From support at bioontology.org Mon Feb 4 16:06:42 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 04 Feb 2019 16:06:42 -0800 Subject: [bioontology-support] [BioPortal] Feedback from mkalas Message-ID: <5c58d39265ca0_69872aed01419ad8224b@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Feb 6 04:18:24 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 06 Feb 2019 04:18:24 -0800 Subject: [bioontology-support] [BioPortal] Feedback from bramdewilde Message-ID: <5c5ad0904b10c_41d62ac720bda6e8497b3@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mmorine at gmail.com Wed Feb 6 08:28:02 2019 From: mmorine at gmail.com (Melissa M) Date: Wed, 6 Feb 2019 12:28:02 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance Message-ID: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO , then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-02-06 at 11.54.52 AM.png Type: image/png Size: 131035 bytes Desc: not available URL: From support at bioontology.org Wed Feb 6 11:06:31 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 06 Feb 2019 11:06:31 -0800 Subject: [bioontology-support] [BioPortal] Feedback from davidnarganes Message-ID: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Feb 6 11:23:48 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 6 Feb 2019 19:23:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from bramdewilde In-Reply-To: <5c5ad0904b10c_41d62ac720bda6e8497b3@ncbo-prd-app-08.stanford.edu.mail> References: <5c5ad0904b10c_41d62ac720bda6e8497b3@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Bram, Thank you for contacting us. The browser tab page may have been unavailable briefly due to a brief downtime we?ve experienced. You should be able to submit your ontology now. http://bioportal.bioontology.org/ontologies/new Let us know if you require additional assistance. Thanks, Michael On Feb 6, 2019, at 4:18 AM, support at bioontology.org wrote: Name: bramdewilde Email: bram.dewilde at uzgent.be Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hi guys, Great resource, we use it as an input for our redcap instance. I wanted to submit ICD-0-3 codes as an ontology resource, but the browse tab seems to be down. kind regards, Bram _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Feb 6 11:42:55 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 6 Feb 2019 19:42:55 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Feb 6 17:02:06 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 7 Feb 2019 01:02:06 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: Hi Melissa, Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. Thanks, Michael On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Feb 6 18:27:53 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 7 Feb 2019 02:27:53 +0000 Subject: [bioontology-support] [BioPortal] Feedback from davidnarganes In-Reply-To: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail> References: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <94126083-E43E-4225-86A7-0371F84CAF3C@stanford.edu> Hi David, Thank you for contacting us. Just to clarify, are you attempting to use our publicly available SPARQL endpoint? http://sparql.bioontology.org/ If that?s the case, please note that we haven?t been maintaining it consistent with our latest code releases and ontology repository. The data contained in that endpoint is at least five-to-six years old. We have a very small engineering team, and we try to focus our efforts on a path of providing new services with an up-to-date content. Unfortunately, the SPARQL endpoint (at least at present) isn?t on that list. That said, if you are trying to retrieve subclasses of the term ?disease? in SNOMEDCT, the two REST services below are available to assist you. They both return a paginated list that you can iterate over programmatically. Direct children: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/children All descendants: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/descendants For more info on our REST API, navigate here: http://data.bioontology.org/documentation Hope this helps! Michael On Feb 6, 2019, at 11:06 AM, support at bioontology.org wrote: Name: davidnarganes Email: dnarganes at dundee.ac.uk Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3D404177007 Feedback: email: david.narganes95 at gmail.com Dear Sir/Madame, I can't use the property path expressions in SPARQL 1.1. Please see ```rdfs:subClassOf*``` in the SPARQL query below. I cannot get all the direct and indirect subclasses of the concept "disease". Could you please actualise it? Many thanks, David SPARQL query: ``` PREFIX rdfs: PREFIX rdf: PREFIX snomedct: PREFIX skos: SELECT DISTINCT ?x ?label ?syn FROM WHERE { ?x rdfs:subClassOf* snomedct:64572001 . ?x skos:prefLabel ?label . ?x skos:altLabel ?syn } ORDER BY ?label ``` _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonquet at lirmm.fr Wed Feb 6 23:24:21 2019 From: jonquet at lirmm.fr (Clement Jonquet) Date: Thu, 7 Feb 2019 08:24:21 +0100 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: Melissa, A complementary note: @misha, @john BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented. But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly. NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export. MeSH is also concerned as there is now an OWL file produced by NLM. @melissa I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the ? Edit submission information ? page. Bye Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- > Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : > > Hi Melissa, > > Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. > > Thanks, > > Michael > > > >> On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: >> >> Hi Michael, >> Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? >> Thanks again, >> Melissa >> >> >> On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: >> Hi Melissa, >> >> Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: >> >> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >> >> The page contains an alphabetical list of all the terminologies contained in the UMLS. >> >> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. >> >> Thanks, >> >> Michael >> >> [1] https://www.nlm.nih.gov/research/umls/ >> >> >> >> >>> On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: >>> >>> Hello, >>> I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. >>> So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jarprovided by IHTSDO , then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. >>> So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. >>> My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? >>> Thanks in advance for any info, >>> Melissa >>> >>> _______________________________________________ >>> 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 mmorine at gmail.com Wed Feb 6 12:10:03 2019 From: mmorine at gmail.com (Melissa M) Date: Wed, 6 Feb 2019 16:10:03 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: > Hi Melissa, > > Thanks for contacting us again. Twice per year we do a bulk import of > terminologies distributed by the UMLS [1]. (They have a twice per year > release schedule, e.g., for this year it will be 2019AA and 2019AB). > SNOMEDCT is one of the terminologies contained in the UMLS distribution. > So, the version numbers for SNOMEDCT that you see in BioPortal correspond > to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their > distributions can be found here: > > https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html > > The page contains an alphabetical list of all the terminologies contained > in the UMLS. > > Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only > assume that may contain either a different version from the one we have in > BioPortal; or a version that may not have all the properties fully > populated. > > Thanks, > > Michael > > [1] https://www.nlm.nih.gov/research/umls/ > > > > > On Feb 6, 2019, at 8:28 AM, Melissa M wrote: > > Hello, > I've recently been discussing with your team regarding use of FoodOn in > the virtual appliance but thought I'd write separately about this question > since it's unrelated to the other. > So far I've been able to import ontologies and perform annotations more or > less successfully, apart from the FoodOn issue that I've already written > about. Now I'm trying to import SNOMED CT but am noticing some issues. > First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED > OWL toolkit jar provided by IHTSDO > , then imported the > resulting owl into my virtual appliance using default settings (i.e., > selected OWL format, and no changes to prefLabel/altLabel/etc properties). > The resulting ontology appears to contain all classes in the class browser, > and I can annotate text that contains exact prefLabels of the SNOMED > ontology, but it's missing many of the fields that are present in the > SNOMED instance on the bioportal server (such as synonyms, altLabels, > etc.). I therefore can't annotate any text that contains SNOMED altLabels > and synonyms. I've attached a screenshot of the SNOMED class browser in my > virtual appliance to hopefully show what I mean. > So I'm trying to figure out if I went wrong in my conversion to owl, or > import into the VA. > My question is, was the instance of SNOMED on the bioportal server > produced using the toolkit from IHTSDO? And when importing into bioportal, > were non-default settings used? > Thanks in advance for any info, > Melissa > > > _______________________________________________ > 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 mmorine at gmail.com Thu Feb 7 03:22:10 2019 From: mmorine at gmail.com (Melissa M) Date: Thu, 7 Feb 2019 07:22:10 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: Hi Clement, Thanks very much for your reply. Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look? About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS. Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions? Thanks again for your help! Melissa On Thu, 7 Feb 2019 at 03:24, Clement Jonquet wrote: > Melissa, > > A complementary note: > > @misha, @john > BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool > as documented. > But eventually, now that Snomed International (new name for IHTSDO) > provide an OWL file directly, it will be interesting one day to drop the > import from UMLS and take the OWL directly. > NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS > but not imported thru the UMLS export. > MeSH is also concerned as there is now an OWL file produced by NLM. > > @melissa > I bet the problem you have with the synonyms in the OWL version of > SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right > property for synonyms in the ? Edit submission information ? page. > > Bye > Clement > > ------------------------------------------------------------------------------------------- > Dr. Clement JONQUET - PhD in Informatics - Assistant Professor > University of Montpellier (LIRMM) > > ------------------------------------------------------------------------------------------- > > Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : > > Hi Melissa, > > Yes, that is the script that is being used to import UMLS ontologies into > a virtual appliance. It hasn?t been updated since 2016, but it should > still be valid. Let us know if you run into any issues importing. > > Thanks, > > Michael > > > > On Feb 6, 2019, at 12:10 PM, Melissa M wrote: > > Hi Michael, > Thank you very much for your response. Can you confirm that the pipeline > described here > is > the one currently used to import UMLS content into bioportal? I'm assuming > that NCBO does not provide downloads of the output files from this pipeline > (I think in ttl format)? > Thanks again, > Melissa > > > On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: > >> Hi Melissa, >> >> Thanks for contacting us again. Twice per year we do a bulk import of >> terminologies distributed by the UMLS [1]. (They have a twice per year >> release schedule, e.g., for this year it will be 2019AA and 2019AB). >> SNOMEDCT is one of the terminologies contained in the UMLS distribution. >> So, the version numbers for SNOMEDCT that you see in BioPortal correspond >> to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their >> distributions can be found here: >> >> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >> >> The page contains an alphabetical list of all the terminologies contained >> in the UMLS. >> >> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only >> assume that may contain either a different version from the one we have in >> BioPortal; or a version that may not have all the properties fully >> populated. >> >> Thanks, >> >> Michael >> >> [1] https://www.nlm.nih.gov/research/umls/ >> >> >> >> >> On Feb 6, 2019, at 8:28 AM, Melissa M wrote: >> >> Hello, >> I've recently been discussing with your team regarding use of FoodOn in >> the virtual appliance but thought I'd write separately about this question >> since it's unrelated to the other. >> So far I've been able to import ontologies and perform annotations more >> or less successfully, apart from the FoodOn issue that I've already written >> about. Now I'm trying to import SNOMED CT but am noticing some issues. >> First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED >> OWL toolkit jar provided by IHTSDO >> , then imported the >> resulting owl into my virtual appliance using default settings (i.e., >> selected OWL format, and no changes to prefLabel/altLabel/etc properties). >> The resulting ontology appears to contain all classes in the class browser, >> and I can annotate text that contains exact prefLabels of the SNOMED >> ontology, but it's missing many of the fields that are present in the >> SNOMED instance on the bioportal server (such as synonyms, altLabels, >> etc.). I therefore can't annotate any text that contains SNOMED altLabels >> and synonyms. I've attached a screenshot of the SNOMED class browser in my >> virtual appliance to hopefully show what I mean. >> So I'm trying to figure out if I went wrong in my conversion to owl, or >> import into the VA. >> My question is, was the instance of SNOMED on the bioportal server >> produced using the toolkit from IHTSDO? And when importing into bioportal, >> were non-default settings used? >> Thanks in advance for any info, >> Melissa >> >> >> _______________________________________________ >> 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 d.narganes at dundee.ac.uk Thu Feb 7 03:08:59 2019 From: d.narganes at dundee.ac.uk (David Narganes (PG Research)) Date: Thu, 7 Feb 2019 11:08:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from davidnarganes In-Reply-To: <94126083-E43E-4225-86A7-0371F84CAF3C@stanford.edu> References: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail>, <94126083-E43E-4225-86A7-0371F84CAF3C@stanford.edu> Message-ID: Hi Michael, Many thanks, I have what I wanted now. One last thing, the REST services do not contain all "synonyms/altLabels". E.g. Anemia: REST: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2 but I found them here: http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=271737000 Thanks again. Best regards, David ________________________________ From: Michael Dorf Sent: 07 February 2019 02:27 To: support at bioontology.org Cc: David Narganes (PG Research) Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes Hi David, Thank you for contacting us. Just to clarify, are you attempting to use our publicly available SPARQL endpoint? http://sparql.bioontology.org/ If that?s the case, please note that we haven?t been maintaining it consistent with our latest code releases and ontology repository. The data contained in that endpoint is at least five-to-six years old. We have a very small engineering team, and we try to focus our efforts on a path of providing new services with an up-to-date content. Unfortunately, the SPARQL endpoint (at least at present) isn?t on that list. That said, if you are trying to retrieve subclasses of the term ?disease? in SNOMEDCT, the two REST services below are available to assist you. They both return a paginated list that you can iterate over programmatically. Direct children: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/children All descendants: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/descendants For more info on our REST API, navigate here: http://data.bioontology.org/documentation Hope this helps! Michael On Feb 6, 2019, at 11:06 AM, support at bioontology.org wrote: Name: davidnarganes Email: dnarganes at dundee.ac.uk Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3D404177007 Feedback: email: david.narganes95 at gmail.com Dear Sir/Madame, I can't use the property path expressions in SPARQL 1.1. Please see ```rdfs:subClassOf*``` in the SPARQL query below. I cannot get all the direct and indirect subclasses of the concept "disease". Could you please actualise it? Many thanks, David SPARQL query: ``` PREFIX rdfs: PREFIX rdf: PREFIX snomedct: PREFIX skos: SELECT DISTINCT ?x ?label ?syn FROM WHERE { ?x rdfs:subClassOf* snomedct:64572001 . ?x skos:prefLabel ?label . ?x skos:altLabel ?syn } ORDER BY ?label ``` _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Feb 7 09:36:46 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 7 Feb 2019 17:36:46 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: , Message-ID: Hi Melissa, let me refresh my memory about the .ttl and get back to you directly. John ________________________________ From: bioontology-support on behalf of Melissa M Sent: Thursday, February 7, 2019 09:28 To: Clement Jonquet Cc: support at bioontology.org Subject: Re: [bioontology-support] Use of SNOMED CT in virtual appliance Hi Clement, Thanks very much for your reply. Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look? About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS. Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions? Thanks again for your help! Melissa On Thu, 7 Feb 2019 at 03:24, Clement Jonquet > wrote: Melissa, A complementary note: @misha, @john BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented. But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly. NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export. MeSH is also concerned as there is now an OWL file produced by NLM. @melissa I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the ? Edit submission information ? page. Bye Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- Le 7 f?vr. 2019 ? 02:02, Michael Dorf > a ?crit : Hi Melissa, Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. Thanks, Michael On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Feb 7 13:36:01 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 7 Feb 2019 21:36:01 +0000 Subject: [bioontology-support] [BioPortal] Feedback from davidnarganes In-Reply-To: References: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail> <94126083-E43E-4225-86A7-0371F84CAF3C@stanford.edu> Message-ID: Hi David, The properties that we don?t store directly in our ontology model are placed in the ?properties? collection. You can get these values by adding a few extra parameters to the REST call: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2&include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties Let me know if this is what you wanted. Michael On Feb 7, 2019, at 3:08 AM, David Narganes (PG Research) > wrote: Hi Michael, Many thanks, I have what I wanted now. One last thing, the REST services do not contain all "synonyms/altLabels". E.g. Anemia: REST: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2 but I found them here: http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=271737000 Thanks again. Best regards, David ________________________________ From: Michael Dorf > Sent: 07 February 2019 02:27 To: support at bioontology.org Cc: David Narganes (PG Research) Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes Hi David, Thank you for contacting us. Just to clarify, are you attempting to use our publicly available SPARQL endpoint? http://sparql.bioontology.org/ If that?s the case, please note that we haven?t been maintaining it consistent with our latest code releases and ontology repository. The data contained in that endpoint is at least five-to-six years old. We have a very small engineering team, and we try to focus our efforts on a path of providing new services with an up-to-date content. Unfortunately, the SPARQL endpoint (at least at present) isn?t on that list. That said, if you are trying to retrieve subclasses of the term ?disease? in SNOMEDCT, the two REST services below are available to assist you. They both return a paginated list that you can iterate over programmatically. Direct children: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/children All descendants: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/descendants For more info on our REST API, navigate here: http://data.bioontology.org/documentation Hope this helps! Michael On Feb 6, 2019, at 11:06 AM, support at bioontology.org wrote: Name: davidnarganes Email: dnarganes at dundee.ac.uk Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3D404177007 Feedback: email: david.narganes95 at gmail.com Dear Sir/Madame, I can't use the property path expressions in SPARQL 1.1. Please see ```rdfs:subClassOf*``` in the SPARQL query below. I cannot get all the direct and indirect subclasses of the concept "disease". Could you please actualise it? Many thanks, David SPARQL query: ``` PREFIX rdfs: PREFIX rdf: PREFIX snomedct: PREFIX skos: SELECT DISTINCT ?x ?label ?syn FROM WHERE { ?x rdfs:subClassOf* snomedct:64572001 . ?x skos:prefLabel ?label . ?x skos:altLabel ?syn } ORDER BY ?label ``` _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.narganes at dundee.ac.uk Fri Feb 8 01:54:02 2019 From: d.narganes at dundee.ac.uk (David Narganes (PG Research)) Date: Fri, 8 Feb 2019 09:54:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from davidnarganes In-Reply-To: References: <5c5b30378c6bd_60f82b0469708af832620@ncbo-prd-app-08.stanford.edu.mail> <94126083-E43E-4225-86A7-0371F84CAF3C@stanford.edu> , Message-ID: Hi Michael, Yes, thanks. It is what I wanted. Nevertheless, I receive an internal server error when querying for all "descendants" of disease AND their "properties": http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/descendants?page=2&include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties but it's fine with "descendants" but not "properties": http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/descendants?page=2&include=prefLabel,synonym,definition,cui,semanticType,obsolete Don't worry, I got all the altLabels with a webcrawler with the URIs of the descendants. Many thanks Michael, Regards, David ________________________________ From: Michael Dorf Sent: 07 February 2019 21:36 To: David Narganes (PG Research) Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes Hi David, The properties that we don?t store directly in our ontology model are placed in the ?properties? collection. You can get these values by adding a few extra parameters to the REST call: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2&include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties Let me know if this is what you wanted. Michael On Feb 7, 2019, at 3:08 AM, David Narganes (PG Research) > wrote: Hi Michael, Many thanks, I have what I wanted now. One last thing, the REST services do not contain all "synonyms/altLabels". E.g. Anemia: REST: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2 but I found them here: http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=271737000 Thanks again. Best regards, David ________________________________ From: Michael Dorf > Sent: 07 February 2019 02:27 To: support at bioontology.org Cc: David Narganes (PG Research) Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes Hi David, Thank you for contacting us. Just to clarify, are you attempting to use our publicly available SPARQL endpoint? http://sparql.bioontology.org/ If that?s the case, please note that we haven?t been maintaining it consistent with our latest code releases and ontology repository. The data contained in that endpoint is at least five-to-six years old. We have a very small engineering team, and we try to focus our efforts on a path of providing new services with an up-to-date content. Unfortunately, the SPARQL endpoint (at least at present) isn?t on that list. That said, if you are trying to retrieve subclasses of the term ?disease? in SNOMEDCT, the two REST services below are available to assist you. They both return a paginated list that you can iterate over programmatically. Direct children: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/children All descendants: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/descendants For more info on our REST API, navigate here: http://data.bioontology.org/documentation Hope this helps! Michael On Feb 6, 2019, at 11:06 AM, support at bioontology.org wrote: Name: davidnarganes Email: dnarganes at dundee.ac.uk Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3D404177007 Feedback: email: david.narganes95 at gmail.com Dear Sir/Madame, I can't use the property path expressions in SPARQL 1.1. Please see ```rdfs:subClassOf*``` in the SPARQL query below. I cannot get all the direct and indirect subclasses of the concept "disease". Could you please actualise it? Many thanks, David SPARQL query: ``` PREFIX rdfs: PREFIX rdf: PREFIX snomedct: PREFIX skos: SELECT DISTINCT ?x ?label ?syn FROM WHERE { ?x rdfs:subClassOf* snomedct:64572001 . ?x skos:prefLabel ?label . ?x skos:altLabel ?syn } ORDER BY ?label ``` _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support The University of Dundee is a registered Scottish Charity, No: SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mmorine at gmail.com Fri Feb 8 08:04:39 2019 From: mmorine at gmail.com (Melissa M) Date: Fri, 8 Feb 2019 12:04:39 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: <23537ED9-F37F-4B72-B2C4-013DB52C65B3@lirmm.fr> References: <23537ED9-F37F-4B72-B2C4-013DB52C65B3@lirmm.fr> Message-ID: Hi Clement, Thanks for your reply. Here are a few examples: Looking at the FoodOn entry here (which comes from the langual_import.owl file), I find that searching the "Preferred Name" and "Synonyms" (which has the same entries as "has narrow synonym") fields in the annotator do produce results. However none of the synonyms in the "has synonym" field produce any result. An example from the base foodon.owl file is here . The preferred name is searchable but "has synonym" field is not. I found that the entries that are pulled in from the ncbi_taxon.owl import do not have the same problem. For example in this entry, both the preferred name and synonyms are searchable, however the synonyms are tagged as "hasExactSynonym" instead. So basically the problem seems to be related to the "has synonym" field, and exists across multiple files (that is, both the base foodon.owl and at least langual_import.owl). I've looked in the .owl files to see if there are obvious differences in the metadata for these different fields and don't see anything, but then I'm still learning and am not sure exactly what I'm looking for. Thank you for your help and have a nice weekend. Melissa On Fri, 8 Feb 2019 at 05:41, Clement Jonquet wrote: > Hi Melissa, all, > > See inline. > > Le 7 f?vr. 2019 ? 12:22, Melissa M a ?crit : > > Hi Clement, > Thanks very much for your reply. > > Regarding the FoodOn issue, I should mention 2 things: 1) I have the same > problem both on my VA and on bioportal, and 2) synonyms are properly > recognized for some classes and not for others. I've looked at the .owl > files to see if I could find any differences in specification of classes > whose synonyms are recognized and those whose synonyms aren't recognized, > and I couldn't find anything. I'd be happy to provide a few class names as > examples if you have time to have a look? > > > Please do so. > > About the SNOMED issue, I contacted IHTSDO and just heard back this > morning that the "toolkit is only currently capable of including the Fully > Specified Name of concepts" but they're opening my issue as a new feature. > In the meantime I'll start working through the pipeline that you use for > importing UMLS. > > > Interesting ;) > It means it worth asking. Indeed, there is n o point doing a semantic > resource, if it does not include the synonyms. > > > Alternatively, would you be able to provide access to the SNOMED .ttl or > are there license restrictions? > > Thanks again for your help! > Melissa > > > > On Thu, 7 Feb 2019 at 03:24, Clement Jonquet wrote: > >> Melissa, >> >> A complementary note: >> >> @misha, @john >> BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool >> as documented. >> But eventually, now that Snomed International (new name for IHTSDO) >> provide an OWL file directly, it will be interesting one day to drop the >> import from UMLS and take the OWL directly. >> NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS >> but not imported thru the UMLS export. >> MeSH is also concerned as there is now an OWL file produced by NLM. >> >> @melissa >> I bet the problem you have with the synonyms in the OWL version of >> SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right >> property for synonyms in the ? Edit submission information ? page. >> >> Bye >> Clement >> >> ------------------------------------------------------------------------------------------- >> Dr. Clement JONQUET - PhD in Informatics - Assistant Professor >> University of Montpellier (LIRMM) >> >> ------------------------------------------------------------------------------------------- >> >> Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : >> >> Hi Melissa, >> >> Yes, that is the script that is being used to import UMLS ontologies into >> a virtual appliance. It hasn?t been updated since 2016, but it should >> still be valid. Let us know if you run into any issues importing. >> >> Thanks, >> >> Michael >> >> >> >> On Feb 6, 2019, at 12:10 PM, Melissa M wrote: >> >> Hi Michael, >> Thank you very much for your response. Can you confirm that the pipeline >> described here >> is >> the one currently used to import UMLS content into bioportal? I'm assuming >> that NCBO does not provide downloads of the output files from this pipeline >> (I think in ttl format)? >> Thanks again, >> Melissa >> >> >> On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: >> >>> Hi Melissa, >>> >>> Thanks for contacting us again. Twice per year we do a bulk import of >>> terminologies distributed by the UMLS [1]. (They have a twice per year >>> release schedule, e.g., for this year it will be 2019AA and 2019AB). >>> SNOMEDCT is one of the terminologies contained in the UMLS distribution. >>> So, the version numbers for SNOMEDCT that you see in BioPortal correspond >>> to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their >>> distributions can be found here: >>> >>> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >>> >>> The page contains an alphabetical list of all the terminologies >>> contained in the UMLS. >>> >>> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only >>> assume that may contain either a different version from the one we have in >>> BioPortal; or a version that may not have all the properties fully >>> populated. >>> >>> Thanks, >>> >>> Michael >>> >>> [1] https://www.nlm.nih.gov/research/umls/ >>> >>> >>> >>> >>> On Feb 6, 2019, at 8:28 AM, Melissa M wrote: >>> >>> Hello, >>> I've recently been discussing with your team regarding use of FoodOn in >>> the virtual appliance but thought I'd write separately about this question >>> since it's unrelated to the other. >>> So far I've been able to import ontologies and perform annotations more >>> or less successfully, apart from the FoodOn issue that I've already written >>> about. Now I'm trying to import SNOMED CT but am noticing some issues. >>> First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED >>> OWL toolkit jar provided by IHTSDO >>> , then imported the >>> resulting owl into my virtual appliance using default settings (i.e., >>> selected OWL format, and no changes to prefLabel/altLabel/etc properties). >>> The resulting ontology appears to contain all classes in the class browser, >>> and I can annotate text that contains exact prefLabels of the SNOMED >>> ontology, but it's missing many of the fields that are present in the >>> SNOMED instance on the bioportal server (such as synonyms, altLabels, >>> etc.). I therefore can't annotate any text that contains SNOMED altLabels >>> and synonyms. I've attached a screenshot of the SNOMED class browser in my >>> virtual appliance to hopefully show what I mean. >>> So I'm trying to figure out if I went wrong in my conversion to owl, or >>> import into the VA. >>> My question is, was the instance of SNOMED on the bioportal server >>> produced using the toolkit from IHTSDO? And when importing into bioportal, >>> were non-default settings used? >>> Thanks in advance for any info, >>> Melissa >>> >>> >>> _______________________________________________ >>> 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 support at bioontology.org Thu Feb 7 12:58:45 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 07 Feb 2019 12:58:45 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Amelie GYRARD Message-ID: <5c5c9c05219b5_32222ababdf7bb18464f@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From john.zobolas at ntnu.no Fri Feb 8 03:57:15 2019 From: john.zobolas at ntnu.no (John Zobolas) Date: Fri, 8 Feb 2019 11:57:15 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> References: , <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> Message-ID: <1549627035257.30535@ntnu.no> Hi, The issue is that the MI ontology in the OBOfoundry page is updated but the BioPortal version? in not synced yet to the current/newest version. Could you please update it? BR, John ________________________________________ From: Pablo Porras Millan Sent: Friday, February 8, 2019 12:41 PM To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk) Cc: John Zobolas Subject: Re: MI update on Bioportal? Dear Vasundra, I have no idea how BioPortal gets updated, but our reference github repo is up to date and shows the latest version of the CV in OLS: https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. Our OBOfoundry page also seems tobe up to date (http://obofoundry.org/ontology/mi.html). We have never updated BioPortal manually and I am certainly not willing to start now, so I assume they have some sort of procedure to do these updates. Can you use an alternative source for theCV? Cheers, Pablo. On 08/02/2019 08:28, Vasundra Tour? wrote: > Dear Pablo and Sandra, > > I have looked at the MI terms in Bioportal and it seems like they are > not updated. (see Causal Regulatory Mechanism branch > https://bit.ly/2DYI5VM). > > Isn't it suppose to be an automatic update from Bioportal? Or do you > have to submit the changes from your side? > > Just wanted to point out this issue. > > Thanks! > > Best regards, > Vasundra > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 8 12:45:11 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 8 Feb 2019 20:45:11 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: <1549627035257.30535@ntnu.no> References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no> Message-ID: Hello Pablo & Vasundra, BioPortal provides functionality that gives end users the ability to enter a URL that is checked on a nightly basis for new versions of their ontology. The MI ontology entry in BioPortal is currently configured to check the following URL nightly: http://purl.obolibrary.org/obo/mi.owl We got this URL from your OBO Foundry page. One thing to note here is that we are currently serving the OWL version of your ontology. The GitHub URL you provided below references the OBO version of your ontology. Is the implication here that you?d rather we be serving the OBO version, and have our system configured to pull from GitHub? Thanks for any clarification you can provide here. Kind regards, Jennifer On Feb 8, 2019, at 3:57 AM, John Zobolas > wrote: Hi, The issue is that the MI ontology in the OBOfoundry page is updated but the BioPortal version? in not synced yet to the current/newest version. Could you please update it? BR, John ________________________________________ From: Pablo Porras Millan > Sent: Friday, February 8, 2019 12:41 PM To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk) Cc: John Zobolas Subject: Re: MI update on Bioportal? Dear Vasundra, I have no idea how BioPortal gets updated, but our reference github repo is up to date and shows the latest version of the CV in OLS: https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. Our OBOfoundry page also seems tobe up to date (http://obofoundry.org/ontology/mi.html). We have never updated BioPortal manually and I am certainly not willing to start now, so I assume they have some sort of procedure to do these updates. Can you use an alternative source for theCV? Cheers, Pablo. On 08/02/2019 08:28, Vasundra Tour? wrote: > Dear Pablo and Sandra, > > I have looked at the MI terms in Bioportal and it seems like they are > not updated. (see Causal Regulatory Mechanism branch > https://bit.ly/2DYI5VM). > > Isn't it suppose to be an automatic update from Bioportal? Or do you > have to submit the changes from your side? > > Just wanted to point out this issue. > > Thanks! > > Best regards, > Vasundra > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- _______________________________________________ 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 Fri Feb 8 14:36:18 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 8 Feb 2019 22:36:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Amelie GYRARD In-Reply-To: <5c5c9c05219b5_32222ababdf7bb18464f@ncbo-prd-app-09.stanford.edu.mail> References: <5c5c9c05219b5_32222ababdf7bb18464f@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Amelie, Thanks for your questions. A) The reason there are no OWL links for the MEDDRA ontology is that its UMLS license precludes re-distribution of the ontology. You may wish to explore using our umls2rdf software at https://github.com/ncbo/umls2rdf to do the conversion yourself, or pursue getting the ontology directly through MEDDRA. B) You are correct, that widget (and the ones below it) are not operational right now. We have an open ticket at https://github.com/ncbo/bioportal_web_ui/issues/79 and intend to address this as soon as we can, but it is not something we will get to in the short term. C) We have a SPARQL endpoint, but it is a beta service and its content is several years old. You can find more about it at https://sparql.bioontology.org. Our intention is to replace this service once we have upgraded our back end triple store; that will not be for at least several months. Sorry for all the unfortunate news; rest assured we are trying to work through these services to provide and update them as soon as we can we can. John On Feb 7, 2019, at 12:58 PM, support at bioontology.org wrote: Name: Amelie GYRARD Email: amelie at knoesis.org Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses Feedback: I would like to download the MEDDRA ontology code, but links are unsuccessful. Example 1: http://bioportal.bioontology.org/ontologies/MEDDRA I clicked on Submissions/Version 2018 AAAA which redirects to http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes Example 2: http://bioportal.bioontology.org/ontologies/MEDDRA?p=widgets When I clicked on Widget type Jumpt to get code notting happens. I would like to later write SPARQL queries. Is there any SPARQL endpoints? Thank you very much for your precious help. _______________________________________________ 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 john.zobolas at ntnu.no Sat Feb 9 01:35:32 2019 From: john.zobolas at ntnu.no (John Zobolas) Date: Sat, 9 Feb 2019 09:35:32 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no>, Message-ID: <1549704933590.54763@ntnu.no> ?Hi Pablo, See the issue below. Maybe the .owl file that they pull is not the one with the changes? BR, John. ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 8, 2019 9:45 PM To: John Zobolas Cc: support at bioontology.org; Vasundra Tour? Subject: Re: [bioontology-support] MI update on Bioportal? Hello Pablo & Vasundra, BioPortal provides functionality that gives end users the ability to enter a URL that is checked on a nightly basis for new versions of their ontology. The MI ontology entry in BioPortal is currently configured to check the following URL nightly: http://purl.obolibrary.org/obo/mi.owl We got this URL from your OBO Foundry page. One thing to note here is that we are currently serving the OWL version of your ontology. The GitHub URL you provided below references the OBO version of your ontology. Is the implication here that you'd rather we be serving the OBO version, and have our system configured to pull from GitHub? Thanks for any clarification you can provide here. Kind regards, Jennifer On Feb 8, 2019, at 3:57 AM, John Zobolas > wrote: Hi, The issue is that the MI ontology in the OBOfoundry page is updated but the BioPortal version? in not synced yet to the current/newest version. Could you please update it? BR, John ________________________________________ From: Pablo Porras Millan > Sent: Friday, February 8, 2019 12:41 PM To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk) Cc: John Zobolas Subject: Re: MI update on Bioportal? Dear Vasundra, I have no idea how BioPortal gets updated, but our reference github repo is up to date and shows the latest version of the CV in OLS: https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. Our OBOfoundry page also seems tobe up to date (http://obofoundry.org/ontology/mi.html). We have never updated BioPortal manually and I am certainly not willing to start now, so I assume they have some sort of procedure to do these updates. Can you use an alternative source for theCV? Cheers, Pablo. On 08/02/2019 08:28, Vasundra Tour? wrote: > Dear Pablo and Sandra, > > I have looked at the MI terms in Bioportal and it seems like they are > not updated. (see Causal Regulatory Mechanism branch > https://bit.ly/2DYI5VM). > > Isn't it suppose to be an automatic update from Bioportal? Or do you > have to submit the changes from your side? > > Just wanted to point out this issue. > > Thanks! > > Best regards, > Vasundra > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- _______________________________________________ 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 Jamie.OSBORNE at swift.com Sun Feb 10 12:52:42 2019 From: Jamie.OSBORNE at swift.com (OSBORNE Jamie) Date: Sun, 10 Feb 2019 20:52:42 +0000 Subject: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? Message-ID: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> Hi NCBO team, Impressive work - I?d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I?m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022 and ISO 15022 financial information interchange standards. Under ISO TC68/SC9/WG1 , I?m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance. Our work is currently too experimental to be shared more broadly, so we?d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature. Greatly appreciate your help to get up and running with a local instance. Thanks! Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 4566 bytes Desc: not available URL: From john.zobolas at ntnu.no Mon Feb 11 02:20:16 2019 From: john.zobolas at ntnu.no (John Zobolas) Date: Mon, 11 Feb 2019 10:20:16 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: <435b7c31-5087-d011-c7c8-0b9b4f17b752@ebi.ac.uk> References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no> <1549704933590.54763@ntnu.no>, <435b7c31-5087-d011-c7c8-0b9b4f17b752@ebi.ac.uk> Message-ID: <1549880415913.73989@ntnu.no> Hi Jennifer and Pablo, This issue was found by Vasundra when she saw that terms like 'indirect causal regulation' are still mentioned in the BioPortal GUI (see here). If you ask the BioPortal API for the same term and ontology, you get the same data (you will probably need an api- key to see this): http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI. Note also that the results that are returned with this API are automatically filtered to obsolete": false,so they are not obsolete :) In the latest version of the MI ontology though these terms are obsolete/deleted (I took the files from http://obofoundry.org/ontology/mi.html)?: .obo file [Term] id: MI:2246 name: indirect causal regulation def: "The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B." [PMID:15845847] subset: PSI-MI_slim synonym: "indirect" EXACT PSI-MI-alternate [] synonym: "indirect causal regulation" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T15:45:44Z .owl file: ppm 2017-01-19T15:45:44Z indirect indirect causal regulation PSI-MI MI:2246 indirect causal regulation true Jennifer, it seems thus that there has to be a synchronization problem from your side then? (since Pablo has checked that both versions of the ontology are pretty much up to date). Or there could be another issue that does not allow you to get the latest version? Might I suggest also that you pull from the .obo version of the MI ontology since it is the one Pablo actively maintains (this is the Github link I think you want)? BR, John. ________________________________ From: Pablo Porras Millan Sent: Monday, February 11, 2019 10:46 AM To: John Zobolas Cc: support at bioontology.org; Vasundra Tour?; Jennifer Leigh Vendetti; Sandra Orchard Subject: Re: [bioontology-support] MI update on Bioportal? Hi John, We do not generate the ontology as an owl file, this must be automatically generated from the obo file we actively maintain. If there is a problem ,it probaly comes from the frequency of the conversion between obo and owl. In any case, I was checking through the changes in the owl file and it seems, as far as I cantell, to be more or less up to date. I see that terms such as 'indirect causal regulation' are correctly marked as 'deprecated' or 'obsolete'. Can you please bespecific about hte changes you were expecting to see but are not there? Just to be sure there is really a synchronization problem and not an update one on our side. Cheers, Pablo. On 09/02/2019 09:35, John Zobolas wrote: ?Hi Pablo, See the issue below. Maybe the .owl file that they pull is not the one with the changes? BR, John. ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 8, 2019 9:45 PM To: John Zobolas Cc: support at bioontology.org; Vasundra Tour? Subject: Re: [bioontology-support] MI update on Bioportal? Hello Pablo & Vasundra, BioPortal provides functionality that gives end users the ability to enter a URL that is checked on a nightly basis for new versions of their ontology. The MI ontology entry in BioPortal is currently configured to check the following URL nightly: http://purl.obolibrary.org/obo/mi.owl We got this URL from your OBO Foundry page. One thing to note here is that we are currently serving the OWL version of your ontology. The GitHub URL you provided below references the OBO version of your ontology. Is the implication here that you?d rather we be serving the OBO version, and have our system configured to pull from GitHub? Thanks for any clarification you can provide here. Kind regards, Jennifer On Feb 8, 2019, at 3:57 AM, John Zobolas > wrote: Hi, The issue is that the MI ontology in the OBOfoundry page is updated but the BioPortal version? in not synced yet to the current/newest version. Could you please update it? BR, John ________________________________________ From: Pablo Porras Millan > Sent: Friday, February 8, 2019 12:41 PM To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk) Cc: John Zobolas Subject: Re: MI update on Bioportal? Dear Vasundra, I have no idea how BioPortal gets updated, but our reference github repo is up to date and shows the latest version of the CV in OLS: https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. Our OBOfoundry page also seems tobe up to date (http://obofoundry.org/ontology/mi.html). We have never updated BioPortal manually and I am certainly not willing to start now, so I assume they have some sort of procedure to do these updates. Can you use an alternative source for theCV? Cheers, Pablo. On 08/02/2019 08:28, Vasundra Tour? wrote: > Dear Pablo and Sandra, > > I have looked at the MI terms in Bioportal and it seems like they are > not updated. (see Causal Regulatory Mechanism branch > https://bit.ly/2DYI5VM). > > Isn't it suppose to be an automatic update from Bioportal? Or do you > have to submit the changes from your side? > > Just wanted to point out this issue. > > Thanks! > > Best regards, > Vasundra > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Feb 11 05:23:58 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 11 Feb 2019 05:23:58 -0800 Subject: [bioontology-support] [BioPortal] Feedback from darys Message-ID: <5c61776ea2458_62f52aedc2d43f9889489@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From pporras at ebi.ac.uk Mon Feb 11 01:46:05 2019 From: pporras at ebi.ac.uk (Pablo Porras Millan) Date: Mon, 11 Feb 2019 09:46:05 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: <1549704933590.54763@ntnu.no> References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no> <1549704933590.54763@ntnu.no> Message-ID: <435b7c31-5087-d011-c7c8-0b9b4f17b752@ebi.ac.uk> Hi John, We do not generate the ontology as an owl file, this must be automatically generated from the obo file we actively maintain. If there is a problem ,it probaly comes from the frequency of the conversion between obo and owl. In any case, I was checking through the changes in the owl file and it seems, as far as I cantell, to be more or less up to date. I see that terms such as 'indirect causal regulation' are correctly marked as 'deprecated' or 'obsolete'. Can you please bespecific about hte changes you were expecting to see but are not there? Just to be sure there is really a synchronization problem and not an update one on our side. Cheers, Pablo. On 09/02/2019 09:35, John Zobolas wrote: > > ?Hi Pablo, > > > See the issue below. Maybe the .owl file that they pull is not the one > with the changes? > > > BR, John. > > ------------------------------------------------------------------------ > *From:* Jennifer Leigh Vendetti > *Sent:* Friday, February 8, 2019 9:45 PM > *To:* John Zobolas > *Cc:* support at bioontology.org; Vasundra Tour? > *Subject:* Re: [bioontology-support] MI update on Bioportal? > Hello Pablo & Vasundra, > > BioPortal provides functionality that gives end users the ability to > enter a URL that is checked on a nightly basis for new versions of > their ontology. The MI ontology entry in BioPortal is currently > configured to check the following URL nightly: > > http://purl.obolibrary.org/obo/mi.owl > > We got this URL from your OBO Foundry page. > > One thing to note here is that we are currently serving the OWL > version of your ontology. The GitHub URL you provided below references > the OBO version of your ontology. Is the implication here that you?d > rather we be serving the OBO version, and have our system configured > to pull from GitHub? > > Thanks for any clarification you can provide here. > > Kind regards, > Jennifer > > > > >> On Feb 8, 2019, at 3:57 AM, John Zobolas > > wrote: >> >> Hi, >> >> The issue is that the MI ontology in theOBOfoundry page >> is updated but theBioPortal >> version? in not >> synced yet to the current/newest version. Could you please update it? >> >> BR, John >> ________________________________________ >> From: Pablo Porras Millan > >> Sent: Friday, February 8, 2019 12:41 PM >> To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk >> ) >> Cc: John Zobolas >> Subject: Re: MI update on Bioportal? >> >> Dear Vasundra, >> >> I have no idea how BioPortal gets updated, but our reference github repo >> is up to date and shows the latest version of the CV in OLS: >> https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. >> Our OBOfoundry page also seems tobe up to date >> (http://obofoundry.org/ontology/mi.html). >> >> We have never updated BioPortal manually and I am certainly not willing >> to start now, so I assume they have some sort of procedure to do these >> updates. Can you use an alternative source for theCV? >> >> Cheers, >> >> Pablo. >> >> >> >> On 08/02/2019 08:28, Vasundra Tour? wrote: >> > Dear Pablo and Sandra, >> > >> > I have looked at the MI terms in Bioportal and it seems like they are >> > not updated. (see Causal Regulatory Mechanism branch >> >https://bit.ly/2DYI5VM). >> > >> > Isn't it suppose to be an automatic update from Bioportal? Or do you >> > have to submit the changes from your side? >> > >> > Just wanted to point out this issue. >> > >> > Thanks! >> > >> > Best regards, >> > Vasundra >> > >> >> -- >> ------------------------------------------------------ >> Pablo Porras Mill?n, Ph.D. >> Molecular Interactions Team Coordinator >> European Molecular Biology Laboratory >> European Bioinformatics Institute (EMBL-EBI) >> Wellcome Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel:??? +44 1223 494482 >> email: pporras at ebi.ac.uk >> URLs: www.ebi.ac.uk/about/people/pablo-porras-millan >> >> www.ebi.ac.uk/intact >> www.ebi.ac.uk/complexportal >> ------------------------------------------------------- >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Feb 11 10:52:21 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 Feb 2019 18:52:21 +0000 Subject: [bioontology-support] [BioPortal] Feedback from darys In-Reply-To: <5c61776ea2458_62f52aedc2d43f9889489@ncbo-prd-app-08.stanford.edu.mail> References: <5c61776ea2458_62f52aedc2d43f9889489@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9A07EC19-D34C-44CC-B25A-3E7B679D15D2@stanford.edu> Hello Dinah, We're sorry, but we don't manage the REDCap application, and as far as I know we do not have the answer to this question. You would need to check with REDCap support, or whoever manages your local installation. John On Feb 11, 2019, at 5:23 AM, support at bioontology.org wrote: Name: darys Email: dinah.arys at uzbrussel.be Location: http%3A%2F%2Fbioportal.bioontology.org%2Fhelp Feedback: Dear, I have a question about adding multiple ontologies to REDCap. I currently have one ontology coupled to REDCap (CTCAE), but I don't know how to add another one. I have read that there are 400 available ontologies to chose from. I tried "submit a new ontology", but that didn't work out. My e-mail adress is: dinah.arys at uzbrussel.be Hoping for a quick feedback. Many thanks, Dinah _______________________________________________ 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 Mon Feb 11 11:24:48 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 Feb 2019 19:24:48 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: Message-ID: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> Melissa, Were you aware SNOMEDCT is available as an OWL file at https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? (Thank you Clement!) Does this address your need? We will look into incorporating this version into BioPortal directly, but will not have time to investigate it in the short term. John On Feb 7, 2019, at 9:36 AM, John Graybeal > wrote: Hi Melissa, let me refresh my memory about the .ttl and get back to you directly. John ________________________________ From: bioontology-support > on behalf of Melissa M > Sent: Thursday, February 7, 2019 09:28 To: Clement Jonquet Cc: support at bioontology.org Subject: Re: [bioontology-support] Use of SNOMED CT in virtual appliance Hi Clement, Thanks very much for your reply. Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look? About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS. Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions? Thanks again for your help! Melissa On Thu, 7 Feb 2019 at 03:24, Clement Jonquet > wrote: Melissa, A complementary note: @misha, @john BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented. But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly. NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export. MeSH is also concerned as there is now an OWL file produced by NLM. @melissa I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the ? Edit submission information ? page. Bye Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- Le 7 f?vr. 2019 ? 02:02, Michael Dorf > a ?crit : Hi Melissa, Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. Thanks, Michael On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== 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 mmorine at gmail.com Mon Feb 11 11:45:47 2019 From: mmorine at gmail.com (Melissa M) Date: Mon, 11 Feb 2019 15:45:47 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> References: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> Message-ID: Hi John, My understanding is that this OWL needs to be generated using the IHSTDO toolkit that I mentioned before. On that page they indicate a perl script, but that's now been replaced with a command line tool + java API. The command line tool produces the OWL without synonyms that I was mentioning earlier. The java API might do part of what I need but I'm still looking into it. As far as I know, they don't provide a direct download of the OWL file. As for generating a ttl from the UMLS distribution, I've had no problem with most of the pipeline that you use at NCBO except I'm stuck on the last step. It looks like an issue with the MySQLdb library, but the tips indicated in the umls2rdf repository don't help since I'm using a different OS. I'll keep working on a fix but if it turns out that you're able to provide access to the SNOMED ttl that would be a great help. Thanks! Melissa On Mon, 11 Feb 2019 at 15:24, John Graybeal wrote: > Melissa, > > Were you aware SNOMEDCT is available as an OWL file at > https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? > (Thank you Clement!) Does this address your need? > > We will look into incorporating this version into BioPortal directly, but > will not have time to investigate it in the short term. > > John > > On Feb 7, 2019, at 9:36 AM, John Graybeal wrote: > > Hi Melissa, let me refresh my memory about the .ttl and get back to you > directly. > > John > > > ------------------------------ > *From:* bioontology-support < > bioontology-support-bounces at lists.stanford.edu> on behalf of Melissa M < > mmorine at gmail.com> > *Sent:* Thursday, February 7, 2019 09:28 > *To:* Clement Jonquet > *Cc:* support at bioontology.org > *Subject:* Re: [bioontology-support] Use of SNOMED CT in virtual > appliance > > Hi Clement, > Thanks very much for your reply. > > Regarding the FoodOn issue, I should mention 2 things: 1) I have the same > problem both on my VA and on bioportal, and 2) synonyms are properly > recognized for some classes and not for others. I've looked at the .owl > files to see if I could find any differences in specification of classes > whose synonyms are recognized and those whose synonyms aren't recognized, > and I couldn't find anything. I'd be happy to provide a few class names as > examples if you have time to have a look? > > About the SNOMED issue, I contacted IHTSDO and just heard back this > morning that the "toolkit is only currently capable of including the Fully > Specified Name of concepts" but they're opening my issue as a new feature. > In the meantime I'll start working through the pipeline that you use for > importing UMLS. > > Alternatively, would you be able to provide access to the SNOMED .ttl or > are there license restrictions? > > Thanks again for your help! > Melissa > > > > On Thu, 7 Feb 2019 at 03:24, Clement Jonquet wrote: > >> Melissa, >> >> A complementary note: >> >> @misha, @john >> BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool >> as documented. >> But eventually, now that Snomed International (new name for IHTSDO) >> provide an OWL file directly, it will be interesting one day to drop the >> import from UMLS and take the OWL directly. >> NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS >> but not imported thru the UMLS export. >> MeSH is also concerned as there is now an OWL file produced by NLM. >> >> @melissa >> I bet the problem you have with the synonyms in the OWL version of >> SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right >> property for synonyms in the ? Edit submission information ? page. >> >> Bye >> Clement >> >> ------------------------------------------------------------------------------------------- >> Dr. Clement JONQUET - PhD in Informatics - Assistant Professor >> University of Montpellier (LIRMM) >> >> ------------------------------------------------------------------------------------------- >> >> Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : >> >> Hi Melissa, >> >> Yes, that is the script that is being used to import UMLS ontologies into >> a virtual appliance. It hasn?t been updated since 2016, but it should >> still be valid. Let us know if you run into any issues importing. >> >> Thanks, >> >> Michael >> >> >> >> On Feb 6, 2019, at 12:10 PM, Melissa M wrote: >> >> Hi Michael, >> Thank you very much for your response. Can you confirm that the pipeline >> described here >> is >> the one currently used to import UMLS content into bioportal? I'm assuming >> that NCBO does not provide downloads of the output files from this pipeline >> (I think in ttl format)? >> Thanks again, >> Melissa >> >> >> On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: >> >>> Hi Melissa, >>> >>> Thanks for contacting us again. Twice per year we do a bulk import of >>> terminologies distributed by the UMLS [1]. (They have a twice per year >>> release schedule, e.g., for this year it will be 2019AA and 2019AB). >>> SNOMEDCT is one of the terminologies contained in the UMLS distribution. >>> So, the version numbers for SNOMEDCT that you see in BioPortal correspond >>> to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their >>> distributions can be found here: >>> >>> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >>> >>> The page contains an alphabetical list of all the terminologies >>> contained in the UMLS. >>> >>> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only >>> assume that may contain either a different version from the one we have in >>> BioPortal; or a version that may not have all the properties fully >>> populated. >>> >>> Thanks, >>> >>> Michael >>> >>> [1] https://www.nlm.nih.gov/research/umls/ >>> >>> >>> >>> >>> On Feb 6, 2019, at 8:28 AM, Melissa M wrote: >>> >>> Hello, >>> I've recently been discussing with your team regarding use of FoodOn in >>> the virtual appliance but thought I'd write separately about this question >>> since it's unrelated to the other. >>> So far I've been able to import ontologies and perform annotations more >>> or less successfully, apart from the FoodOn issue that I've already written >>> about. Now I'm trying to import SNOMED CT but am noticing some issues. >>> First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED >>> OWL toolkit jar provided by IHTSDO >>> , then imported the >>> resulting owl into my virtual appliance using default settings (i.e., >>> selected OWL format, and no changes to prefLabel/altLabel/etc properties). >>> The resulting ontology appears to contain all classes in the class browser, >>> and I can annotate text that contains exact prefLabels of the SNOMED >>> ontology, but it's missing many of the fields that are present in the >>> SNOMED instance on the bioportal server (such as synonyms, altLabels, >>> etc.). I therefore can't annotate any text that contains SNOMED altLabels >>> and synonyms. I've attached a screenshot of the SNOMED class browser in my >>> virtual appliance to hopefully show what I mean. >>> So I'm trying to figure out if I went wrong in my conversion to owl, or >>> import into the VA. >>> My question is, was the instance of SNOMED on the bioportal server >>> produced using the toolkit from IHTSDO? And when importing into bioportal, >>> were non-default settings used? >>> Thanks in advance for any info, >>> Melissa >>> >>> >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> >> _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > ======================== > 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 Feb 11 13:20:31 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 11 Feb 2019 21:20:31 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: <1549880415913.73989@ntnu.no> References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no> <1549704933590.54763@ntnu.no> <435b7c31-5087-d011-c7c8-0b9b4f17b752@ebi.ac.uk> <1549880415913.73989@ntnu.no> Message-ID: Hi John et al., It sounds like the OBO version of MI in GitHub is the one that?s more actively maintained, so I went ahead and modified BioPortal to serve that version. I also configured the MI ontology entry to check your GitHub URL [1] on a nightly basis for new versions. We have a number of ontologies that are configured this way, so I don?t anticipate problems with pulling new versions. However, if anyone notices something awry, please feel free to contact us via the support list and we?ll look into it ASAP. The new upload is finished processing in BioPortal. The ?indirect causal regulation? class no longer appears in the tree in the BioPortal user interface. Using the search functionality of our REST API with the require_exact_match parameter set to true [2], there is still one result returned since ?indirect causal regulation? is listed as a synonym for the "causal regulatory mechanism? term. I verified that the synonym is declared in the OBO source file (beginning on line 13,157): [Term] id: MI:2245 name: causal regulatory mechanism def: "Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B." [PMID:26467481] synonym: "causal regulatory mechanism" EXACT PSI-MI-short [] synonym: "indirect causal regulation" EXACT PSI-MI-alternate [] is_a: MI:2233 ! causal interaction created_by: ppm creation_date: 2017-01-19T15:44:29Z Kind regards, Jennifer [1] https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo [2] http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI&require_exact_match=true On Feb 11, 2019, at 2:20 AM, John Zobolas > wrote: Hi Jennifer and Pablo, This issue was found by Vasundra when she saw that terms like 'indirect causal regulation' are still mentioned in the BioPortal GUI (see here). If you ask the BioPortal API for the same term and ontology, you get the same data (you will probably need an api- key to see this): http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI. Note also that the results that are returned with this API are automatically filtered to obsolete": false,so they are not obsolete :) In the latest version of the MI ontology though these terms are obsolete/deleted (I took the files from http://obofoundry.org/ontology/mi.html)?: .obo file [Term] id: MI:2246 name: indirect causal regulation def: "The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B." [PMID:15845847] subset: PSI-MI_slim synonym: "indirect" EXACT PSI-MI-alternate [] synonym: "indirect causal regulation" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T15:45:44Z .owl file: ppm 2017-01-19T15:45:44Z indirect indirect causal regulation PSI-MI MI:2246 indirect causal regulation true Jennifer, it seems thus that there has to be a synchronization problem from your side then? (since Pablo has checked that both versions of the ontology are pretty much up to date). Or there could be another issue that does not allow you to get the latest version? Might I suggest also that you pull from the .obo version of the MI ontology since it is the one Pablo actively maintains (this is the Github link I think you want)? BR, John. ________________________________ From: Pablo Porras Millan > Sent: Monday, February 11, 2019 10:46 AM To: John Zobolas Cc: support at bioontology.org; Vasundra Tour?; Jennifer Leigh Vendetti; Sandra Orchard Subject: Re: [bioontology-support] MI update on Bioportal? Hi John, We do not generate the ontology as an owl file, this must be automatically generated from the obo file we actively maintain. If there is a problem ,it probaly comes from the frequency of the conversion between obo and owl. In any case, I was checking through the changes in the owl file and it seems, as far as I cantell, to be more or less up to date. I see that terms such as 'indirect causal regulation' are correctly marked as 'deprecated' or 'obsolete'. Can you please bespecific about hte changes you were expecting to see but are not there? Just to be sure there is really a synchronization problem and not an update one on our side. Cheers, Pablo. On 09/02/2019 09:35, John Zobolas wrote: ?Hi Pablo, See the issue below. Maybe the .owl file that they pull is not the one with the changes? BR, John. ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, February 8, 2019 9:45 PM To: John Zobolas Cc: support at bioontology.org; Vasundra Tour? Subject: Re: [bioontology-support] MI update on Bioportal? Hello Pablo & Vasundra, BioPortal provides functionality that gives end users the ability to enter a URL that is checked on a nightly basis for new versions of their ontology. The MI ontology entry in BioPortal is currently configured to check the following URL nightly: http://purl.obolibrary.org/obo/mi.owl We got this URL from your OBO Foundry page. One thing to note here is that we are currently serving the OWL version of your ontology. The GitHub URL you provided below references the OBO version of your ontology. Is the implication here that you?d rather we be serving the OBO version, and have our system configured to pull from GitHub? Thanks for any clarification you can provide here. Kind regards, Jennifer On Feb 8, 2019, at 3:57 AM, John Zobolas > wrote: Hi, The issue is that the MI ontology in the OBOfoundry page is updated but the BioPortal version? in not synced yet to the current/newest version. Could you please update it? BR, John ________________________________________ From: Pablo Porras Millan > Sent: Friday, February 8, 2019 12:41 PM To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk) Cc: John Zobolas Subject: Re: MI update on Bioportal? Dear Vasundra, I have no idea how BioPortal gets updated, but our reference github repo is up to date and shows the latest version of the CV in OLS: https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. Our OBOfoundry page also seems tobe up to date (http://obofoundry.org/ontology/mi.html). We have never updated BioPortal manually and I am certainly not willing to start now, so I assume they have some sort of procedure to do these updates. Can you use an alternative source for theCV? Cheers, Pablo. On 08/02/2019 08:28, Vasundra Tour? wrote: > Dear Pablo and Sandra, > > I have looked at the MI terms in Bioportal and it seems like they are > not updated. (see Causal Regulatory Mechanism branch > https://bit.ly/2DYI5VM). > > Isn't it suppose to be an automatic update from Bioportal? Or do you > have to submit the changes from your side? > > Just wanted to point out this issue. > > Thanks! > > Best regards, > Vasundra > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From pporras at ebi.ac.uk Mon Feb 11 13:47:10 2019 From: pporras at ebi.ac.uk (Pablo Porras Millan) Date: Mon, 11 Feb 2019 21:47:10 +0000 Subject: [bioontology-support] MI update on Bioportal? In-Reply-To: References: <20190208114206.CD43962A6D3_C5D6B0EB@hh-mx3.ebi.ac.uk> <1549627035257.30535@ntnu.no> <1549704933590.54763@ntnu.no> <435b7c31-5087-d011-c7c8-0b9b4f17b752@ebi.ac.uk> <1549880415913.73989@ntnu.no> Message-ID: Many thanks for your help, Jennifer. We will keep an eye on this and pass through any issues that our users report. Best regards, Pablo. On 11/02/2019 21:20, Jennifer Leigh Vendetti wrote: > Hi John et al., > > It sounds like the OBO version of MI in GitHub is the one that?s more > actively maintained, so I went ahead and modified BioPortal to serve > that version. I also configured the MI ontology entry to check your > GitHub URL [1] on a nightly basis for new versions. We have a number > of ontologies that are configured this way, so I don?t anticipate > problems with pulling new versions. However, if anyone notices > something awry, please feel free to contact us via the support list > and we?ll look into it ASAP. > > The new upload is finished processing in BioPortal. The ?indirect > causal regulation? class no longer appears in the tree in the > BioPortal user interface. Using the search functionality of our REST > API with the require_exact_match parameter set to true [2], there is > still one result returned since ?indirect causal regulation? is listed > as a synonym for the "causal regulatory mechanism? term. I verified > that the synonym is declared in the OBO source file (beginning on line > 13,157): > > [Term] > id: MI:2245 > name: causal regulatory mechanism > def: "Type of relationship between entities involved in a causal > interaction. This term is to be used only to describe the effect of a > modulator entity A on a modulated entity B when A is not immediately > upstream of B." [PMID:26467481] > synonym: "causal regulatory mechanism" EXACT PSI-MI-short [] > *synonym: "indirect causal regulation"* EXACT PSI-MI-alternate [] > is_a: MI:2233 ! causal interaction > created_by: ppm > creation_date: 2017-01-19T15:44:29Z > > Kind regards, > Jennifer > > [1] https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo > [2] > http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI&require_exact_match=true > regulation&ontologies=MI&require_exact_match=true> > > > >> On Feb 11, 2019, at 2:20 AM, John Zobolas > > wrote: >> >> Hi Jennifer and Pablo, >> >> This issue was found by?Vasundra when she saw?that terms like >> 'indirect causal regulation' are?still mentioned in the BioPortal?GUI >> (see here >> ). >> If you?ask the BioPortal API for the same term and ontology, you >> get?the same data?(you will probably need an api- key to see this): >> http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI. >> Note also?that?the?results that are returned with this API are >> automatically filtered to obsolete": false,so they are not obsolete?:) >> >> In the latest version of the MI ontology >> though?these >> terms are obsolete/deleted (I took the files from >> http://obofoundry.org/ontology/mi.html) >> ?: >> >> *.obo file* >> [Term] >> id: MI:2246 >> name:indirect causal regulation >> def: "The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B." [PMID:15845847] >> subset: PSI-MI_slim >> synonym: "indirect" EXACT PSI-MI-alternate [] >> synonym: "indirect causal regulation" EXACT PSI-MI-short [] >> is_obsolete: true >> created_by: ppm >> creation_date: 2017-01-19T15:45:44Z >> *.owl file:* >> > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ppm >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2017-01-19T15:45:44Z >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect >> causal regulation >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSI-MI >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MI:2246 >> ? ? ? ? > rdf:resource="http://purl.obolibrary.org/obo/mi#PSI-MI_slim"/> >> ? ? ? ? > rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect >> causal regulation >> ? ? ? ? >> true >> >> >> Jennifer, it?seems thus?that there has to be a synchronization >> problem from your side then? (since Pablo has checked that both >> versions of the ontology are pretty much?up to date). Or there could >> be another issue?that does not allow you to get the latest >> version??Might I suggest also?that you pull from the?.obo version of >> the MI ontology since?it is the one?Pablo actively maintains?(this >> is?the Github link ?I think >> you want)? >> >> BR, John. >> ------------------------------------------------------------------------ >> *From:*Pablo Porras Millan > >> *Sent:*Monday, February 11, 2019 10:46 AM >> *To:*John Zobolas >> *Cc:*support at bioontology.org ; >> Vasundra Tour?; Jennifer Leigh Vendetti; Sandra Orchard >> *Subject:*Re: [bioontology-support] MI update on Bioportal? >> Hi John, >> >> We do not generate the ontology as an owl file, this must be >> automatically generated from the obo file we actively maintain. If >> there is a problem ,it probaly comes from the frequency of the >> conversion between obo and owl. >> >> In any case, I was checking through the changes in the owl file and >> it seems, as far as I cantell, to be more or less up to date. I see >> that terms such as 'indirect causal regulation' are correctly marked >> as 'deprecated' or 'obsolete'. Can you please bespecific about hte >> changes you were expecting to see but are not there? Just to be sure >> there is really a synchronization problem and not an update one on >> our side. >> >> Cheers, >> >> Pablo. >> >> On 09/02/2019 09:35, John Zobolas wrote: >>> ?Hi Pablo, >>> >>> See the issue below. Maybe the .owl file that they pull is not the >>> one with the changes? >>> >>> BR, John. >>> ------------------------------------------------------------------------ >>> *From:*Jennifer Leigh Vendetti >>> *Sent:*Friday, February 8, 2019 9:45 PM >>> *To:*John Zobolas >>> *Cc:*support at bioontology.org; Vasundra Tour? >>> *Subject:*Re: [bioontology-support] MI update on Bioportal? >>> Hello Pablo & Vasundra, >>> >>> BioPortal provides functionality that gives end users the ability to >>> enter a URL that is checked on a nightly basis for new versions of >>> their ontology. The MI ontology entry in BioPortal is currently >>> configured to check the following URL nightly: >>> >>> http://purl.obolibrary.org/obo/mi.owl >>> >>> We got this URL from your OBO Foundry page. >>> >>> One thing to note here is that we are currently serving the OWL >>> version of your ontology. The GitHub URL you provided below >>> references the OBO version of your ontology. Is the implication here >>> that you?d rather we be serving the OBO version, and have our system >>> configured to pull from GitHub? >>> >>> Thanks for any clarification you can provide here. >>> >>> Kind regards, >>> Jennifer >>> >>> >>> >>> >>>> On Feb 8, 2019, at 3:57 AM, John Zobolas >>> > wrote: >>>> >>>> Hi, >>>> >>>> The issue is that the MI ontology in theOBOfoundry page >>>> is updated but theBioPortal >>>> version? in not >>>> synced yet to the current/newest version. Could you please update it? >>>> >>>> BR, John >>>> ________________________________________ >>>> From: Pablo Porras Millan >>> > >>>> Sent: Friday, February 8, 2019 12:41 PM >>>> To: Vasundra Tour?; Sandra Orchard (orchard at ebi.ac.uk >>>> ) >>>> Cc: John Zobolas >>>> Subject: Re: MI update on Bioportal? >>>> >>>> Dear Vasundra, >>>> >>>> I have no idea how BioPortal gets updated, but our reference github >>>> repo >>>> is up to date and shows the latest version of the CV in OLS: >>>> https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233. >>>> Our OBOfoundry page also seems tobe up to date >>>> (http://obofoundry.org/ontology/mi.html). >>>> >>>> We have never updated BioPortal manually and I am certainly not willing >>>> to start now, so I assume they have some sort of procedure to do these >>>> updates. Can you use an alternative source for theCV? >>>> >>>> Cheers, >>>> >>>> Pablo. >>>> >>>> >>>> >>>> On 08/02/2019 08:28, Vasundra Tour? wrote: >>>> > Dear Pablo and Sandra, >>>> > >>>> > I have looked at the MI terms in Bioportal and it seems like they are >>>> > not updated. (see Causal Regulatory Mechanism branch >>>> >https://bit.ly/2DYI5VM). >>>> > >>>> > Isn't it suppose to be an automatic update from Bioportal? Or do you >>>> > have to submit the changes from your side? >>>> > >>>> > Just wanted to point out this issue. >>>> > >>>> > Thanks! >>>> > >>>> > Best regards, >>>> > Vasundra >>>> > >>>> >>>> -- >>>> ------------------------------------------------------ >>>> Pablo Porras Mill?n, Ph.D. >>>> Molecular Interactions Team Coordinator >>>> European Molecular Biology Laboratory >>>> European Bioinformatics Institute (EMBL-EBI) >>>> Wellcome Genome Campus >>>> Hinxton >>>> Cambridge CB10 1SD >>>> United Kingdom >>>> Tel:??? +44 1223 494482 >>>> email: pporras at ebi.ac.uk >>>> URLs: www.ebi.ac.uk/about/people/pablo-porras-millan >>>> >>>> www.ebi.ac.uk/intact >>>> www.ebi.ac.uk/complexportal >>>> ------------------------------------------------------- >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >> >> -- >> ------------------------------------------------------ >> Pablo Porras Mill?n, Ph.D. >> Molecular Interactions Team Coordinator >> European Molecular Biology Laboratory >> European Bioinformatics Institute (EMBL-EBI) >> Wellcome Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Tel: +44 1223 494482 >> email:pporras at ebi.ac.uk >> URLs:www.ebi.ac.uk/about/people/pablo-porras-millan >> www.ebi.ac.uk/intact >> www.ebi.ac.uk/complexportal >> ------------------------------------------------------- > -- ------------------------------------------------------ Pablo Porras Mill?n, Ph.D. Molecular Interactions Team Coordinator European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras at ebi.ac.uk URLs: www.ebi.ac.uk/about/people/pablo-porras-millan www.ebi.ac.uk/intact www.ebi.ac.uk/complexportal ------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Feb 11 14:09:29 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 Feb 2019 22:09:29 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> Message-ID: Sorry, I think you're right about that. At least, I can't find anything OWLish on that page. (I just assumed the link ending in /owl was an OWL file. Silly me.) Back to my licensing studies! John On Feb 11, 2019, at 11:45 AM, Melissa M > wrote: Hi John, My understanding is that this OWL needs to be generated using the IHSTDO toolkit that I mentioned before. On that page they indicate a perl script, but that's now been replaced with a command line tool + java API. The command line tool produces the OWL without synonyms that I was mentioning earlier. The java API might do part of what I need but I'm still looking into it. As far as I know, they don't provide a direct download of the OWL file. As for generating a ttl from the UMLS distribution, I've had no problem with most of the pipeline that you use at NCBO except I'm stuck on the last step. It looks like an issue with the MySQLdb library, but the tips indicated in the umls2rdf repository don't help since I'm using a different OS. I'll keep working on a fix but if it turns out that you're able to provide access to the SNOMED ttl that would be a great help. Thanks! Melissa On Mon, 11 Feb 2019 at 15:24, John Graybeal > wrote: Melissa, Were you aware SNOMEDCT is available as an OWL file at https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? (Thank you Clement!) Does this address your need? We will look into incorporating this version into BioPortal directly, but will not have time to investigate it in the short term. John On Feb 7, 2019, at 9:36 AM, John Graybeal > wrote: Hi Melissa, let me refresh my memory about the .ttl and get back to you directly. John ________________________________ From: bioontology-support > on behalf of Melissa M > Sent: Thursday, February 7, 2019 09:28 To: Clement Jonquet Cc: support at bioontology.org Subject: Re: [bioontology-support] Use of SNOMED CT in virtual appliance Hi Clement, Thanks very much for your reply. Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look? About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS. Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions? Thanks again for your help! Melissa On Thu, 7 Feb 2019 at 03:24, Clement Jonquet > wrote: Melissa, A complementary note: @misha, @john BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented. But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly. NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export. MeSH is also concerned as there is now an OWL file produced by NLM. @melissa I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the ? Edit submission information ? page. Bye Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- Le 7 f?vr. 2019 ? 02:02, Michael Dorf > a ?crit : Hi Melissa, Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. Thanks, Michael On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== 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 mmorine at gmail.com Tue Feb 12 11:27:03 2019 From: mmorine at gmail.com (Melissa M) Date: Tue, 12 Feb 2019 15:27:03 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> Message-ID: Hi John, I wanted to let you know that I just got the last step of the pipeline working and have generated the SNOMED ttl. I'm now loading it in my VA and will let you know if I have any issues. Thanks again for your responsiveness to all of my questions! Melissa On Mon, 11 Feb 2019 at 18:09, John Graybeal wrote: > Sorry, I think you're right about that. At least, I can't find anything > OWLish on that page. (I just assumed the link ending in /owl was an OWL > file. Silly me.) > > Back to my licensing studies! > > John > > On Feb 11, 2019, at 11:45 AM, Melissa M wrote: > > Hi John, > My understanding is that this OWL needs to be generated > > using the IHSTDO toolkit that I mentioned before. On that page they > indicate a perl script, but that's now been replaced with a command line > tool + java API. The command line tool produces the OWL without synonyms > that I was mentioning earlier. The java API might do part of what I need > but I'm still looking into it. As far as I know, they don't provide a > direct download of the OWL file. > > As for generating a ttl from the UMLS distribution, I've had no problem > with most of the pipeline that you use at NCBO except I'm stuck on the last > step. It looks like an issue with the MySQLdb library, but the tips > indicated in the umls2rdf repository don't help since I'm using a different > OS. I'll keep working on a fix but if it turns out that you're able to > provide access to the SNOMED ttl that would be a great help. > > Thanks! > Melissa > > > On Mon, 11 Feb 2019 at 15:24, John Graybeal > wrote: > >> Melissa, >> >> Were you aware SNOMEDCT is available as an OWL file at >> https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? >> (Thank you Clement!) Does this address your need? >> >> We will look into incorporating this version into BioPortal directly, but >> will not have time to investigate it in the short term. >> >> John >> >> On Feb 7, 2019, at 9:36 AM, John Graybeal wrote: >> >> Hi Melissa, let me refresh my memory about the .ttl and get back to you >> directly. >> >> John >> >> >> ------------------------------ >> *From:* bioontology-support < >> bioontology-support-bounces at lists.stanford.edu> on behalf of Melissa M < >> mmorine at gmail.com> >> *Sent:* Thursday, February 7, 2019 09:28 >> *To:* Clement Jonquet >> *Cc:* support at bioontology.org >> *Subject:* Re: [bioontology-support] Use of SNOMED CT in virtual >> appliance >> >> Hi Clement, >> Thanks very much for your reply. >> >> Regarding the FoodOn issue, I should mention 2 things: 1) I have the same >> problem both on my VA and on bioportal, and 2) synonyms are properly >> recognized for some classes and not for others. I've looked at the .owl >> files to see if I could find any differences in specification of classes >> whose synonyms are recognized and those whose synonyms aren't recognized, >> and I couldn't find anything. I'd be happy to provide a few class names as >> examples if you have time to have a look? >> >> About the SNOMED issue, I contacted IHTSDO and just heard back this >> morning that the "toolkit is only currently capable of including the Fully >> Specified Name of concepts" but they're opening my issue as a new feature. >> In the meantime I'll start working through the pipeline that you use for >> importing UMLS. >> >> Alternatively, would you be able to provide access to the SNOMED .ttl or >> are there license restrictions? >> >> Thanks again for your help! >> Melissa >> >> >> >> On Thu, 7 Feb 2019 at 03:24, Clement Jonquet wrote: >> >>> Melissa, >>> >>> A complementary note: >>> >>> @misha, @john >>> BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF >>> tool as documented. >>> But eventually, now that Snomed International (new name for IHTSDO) >>> provide an OWL file directly, it will be interesting one day to drop the >>> import from UMLS and take the OWL directly. >>> NCBO already does it for NCIt, GO, and a bunch of others that are in >>> UMLS but not imported thru the UMLS export. >>> MeSH is also concerned as there is now an OWL file produced by NLM. >>> >>> @melissa >>> I bet the problem you have with the synonyms in the OWL version of >>> SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right >>> property for synonyms in the ? Edit submission information ? page. >>> >>> Bye >>> Clement >>> >>> ------------------------------------------------------------------------------------------- >>> Dr. Clement JONQUET - PhD in Informatics - Assistant Professor >>> University of Montpellier (LIRMM) >>> >>> ------------------------------------------------------------------------------------------- >>> >>> Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : >>> >>> Hi Melissa, >>> >>> Yes, that is the script that is being used to import UMLS ontologies >>> into a virtual appliance. It hasn?t been updated since 2016, but it should >>> still be valid. Let us know if you run into any issues importing. >>> >>> Thanks, >>> >>> Michael >>> >>> >>> >>> On Feb 6, 2019, at 12:10 PM, Melissa M wrote: >>> >>> Hi Michael, >>> Thank you very much for your response. Can you confirm that the pipeline >>> described here >>> is >>> the one currently used to import UMLS content into bioportal? I'm assuming >>> that NCBO does not provide downloads of the output files from this pipeline >>> (I think in ttl format)? >>> Thanks again, >>> Melissa >>> >>> >>> On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: >>> >>>> Hi Melissa, >>>> >>>> Thanks for contacting us again. Twice per year we do a bulk import of >>>> terminologies distributed by the UMLS [1]. (They have a twice per year >>>> release schedule, e.g., for this year it will be 2019AA and 2019AB). >>>> SNOMEDCT is one of the terminologies contained in the UMLS distribution. >>>> So, the version numbers for SNOMEDCT that you see in BioPortal correspond >>>> to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their >>>> distributions can be found here: >>>> >>>> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >>>> >>>> The page contains an alphabetical list of all the terminologies >>>> contained in the UMLS. >>>> >>>> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only >>>> assume that may contain either a different version from the one we have in >>>> BioPortal; or a version that may not have all the properties fully >>>> populated. >>>> >>>> Thanks, >>>> >>>> Michael >>>> >>>> [1] https://www.nlm.nih.gov/research/umls/ >>>> >>>> >>>> >>>> >>>> On Feb 6, 2019, at 8:28 AM, Melissa M wrote: >>>> >>>> Hello, >>>> I've recently been discussing with your team regarding use of FoodOn in >>>> the virtual appliance but thought I'd write separately about this question >>>> since it's unrelated to the other. >>>> So far I've been able to import ontologies and perform annotations more >>>> or less successfully, apart from the FoodOn issue that I've already written >>>> about. Now I'm trying to import SNOMED CT but am noticing some issues. >>>> First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED >>>> OWL toolkit jar provided by IHTSDO >>>> , then imported the >>>> resulting owl into my virtual appliance using default settings (i.e., >>>> selected OWL format, and no changes to prefLabel/altLabel/etc properties). >>>> The resulting ontology appears to contain all classes in the class browser, >>>> and I can annotate text that contains exact prefLabels of the SNOMED >>>> ontology, but it's missing many of the fields that are present in the >>>> SNOMED instance on the bioportal server (such as synonyms, altLabels, >>>> etc.). I therefore can't annotate any text that contains SNOMED altLabels >>>> and synonyms. I've attached a screenshot of the SNOMED class browser in my >>>> virtual appliance to hopefully show what I mean. >>>> So I'm trying to figure out if I went wrong in my conversion to owl, or >>>> import into the VA. >>>> My question is, was the instance of SNOMED on the bioportal server >>>> produced using the toolkit from IHTSDO? And when importing into bioportal, >>>> were non-default settings used? >>>> Thanks in advance for any info, >>>> Melissa >>>> >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>>> >>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> >> ======================== >> 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 jgraybeal at stanford.edu Tue Feb 12 14:12:09 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 12 Feb 2019 22:12:09 +0000 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: References: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> Message-ID: <279141E7-564E-4B76-9ED9-D52ECC687A50@stanford.edu> Melissa, you're welcome, and we're very glad to hear it. (if you want to share your experience, we could perhaps turn it into advice in the documentation?) I appreciate the news and your willingness to work with us to find solutions. Best of luck! John On Feb 12, 2019, at 11:27 AM, Melissa M > wrote: Hi John, I wanted to let you know that I just got the last step of the pipeline working and have generated the SNOMED ttl. I'm now loading it in my VA and will let you know if I have any issues. Thanks again for your responsiveness to all of my questions! Melissa On Mon, 11 Feb 2019 at 18:09, John Graybeal > wrote: Sorry, I think you're right about that. At least, I can't find anything OWLish on that page. (I just assumed the link ending in /owl was an OWL file. Silly me.) Back to my licensing studies! John On Feb 11, 2019, at 11:45 AM, Melissa M > wrote: Hi John, My understanding is that this OWL needs to be generated using the IHSTDO toolkit that I mentioned before. On that page they indicate a perl script, but that's now been replaced with a command line tool + java API. The command line tool produces the OWL without synonyms that I was mentioning earlier. The java API might do part of what I need but I'm still looking into it. As far as I know, they don't provide a direct download of the OWL file. As for generating a ttl from the UMLS distribution, I've had no problem with most of the pipeline that you use at NCBO except I'm stuck on the last step. It looks like an issue with the MySQLdb library, but the tips indicated in the umls2rdf repository don't help since I'm using a different OS. I'll keep working on a fix but if it turns out that you're able to provide access to the SNOMED ttl that would be a great help. Thanks! Melissa On Mon, 11 Feb 2019 at 15:24, John Graybeal > wrote: Melissa, Were you aware SNOMEDCT is available as an OWL file at https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? (Thank you Clement!) Does this address your need? We will look into incorporating this version into BioPortal directly, but will not have time to investigate it in the short term. John On Feb 7, 2019, at 9:36 AM, John Graybeal > wrote: Hi Melissa, let me refresh my memory about the .ttl and get back to you directly. John ________________________________ From: bioontology-support > on behalf of Melissa M > Sent: Thursday, February 7, 2019 09:28 To: Clement Jonquet Cc: support at bioontology.org Subject: Re: [bioontology-support] Use of SNOMED CT in virtual appliance Hi Clement, Thanks very much for your reply. Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look? About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS. Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions? Thanks again for your help! Melissa On Thu, 7 Feb 2019 at 03:24, Clement Jonquet > wrote: Melissa, A complementary note: @misha, @john BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented. But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly. NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export. MeSH is also concerned as there is now an OWL file produced by NLM. @melissa I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the ? Edit submission information ? page. Bye Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- Le 7 f?vr. 2019 ? 02:02, Michael Dorf > a ?crit : Hi Melissa, Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance. It hasn?t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing. Thanks, Michael On Feb 6, 2019, at 12:10 PM, Melissa M > wrote: Hi Michael, Thank you very much for your response. Can you confirm that the pipeline described here is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)? Thanks again, Melissa On Wed, 6 Feb 2019 at 15:42, Michael Dorf > wrote: Hi Melissa, Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1]. (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB). SNOMEDCT is one of the terminologies contained in the UMLS distribution. So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html The page contains an alphabetical list of all the terminologies contained in the UMLS. Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated. Thanks, Michael [1] https://www.nlm.nih.gov/research/umls/ On Feb 6, 2019, at 8:28 AM, Melissa M > wrote: Hello, I've recently been discussing with your team regarding use of FoodOn in the virtual appliance but thought I'd write separately about this question since it's unrelated to the other. So far I've been able to import ontologies and perform annotations more or less successfully, apart from the FoodOn issue that I've already written about. Now I'm trying to import SNOMED CT but am noticing some issues. First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED OWL toolkit jar provided by IHTSDO, then imported the resulting owl into my virtual appliance using default settings (i.e., selected OWL format, and no changes to prefLabel/altLabel/etc properties). The resulting ontology appears to contain all classes in the class browser, and I can annotate text that contains exact prefLabels of the SNOMED ontology, but it's missing many of the fields that are present in the SNOMED instance on the bioportal server (such as synonyms, altLabels, etc.). I therefore can't annotate any text that contains SNOMED altLabels and synonyms. I've attached a screenshot of the SNOMED class browser in my virtual appliance to hopefully show what I mean. So I'm trying to figure out if I went wrong in my conversion to owl, or import into the VA. My question is, was the instance of SNOMED on the bioportal server produced using the toolkit from IHTSDO? And when importing into bioportal, were non-default settings used? Thanks in advance for any info, Melissa _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== 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 jgraybeal at stanford.edu Tue Feb 12 14:15:41 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 12 Feb 2019 22:15:41 +0000 Subject: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? In-Reply-To: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> References: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> Message-ID: Hi Jamie, I'm sorry my response was delayed, I will be happy to provide you access. I'll respond off-line shortly with additional information. John On Feb 10, 2019, at 12:52 PM, OSBORNE Jamie > wrote: Hi NCBO team, Impressive work - I?d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I?m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022 and ISO 15022 financial information interchange standards. Under ISO TC68/SC9/WG1, I?m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance. Our work is currently too experimental to be shared more broadly, so we?d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature. Greatly appreciate your help to get up and running with a local instance. Thanks! Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. _______________________________________________ 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 Tue Feb 12 14:32:48 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 12 Feb 2019 22:32:48 +0000 Subject: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? In-Reply-To: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> References: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> Message-ID: Hi again Jamie, Thank you for providing your information with your request. You can now access this page that contains the download and documentation links: http://bioportal.bioontology.org/virtual_appliance We are now providing version 2.5 of the Virtual Appliance, which implements a "call home" feature to determine whether there is an update available. I notice that you want to work with an AWS instance; unfortunately this is still at version 2.4. We hope to have a new AMI available before too long, but perhaps you'd like to contact me about your specific situation. Also, if you have any questions or thoughts about your use of the Virtual Appliance, please feel free to contact me. Our licensing may be change before too long and it will be good to give you an update on that as well. For any questions about the installation or ontology population process, please email support at bioontology.org. And since requests for Virtual Appliance support are made through this NCBO Support email list, we suggest you sign up for the email list at https://mailman.stanford.edu/mailman/listinfo/bioontology-support. This will help you keep up to date on the BioPortal and Virtual Appliance systems. John On Feb 10, 2019, at 12:52 PM, OSBORNE Jamie > wrote: Hi NCBO team, Impressive work - I?d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I?m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022 and ISO 15022 financial information interchange standards. Under ISO TC68/SC9/WG1, I?m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance. Our work is currently too experimental to be shared more broadly, so we?d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature. Greatly appreciate your help to get up and running with a local instance. Thanks! Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. _______________________________________________ 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 Tue Feb 12 14:40:11 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 12 Feb 2019 22:40:11 +0000 Subject: [bioontology-support] CPT csv file In-Reply-To: References: Message-ID: Hello Paymon, Sincere apologies for the late reply. Unfortunately, we can?t offer downloads of the CPT ontology source file in any format due to licensing restrictions. Kind regards, Jennifer On Jan 29, 2019, at 10:13 AM, Paymon Garakani Rezaii > wrote: Hi, Would it be possible to receive/download a .csv file containing all CPT data (specifically with the following columns: CPT codes, preferred names, *classes, subclasses, date created)? Also, would you by chance have this data for previous years? If so, would you mind providing this data as well (earliest year available after 2006)? Thank you in advance! Paymon _______________________________________________ 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 Jamie.OSBORNE at swift.com Wed Feb 13 01:51:54 2019 From: Jamie.OSBORNE at swift.com (OSBORNE Jamie) Date: Wed, 13 Feb 2019 09:51:54 +0000 Subject: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? In-Reply-To: References: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> Message-ID: <3ad8da14d88b4cdc82cec3392dd8648d@BEEXCL32.swift.corp> Thanks John ? downloading and getting setup now ? One question that I have already after digging around on the online portal is whether the ontoportal technical stack has built-in any assumptions/requirements that ontologies are compliant with BFO? While I appreciate the benefits of a foundational/operational ontology, we haven?t yet reached any agreement in Finance about which, if any, we will implement. Some of my peers have raised concerns that BFO is not well suited to our industry and have proposed (or developed) alternatives. Do you have any thoughts, warnings, or expert advice for us? Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: 12 February 2019 23:33 To: OSBORNE Jamie Cc: support at bioontology.org Subject: Re: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? Mail originates from outside SWIFT ! Be vigilant before you click on a link, open attachments or reply ! ------------------------------------------------------------------------- Hi again Jamie, Thank you for providing your information with your request. You can now access this page that contains the download and documentation links: http://bioportal.bioontology.org/virtual_appliance We are now providing version 2.5 of the Virtual Appliance, which implements a "call home" feature to determine whether there is an update available. I notice that you want to work with an AWS instance; unfortunately this is still at version 2.4. We hope to have a new AMI available before too long, but perhaps you'd like to contact me about your specific situation. Also, if you have any questions or thoughts about your use of the Virtual Appliance, please feel free to contact me. Our licensing may be change before too long and it will be good to give you an update on that as well. For any questions about the installation or ontology population process, please email support at bioontology.org. And since requests for Virtual Appliance support are made through this NCBO Support email list, we suggest you sign up for the email list at https://mailman.stanford.edu/mailman/listinfo/bioontology-support. This will help you keep up to date on the BioPortal and Virtual Appliance systems. John On Feb 10, 2019, at 12:52 PM, OSBORNE Jamie wrote: Hi NCBO team, Impressive work - I?d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I?m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022 and ISO 15022 financial information interchange standards. Under ISO TC68/SC9/WG1, I?m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance. Our work is currently too experimental to be shared more broadly, so we?d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature. Greatly appreciate your help to get up and running with a local instance. Thanks! Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. _______________________________________________ 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: smime.p7s Type: application/pkcs7-signature Size: 4566 bytes Desc: not available URL: From mmorine at gmail.com Wed Feb 13 05:57:48 2019 From: mmorine at gmail.com (Melissa M) Date: Wed, 13 Feb 2019 09:57:48 -0400 Subject: [bioontology-support] Use of SNOMED CT in virtual appliance In-Reply-To: <279141E7-564E-4B76-9ED9-D52ECC687A50@stanford.edu> References: <59254943-02A2-4A7F-8DAD-2A002A93BF49@stanford.edu> <279141E7-564E-4B76-9ED9-D52ECC687A50@stanford.edu> Message-ID: Hi John, For sure. I meant to send this before but had to leave to pick up my son. I was getting an error when installing the MySQL-python python library, so I tried the solution indicated here and it worked. From that solution it looks like I needed to first install the MySQL/C connector before installing MySQL-python. I'm using macOS version 10.14. Thanks! Melissa On Tue, 12 Feb 2019 at 18:12, John Graybeal wrote: > Melissa, > > you're welcome, and we're very glad to hear it. (if you want to share your > experience, we could perhaps turn it into advice in the documentation?) > > I appreciate the news and your willingness to work with us to find > solutions. Best of luck! > > John > > On Feb 12, 2019, at 11:27 AM, Melissa M wrote: > > Hi John, > I wanted to let you know that I just got the last step of the pipeline > working and have generated the SNOMED ttl. I'm now loading it in my VA and > will let you know if I have any issues. > Thanks again for your responsiveness to all of my questions! > Melissa > > > > On Mon, 11 Feb 2019 at 18:09, John Graybeal > wrote: > >> Sorry, I think you're right about that. At least, I can't find anything >> OWLish on that page. (I just assumed the link ending in /owl was an OWL >> file. Silly me.) >> >> Back to my licensing studies! >> >> John >> >> On Feb 11, 2019, at 11:45 AM, Melissa M wrote: >> >> Hi John, >> My understanding is that this OWL needs to be generated >> >> using the IHSTDO toolkit that I mentioned before. On that page they >> indicate a perl script, but that's now been replaced with a command line >> tool + java API. The command line tool produces the OWL without synonyms >> that I was mentioning earlier. The java API might do part of what I need >> but I'm still looking into it. As far as I know, they don't provide a >> direct download of the OWL file. >> >> As for generating a ttl from the UMLS distribution, I've had no problem >> with most of the pipeline that you use at NCBO except I'm stuck on the last >> step. It looks like an issue with the MySQLdb library, but the tips >> indicated in the umls2rdf repository don't help since I'm using a different >> OS. I'll keep working on a fix but if it turns out that you're able to >> provide access to the SNOMED ttl that would be a great help. >> >> Thanks! >> Melissa >> >> >> On Mon, 11 Feb 2019 at 15:24, John Graybeal >> wrote: >> >>> Melissa, >>> >>> Were you aware SNOMEDCT is available as an OWL file at >>> https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ? >>> (Thank you Clement!) Does this address your need? >>> >>> We will look into incorporating this version into BioPortal directly, >>> but will not have time to investigate it in the short term. >>> >>> John >>> >>> On Feb 7, 2019, at 9:36 AM, John Graybeal >>> wrote: >>> >>> Hi Melissa, let me refresh my memory about the .ttl and get back to you >>> directly. >>> >>> John >>> >>> >>> ------------------------------ >>> *From:* bioontology-support < >>> bioontology-support-bounces at lists.stanford.edu> on behalf of Melissa M < >>> mmorine at gmail.com> >>> *Sent:* Thursday, February 7, 2019 09:28 >>> *To:* Clement Jonquet >>> *Cc:* support at bioontology.org >>> *Subject:* Re: [bioontology-support] Use of SNOMED CT in virtual >>> appliance >>> >>> Hi Clement, >>> Thanks very much for your reply. >>> >>> Regarding the FoodOn issue, I should mention 2 things: 1) I have the >>> same problem both on my VA and on bioportal, and 2) synonyms are properly >>> recognized for some classes and not for others. I've looked at the .owl >>> files to see if I could find any differences in specification of classes >>> whose synonyms are recognized and those whose synonyms aren't recognized, >>> and I couldn't find anything. I'd be happy to provide a few class names as >>> examples if you have time to have a look? >>> >>> About the SNOMED issue, I contacted IHTSDO and just heard back this >>> morning that the "toolkit is only currently capable of including the Fully >>> Specified Name of concepts" but they're opening my issue as a new feature. >>> In the meantime I'll start working through the pipeline that you use for >>> importing UMLS. >>> >>> Alternatively, would you be able to provide access to the SNOMED .ttl or >>> are there license restrictions? >>> >>> Thanks again for your help! >>> Melissa >>> >>> >>> >>> On Thu, 7 Feb 2019 at 03:24, Clement Jonquet wrote: >>> >>>> Melissa, >>>> >>>> A complementary note: >>>> >>>> @misha, @john >>>> BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF >>>> tool as documented. >>>> But eventually, now that Snomed International (new name for IHTSDO) >>>> provide an OWL file directly, it will be interesting one day to drop the >>>> import from UMLS and take the OWL directly. >>>> NCBO already does it for NCIt, GO, and a bunch of others that are in >>>> UMLS but not imported thru the UMLS export. >>>> MeSH is also concerned as there is now an OWL file produced by NLM. >>>> >>>> @melissa >>>> I bet the problem you have with the synonyms in the OWL version of >>>> SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right >>>> property for synonyms in the ? Edit submission information ? page. >>>> >>>> Bye >>>> Clement >>>> >>>> ------------------------------------------------------------------------------------------- >>>> Dr. Clement JONQUET - PhD in Informatics - Assistant Professor >>>> University of Montpellier (LIRMM) >>>> >>>> ------------------------------------------------------------------------------------------- >>>> >>>> Le 7 f?vr. 2019 ? 02:02, Michael Dorf a ?crit : >>>> >>>> Hi Melissa, >>>> >>>> Yes, that is the script that is being used to import UMLS ontologies >>>> into a virtual appliance. It hasn?t been updated since 2016, but it should >>>> still be valid. Let us know if you run into any issues importing. >>>> >>>> Thanks, >>>> >>>> Michael >>>> >>>> >>>> >>>> On Feb 6, 2019, at 12:10 PM, Melissa M wrote: >>>> >>>> Hi Michael, >>>> Thank you very much for your response. Can you confirm that the >>>> pipeline described here >>>> is >>>> the one currently used to import UMLS content into bioportal? I'm assuming >>>> that NCBO does not provide downloads of the output files from this pipeline >>>> (I think in ttl format)? >>>> Thanks again, >>>> Melissa >>>> >>>> >>>> On Wed, 6 Feb 2019 at 15:42, Michael Dorf wrote: >>>> >>>>> Hi Melissa, >>>>> >>>>> Thanks for contacting us again. Twice per year we do a bulk import of >>>>> terminologies distributed by the UMLS [1]. (They have a twice per year >>>>> release schedule, e.g., for this year it will be 2019AA and 2019AB). >>>>> SNOMEDCT is one of the terminologies contained in the UMLS distribution. >>>>> So, the version numbers for SNOMEDCT that you see in BioPortal correspond >>>>> to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their >>>>> distributions can be found here: >>>>> >>>>> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html >>>>> >>>>> The page contains an alphabetical list of all the terminologies >>>>> contained in the UMLS. >>>>> >>>>> Unfortunately, I?m not familiar with the IHTSDO toolkit, but I can >>>>> only assume that may contain either a different version from the one we >>>>> have in BioPortal; or a version that may not have all the properties fully >>>>> populated. >>>>> >>>>> Thanks, >>>>> >>>>> Michael >>>>> >>>>> [1] https://www.nlm.nih.gov/research/umls/ >>>>> >>>>> >>>>> >>>>> >>>>> On Feb 6, 2019, at 8:28 AM, Melissa M wrote: >>>>> >>>>> Hello, >>>>> I've recently been discussing with your team regarding use of FoodOn >>>>> in the virtual appliance but thought I'd write separately about this >>>>> question since it's unrelated to the other. >>>>> So far I've been able to import ontologies and perform annotations >>>>> more or less successfully, apart from the FoodOn issue that I've already >>>>> written about. Now I'm trying to import SNOMED CT but am noticing some >>>>> issues. First, I converted the SNOMED RF2 snapshot files to owl using the >>>>> SNOMED OWL toolkit jar provided by IHTSDO >>>>> , then imported the >>>>> resulting owl into my virtual appliance using default settings (i.e., >>>>> selected OWL format, and no changes to prefLabel/altLabel/etc properties). >>>>> The resulting ontology appears to contain all classes in the class browser, >>>>> and I can annotate text that contains exact prefLabels of the SNOMED >>>>> ontology, but it's missing many of the fields that are present in the >>>>> SNOMED instance on the bioportal server (such as synonyms, altLabels, >>>>> etc.). I therefore can't annotate any text that contains SNOMED altLabels >>>>> and synonyms. I've attached a screenshot of the SNOMED class browser in my >>>>> virtual appliance to hopefully show what I mean. >>>>> So I'm trying to figure out if I went wrong in my conversion to owl, >>>>> or import into the VA. >>>>> My question is, was the instance of SNOMED on the bioportal server >>>>> produced using the toolkit from IHTSDO? And when importing into bioportal, >>>>> were non-default settings used? >>>>> Thanks in advance for any info, >>>>> Melissa >>>>> >>>>> >>>>> _______________________________________________ >>>>> bioontology-support mailing list >>>>> bioontology-support at lists.stanford.edu >>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>>> >>>> _______________________________________________ >>> bioontology-support mailing list >>> bioontology-support at lists.stanford.edu >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >>> >>> ======================== >>> 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 jonquet at lirmm.fr Wed Feb 13 07:49:24 2019 From: jonquet at lirmm.fr (Clement Jonquet) Date: Wed, 13 Feb 2019 16:49:24 +0100 Subject: [bioontology-support] OBO upload, class browser issue In-Reply-To: <2FB582DB-C79C-4868-A87A-87635602E4E5@stanford.edu> References: <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu> <2FB582DB-C79C-4868-A87A-87635602E4E5@stanford.edu> Message-ID: <170AE375-0B23-49F9-B693-B82B098DB263@lirmm.fr> 14 months is never too late? Benjamin, if you want to know what we have done for storing ? Inter-portal ? and ? external ? mappings check out: https://github.com/agroportal/documentation/wiki/Mappings Or contact me if needed. Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) ------------------------------------------------------------------------------------------- > Le 23 nov. 2017 ? 03:54, John Graybeal a ?crit : > > The AgroPortal group, led by Clement Jonquet, has customized a virtual appliance instance of BioPortal to handle external mappings. Unfortunately, it appears to incur a significant performance hit, that has prevented us from doing the same with BioPortal, at least without a lot of work. > >> Another question I had is about mapping to outside ontologies. In this ontology xrefs, inverse_is_a and has_part relationships often link to outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc. What is the preferred way to add links to such outside ontologies in the OBO file I upload? Currently, I encode them as, for instance "has_part: HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could be linked out to the given outside resources via the web interface. > > > When you say 'outside ontologies', do you mean outside OBO or outside BioPortal? We should be able to process mappings to other terms in BioPortal (NCIT for example). > > With regard to OBO references to terms of ontologies in BioPortal, I am not sure how BioPortal processes the CURIE format for those mappings. (Perhaps a full IRI would be better?) I'll see if we can dig up any additional answers in that regard. (There might be some information in the OBO support lists also.) > > John > > >> On Nov 22, 2017, at 12:52 PM, Jennifer Leigh Vendetti > wrote: >> >> Hi Ben, >> >> >>> On Nov 20, 2017, at 8:19 PM, Benjamin Gyori > wrote: >>> >>> I modified the root node to be part of the BE ontology, and now the classes are loaded correctly. >> >> >> OK, good to hear. >> >> >>> I also really like the visualization on some of the other ontologies and would like to make it work for this one. But for some reason I get this blank view when I click on the Visualization tab: Could you help figure out what I need to change to make visualization work? >> >> >> The visualization software you?re referring to is 3rd party, developed by the University of Victoria for BioPortal a few years ago. There?s a known issue that?s cropped up where the software doesn?t work over HTTPS [1]. As of yet, we haven?t been able to secure the resources to take over development and maintenance of their code. There?s a simple workaround in the mean time though. If you modify the URL in the address bar to use HTTP, you?ll be able to see the visualizations: >> >> >> >> >> >> >>> >>> Another question I had is about mapping to outside ontologies. In this ontology xrefs, inverse_is_a and has_part relationships often link to outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc. What is the preferred way to add links to such outside ontologies in the OBO file I upload? Currently, I encode them as, for instance "has_part: HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could be linked out to the given outside resources via the web interface. >> >> If I understood your question correctly, we don?t offer this kind of functionality. The mappings we generate are between ontology classes from the set of ontologies that exist in BioPortal. I did a quick search and the ontologies you mentioned above don?t appear to have been uploaded into our application, although they could be if they are published in a format we can handle. >> >> I vaguely recall a research group that may have customized a virtual appliance instance of BioPortal to handle external mappings. Let me see if I can track that information down. >> >> Kind regards, >> Jennifer >> >> [1] https://github.com/ncbo/biomixer/issues/2 >> >> >> _______________________________________________ >> 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 Wed Feb 13 07:28:29 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 13 Feb 2019 07:28:29 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Dino Fanfan Message-ID: <5c64379d515ee_330e2abf8963121c6637a@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Feb 13 12:39:16 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 13 Feb 2019 20:39:16 +0000 Subject: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? In-Reply-To: <3ad8da14d88b4cdc82cec3392dd8648d@BEEXCL32.swift.corp> References: <25191a1a769d4bce8b18de595488ea4b@BEEXCL32.swift.corp> <3ad8da14d88b4cdc82cec3392dd8648d@BEEXCL32.swift.corp> Message-ID: No, BIoPortal is agnostic with regard to compliance with upper ontologies including BFO. BioPortal does have one accommodation that relates to BFO. The class trees displayed by BioPortal do not show 'continuant' and 'occurent' classes at the head of these trees. because we found it confusing for many users over the years. My warning is that opinions tend to be strongly held in this regard. One bit of advice is to consider the tooling and community resources available when you choose to use (or not use) an ontology framework. Your ability to communicate, collaborate, and get advice about your ontology may be more important than the actual representations (and constraints) offered by a particular framework. You may want to send an email to the Protege support list (see https://protege.stanford.edu/support.php) soliciting more advice, particularly if you want to put forward specific modeling concerns or goals of your effort. (You may also find out about existing related efforts via that support list.) John On Feb 13, 2019, at 1:51 AM, OSBORNE Jamie > wrote: Thanks John ? downloading and getting setup now ? One question that I have already after digging around on the online portal is whether the ontoportal technical stack has built-in any assumptions/requirements that ontologies are compliant with BFO? While I appreciate the benefits of a foundational/operational ontology, we haven?t yet reached any agreement in Finance about which, if any, we will implement. Some of my peers have raised concerns that BFO is not well suited to our industry and have proposed (or developed) alternatives. Do you have any thoughts, warnings, or expert advice for us? Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: 12 February 2019 23:33 To: OSBORNE Jamie Cc: support at bioontology.org Subject: Re: [bioontology-support] Access to a copy of the VMWare Virtual Appliance? Mail originates from outside SWIFT ! Be vigilant before you click on a link, open attachments or reply ! ------------------------------------------------------------------------- Hi again Jamie, Thank you for providing your information with your request. You can now access this page that contains the download and documentation links: http://bioportal.bioontology.org/virtual_appliance We are now providing version 2.5 of the Virtual Appliance, which implements a "call home" feature to determine whether there is an update available. I notice that you want to work with an AWS instance; unfortunately this is still at version 2.4. We hope to have a new AMI available before too long, but perhaps you'd like to contact me about your specific situation. Also, if you have any questions or thoughts about your use of the Virtual Appliance, please feel free to contact me. Our licensing may be change before too long and it will be good to give you an update on that as well. For any questions about the installation or ontology population process, please email support at bioontology.org. And since requests for Virtual Appliance support are made through this NCBO Support email list, we suggest you sign up for the email list at https://mailman.stanford.edu/mailman/listinfo/bioontology-support. This will help you keep up to date on the BioPortal and Virtual Appliance systems. John On Feb 10, 2019, at 12:52 PM, OSBORNE Jamie > wrote: Hi NCBO team, Impressive work - I?d like to get my hands on a copy of the appliance to explore whether we can use it to publish some Financial Services ontologies that we are developing. I?m reaching out on behalf of SWIFT Standards, where I am responsible for developing and publishing ontologies for the ISO 20022 and ISO 15022 financial information interchange standards. Under ISO TC68/SC9/WG1, I?m working with technical and business colleagues from all other significant financial standardisation bodies to design and deliver a common ontology for Finance. Our work is currently too experimental to be shared more broadly, so we?d prefer to work locally on our own machines, and with a more privately share AWS instance until we are a little more mature. Greatly appreciate your help to get up and running with a local instance. Thanks! Kind regards, Jamie OSBORNE Systems Architect Standards Research S.W.I.F.T. SCRL Tel: +32 (0)2 655 3229 Mob: +32 (0)474 990 988 E-mail: jamie.osborne at swift.com Twitter: JamieAtSWIFT LinkedIn *** Check out our new API Whitepaper and API Developer Portal *** ? Please consider the environment before printing This e-mail and any attachments thereto may contain information which is confidential and/or proprietary and intended for the sole use of the recipient(s) named above. If you have received this e-mail in error, please immediately notify the sender and delete the mail. Thank you for your co-operation. SWIFT reserves the right to retain e-mail messages on its systems and, under circumstances permitted by applicable law, to monitor and intercept e-mail messages to and from its systems. Please visit www.swift.com for more information about SWIFT. _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Feb 13 12:54:55 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 13 Feb 2019 20:54:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Dino Fanfan In-Reply-To: <5c64379d515ee_330e2abf8963121c6637a@ncbo-prd-app-08.stanford.edu.mail> References: <5c64379d515ee_330e2abf8963121c6637a@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Dino, Thank you for contacting us. You can submit a new ontology to BioPortal by following these steps: 1. Create a BioPortal account by visiting this page: https://bioportal.bioontology.org/accounts/new 2. Login to your BioPortal account and navigate to: https://bioportal.bioontology.org/ontologies 3. Click on ?Submit New Ontology? button and follow a series of forms that create a general ontology record as well as a version specific ontology submission record. If you need to keep any of your ontologies private, but still want them available to REDCap, please contact us for further instructions. If you run into any issues during the submission, please don?t hesitate to write to us. (Note that we are not experienced ourselves with REDCap, and can not offer directions on how to configure it to work with BioPortal.) John On Feb 13, 2019, at 7:28 AM, support at bioontology.org wrote: Name: Dino Fanfan Email: dfanfan at miami.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Good Morning, My name is Dino Fanfan and I'm a project coordinator at the University of Miami's Sylvester Comprehensive Cancer Center. I emailing to inquire what the steps are to register an ontology with your service. A lot of the processes we use in our center could benefit from a standardize list which would be incorporated into RedCap and would improve our data processing methods greatly. Thank you for taking the time to read this, and I'll look forward to hearing from you. Regards, Dino Fanfan _______________________________________________ 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 support at bioontology.org Wed Feb 13 20:24:22 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 13 Feb 2019 20:24:22 -0800 Subject: [bioontology-support] [BioPortal] Feedback from rakesh Message-ID: <5c64ed76392ad_5e5d2b22eed0ef588871d@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Feb 14 11:41:18 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 14 Feb 2019 19:41:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from rakesh In-Reply-To: <5c64ed76392ad_5e5d2b22eed0ef588871d@ncbo-prd-app-08.stanford.edu.mail> References: <5c64ed76392ad_5e5d2b22eed0ef588871d@ncbo-prd-app-08.stanford.edu.mail> Message-ID: hello Rakesh, To get all the fields shown in the UI, you can modify your REST call to use the ?include=all? parameter, e.g.: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C71721?include=all You may be interested to look over the ?common parameters? section of our REST API documentation, which describes parameters like ?include?: http://data.bioontology.org/documentation#nav_usage John On Feb 13, 2019, at 8:24 PM, support at bioontology.org wrote: Name: rakesh Email: rakesh at pieriandx.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F500%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fncicb.nci.nih.gov%252Fxml%252Fowl%252FEVS%252FThesaurus.owl%2523C71721%26jump_to_nav%3Dtrue Feedback: Hello, Using the API how can I get all the fileds shown in the UI. I only see a subset when using the classes endpoint of your API. Thanks, Rakesh _______________________________________________ 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 sebastian.luehr at bayer.com Fri Feb 15 00:49:41 2019 From: sebastian.luehr at bayer.com (Sebastian Luehr) Date: Fri, 15 Feb 2019 08:49:41 +0000 Subject: [bioontology-support] install instruction for bioportal_web_ui Message-ID: Hello BioPortal Team, Thank you for developing such an awesome product for the scientific community. If used it a lot during my studies in biology. Currently we are evaluating ontology browsers I would love to test the technical side of bioportal. Unfortunately, we are not allowed to run any VM or AMI from external sources. So it would be nice if you can maybe provide an instruction on how to install the bioportal_web_ui, which is present in your git repository. (https://github.com/ncbo/bioportal_web_ui/) Many thanks in advance Sebastian -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.day at pinky.co.uk Fri Feb 15 06:25:42 2019 From: chris.day at pinky.co.uk (chris.day at pinky.co.uk) Date: Fri, 15 Feb 2019 14:25:42 -0000 Subject: [bioontology-support] Request for the virtual appliance Message-ID: <003401d4c53a$55ec1fa0$01c45ee0$@pinky.co.uk> Hi NCBO Support - I'm working within ISO TC68/SC9/WG1, to design and deliver a common ontology for Finance and would appreciate your help to get a local virtual appliance . You've been in contact with one of my colleagues, Jamie Osborne, from SWIFT over the weekend about this. My username/account is chrisday Cheers Chris Day c: +44 7930 909 297 p: +44 115 714 0869 s: bigchrisday https://www.linkedin.com/in/chrisdayabinitio/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 15 16:20:28 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 16 Feb 2019 00:20:28 +0000 Subject: [bioontology-support] install instruction for bioportal_web_ui In-Reply-To: References: Message-ID: <13CACEB1-7EED-4C49-A83E-A783C36AF7EE@stanford.edu> Hi Sebastian, On Feb 15, 2019, at 12:49 AM, Sebastian Luehr > wrote: Currently we are evaluating ontology browsers I would love to test the technical side of bioportal. Unfortunately, we are not allowed to run any VM or AMI from external sources. So it would be nice if you can maybe provide an instruction on how to install the bioportal_web_ui, which is present in your git repository. (https://github.com/ncbo/bioportal_web_ui/) Apologies - I don?t have anything to point you at immediately. We?re a very small team and haven?t dedicated resources as of yet to thoroughly documenting our local development environment. The project you mention above only encapsulates our front end code. There are a number of other GitHub repositories in our organization that make up the back end code for our REST API. Please give us a day or so to discuss this internally and we?ll get back to you early next week. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From tai at brookpath.com Tue Feb 19 07:41:15 2019 From: tai at brookpath.com (Lisa Taikitsadaporn) Date: Tue, 19 Feb 2019 10:41:15 -0500 Subject: [bioontology-support] Access to NCBO Virtual Appliance Message-ID: <00ae01d4c869$8cff4d50$a6fde7f0$@brookpath.com> Dear NCBO Support team I am contacting you as a representative of the FIX Protocol (www.fixtrading.org) , an open source financial messaging standard. We are working with a number of experts under the ISO TC68/SC9/WG1 and you may have already heard from my fellow working group members Jamie Osborne and Chris Day with their request to obtain access to the Virtual Appliance for their local environment. At FIX we are standing up an AWS instance to host the NCBO virtual appliance for the working group to continue our collaboration on ontology development. For the time being this will be private until such time we can open it up to the public as much of our semantic and ontology development is still not mature enough. I have also copied a colleague of mine, Rich Shriver, who will be the one responsible for the installation on our AWS instance. I would greatly appreciate your help in providing us with the access to the imagine and getting this up and running. Best regards, Lisa Taikitsadaporn FIX Protocol Ltd., Technical Project Manager TC68/SC9/WG1 Convenor -- Managing Partner Brook Path Partners, Inc. 60 State Street, Suite 700 Boston, MA 02109, USA Tel: +1.617.988.2729 Ext. 00216 Web: http://www.brookpath.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Feb 19 13:36:43 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 19 Feb 2019 21:36:43 +0000 Subject: [bioontology-support] Access to NCBO Virtual Appliance In-Reply-To: <00ae01d4c869$8cff4d50$a6fde7f0$@brookpath.com> References: <00ae01d4c869$8cff4d50$a6fde7f0$@brookpath.com> Message-ID: <433D8068-79A3-461D-913A-3EA7C2C1A326@stanford.edu> Hello Lisa, Yes, we've been working with Jamie Osborne. I will contact you offline to clarify next steps. John On Feb 19, 2019, at 7:41 AM, Lisa Taikitsadaporn > wrote: Dear NCBO Support team I am contacting you as a representative of the FIX Protocol (www.fixtrading.org) , an open source financial messaging standard. We are working with a number of experts under the ISO TC68/SC9/WG1 and you may have already heard from my fellow working group members Jamie Osborne and Chris Day with their request to obtain access to the Virtual Appliance for their local environment. At FIX we are standing up an AWS instance to host the NCBO virtual appliance for the working group to continue our collaboration on ontology development. For the time being this will be private until such time we can open it up to the public as much of our semantic and ontology development is still not mature enough. I have also copied a colleague of mine, Rich Shriver, who will be the one responsible for the installation on our AWS instance. I would greatly appreciate your help in providing us with the access to the imagine and getting this up and running. Best regards, Lisa Taikitsadaporn FIX Protocol Ltd., Technical Project Manager TC68/SC9/WG1 Convenor -- Managing Partner Brook Path Partners, Inc. 60 State Street, Suite 700 Boston, MA 02109, USA Tel: +1.617.988.2729 Ext. 00216 Web: http://www.brookpath.com _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Feb 20 08:02:44 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 20 Feb 2019 08:02:44 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Warren Welch Message-ID: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From RFollett at mednet.ucla.edu Wed Feb 20 09:24:59 2019 From: RFollett at mednet.ucla.edu (Follett, Robert W.) Date: Wed, 20 Feb 2019 17:24:59 +0000 Subject: [bioontology-support] Problem with Page 544 in LOINC ontology Message-ID: Hello, I am running the NCBO Extract tool to download the LOINC 2018AA ontology and kept receiving a timeout on page 544. When I restart at page 545, it continues just fine. I cannot access the page manually either: http://data.bioontology.org/ontologies/LOINC/classes?include=properties,synonym,children&format=xml&apikey=YOURKEY&page=544 Thanks, Rob Follett Lead Data Analyst Biomedical Informatics Program Clinical and Translational Science Institute (CTSI) (310) 794-8044 rfollett at mednet.ucla.edu This message and any included attachments are intended only for the addressee. The information contained in this message is confidential and may constitute proprietary or non-public information under international, federal, or state laws. Unauthorized forwarding, printing, copying, distribution, or use of such information is strictly prohibited and may be unlawful. If you are not the addressee, please promptly delete this message and notify the sender of the delivery error by e-mail * CTSI Investigators: Please cite NIH/NCATS Grant #UL1TR001881 ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Feb 20 16:10:32 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 21 Feb 2019 00:10:32 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Warren Welch In-Reply-To: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> References: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Warren, I am able to find the resource for DRON_00087099 using the general ontology search, but only by going to the Advanced Search option and checking the Include Property Values box: http://bioportal.bioontology.org/search?q=DRON_00087099&ontologies=&include_properties=true&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories= Similarly, I can find Biotene Dry Mouth in two references using a similar strategy and 'Biotene' as the search string (http://bioportal.bioontology.org/ontologies/DRON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDRON_00086792): * http://bioportal.bioontology.org/ontologies/DRON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDRON_00086792 * http://bioportal.bioontology.org/ontologies/DRON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDRON_00087099 I am unable to tell you if the exact term you are looking for was eliminated in error, and our ontology expert is unavailable to investigate this further in the next few days, but perhaps one of the two other concepts would be useful to you for now. I see that the ontobee lookup for this concept shows it as you describe: http://www.ontobee.org/ontology/DRON?iri=http://purl.obolibrary.org/obo/DRON_00087099 Since we both seem to have the same ontology version for DRON, we will investigate the discrepancy further and let you know what we find. If you need further assistance please feel free to check again. John On Feb 20, 2019, at 8:02 AM, support at bioontology.org wrote: Name: Warren Welch Email: Warren.welch at cchmc.org Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDRON%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDRON_00087099%26jump_to_nav%3Dtrue Feedback: Good morning, Biotene Dry Mouth is coded as 1147902 seems to have disappeared from the drug ontology search. Is there a substitution or was this eliminated in error? Any information you can provide is appreciated _______________________________________________ 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 Wed Feb 20 21:22:44 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 21 Feb 2019 05:22:44 +0000 Subject: [bioontology-support] Problem with Page 544 in LOINC ontology In-Reply-To: References: Message-ID: <397E6152-657D-479B-B910-7F4A4B96ECB3@stanford.edu> Hi Robert, Sorry for the trouble. We're a bit short-handed at the moment but we'll have a look as soon as we can. John On Feb 20, 2019, at 9:24 AM, Follett, Robert W. > wrote: Hello, I am running the NCBO Extract tool to download the LOINC 2018AA ontology and kept receiving a timeout on page 544. When I restart at page 545, it continues just fine. I cannot access the page manually either: http://data.bioontology.org/ontologies/LOINC/classes?include=properties,synonym,children&format=xml&apikey=YOURKEY&page=544 Thanks, Rob Follett Lead Data Analyst Biomedical Informatics Program Clinical and Translational Science Institute (CTSI) (310) 794-8044 rfollett at mednet.ucla.edu This message and any included attachments are intended only for the addressee. The information contained in this message is confidential and may constitute proprietary or non-public information under international, federal, or state laws. Unauthorized forwarding, printing, copying, distribution, or use of such information is strictly prohibited and may be unlawful. If you are not the addressee, please promptly delete this message and notify the sender of the delivery error by e-mail * CTSI Investigators: Please cite NIH/NCATS Grant #UL1TR001881 ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ 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 support at bioontology.org Thu Feb 21 10:47:08 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 21 Feb 2019 10:47:08 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Thomas Chong Message-ID: <5c6ef22ce8726_2fcf2ab3ceacb3e8838dd@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Feb 21 11:30:00 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 21 Feb 2019 19:30:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Warren Welch In-Reply-To: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> References: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <3334E9B9-0EEC-4EC3-AC4C-9A1B630AFB0E@stanford.edu> Hello Warren, On Feb 20, 2019, at 8:02 AM, support at bioontology.org wrote: Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDRON%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDRON_00087099%26jump_to_nav%3Dtrue Biotene Dry Mouth is coded as 1147902 seems to have disappeared from the drug ontology search. Is there a substitution or was this eliminated in error? BioPortal is configured to pull new versions of the Drug Ontology from this URL: http://purl.obolibrary.org/obo/dron.owl Our application pulled and processed a new version of DRON about a week ago on Feb. 15th (version # "2019-02-15?). It?s unclear to me from your message if you weren?t able to find the class via search, or if you were asking about the code associated with that class. I downloaded and looked at the content of the ontology source file. The class that you refer to above (with ID http://purl.obolibrary.org/obo/DRON_00087099) is declared with has_RxCUI of 1147905. I don?t see any indication that BioPortal is displaying the code data incorrectly. Could you please clarify? Kind regards, Jennifer [cid:F325505B-4744-4FEC-97D1-211B038D4000 at stanford.edu][cid:B9F0AA7F-1816-41D7-8D54-A0F516C751C6 at stanford.edu] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-02-21 11.25.06.png Type: image/png Size: 753523 bytes Desc: Screenshot 2019-02-21 11.25.06.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2019-02-21 11.27.04.png Type: image/png Size: 546866 bytes Desc: Screenshot 2019-02-21 11.27.04.png URL: From vendetti at stanford.edu Thu Feb 21 12:19:53 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 21 Feb 2019 20:19:53 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Warren Welch In-Reply-To: References: <5c6d7a2462fd2_7ee72afa321575002237a@ncbo-prd-app-08.stanford.edu.mail> <3334E9B9-0EEC-4EC3-AC4C-9A1B630AFB0E@stanford.edu> Message-ID: <4CAD6F0E-857C-439C-B4A7-283DE9CB8D71@stanford.edu> Hi Warren, I downloaded the two previous versions of the Drug Ontology source files from our system from 2016 and 2015 respectively. I searched the source files for the code ?1147902? and found no results. There are no results for this code in the most recent version from 2019 either. Apologies, but I?m not sure how I can be of assistance here. It looks like we?re serving the correct code from both the BioPortal application, and our REST API. Kind regards, Jennifer On Feb 21, 2019, at 11:41 AM, Welch, Warren > wrote: Hi Jennifer, We are using an ontology search in REDCap which points to your portal (I?m not sure which url it actually uses). They used to just search for Biotene and then it would come up with 1147902. Sorry, I really don?t have any more detail than that. Warren From: Jennifer Leigh Vendetti > Date: Thursday, February 21, 2019 at 2:30 PM To: "support at bioontology.org" > Cc: Warren Welch > Subject: Re: [bioontology-support] [BioPortal] Feedback from Warren Welch Hello Warren, On Feb 20, 2019, at 8:02 AM, support at bioontology.org wrote: Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDRON%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDRON_00087099%26jump_to_nav%3Dtrue Biotene Dry Mouth is coded as 1147902 seems to have disappeared from the drug ontology search. Is there a substitution or was this eliminated in error? BioPortal is configured to pull new versions of the Drug Ontology from this URL: http://purl.obolibrary.org/obo/dron.owl Our application pulled and processed a new version of DRON about a week ago on Feb. 15th (version # "2019-02-15?). It?s unclear to me from your message if you weren?t able to find the class via search, or if you were asking about the code associated with that class. I downloaded and looked at the content of the ontology source file. The class that you refer to above (with ID http://purl.obolibrary.org/obo/DRON_00087099) is declared with has_RxCUI of 1147905. I don?t see any indication that BioPortal is displaying the code data incorrectly. Could you please clarify? Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From beijingcdy at yeah.net Thu Feb 21 21:31:30 2019 From: beijingcdy at yeah.net (truename) Date: Fri, 22 Feb 2019 13:31:30 +0800 (CST) Subject: [bioontology-support] VMWare Virtual Appliance Message-ID: <3c39f1ae.693b6.16913afedcd.Coremail.beijingcdy@yeah.net> Dear Bioportal: We are a team in the Institute of Medicinal Plant Development. We apply to obtain the VMWare Virtual Appliance, and want to establish Herbal Semantic Web. Thanks very much for your helps. Best regards. Yours Dayong Cai 2019-02-22 Email: dycai at implad.ac.cn, beijingcdy at yeah.net Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College Add No151, Malianwa North Road, Haidian District, Beijing, China. 100193 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 21 22:42:07 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 21 Feb 2019 22:42:07 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Claudiu Aeptrei Message-ID: <5c6f99bfe0f2a_75242ae5c2383704103e6@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 21 23:15:31 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 21 Feb 2019 23:15:31 -0800 Subject: [bioontology-support] [BioPortal] Feedback from katoh_nobutake Message-ID: <5c6fa1935926b_73552ae5c238376810345@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Fri Feb 22 05:04:24 2019 From: support at bioontology.org (support at bioontology.org) Date: Fri, 22 Feb 2019 05:04:24 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Bhavani Gunasekaran Message-ID: <5c6ff35850976_32f62b01584bec988184e@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 22 09:48:38 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 22 Feb 2019 17:48:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Claudiu Aeptrei In-Reply-To: <5c6f99bfe0f2a_75242ae5c2383704103e6@ncbo-prd-app-08.stanford.edu.mail> References: <5c6f99bfe0f2a_75242ae5c2383704103e6@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <2F4A018F-0041-40F6-A0DD-EF5D2E5F8914@stanford.edu> Hello Claudia, On Feb 21, 2019, at 10:42 PM, support at bioontology.org wrote: Hi, Don't know if you noticed but the website & api seem to be down. Yes - we experienced some difficulties with BioPortal overnight. The site and API are restored now. Apologies for the inconvenience. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 22 09:56:55 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 22 Feb 2019 17:56:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Bhavani Gunasekaran In-Reply-To: <5c6ff35850976_32f62b01584bec988184e@ncbo-prd-app-08.stanford.edu.mail> References: <5c6ff35850976_32f62b01584bec988184e@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <4322C47D-FC84-4CDA-8A29-BB3A8C3075E2@stanford.edu> Hello Bhavani, On Feb 22, 2019, at 5:04 AM, support at bioontology.org wrote: Name: Bhavani Gunasekaran Email: bhavani at azidus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2F404%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FMEDDRA%252F10024689%26jump_to_nav%3Dtrue Feedback: Hi I have been using the portal for coding but unfortunately when I tried using it today an error message pops up. Kindly rectify the error at the earliest to continue using the portal. We had some technical difficulties with BioPortal overnight. The site is restored now. Apologies for the inconvenience. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Feb 22 10:01:18 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 22 Feb 2019 18:01:18 +0000 Subject: [bioontology-support] [BioPortal] Feedback from katoh_nobutake In-Reply-To: <5c6fa1935926b_73552ae5c238376810345@ncbo-prd-app-08.stanford.edu.mail> References: <5c6fa1935926b_73552ae5c238376810345@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Kato, We had some technical difficulties with BioPortal overnight, which I think is the reason you were seeing error messages from our user interface. The site is restored now. I looked at your ontology. Submission 1 was deleted, and submission 2 is visible in the user interface. Everything seems to be in order. Let us know if you?re still having difficulties. Apologies for the inconvenience. Kind regards, Jennifer On Feb 21, 2019, at 11:15 PM, support at bioontology.org wrote: Name: katoh_nobutake Email: kato.nobutake at cij.co.jp Location: https%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: Hi, I'm editing an Ontology data(Acronym "TXPO"). I had two submissions of that. Their ID are "1" and "2". And deleted submissionID "1" by the command below. >curl -X DELETE "https://data.bioontology.org/ontologies/TXPO/submissions/1?apikey={apikey}" Then, The server returned the message " Internal Server Error ". After that, I accessed the URI below, http://data.bioontology.org/ontologies/TXPO/submissions?display=submissionId,version the data submission "1" was deleted, so I thought it succeed. But, then I accessed the URI below, https://bioportal.bioontology.org/ontologies/TXPO and an error happened. The error message is below. "We're sorry but something has gone wrong. We have been notified of this error." I'm afraid I took some wrong processes to delete a data. Tell me how I should do. Thanks. -- kato.nobutake at cij.co.jp _______________________________________________ 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 Fri Feb 22 11:14:19 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 22 Feb 2019 19:14:19 +0000 Subject: [bioontology-support] VMWare Virtual Appliance In-Reply-To: <3c39f1ae.693b6.16913afedcd.Coremail.beijingcdy@yeah.net> References: <3c39f1ae.693b6.16913afedcd.Coremail.beijingcdy@yeah.net> Message-ID: <7383EB35-F825-4ACB-98D8-6F9F4A1C151A@stanford.edu> Hello, Thank you for your interest in the virtual appliance, I will be happy to help you with your request. To implement your request, please give us the following information: - your BioPortal user name -- if you need a BioPortal user name go to http://bioportal.bioontology.org/accounts/new - a one to two sentence description of your project We usually respond within a business day upon receiving this information. Also, while you are waiting, please note that requests for Virtual Appliance support are also made through the NCBO Support email list. Therefore, we suggest you sign up for that email list at https://mailman.stanford.edu/mailman/listinfo/bioontology-support. This will help you keep up to date on the BioPortal and Virtual Appliance systems. John On Feb 21, 2019, at 9:31 PM, truename > wrote: Dear Bioportal: We are a team in the Institute of Medicinal Plant Development. We apply to obtain the VMWare Virtual Appliance, and want to establish Herbal Semantic Web. Thanks very much for your helps. Best regards. Yours Dayong Cai 2019-02-22 Email: dycai at implad.ac.cn, beijingcdy at yeah.net Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College Add No151, Malianwa North Road, Haidian District, Beijing, China. 100193 _______________________________________________ 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 jonquet at lirmm.fr Fri Feb 22 12:03:24 2019 From: jonquet at lirmm.fr (Clement Jonquet) Date: Fri, 22 Feb 2019 21:03:24 +0100 Subject: [bioontology-support] Multiple postions in the semantic web area: research engineer, postdoc and 2 doctorate at LIRMM (Montpellier, France) Message-ID: <47FA8136-A89B-4BA4-8893-3B641E915A63@lirmm.fr> Hello everyone, The French ANR D2KAB (Data to Knowledge in Agronomy and Biodiversity) project, offers several positions in the semantic web domain at LIRMM in Montpellier, France: http://d2kab.strikingly.com/#positions Two positions (minimum 18 months) to work on the platform AgroPortal, a portal of ontologies and vocabularies in agronomy: - Research Engineer / Developer (semantic web, ontology-based service) - Postdoc / Researcher (semantic Web , ontology management and alignment) Two PhD project: - PhD (ontology alignment and property graph) - PhD (data linking and enrichment) Do not hesitate to contact us for more information.Applications by email will not be accepted, please use the links provided. Best regards, Clement Jonquet ------------------------------------------------------------------------------------------- Dr. Clement JONQUET - PhD in Informatics - Assistant Professor University of Montpellier (LIRMM) Coordinator of the SIFR and AgroPortal projects EU Marie Curie fellow jonquet at lirmm.fr http://www.lirmm.fr/~jonquet @Montpellier : +33/0 4 67 14 97 43 ------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Feb 25 22:35:11 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 25 Feb 2019 22:35:11 -0800 Subject: [bioontology-support] [BioPortal] Feedback from hyehyeon2 Message-ID: <5c74de1f82793_c442b1fca0cdef042351@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Feb 26 12:16:02 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 26 Feb 2019 20:16:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from hyehyeon2 In-Reply-To: <5c74de1f82793_c442b1fca0cdef042351@ncbo-prd-app-08.stanford.edu.mail> References: <5c74de1f82793_c442b1fca0cdef042351@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello, I assume you?re referring to the CMDO ontology: http://bioportal.bioontology.org/ontologies/CMDO ? You didn?t specify which ontology in your message. I?m not able to reproduce this issue - I can see the class tree without errors in BioPortal. I downloaded your ontology source file and opened it in the Protege ontology editor. The number of classes reported by Protege is the same as BioPortal (182). Please clarify what sort of issue you?re having with the class metrics. Jennifer [cid:8AB51F3C-0EEF-42D3-A653-F525C12B8E9D at stanford.edu] [cid:6E5F093E-723E-448C-9F91-EA95FE83505D at stanford.edu] [cid:7636264E-B439-4053-B037-7A72660650CD at stanford.edu] On Feb 25, 2019, at 10:35 PM, support at bioontology.org wrote: Name: hyehyeon2 Email: hyehyeon2 at snu.ac.kr Location: https%3A%2F%2Fbioportal.bioontology.org%2Fhelp Feedback: We have a problem to upload a new version of our ontology. The classes of new version ontology were not able to see in the browser. The number of classes were changed from 161 to 188 in the new version. _______________________________________________ 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... 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URL: From support at bioontology.org Wed Feb 27 05:49:15 2019 From: support at bioontology.org (support at bioontology.org) Date: Wed, 27 Feb 2019 05:49:15 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Osnat Hakimi Message-ID: <5c76955b6e13f_70502aff8bc84e10717c2@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Feb 27 11:32:00 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 27 Feb 2019 19:32:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mikkel I. Christensen In-Reply-To: <5c7647aac36d3_46292af7b4cb8f50304fb@ncbo-prd-app-09.stanford.edu.mail> References: <5c7647aac36d3_46292af7b4cb8f50304fb@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <6E2D5631-3C65-4CB7-A17A-938DA36A4FBE@stanford.edu> I'm sorry Mikkel, but we are unable to help you with the specifics of this ontology. I encourage you to contact the ontology contact given on the ontology summary page (http://bioportal.bioontology.org/ontologies/MEDDRA). In this case that is "MedDRA MSSO, mssohelp at meddra.org". That contact will be more familiar with the ontology itself, and may be able to respond to your question. john On Feb 27, 2019, at 12:17 AM, support at bioontology.org wrote: Name: Mikkel I. Christensen Email: mikkelch at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FMEDDRA%252F10043554 Feedback: Hello I am a third year medical student in Denmark. While writing a report on the effect of Elotuzumab vs Carfilzomib in the treatment of relapsed and/or refractory Multiple Myeloma patients, I came across some terms in the adverse effects(AE) section that caused me some confusion. I have two oberservations which i hope you could shed some light on 1) In one study (DOI: 10.1002/cncr.31680), they list in the same table two AE's (Lymphocytopenia vs Lymphopenia),which share a similar name and when you google the difference, there seem to be none. Lymphocytopenia is listed under "common hematologic toxic effects" and Lymphopenia is listed under "common non-hematologic adverse effects" The values are different, but what is the difference between the two terms? 2)In another study (DOI: 10.1200/JCO.2017. 76.5032) They list Thrombocytopenia under "most common events" and Hematopoetic Thrombocytopenia under "Events of interest" again with different values. Again, confusion strikes me. What is the difference between those two terms? I hope you can help Best regards Mikkel _______________________________________________ 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 Wed Feb 27 11:34:37 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 27 Feb 2019 19:34:37 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Osnat Hakimi In-Reply-To: <5c76955b6e13f_70502aff8bc84e10717c2@ncbo-prd-app-08.stanford.edu.mail> References: <5c76955b6e13f_70502aff8bc84e10717c2@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9A82D237-A124-451F-9278-F61449D91A25@stanford.edu> Hello Dr. Hakimi, It is generally our expectation that public ontologies that do not explicitly list a license do not have restrictions regarding their use. However, to confirm this I would encourage you to contact the ontology contact, listed on its summary page as Federica Viti (and Alessandro Orro), federica.viti at itb.cnr.it. John On Feb 27, 2019, at 5:49 AM, support at bioontology.org wrote: Name: Osnat Hakimi Email: osnat.hakimi at upc.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBCTEO Feedback: Dear sir/Madam, I am writing to inquire about ontology: Bone/Cartilage Tissue Engineering Ontology (BCTEO) Is it freely available for public use? are there any restrictions regarding importation of the ontology into a new one? Many thanks Dr Osnat Hakimi MSCA-IF Fellow Universitat Polit?cnica de Catalunya Biomaterials, Biomechanics and Tissue Engineering Group Dept. Materials Science and Metallurgical Engineering Av. Eduard Maristany 16, edif i4.5 08930 Barcelona, Spain Tel: +34 93 413 7218 Email: osnat.hakimi at upc.edu _______________________________________________ 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 john.zobolas at ntnu.no Thu Feb 28 03:54:18 2019 From: john.zobolas at ntnu.no (John Zobolas) Date: Thu, 28 Feb 2019 11:54:18 +0000 Subject: [bioontology-support] Questions regarding the REST API In-Reply-To: <1541967499734.46992@ntnu.no> References: <1541771841693.45184@ntnu.no>, , <1541967499734.46992@ntnu.no> Message-ID: <1551354858511.5081@ntnu.no> Hi Michael, Regarding point No. 4 (format of error responses) I have noticed that when no proper API key is used, you get a result back in the form: { * "status": 401, * "error": "You must provide a valid API Key. Your API Key can be obtained by logging in at bioportal.bioontology.org/account" } which is different than the "standard" you mention: { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } Just mentioning it, I don't know if its something you want to change or why it is that way (and probably you know it already). BR, John. ________________________________ From: Michael Dorf Sent: Saturday, November 10, 2018 12:46 AM To: John Zobolas Cc: support at bioontology.org Subject: Re: [bioontology-support] Questions regarding the REST API Hi John, Thanks for contacting us. See my answers inline below. On Nov 9, 2018, at 5:57 AM, John Zobolas > wrote: Hi, I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things: 1. ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma) which almost always (as far as I can tell) isfalse. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:falseones? The results are by default filtered on obsolete:false. There is a parameter called also_search_obsolete={true|false} if you want a more granular control over this flag. 1. Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!) Both paramours work, but the correct one to use is display_context={true|false}, which is the one advertised in our documentation. 1. I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym, will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type). You can create ontologies/groups programmatically using your own API key via a POST call, but you cannot delete anything from the system. That function is limited to admins only. 1. The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr Yes, the errors should all have a uniform response. If you notice otherwise, that would probably constitute a bug. Let us know if you find an error that deviates from this format. { * - "errors": [ * "You must provide a valid `acronym` to retrieve an ontology" ], * "status": 404 } { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } 1. If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right? Correct. These two endpoints appear to have a slightly different handling of the empty fields. The classes endpoint displays empty lists, where as the search endpoint just drops the empty attributes from the response. Example: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 http://data.bioontology.org/search?q=CALR%20NM_004343.3:c.1092_1143del52&ontologies=NCIT&require_exact_match=true 1. Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string? You can try calling the search endpoint without passing in a search string and limiting the results to a specific ontology. You need to pass a ?special? parameter called ?ontology_types=ONTOLOGY? in order for the queriless search to work: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY This will give you ALL results stored in our search index for the ontology NCIT. This isn?t the ?advertised? method of getting all classes, rather a ?workaround? that let?s you execute a search call without passing a query string. Really helpful!!! I noticed also that when you do: http://data.bioontology.org/ontologies/NCIT/classes/ you get a total count of 144695 classes, while the query http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY returns 140329 as a total count and the difference must be that the first has the obsolete terms as well, right? Because if I do: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY&also_search_obsolete=true, then I get 144695! Is there a specific ordering on the returned results on the query: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY? Are the results ordered by prefLabel or @id for example?(doesn't seem to be the case) Also, does this query return all classes in all ontologies in BioPortal: http://data.bioontology.org/search?ontologies=&ontology_types=ONTOLOGY ? And if so, what ordering is applied to the results? 1. I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does. Again, correct! The @id represents the class ID as defined in the original source ontology. The same class can be reused in multiple ontologies. The ?unique? ID of a class in BioPortal is a combination of the @id and the ontology acronym, as in: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 Useful to know! 1. Is there a way to get results by id? Something like: /searchByID/id=URLid (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,?}? Yes, you can pass the URL-encoded full ID in the ?q? parameter to the /search endpoint: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true Actually I kinda though that the `search?q=something` searched for `something` in the prefLabel and synonyms only! (but it seems this is not the case, since it searchs for a match with the @id as well :) Which other fields does it look for a match? Also I noticed that the `something` must always be URL encoded (otherwise you get no results). Do you think that the `ontologies=GO,BAO` part should be also (for the comma mostly)? Do you know if there is an id I can request that has more than 50 matches (a class that is included in more than 50 ontologies)? This would mean that I would have a second page of results (since the default pagesize is 50). You cannot search by multiple IDs. 1. Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty! If you want to limit results to a given class within a given ontology(ies), just add the ?ontologies=?BAO,DOID? to the query: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO,DOID Here, is there a preferential sorting happening for these results (first BAO entry and then DOID for example? - though I see you get them the other way around) http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO Hope this helps! Feel free to reach out if you have further questions. 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 ---------------------------------------------------- ?BR, John. ?------------------ John Zobolas PhD Student Department of Biology, Faculty of Natural Sciences, NTNU Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU _______________________________________________ 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 osnat.hakimi at upc.edu Thu Feb 28 03:49:56 2019 From: osnat.hakimi at upc.edu (Osnat Hakimi) Date: Thu, 28 Feb 2019 12:49:56 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Osnat Hakimi In-Reply-To: <9A82D237-A124-451F-9278-F61449D91A25@stanford.edu> References: <5c76955b6e13f_70502aff8bc84e10717c2@ncbo-prd-app-08.stanford.edu.mail> <9A82D237-A124-451F-9278-F61449D91A25@stanford.edu> Message-ID: Dear John, I have contacted Dr Viti as you advised and received her permission, Many thanks for your assistance and I hope I can submit my ontology when it is ready, Best regards Osnat On 27/02/2019 20:34, John Graybeal wrote: > Hello Dr. Hakimi, > > It is generally our expectation that public ontologies that do not > explicitly list a license do not have restrictions regarding their > use. ?However, to confirm this I would encourage you to contact the > ontology contact, listed on its summary page as?Federica Viti (and > Alessandro Orro), federica.viti at itb.cnr.it > . > > John > > >> On Feb 27, 2019, at 5:49 AM, support at bioontology.org >> wrote: >> >> Name: Osnat Hakimi >> >> Email: osnat.hakimi at upc.edu >> >> Location: https%3A%2F%2Fbioportal.bioontology.org >> %2Fontologies%2FBCTEO >> >> >> *Feedback:* >> >> Dear sir/Madam, >> I am writing to inquire about ontology: Bone/Cartilage Tissue >> Engineering Ontology (BCTEO) >> >> Is it freely available for public use? are there any restrictions >> regarding importation of the ontology into a new one? >> >> Many thanks >> >> Dr Osnat Hakimi >> MSCA-IF Fellow >> Universitat Polit?cnica de Catalunya >> Biomaterials, Biomechanics and Tissue Engineering Group >> Dept. Materials Science and Metallurgical Engineering >> Av. Eduard Maristany 16, edif i4.5 >> 08930 Barcelona, Spain >> Tel: +34 93 413 7218 >> Email: osnat.hakimi at upc.edu >> >> >> _______________________________________________ >> 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 > > -- Dr Osnat Hakimi MSCA-IF Fellow Universitat Polit?cnica de Catalunya Biomaterials, Biomechanics and Tissue Engineering Group Dept. Materials Science and Metallurgical Engineering Av. Eduard Maristany 16, edif i4.5 08930 Barcelona, Spain Tel: +34 93 413 7218 Email: osnat.hakimi at upc.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From akemisetti at dons.usfca.edu Wed Feb 27 20:36:44 2019 From: akemisetti at dons.usfca.edu (Anil Kemisetti) Date: Wed, 27 Feb 2019 20:36:44 -0800 Subject: [bioontology-support] Request for access to the ONTOPortal VMWare Virtual Appliance Message-ID: Hi, I am a masters student in "University of San Francisco" "Masters of Science Health Informatics" program. We study Ontology for our course work. I need access to ONTOPortal VMWare Virtual Appliance. Please let me know what is needed and process to get this access. Thanks Anil -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Feb 28 15:40:11 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 28 Feb 2019 23:40:11 +0000 Subject: [bioontology-support] Questions regarding the REST API In-Reply-To: <1551354858511.5081@ntnu.no> References: <1541771841693.45184@ntnu.no> <1541967499734.46992@ntnu.no> <1551354858511.5081@ntnu.no> Message-ID: <1802A3DC-CFF2-4520-9DD7-D61EE4D8E86F@stanford.edu> Hi John, Thank you, that?s a great catch! Indeed, the error response should have a consistent output, and what you?re seeing is a bug. I?ve logged it here: https://github.com/ncbo/ontologies_api/issues/55 Thanks again for your report. We very much appreciate it! Michael On Feb 28, 2019, at 3:54 AM, John Zobolas > wrote: { * "status": 401, * "error": "You must provide a valid API Key. Your API Key can be obtained by logging in at bioportal.bioontology.org/account" } which is different than the "standard" you mention: { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Feb 28 18:35:27 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 28 Feb 2019 18:35:27 -0800 Subject: [bioontology-support] [BioPortal] Feedback from rakesh Message-ID: <5c789a6f75c57_29652b0afabbfdd41476d@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: