From 68sharmaani at gmail.com Thu Jan 3 03:17:05 2019 From: 68sharmaani at gmail.com (Anirudh Sharma) Date: Thu, 3 Jan 2019 11:17:05 +0000 Subject: [bioontology-support] Using the API Message-ID: Dear support team, Greetings! I'm a medical student at Cambridge university and I was wondering if I could have access to the API for a trial period for research purposes in medical natural language processing. Kindly let me know. Sincerely, Anirudh Sharma as2659 at cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 7 06:18:25 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 07 Jan 2019 06:18:25 -0800 Subject: [bioontology-support] [BioPortal] Feedback from seandavi@gmail.com Message-ID: <5c335fb12fa56_626e2aff65e289a4649a4@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 7 08:18:33 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Jan 2019 16:18:33 +0000 Subject: [bioontology-support] Using the API In-Reply-To: References: Message-ID: Hello Anirudh, On Jan 3, 2019, at 3:17 AM, Anirudh Sharma <68sharmaani at gmail.com> wrote: I'm a medical student at Cambridge university and I was wondering if I could have access to the API for a trial period for research purposes in medical natural language processing. Kindly let me know. Apologies for the late reply. The REST API is free and open source to use as you?d like. You?ll need an API key in order to issue requests. There are instructions for getting a key on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 7 08:25:02 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 7 Jan 2019 16:25:02 +0000 Subject: [bioontology-support] [BioPortal] Feedback from seandavi@gmail.com In-Reply-To: <5c335fb12fa56_626e2aff65e289a4649a4@ncbo-prd-app-09.stanford.edu.mail> References: <5c335fb12fa56_626e2aff65e289a4649a4@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <410982B9-53FA-4350-98DE-E5EE2EF683E0@stanford.edu> Hi Sean, Apologies that there?s not a way for you to do this via the BioPortal application. If you?d like, I could manually delete your account from our system, and you could then recreate on the new account page: https://bioportal.bioontology.org/accounts/new Kind regards, Jennifer On Jan 7, 2019, at 6:18 AM, support at bioontology.org wrote: Name: seandavi at gmail.com Email: seandavi at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccount Feedback: Is it possible to reset my API key? I recently shared it with another group inadvertently. Thanks, Sean _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 7 08:14:43 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 07 Jan 2019 08:14:43 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Message-ID: <5c337af3e03cc_9d62acb0a88d7b823c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jonquet at lirmm.fr Mon Jan 7 13:00:08 2019 From: jonquet at lirmm.fr (Clement Jonquet) Date: Mon, 7 Jan 2019 22:00:08 +0100 Subject: [bioontology-support] [BioPortal] Feedback from Melissa In-Reply-To: <5c337af3e03cc_9d62acb0a88d7b823c@ncbo-prd-app-09.stanford.edu.mail> References: <5c337af3e03cc_9d62acb0a88d7b823c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <122482A0-4951-40E3-989F-A3C3DD9C7802@lirmm.fr> Dar Melissa, If you annotate with Langual you can consider annotating with FoodOn also: https://bioportal.bioontology.org/ontologies/FOODON We also have FoodOn and a bunch of other Agri-Food related ontologies/vocabularies in AgroPortal: http://agroportal.lirmm.fr/ontologies/FOODON Note that you will not be that first one to annotate 5M of PubMe abstract with the NCBO Annotator ;) Bye Clement ------------------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------------------- > Le 7 janv. 2019 ? 17:14, support at bioontology.org a ?crit : > > Name: Melissa > > Email: mmorine at gmail.com > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator > > > Feedback: > > Hi, > I'm looking to use the annotator to annotate a large corpus (>5M pubmed abstracts) with a custom ontology that is not present in BioPortal (the LanguaL thesaurus). Could you kindly advise on 1) whether custom ontologies can be used, and 2) what is the best approach for using the annotator on such a large corpus. > Thanks in advance, > 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 jgraybeal at stanford.edu Mon Jan 7 17:38:03 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 8 Jan 2019 01:38:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Melissa In-Reply-To: <5c337af3e03cc_9d62acb0a88d7b823c@ncbo-prd-app-09.stanford.edu.mail> References: <5c337af3e03cc_9d62acb0a88d7b823c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Melissa, Thank you for your inquiry. While it seems simple to submit your ontology (even privately) directly to BioPortal, that number of annotation requests you would cause inefficiencies: network delays, BioPortal slowdowns (or worse), and the coding you'd need (please) to make sure you weren't overloading BioPortal. I expect the same concerns would apply to using AgroPortal directly, but Clement can comment on that. Of course, you could use BioPortal for a small proof of concept, submit your ontology to BioPortal and writing your script against it, using just a small number of abstracts (maybe 25) to work out initial algorithms. But using BioPortal remotely at full scale is not recommended for this project. The recommended option is to deploy a BioPortal Virtual Appliance in your own system, and submit just your ontology to your local Virtual Appliance. Then you could run your algorithm locally, and use the full bandwidth and computer power you have available in your local machine. This is arguably the best option, due to a combination of speed and practicality. It may also be possible to use our Resource Index scripts (see next paragraph) against your Virtual Appliance. A third option is to leverage work we have already done; as you likely know, BioPortal as indexed all its ontologies against 24 million PubMed abstracts as recently as 2017. (See http://bioportal.bioontology.org/resource_index/; example here.) The code we used to do this is available on GitHub, and might be considerably more efficient than running the Annotator against those entries. We could at least tell you what we did, if that is useful. (We'd even be willing to consider re-running the PubMed index for our system, but it would take a fair amount of time, so would probably involve additional cost in time and/or money to you. Contact me off-thread if you are interested in more information on this possibility.) John On Jan 7, 2019, at 8:14 AM, support at bioontology.org wrote: Name: Melissa Email: mmorine at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hi, I'm looking to use the annotator to annotate a large corpus (>5M pubmed abstracts) with a custom ontology that is not present in BioPortal (the LanguaL thesaurus). Could you kindly advise on 1) whether custom ontologies can be used, and 2) what is the best approach for using the annotator on such a large corpus. Thanks in advance, Melissa _______________________________________________ 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 jgraybeal at stanford.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 8 16:51:13 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 08 Jan 2019 16:51:13 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Shawna Froese Message-ID: <5c354581602da_2e092af79d1c0d083333f@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 8 16:56:48 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 9 Jan 2019 00:56:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Shawna Froese In-Reply-To: <5c354581602da_2e092af79d1c0d083333f@ncbo-prd-app-09.stanford.edu.mail> References: <5c354581602da_2e092af79d1c0d083333f@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Shawna, We had a roughly 50 minute outage from 4 to 4:47PM Pacific Time. The system is back up and you should be able to create an account now. Apologies for the inconvenience. Jennifer On Jan 8, 2019, at 4:51 PM, support at bioontology.org wrote: Name: Shawna Froese Email: Shawna.Froese at kingstonhsc.ca Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccounts%2Fnew Feedback: We're sorry but something has gone wrong. We have been notified of this error. I've tried to register 3 times and keep getting the above error. I've tried different account names and possible passwords and I don't understand why I can't create an account. Shawna _______________________________________________ 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 david.channin at dhin.org Wed Jan 9 07:18:36 2019 From: david.channin at dhin.org (David Channin) Date: Wed, 9 Jan 2019 15:18:36 +0000 Subject: [bioontology-support] A little help, please Message-ID: <97D0C18078E2754C8FDA3F62439D7E6A0929953D@DHIN-SBS.AIM.local> Hello, I'm trying to query RXNORM by NDC code. I can query by CUI but can't figure out how to query by NDC: http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=C0694079 works and you will see 68788924909 as one of the NDCs of the classes. http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=68788924909 does not work nor does http://data.bioontology.org/property_search?apikey=&ontologies=RXNORM&q=68788924909 How to query on the property NDC? Thank you, Dave David S. Channin MD Chief Health Information Officer Delaware Health Information Network David.Channin at dhin.org O:+1.302.450.1960 C:+1.570.431.9729 www.dhin.org [DHIN-logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3898 bytes Desc: image001.jpg URL: From mdorf at stanford.edu Wed Jan 9 14:56:40 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 9 Jan 2019 22:56:40 +0000 Subject: [bioontology-support] A little help, please In-Reply-To: <97D0C18078E2754C8FDA3F62439D7E6A0929953D@DHIN-SBS.AIM.local> References: <97D0C18078E2754C8FDA3F62439D7E6A0929953D@DHIN-SBS.AIM.local> Message-ID: <5BD447A7-6D1C-4661-99AF-41589F5B0D90@stanford.edu> Hi David, Thank you for reaching out to us! The link below should give you the result you are looking for: http://data.bioontology.org/search?ontologies=RXNORM&q=68788924909&also_search_properties=true While we don?t store every class property with its associated value individually in our search index, we do store ALL of the properties for each class as a collection. This effectively translates to: ?ontologies=RXNORM&NDC=68788924909 <= CANNOT DO! ?ontologies=RXNORM&q=68788924909&also_search_properties=true <= CAN DO! CUI is an exception to this rule, where its value is actually stored individually and is included in our default search algorithm. This is why the first link in your email works without the ?also_search_properties? flag enabled. The /property_search endpoint searches for the names (labels) of the properties associated with an ontology rather than class specific values of each property. Thanks again and let us know if you run into any other issues. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 9, 2019, at 7:18 AM, David Channin > wrote: Hello, I?m trying to query RXNORM by NDC code. I can query by CUI but can?t figure out how to query by NDC: http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=C0694079 works and you will see 68788924909 as one of the NDCs of the classes. http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=68788924909 does not work nor does http://data.bioontology.org/property_search?apikey=&ontologies=RXNORM&q=68788924909 How to query on the property NDC? Thank you, Dave David S. Channin MD Chief Health Information Officer Delaware Health Information Network David.Channin at dhin.org O:+1.302.450.1960 C:+1.570.431.9729 www.dhin.org _______________________________________________ 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 Jan 10 17:52:08 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 11 Jan 2019 01:52:08 +0000 Subject: [bioontology-support] A little help, please In-Reply-To: <5E0570F733524170.d009df1f-7eb2-4b0d-b943-bfce820f2e74@mail.outlook.com> References: <97D0C18078E2754C8FDA3F62439D7E6A0929953D@DHIN-SBS.AIM.local> <5BD447A7-6D1C-4661-99AF-41589F5B0D90@stanford.edu> <5E0570F733524170.d009df1f-7eb2-4b0d-b943-bfce820f2e74@mail.outlook.com> Message-ID: <81B1722A-FF34-4319-B786-B8A9CDE6AEAC@stanford.edu> Hi David, Unfortunately, not. As mentioned previously, the properties are indexed as a block of value pairs, rather than each individually. A possible workaround could be a query below, which displays all the property values. You can then programmatically examine the value of the field "properties" for each result, filtering out the entries that did not meet your search criteria: http://data.bioontology.org/search?ontologies=RXNORM&q=68788924909&also_search_properties=true&no_links=true&no_context=true&display=prefLabel,synonym,definition,notation,cui,semanticType,properties Hope this helps! Michael On Jan 9, 2019, at 15:49, David Channin > wrote: Michael, One other question that I just thought of... suppose the q value (in my example), 68788924909 appears in two properties. Is there a way to specify which property I am interested in (in my example, NDC)? Again, thank you very much, Dave From: Michael Dorf Sent: Wednesday, January 9, 18:12 Subject: Re: [bioontology-support] A little help, please To: David Channin Cc: support at bioontology.org Hi David, Thank you for reaching out to us! The link below should give you the result you are looking for: http://data.bioontology.org/search?ontologies=RXNORM&q=68788924909&also_search_properties=true While we don?t store every class property with its associated value individually in our search index, we do store ALL of the properties for each class as a collection. This effectively translates to: ?ontologies=RXNORM&NDC=68788924909 <= CANNOT DO! ?ontologies=RXNORM&q=68788924909&also_search_properties=true <= CAN DO! CUI is an exception to this rule, where its value is actually stored individually and is included in our default search algorithm. This is why the first link in your email works without the ?also_search_properties? flag enabled. The /property_search endpoint searches for the names (labels) of the properties associated with an ontology rather than class specific values of each property. Thanks again and let us know if you run into any other issues. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jan 9, 2019, at 7:18 AM, David Channin > wrote: Hello, I?m trying to query RXNORM by NDC code. I can query by CUI but can?t figure out how to query by NDC: http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=C0694079 works and you will see 68788924909 as one of the NDCs of the classes. http://data.bioontology.org/search?apikey=&ontologies=RXNORM&q=68788924909 does not work nor does http://data.bioontology.org/property_search?apikey=&ontologies=RXNORM&q=68788924909 How to query on the property NDC? Thank you, Dave David S. Channin MD Chief Health Information Officer Delaware Health Information Network David.Channin at dhin.org O:+1.302.450.1960 C:+1.570.431.9729 www.dhin.org _______________________________________________ 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 neerajhaharihar at oakland.edu Sun Jan 13 18:57:59 2019 From: neerajhaharihar at oakland.edu (Neerajha Hariharakumar) Date: Sun, 13 Jan 2019 21:57:59 -0500 Subject: [bioontology-support] Help with API Documentation Message-ID: Hi Team, I am a graduate student from Oakland University and I would like to use the API examples provided with data.bioontology.org. Can you please help me with this? Can you provide details about the APIKey, its working and how should I be using it? Any help is appreciated. Thanks in advance! Regards, Neerajha -- Neerajha Hariharakumar Graduate Student (MS ITM) Oakland University -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 14 07:36:54 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 14 Jan 2019 07:36:54 -0800 Subject: [bioontology-support] [BioPortal] Feedback from utjingchengdu Message-ID: <5c3cac96aec65_1e662b24519a7eb4285d7@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 14 08:04:29 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 14 Jan 2019 16:04:29 +0000 Subject: [bioontology-support] [BioPortal] Feedback from utjingchengdu In-Reply-To: <5c3cac96aec65_1e662b24519a7eb4285d7@ncbo-prd-app-09.stanford.edu.mail> References: <5c3cac96aec65_1e662b24519a7eb4285d7@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <5F5EE587-DAE6-4243-81F5-66881D6F313C@stanford.edu> Hello, On Jan 14, 2019, at 7:36 AM, support at bioontology.org wrote: Name: utjingchengdu Email: jingcheng.du at uth.tmc.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2F404 Feedback: I'm the administrator of Time Event Ontology (TEO) project. After I log in, when I click the ontology: https://bioportal.bioontology.org/ontologies/TEO I always get "The page you are looking for wasn't found. Please try again." Could anyone help me on this issue? My account: utdujingcheng I looked at the list of administrators for the TEO ontology. There is only one with an account name of ?taocui?. Are you familiar with who this account belongs to? Would you like us to add the account you list above? Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 14 08:09:40 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 14 Jan 2019 16:09:40 +0000 Subject: [bioontology-support] Help with API Documentation In-Reply-To: References: Message-ID: <3CAE4664-ECF4-41AF-9E96-1390D555A6E0@stanford.edu> Hello Neerajha, On Jan 13, 2019, at 6:57 PM, Neerajha Hariharakumar > wrote: Hi Team, I am a graduate student from Oakland University and I would like to use the API examples provided with data.bioontology.org. Can you please help me with this? Can you provide details about the APIKey, its working and how should I be using it? There are instructions for obtaining an API key on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Once you have an API key, you pass it as a parameter when making API calls, e.g.: http://data.bioontology.org/ontologies/SNOMEDCT?apikey=your_api_key_goes_here The API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.nikolopoulos at student.vu.nl Mon Jan 14 11:07:48 2019 From: d.nikolopoulos at student.vu.nl (Nikolopoulos, D.) Date: Mon, 14 Jan 2019 19:07:48 +0000 Subject: [bioontology-support] Downloading mappings in ttl Message-ID: Greetings, I was wondering if there is a way to download all the mappings between two ontologies in ttl format. I am interested for the MeSH and ICD10 mappings, however I suspect that it won't be possible due to licensing of ICD10 (?). Even if it's not possible, I would like to know the way for any pair of ontologies, Kind regards, Dimitris From mdorf at stanford.edu Mon Jan 14 12:36:28 2019 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 14 Jan 2019 20:36:28 +0000 Subject: [bioontology-support] Downloading mappings in ttl In-Reply-To: References: Message-ID: Hi Dimitris, Thank you for contacting us. Unfortunately, at this point, mappings are not available as a bulk download. We've had similar requests in the past and have an existing open ticket in Github that tracks this issue: https://github.com/ncbo/bioportal-project/issues/84 You can, however, use our REST service to get mappings between two ontologies. This call, documented at http://data.bioontology.org/documentation#Mapping, returns JSON output: http://data.bioontology.org/mappings?ontologies=MESH,ICD10 This returns each mapped pair as an array of JSON objects. The @id: values contain the two class IDs that are mapped. Michael On Jan 14, 2019, at 11:07, Nikolopoulos, D. > wrote: Greetings, I was wondering if there is a way to download all the mappings between two ontologies in ttl format. I am interested for the MeSH and ICD10 mappings, however I suspect that it won't be possible due to licensing of ICD10 (?). Even if it's not possible, I would like to know the way for any pair of ontologies, Kind regards, Dimitris _______________________________________________ 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.nikolopoulos at student.vu.nl Sat Jan 19 09:44:02 2019 From: d.nikolopoulos at student.vu.nl (Nikolopoulos, D.) Date: Sat, 19 Jan 2019 17:44:02 +0000 Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT Message-ID: <9cdb1c5fb4824046b77e44e9b70c27ab@student.vu.nl> Greetings to all, I would like to have the latest UMLS versions of ICD10, ICD10CM and SNOMEDCT ttl files, or some of them. I know that I can access data through the REST api, but I would like to have the ontology versions of the datasets in order to work on my master project thesis. I possess a UMLS license and I wonder whether an offline download is possible, as I have seen in previous thread that there was this option. I suppose that I could also use umls2rdf script in order to generate the ontologies myself. However, I am not familiar with the database set up of UMLS and it would take me some time to familiarize with the technicalities of it. Do I have options of downloading? Thank you kindly in advance! Best, Dimitris From d.nikolopoulos at student.vu.nl Sat Jan 19 09:58:46 2019 From: d.nikolopoulos at student.vu.nl (Nikolopoulos, D.) Date: Sat, 19 Jan 2019 17:58:46 +0000 Subject: [bioontology-support] Questions on mappings between ontologies Message-ID: Hello again, I have one more inquiry. I am able to download mappings with the REST API between the following pairs: ICD10 - ICD10CM MeSH-ICD10 MeSH-ICD10CM SNOMEDCT - MeSH SNOMEDCT - ICD10 SNOMEDCT - ICD10CM My question is how does someone represent these mappings in rdf? In the documentation you mention some of the relations, but it is quite unclear to me how I can see the type of relation. Some sub-questions: 1. Is there any way to see what relation describes a mapping? 2. Is there any confidence metric of a mapping? 3. Do the mappings of the above mentioned ontology pairs come from UMLS CUIs? (skos:closeMatch) 4. In case of LOOM matching, you mention two types: NCBO lexical mapping (loom) and NCBO Identical URI (loom). How do I distinguish between these two mappigns? 5. Can I download the mapping in rdf format with the REST api? Something like this -> http://data.bioontology.org/mappings?ontologies=MESH,ICD10&download_format=rdf seems to return json format. Best, Dimitris Nikolopoulos From d.nikolopoulos at student.vu.nl Mon Jan 21 05:31:20 2019 From: d.nikolopoulos at student.vu.nl (Nikolopoulos, D.) Date: Mon, 21 Jan 2019 13:31:20 +0000 Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT In-Reply-To: <9cdb1c5fb4824046b77e44e9b70c27ab@student.vu.nl> References: <9cdb1c5fb4824046b77e44e9b70c27ab@student.vu.nl> Message-ID: I managed to set up a mysql database and run umls2rdf for ICD10 and ICD10CM. Unfortunately, trying to run umls2rdf upon SNOMED-CT turns out to be impossible through my laptop. My RAM is 16GB and the process is taking over my RAM and swap. Do I have any other option? I have the necessary licenses. Thank you in advance! Dimitris ________________________________________ From: bioontology-support [bioontology-support-bounces at lists.stanford.edu] on behalf of Nikolopoulos, D. [d.nikolopoulos at student.vu.nl] Sent: 19 January 2019 18:44 To: bioontology-support at lists.stanford.edu Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT Greetings to all, I would like to have the latest UMLS versions of ICD10, ICD10CM and SNOMEDCT ttl files, or some of them. I know that I can access data through the REST api, but I would like to have the ontology versions of the datasets in order to work on my master project thesis. I possess a UMLS license and I wonder whether an offline download is possible, as I have seen in previous thread that there was this option. I suppose that I could also use umls2rdf script in order to generate the ontologies myself. However, I am not familiar with the database set up of UMLS and it would take me some time to familiarize with the technicalities of it. Do I have options of downloading? Thank you kindly in advance! Best, Dimitris _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support From isaaccf at gmail.com Tue Jan 22 05:46:34 2019 From: isaaccf at gmail.com (Isaac Cano) Date: Tue, 22 Jan 2019 14:46:34 +0100 Subject: [bioontology-support] Bioportal down Message-ID: Dears, We have noticed that the bioportal ( https://bioportal.bioontology.org/ontologies) is down. Since we use a BioPortal API token for searching biomedical ontologies in REDCap this situation may jeopardise data collection in our clinical trials. Are you already aware of this situation? If so, do you have an estimation to restore the service? Thanks in advance, -- *Isaac Cano*, BSc, MSd, PhD Institut d'Investigacions Biom?diques August Pi i Sunyer (IDIBAPS) *Associate professor, School of Medicine - University of Barcelona* *Hospital Cl?nic de Barcelona* Respiratory Diagnostic Center Villarroel, 170 | 08036 Barcelona, Catalonia T: +34 932 275 747 | E1: iscano at clinic.cat | E2: iscano at ub.edu www.nextcarecat.cat | researchgate.net profile | Skype ID: is.cano -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Jan 22 14:09:06 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 22 Jan 2019 22:09:06 +0000 Subject: [bioontology-support] Bioportal down In-Reply-To: References: Message-ID: Hello Isaac, I see the service was having some intermittent operations around the time you sent your email, and our team performed some recovery operations that brought it back on-line shortly thereafter. Typically this can happen when one or more requestors overwhelm the system with complicated requests, though our average monthly uptime has remained in the 98.0-99.5% range for many years. That said, I'll repeat a message I've sent to the BioPortal support list before: The free and public BioPortal service is not funded as a mission-critical service, and is not capable, as a research service, of providing extremely high availability. We especially discourage any use that could jeopardize data collection for clinical trials. To the extent your software solution relies on the research-grade BioPortal deployment for a mission-critical operation, that will put those operations at risk. If you have a need for mission-critical support, we would be happy to discuss providing a BioPortal service that meets your Service Level Agreement requirements. Please contact me if you are interested in such an arrangement. John On Jan 22, 2019, at 5:46 AM, Isaac Cano > wrote: Dears, We have noticed that the bioportal (https://bioportal.bioontology.org/ontologies) is down. Since we use a BioPortal API token for searching biomedical ontologies in REDCap this situation may jeopardise data collection in our clinical trials. Are you already aware of this situation? If so, do you have an estimation to restore the service? Thanks in advance, -- Isaac Cano, BSc, MSd, PhD Institut d'Investigacions Biom?diques August Pi i Sunyer (IDIBAPS) Associate professor, School of Medicine - University of Barcelona Hospital Cl?nic de Barcelona Respiratory Diagnostic Center Villarroel, 170 | 08036 Barcelona, Catalonia T: +34 932 275 747 | E1: iscano at clinic.cat | E2: iscano at ub.edu www.nextcarecat.cat | researchgate.net profile | Skype ID: is.cano _______________________________________________ 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 isaaccf at gmail.com Tue Jan 22 23:06:55 2019 From: isaaccf at gmail.com (Isaac Cano) Date: Wed, 23 Jan 2019 08:06:55 +0100 Subject: [bioontology-support] Bioportal down In-Reply-To: References: Message-ID: Thanks John, we will discuss internally if the current average monthly uptime is enough and if not I will come back to you to request a SLA-based Bioportal service. Isaac El mar., 22 ene. 2019 23:09, John Graybeal escribi?: > Hello Isaac, > > I see the service was having some intermittent operations around the time > you sent your email, and our team performed some recovery operations that > brought it back on-line shortly thereafter. Typically this can happen when > one or more requestors overwhelm the system with complicated requests, > though our average monthly uptime has remained in the 98.0-99.5% range for > many years. > > That said, I'll repeat a message I've sent to the BioPortal support list > before: The free and public BioPortal service is not funded as a > mission-critical service, and is not capable, as a research service, of > providing extremely high availability. We especially discourage any use > that could jeopardize data collection for clinical trials. To the extent > your software solution relies on the research-grade BioPortal deployment > for a mission-critical operation, that will put those operations at risk. > > If you have a need for mission-critical support, we would be happy to > discuss providing a BioPortal service that meets your Service Level > Agreement requirements. Please contact me if you are interested in such an > arrangement. > > John > > > On Jan 22, 2019, at 5:46 AM, Isaac Cano wrote: > > Dears, > > We have noticed that the bioportal ( > https://bioportal.bioontology.org/ontologies) is down. Since we use > a BioPortal API token for searching biomedical ontologies in REDCap this > situation may jeopardise data collection in our clinical trials. > > Are you already aware of this situation? If so, do you have an estimation > to restore the service? > > Thanks in advance, > > -- > > *Isaac Cano*, BSc, MSd, PhD > > Institut d'Investigacions Biom?diques August Pi i Sunyer (IDIBAPS) > > *Associate professor, School of Medicine - University of Barcelona* > > *Hospital Cl?nic de Barcelona* > > Respiratory Diagnostic Center > > Villarroel, 170 | 08036 Barcelona, Catalonia > > T: +34 932 275 747 | E1: iscano at clinic.cat | E2: iscano at ub.edu > > www.nextcarecat.cat | researchgate.net profile > | Skype ID: is.cano > > > > > _______________________________________________ > 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 Jan 23 09:29:46 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 23 Jan 2019 17:29:46 +0000 Subject: [bioontology-support] Bioportal down In-Reply-To: References: Message-ID: Sounds good Isaac. In my last email, I also should have noted that we target an up time of 99.5%, and already we have projects under way to increase the reliability. However, lately we have had a number of different types of outages, and addressing these can take time for analysis and developing systematic responses. John On Jan 22, 2019, at 11:06 PM, Isaac Cano > wrote: Thanks John, we will discuss internally if the current average monthly uptime is enough and if not I will come back to you to request a SLA-based Bioportal service. Isaac El mar., 22 ene. 2019 23:09, John Graybeal > escribi?: Hello Isaac, I see the service was having some intermittent operations around the time you sent your email, and our team performed some recovery operations that brought it back on-line shortly thereafter. Typically this can happen when one or more requestors overwhelm the system with complicated requests, though our average monthly uptime has remained in the 98.0-99.5% range for many years. That said, I'll repeat a message I've sent to the BioPortal support list before: The free and public BioPortal service is not funded as a mission-critical service, and is not capable, as a research service, of providing extremely high availability. We especially discourage any use that could jeopardize data collection for clinical trials. To the extent your software solution relies on the research-grade BioPortal deployment for a mission-critical operation, that will put those operations at risk. If you have a need for mission-critical support, we would be happy to discuss providing a BioPortal service that meets your Service Level Agreement requirements. Please contact me if you are interested in such an arrangement. John On Jan 22, 2019, at 5:46 AM, Isaac Cano > wrote: Dears, We have noticed that the bioportal (https://bioportal.bioontology.org/ontologies) is down. Since we use a BioPortal API token for searching biomedical ontologies in REDCap this situation may jeopardise data collection in our clinical trials. Are you already aware of this situation? If so, do you have an estimation to restore the service? Thanks in advance, -- Isaac Cano, BSc, MSd, PhD Institut d'Investigacions Biom?diques August Pi i Sunyer (IDIBAPS) Associate professor, School of Medicine - University of Barcelona Hospital Cl?nic de Barcelona Respiratory Diagnostic Center Villarroel, 170 | 08036 Barcelona, Catalonia T: +34 932 275 747 | E1: iscano at clinic.cat | E2: iscano at ub.edu www.nextcarecat.cat | researchgate.net profile | Skype ID: is.cano _______________________________________________ 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 u0597274 at utah.edu Fri Jan 25 00:44:09 2019 From: u0597274 at utah.edu (Trevor Tanner) Date: Fri, 25 Jan 2019 01:44:09 -0700 Subject: [bioontology-support] VMWare Virtual Application Message-ID: Greetings, I am wondering if it is possible to obtain a copy of the Bioportal VMWare Virtual Appliance? I am hoping to use the local installation in conjunction with cheminformatics and machine learning to search for ontologies that may be predicted by chemical structure and animal models. My Bioportal username is "u0597274" - please just let me know if you need any additional information. Thank you for your time. Thanks again, Trevor Tanner (801) 742-5366 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 24 10:11:03 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 24 Jan 2019 10:11:03 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Chris Grove Message-ID: <5c49ffb72eac4_7b4a2b192532a5c848693@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Jan 24 14:41:00 2019 From: support at bioontology.org (support at bioontology.org) Date: Thu, 24 Jan 2019 14:41:00 -0800 Subject: [bioontology-support] [BioPortal] Feedback from helenadeus Message-ID: <5c4a3efcd39a8_541e2ad1790ad61826fa@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Jan 25 13:41:55 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 25 Jan 2019 21:41:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from helenadeus In-Reply-To: <5c4a3efcd39a8_541e2ad1790ad61826fa@ncbo-prd-app-08.stanford.edu.mail> References: <5c4a3efcd39a8_541e2ad1790ad61826fa@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Helena, We're sorry for the discrepancy. Our Beta SPARQL endpoint data is not maintained due to resource constraints. We hope to make a new SPARQL service available at some point, but in the meantime that resource is simply a historical archive to let people play with a SPARQL system. We are happy to entertain use cases and offers of resources to bring a new, up-to-date endpoint online faster. John On Jan 24, 2019, at 2:41 PM, support at bioontology.org wrote: Name: helenadeus Email: hdeus.elsevier at gmail.com Location: http://sparql.bioontology.org/ Feedback: Got 67 results on this query: PREFIX rdfs: PREFIX snomed-term: PREFIX skos: SELECT ( COUNT(Distinct ?x) as ?xcnt) FROM WHERE { ?x rdfs:subClassOf snomed-term:40733004 . ?x skos:prefLabel ?label. } But according to the SNOMED CT browser (ihtsdotools) there are 121 children to that term. Can you clarify where the gap is? _______________________________________________ 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 Fri Jan 25 13:49:13 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 25 Jan 2019 21:49:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Chris Grove In-Reply-To: <5c49ffb72eac4_7b4a2b192532a5c848693@ncbo-prd-app-09.stanford.edu.mail> References: <5c49ffb72eac4_7b4a2b192532a5c848693@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Chris, Our apologies, in our last outage early this morning Pacific Time (around 3 AM) some features of the site went offline for a few minutes, but it self-recovered. I am not able to see any other indication of an outage since then. Can you replicate the problem at this point, and after force-reloading the web page? John On Jan 24, 2019, at 10:11 AM, support at bioontology.org wrote: Name: Chris Grove Email: cgrove at caltech.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2F500 Feedback: NCBO BioPortal site appears to be down _______________________________________________ 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 d.nikolopoulos at student.vu.nl Sat Jan 26 04:59:48 2019 From: d.nikolopoulos at student.vu.nl (Nikolopoulos, D.) Date: Sat, 26 Jan 2019 12:59:48 +0000 Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT In-Reply-To: References: <9cdb1c5fb4824046b77e44e9b70c27ab@student.vu.nl>, Message-ID: <6126a033df084995a89fff1b6003bbae@student.vu.nl> Hello, I am wondering if someone can answer my question on how to receive SNOMEDCT owl dataset from BioPortal. I see there is activity in the mailing list, but my messages appear to be unanswered. I would appreciate it if someone could help me out because I am one 1 week behind with my project. Thanks in advance! Best regards, Dimitris ________________________________________ From: bioontology-support [bioontology-support-bounces at lists.stanford.edu] on behalf of Nikolopoulos, D. [d.nikolopoulos at student.vu.nl] Sent: 21 January 2019 14:31 To: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT I managed to set up a mysql database and run umls2rdf for ICD10 and ICD10CM. Unfortunately, trying to run umls2rdf upon SNOMED-CT turns out to be impossible through my laptop. My RAM is 16GB and the process is taking over my RAM and swap. Do I have any other option? I have the necessary licenses. Thank you in advance! Dimitris ________________________________________ From: bioontology-support [bioontology-support-bounces at lists.stanford.edu] on behalf of Nikolopoulos, D. [d.nikolopoulos at student.vu.nl] Sent: 19 January 2019 18:44 To: bioontology-support at lists.stanford.edu Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT Greetings to all, I would like to have the latest UMLS versions of ICD10, ICD10CM and SNOMEDCT ttl files, or some of them. I know that I can access data through the REST api, but I would like to have the ontology versions of the datasets in order to work on my master project thesis. I possess a UMLS license and I wonder whether an offline download is possible, as I have seen in previous thread that there was this option. I suppose that I could also use umls2rdf script in order to generate the ontologies myself. However, I am not familiar with the database set up of UMLS and it would take me some time to familiarize with the technicalities of it. Do I have options of downloading? Thank you kindly in advance! Best, Dimitris _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support From jgraybeal at stanford.edu Sat Jan 26 08:46:45 2019 From: jgraybeal at stanford.edu (John Graybeal) Date: Sat, 26 Jan 2019 16:46:45 +0000 Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT In-Reply-To: <6126a033df084995a89fff1b6003bbae@student.vu.nl> References: <9cdb1c5fb4824046b77e44e9b70c27ab@student.vu.nl>, , <6126a033df084995a89fff1b6003bbae@student.vu.nl> Message-ID: Sorry Dimitris, I need to double-check previous research I did for a previous request and haven?t had time to do so. Unfortunately, I think the license may not allow this, but I will check and reply offline as soon as I verify. (Likely Monday.) John ________________________________ From: bioontology-support on behalf of Nikolopoulos, D. Sent: Saturday, January 26, 2019 04:59 To: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT Hello, I am wondering if someone can answer my question on how to receive SNOMEDCT owl dataset from BioPortal. I see there is activity in the mailing list, but my messages appear to be unanswered. I would appreciate it if someone could help me out because I am one 1 week behind with my project. Thanks in advance! Best regards, Dimitris ________________________________________ From: bioontology-support [bioontology-support-bounces at lists.stanford.edu] on behalf of Nikolopoulos, D. [d.nikolopoulos at student.vu.nl] Sent: 21 January 2019 14:31 To: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT I managed to set up a mysql database and run umls2rdf for ICD10 and ICD10CM. Unfortunately, trying to run umls2rdf upon SNOMED-CT turns out to be impossible through my laptop. My RAM is 16GB and the process is taking over my RAM and swap. Do I have any other option? I have the necessary licenses. Thank you in advance! Dimitris ________________________________________ From: bioontology-support [bioontology-support-bounces at lists.stanford.edu] on behalf of Nikolopoulos, D. [d.nikolopoulos at student.vu.nl] Sent: 19 January 2019 18:44 To: bioontology-support at lists.stanford.edu Subject: [bioontology-support] Download options of ICD10, ICD10CM and SNOMEDCT Greetings to all, I would like to have the latest UMLS versions of ICD10, ICD10CM and SNOMEDCT ttl files, or some of them. I know that I can access data through the REST api, but I would like to have the ontology versions of the datasets in order to work on my master project thesis. I possess a UMLS license and I wonder whether an offline download is possible, as I have seen in previous thread that there was this option. I suppose that I could also use umls2rdf script in order to generate the ontologies myself. However, I am not familiar with the database set up of UMLS and it would take me some time to familiarize with the technicalities of it. Do I have options of downloading? Thank you kindly in advance! Best, Dimitris _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Jan 28 09:16:58 2019 From: support at bioontology.org (support at bioontology.org) Date: Mon, 28 Jan 2019 09:16:58 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Alex Message-ID: <5c4f390a8d476_39eb2b03f09cb5e889560@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 28 11:31:03 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 28 Jan 2019 19:31:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Alex In-Reply-To: <5c4f390a8d476_39eb2b03f09cb5e889560@ncbo-prd-app-09.stanford.edu.mail> References: <5c4f390a8d476_39eb2b03f09cb5e889560@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Alex, On Jan 28, 2019, at 9:16 AM, support at bioontology.org wrote: Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FMEDDRA%252F10075733 Feedback: I just wanted to let you know that the link to the "Ontology home page" at the top, right of the below page (and all MedDRA term pages) is broken. http://bioportal.bioontology.org/ontologies/MEDDRA Thanks for alerting us to that. I updated the ontology metadata so that the home page is now accessible. The 500 error you encountered when attempting to select the ?Venous perforation? class is the result of a known issue [1]. We have a fix for this that we?re planning to get deployed over the next couple of days. In the mean time, if you log out of your BioPortal account, you?ll be able to see all the MedDRA classes without errors. Kind regards, Jennifer [1] https://github.com/ncbo/bioportal_web_ui/issues/86 -------------- next part -------------- An HTML attachment was scrubbed... URL: From teftimov at stanford.edu Mon Jan 28 18:46:36 2019 From: teftimov at stanford.edu (Tome Eftimov) Date: Tue, 29 Jan 2019 02:46:36 +0000 Subject: [bioontology-support] NCBO annotator in R Message-ID: <8A8F08A7-BB29-4DF9-A9C3-0B176F0A5A9D@stanford.edu> Dear, Is it possible to have the source code for the NCBO Annotator API in R? Thanks in advance! Best, Tome -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jan 28 20:48:22 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Jan 2019 04:48:22 +0000 Subject: [bioontology-support] NCBO annotator in R In-Reply-To: <8A8F08A7-BB29-4DF9-A9C3-0B176F0A5A9D@stanford.edu> References: <8A8F08A7-BB29-4DF9-A9C3-0B176F0A5A9D@stanford.edu> Message-ID: <8AFDC20A-0583-4E23-BC2C-A80CC1333F71@stanford.edu> Hi Tome, We offer example code in a number of languages [1], but we?ve not included anything in R (I don?t think anyone on our current team knows R). There is however, an example in R from an end user here: https://github.com/muntisa/RNCBO I don?t believe they are making any calls to the Annotator, but they do make calls to the Recommender service, so you could probably get a good idea from their code of how to proceed. Our API is documented here: http://data.bioontology.org/documentation Hope that helps. Kind regards, Jennifer [1] https://github.com/ncbo/ncbo_rest_sample_code On Jan 28, 2019, at 6:46 PM, Tome Eftimov > wrote: Dear, Is it possible to have the source code for the NCBO Annotator API in R? Thanks in advance! Best, Tome _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 29 00:15:57 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Jan 2019 00:15:57 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Dharani P Message-ID: <5c500bbda3487_4f0c2af53af2c97090965@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Jan 29 08:50:56 2019 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 29 Jan 2019 16:50:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Dharani P In-Reply-To: <5c500bbda3487_4f0c2af53af2c97090965@ncbo-prd-app-09.stanford.edu.mail> References: <5c500bbda3487_4f0c2af53af2c97090965@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <766AC4BC-4119-452A-BB1D-76E25EA6EAE8@stanford.edu> Hello Dharani, On Jan 29, 2019, at 12:15 AM, support at bioontology.org wrote: Name: Dharani P Email: dharaninirmala661998 at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fsearch Feedback: I have downloaded DDO-Diabetes Mellitus diagnosis ontology owl file form your website.one day after download process when I open the downloaded file, there is an problem that some of the imports being missed in that ontology. I have a problem in adding SWRL rules additional to that ontology and saving them. I downloaded and looked at the DDO_v1.owl source file. The ontology author lists 3 imports: http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl http://purl.obolibrary.org/obo/bfo.owl I navigated to all 3 of these URLs and they are all valid. I?m not sure what you are referring to when you say that the imports are missing. Could you be more specific? Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Jan 29 10:10:31 2019 From: support at bioontology.org (support at bioontology.org) Date: Tue, 29 Jan 2019 10:10:31 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Paymon Rezaii Message-ID: <5c509717f3ec8_22f92ad6fc5469a8565b9@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From prezaii at stanford.edu Tue Jan 29 10:13:13 2019 From: prezaii at stanford.edu (Paymon Garakani Rezaii) Date: Tue, 29 Jan 2019 18:13:13 +0000 Subject: [bioontology-support] CPT csv file Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: