specific example of a class where you?ve detected empty fields that you think are incorrect? Kind regards, Jennifer [1] http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false On Sep 30, 2019, at 7:13 AM, support at bioontology.org wrote: Name: Maria Herrero Email: maria at ebi.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDINTO Feedback: Dear colleagues, Thank you very much for publishing our ontology DINTO on your website and making it available for the public. We have been recently using the CSV file that you published in BioPortal for our latest version DINTO 1.3. to load a graph database, in which we have also implemented some rules for the inference of new relationships (unknown DDIs) between entities. This CSV version of the ontology is very useful, however, during the process we observed that some fields in the CSV are empty. They are very important for our project and we would like to know if it would be possible for you to look into the reason for these fields to be missing. In particular, we really need the following fields: carries facilitates has DDI effect has participant has substrate impairs is carried by is DDI effect of is facilitated by is impaired by is participant in We would really appreciate if you could help us with this by creating a new CSV from DINTO 1.3 with values for these fields. Kind regards, Maria Herrero maria at ebi.ac.uk maria.herrero at kcl.ac.uk _______________________________________________ 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 Oct 7 16:57:48 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Oct 2019 23:57:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> Message-ID: Hi Maria, I have a question for you (below) before I proceed further with troubleshooting the CSV content. I searched DINTO in BioPortal for both "naloxone/morphine DDI? and "propafenone/mirtazapine DDI? and couldn?t find any classes with those labels. I downloaded your ontology source file and opened it outside of the BioPortal system using the Protege ontology editing tool. I performed searches using that tool as well, and couldn?t find any matches. I noticed the last time DINTO was uploaded to our system was February 11, 2016. Is it possible you?re referring to a newer version of the ontology than what is hosted in our BioPortal system? Kind regards, Jennifer On Oct 3, 2019, at 6:08 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for having a look into this so quickly. I?m afraid this has been an error. We made a mistake and ?has substrate? is not empty. I have updated the list of empty fields below and I provide two examples: * The DDI with preferredLabel "naloxone/morphine DDI" should have two relationships has participant with the classes with preferredLabel "naloxone" and "morphine". * The DDI with preferredLabel "propafenone/mirtazapine DDI" should have a relationship has DDI effect with the class with preferredLabel "bradycardia AE". Sorry for the misunderstanding, Kind regards, Maria adsorbs alters carries decreases describes determines facilitates has agent has DDI effect has metabolite has object has parameter has participant has precipitant has product has quality has study entity has study subject impaires increases is adsorbed by is agent in is altered by is carried by is DDI effect of is decreased by is described in is determined by is effect of is facilitated by is impaired by is increased by is metabolite of is object in is parameter of is participant in is precipitant in is product of is quality of is regulated by is role of is undergone by precedes regulates undergoes On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: Hi Maria, I looked at one example in BioPortal from the list of fields that you gave below. I chose the "alpha-1-acid glycoprotein 1? class from your DINTO ontology: http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true ? that uses ?has substrate?. The ?has substrate? field is populated with 14 values in the BioPortal user interface: I double checked this against the contents of the CSV file that we generated. To follow is a screen shot from Excel where the line for the above class is shown. The column for has_substrate does contain all 14 values (separated by the pipe character) of class IDs that were used to populate this field: It appears in this case the the CSV content matches what BioPortal serves, both in the user interface and via our REST API [1]. Could you provide us with a specific example of a class where you?ve detected empty fields that you think are incorrect? Kind regards, Jennifer [1] http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false On Sep 30, 2019, at 7:13 AM, support at bioontology.org wrote: Name: Maria Herrero Email: maria at ebi.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDINTO Feedback: Dear colleagues, Thank you very much for publishing our ontology DINTO on your website and making it available for the public. We have been recently using the CSV file that you published in BioPortal for our latest version DINTO 1.3. to load a graph database, in which we have also implemented some rules for the inference of new relationships (unknown DDIs) between entities. This CSV version of the ontology is very useful, however, during the process we observed that some fields in the CSV are empty. They are very important for our project and we would like to know if it would be possible for you to look into the reason for these fields to be missing. In particular, we really need the following fields: carries facilitates has DDI effect has participant has substrate impairs is carried by is DDI effect of is facilitated by is impaired by is participant in We would really appreciate if you could help us with this by creating a new CSV from DINTO 1.3 with values for these fields. Kind regards, Maria Herrero maria at ebi.ac.uk maria.herrero at kcl.ac.uk _______________________________________________ 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 ypandelidis at hc1.com Tue Oct 8 11:52:58 2019 From: ypandelidis at hc1.com (ypandelidis at hc1.com) Date: Tue, 8 Oct 2019 14:52:58 -0400 Subject: [bioontology-support] CPT hierarchy Message-ID: <002401d57e09$9abb76c0$d0326440$@hc1.com> Hello, I would like to download the CPT hierarchy, ideally in rdf, ttle, Jason-ld, owl, or shacl format. I am primarily interested in the CPT Pathology and Laboratory codes. Is that possible? If it not free, how much would it cost? Regards, Yanni Yanni Pandelidis, Ph.D. Data Scientist Hc1 Email: ypandelidis at hc1.com Mobile: 617-201-2716 | Right Patient. Right Test. Right Prescription.T -- This e-mail message and any file transmitted with it is confidential to the intended recipient and may contain confidential and or legally privileged information. If you are not the intended recipient, you may not copy, distribute or disclose the contents to anyone, nor take any action in reliance on its contents. Should you receive this message in error, please delete it and all copies of it from your system immediately, destroying any hard copies and notifying the sender. Please note that any email sent to, or from hc1.com Inc. may be monitored for content. Virus checking is the responsibility of the recipient. hc1.com Inc. does not accept any legal responsibility for the content of this message or any attachments. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Oct 8 17:00:49 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 9 Oct 2019 00:00:49 +0000 Subject: [bioontology-support] CPT hierarchy In-Reply-To: <002401d57e09$9abb76c0$d0326440$@hc1.com> References: <002401d57e09$9abb76c0$d0326440$@hc1.com> Message-ID: <92AE856B-5A4E-4921-9D5E-8B4D11247F76@stanford.edu> Yanni, You can request all the classes via the BioPortal API. You will have to page through them to get them all?see the API instructions at https://www.bioontology.org/wiki/BioPortal_Help#Programming_with_the_BioPortal_API and http://data.bioontology.org/documentation. Your top level search would look something like http://data.bioontology.org/ontologies/CPT/classes, with the API apended per the examples in the documentation. From there you can follow the 'children' links to traverse the tree until hasChildren = false. John On Oct 8, 2019, at 11:52 AM, ypandelidis at hc1.com wrote: Hello, I would like to download the CPT hierarchy, ideally in rdf, ttle, Jason-ld, owl, or shacl format. I am primarily interested in the CPT Pathology and Laboratory codes. Is that possible? If it not free, how much would it cost? Regards, Yanni Yanni Pandelidis, Ph.D. Data Scientist Hc1 Email: ypandelidis at hc1.com Mobile: 617-201-2716 [https://cdn2.hubspot.net/hubfs/2718424/hc1%20logos%20and%20marketing%20images/hc1%20logo%20copy.png]| Right Patient. Right Test. Right Prescription.? This e-mail message and any file transmitted with it is confidential to the intended recipient and may contain confidential and or legally privileged information. If you are not the intended recipient, you may not copy, distribute or disclose the contents to anyone, nor take any action in reliance on its contents. Should you receive this message in error, please delete it and all copies of it from your system immediately, destroying any hard copies and notifying the sender. Please note that any email sent to, or from hc1.com Inc. may be monitored for content. Virus checking is the responsibility of the recipient. hc1.com Inc. does not accept any legal responsibility for the content of this message or any attachments._______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Oct 9 09:53:38 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 9 Oct 2019 16:53:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from fathalla In-Reply-To: <311324667.2860755.1570398561528@mail.yahoo.com> References: <5d91fa0cf0a7e_155e2b222f37b924557fe@ncbo-prd-app-08.stanford.edu.mail> <2039425837.1195255.1569911219988@mail.yahoo.com> <1059291E-16C1-4C51-A79F-757E4776F7AD@stanford.edu> <311324667.2860755.1570398561528@mail.yahoo.com> Message-ID: <0308CE0B-C14C-4B2E-ADC4-85DEA4A24BC3@stanford.edu> Hello Said, Thanks for sending a new copy of the source file. I downloaded your attachment and opened it in Protege, but I still see the ?Attempt to transform an axiom?? errors in the log. Screen shot below. I spoke to a member of the Protege team yesterday to see if they could help resolve those errors and received this advice: "I think the problem is that the ontology imports the skos and foaf vocabularies explicitly. Generally, there is no need to do that. One can just use whatever property from skos (e.g., prefLabel) or from foaf. By removing those 2 imported ontologies, the ModSci ontology loads without errors/warnings in Protege? I removed the skos and foaf imports statements, and was then able to load your ontology in Protege without any errors. I resubmitted the newly modified file to BioPortal, but we are still running into some processing errors in our system. I?ve entered an issue in our tracker [1], and we?ll continue to troubleshoot. Apologies for the inconvenience. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal-project/issues/138 [cid:0BD602E8-C7C5-49EC-8BAA-2B103145111E at lan] On Oct 6, 2019, at 2:49 PM, said fathalla > wrote: Kindly find the source file of the ontology Mit freundlichen Gr??en, Said Fathalla On Tuesday, October 1, 2019, 09:23:19 PM GMT+2, Jennifer Leigh Vendetti > wrote: Hi Said, I?m not sure if something went wrong with the upload of the new version. I retrieved it from our server, but I still see those errors when I open in Protege. Could you send me a copy of the latest version of your ontology source file privately (vendetti at stanford.edu)? Thank you, Jennifer On Sep 30, 2019, at 11:26 PM, said fathalla > wrote: Hello Jennifer, I checked the ontology and I fixed these errors and uploaded the new version after opening it with Protege and checked the syntax using W3C RDF Validation Results but the problem still exist. W3C RDF Validation Results Mit freundlichen Gr??en, Said Fathalla On Tuesday, October 1, 2019, 01:30:50 AM GMT+2, Jennifer Leigh Vendetti > wrote: Hello, I?ve been attempting to load / examine your ontology outside of the BioPortal system. I used a programmatic approach with the OWL API [1], and also tried manually opening the ontology file in the Protege ontology editing application [2]. In both cases, there are a number of errors. If you happen to use Protege, you can see them via Window | Show log? menu: Here is the complete text of one of the errors: ERROR 16:16:32 Attempt to transform an axiom to correct misuse of properties failed. Property replacement: {=, =, =, =, =}, axiom: AnnotationAssertion( "A top level concept in the concept scheme."@en), error: uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplPlain cannot be cast to org.semanticweb.owlapi.model.IRI We can more readily help with getting an ontology uploaded / displaying properly in BioPortal when parsing errors like this aren?t present. Kind regards, Jennifer [1] http://owlcs.github.io/owlapi/ [2] https://protege.stanford.edu/ On Sep 30, 2019, at 5:50 AM, support at bioontology.org wrote: Name: fathalla Email: sm_fathalla at yahoo.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMODSCI%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fwww.w3.org%252F2003%252F01%252Fgeo%252Fwgs84_pos%2523SpatialThing Feedback: class names for my ontology do not appear well : http://bioportal.bioontology.org/ontologies/MODSCI/ _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-10-08 16.30.44.png Type: image/png Size: 308987 bytes Desc: Screenshot 2019-10-08 16.30.44.png URL: From support at bioontology.org Wed Oct 9 06:03:18 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 09 Oct 2019 06:03:18 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero Message-ID: <5d9dda96762a5_21742ae5655564806709c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Oct 9 15:05:26 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 9 Oct 2019 22:05:26 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: <5d9dda96762a5_21742ae5655564806709c@ncbo-prd-app-09.stanford.edu.mail> References: <5d9dda96762a5_21742ae5655564806709c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <11D737BB-829B-4C1D-B305-92D7ED1244BB@stanford.edu> Hi Maria, With help from my colleagues, we've manually modified your email address to the one you've been using on the support list (maria at ebi.ac.uk). Now you should be able to go to the lost password page in BP, and enter your account name and email address to get a password reminder: https://bioportal.bioontology.org/lost_pass. I'll send your account name privately. Jennifer On Oct 9, 2019, at 6:03 AM, support at bioontology.org wrote: Name: Maria Herrero Email: maria at ebi.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccounts%2Fnew Feedback: Good afternoon, I don't remember my login details. It has been a while since last time I uploaded my ontology DINTO and I would like to check the latests versions. My e-mail address has changed since then. It could be maria.herrero at kcl.ac.uk or my personal address asmarahz84 at gmail.com. It could also be my previous e-mail address mhzazo at pa.uc3m.es (although I don't have access to this address any more) Could you please assist me on this? Kind regards, Maria _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maria at ebi.ac.uk Thu Oct 10 08:16:47 2019 From: maria at ebi.ac.uk (Maria Herrero) Date: Thu, 10 Oct 2019 16:16:47 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> Message-ID: <04ca58f1-f6b0-5f1c-e332-24e23f13216e@ebi.ac.uk> Hi Jennifer, Thanks a lot for your feedback. We've had a look at the latest version of DINTO and it looks like the problem might be that the relationships "has_participant" is defined as a "EquivalentTo" axiom, and not as a "SubClass Of" axiom. You can see an example of a entity class in Protege in the image below. We think that the issue might be that the CSV version includes only the SubClassOf axioms (for example, the "is preceded by" some "target activity alteration" for the class "abciximab/tirofiban DDI"). We are considering solving this issue along to other relevant changes and upload a version 1.4, but I would appreciate if you could confirm first that this is the case and that, if we change the "Equivalent To" axiom to two "SubClass Of" axioms "'has participant' some 'abciximab'" and " 'has participant' some 'tirofiban' ", these relationships will be shown in the CSV. Thanks a lot, Maria example On 08/10/2019 00:57, Jennifer Leigh Vendetti wrote: > Hi Maria, > > I have a question for you (below) before I proceed further with > troubleshooting the CSV content. > > I searched DINTO in BioPortal for both?"naloxone/morphine DDI? > and?"propafenone/mirtazapine DDI? and couldn?t find any classes with > those labels. I downloaded your ontology source file and opened it > outside of the BioPortal system using the Protege ontology editing > tool. I performed searches using that tool as well, and couldn?t find > any matches. I noticed the last time DINTO was uploaded to our system > was February 11, 2016. Is it possible you?re referring to a newer > version of the ontology than what is hosted in our BioPortal system? > > Kind regards, > Jennifer > > >> On Oct 3, 2019, at 6:08 AM, Maria Herrero > > wrote: >> >> >> Hi Jennifer, >> Thanks a lot for having a look into this so quickly. I?m afraid this >> has been an error. We made a mistake and ?has substrate? is not >> empty. I have updated the list of empty fields below and I provide >> two examples: >> >> * The DDI withpreferredLabel"naloxone/morphine DDI" should have two >> relationshipshas participantwith the classes >> withpreferredLabel"naloxone" and "morphine". >> * The DDI withpreferredLabel"propafenone/mirtazapine DDI" should >> have a relationshiphas DDI effectwith the class >> withpreferredLabel"bradycardia AE". >> >> >> Sorry for the misunderstanding, >> >> Kind regards, >> Maria >> >> adsorbs >> alters >> *_carries_* >> decreases >> describes >> determines >> *_facilitates_* >> has agent >> *_has DDI effect_* >> has metabolite >> has object >> has parameter >> *_has participant_* >> has precipitant >> has product >> has quality >> has study entity >> has study subject >> *_impaires_* >> increases >> is adsorbed by >> is agent in >> is altered by >> *_is carried by_* >> *_is DDI effect of_* >> is decreased by >> is described in >> is determined by >> is effect of >> *_is facilitated by_* >> *_is impaired by_* >> is increased by >> is metabolite of >> is object in >> is parameter of >> *_is participant in_* >> is precipitant in >> is product of >> is quality of >> is regulated by >> is role of >> is undergone by >> precedes >> regulates >> undergoes >> >> >> On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: >>> Hi Maria, >>> >>> I looked at one example in BioPortal from the list of fields that >>> you gave below. I chose the "alpha-1-acid glycoprotein 1? class from >>> your DINTO ontology: >>> >>> http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true >>> >>> >>> ? that uses ?has substrate?. The ?has substrate? field is populated >>> with 14 values in the BioPortal user interface: >>> >>> >>> >>> >>> I double checked this against the contents of the CSV file that we >>> generated. To follow is a screen shot from Excel where the line for >>> the above class is shown. The column for has_substrate does contain >>> all 14 values (separated by the pipe character) of class IDs that >>> were used to populate this field: >>> >>> >>> >>> >>> >>> It appears in this case the the CSV content matches what BioPortal >>> serves, both in the user interface and via our REST API [1]. Could >>> you provide us with a specific example of a class where you?ve >>> detected empty fields that you think are incorrect? >>> >>> Kind regards, >>> Jennifer >>> >>> [1] >>> http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false >>> >>> >>> >>>> On Sep 30, 2019, at 7:13 AM,support at bioontology.org >>>> wrote: >>>> >>>> Name: Maria Herrero >>>> >>>> Email: maria at ebi.ac.uk >>>> >>>> Location: https%3A%2F%2Fbioportal.bioontology.org >>>> %2Fontologies%2FDINTO >>>> >>>> >>>> *Feedback:* >>>> >>>> Dear colleagues, >>>> >>>> Thank you very much for publishing our ontology DINTO on your >>>> website and making it available for the public. >>>> We have been recently using the CSV file that you published in >>>> BioPortal for our latest version DINTO 1.3. to load a graph >>>> database, in which we have also implemented some rules for the >>>> inference of new relationships (unknown DDIs) between entities. >>>> This CSV version of the ontology is very useful, however, during >>>> the process we observed that some fields in the CSV are empty. They >>>> are very important for our project and we would like to know if it >>>> would be possible for you to look into the reason for these fields >>>> to be missing. In particular, we really need the following fields: >>>> >>>> carries >>>> facilitates >>>> has DDI effect >>>> has participant >>>> has substrate >>>> impairs >>>> is carried by >>>> is DDI effect of >>>> is facilitated by >>>> is impaired by >>>> is participant in >>>> >>>> We would really appreciate if you could help us with this by >>>> creating a new CSV from DINTO 1.3 with values for these fields. >>>> >>>> Kind regards, >>>> Maria Herrero >>>> maria at ebi.ac.uk >>>> maria.herrero at kcl.ac.uk >>>> >>>> >>>> _______________________________________________ >>>> 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: Screen Shot 2019-10-10 at 10.59.45.png Type: image/png Size: 1026802 bytes Desc: not available URL: From jgraybeal at stanford.edu Thu Oct 10 12:12:13 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 10 Oct 2019 19:12:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: <04ca58f1-f6b0-5f1c-e332-24e23f13216e@ebi.ac.uk> References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> <04ca58f1-f6b0-5f1c-e332-24e23f13216e@ebi.ac.uk> Message-ID: <99E311F0-A9EF-4B4C-9F95-912688B634D7@stanford.edu> Hi Maria, I'm responding to this as I'm the support list person this week. As much as we'd like to provide individualized responses to ontology scenarios, the way we would have to answer a complex question like this is simply to test it in BioPortal, which you can do more quickly (and more often) yourself. To do this without affecting your primary ontology submission, you can create a Private submission (set using the Visibility attribute when creating the ontology) with another name (we encourage including Test in the name). That way only you (and us) can see it, and you can try whatever relationships you think might be worth trying and see how the CSV reflects those relationships. If you complete your work and no longer need your test submissions, we can delete them for you. I also will ask any members of the team who can offer a precise description of the CSV feature to do so. I believe it has been documented before on the mailing list, so with a search (at http://ncbo-support.2288202.n4.nabble.com/) you might find additional information that would be useful for your project. I note that the relationships you are describing (for EquivalentTo and SubClass Of axioms) are not making intuitive ontological sense to me, so I am not sure what to expect as far as the CSV goes. It is possible that with close examination of your ontology we could appreciate what you are trying to do more thoroughly and offer better advice, but we aren't staffed to provide that level of consultation. For the best feedback about your ontology construction, we recommend the Protege mailing list, where ontological experts will often be able to offer precise advice about the best constructs to use. John On Oct 10, 2019, at 8:16 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for your feedback. We've had a look at the latest version of DINTO and it looks like the problem might be that the relationships "has_participant" is defined as a "EquivalentTo" axiom, and not as a "SubClass Of" axiom. You can see an example of a entity class in Protege in the image below. We think that the issue might be that the CSV version includes only the SubClassOf axioms (for example, the "is preceded by" some "target activity alteration" for the class "abciximab/tirofiban DDI"). We are considering solving this issue along to other relevant changes and upload a version 1.4, but I would appreciate if you could confirm first that this is the case and that, if we change the "Equivalent To" axiom to two "SubClass Of" axioms "'has participant' some 'abciximab'" and " 'has participant' some 'tirofiban' ", these relationships will be shown in the CSV. Thanks a lot, Maria On 08/10/2019 00:57, Jennifer Leigh Vendetti wrote: Hi Maria, I have a question for you (below) before I proceed further with troubleshooting the CSV content. I searched DINTO in BioPortal for both "naloxone/morphine DDI? and "propafenone/mirtazapine DDI? and couldn?t find any classes with those labels. I downloaded your ontology source file and opened it outside of the BioPortal system using the Protege ontology editing tool. I performed searches using that tool as well, and couldn?t find any matches. I noticed the last time DINTO was uploaded to our system was February 11, 2016. Is it possible you?re referring to a newer version of the ontology than what is hosted in our BioPortal system? Kind regards, Jennifer On Oct 3, 2019, at 6:08 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for having a look into this so quickly. I?m afraid this has been an error. We made a mistake and ?has substrate? is not empty. I have updated the list of empty fields below and I provide two examples: * The DDI with preferredLabel "naloxone/morphine DDI" should have two relationships has participant with the classes with preferredLabel "naloxone" and "morphine". * The DDI with preferredLabel "propafenone/mirtazapine DDI" should have a relationship has DDI effect with the class with preferredLabel "bradycardia AE". Sorry for the misunderstanding, Kind regards, Maria adsorbs alters carries decreases describes determines facilitates has agent has DDI effect has metabolite has object has parameter has participant has precipitant has product has quality has study entity has study subject impaires increases is adsorbed by is agent in is altered by is carried by is DDI effect of is decreased by is described in is determined by is effect of is facilitated by is impaired by is increased by is metabolite of is object in is parameter of is participant in is precipitant in is product of is quality of is regulated by is role of is undergone by precedes regulates undergoes On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: Hi Maria, I looked at one example in BioPortal from the list of fields that you gave below. I chose the "alpha-1-acid glycoprotein 1? class from your DINTO ontology: http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true ? that uses ?has substrate?. The ?has substrate? field is populated with 14 values in the BioPortal user interface: I double checked this against the contents of the CSV file that we generated. To follow is a screen shot from Excel where the line for the above class is shown. The column for has_substrate does contain all 14 values (separated by the pipe character) of class IDs that were used to populate this field: It appears in this case the the CSV content matches what BioPortal serves, both in the user interface and via our REST API [1]. Could you provide us with a specific example of a class where you?ve detected empty fields that you think are incorrect? Kind regards, Jennifer [1] http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false On Sep 30, 2019, at 7:13 AM, support at bioontology.org wrote: Name: Maria Herrero Email: maria at ebi.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDINTO Feedback: Dear colleagues, Thank you very much for publishing our ontology DINTO on your website and making it available for the public. We have been recently using the CSV file that you published in BioPortal for our latest version DINTO 1.3. to load a graph database, in which we have also implemented some rules for the inference of new relationships (unknown DDIs) between entities. This CSV version of the ontology is very useful, however, during the process we observed that some fields in the CSV are empty. They are very important for our project and we would like to know if it would be possible for you to look into the reason for these fields to be missing. In particular, we really need the following fields: carries facilitates has DDI effect has participant has substrate impairs is carried by is DDI effect of is facilitated by is impaired by is participant in We would really appreciate if you could help us with this by creating a new CSV from DINTO 1.3 with values for these fields. Kind regards, Maria Herrero maria at ebi.ac.uk maria.herrero at kcl.ac.uk _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Oct 10 16:51:37 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 10 Oct 2019 23:51:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maria Herrero In-Reply-To: <99E311F0-A9EF-4B4C-9F95-912688B634D7@stanford.edu> References: <5d920d7e39183_24fb2ac74f4896e4338e8@ncbo-prd-app-09.stanford.edu.mail> <3972bf31-f55e-cbaa-f951-8680bc6a58cc@ebi.ac.uk> <04ca58f1-f6b0-5f1c-e332-24e23f13216e@ebi.ac.uk> <99E311F0-A9EF-4B4C-9F95-912688B634D7@stanford.edu> Message-ID: Hi Maria, BioPortal has limited support for equivalence axioms. This is discussed in a little more detail in the following post in our mailing list archive: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Class-equivalence-in-BioPortal-tp4653553p4653560.html The ontology mentioned in the above post is still present in BioPortal: http://bioportal.bioontology.org/ontologies/OBOE/?p=summary The BioPortal UI will display simple equivalent class axioms in the Details pane, e.g., Hectopascal Equivalent To Millibar: http://bioportal.bioontology.org/ontologies/OBOE/?p=classes&conceptid=http%3A%2F%2Fecoinformatics.org%2Foboe%2Foboe.1.2%2Foboe-standards.owl%23Hectopascal&jump_to_nav=true However, I checked the CSV output for this ontology and it does not contain content for equivalent classes. More detail on what is provided in the CSV files is mentioned in this post in the mailing list archive: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Kathryn-Stout-tp4654915p4654926.html Kind regards, Jennifer On Oct 10, 2019, at 12:12 PM, John Graybeal > wrote: Hi Maria, I'm responding to this as I'm the support list person this week. As much as we'd like to provide individualized responses to ontology scenarios, the way we would have to answer a complex question like this is simply to test it in BioPortal, which you can do more quickly (and more often) yourself. To do this without affecting your primary ontology submission, you can create a Private submission (set using the Visibility attribute when creating the ontology) with another name (we encourage including Test in the name). That way only you (and us) can see it, and you can try whatever relationships you think might be worth trying and see how the CSV reflects those relationships. If you complete your work and no longer need your test submissions, we can delete them for you. I also will ask any members of the team who can offer a precise description of the CSV feature to do so. I believe it has been documented before on the mailing list, so with a search (at http://ncbo-support.2288202.n4.nabble.com/) you might find additional information that would be useful for your project. I note that the relationships you are describing (for EquivalentTo and SubClass Of axioms) are not making intuitive ontological sense to me, so I am not sure what to expect as far as the CSV goes. It is possible that with close examination of your ontology we could appreciate what you are trying to do more thoroughly and offer better advice, but we aren't staffed to provide that level of consultation. For the best feedback about your ontology construction, we recommend the Protege mailing list, where ontological experts will often be able to offer precise advice about the best constructs to use. John On Oct 10, 2019, at 8:16 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for your feedback. We've had a look at the latest version of DINTO and it looks like the problem might be that the relationships "has_participant" is defined as a "EquivalentTo" axiom, and not as a "SubClass Of" axiom. You can see an example of a entity class in Protege in the image below. We think that the issue might be that the CSV version includes only the SubClassOf axioms (for example, the "is preceded by" some "target activity alteration" for the class "abciximab/tirofiban DDI"). We are considering solving this issue along to other relevant changes and upload a version 1.4, but I would appreciate if you could confirm first that this is the case and that, if we change the "Equivalent To" axiom to two "SubClass Of" axioms "'has participant' some 'abciximab'" and " 'has participant' some 'tirofiban' ", these relationships will be shown in the CSV. Thanks a lot, Maria On 08/10/2019 00:57, Jennifer Leigh Vendetti wrote: Hi Maria, I have a question for you (below) before I proceed further with troubleshooting the CSV content. I searched DINTO in BioPortal for both "naloxone/morphine DDI? and "propafenone/mirtazapine DDI? and couldn?t find any classes with those labels. I downloaded your ontology source file and opened it outside of the BioPortal system using the Protege ontology editing tool. I performed searches using that tool as well, and couldn?t find any matches. I noticed the last time DINTO was uploaded to our system was February 11, 2016. Is it possible you?re referring to a newer version of the ontology than what is hosted in our BioPortal system? Kind regards, Jennifer On Oct 3, 2019, at 6:08 AM, Maria Herrero > wrote: Hi Jennifer, Thanks a lot for having a look into this so quickly. I?m afraid this has been an error. We made a mistake and ?has substrate? is not empty. I have updated the list of empty fields below and I provide two examples: * The DDI with preferredLabel "naloxone/morphine DDI" should have two relationships has participant with the classes with preferredLabel "naloxone" and "morphine". * The DDI with preferredLabel "propafenone/mirtazapine DDI" should have a relationship has DDI effect with the class with preferredLabel "bradycardia AE". Sorry for the misunderstanding, Kind regards, Maria adsorbs alters carries decreases describes determines facilitates has agent has DDI effect has metabolite has object has parameter has participant has precipitant has product has quality has study entity has study subject impaires increases is adsorbed by is agent in is altered by is carried by is DDI effect of is decreased by is described in is determined by is effect of is facilitated by is impaired by is increased by is metabolite of is object in is parameter of is participant in is precipitant in is product of is quality of is regulated by is role of is undergone by precedes regulates undergoes On 30/09/2019 20:05, Jennifer Leigh Vendetti wrote: Hi Maria, I looked at one example in BioPortal from the list of fields that you gave below. I chose the "alpha-1-acid glycoprotein 1? class from your DINTO ontology: http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true ? that uses ?has substrate?. The ?has substrate? field is populated with 14 values in the BioPortal user interface: I double checked this against the contents of the CSV file that we generated. To follow is a screen shot from Excel where the line for the above class is shown. The column for has_substrate does contain all 14 values (separated by the pipe character) of class IDs that were used to populate this field: It appears in this case the the CSV content matches what BioPortal serves, both in the user interface and via our REST API [1]. Could you provide us with a specific example of a class where you?ve detected empty fields that you think are incorrect? Kind regards, Jennifer [1] http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false On Sep 30, 2019, at 7:13 AM, support at bioontology.org wrote: Name: Maria Herrero Email: maria at ebi.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDINTO Feedback: Dear colleagues, Thank you very much for publishing our ontology DINTO on your website and making it available for the public. We have been recently using the CSV file that you published in BioPortal for our latest version DINTO 1.3. to load a graph database, in which we have also implemented some rules for the inference of new relationships (unknown DDIs) between entities. This CSV version of the ontology is very useful, however, during the process we observed that some fields in the CSV are empty. They are very important for our project and we would like to know if it would be possible for you to look into the reason for these fields to be missing. In particular, we really need the following fields: carries facilitates has DDI effect has participant has substrate impairs is carried by is DDI effect of is facilitated by is impaired by is participant in We would really appreciate if you could help us with this by creating a new CSV from DINTO 1.3 with values for these fields. Kind regards, Maria Herrero maria at ebi.ac.uk maria.herrero at kcl.ac.uk _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Oct 15 14:01:21 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 15 Oct 2019 21:01:21 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> Message-ID: <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. Thank you for your patience. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Tue Oct 15 09:12:23 2019 From: vk396 at njit.edu (Kuttichikeloth, Vipina) Date: Tue, 15 Oct 2019 12:12:23 -0400 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> Message-ID: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal wrote: > Hi Vipina, > > Our team discussed your experience Friday and I am offering our latest > thoughts for the list, and some of my own observations. (I have the > specific example you sent Jennifer but have not copied it here.) > > When I remove '(finding)' from Jennifer's example, I still see an > annotation for CC-SNOMED. It does not matter what boxes are or are not > checked, this still works. > > Now, I see that your class ( > https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006 > ) is > currently called simply 'abdominal aortic bruit', and so it seems likely > that you have removed the parenthetical expressions from your latest > submission. Based on some further examples (using 'abdominal' and > 'abdominal aortic'), here is the likely explanation. > > When Annotator is looking for matches, it is only looking for class names > that exactly match a string in the source text. (If Annotator matched any > class that *contained* a string in your text, there would be an impossibly > large number of matches for any significant text, and the vast majority of > them would be incorrect.) > > So for example, Annotator will not match 'abdominal' to the class > 'abdominal aortic bruit', because text describing 'abdominal pain' should > not result in a match to that detailed class. > > So if we reconsider your class name that contains '(finding)', if you > remove that from the text that you are trying to annotate, the Annotator > will no longer consider it a match (because Annotator will not want to > assume the more general phrase 'abdominal aortic bruit' matches the more > specific phrase 'abdominal aortic bruit (finding)'). This seems > appropriately conservative, considering the above example of matching > 'abdominal' to the longer phrase. > > Checking 'Match partial words' does not have any impact on this behavior; > it is simply used to enable a short word to match a longer word, for > example, to match suffixed words. > > On another point, if you compare your results with the matches found in > SNOMED-CT, there you will find matches to the shorter strings?but only > because SNOMED-CT has those exact shorter strings as classes. > > This matching behavior is different than searching, which will match any > appearance of the string in a class name, but will prioritize more complete > matches. This is appropriate also, to let people find classes that may have > only some of the entered search string. > > I hope this explains your experience so far. Pleae feel free to follow up > with further questions or concerns. > > John > > > On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti < > vendetti at stanford.edu> wrote: > >> Hello Vipina, >> >> Could you give me a specific example of the text you are entering where >> you don?t see results that you think should be present? I looked at your >> ontology with the Annotator just now. I entered the text of one of your >> class names in the Annotator and selected CC_SNOMED under advanced options. >> The Annotator returned results as I would have expected: >> >> >> >> Kind regards, >> Jennifer >> >> >> >> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >> wrote: >> >> Hi, >> >> Recently I uploaded an ontology named Cardiology Component of SNOMED CT >> (CC_SNOMED). The visibility is set to private. I can see and browse the >> classes on BioPortal. >> >> I want to annotate some medical text using this ontology that I created. >> In the advanced options under "select ontologies", I am able to select >> CC_SNOMED but when I click "Get annotations" no results appear. I have >> tried putting the concepts that exist in CC_SNOMED in the medical text >> still no results. Also, if I select SNOMED CT then the text gets annotated >> and all these concepts are shown. Is there anything I am missing and please >> let me know why this is not working? >> >> Thank you. >> Vipina >> >> >> >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> > On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti < > vendetti at stanford.edu> wrote: > > Hello Vipina, > > Could you give me a specific example of the text you are entering where > you don?t see results that you think should be present? I looked at your > ontology with the Annotator just now. I entered the text of one of your > class names in the Annotator and selected CC_SNOMED under advanced options. > The Annotator returned results as I would have expected: > > > > > Kind regards, > Jennifer > > > > On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina wrote: > > Hi, > > Recently I uploaded an ontology named Cardiology Component of SNOMED CT > (CC_SNOMED). The visibility is set to private. I can see and browse the > classes on BioPortal. > > I want to annotate some medical text using this ontology that I created. > In the advanced options under "select ontologies", I am able to select > CC_SNOMED but when I click "Get annotations" no results appear. I have > tried putting the concepts that exist in CC_SNOMED in the medical text > still no results. Also, if I select SNOMED CT then the text gets annotated > and all these concepts are shown. Is there anything I am missing and please > let me know why this is not working? > > Thank you. > Vipina > > > > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-10-02 11.27.49.png Type: image/png Size: 220584 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: annotator.png Type: image/png Size: 37098 bytes Desc: not available URL: From mdorf at stanford.edu Thu Oct 17 14:14:22 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 17 Oct 2019 21:14:22 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> Message-ID: <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Hi Vipina, I was finally able to identify the issue that was causing the behavior you reported. The culprit is an earlier version of CC_SNOMED ontology, in which the terms in question contained different labels: Earlier version (cc_v6.owl): Left Latest version: Left (non-mitral) atrioventricular valve structure Left (non-mitral) atrioventricular valve structure (body structure) The same applies to the other false match, the term with the id "http://snomed.info/id/312524003?: Earlier version (cc_v6.owl): Right Latest version: Right (non-tricuspid) atrioventricular valve structure Right (non-tricuspid) atrioventricular valve structure (body structure) We currently have a limitation in the Annotator that prevents us from removing older records on ontology re-processing. So when the pref labels got changed, both the old and the new values ended up being stored in the Annotator. As a workaround for this specific case, I have removed the old values from the Annotator datastore. Your text "left right left? no longer returns annotations. I?ve logged this issue in our Github repository: https://github.com/ncbo/ncbo_annotator/issues/8 Thank you again for your patience. 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 Oct 15, 2019, at 2:01 PM, Michael Dorf > wrote: Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. Thank you for your patience. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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 Oct 21 17:00:31 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 21 Oct 2019 17:00:31 -0700 Subject: [bioontology-support] [BioPortal] Feedback from BrandonRose Message-ID: <5dae469f576_5d462ab0bae62b1c58b2@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Oct 21 17:14:07 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Oct 2019 00:14:07 +0000 Subject: [bioontology-support] [BioPortal] Feedback from BrandonRose In-Reply-To: <5dae469f576_5d462ab0bae62b1c58b2@ncbo-prd-app-09.stanford.edu.mail> References: <5dae469f576_5d462ab0bae62b1c58b2@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Brandon, Due to licensing restrictions, we?re unable to provide downloads of the RCD ontology in any format. The ontology content is however accessible via our REST API [1]. We have sample code in various languages for working with the API in one of our GitHub repositories [2]. We don?t have anyone on the current team that knows R, but someone external to Stanford provided an R example in their repository [3]. Kind regards, Jennifer [1] http://data.bioontology.org/documentation [2] https://github.com/ncbo/ncbo_rest_sample_code [3] https://github.com/muntisa/RNCBO On Oct 21, 2019, at 5:00 PM, support at bioontology.org wrote: Name: BrandonRose Email: brandon.ed.rose at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FRCD%3Fp%3Dclasses Feedback: brandon.ed.rose at gmail.com I there a way to download an R friendly version of your ontology on Read Codes (CTV3). I'm trying to work with the drug section for a conversion project. I need a csv or xml of that ontology to merge the text with another dataframe. Do I have to go through UMLS for that? _______________________________________________ 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 mrbarnes at uw.edu Tue Oct 22 09:55:30 2019 From: mrbarnes at uw.edu (Megan Barnes) Date: Tue, 22 Oct 2019 09:55:30 -0700 Subject: [bioontology-support] VMWare Virtual Appliance Message-ID: Hello, I would like to request the NCBO Virtual Appliance product. I am working on a project using the annotator that requires that sensitive health record data remain on our servers, so a local installation of NCBO is necessary. Thanks, Megan Barnes -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Oct 22 03:00:00 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 22 Oct 2019 03:00:00 -0700 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister Message-ID: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Oct 22 04:14:39 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 22 Oct 2019 04:14:39 -0700 Subject: [bioontology-support] [BioPortal] Feedback from BRENDA-BTO Message-ID: <5daee49f6853_29c02b106bb06ebc2c2@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Oct 22 11:03:16 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Oct 2019 18:03:16 +0000 Subject: [bioontology-support] [BioPortal] Feedback from BrandonRose In-Reply-To: References: <5dae469f576_5d462ab0bae62b1c58b2@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Brandon, Apologies, no. We only serve content from the latest submission of each ontology. Kind regards, Jennifer On Oct 22, 2019, at 1:45 AM, Brandon Rose > wrote: Thanks for your help. Am I able to use archived versions of an ontology using the API? Regards, Brandon Rose On Mon, Oct 21, 2019 at 8:14 PM Jennifer Leigh Vendetti > wrote: Hello Brandon, Due to licensing restrictions, we?re unable to provide downloads of the RCD ontology in any format. The ontology content is however accessible via our REST API [1]. We have sample code in various languages for working with the API in one of our GitHub repositories [2]. We don?t have anyone on the current team that knows R, but someone external to Stanford provided an R example in their repository [3]. Kind regards, Jennifer [1] http://data.bioontology.org/documentation [2] https://github.com/ncbo/ncbo_rest_sample_code [3] https://github.com/muntisa/RNCBO On Oct 21, 2019, at 5:00 PM, support at bioontology.org wrote: Name: BrandonRose Email: brandon.ed.rose at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FRCD%3Fp%3Dclasses Feedback: brandon.ed.rose at gmail.com I there a way to download an R friendly version of your ontology on Read Codes (CTV3). I'm trying to work with the drug section for a conversion project. I need a csv or xml of that ontology to merge the text with another dataframe. Do I have to go through UMLS for that? _______________________________________________ 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 Oct 22 11:10:11 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Oct 2019 18:10:11 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> Hi Allyson, Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. Let us know if you have any further questions about updating the ontology metadata. Kind regards, Jennifer On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: Name: allysonlister Email: allyson.lister at oerc.ox.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. Thanks, Allyson _______________________________________________ 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 allyson.lister at oerc.ox.ac.uk Tue Oct 22 11:51:13 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Tue, 22 Oct 2019 18:51:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail>, <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> Message-ID: Thanks very much! :) Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 22 October 2019 19:10 To: support at bioontology.org Cc: Allyson Lister Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi Allyson, Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. Let us know if you have any further questions about updating the ontology metadata. Kind regards, Jennifer On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: Name: allysonlister Email: allyson.lister at oerc.ox.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. Thanks, Allyson _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support From matthew.landowski at aspeninsights.com Tue Oct 22 13:27:11 2019 From: matthew.landowski at aspeninsights.com (Matt Landowski) Date: Tue, 22 Oct 2019 20:27:11 +0000 Subject: [bioontology-support] Virtual Appliance Request Message-ID: Username: mlando Org: Aspen Insights, LLC Goals: Annotate clinical trial text Why Local Appliance: Annotating a lot of sections individually and the IO per request makes it take several hours. If you have a docker image that would be preferred, but we can handle a OVF or other VM format. Thank you, Matt Landowski, Aspen Insights, LLC -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Oct 22 14:17:49 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 22 Oct 2019 21:17:49 +0000 Subject: [bioontology-support] [BioPortal] Feedback from BRENDA-BTO In-Reply-To: <5daee49f6853_29c02b106bb06ebc2c2@ncbo-prd-app-09.stanford.edu.mail> References: <5daee49f6853_29c02b106bb06ebc2c2@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Antje, On Oct 22, 2019, at 4:14 AM, support at bioontology.org wrote: I am working for the BRENDA ENzyme database and I have noticed, that the latest version of the BRENDA Tissue Ontology (BTO) on your plattform was uploaded in 2016 (https://bioportal.bioontology.org/ontologies/BTO). The BTO is still maintained and we would like to upload the newest version of the BTO. Unfortunately I am not quite sure, whether your team automatically parse our website or if we upload the versions manually? The BTO is downloadable here: https://www.brenda-enzymes.org/ontology.php https://www.brenda-enzymes.org/ontology/tissue/tree/update/update_files/BrendaTissueOBO It appears in the past that new versions have been uploaded manually. We do provide functionality whereby end users can enter a URL that we check daily for new versions. I entered the second URL you provided above. The latest version of BTO was pulled and processed from your website successfully. On a related note, I noticed there is only one account with administrative privileges for this ontology with an email address of marion.gremse at uni-koeln.de. Let me know if you?d like me to add you as well so that you have appropriate permissions to make any other desired modifications. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From allyson.lister at oerc.ox.ac.uk Wed Oct 23 04:00:57 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Wed, 23 Oct 2019 11:00:57 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail>, <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu>, Message-ID: Dear Jennifer, Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? thanks very much, Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Allyson Lister Sent: 22 October 2019 19:51 To: Jennifer Leigh Vendetti; support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Thanks very much! :) Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 22 October 2019 19:10 To: support at bioontology.org Cc: Allyson Lister Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi Allyson, Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. Let us know if you have any further questions about updating the ontology metadata. Kind regards, Jennifer On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: Name: allysonlister Email: allyson.lister at oerc.ox.ac.uk Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. Thanks, Allyson _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support From mdorf at stanford.edu Wed Oct 23 09:28:01 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 23 Oct 2019 16:28:01 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: Hi Vipina, Thank you for reaching out. I?ve looked at the term you are referring to, but I am seeing a different picture on my end. None of the synonyms from your screenshot are listed under the term ?24 hour diastolic blood pressure (observable entity)?: [cid:B63578C8-DA37-4351-A7EC-46DF89D7CB37] These synonyms ARE, however, listed under the term ?Cardiac disorder? (see below), so your Annotator results appear to be consistent. I?ve flushed our caches, but it hasn?t changed the structure of the ?24 hour?.? term. [cid:44A22852-EA07-4FBE-9D88-4B74398A0B98] The REST endpoint results are also consistent with my screenshot above: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all Is it possible that that page is somehow browser-cached on your end? Thanks, Michael On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina > wrote: Hi, I am having an issue trying to annotate synonyms. Some synonyms are getting annotated while some others are not. For example, for the concept "Cardiac disorder" the first image attached shows all the alternate labels for the concept in CC_SNOMED. The second image is the result of the Annotator. I read about sort of a similar issue here https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that it has something to do with the way the ontology is designed. Is this also an issue with the design of the ontology? But then why are some synonyms getting annotated. Thank you, Vipina On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina > wrote: Thank you so much for your help and explanation. ~Vipina On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf > wrote: Hi Vipina, I was finally able to identify the issue that was causing the behavior you reported. The culprit is an earlier version of CC_SNOMED ontology, in which the terms in question contained different labels: Earlier version (cc_v6.owl): Left Latest version: Left (non-mitral) atrioventricular valve structure Left (non-mitral) atrioventricular valve structure (body structure) The same applies to the other false match, the term with the id "http://snomed.info/id/312524003?: Earlier version (cc_v6.owl): Right Latest version: Right (non-tricuspid) atrioventricular valve structure Right (non-tricuspid) atrioventricular valve structure (body structure) We currently have a limitation in the Annotator that prevents us from removing older records on ontology re-processing. So when the pref labels got changed, both the old and the new values ended up being stored in the Annotator. As a workaround for this specific case, I have removed the old values from the Annotator datastore. Your text "left right left? no longer returns annotations. I?ve logged this issue in our Github repository: https://github.com/ncbo/ncbo_annotator/issues/8 Thank you again for your patience. 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 Oct 15, 2019, at 2:01 PM, Michael Dorf > wrote: Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. Thank you for your patience. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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: Screen Shot 2019-10-23 at 9.17.50 AM.png Type: image/png Size: 206884 bytes Desc: Screen Shot 2019-10-23 at 9.17.50 AM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-23 at 9.20.10 AM.png Type: image/png Size: 356095 bytes Desc: Screen Shot 2019-10-23 at 9.20.10 AM.png URL: From mdorf at stanford.edu Wed Oct 23 09:40:12 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 23 Oct 2019 16:40:12 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: Hi Vipina, Actually, please scratch my previous response. I think the confusion was that the highlighted entry on the left of your screenshot did not match the entry on the right (not sure why that is), but I AM seeing the issue you're describing. At least two synonyms, ?Morbus cordis? and "Cardiopathy? did not get annotated properly. Let me do a bit more investigating on this. My quick guess is that there is still an inconsistency between the latest version of CC_SNOMED and our Annotator datastore that causes these bits of behavior. I will have a look to confirm and keep you posted. Thanks, Michael On Oct 23, 2019, at 9:28 AM, Michael Dorf > wrote: Hi Vipina, Thank you for reaching out. I?ve looked at the term you are referring to, but I am seeing a different picture on my end. None of the synonyms from your screenshot are listed under the term ?24 hour diastolic blood pressure (observable entity)?: These synonyms ARE, however, listed under the term ?Cardiac disorder? (see below), so your Annotator results appear to be consistent. I?ve flushed our caches, but it hasn?t changed the structure of the ?24 hour?.? term. The REST endpoint results are also consistent with my screenshot above: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all Is it possible that that page is somehow browser-cached on your end? Thanks, Michael On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina > wrote: Hi, I am having an issue trying to annotate synonyms. Some synonyms are getting annotated while some others are not. For example, for the concept "Cardiac disorder" the first image attached shows all the alternate labels for the concept in CC_SNOMED. The second image is the result of the Annotator. I read about sort of a similar issue here https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that it has something to do with the way the ontology is designed. Is this also an issue with the design of the ontology? But then why are some synonyms getting annotated. Thank you, Vipina On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina > wrote: Thank you so much for your help and explanation. ~Vipina On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf > wrote: Hi Vipina, I was finally able to identify the issue that was causing the behavior you reported. The culprit is an earlier version of CC_SNOMED ontology, in which the terms in question contained different labels: Earlier version (cc_v6.owl): Left Latest version: Left (non-mitral) atrioventricular valve structure Left (non-mitral) atrioventricular valve structure (body structure) The same applies to the other false match, the term with the id "http://snomed.info/id/312524003?: Earlier version (cc_v6.owl): Right Latest version: Right (non-tricuspid) atrioventricular valve structure Right (non-tricuspid) atrioventricular valve structure (body structure) We currently have a limitation in the Annotator that prevents us from removing older records on ontology re-processing. So when the pref labels got changed, both the old and the new values ended up being stored in the Annotator. As a workaround for this specific case, I have removed the old values from the Annotator datastore. Your text "left right left? no longer returns annotations. I?ve logged this issue in our Github repository: https://github.com/ncbo/ncbo_annotator/issues/8 Thank you again for your patience. 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 Oct 15, 2019, at 2:01 PM, Michael Dorf > wrote: Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. Thank you for your patience. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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 vk396 at njit.edu Wed Oct 23 08:55:36 2019 From: vk396 at njit.edu (Kuttichikeloth, Vipina) Date: Wed, 23 Oct 2019 11:55:36 -0400 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: Hi, I am having an issue trying to annotate synonyms. Some synonyms are getting annotated while some others are not. For example, for the concept "Cardiac disorder" the first image attached shows all the alternate labels for the concept in CC_SNOMED. The second image is the result of the Annotator. I read about sort of a similar issue here https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that it has something to do with the way the ontology is designed. Is this also an issue with the design of the ontology? But then why are some synonyms getting annotated. Thank you, Vipina On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina wrote: > Thank you so much for your help and explanation. > > ~Vipina > > > > On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf wrote: > >> Hi Vipina, >> >> I was finally able to identify the issue that was causing the behavior >> you reported. The culprit is an earlier version of CC_SNOMED ontology, in >> which the terms in question contained different labels: >> >> Earlier version (cc_v6.owl): >> >> >> >> >> >> Left >> >> >> Latest version: >> >> >> >> >> >> Left >> (non-mitral) atrioventricular valve structure >> Left >> (non-mitral) atrioventricular valve structure (body structure) >> >> >> The same applies to the other false match, the term with the id " >> http://snomed.info/id/312524003?: >> >> Earlier version (cc_v6.owl): >> >> >> >> >> >> Right >> >> >> Latest version: >> >> >> >> >> >> Right >> (non-tricuspid) atrioventricular valve structure >> Right >> (non-tricuspid) atrioventricular valve structure (body >> structure) >> >> >> We currently have a limitation in the Annotator that prevents us from >> removing older records on ontology re-processing. So when the pref labels >> got changed, both the old and the new values ended up being stored in the >> Annotator. As a workaround for this specific case, I have removed the old >> values from the Annotator datastore. Your text "left right left? no longer >> returns annotations. I?ve logged this issue in our Github repository: >> >> https://github.com/ncbo/ncbo_annotator/issues/8 >> >> Thank you again for your patience. >> >> 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 Oct 15, 2019, at 2:01 PM, Michael Dorf wrote: >> >> Hi Vipina, >> >> Thanks for your report. I need a bit of time to investigate this. Indeed, >> this does not appear to be an expected behavior. I?ll keep you posted as >> soon as I get to the bottom of it. >> >> Thank you for your patience. >> >> 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina >> wrote: >> >> Thank you for the response. I played a little bit more with the ontology >> to add multiple labels to each concept (synonyms) and then annotating some >> text. >> I noticed that every mention of "left" or "right" in the text is getting >> annotated with a concept as shown in the attached image. >> I gave the text to be annotated as "left right left". >> I thought I understood what you said in your response, but in that case >> (and if I understood it correctly), it shouldn't be matching "left" which >> is a part of the entire label >> "Left (non-mitral) atrioventricular valve structure". Am I missing >> something else here? >> >> Thank you. >> Vipina >> >> On Sat, Oct 5, 2019 at 9:37 PM John Graybeal >> wrote: >> >>> Hi Vipina, >>> >>> Our team discussed your experience Friday and I am offering our latest >>> thoughts for the list, and some of my own observations. (I have the >>> specific example you sent Jennifer but have not copied it here.) >>> >>> When I remove '(finding)' from Jennifer's example, I still see an >>> annotation for CC-SNOMED. It does not matter what boxes are or are not >>> checked, this still works. >>> >>> Now, I see that your class ( >>> https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006 >>> ) is >>> currently called simply 'abdominal aortic bruit', and so it seems likely >>> that you have removed the parenthetical expressions from your latest >>> submission. Based on some further examples (using 'abdominal' and >>> 'abdominal aortic'), here is the likely explanation. >>> >>> When Annotator is looking for matches, it is only looking for class >>> names that exactly match a string in the source text. (If Annotator matched >>> any class that *contained* a string in your text, there would be an >>> impossibly large number of matches for any significant text, and the vast >>> majority of them would be incorrect.) >>> >>> So for example, Annotator will not match 'abdominal' to the class >>> 'abdominal aortic bruit', because text describing 'abdominal pain' should >>> not result in a match to that detailed class. >>> >>> So if we reconsider your class name that contains '(finding)', if you >>> remove that from the text that you are trying to annotate, the Annotator >>> will no longer consider it a match (because Annotator will not want to >>> assume the more general phrase 'abdominal aortic bruit' matches the more >>> specific phrase 'abdominal aortic bruit (finding)'). This seems >>> appropriately conservative, considering the above example of matching >>> 'abdominal' to the longer phrase. >>> >>> Checking 'Match partial words' does not have any impact on this >>> behavior; it is simply used to enable a short word to match a longer word, >>> for example, to match suffixed words. >>> >>> On another point, if you compare your results with the matches found in >>> SNOMED-CT, there you will find matches to the shorter strings?but only >>> because SNOMED-CT has those exact shorter strings as classes. >>> >>> This matching behavior is different than searching, which will match any >>> appearance of the string in a class name, but will prioritize more complete >>> matches. This is appropriate also, to let people find classes that may have >>> only some of the entered search string. >>> >>> I hope this explains your experience so far. Pleae feel free to follow >>> up with further questions or concerns. >>> >>> John >>> >>> >>> On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti < >>> vendetti at stanford.edu> wrote: >>> >>>> Hello Vipina, >>>> >>>> Could you give me a specific example of the text you are entering where >>>> you don?t see results that you think should be present? I looked at your >>>> ontology with the Annotator just now. I entered the text of one of your >>>> class names in the Annotator and selected CC_SNOMED under advanced options. >>>> The Annotator returned results as I would have expected: >>>> >>>> >>>> >>>> >>>> Kind regards, >>>> Jennifer >>>> >>>> >>>> >>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>>> wrote: >>>> >>>> Hi, >>>> >>>> Recently I uploaded an ontology named Cardiology Component of SNOMED CT >>>> (CC_SNOMED). The visibility is set to private. I can see and browse the >>>> classes on BioPortal. >>>> >>>> I want to annotate some medical text using this ontology that I >>>> created. In the advanced options under "select ontologies", I am able to >>>> select CC_SNOMED but when I click "Get annotations" no results appear. I >>>> have tried putting the concepts that exist in CC_SNOMED in the medical text >>>> still no results. Also, if I select SNOMED CT then the text gets annotated >>>> and all these concepts are shown. Is there anything I am missing and please >>>> let me know why this is not working? >>>> >>>> Thank you. >>>> Vipina >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>> On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti < >>> vendetti at stanford.edu> wrote: >>> >>> Hello Vipina, >>> >>> Could you give me a specific example of the text you are entering where >>> you don?t see results that you think should be present? I looked at your >>> ontology with the Annotator just now. I entered the text of one of your >>> class names in the Annotator and selected CC_SNOMED under advanced options. >>> The Annotator returned results as I would have expected: >>> >>> >>> >>> >>> Kind regards, >>> Jennifer >>> >>> >>> >>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>> wrote: >>> >>> Hi, >>> >>> Recently I uploaded an ontology named Cardiology Component of SNOMED CT >>> (CC_SNOMED). The visibility is set to private. I can see and browse the >>> classes on BioPortal. >>> >>> I want to annotate some medical text using this ontology that I created. >>> In the advanced options under "select ontologies", I am able to select >>> CC_SNOMED but when I click "Get annotations" no results appear. I have >>> tried putting the concepts that exist in CC_SNOMED in the medical text >>> still no results. Also, if I select SNOMED CT then the text gets annotated >>> and all these concepts are shown. Is there anything I am missing and please >>> let me know why this is not working? >>> >>> Thank you. >>> Vipina >>> >>> >>> >>> >>> >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> ======================== >>> John Graybeal >>> Technical Program Manager >>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal >>> Stanford Center for Biomedical Informatics Research >>> 650-736-1632 >>> >>> >>> >> >> >> _______________________________________________ >> 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: cardiac disorder.png Type: image/png Size: 69856 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cardiac_annotated.png Type: image/png Size: 29920 bytes Desc: not available URL: From vk396 at njit.edu Wed Oct 23 09:40:28 2019 From: vk396 at njit.edu (Kuttichikeloth, Vipina) Date: Wed, 23 Oct 2019 12:40:28 -0400 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: I am sorry about not explaining it properly. I am talking about "Cardiac disorder" and sorry that "24 hour ....." was highlighted. >From the synonyms of Cardiac disorder in the attached figure, you can see that "Morbus cordis" and "Cardiopathy" and "Heart disease" are synonyms. Now when I give the text "*Cardiac disorder, Heart disease, Morbus cordis, Cardiopathy*" to the Annotator, Cardiac disorder and Heart disease are annotated to "Cardiac disorder" (preferred label in this case) as you can see in the second screenshot I attached while "Morbus cordis and Cardiopathy" are not annotated. On Wed, Oct 23, 2019 at 12:28 PM Michael Dorf wrote: > Hi Vipina, > > Thank you for reaching out. I?ve looked at the term you are referring to, > but I am seeing a different picture on my end. None of the synonyms from > your screenshot are listed under the term ?24 hour diastolic blood pressure > (observable entity)?: > > > These synonyms ARE, however, listed under the term ?Cardiac disorder? (see > below), so your Annotator results appear to be consistent. I?ve flushed our > caches, but it hasn?t changed the structure of the ?24 hour?.? term. > > > > > The REST endpoint results are also consistent with my screenshot above: > > > http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all > > > Is it possible that that page is somehow browser-cached on your end? > > Thanks, > > Michael > > > > > On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina > wrote: > > Hi, > > I am having an issue trying to annotate synonyms. Some synonyms are > getting annotated while some others are not. > For example, for the concept "Cardiac disorder" the first image attached > shows all the alternate labels for the concept in CC_SNOMED. > The second image is the result of the Annotator. > I read about sort of a similar issue here > https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that > it has something to do with the way the ontology is designed. > > Is this also an issue with the design of the ontology? But then why are > some synonyms getting annotated. > > Thank you, > Vipina > > On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina > wrote: > >> Thank you so much for your help and explanation. >> >> ~Vipina >> >> >> >> On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf wrote: >> >>> Hi Vipina, >>> >>> I was finally able to identify the issue that was causing the behavior >>> you reported. The culprit is an earlier version of CC_SNOMED ontology, in >>> which the terms in question contained different labels: >>> >>> Earlier version (cc_v6.owl): >>> >>> >>> >>> >>> >>> Left >>> >>> >>> Latest version: >>> >>> >>> >>> >>> >>> Left (non-mitral) >>> atrioventricular valve structure >>> Left (non-mitral) >>> atrioventricular valve structure (body structure) >>> >>> >>> The same applies to the other false match, the term with the id " >>> http://snomed.info/id/312524003?: >>> >>> Earlier version (cc_v6.owl): >>> >>> >>> >>> >>> >>> Right >>> >>> >>> Latest version: >>> >>> >>> >>> >>> >>> Right (non-tricuspid) >>> atrioventricular valve structure >>> Right (non-tricuspid) >>> atrioventricular valve structure (body structure) >>> >>> >>> We currently have a limitation in the Annotator that prevents us from >>> removing older records on ontology re-processing. So when the pref labels >>> got changed, both the old and the new values ended up being stored in the >>> Annotator. As a workaround for this specific case, I have removed the old >>> values from the Annotator datastore. Your text "left right left? no longer >>> returns annotations. I?ve logged this issue in our Github repository: >>> >>> https://github.com/ncbo/ncbo_annotator/issues/8 >>> >>> Thank you again for your patience. >>> >>> 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 Oct 15, 2019, at 2:01 PM, Michael Dorf wrote: >>> >>> Hi Vipina, >>> >>> Thanks for your report. I need a bit of time to investigate this. >>> Indeed, this does not appear to be an expected behavior. I?ll keep you >>> posted as soon as I get to the bottom of it. >>> >>> Thank you for your patience. >>> >>> 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina >>> wrote: >>> >>> Thank you for the response. I played a little bit more with the ontology >>> to add multiple labels to each concept (synonyms) and then annotating some >>> text. >>> I noticed that every mention of "left" or "right" in the text is getting >>> annotated with a concept as shown in the attached image. >>> I gave the text to be annotated as "left right left". >>> I thought I understood what you said in your response, but in that case >>> (and if I understood it correctly), it shouldn't be matching "left" which >>> is a part of the entire label >>> "Left (non-mitral) atrioventricular valve structure". Am I missing >>> something else here? >>> >>> Thank you. >>> Vipina >>> >>> On Sat, Oct 5, 2019 at 9:37 PM John Graybeal >>> wrote: >>> >>>> Hi Vipina, >>>> >>>> Our team discussed your experience Friday and I am offering our latest >>>> thoughts for the list, and some of my own observations. (I have the >>>> specific example you sent Jennifer but have not copied it here.) >>>> >>>> When I remove '(finding)' from Jennifer's example, I still see an >>>> annotation for CC-SNOMED. It does not matter what boxes are or are not >>>> checked, this still works. >>>> >>>> Now, I see that your class ( >>>> https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006 >>>> ) is >>>> currently called simply 'abdominal aortic bruit', and so it seems likely >>>> that you have removed the parenthetical expressions from your latest >>>> submission. Based on some further examples (using 'abdominal' and >>>> 'abdominal aortic'), here is the likely explanation. >>>> >>>> When Annotator is looking for matches, it is only looking for class >>>> names that exactly match a string in the source text. (If Annotator matched >>>> any class that *contained* a string in your text, there would be an >>>> impossibly large number of matches for any significant text, and the vast >>>> majority of them would be incorrect.) >>>> >>>> So for example, Annotator will not match 'abdominal' to the class >>>> 'abdominal aortic bruit', because text describing 'abdominal pain' should >>>> not result in a match to that detailed class. >>>> >>>> So if we reconsider your class name that contains '(finding)', if you >>>> remove that from the text that you are trying to annotate, the Annotator >>>> will no longer consider it a match (because Annotator will not want to >>>> assume the more general phrase 'abdominal aortic bruit' matches the more >>>> specific phrase 'abdominal aortic bruit (finding)'). This seems >>>> appropriately conservative, considering the above example of matching >>>> 'abdominal' to the longer phrase. >>>> >>>> Checking 'Match partial words' does not have any impact on this >>>> behavior; it is simply used to enable a short word to match a longer word, >>>> for example, to match suffixed words. >>>> >>>> On another point, if you compare your results with the matches found in >>>> SNOMED-CT, there you will find matches to the shorter strings?but only >>>> because SNOMED-CT has those exact shorter strings as classes. >>>> >>>> This matching behavior is different than searching, which will match >>>> any appearance of the string in a class name, but will prioritize more >>>> complete matches. This is appropriate also, to let people find classes that >>>> may have only some of the entered search string. >>>> >>>> I hope this explains your experience so far. Pleae feel free to follow >>>> up with further questions or concerns. >>>> >>>> John >>>> >>>> >>>> On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti < >>>> vendetti at stanford.edu> wrote: >>>> >>>>> Hello Vipina, >>>>> >>>>> Could you give me a specific example of the text you are entering >>>>> where you don?t see results that you think should be present? I looked at >>>>> your ontology with the Annotator just now. I entered the text of one of >>>>> your class names in the Annotator and selected CC_SNOMED under advanced >>>>> options. The Annotator returned results as I would have expected: >>>>> >>>>> >>>>> >>>>> >>>>> Kind regards, >>>>> Jennifer >>>>> >>>>> >>>>> >>>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Recently I uploaded an ontology named Cardiology Component of SNOMED >>>>> CT (CC_SNOMED). The visibility is set to private. I can see and browse the >>>>> classes on BioPortal. >>>>> >>>>> I want to annotate some medical text using this ontology that I >>>>> created. In the advanced options under "select ontologies", I am able to >>>>> select CC_SNOMED but when I click "Get annotations" no results appear. I >>>>> have tried putting the concepts that exist in CC_SNOMED in the medical text >>>>> still no results. Also, if I select SNOMED CT then the text gets annotated >>>>> and all these concepts are shown. Is there anything I am missing and please >>>>> let me know why this is not working? >>>>> >>>>> Thank you. >>>>> Vipina >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> bioontology-support mailing list >>>>> bioontology-support at lists.stanford.edu >>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>> >>>>> >>>> On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti < >>>> vendetti at stanford.edu> wrote: >>>> >>>> Hello Vipina, >>>> >>>> Could you give me a specific example of the text you are entering where >>>> you don?t see results that you think should be present? I looked at your >>>> ontology with the Annotator just now. I entered the text of one of your >>>> class names in the Annotator and selected CC_SNOMED under advanced options. >>>> The Annotator returned results as I would have expected: >>>> >>>> >>>> >>>> >>>> Kind regards, >>>> Jennifer >>>> >>>> >>>> >>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina >>>> wrote: >>>> >>>> Hi, >>>> >>>> Recently I uploaded an ontology named Cardiology Component of SNOMED CT >>>> (CC_SNOMED). The visibility is set to private. I can see and browse the >>>> classes on BioPortal. >>>> >>>> I want to annotate some medical text using this ontology that I >>>> created. In the advanced options under "select ontologies", I am able to >>>> select CC_SNOMED but when I click "Get annotations" no results appear. I >>>> have tried putting the concepts that exist in CC_SNOMED in the medical text >>>> still no results. Also, if I select SNOMED CT then the text gets annotated >>>> and all these concepts are shown. Is there anything I am missing and please >>>> let me know why this is not working? >>>> >>>> Thank you. >>>> Vipina >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>>> ======================== >>>> John Graybeal >>>> Technical Program Manager >>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal >>>> Stanford Center for Biomedical Informatics Research >>>> 650-736-1632 >>>> >>>> >>>> >>> >>> >>> _______________________________________________ >>> 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: Screen Shot 2019-10-23 at 9.17.50 AM.png Type: image/png Size: 206884 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-10-23 at 9.20.10 AM.png Type: image/png Size: 356095 bytes Desc: not available URL: From vendetti at stanford.edu Wed Oct 23 11:37:29 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 23 Oct 2019 18:37:29 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> Message-ID: <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> Hi Allyson, I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. Kind regards, Jennifer > On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: > > Dear Jennifer, > > Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? > > thanks very much, > Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Allyson Lister > Sent: 22 October 2019 19:51 > To: Jennifer Leigh Vendetti; support at bioontology.org > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Thanks very much! > > :) Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Jennifer Leigh Vendetti > Sent: 22 October 2019 19:10 > To: support at bioontology.org > Cc: Allyson Lister > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Hi Allyson, > > Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. > > Let us know if you have any further questions about updating the ontology metadata. > > Kind regards, > Jennifer > > > On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: > > > Name: allysonlister > > Email: allyson.lister at oerc.ox.ac.uk > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount > > Feedback: > > Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com > > I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. > > Thanks, > Allyson > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > From allyson.lister at oerc.ox.ac.uk Wed Oct 23 11:39:18 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Wed, 23 Oct 2019 18:39:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> , <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> Message-ID: Thanks very much, I appreciate it! :) Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 23 October 2019 19:37 To: Allyson Lister Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi Allyson, I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. Kind regards, Jennifer > On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: > > Dear Jennifer, > > Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? > > thanks very much, > Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Allyson Lister > Sent: 22 October 2019 19:51 > To: Jennifer Leigh Vendetti; support at bioontology.org > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Thanks very much! > > :) Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Jennifer Leigh Vendetti > Sent: 22 October 2019 19:10 > To: support at bioontology.org > Cc: Allyson Lister > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Hi Allyson, > > Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. > > Let us know if you have any further questions about updating the ontology metadata. > > Kind regards, > Jennifer > > > On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: > > > Name: allysonlister > > Email: allyson.lister at oerc.ox.ac.uk > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount > > Feedback: > > Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com > > I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. > > Thanks, > Allyson > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > From mdorf at stanford.edu Wed Oct 23 12:05:44 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 23 Oct 2019 19:05:44 +0000 Subject: [bioontology-support] Annotator issues In-Reply-To: References: <04064BB8-F978-4C8C-811E-BE1D8CD5ECEF@stanford.edu> <68D813D3-9F9D-49F7-88D2-7FF9A49AD1C3@stanford.edu> <6BE4E749-AED7-4125-B264-385AF8CB84BD@stanford.edu> Message-ID: Hi Vipina, There are two issues at play here. The first is that the ontology does not properly define synonyms. The second is the earlier mentioned issue that prevents regular Annotator refreshes (https://github.com/ncbo/ncbo_annotator/issues/8). The term ?Cardiac disorder? contains multiple entries of "http://www.w3.org/2000/01/rdf-schema#label?, which does not translate into synonyms. By default, BioPortal uses these properties to define its own reserved property called ?synonym?. A custom synonym property is allowed, but the ontology submitter must specify it on the metadata form when uploading the ontology. http://www.w3.org/2004/02/skos/core#altLabel http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym http://purl.obolibrary.org/obo/synonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym The default ?prefLabel" property is set using one these properties (unless the user specified a custom one): http://www.w3.org/2004/02/skos/core#prefLabel http://www.w3.org/2000/01/rdf-schema#label http://data.bioontology.org/metadata/def/prefLabel As you can see, the "http://www.w3.org/2000/01/rdf-schema#label? property is used to determine a prefLabel for the term. When there are multiple entries, BioPortal either picks the English one (if multiple languages are used), or the very first one as the de-facto prefLabel. In your older version of the ontology (v6), the term ?Cardiac disorder? is defined as: Heart disease In the latest version, the same term is defined as: Cardiac disorder Cardiopathy Cardiopathy, NOS Disorder of heart Heart disease Heart disease (disorder) Heart disease, NOS Morbus cordis Morbus cordis, NOS Because of the Annotator refresh issue, both, the original prefLabel, "Heart disease? and the new prefLabel, ?Cardiac disorder? are being stored in the Annotator, that?s why you're seeing two annotations in your results. However, there are NO matches on synonyms, since none are defined. Note the result of this API call: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F56265001?display=all As you can see, the ?synonym? property contains an empty array. I am going to try to refresh our Annotator repository in the upcoming days, so that at least for the time being it is synchronized with the latest version of CC_SNOMED. Thanks again for your inquiry. 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 Oct 23, 2019, at 9:40 AM, Kuttichikeloth, Vipina > wrote: I am sorry about not explaining it properly. I am talking about "Cardiac disorder" and sorry that "24 hour ....." was highlighted. From the synonyms of Cardiac disorder in the attached figure, you can see that "Morbus cordis" and "Cardiopathy" and "Heart disease" are synonyms. Now when I give the text "Cardiac disorder, Heart disease, Morbus cordis, Cardiopathy" to the Annotator, Cardiac disorder and Heart disease are annotated to "Cardiac disorder" (preferred label in this case) as you can see in the second screenshot I attached while "Morbus cordis and Cardiopathy" are not annotated. On Wed, Oct 23, 2019 at 12:28 PM Michael Dorf > wrote: Hi Vipina, Thank you for reaching out. I?ve looked at the term you are referring to, but I am seeing a different picture on my end. None of the synonyms from your screenshot are listed under the term ?24 hour diastolic blood pressure (observable entity)?: These synonyms ARE, however, listed under the term ?Cardiac disorder? (see below), so your Annotator results appear to be consistent. I?ve flushed our caches, but it hasn?t changed the structure of the ?24 hour?.? term. The REST endpoint results are also consistent with my screenshot above: http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all Is it possible that that page is somehow browser-cached on your end? Thanks, Michael On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina > wrote: Hi, I am having an issue trying to annotate synonyms. Some synonyms are getting annotated while some others are not. For example, for the concept "Cardiac disorder" the first image attached shows all the alternate labels for the concept in CC_SNOMED. The second image is the result of the Annotator. I read about sort of a similar issue here https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned that it has something to do with the way the ontology is designed. Is this also an issue with the design of the ontology? But then why are some synonyms getting annotated. Thank you, Vipina On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina > wrote: Thank you so much for your help and explanation. ~Vipina On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf > wrote: Hi Vipina, I was finally able to identify the issue that was causing the behavior you reported. The culprit is an earlier version of CC_SNOMED ontology, in which the terms in question contained different labels: Earlier version (cc_v6.owl): Left Latest version: Left (non-mitral) atrioventricular valve structure Left (non-mitral) atrioventricular valve structure (body structure) The same applies to the other false match, the term with the id "http://snomed.info/id/312524003?: Earlier version (cc_v6.owl): Right Latest version: Right (non-tricuspid) atrioventricular valve structure Right (non-tricuspid) atrioventricular valve structure (body structure) We currently have a limitation in the Annotator that prevents us from removing older records on ontology re-processing. So when the pref labels got changed, both the old and the new values ended up being stored in the Annotator. As a workaround for this specific case, I have removed the old values from the Annotator datastore. Your text "left right left? no longer returns annotations. I?ve logged this issue in our Github repository: https://github.com/ncbo/ncbo_annotator/issues/8 Thank you again for your patience. 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 Oct 15, 2019, at 2:01 PM, Michael Dorf > wrote: Hi Vipina, Thanks for your report. I need a bit of time to investigate this. Indeed, this does not appear to be an expected behavior. I?ll keep you posted as soon as I get to the bottom of it. Thank you for your patience. 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 Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina > wrote: Thank you for the response. I played a little bit more with the ontology to add multiple labels to each concept (synonyms) and then annotating some text. I noticed that every mention of "left" or "right" in the text is getting annotated with a concept as shown in the attached image. I gave the text to be annotated as "left right left". I thought I understood what you said in your response, but in that case (and if I understood it correctly), it shouldn't be matching "left" which is a part of the entire label "Left (non-mitral) atrioventricular valve structure". Am I missing something else here? Thank you. Vipina On Sat, Oct 5, 2019 at 9:37 PM John Graybeal > wrote: Hi Vipina, Our team discussed your experience Friday and I am offering our latest thoughts for the list, and some of my own observations. (I have the specific example you sent Jennifer but have not copied it here.) When I remove '(finding)' from Jennifer's example, I still see an annotation for CC-SNOMED. It does not matter what boxes are or are not checked, this still works. Now, I see that your class (https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006) is currently called simply 'abdominal aortic bruit', and so it seems likely that you have removed the parenthetical expressions from your latest submission. Based on some further examples (using 'abdominal' and 'abdominal aortic'), here is the likely explanation. When Annotator is looking for matches, it is only looking for class names that exactly match a string in the source text. (If Annotator matched any class that *contained* a string in your text, there would be an impossibly large number of matches for any significant text, and the vast majority of them would be incorrect.) So for example, Annotator will not match 'abdominal' to the class 'abdominal aortic bruit', because text describing 'abdominal pain' should not result in a match to that detailed class. So if we reconsider your class name that contains '(finding)', if you remove that from the text that you are trying to annotate, the Annotator will no longer consider it a match (because Annotator will not want to assume the more general phrase 'abdominal aortic bruit' matches the more specific phrase 'abdominal aortic bruit (finding)'). This seems appropriately conservative, considering the above example of matching 'abdominal' to the longer phrase. Checking 'Match partial words' does not have any impact on this behavior; it is simply used to enable a short word to match a longer word, for example, to match suffixed words. On another point, if you compare your results with the matches found in SNOMED-CT, there you will find matches to the shorter strings?but only because SNOMED-CT has those exact shorter strings as classes. This matching behavior is different than searching, which will match any appearance of the string in a class name, but will prioritize more complete matches. This is appropriate also, to let people find classes that may have only some of the entered search string. I hope this explains your experience so far. Pleae feel free to follow up with further questions or concerns. John On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti > wrote: Hello Vipina, Could you give me a specific example of the text you are entering where you don?t see results that you think should be present? I looked at your ontology with the Annotator just now. I entered the text of one of your class names in the Annotator and selected CC_SNOMED under advanced options. The Annotator returned results as I would have expected: Kind regards, Jennifer On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina > wrote: Hi, Recently I uploaded an ontology named Cardiology Component of SNOMED CT (CC_SNOMED). The visibility is set to private. I can see and browse the classes on BioPortal. I want to annotate some medical text using this ontology that I created. In the advanced options under "select ontologies", I am able to select CC_SNOMED but when I click "Get annotations" no results appear. I have tried putting the concepts that exist in CC_SNOMED in the medical text still no results. Also, if I select SNOMED CT then the text gets annotated and all these concepts are shown. Is there anything I am missing and please let me know why this is not working? Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 _______________________________________________ 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 Wed Oct 23 15:20:43 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 23 Oct 2019 22:20:43 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> Message-ID: <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu> Hi again Allyson, OK - SWO is displaying without errors in BioPortal now. Turns out there was a caching issue, unrelated to your ontology. I looked at the contents of the folder on our server that contains the files for the latest submission of SWO. I found two ontology source files in the directory: 1) swo_inferred.owl (with an underscore in the name), uploaded Feb. 24, 2017. This older file has two owl:versionInfo properties. One is set to ?0.4? and one is set to ?1.6?. It also has a ?date? ontology-level annotation of "31.10.2016 23:58 GMT" 2) swo-inferred.owl (with a hyphen in the name), uploaded Oct. 22, 2019. This newer file has one owl:versionInfo property set to ?1.7?. It also has an rdfs:comment property set to "Date of release: 21.10.2019?. It appears that BioPortal successfully pulled the latest version of your ontology from the location you specified as a pull URL in GitHub. There is no need to do a manual upload first, then specify a pull URL for going forward. BioPortal will pull the initial version of your ontology from the URL you specify. With regard to the upload date, I?m guessing you edited the latest submission using the ?Edit latest submission? button, vs. adding a new submission? Submission objects are distinct in our data store. Historically speaking, we haven?t allowed the upload date of a submission to be modified once that submission is created in our system. For example, if you specify a pull URL for us to check nightly, every time BioPortal detects a new ontology source file at that location, the system will create a new submission object to represent that new version, and leave the prior version intact. However, there do appear to be situations like the one you describe below where editing an *existing* submission with a new ontology source file ends up showing a current date as the release date, but keeps the upload date as the old date when the submission object was initially created. We generally recommend creating a new submission if you?re uploading a new version and/or specifying a new pull URL for your ontology. I?m hoping that explanation was relatively clear. All of that said, I could do some manual work on your behalf to clean up current display of SWO. Possibilities that come to mind are deleting and recreating the 1.7 submission so that it has a current upload date, or deleting 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for your latest 1.7 version. Let me know. Kind regards, Jennifer > On Oct 23, 2019, at 11:37 AM, Jennifer Leigh Vendetti wrote: > > Hi Allyson, > > I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. > > Kind regards, > Jennifer > > >> On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: >> >> Dear Jennifer, >> >> Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? >> >> thanks very much, >> Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Allyson Lister >> Sent: 22 October 2019 19:51 >> To: Jennifer Leigh Vendetti; support at bioontology.org >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Thanks very much! >> >> :) Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Jennifer Leigh Vendetti >> Sent: 22 October 2019 19:10 >> To: support at bioontology.org >> Cc: Allyson Lister >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Hi Allyson, >> >> Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. >> >> Let us know if you have any further questions about updating the ontology metadata. >> >> Kind regards, >> Jennifer >> >> >> On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: >> >> >> Name: allysonlister >> >> Email: allyson.lister at oerc.ox.ac.uk >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount >> >> Feedback: >> >> Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com >> >> I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. >> >> Thanks, >> Allyson >> >> _______________________________________________ >> 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 From allyson.lister at oerc.ox.ac.uk Thu Oct 24 02:23:32 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Thu, 24 Oct 2019 09:23:32 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu>, <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu> Message-ID: Dear Jennifer, Thanks very much for your reply. Yes, I began by making a new submission (originally) but deleted that and edited the most recent submission after I read this in the help pages: "If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology." I think I misunderstood what it said, and I thought that meant I should use an existing submission. Next time I'll make a new one. I really appreciate the full explanation, it's made things clearer for me. Please could you help me revert the original submission, by choosing your option above where we delete the 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for the latest 1.7 version? Thanks :) Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 23 October 2019 23:20 To: Allyson Lister Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi again Allyson, OK - SWO is displaying without errors in BioPortal now. Turns out there was a caching issue, unrelated to your ontology. I looked at the contents of the folder on our server that contains the files for the latest submission of SWO. I found two ontology source files in the directory: 1) swo_inferred.owl (with an underscore in the name), uploaded Feb. 24, 2017. This older file has two owl:versionInfo properties. One is set to ?0.4? and one is set to ?1.6?. It also has a ?date? ontology-level annotation of "31.10.2016 23:58 GMT" 2) swo-inferred.owl (with a hyphen in the name), uploaded Oct. 22, 2019. This newer file has one owl:versionInfo property set to ?1.7?. It also has an rdfs:comment property set to "Date of release: 21.10.2019?. It appears that BioPortal successfully pulled the latest version of your ontology from the location you specified as a pull URL in GitHub. There is no need to do a manual upload first, then specify a pull URL for going forward. BioPortal will pull the initial version of your ontology from the URL you specify. With regard to the upload date, I?m guessing you edited the latest submission using the ?Edit latest submission? button, vs. adding a new submission? Submission objects are distinct in our data store. Historically speaking, we haven?t allowed the upload date of a submission to be modified once that submission is created in our system. For example, if you specify a pull URL for us to check nightly, every time BioPortal detects a new ontology source file at that location, the system will create a new submission object to represent that new version, and leave the prior version intact. However, there do appear to be situations like the one you describe below where editing an *existing* submission with a new ontology source file ends up showing a current date as the release date, but keeps the upload date as the old date when the submission object was initially created. We generally recommend creating a new submission if you?re uploading a new version and/or specifying a new pull URL for your ontology. I?m hoping that explanation was relatively clear. All of that said, I could do some manual work on your behalf to clean up current display of SWO. Possibilities that come to mind are deleting and recreating the 1.7 submission so that it has a current upload date, or deleting 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for your latest 1.7 version. Let me know. Kind regards, Jennifer > On Oct 23, 2019, at 11:37 AM, Jennifer Leigh Vendetti wrote: > > Hi Allyson, > > I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. > > Kind regards, > Jennifer > > >> On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: >> >> Dear Jennifer, >> >> Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? >> >> thanks very much, >> Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Allyson Lister >> Sent: 22 October 2019 19:51 >> To: Jennifer Leigh Vendetti; support at bioontology.org >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Thanks very much! >> >> :) Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Jennifer Leigh Vendetti >> Sent: 22 October 2019 19:10 >> To: support at bioontology.org >> Cc: Allyson Lister >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Hi Allyson, >> >> Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. >> >> Let us know if you have any further questions about updating the ontology metadata. >> >> Kind regards, >> Jennifer >> >> >> On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: >> >> >> Name: allysonlister >> >> Email: allyson.lister at oerc.ox.ac.uk >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount >> >> Feedback: >> >> Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com >> >> I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. >> >> Thanks, >> Allyson >> >> _______________________________________________ >> 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 From allyson.lister at oerc.ox.ac.uk Thu Oct 24 02:48:16 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Thu, 24 Oct 2019 09:48:16 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu>, <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu>, Message-ID: Hi Jennifer, I just realized I hadn't replied to the part of your message asking about the issue with version numbers. This was something I only noticed as I built the 1.7 release. What seems to have happened with the last couple of releases (and didn't happen with 1.7 due to a change in the way that we have built the ontology) is that some of EDAM's ontology annotation accidentally got copied across to SWO. So some of its descriptions/versions/titles were there mixed up with the SWO ontology annotations. That's been fixed, and you shouldn't see it again, and 1.6 is the correct value for the release before this one. Thanks again, Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Allyson Lister Sent: 24 October 2019 10:23 To: Jennifer Leigh Vendetti Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Dear Jennifer, Thanks very much for your reply. Yes, I began by making a new submission (originally) but deleted that and edited the most recent submission after I read this in the help pages: "If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology." I think I misunderstood what it said, and I thought that meant I should use an existing submission. Next time I'll make a new one. I really appreciate the full explanation, it's made things clearer for me. Please could you help me revert the original submission, by choosing your option above where we delete the 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for the latest 1.7 version? Thanks :) Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 23 October 2019 23:20 To: Allyson Lister Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi again Allyson, OK - SWO is displaying without errors in BioPortal now. Turns out there was a caching issue, unrelated to your ontology. I looked at the contents of the folder on our server that contains the files for the latest submission of SWO. I found two ontology source files in the directory: 1) swo_inferred.owl (with an underscore in the name), uploaded Feb. 24, 2017. This older file has two owl:versionInfo properties. One is set to ?0.4? and one is set to ?1.6?. It also has a ?date? ontology-level annotation of "31.10.2016 23:58 GMT" 2) swo-inferred.owl (with a hyphen in the name), uploaded Oct. 22, 2019. This newer file has one owl:versionInfo property set to ?1.7?. It also has an rdfs:comment property set to "Date of release: 21.10.2019?. It appears that BioPortal successfully pulled the latest version of your ontology from the location you specified as a pull URL in GitHub. There is no need to do a manual upload first, then specify a pull URL for going forward. BioPortal will pull the initial version of your ontology from the URL you specify. With regard to the upload date, I?m guessing you edited the latest submission using the ?Edit latest submission? button, vs. adding a new submission? Submission objects are distinct in our data store. Historically speaking, we haven?t allowed the upload date of a submission to be modified once that submission is created in our system. For example, if you specify a pull URL for us to check nightly, every time BioPortal detects a new ontology source file at that location, the system will create a new submission object to represent that new version, and leave the prior version intact. However, there do appear to be situations like the one you describe below where editing an *existing* submission with a new ontology source file ends up showing a current date as the release date, but keeps the upload date as the old date when the submission object was initially created. We generally recommend creating a new submission if you?re uploading a new version and/or specifying a new pull URL for your ontology. I?m hoping that explanation was relatively clear. All of that said, I could do some manual work on your behalf to clean up current display of SWO. Possibilities that come to mind are deleting and recreating the 1.7 submission so that it has a current upload date, or deleting 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for your latest 1.7 version. Let me know. Kind regards, Jennifer > On Oct 23, 2019, at 11:37 AM, Jennifer Leigh Vendetti wrote: > > Hi Allyson, > > I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. > > Kind regards, > Jennifer > > >> On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: >> >> Dear Jennifer, >> >> Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? >> >> thanks very much, >> Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Allyson Lister >> Sent: 22 October 2019 19:51 >> To: Jennifer Leigh Vendetti; support at bioontology.org >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Thanks very much! >> >> :) Allyson >> >> -- >> Dr. Allyson Lister >> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >> University of Oxford >> >> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >> https://www.eng.ox.ac.uk/people/allyson-lister/ >> >> ORCiD: 0000-0002-7702-4495 >> @allysonlister >> >> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >> >> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >> >> >> ________________________________________ >> From: Jennifer Leigh Vendetti >> Sent: 22 October 2019 19:10 >> To: support at bioontology.org >> Cc: Allyson Lister >> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >> >> Hi Allyson, >> >> Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. >> >> Let us know if you have any further questions about updating the ontology metadata. >> >> Kind regards, >> Jennifer >> >> >> On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: >> >> >> Name: allysonlister >> >> Email: allyson.lister at oerc.ox.ac.uk >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount >> >> Feedback: >> >> Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com >> >> I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. >> >> Thanks, >> Allyson >> >> _______________________________________________ >> 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 From vendetti at stanford.edu Thu Oct 24 13:00:14 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 24 Oct 2019 20:00:14 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu> Message-ID: <92D1327E-761B-4948-9D5A-DCBF63996449@stanford.edu> Hi Allyson, I deleted the last 1.7 submission, and recreated two new ones for 1.6 and 1.7. Let me know if you see anything that looks awry. Kind regards, Jennifer > On Oct 24, 2019, at 2:23 AM, Allyson Lister wrote: > > Dear Jennifer, > > Thanks very much for your reply. Yes, I began by making a new submission (originally) but deleted that and edited the most recent submission after I read this in the help pages: "If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology." I think I misunderstood what it said, and I thought that meant I should use an existing submission. Next time I'll make a new one. > > I really appreciate the full explanation, it's made things clearer for me. Please could you help me revert the original submission, by choosing your option above where we delete the 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for the latest 1.7 version? > > Thanks :) Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Jennifer Leigh Vendetti > Sent: 23 October 2019 23:20 > To: Allyson Lister > Cc: support at bioontology.org > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Hi again Allyson, > > OK - SWO is displaying without errors in BioPortal now. Turns out there was a caching issue, unrelated to your ontology. > > I looked at the contents of the folder on our server that contains the files for the latest submission of SWO. I found two ontology source files in the directory: > > 1) swo_inferred.owl (with an underscore in the name), uploaded Feb. 24, 2017. This older file has two owl:versionInfo properties. One is set to ?0.4? and one is set to ?1.6?. It also has a ?date? ontology-level annotation of "31.10.2016 23:58 GMT" > > 2) swo-inferred.owl (with a hyphen in the name), uploaded Oct. 22, 2019. This newer file has one owl:versionInfo property set to ?1.7?. It also has an rdfs:comment property set to "Date of release: 21.10.2019?. > > It appears that BioPortal successfully pulled the latest version of your ontology from the location you specified as a pull URL in GitHub. There is no need to do a manual upload first, then specify a pull URL for going forward. BioPortal will pull the initial version of your ontology from the URL you specify. > > With regard to the upload date, I?m guessing you edited the latest submission using the ?Edit latest submission? button, vs. adding a new submission? > > Submission objects are distinct in our data store. Historically speaking, we haven?t allowed the upload date of a submission to be modified once that submission is created in our system. For example, if you specify a pull URL for us to check nightly, every time BioPortal detects a new ontology source file at that location, the system will create a new submission object to represent that new version, and leave the prior version intact. > > However, there do appear to be situations like the one you describe below where editing an *existing* submission with a new ontology source file ends up showing a current date as the release date, but keeps the upload date as the old date when the submission object was initially created. > > We generally recommend creating a new submission if you?re uploading a new version and/or specifying a new pull URL for your ontology. > > I?m hoping that explanation was relatively clear. All of that said, I could do some manual work on your behalf to clean up current display of SWO. Possibilities that come to mind are deleting and recreating the 1.7 submission so that it has a current upload date, or deleting 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for your latest 1.7 version. Let me know. > > Kind regards, > Jennifer > > >> On Oct 23, 2019, at 11:37 AM, Jennifer Leigh Vendetti wrote: >> >> Hi Allyson, >> >> I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. >> >> Kind regards, >> Jennifer >> >> >>> On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: >>> >>> Dear Jennifer, >>> >>> Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? >>> >>> thanks very much, >>> Allyson >>> >>> -- >>> Dr. Allyson Lister >>> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >>> University of Oxford >>> >>> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >>> https://www.eng.ox.ac.uk/people/allyson-lister/ >>> >>> ORCiD: 0000-0002-7702-4495 >>> @allysonlister >>> >>> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >>> >>> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >>> >>> >>> ________________________________________ >>> From: Allyson Lister >>> Sent: 22 October 2019 19:51 >>> To: Jennifer Leigh Vendetti; support at bioontology.org >>> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >>> >>> Thanks very much! >>> >>> :) Allyson >>> >>> -- >>> Dr. Allyson Lister >>> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >>> University of Oxford >>> >>> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >>> https://www.eng.ox.ac.uk/people/allyson-lister/ >>> >>> ORCiD: 0000-0002-7702-4495 >>> @allysonlister >>> >>> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >>> >>> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >>> >>> >>> ________________________________________ >>> From: Jennifer Leigh Vendetti >>> Sent: 22 October 2019 19:10 >>> To: support at bioontology.org >>> Cc: Allyson Lister >>> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >>> >>> Hi Allyson, >>> >>> Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. >>> >>> Let us know if you have any further questions about updating the ontology metadata. >>> >>> Kind regards, >>> Jennifer >>> >>> >>> On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: >>> >>> >>> Name: allysonlister >>> >>> Email: allyson.lister at oerc.ox.ac.uk >>> >>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount >>> >>> Feedback: >>> >>> Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com >>> >>> I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. >>> >>> Thanks, >>> Allyson >>> >>> _______________________________________________ >>> 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 > From allyson.lister at oerc.ox.ac.uk Tue Oct 29 12:38:47 2019 From: allyson.lister at oerc.ox.ac.uk (Allyson Lister) Date: Tue, 29 Oct 2019 19:38:47 +0000 Subject: [bioontology-support] [BioPortal] Feedback from allysonlister In-Reply-To: <92D1327E-761B-4948-9D5A-DCBF63996449@stanford.edu> References: <5daed32039520_43bf2b09e77f50c872777@ncbo-prd-app-09.stanford.edu.mail> <8DBD822F-2FE6-49B1-B86A-91031794B853@stanford.edu> <58AD71CE-1CC1-48BC-9BE4-48EDFC407972@stanford.edu> <0795B562-EF25-47AA-B733-3A1358872B68@stanford.edu> , <92D1327E-761B-4948-9D5A-DCBF63996449@stanford.edu> Message-ID: Thanks very much, Jennifer, it all looks great. I really appreciate all your help, especially, as I didn't upload the new release correctly! Thanks again, and best wishes, Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing, Oxford e-Research Centre University of Oxford Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ https://www.eng.ox.ac.uk/people/allyson-lister/ ORCiD: 0000-0002-7702-4495 @allysonlister Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 ________________________________________ From: Jennifer Leigh Vendetti Sent: 24 October 2019 21:00 To: Allyson Lister Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister Hi Allyson, I deleted the last 1.7 submission, and recreated two new ones for 1.6 and 1.7. Let me know if you see anything that looks awry. Kind regards, Jennifer > On Oct 24, 2019, at 2:23 AM, Allyson Lister wrote: > > Dear Jennifer, > > Thanks very much for your reply. Yes, I began by making a new submission (originally) but deleted that and edited the most recent submission after I read this in the help pages: "If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology." I think I misunderstood what it said, and I thought that meant I should use an existing submission. Next time I'll make a new one. > > I really appreciate the full explanation, it's made things clearer for me. Please could you help me revert the original submission, by choosing your option above where we delete the 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for the latest 1.7 version? > > Thanks :) Allyson > > -- > Dr. Allyson Lister > Knowledge Engineer, FAIRsharing, Oxford e-Research Centre > University of Oxford > > Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ > https://www.eng.ox.ac.uk/people/allyson-lister/ > > ORCiD: 0000-0002-7702-4495 > @allysonlister > > Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. > > For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 > > > ________________________________________ > From: Jennifer Leigh Vendetti > Sent: 23 October 2019 23:20 > To: Allyson Lister > Cc: support at bioontology.org > Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister > > Hi again Allyson, > > OK - SWO is displaying without errors in BioPortal now. Turns out there was a caching issue, unrelated to your ontology. > > I looked at the contents of the folder on our server that contains the files for the latest submission of SWO. I found two ontology source files in the directory: > > 1) swo_inferred.owl (with an underscore in the name), uploaded Feb. 24, 2017. This older file has two owl:versionInfo properties. One is set to ?0.4? and one is set to ?1.6?. It also has a ?date? ontology-level annotation of "31.10.2016 23:58 GMT" > > 2) swo-inferred.owl (with a hyphen in the name), uploaded Oct. 22, 2019. This newer file has one owl:versionInfo property set to ?1.7?. It also has an rdfs:comment property set to "Date of release: 21.10.2019?. > > It appears that BioPortal successfully pulled the latest version of your ontology from the location you specified as a pull URL in GitHub. There is no need to do a manual upload first, then specify a pull URL for going forward. BioPortal will pull the initial version of your ontology from the URL you specify. > > With regard to the upload date, I?m guessing you edited the latest submission using the ?Edit latest submission? button, vs. adding a new submission? > > Submission objects are distinct in our data store. Historically speaking, we haven?t allowed the upload date of a submission to be modified once that submission is created in our system. For example, if you specify a pull URL for us to check nightly, every time BioPortal detects a new ontology source file at that location, the system will create a new submission object to represent that new version, and leave the prior version intact. > > However, there do appear to be situations like the one you describe below where editing an *existing* submission with a new ontology source file ends up showing a current date as the release date, but keeps the upload date as the old date when the submission object was initially created. > > We generally recommend creating a new submission if you?re uploading a new version and/or specifying a new pull URL for your ontology. > > I?m hoping that explanation was relatively clear. All of that said, I could do some manual work on your behalf to clean up current display of SWO. Possibilities that come to mind are deleting and recreating the 1.7 submission so that it has a current upload date, or deleting 1.7 and recreating two new submissions - one for the 1.6 version that got overwritten, and one for your latest 1.7 version. Let me know. > > Kind regards, > Jennifer > > >> On Oct 23, 2019, at 11:37 AM, Jennifer Leigh Vendetti wrote: >> >> Hi Allyson, >> >> I looked at SWO this morning, but BioPortal is displaying a 500 error for that ontology now. I?ll need to investigate further to see if I can get it cleaned up and displaying properly. Will keep you posted. >> >> Kind regards, >> Jennifer >> >> >>> On Oct 23, 2019, at 4:00 AM, Allyson Lister wrote: >>> >>> Dear Jennifer, >>> >>> Thanks again for your help. I've attempted to add a new release of SWO into the BioPortal entry. It shows that I updated the release yesterday, but that it hasn't been uploaded yet. I tried to upload it manually, and then reset it to pull automatically every night, but the upload date is still from 2017. Do you know if BioPortal attempted to download the new SWO file automatically last night? >>> >>> thanks very much, >>> Allyson >>> >>> -- >>> Dr. Allyson Lister >>> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >>> University of Oxford >>> >>> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >>> https://www.eng.ox.ac.uk/people/allyson-lister/ >>> >>> ORCiD: 0000-0002-7702-4495 >>> @allysonlister >>> >>> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >>> >>> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >>> >>> >>> ________________________________________ >>> From: Allyson Lister >>> Sent: 22 October 2019 19:51 >>> To: Jennifer Leigh Vendetti; support at bioontology.org >>> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >>> >>> Thanks very much! >>> >>> :) Allyson >>> >>> -- >>> Dr. Allyson Lister >>> Knowledge Engineer, FAIRsharing, Oxford e-Research Centre >>> University of Oxford >>> >>> Data Readiness Group: https://datareadiness.eng.ox.ac.uk/ >>> https://www.eng.ox.ac.uk/people/allyson-lister/ >>> >>> ORCiD: 0000-0002-7702-4495 >>> @allysonlister >>> >>> Please note that I work part time. If the matter is urgent, you may wish to email contact at fairsharing.org instead. >>> >>> For more on FAIRsharing, please see https://doi.org/10.1038/s41587-019-0080-8 >>> >>> >>> ________________________________________ >>> From: Jennifer Leigh Vendetti >>> Sent: 22 October 2019 19:10 >>> To: support at bioontology.org >>> Cc: Allyson Lister >>> Subject: Re: [bioontology-support] [BioPortal] Feedback from allysonlister >>> >>> Hi Allyson, >>> >>> Sure, no problem. I added your ?allysonlister? account as an administrator on SWO just now, and updated James Malone?s email address. >>> >>> Let us know if you have any further questions about updating the ontology metadata. >>> >>> Kind regards, >>> Jennifer >>> >>> >>> On Oct 22, 2019, at 3:00 AM, support at bioontology.org wrote: >>> >>> >>> Name: allysonlister >>> >>> Email: allyson.lister at oerc.ox.ac.uk >>> >>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount >>> >>> Feedback: >>> >>> Please could I be set as a manager of SWO (https://bioportal.bioontology.org/ontologies/SWO) as I am one of its main developers? James Malone is still involved, but he is better reached these days at james at scibite.com >>> >>> I'd like to ensure our latest release is uploaded to BioPortal properly, and to check and update the metadata. >>> >>> Thanks, >>> Allyson >>> >>> _______________________________________________ >>> 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 > From support at bioontology.org Tue Oct 29 10:19:47 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Oct 2019 10:19:47 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Hernis De La Cruz Message-ID: <5db874b312fa6_32a72b221ecb7c3880423@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mrbarnes at uw.edu Tue Oct 29 15:45:04 2019 From: mrbarnes at uw.edu (Megan Barnes) Date: Tue, 29 Oct 2019 15:45:04 -0700 Subject: [bioontology-support] VMWare Virtual Appliance Message-ID: Hello, I would like to request the NCBO Virtual Appliance product. I am working on a project using the annotator that requires that sensitive health record data remain on our servers, so a local installation of NCBO is necessary. Thanks, Megan Barnes -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Oct 31 14:00:13 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 31 Oct 2019 21:00:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Hernis De La Cruz In-Reply-To: <5db874b312fa6_32a72b221ecb7c3880423@ncbo-prd-app-09.stanford.edu.mail> References: <5db874b312fa6_32a72b221ecb7c3880423@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <37776023-1B55-43A5-94F9-448143887FDF@stanford.edu> Hi Hernis, Thank you for getting in touch with us. We obtain MEDDRA content via the UMLS Metathesaurus [1], released twice per year by the National Library of Medicine. The version we currently serve is 2019AA, which, for the moment, appears to be their latest release. According to their metadata for MEDDRA [2], UMLS 2019AA contains MEDDRA version "MDR21_1?. If that?s not the info you were looking for, your best bet is to contact the ontology maintainers to find out the specifics of their current release. Contact information is available at the link I provided below [2]. Thank you, Michael [1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html On Oct 29, 2019, at 10:19 AM, support at bioontology.org wrote: Name: Hernis De La Cruz Email: hernis.delacruz at mountsinai.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses Feedback: Hi, Is there a way to figure out what version the MedDRA database is currently? _______________________________________________ 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: