From wynner at mail.nih.gov Tue Sep 4 09:14:21 2018 From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C]) Date: Tue, 4 Sep 2018 16:14:21 +0000 Subject: [bioontology-support] searching by synonyms In-Reply-To: References: Message-ID: Yes! Jennifer, this is great. I will bronze this thread. Thank you so much. Rob From: Jennifer Leigh Vendetti Sent: Thursday, August 30, 2018 7:51 PM To: Wynne, Robert (NIH/NCI) [C] Cc: support at bioontology.org; De Coronado, Sherri (NIH/NCI) [E] Subject: Re: [bioontology-support] searching by synonyms Hi Rob, On Aug 18, 2018, at 12:52 PM, Wynne, Robert (NIH/NCI) [C] > wrote: Hi Jennifer, Yes. I took a look at the documentation and have tried the following calls using my key. Neither seem to return what I?m looking for, so maybe I?m doing something wrong. http://data.bioontology.org/property_search?q=P90&ontologies=NCIT http://data.bioontology.org/property_search?q=P90&ontologies=NCIT/search?q=Malignant I?d like to restrict my search to just synonyms, and have classes returned that match the search value (a contains or exact match). You can use the ?include? parameter to limit what?s returned by the API. That parameter is documented in the Common Parameters section of our API documentation: http://data.bioontology.org/documentation#nav_usage You can also set the display_links parameter to false to eliminate the hypermedia links that are returned by default. For example (this is the /search endpoint, not the /property_search endpoint): http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&display_links=false ? the above call retrieves all classes from the NCIT ontology where the class name contains ?Malignant?. For each class in the resulting JSON, only the preferred label and synonyms are returned: [cid:image001.png at 01D44448.CE9A9BC0] For an exact match search, you would add the require_exact_match parameter: http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&require_exact_match=true&display_links=false [cid:image002.png at 01D44448.CE9A9BC0] Is this the type of search you?re trying to accomplish? Kind regards, Jennifer Can this be done through BioPortal instead? If I go to the Advanced Search there is an option to select all properties, but is there a way to search by a single property? Thanks! Rob From: Jennifer Leigh Vendetti > Sent: Thursday, August 16, 2018 7:57 PM To: Wynne, Robert (NIH/NCI) [C] > Cc: support at bioontology.org; De Coronado, Sherri (NIH/NCI) [E] > Subject: Re: [bioontology-support] searching by synonyms Hi Rob, Apologies, but I?m not sure I followed your question. We do have a search endpoint in the REST API for searching by ontology properties. It?s documented here: http://data.bioontology.org/documentation#nav_prop_search Is this what you meant? Kind regards, Jennifer On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] > wrote: Hi all, How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes? I guess this would go for any one specific text property. If I do this search using REST, could I specify my property? Thanks, Rob _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 267417 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 102224 bytes Desc: image002.png URL: From hideki at biosciencedbc.jp Mon Sep 3 21:44:31 2018 From: hideki at biosciencedbc.jp (Hideki Hatanaka) Date: Tue, 4 Sep 2018 13:44:31 +0900 Subject: [bioontology-support] [BioPortal] Feedback from Hideki Hatanaka In-Reply-To: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail> References: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Dear Sirs, the content of the email is different from that I input into the support form. I wanted to show downloading was suddenly interrupted. Sincerely yours, Hideki 2018?9?4?(?) 13:27 : > > Name: Hideki Hatanaka > > Email: hideki at biosciencedbc.jp > > Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FGAZ > > > Feedback: > > Downloading PR, GAZ or NCBITAXON seems to stop at 1 GB . > For example, results from downloading RDF/XML at https://bioportal.bioontology.org/ontologies/PR are : > > $ ls -l > total 2129944 > -rw-r--r--@ 1 hatanaka staff 8094 9 4 05:42 Info.plist > -rw-r--r--@ 1 hatanaka staff 1074126848 9 4 05:42 owlapi.xrdf > > $ tail -5 owlapi.xrdf > > > > A protein coding gene wdr68 in Dictyostelium discoideum. -- Hideki Hatanaka, D.Sc. National Bioscience Database Center (NBDC), JST 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan Phone:+81-90-1114-6896, +81-3-5214-8491 From nick.kennedy1 at nhs.net Tue Sep 4 04:13:02 2018 From: nick.kennedy1 at nhs.net (KENNEDY, Nick (ROYAL DEVON AND EXETER NHS FOUNDATION TRUST)) Date: Tue, 4 Sep 2018 11:13:02 +0000 Subject: [bioontology-support] MEDDRA version Message-ID: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET> Dear Bioontology support, The version of MEDDRA currently used on bioontology doesn't seem to be displayed anywhere. I've checked on http://bioportal.bioontology.org/ontologies/MEDDRA?p=summary and browsed through the other tabs on that page. From the release date given as June 2017, it seems likely that you are using version 20.0 released March 2017. Is that correct? Best wishes, Dr Nick Kennedy Consultant Gastroenterologist Direct line (01392) 40 8457 Secretary (01392) 40 2783 ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services. For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Sep 3 21:27:24 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 03 Sep 2018 21:27:24 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Hideki Hatanaka Message-ID: <5b8e09ac821b9_16553f8a400b73f4543fc@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Tue Sep 4 03:23:22 2018 From: support at bioontology.org (support at bioontology.org) Date: Tue, 04 Sep 2018 03:23:22 -0700 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be Message-ID: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Sep 4 10:59:22 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 4 Sep 2018 17:59:22 +0000 Subject: [bioontology-support] MEDDRA version In-Reply-To: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET> References: <6fa22fb7ddcc47eaa5696e1c1e925326@NH-SLPEX095.AD1.NHS.NET> Message-ID: <3DDE4CDC-2D88-4A61-8074-EC25523FD54A@stanford.edu> Hello Nick, On Sep 4, 2018, at 4:13 AM, KENNEDY, Nick (ROYAL DEVON AND EXETER NHS FOUNDATION TRUST) > wrote: The version of MEDDRA currently used on bioontology doesn?t seem to be displayed anywhere. I?ve checked on http://bioportal.bioontology.org/ontologies/MEDDRA?p=summary and browsed through the other tabs on that page. From the release date given as June 2017, it seems likely that you are using version 20.0 released March 2017. Is that correct? We import MEDDRA into BioPortal from the National Library of Medicine?s UMLS [1]. The last release of the UMLS was 2018AA. According to their documentation, 2018AA included version 20.1 of MEDDRA from Sept., 2017. More specifics are available on their website [2]. Kind regards, Jennifer [1] https://www.nlm.nih.gov/research/umls/ [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Sep 4 11:11:46 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 4 Sep 2018 18:11:46 +0000 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be In-Reply-To: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail> References: <5b8e5d1ad21ce_53523ff5d50e3fc023d7@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <9A3C2435-B22C-45A2-8287-9A5219CA6FCF@stanford.edu> Hello Chen, On Sep 4, 2018, at 3:23 AM, support at bioontology.org wrote: Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFOODON_03400361 Feedback: Dear, 1) If I want to make permanent link/ID for classes (i.e. I can access the class on BioPortal by the url/ID), should I use "http://purl.bioontology.org/ontology/ONE/XXXX"? You can access a permanent link for a class in the BioPortal user interface on the Classes tab. I noticed a bug while looking at this functionality, in that the icon for displaying the dialog with the permanent link is barely visible. We?ll need to fix that. To get to what you?re looking for, you can use the following steps: 1. Navigate to the Classes tab for your ontology: https://bioportal.bioontology.org/ontologies/ONE?p=classes. 2. Select any class in the class tree on the left-hand side. 3. In the Details pane on the right-hand side, hover your mouse in the toolbar to the right of the "Class Mappings" tab. You should be able to see a tooltip that says ?Get a permanent link to this class?. 4. Click the link and a dialog will pop up that contains the permanent link to the class. 2) In my ontology (ONE), there are always some classes without labels randomly. But I added labels actually. Please give an example of a class that you feel should have a label, but doesn?t. 3) For the terms I borrowed from other ontology (e.g. MeSH), if I don't add label by myself, the original label put by MeSH ontology will be used or not? i.e. in my ontology I will see "MESH:D003223" or "Congo" as label? You?ll see Congo. This is something you can check yourself by entering what you think the label would be in the ?Jump To? search box on the Classes tab: [cid:E62221BE-89B3-4CED-BE99-1BA0E69E3B8F at stanford.edu] Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-09-04 11.10.01.png Type: image/png Size: 117509 bytes Desc: Screenshot 2018-09-04 11.10.01.png URL: From Thomas.Schneider2 at mountsinai.org Wed Sep 5 08:31:17 2018 From: Thomas.Schneider2 at mountsinai.org (Schneider, Thomas) Date: Wed, 5 Sep 2018 15:31:17 +0000 Subject: [bioontology-support] Problem with registration to website Message-ID: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org> Hi, I am having difficulty registering to your website. Whenever I try to register it stalls and then I get the error below. We're sorry but something has gone wrong. We have been notified of this error. Please let me know how I can register for this website. Thanks, Tom From support at bioontology.org Wed Sep 5 04:53:29 2018 From: support at bioontology.org (support at bioontology.org) Date: Wed, 05 Sep 2018 04:53:29 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Gerhard Mayer Message-ID: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Sep 5 11:56:00 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 5 Sep 2018 18:56:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Gerhard Mayer In-Reply-To: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail> References: <5b8fc3b985433_564f3fe9c4eb3488564b4@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <97C43287-AC94-4068-A628-7D57DF8FA810@stanford.edu> Hello Gerhard, The process for submitting an ontology to BioPortal is described on this wiki page: https://www.bioontology.org/wiki/BioPortal_Help#Submitting_an_ontology Let us know if you experience any difficulties. Kind regards, Jennifer On Sep 5, 2018, at 4:53 AM, support at bioontology.org wrote: Hello, we developed a new cross-linker and derivatization reagents ontology. It's a structured controlled vocabulary for cross-linking reagents and derivatization reagents used within the proteomics mass spectrometry standard mzIdenML1.2 and mzTab-M / mzTab-L The link to the .obo file is https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo How can we trigger the inclusion into the BioPortal portal? Best regards, Gerhard Mayer HUPO-PSI ontology coordinator -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Sep 5 18:16:00 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 6 Sep 2018 01:16:00 +0000 Subject: [bioontology-support] Problem with registration to website In-Reply-To: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org> References: <1DC6254D8AC2924BACB3BAAE6975FC480C0866D2@SMESEXCP014034.msnyuhealth.org> Message-ID: Hi Tom, Apologies that our site has been experiencing some instability since early this morning. We?re still investigating / doing some troubleshooting. It?s up at the moment if you?d like to do another attempt at registration. Kind regards, Jennifer > On Sep 5, 2018, at 8:31 AM, Schneider, Thomas wrote: > > Hi, > > I am having difficulty registering to your website. Whenever I try to register it stalls and then I get the error below. > > > We're sorry but something has gone wrong. We have been notified of this error. > > > Please let me know how I can register for this website. > > > Thanks, > Tom > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From amassengale at rsna.org Thu Sep 6 12:13:37 2018 From: amassengale at rsna.org (Andrew Massengale) Date: Thu, 6 Sep 2018 19:13:37 +0000 Subject: [bioontology-support] BioPortal API route not working Message-ID: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org> Hi all, We have been using the following API call without issue up until a few days ago (API key removed): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000 Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000 Here is a visual representation of what I?m trying to do: [cid:image001.png at 01D445EB.CD3BDAB0] I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned. Let me know if you need any more information, Andrew M Andrew Massengale Team Lead | Senior Software Engineer IT: Development amassengale at rsna.org CEL: 815-614-8296 TEL: 630-481-1012 FAX: 630-571-7837 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2018 Annual Meeting November 25th ? 30th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 93077 bytes Desc: image001.png URL: From vendetti at stanford.edu Thu Sep 6 13:16:19 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 6 Sep 2018 20:16:19 +0000 Subject: [bioontology-support] BioPortal API route not working In-Reply-To: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org> References: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org> Message-ID: <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu> Hi Andrew, This appears to have been a caching issue, possibly related to some system instability we experienced yesterday. I?ve reset the application caches and the call you list below now returns results. Apologies for the difficulty. Kind regards, Jennifer On Sep 6, 2018, at 12:13 PM, Andrew Massengale > wrote: Hi all, We have been using the following API call without issue up until a few days ago (API key removed): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000 Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000 Here is a visual representation of what I?m trying to do: I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned. Let me know if you need any more information, Andrew M Andrew Massengale Team Lead | Senior Software Engineer IT: Development amassengale at rsna.org CEL: 815-614-8296 TEL: 630-481-1012 FAX: 630-571-7837 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2018 Annual Meeting November 25th ? 30th McCormick Place, Chicago _______________________________________________ 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 amassengale at rsna.org Thu Sep 6 13:18:43 2018 From: amassengale at rsna.org (Andrew Massengale) Date: Thu, 6 Sep 2018 20:18:43 +0000 Subject: [bioontology-support] BioPortal API route not working In-Reply-To: <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu> References: <51FE1A25-0645-439F-8848-76CA23206C97@hq.rsna.org> <07AE9960-C21D-464C-A0CF-BA73DE890C05@stanford.edu> Message-ID: <807C8BFB-0347-4B03-BA81-EECAEC45EA5D@hq.rsna.org> Confirmed that it?s working from our end again. Thanks Jennifer! From: Jennifer Leigh Vendetti Date: Thursday, September 6, 2018 at 3:16 PM To: Andrew Massengale Cc: "support at bioontology.org" Subject: Re: [bioontology-support] BioPortal API route not working Hi Andrew, This appears to have been a caching issue, possibly related to some system instability we experienced yesterday. I?ve reset the application caches and the call you list below now returns results. Apologies for the difficulty. Kind regards, Jennifer On Sep 6, 2018, at 12:13 PM, Andrew Massengale > wrote: Hi all, We have been using the following API call without issue up until a few days ago (API key removed): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000 Now it is returning 0 results. What is interesting is that, considering that this query is using the subtree_root_id option, if I use a subtree directly under the root ID I?m passing in, then it returns results. This seems to be in error to be, because if I try and query a subtree on a parent of a child element, than at least that child?s elements should be returned, but instead nothing is being returned. Here is the query for the child (API key removed again): https://data.bioontology.org/search?ontology=RADLEX&q=head&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID13230&roots_only=true&page=1&pagesize=1000 Here is a visual representation of what I?m trying to do: I?m trying to query the ?Anatomical entity? subtree (RID3), which returns 0 results. However, as mentioned above, when I use the ?Anatomical set? subtree (RID13230), I get some results returned. Let me know if you need any more information, Andrew M Andrew Massengale Team Lead | Senior Software Engineer IT: Development amassengale at rsna.org CEL: 815-614-8296 TEL: 630-481-1012 FAX: 630-571-7837 Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2018 Annual Meeting November 25th ? 30th McCormick Place, Chicago _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support Radiological Society of North America 820 Jorie Blvd, Oak Brook, IL 60523 TEL 1-630-571-2670 FAX 1-630-571-7837 RSNA.org Facebook Twitter RSNA 2018 Annual Meeting November 25th ? 30th McCormick Place, Chicago -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elcio.Abrahao at lirmm.fr Mon Sep 10 06:23:54 2018 From: Elcio.Abrahao at lirmm.fr (abrahao) Date: Mon, 10 Sep 2018 15:23:54 +0200 Subject: [bioontology-support] Problem on the respose from the REST API for mappigs submission Message-ID: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr> Hi! My name is Elcio Abrah?o. I worked with Clement Jonquet at Agroportal, FR. I am testing the REST API from Bioportal to submit Mappings on the JSON format and I notice that the response JSON did not include a valid ID for that mapping. The ID field come with the content NULL. I would like to asked you if this an error or I missing something.... The request and response are attached bellow: Thanks, -- Elcio Abrah?o AgroPortal Project - LIRMM - University of Montpellier, France. HTTP POST with APIKEY on the headers. REST URL: https://data.bioontology.org/mappings REST API Key: OMITTED HERE for security REQUEST: { "creator": "http://data.bioontology.org/users/elcioabrahao", "source_contact_info": "pirmail at georgetown.edu,dan5 at georgetown.edu", "relation": [ "http://www.geneontology.org/formats/oboinowl#hasdbxref" ], "source": "RESTTEST", "source_name": "PR", "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR", "classes" : { "http://purl.bioontology.org/ontology/STY/T052": "STY", "http://www.drugtargetontology.org/dto/DTO_03100518": "DTO" } } RESPONSE: { "id": null, "source": "REST", "classes": [ { "obsolete": false, "@id": "http://purl.bioontology.org/ontology/STY/T052", "@type": "http://www.w3.org/2002/07/owl#Class", "links": { "self": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052", "ontology": "http://data.bioontology.org/ontologies/STY", "children": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/children", "parents": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/parents", "descendants": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/descendants", "ancestors": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/ancestors", "instances": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/instances", "tree": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/tree", "notes": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/notes", "mappings": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/mappings", "ui": "http://bioportal.bioontology.org/ontologies/STY?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052", "@context": { "self": "http://www.w3.org/2002/07/owl#Class", "ontology": "http://data.bioontology.org/metadata/Ontology", "children": "http://www.w3.org/2002/07/owl#Class", "parents": "http://www.w3.org/2002/07/owl#Class", "descendants": "http://www.w3.org/2002/07/owl#Class", "ancestors": "http://www.w3.org/2002/07/owl#Class", "instances": "http://data.bioontology.org/metadata/Instance", "tree": "http://www.w3.org/2002/07/owl#Class", "notes": "http://data.bioontology.org/metadata/Note", "mappings": "http://data.bioontology.org/metadata/Mapping", "ui": "http://www.w3.org/2002/07/owl#Class" } }, "@context": { "@vocab": "http://data.bioontology.org/metadata/", "obsolete": "http://data.bioontology.org/metadata/owlobsolete" } }, { "obsolete": false, "@id": "http://www.drugtargetontology.org/dto/DTO_03100518", "@type": "http://www.w3.org/2002/07/owl#Class", "links": { "self": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518", "ontology": "http://data.bioontology.org/ontologies/DTO", "children": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/children", "parents": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/parents", "descendants": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/descendants", "ancestors": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/ancestors", "instances": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/instances", "tree": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/tree", "notes": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/notes", "mappings": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/mappings", "ui": "http://bioportal.bioontology.org/ontologies/DTO?p=classes&conceptid=http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518", "@context": { "self": "http://www.w3.org/2002/07/owl#Class", "ontology": "http://data.bioontology.org/metadata/Ontology", "children": "http://www.w3.org/2002/07/owl#Class", "parents": "http://www.w3.org/2002/07/owl#Class", "descendants": "http://www.w3.org/2002/07/owl#Class", "ancestors": "http://www.w3.org/2002/07/owl#Class", "instances": "http://data.bioontology.org/metadata/Instance", "tree": "http://www.w3.org/2002/07/owl#Class", "notes": "http://data.bioontology.org/metadata/Note", "mappings": "http://data.bioontology.org/metadata/Mapping", "ui": "http://www.w3.org/2002/07/owl#Class" } }, "@context": { "@vocab": "http://data.bioontology.org/metadata/", "obsolete": "http://data.bioontology.org/metadata/owlobsolete" } } ], "process": { "id": "http://data.bioontology.org/metadata/mapping_processes/-elcioabrahao-0831b590-9723-0136-cc8e-005056010074", "name": "REST Mapping", "creator": "http://data.bioontology.org/users/elcioabrahao", "source": "RESTTEST", "relation": "[\"http://www.geneontology.org/formats/oboinowl#hasdbxref\"]", "source_name": "PR", "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR", "date": "2018-09-10T05:29:05-07:00" }, "@id": "", "@type": "http://data.bioontology.org/metadata/Mapping" } From Elcio.Abrahao at lirmm.fr Mon Sep 10 06:13:32 2018 From: Elcio.Abrahao at lirmm.fr (abrahao) Date: Mon, 10 Sep 2018 15:13:32 +0200 Subject: [bioontology-support] Problem when trying to see class details Message-ID: Hi ! My name is Elcio Abrah?o. I worked with CLement Jonquet at Agroportal, FR. I just trying to query same classes on PR ontology but I only could access the class details when I am logged out... If I login then cames the folow error message only when try to access class details or the cls tree: "We're sorry but something has gone wrong. We have been notified of this error." Finnaly, I have 2 accounts: "elcioabrahao" and "abrahao". Could you delete the account with ID "abrahao" please ? I notice a problem when sumiting mappings, but I will send other email for this problem. Thanks, -- Elcio Abrah?o AgroPortal Project - LIRMM - University of Montpellier, France. From csongor.nyulas at stanford.edu Mon Sep 10 12:31:17 2018 From: csongor.nyulas at stanford.edu (Csongor Nyulas) Date: Mon, 10 Sep 2018 12:31:17 -0700 Subject: [bioontology-support] =?utf-8?q?Fwd=3A_Early_bird_deadline_approa?= =?utf-8?q?ching=3A_Register_today_to_the_Protege_Short_Course_at_Stanford?= =?utf-8?q?_University=2C_October_22_=E2=80=93_24=2C_2018!?= In-Reply-To: <6ef02961-ec36-881a-6695-54723cf3df75@stanford.edu> References: <6ef02961-ec36-881a-6695-54723cf3df75@stanford.edu> Message-ID: <57d05cfa-3742-9c82-b487-53a02bdbd27a@stanford.edu> In case anyone is interested in participating at the Prot?g? Short Course please check out the announcement below... Csongor -------- Forwarded Message -------- Subject: Early bird deadline approaching: Register today to the Protege Short Course at Stanford University, October 22 ? 24, 2018! Date: Mon, 10 Sep 2018 12:05:09 -0700 From: Csongor Nyulas To: protege-announce at lists.stanford.edu CC: User support for WebProtege and Protege Desktop , Developer support for WebProtege and Protege Desktop Dear all, Don't miss the chance to register at reduced rate to the next Prot?g? Short Course, to be held at Stanford University, California between October 22 ? 24, 2018. *There are only two weeks until the "early bird" deadline!* Register here: https://protege.stanford.edu/shortcourse/201810/registration.html The Prot?g? Short Course offers a 3-day intensive training in use of the Prot?g? toolset, ontology development, and OWL. We cover best practices in ontology building and the latest Semantic Web technologies, including OWL 2, RDF, and SPARQL. We also cover topics such as real-world applications with ontologies, and data access and import from different data sources. The course is hands-on and is taught by the members of the Prot?g? team. Read more about it at: https://protege.stanford.edu/shortcourse/201810/ If you have any questions about the Prot?g? Short Course, please email: protege-shortcourse at lists.stanford.edu Please feel free to forward this announcement to anyone who might be interested in the course. Thank you! We look forward to seeing you in October! Best regards, The Prot?g? Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Sep 10 19:52:01 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 10 Sep 2018 19:52:01 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Chad Vanderbilt Message-ID: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Sep 10 18:39:54 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 10 Sep 2018 18:39:54 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Syanne Fonda Message-ID: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From james at overton.ca Mon Sep 10 12:36:00 2018 From: james at overton.ca (James A. Overton) Date: Mon, 10 Sep 2018 15:36:00 -0400 Subject: [bioontology-support] Some trouble with OBI on Bioportal Message-ID: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca> Hello, I'm a developer for the Ontology for Biomedical Investigations (OBI). A new OBI release was published last week. On Bioportal's OBI page, I see that a new release was uploaded last week, but the ontology date is wrong, and the new classes are not appearing in the class view. I have access to the "ontology.bio.investigations" user that administers the OBI account, but I can't figure out how to fix this. In general I've seen a lot of errors while trying to use the OBI class view over the past week. Some help would be appreciated. James From mdorf at stanford.edu Tue Sep 11 13:19:00 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 11 Sep 2018 20:19:00 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Chad Vanderbilt In-Reply-To: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail> References: <5b972dd180603_177e2acee3c42f3448e0@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <93ED9B89-B47D-492A-B0AB-DD0E28AC91D2@stanford.edu> Hi Chad, Thank you for contacting us. Our site has experienced several outages last week, which may have been the cause of the issues you?ve experienced. It is back to normal now, and I?ve verified that the URL below works as expected. Please let us know if you continue experiencing issues with BioPortal. Thanks, Michael On Sep 10, 2018, at 7:52 PM, support at bioontology.org wrote: Name: Chad Vanderbilt Email: vanderbilt.chad at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2F500%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FICD10PCS%252FGZC Feedback: Hi, I have noticed a lot of performance issues, particularly with the CPT section in the last 2 weeks. Thank you. -Chad Vanderbilt, MD _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Sep 11 13:21:38 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 11 Sep 2018 20:21:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Syanne Fonda In-Reply-To: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail> References: <5b971cea617f2_79432b28b31c6ec831656@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Syanne, Thank you for contacting us. Thank you for contacting us. Our site has experienced several outages last week and yesterday, which may have been the cause of your issue with CPT. It is back to normal now, and I?ve verified that the URL below works as expected. Please let us know if you continue experiencing issues with CPT and BioPortal. Thanks! Michael On Sep 10, 2018, at 6:39 PM, support at bioontology.org wrote: Name: Syanne Fonda Email: syanne.fonda at docdoc.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F1006069 Feedback: Why is your CPT is not working since yesterday? You need to fix this as soon as possible. Thank you. Best _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Sep 11 14:18:04 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 11 Sep 2018 21:18:04 +0000 Subject: [bioontology-support] Some trouble with OBI on Bioportal In-Reply-To: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca> References: <174F5073-5C3D-448D-93A1-41951AB08D12@overton.ca> Message-ID: Hi James, Thank you for contacting us. I?ve re-processed the latest version of OBI, and it appears to work as expected now. You can adjust the release date by following this link (having previously logged in to BioPortal): http://bioportal.bioontology.org/ontologies/OBI/submissions/37/edit As far as errors, I must apologize, we?ve been experiencing a number of periods of instability both last and this week (Monday). The site is now back to normal, so please let us know if you continue seeing errors you reported. Thanks! Michael On Sep 10, 2018, at 12:36 PM, James A. Overton > wrote: Hello, I'm a developer for the Ontology for Biomedical Investigations (OBI). A new OBI release was published last week. On Bioportal's OBI page, I see that a new release was uploaded last week, but the ontology date is wrong, and the new classes are not appearing in the class view. I have access to the "ontology.bio.investigations" user that administers the OBI account, but I can't figure out how to fix this. In general I've seen a lot of errors while trying to use the OBI class view over the past week. Some help would be appreciated. James _______________________________________________ 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 Sep 12 11:36:54 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 12 Sep 2018 18:36:54 +0000 Subject: [bioontology-support] Problem when trying to see class details In-Reply-To: References: Message-ID: Hi Elcio, Thanks for contacting us. Is the problem still happening on your end. I have not been able to reproduce it on mine. I?ve seen a problem like this reported on the support list before, and it was solved by clearing the browser cache, e.g., in Chrome doing something like Preferences? | Clear Browsing Data? Have you tried this? Another thing to note is that we?ve experienced some pockets of downtime last week, and your use may have coincided with one. When you?re logged out, you are seeing a cached response, which doesn?t always rely on our backend being up and running. When you?re logged in, the caching layer does not kick in (well, to some extent), and you are hitting the rest service. I?ve removed the user ?abrahao? from our system. Thanks! Michael > On Sep 10, 2018, at 6:13 AM, abrahao wrote: > > Hi ! > > My name is Elcio Abrah?o. I worked with CLement Jonquet at Agroportal, FR. > > I just trying to query same classes on PR ontology but I only could access the class details when I am logged out... If I login then cames the folow error message only when try to access class details or the cls tree: "We're sorry but something has gone wrong. We have been notified of this error." > > Finnaly, I have 2 accounts: "elcioabrahao" and "abrahao". Could you delete the account with ID "abrahao" please ? > > I notice a problem when sumiting mappings, but I will send other email for this problem. > > Thanks, > > -- > Elcio Abrah?o > AgroPortal Project - LIRMM - University of Montpellier, France. > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From mdorf at stanford.edu Wed Sep 12 14:51:32 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 12 Sep 2018 21:51:32 +0000 Subject: [bioontology-support] Problem on the respose from the REST API for mappigs submission In-Reply-To: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr> References: <986218a9d71b8dc78cd5b93d9778af29@lirmm.fr> Message-ID: <08A76D05-759D-4955-92F8-65F20B29117B@stanford.edu> Hi again, Elcio, This output is by design. If you look at a sample of our own mappings output, the response would look identical to yours: https://data.bioontology.org/mappings?ontologies=SNOMEDCT,CPT Most of the mappings in our system are of type LOOM, which are auto-inferred on the fly when you make the REST call. The other auto-generated mappings are of type CUI and SAME_URI. They aren?t stored in the system, and therefore, don?t have an ID (or the Process object) associated with them. The mappings of type REST (manually created) are stored in our backend. They have the object ?process? populated, which serves as the identifier for the mapping. So, in short, your output looks correct! :-) Hope this helps! Michael On Sep 10, 2018, at 6:23 AM, abrahao > wrote: Hi! My name is Elcio Abrah?o. I worked with Clement Jonquet at Agroportal, FR. I am testing the REST API from Bioportal to submit Mappings on the JSON format and I notice that the response JSON did not include a valid ID for that mapping. The ID field come with the content NULL. I would like to asked you if this an error or I missing something.... The request and response are attached bellow: Thanks, -- Elcio Abrah?o AgroPortal Project - LIRMM - University of Montpellier, France. HTTP POST with APIKEY on the headers. REST URL: https://data.bioontology.org/mappings REST API Key: OMITTED HERE for security REQUEST: { "creator": "http://data.bioontology.org/users/elcioabrahao", "source_contact_info": "pirmail at georgetown.edu,dan5 at georgetown.edu", "relation": [ "http://www.geneontology.org/formats/oboinowl#hasdbxref" ], "source": "RESTTEST", "source_name": "PR", "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR", "classes" : { "http://purl.bioontology.org/ontology/STY/T052": "STY", "http://www.drugtargetontology.org/dto/DTO_03100518": "DTO" } } RESPONSE: { "id": null, "source": "REST", "classes": [ { "obsolete": false, "@id": "http://purl.bioontology.org/ontology/STY/T052", "@type": "http://www.w3.org/2002/07/owl#Class", "links": { "self": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052", "ontology": "http://data.bioontology.org/ontologies/STY", "children": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/children", "parents": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/parents", "descendants": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/descendants", "ancestors": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/ancestors", "instances": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/instances", "tree": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/tree", "notes": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/notes", "mappings": "http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052/mappings", "ui": "http://bioportal.bioontology.org/ontologies/STY?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT052", "@context": { "self": "http://www.w3.org/2002/07/owl#Class", "ontology": "http://data.bioontology.org/metadata/Ontology", "children": "http://www.w3.org/2002/07/owl#Class", "parents": "http://www.w3.org/2002/07/owl#Class", "descendants": "http://www.w3.org/2002/07/owl#Class", "ancestors": "http://www.w3.org/2002/07/owl#Class", "instances": "http://data.bioontology.org/metadata/Instance", "tree": "http://www.w3.org/2002/07/owl#Class", "notes": "http://data.bioontology.org/metadata/Note", "mappings": "http://data.bioontology.org/metadata/Mapping", "ui": "http://www.w3.org/2002/07/owl#Class" } }, "@context": { "@vocab": "http://data.bioontology.org/metadata/", "obsolete": "http://data.bioontology.org/metadata/owlobsolete" } }, { "obsolete": false, "@id": "http://www.drugtargetontology.org/dto/DTO_03100518", "@type": "http://www.w3.org/2002/07/owl#Class", "links": { "self": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518", "ontology": "http://data.bioontology.org/ontologies/DTO", "children": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/children", "parents": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/parents", "descendants": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/descendants", "ancestors": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/ancestors", "instances": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/instances", "tree": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/tree", "notes": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/notes", "mappings": "http://data.bioontology.org/ontologies/DTO/classes/http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518/mappings", "ui": "http://bioportal.bioontology.org/ontologies/DTO?p=classes&conceptid=http%3A%2F%2Fwww.drugtargetontology.org%2Fdto%2FDTO_03100518", "@context": { "self": "http://www.w3.org/2002/07/owl#Class", "ontology": "http://data.bioontology.org/metadata/Ontology", "children": "http://www.w3.org/2002/07/owl#Class", "parents": "http://www.w3.org/2002/07/owl#Class", "descendants": "http://www.w3.org/2002/07/owl#Class", "ancestors": "http://www.w3.org/2002/07/owl#Class", "instances": "http://data.bioontology.org/metadata/Instance", "tree": "http://www.w3.org/2002/07/owl#Class", "notes": "http://data.bioontology.org/metadata/Note", "mappings": "http://data.bioontology.org/metadata/Mapping", "ui": "http://www.w3.org/2002/07/owl#Class" } }, "@context": { "@vocab": "http://data.bioontology.org/metadata/", "obsolete": "http://data.bioontology.org/metadata/owlobsolete" } } ], "process": { "id": "http://data.bioontology.org/metadata/mapping_processes/-elcioabrahao-0831b590-9723-0136-cc8e-005056010074", "name": "REST Mapping", "creator": "http://data.bioontology.org/users/elcioabrahao", "source": "RESTTEST", "relation": "[\"http://www.geneontology.org/formats/oboinowl#hasdbxref\"]", "source_name": "PR", "comment": "Generated with the Ontology Mapping Harvest Tool - v.1.3 - Agroportal Project - LIRMM - 10/09/2018 11:13 - FR", "date": "2018-09-10T05:29:05-07:00" }, "@id": "", "@type": "http://data.bioontology.org/metadata/Mapping" } _______________________________________________ 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 Sep 12 22:26:23 2018 From: support at bioontology.org (support at bioontology.org) Date: Wed, 12 Sep 2018 22:26:23 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Kristi Brownfield Message-ID: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Sep 13 11:31:56 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 13 Sep 2018 18:31:56 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Kristi Brownfield In-Reply-To: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail> References: <5b99f4ff1c3b7_24b72b29a20ad3a855523@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <1E95416C-95F2-4177-97BE-24D346ECAF60@stanford.edu> Hi Kristi, Thank you for contacting us. I?ve looked up the term you were referring to, but it doesn?t contain any definition: http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F19681004 Can you please clarify what you are looking for? Roughly twice per year the UMLS [1] publishes a release of a group of ontologies, which we import into BioPortal. SNOMED CT is one of the ontologies that?s pulled in when we do the UMLS imports. We don?t have any control over the ontology content. I look forward to further clarification from you. Thanks! Michael [1] https://www.nlm.nih.gov/research/umls/ On Sep 12, 2018, at 10:26 PM, support at bioontology.org wrote: Name: Kristi Brownfield Email: kbrownfield at wregional.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F424008009 Feedback: I am researching Snomed code 19681004 "Nursing evaluation of patient and report (procedure)" for a quality metrix visit type permitted by CMS for a program for CPC+ CQM. I am trying to find the definition or defining term to the "nursing ....(procedure" What required docuemation is required to link this snomed code to the note? Thank you so much. This is a very time sensitive issue that we are trying to resolve on behalf of the CPC+ program and our hospital system and EMR Vendor. _______________________________________________ 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 markampa at pennmedicine.upenn.edu Tue Sep 18 08:43:20 2018 From: markampa at pennmedicine.upenn.edu (Miller, Mark) Date: Tue, 18 Sep 2018 15:43:20 +0000 Subject: [bioontology-support] Download OWL versions of UMLS components? Message-ID: If I try to download MDDB via http://data.bioontology.org/ontologies/MDDB/download?apikey= I get the response at the end of the is email. Are there any conditions under which you allow download of licensed UMLS components? I have a UMLS license! I have done the MetaMorphoSys -> MySQL -> RDF conversion in the past, but would like to avoid that overhead if possible. (I do appreciate your contribution of the RDF conversion tool.) thanks, Mark Miller ontologist, Institute for Biomedical Informatics University of Pennsylvania ____ { * - "errors": [ * "License restrictions on download for MDDB" ], * "status": 403 } -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Sep 18 13:22:12 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 18 Sep 2018 20:22:12 +0000 Subject: [bioontology-support] Download OWL versions of UMLS components? In-Reply-To: References: Message-ID: <418EB8C5-0177-421D-BBC5-D9E809762B5B@stanford.edu> Mark, We handle requests like this on a case-by-case basis, depending on the ontology, its license, the UMLS distribution license, and sometimes my current knowledge of Intellectual Property issues. I'll respond to you off-list once I've explore further. John On Sep 18, 2018, at 8:43 AM, Miller, Mark > wrote: If I try to download MDDB via http://data.bioontology.org/ontologies/MDDB/download?apikey=<my apikey> I get the response at the end of the is email. Are there any conditions under which you allow download of licensed UMLS components? I have a UMLS license! I have done the MetaMorphoSys -> MySQL -> RDF conversion in the past, but would like to avoid that overhead if possible. (I do appreciate your contribution of the RDF conversion tool.) thanks, Mark Miller ontologist, Institute for Biomedical Informatics University of Pennsylvania ____ { * - "errors": [ * "License restrictions on download for MDDB" ], * "status": 403 } _______________________________________________ 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 Mon Sep 17 11:48:05 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 17 Sep 2018 11:48:05 -0700 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be Message-ID: <5b9ff6e54edc2_3fb92b263a0b0dd4660f6@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From yac9016 at nyp.org Tue Sep 18 08:42:47 2018 From: yac9016 at nyp.org (Yael Greenberg) Date: Tue, 18 Sep 2018 15:42:47 +0000 Subject: [bioontology-support] CPT Code Library Message-ID: <834786eeb7c348d5b359e02b19f946a0@nyp.org> Is there a way to download the library of CPT codes and matching descriptions? Thanks, Yael Yael Coppleson Greenberg, MPH Director, NYP Analytics | NewYork-Presbyterian Hospital yac9016 at nyp.org | (c) 646.784.5656 | (o) 212.305.5715 ---------------------------------------------------------------------- This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you. code:d34y -------------- next part -------------- An HTML attachment was scrubbed... URL: From gullyburns at gmail.com Mon Sep 17 13:27:40 2018 From: gullyburns at gmail.com (Gully Burns) Date: Mon, 17 Sep 2018 13:27:40 -0700 Subject: [bioontology-support] Transferring ownership of DSEO ontology Message-ID: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com> Dear Sir, Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary ) to a colleague? The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). Can you advise me what the process is to switch ownership of this ontology? Thanks Gully -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed Sep 19 10:50:45 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 19 Sep 2018 17:50:45 +0000 Subject: [bioontology-support] Transferring ownership of DSEO ontology In-Reply-To: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com> References: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com> Message-ID: <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu> Gully, We can take care of that for you. Do you want both of the people you list as administrator? John On Sep 17, 2018, at 1:27 PM, Gully Burns > wrote: Dear Sir, Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague? The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). Can you advise me what the process is to switch ownership of this ontology? Thanks Gully _______________________________________________ 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 Sep 19 18:17:29 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 20 Sep 2018 01:17:29 +0000 Subject: [bioontology-support] CPT Code Library In-Reply-To: <834786eeb7c348d5b359e02b19f946a0@nyp.org> References: <834786eeb7c348d5b359e02b19f946a0@nyp.org> Message-ID: <92F0973F-539F-4F6D-89D1-9FB3FF57EC66@stanford.edu> Yael, Thanks for your request. I offer the following information for the list, some of which you may have received separately (thanks R Wynne!). As you may know, you are unable to download most UMLS ontologies directly from BioPortal, because license restrictions apply. However, you can download information contained in BioPortal about those ontologies by using the BioPortal REST API. The API is documented at http://data.bioontology.org/documentation. If you decide to use the API, you?ll need to get an API key (see https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key). So for example, REST API calls to retrieve class data will return results: http://data.bioontology.org/ontologies/CPT/classes?apikey= You can use the hypermedia links in the reply to explore things like parents, children, descendants, etc. OR, for UMLS ontologies: There is a way to download this information directly from UMLS, with minimal processing. The following applies for almost all sources in the UMLS Metathesaurus (which includes even more sources than BioPortal captures). You may want to reach out to the source contact for your ontology and let them know you are interested, as there may be a license on the source you are not aware of, it could give you additional access or reuse privileges beyond what UMLS offers in its license. The CPT source is extracted via the UMLS Metathesaurus. You need to obtain a free license[1] from NLM to download Metathesaurus. The download includes a utility to extract a source or sources, named Metamorphosys. Once you have an extract, it can be loaded into a database. Some sources are small enough to load into Excel. You will want to know which files and columns are most important to you. More information on CPT source representation is available through UMLS[2]. John [1] https://uts.nlm.nih.gov/license.html [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/sourcerepresentation.html On Sep 18, 2018, at 8:42 AM, Yael Greenberg > wrote: Is there a way to download the library of CPT codes and matching descriptions? Thanks, Yael Yael Coppleson Greenberg, MPH Director, NYP Analytics | NewYork-Presbyterian Hospital yac9016 at nyp.org | (c) 646.784.5656 | (o) 212.305.5715 ________________________________ This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you. code:d34y _______________________________________________ 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 Thu Sep 20 17:49:56 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 21 Sep 2018 00:49:56 +0000 Subject: [bioontology-support] NCBO virtual appliance In-Reply-To: References: <017BE204-69FE-418C-A83E-B8E381C5A736@stanford.edu> Message-ID: Hi Chad, I'm sorry, but I don't know what version you have right now, so I can't answer your question directly. The Release Notes for the Virtual Appliance software are at https://www.bioontology.org/wiki/BioPortal_Virtual_Appliance_Release_Notes. However, you may also want to know whether it is easily installable on your platform. If you have a Virtual Appliance already, the way to find out the current releases that are available for download is to visit https://bioportal.bioontology.org/virtual_appliance. (You'll need to be logged in to BioPortal, using the account you obtained the Virtual Appliance with, to see that page.) The current listing show: ? Version 2.5 OVF ? Version 2.4 OVF | Amazon EC2 In summary, we have not created an Amazon EC2 version for Version 2.5 yet. I hope this helps. John On Sep 20, 2018, at 3:28 PM, Shaw, Chad A. > wrote: Hi John Is there a new release of the NCBO VM that we could obtain? I think the one we have is pretty old right now. Please let me know Thanks Chad ________________________________ ======================== 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 lfierro at isi.edu Fri Sep 21 09:09:26 2018 From: lfierro at isi.edu (Lily Fierro) Date: Fri, 21 Sep 2018 16:09:26 +0000 Subject: [bioontology-support] Transferring ownership of DSEO ontology In-Reply-To: <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu> References: <283911A2-25A2-4655-BBBC-D1071C7D360E@gmail.com>, <2883DEF7-3A1B-4C6F-89C4-E1BF7165B589@stanford.edu> Message-ID: <528934fd6376469395e3617179128104@ads.isi.edu> Hello John, Thank you very much for your help on this! I just logged into BioPortal and can confirm that I have administrator access. One quick question for you: is there a way to upload mappings to BioPortal in bulk? I noticed that I can add them on a class-by-class basis through the web interface, but could not find any way to upload them for multiple classes. Thanks again! -Lily ________________________________ From: John Graybeal Sent: Wednesday, September 19, 2018 1:50:45 PM To: Gully Burns Cc: support at bioontology.org; Jose-Luis Ambite; Lily Fierro Subject: Re: [bioontology-support] Transferring ownership of DSEO ontology Gully, We can take care of that for you. Do you want both of the people you list as administrator? John On Sep 17, 2018, at 1:27 PM, Gully Burns > wrote: Dear Sir, Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague? The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). Can you advise me what the process is to switch ownership of this ontology? Thanks Gully _______________________________________________ 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 Sep 21 11:43:48 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 21 Sep 2018 18:43:48 +0000 Subject: [bioontology-support] uploading mappings in bulk Message-ID: You're welcome Lily. Yes, you can upload mappings through the API. Example code for creating API mappings is at https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java A past thread on how to do this is at http://ncbo-support.2288202.n4.nabble.com/Uploading-a-Mapping-td4653220.html#a4653222 It mentions the general info on running the above sample code: https://github.com/ncbo/ncbo_rest_sample_code/tree/master/java Links that might be useful: https://www.bioontology.org/wiki/index.php/BioPortal_Mappings http://data.bioontology.org/documentation#Mapping -- the actual API documentation John > On Sep 21, 2018, at 9:09 AM, Lily Fierro wrote: > > Hello John, > > Thank you very much for your help on this! I just logged into BioPortal and can confirm that I have administrator access. > > One quick question for you: is there a way to upload mappings to BioPortal in bulk? I noticed that I can add them on a class-by-class basis through the web interface, but could not find any way to upload them for multiple classes. > > Thanks again! > > -Lily > From: John Graybeal > Sent: Wednesday, September 19, 2018 1:50:45 PM > To: Gully Burns > Cc: support at bioontology.org; Jose-Luis Ambite; Lily Fierro > Subject: Re: [bioontology-support] Transferring ownership of DSEO ontology > > Gully, > > We can take care of that for you. Do you want both of the people you list as administrator? > > John > >> On Sep 17, 2018, at 1:27 PM, Gully Burns wrote: >> >> Dear Sir, >> >> Would it be possible to transfer my administrator role for the DSEO ontology (http://bioportal.bioontology.org/ontologies/DSEO/?p=summary) to a colleague? >> >> The main technical developers responsible for DSEO development is Lily Fierro (lfierro at isi.edu) and the head of the project developing this work is Jose Luis Ambite (jl.ambite at gmail.com). >> >> Can you advise me what the process is to switch ownership of this ontology? >> >> Thanks >> >> Gully >> _______________________________________________ >> 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 From support at bioontology.org Mon Sep 24 02:17:17 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 24 Sep 2018 02:17:17 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Hiba Itani Message-ID: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From a.grigoriu at student.maastrichtuniversity.nl Mon Sep 24 07:06:25 2018 From: a.grigoriu at student.maastrichtuniversity.nl (Grigoriu, Andreea (Stud. DKE)) Date: Mon, 24 Sep 2018 14:06:25 +0000 Subject: [bioontology-support] error report Message-ID: <1537797983389.43171@student.maastrichtuniversity.nl> Hi! While working on my Internship during my Master Studies I have encountered some incosistency in your platform. I was trying to find the metrics for various ontologies ( I was particulary interested in number of classes and properties of an ontology). Some ontologies (eg. PTS, HUGO, HGNC) were showing ( in the metric box on the ontology page->http://bioportal.bioontology.org/ontologies/HGNC/?p=summary) 0 properties but once I check the properties tab (http://bioportal.bioontology.org/ontologies/HGNC/?p=properties?) I can actually see a lot of properties. This was obvious for the examples of 0 properties but now I am also wandering if there might be other inconsistencies as well in other numbers of properties or maybe even classes. Kind regards, Andreea Grigoriu -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Sep 24 08:49:35 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 24 Sep 2018 08:49:35 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh Message-ID: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From Ross.W.Filice at gunet.georgetown.edu Mon Sep 24 10:37:59 2018 From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W) Date: Mon, 24 Sep 2018 13:37:59 -0400 Subject: [bioontology-support] programmatic class mappings In-Reply-To: References: Message-ID: Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error: {"errors":["Input does not contain classes"],"status":400} I'm submitting the JSON object as provided by the github code: { "creator" : "http://data.bioontology.org/user/[USER]", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "[USER]", "source_name" : "[USER] Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "terms" : [ { "ontology" : "NCIT", "term" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ] }, { "ontology" : "SNOMEDCT", "term" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ] } ] } Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings: http://data.bioontology.org/documentation#Mapping It includes parameters "source" "id" "process" and "classes" without any other information. Thanks much, Ross -----Original Message----- From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Thursday, August 30, 2018 7:14 PM To: Filice, Ross W Cc: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hi Ross, BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=. Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept. At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.) But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=: > You can also manually create mappings using our REST API: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e= > > We have example code for programmatically creating mappings in our GitHub sample code repository: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e= I hope all this helps. John > On Aug 28, 2018, at 12:02 PM, Filice, Ross W wrote: > > Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other? > > And similarly is there a way to map subclasses across ontologies? > > Thanks much, > Ross > > Ross W. Filice, M.D. > Associate Professor and Chief, Imaging Informatics > Department of Radiology, MedStar Georgetown University Hospital > Chief, Imaging Informatics > MedStar Medical Group Radiology > Clinical Informatics Scientist > National Center for Human Factors in Healthcare, MedStar Institute for Innovation > > 3800 Reservoir Road NW, CG 201 > Washington DC, 20007 > 202-444-3450 PHONE > 202-444-4899 FAX > ross.w.filice at medstar.net > https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e= > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e= ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 From vendetti at stanford.edu Mon Sep 24 11:35:05 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 24 Sep 2018 18:35:05 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh In-Reply-To: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> Hello Dr. El-Sappagh, It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system. Kind regards, Jennifer On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote: Name: Shaker El-Sappagh Email: Shaker_elsapagh at yahoo.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO Feedback: Please, I have uploaded my FASTO ontology. It has not worked yet. Best regards . _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Sep 24 14:19:13 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 24 Sep 2018 21:19:13 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Hiba Itani In-Reply-To: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail> References: <5ba8ab9de591c_af52b0b2911aef4536aa@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <3D9790D8-1631-4BA8-8F20-F1E7DBF84408@stanford.edu> Hello Hiba, We offer a REST API for accessing all of the ontology data in BioPortal. CPT is one of the ontologies in our repository, so you can use the API to access CPT content. Our API is documented here: http://data.bioontology.org/documentation In order to use the API, you need an API key. Instructions for getting a key are available on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key If you have more specific question about API usage, feel free to follow up with us. Kind regards, Jennifer On Sep 24, 2018, at 2:17 AM, support at bioontology.org wrote: Name: Hiba Itani Email: best.smile1988 at live.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F99241%26jump_to_nav%3Dtrue Feedback: Hello; We are a Healthcare Management Company located in Lebanon and we are looking for a structured coding database or web api for CPT hat will enable us to manage our claims, stratify, and map our provider codes. Kindly Let ya know what solutions can you provide. Anticipating your feedback. Kind Regards, Hiba Itani _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Sep 24 14:13:55 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 24 Sep 2018 21:13:55 +0000 Subject: [bioontology-support] error report In-Reply-To: <1537797983389.43171@student.maastrichtuniversity.nl> References: <1537797983389.43171@student.maastrichtuniversity.nl> Message-ID: <8BEB2827-3B8B-484E-9CCC-33EC361252E1@stanford.edu> Hi Andreea, On Sep 24, 2018, at 7:06 AM, Grigoriu, Andreea (Stud. DKE) > wrote: While working on my Internship during my Master Studies I have encountered some incosistency in your platform. I was trying to find the metrics for various ontologies ( I was particulary interested in number of classes and properties of an ontology). Some ontologies (eg. PTS, HUGO, HGNC) were showing ( in the metric box on the ontology page->http://bioportal.bioontology.org/ontologies/HGNC/?p=summary) 0 properties but once I check the properties tab (http://bioportal.bioontology.org/ontologies/HGNC/?p=properties?) I can actually see a lot of properties. This was obvious for the examples of 0 properties but now I am also wandering if there might be other inconsistencies as well in other numbers of properties or maybe even classes. The number of properties reported in the BioPortal metrics panel includes the total number of data and object properties that are declared in an ontology. It doesn?t include the number of annotation properties, but we do display annotation properties in the user interface, which is why you see more properties on the properties tab than are reported in the metrics panel. Using one of the ontologies you listed above, I opened PTS in the Protege ontology editing environment [1] and confirmed that there are 5 object properties, and no data properties declared: [cid:370C96D0-9508-4724-AFBB-5B3852FCEC9C at stanford.edu] The BioPortal metrics panel reports a total of 5 properties for PTS. I checked the other two ontologies you mentioned above. HUGO and HGNC appear to be the same OWL ontology listed under two different ontology entries in BioPortal. The ontology has no data or object properties, hence the zeros in the metrics panel. It does have 66 annotation properties though, which is why the properties tab in the BioPortal UI shows a property tree. Honestly speaking, I don?t know the historical reason why annotation property counts weren?t included in the total property count in the metrics data. I will ask around among my colleagues to see if anyone has more information on this. Kind regards, Jennifer [1] https://protege.stanford.edu/products.php -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-09-24 11.52.50.png Type: image/png Size: 106235 bytes Desc: Screenshot 2018-09-24 11.52.50.png URL: From vendetti at stanford.edu Mon Sep 24 16:32:28 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 24 Sep 2018 23:32:28 +0000 Subject: [bioontology-support] programmatic class mappings In-Reply-To: References: Message-ID: Hello Ross, Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors. Kind regards, Jennifer > On Sep 24, 2018, at 10:37 AM, Filice, Ross W wrote: > > Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error: > > {"errors":["Input does not contain classes"],"status":400} > > I'm submitting the JSON object as provided by the github code: > > { > "creator" : "http://data.bioontology.org/user/[USER]", > "relation" : "http://www.w3.org/2002/07/owl#sameAs", > "source" : "[USER]", > "source_name" : "[USER] Mapping Data", > "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", > "terms" : [ { > "ontology" : "NCIT", > "term" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ] > }, { > "ontology" : "SNOMEDCT", > "term" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ] > } ] > } > > Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings: > > http://data.bioontology.org/documentation#Mapping > > It includes parameters "source" "id" "process" and "classes" without any other information. > > Thanks much, > Ross > > -----Original Message----- > From: John Graybeal [mailto:jgraybeal at stanford.edu] > Sent: Thursday, August 30, 2018 7:14 PM > To: Filice, Ross W > Cc: bioontology-support at lists.stanford.edu > Subject: Re: [bioontology-support] programmatic class mappings > > > ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. > > Hi Ross, > > > > BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=. > > > > Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept. At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.) > > > > But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=: > > > >> You can also manually create mappings using our REST API: > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e= > >> > >> We have example code for programmatically creating mappings in our GitHub sample code repository: > >> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e= > > > > I hope all this helps. > > > > John > > > > > >> On Aug 28, 2018, at 12:02 PM, Filice, Ross W wrote: > >> > >> Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other? > >> > >> And similarly is there a way to map subclasses across ontologies? > >> > >> Thanks much, > >> Ross > >> > >> Ross W. Filice, M.D. > >> Associate Professor and Chief, Imaging Informatics > >> Department of Radiology, MedStar Georgetown University Hospital > >> Chief, Imaging Informatics > >> MedStar Medical Group Radiology > >> Clinical Informatics Scientist > >> National Center for Human Factors in Healthcare, MedStar Institute for Innovation > >> > >> 3800 Reservoir Road NW, CG 201 > >> Washington DC, 20007 > >> 202-444-3450 PHONE > >> 202-444-4899 FAX > >> ross.w.filice at medstar.net > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e= > >> > >> _______________________________________________ > >> bioontology-support mailing list > >> bioontology-support at lists.stanford.edu > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e= > > > > ======================== > > 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 From Ross.W.Filice at gunet.georgetown.edu Mon Sep 24 18:53:51 2018 From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W) Date: Mon, 24 Sep 2018 21:53:51 -0400 Subject: [bioontology-support] programmatic class mappings In-Reply-To: References: Message-ID: Thanks Jennifer. If I change to classes instead of terms as such: { "creator" : "http://data.bioontology.org/user/rwfilice", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "rwfilice", "source_name" : "rwfilice Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "classes" : [ { "ontology" : "NCIT", "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ] }, { "ontology" : "SNOMEDCT", "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ] } ] } I get an Internal Server Error (500) Any further help would be much appreciated. Thanks much, Ross -----Original Message----- From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Monday, September 24, 2018 7:32 PM To: Filice, Ross W Cc: John Graybeal; bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hello Ross, Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors. Kind regards, Jennifer > On Sep 24, 2018, at 10:37 AM, Filice, Ross W wrote: > > Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error: > > {"errors":["Input does not contain classes"],"status":400} > > I'm submitting the JSON object as provided by the github code: > > { > "creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=", > "relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=", > "source" : "[USER]", > "source_name" : "[USER] Mapping Data", > "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", > "terms" : [ { > "ontology" : "NCIT", > "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ] > }, { > "ontology" : "SNOMEDCT", > "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ] > } ] > } > > Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e= > > It includes parameters "source" "id" "process" and "classes" without any other information. > > Thanks much, > Ross > > -----Original Message----- > From: John Graybeal [mailto:jgraybeal at stanford.edu] > Sent: Thursday, August 30, 2018 7:14 PM > To: Filice, Ross W > Cc: bioontology-support at lists.stanford.edu > Subject: Re: [bioontology-support] programmatic class mappings > > > ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. > > Hi Ross, > > > > BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=. > > > > Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept. At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.) > > > > But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=: > > > >> You can also manually create mappings using our REST API: > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e= > >> > >> We have example code for programmatically creating mappings in our GitHub sample code repository: > >> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e= > > > > I hope all this helps. > > > > John > > > > > >> On Aug 28, 2018, at 12:02 PM, Filice, Ross W wrote: > >> > >> Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other? > >> > >> And similarly is there a way to map subclasses across ontologies? > >> > >> Thanks much, > >> Ross > >> > >> Ross W. Filice, M.D. > >> Associate Professor and Chief, Imaging Informatics > >> Department of Radiology, MedStar Georgetown University Hospital > >> Chief, Imaging Informatics > >> MedStar Medical Group Radiology > >> Clinical Informatics Scientist > >> National Center for Human Factors in Healthcare, MedStar Institute for Innovation > >> > >> 3800 Reservoir Road NW, CG 201 > >> Washington DC, 20007 > >> 202-444-3450 PHONE > >> 202-444-4899 FAX > >> ross.w.filice at medstar.net > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e= > >> > >> _______________________________________________ > >> bioontology-support mailing list > >> bioontology-support at lists.stanford.edu > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e= > > > > ======================== > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e= From shaker_elsapagh at yahoo.com Mon Sep 24 20:31:17 2018 From: shaker_elsapagh at yahoo.com (Shaker El-Sappagh) Date: Tue, 25 Sep 2018 03:31:17 +0000 (UTC) Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh In-Reply-To: <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> Message-ID: <2032047650.1906847.1537846277280@mail.yahoo.com> Dear Dr. Jennifer,Thank you for your kind reply. Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link: http://bioportal.bioontology.org/ontologies/FASTO Thank you for your support. Best Regards. .......................................................... Shaker El-Sappagh, PhD. Post-Doctoral FellowUWB Wireless Communications Research Center, Department of Information and Communication Engineering, Inha University, Incheon, South Korea.Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti wrote: Hello Dr. El-Sappagh, It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system. Kind regards,Jennifer On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote: Name: Shaker El-Sappagh Email: Shaker_elsapagh at yahoo.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO Feedback: Please, I have uploaded my FASTO ontology. It has not worked yet. Best regards . _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Sep 25 17:16:11 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 26 Sep 2018 00:16:11 +0000 Subject: [bioontology-support] programmatic class mappings In-Reply-To: References: Message-ID: <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu> Hi Ross, My apologies that you?ve had to endure some back and forth with us. We?re a small team and I wasn?t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven?t had time to modify the code, so instead I?ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman. This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version): { "creator" : "http://data.bioontology.org/user/vendetti", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "classes" : { "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" : "NCIT", "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":"SNOMEDCT" } } The ?classes? hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side. You can also add the ?source", ?source_name", and ?comment" key value pairs as before, but they aren?t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added: { "creator" : "http://data.bioontology.org/user/vendetti", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "vendetti", "source_name" : "Jennifer's Test Mapping Data", "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)", "classes" : { "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" : "NCIT", "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":?SNOMEDCT" } } If you want to test this in Postman, you?ll need header information like the following (please enter your API key where I?ve indicated): [cid:ED5766D3-FCE4-4255-935C-D0A6B68FE2E1 at stanford.edu] ? and here is the body text: [cid:D3BB66BE-AFEE-4E6D-8FD6-D6A928DB2F5B at stanford.edu] Clicking the Send button should result in a ?201 Created? status with a result that contains the mapping creation date, etc.: [cid:869FDF5B-FA0E-4ED2-99F8-3597C8D29BB0 at stanford.edu] ? and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page): [cid:5BDAE2EA-CE28-4A1E-B9B3-6BE2462EA453 at stanford.edu] You can select the Malignant melanoma class in SNOMEDCT: https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003 ? and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I?ll delete the test mappings in a day or two. Let me know if you?re still having difficulties. Kind regards, Jennifer On Sep 24, 2018, at 6:53 PM, Filice, Ross W > wrote: Thanks Jennifer. If I change to classes instead of terms as such: { "creator" : "http://data.bioontology.org/user/rwfilice", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "rwfilice", "source_name" : "rwfilice Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "classes" : [ { "ontology" : "NCIT", "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ] }, { "ontology" : "SNOMEDCT", "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ] } ] } I get an Internal Server Error (500) Any further help would be much appreciated. Thanks much, Ross -----Original Message----- From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Monday, September 24, 2018 7:32 PM To: Filice, Ross W Cc: John Graybeal; bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hello Ross, Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors. Kind regards, Jennifer On Sep 24, 2018, at 10:37 AM, Filice, Ross W > wrote: Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error: {"errors":["Input does not contain classes"],"status":400} I'm submitting the JSON object as provided by the github code: { "creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=", "relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=", "source" : "[USER]", "source_name" : "[USER] Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "terms" : [ { "ontology" : "NCIT", "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ] }, { "ontology" : "SNOMEDCT", "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ] } ] } Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings: https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e= It includes parameters "source" "id" "process" and "classes" without any other information. Thanks much, Ross -----Original Message----- From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Thursday, August 30, 2018 7:14 PM To: Filice, Ross W Cc: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hi Ross, BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=. Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept. At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.) But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=: You can also manually create mappings using our REST API: https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e= We have example code for programmatically creating mappings in our GitHub sample code repository: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e= I hope all this helps. John On Aug 28, 2018, at 12:02 PM, Filice, Ross W > wrote: Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other? And similarly is there a way to map subclasses across ontologies? Thanks much, Ross Ross W. Filice, M.D. Associate Professor and Chief, Imaging Informatics Department of Radiology, MedStar Georgetown University Hospital Chief, Imaging Informatics MedStar Medical Group Radiology Clinical Informatics Scientist National Center for Human Factors in Healthcare, MedStar Institute for Innovation 3800 Reservoir Road NW, CG 201 Washington DC, 20007 202-444-3450 PHONE 202-444-4899 FAX ross.w.filice at medstar.net https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e= _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e= ======================== 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://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e= -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Screenshot 2018-09-25 17.11.26.png Type: image/png Size: 24587 bytes Desc: Screenshot 2018-09-25 17.11.26.png URL: From Ross.W.Filice at gunet.georgetown.edu Wed Sep 26 07:20:36 2018 From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W) Date: Wed, 26 Sep 2018 10:20:36 -0400 Subject: [bioontology-support] programmatic class mappings In-Reply-To: <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu> References: <9FD014AB-87AF-4283-9A65-45AE983B6E0C@stanford.edu> Message-ID: That worked! Thanks very much. Ross From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Tuesday, September 25, 2018 8:16 PM To: Filice, Ross W Cc: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network. ** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hi Ross, My apologies that you?ve had to endure some back and forth with us. We?re a small team and I wasn?t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven?t had time to modify the code, so instead I?ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman. This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version): { "creator" : "http://data.bioontology.org/user/vendetti", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "classes" : { "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" : "NCIT", "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":"SNOMEDCT" } } The ?classes? hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side. You can also add the ?source", ?source_name", and ?comment" key value pairs as before, but they aren?t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added: { "creator" : "http://data.bioontology.org/user/vendetti", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "vendetti", "source_name" : "Jennifer's Test Mapping Data", "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)", "classes" : { "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224" : "NCIT", "http://purl.bioontology.org/ontology/SNOMEDCT/2092003":?SNOMEDCT" } } If you want to test this in Postman, you?ll need header information like the following (please enter your API key where I?ve indicated): [cid:image001.png at 01D45582.90BA60B0] ? and here is the body text: [cid:image002.png at 01D45582.90BA60B0] Clicking the Send button should result in a ?201 Created? status with a result that contains the mapping creation date, etc.: [cid:image003.png at 01D45582.90BA60B0] ? and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page): [cid:image004.png at 01D45582.90BA60B0] You can select the Malignant melanoma class in SNOMEDCT: https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003 ? and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I?ll delete the test mappings in a day or two. Let me know if you?re still having difficulties. Kind regards, Jennifer On Sep 24, 2018, at 6:53 PM, Filice, Ross W > wrote: Thanks Jennifer. If I change to classes instead of terms as such: { "creator" : "http://data.bioontology.org/user/rwfilice", "relation" : "http://www.w3.org/2002/07/owl#sameAs", "source" : "rwfilice", "source_name" : "rwfilice Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "classes" : [ { "ontology" : "NCIT", "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711" ] }, { "ontology" : "SNOMEDCT", "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006" ] } ] } I get an Internal Server Error (500) Any further help would be much appreciated. Thanks much, Ross -----Original Message----- From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: Monday, September 24, 2018 7:32 PM To: Filice, Ross W Cc: John Graybeal; bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hello Ross, Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you?re still experiencing issues. If so, we?ll try to get the example code updated and running without errors. Kind regards, Jennifer On Sep 24, 2018, at 10:37 AM, Filice, Ross W > wrote: Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error: {"errors":["Input does not contain classes"],"status":400} I'm submitting the JSON object as provided by the github code: { "creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=", "relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=", "source" : "[USER]", "source_name" : "[USER] Mapping Data", "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)", "terms" : [ { "ontology" : "NCIT", "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ] }, { "ontology" : "SNOMEDCT", "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ] } ] } Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings: https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e= It includes parameters "source" "id" "process" and "classes" without any other information. Thanks much, Ross -----Original Message----- From: John Graybeal [mailto:jgraybeal at stanford.edu] Sent: Thursday, August 30, 2018 7:14 PM To: Filice, Ross W Cc: bioontology-support at lists.stanford.edu Subject: Re: [bioontology-support] programmatic class mappings ** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hi Ross, BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=. Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept. At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.) But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=: You can also manually create mappings using our REST API: https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e= We have example code for programmatically creating mappings in our GitHub sample code repository: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e= I hope all this helps. John On Aug 28, 2018, at 12:02 PM, Filice, Ross W > wrote: Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other? And similarly is there a way to map subclasses across ontologies? Thanks much, Ross Ross W. Filice, M.D. Associate Professor and Chief, Imaging Informatics Department of Radiology, MedStar Georgetown University Hospital Chief, Imaging Informatics MedStar Medical Group Radiology Clinical Informatics Scientist National Center for Human Factors in Healthcare, MedStar Institute for Innovation 3800 Reservoir Road NW, CG 201 Washington DC, 20007 202-444-3450 PHONE 202-444-4899 FAX ross.w.filice at medstar.net https://urldefense.proofpoint.com/v2/url?u=http-3A__MedStarHealth.org&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=DnGnwepD_un0eAHcMhVe-VhZfeG3jjAOo1f0JOtIntk&e= _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=f7r2i-ZveGjVEcJkTbeRXQhi5mJI6u_EQ0AD7xpBsGY&e= ======================== 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://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=AF8-u_FYGJ9Bc9prtVxgWktndfWTn0vy_iu-5EXzp3o&e= -------------- next part -------------- An HTML attachment was scrubbed... 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The link is on the "Summary" tab under "License Information". http://bioportal.bioontology.org/ontologies/MEDDRA Also, I tried to submit this comment using the form under Feedback, but there wasn't a "submit" button. If it helps, I accessed the page using Chrome. [cid:image001.jpg at 01D4558B.5FBD65D0] Best, Alex ___________________________________________________________ Alex J. Noury Protocol Coordinator | ETPB, NIMH 301-496-9848 | alex.noury at nih.gov | 10-CRC, 7-5331 Branch website: www.nimh.nih.gov/MoodResearch Adult Bipolar & Depression Research at: www.nimh.nih.gov/JoinAStudy -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 19283 bytes Desc: image001.jpg URL: From vendetti at stanford.edu Wed Sep 26 11:32:45 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 26 Sep 2018 18:32:45 +0000 Subject: [bioontology-support] Broken Link In-Reply-To: References: Message-ID: <06C418A2-5235-4C84-AC5E-287768017CCC@stanford.edu> Hi Alex, On Sep 26, 2018, at 8:23 AM, Noury, Alex (NIH/NIMH) [E] > wrote: The link to "MedDRA MSSO" on the below page is broken. The link is on the "Summary" tab under "License Information". http://bioportal.bioontology.org/ontologies/MEDDRA At the moment we don?t have a way for end users to edit ontology license information via the BioPortal user interface. Rather, if you send us the updated license text, we can add it to the application on your behalf. Also, I tried to submit this comment using the form under Feedback, but there wasn?t a ?submit? button. If it helps, I accessed the page using Chrome. You should be able to resize the dialog window to make it a little bigger, which will reveal the ?Send Feedback? button: [cid:24C66B2E-219D-4C7D-B26A-1FB65FDACF17 at stanford.edu] Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-09-26 11.30.36.png Type: image/png Size: 140195 bytes Desc: Screenshot 2018-09-26 11.30.36.png URL: From vendetti at stanford.edu Wed Sep 26 15:26:50 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 26 Sep 2018 22:26:50 +0000 Subject: [bioontology-support] Broken Link In-Reply-To: References: <06C418A2-5235-4C84-AC5E-287768017CCC@stanford.edu> Message-ID: <4466A436-16D2-464B-9B2D-2EE4C79BAA0F@stanford.edu> Hi Alex, On Sep 26, 2018, at 11:38 AM, Noury, Alex (NIH/NIMH) [E] > wrote: Hi Jennifer, I didn?t realize I could shrink the dialogue box. Thanks! About the link, I was just reporting that it?s broken. It goes to this error page: https://www.meddra.org/node/734. It looks like the page moved. Here?s the current location:https://www.meddra.org/about-meddra/organisation/msso. OK, thanks for pointing that out. I changed the link to point to the new page, and it?s now live on our production site. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Wed Sep 26 17:00:04 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 27 Sep 2018 00:00:04 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh In-Reply-To: <2032047650.1906847.1537846277280@mail.yahoo.com> References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> <2032047650.1906847.1537846277280@mail.yahoo.com> Message-ID: <8E890E4D-A5F5-41D4-8AE0-4A68BA4D5DBB@stanford.edu> Hello Dr. El-Sappagh, Thank you for resubmitting your ontology in the requested format. There were still some errors that occurred during our parsing process, which I am looking into and will report back when I have more information. Kind regards, Jennifer On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh > wrote: Dear Dr. Jennifer, Thank you for your kind reply. Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link: http://bioportal.bioontology.org/ontologies/FASTO Thank you for your support. Best Regards. .......................................................... Shaker El-Sappagh, PhD. Post-Doctoral Fellow UWB Wireless Communications Research Center, Department of Information and Communication Engineering, Inha University, Incheon, South Korea. Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti > wrote: Hello Dr. El-Sappagh, It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system. Kind regards, Jennifer On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote: Name: Shaker El-Sappagh Email: Shaker_elsapagh at yahoo.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO Feedback: Please, I have uploaded my FASTO ontology. It has not worked yet. Best regards . _______________________________________________ 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 Thu Sep 27 10:27:06 2018 From: jonquet at lirmm.fr (Clement Jonquet) Date: Thu, 27 Sep 2018 19:27:06 +0200 Subject: [bioontology-support] =?utf-8?q?Research_engineer_position_in_Mon?= =?utf-8?q?tpellier=2C_France_-_Web_architect_=E2=80=93_Semantic_web_techn?= =?utf-8?q?ologies_=E2=80=93_Text_and_data_mining?= Message-ID: <6AD25A29-F837-4356-9D2B-2072351B2F76@lirmm.fr> Dear all, We have a job opening in Montpellier, France to work on semantic web technologies, ontology managment and text mining workflows? at LIRMM (University of Montpellier & CNRS Informatics Research lab). The position is for 1 year with possible extensions. ******** A key aspect in addressing semantic interoperability is the use of terminologies, vocabularies and ontologies as a common denominator to structure data and make them interoperable. In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories: (i) the SIFR BioPortal (http://bioportal.lirmm.fr ) which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data; (ii) AgroPortal (http://agroportal.lirmm.fr ) a reference repository for semantic resources in agronomy, agriculture, food, plant sciences and biodiversity. These platforms allow us to tackle scientific problems in natural language processing, semantic annotation, ontology engineering, while being driven by concrete use cases with impacts in biomedicine and agronomy. In the context of the ANR PractiKPharma and VisaTM projects, we are seeking a motivated, curious and interested research engineer and web developer to take hands on the platforms and prototypes developed. Your role will be both to support the current platforms and investigate technical decisions to enable the development of new features in relation to text and data mining. Within PractiKPharma, your role will consist in enhancing the SIFR Annotator to facilitate its use to annotate clinical data (in collaboration with HEGP and LORIA). Within the VisaTM project, your role will be to enable interoperation of both AgroProtal and BioPortal with the text and data mining infrastructure developed in the OpenMinTeD project (in collaboration with INRA and INIST). You will work with a small team (4 persons) at LIRMM in both a national and international context. Further extension of the proposed 12-month-contract are possible. ******** See http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf Regards ------------------------------------------------------------------------------------------- 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 Thu Sep 27 09:19:45 2018 From: support at bioontology.org (support at bioontology.org) Date: Thu, 27 Sep 2018 09:19:45 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Mohammad Message-ID: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Sep 27 11:23:54 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 27 Sep 2018 18:23:54 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Mohammad In-Reply-To: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail> References: <5bad032147acd_5c192ac93bce5f5c51971@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <2DCDC503-F953-4F65-AAB7-A70068EA2A4B@stanford.edu> Hello Mohammad, There?s a known issue with the 3rd party visualization software we use where it doesn?t work over HTTPS. You?ll need to change the protocol in your browser?s address bar to HTTP in order to see the visualizations: [cid:5D5DA279-D11D-433F-A1C8-F7DA0B5331E4 at stanford.edu] Apologies for the inconvenience. Jennifer On Sep 27, 2018, at 9:19 AM, support at bioontology.org wrote: Name: Mohammad Email: mohammad.babaei33 at yahoo.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FATOL%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.org%252Fobo%252FowlATOL_0002159 Feedback: Hi, i want to know why vidualization of trait's ontologies( e.g. feed efficiency) don't draw?. Thanks _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-09-27 11.23.11.png Type: image/png Size: 155438 bytes Desc: Screenshot 2018-09-27 11.23.11.png URL: From jonquet at lirmm.fr Thu Sep 27 10:27:06 2018 From: jonquet at lirmm.fr (Clement Jonquet) Date: Thu, 27 Sep 2018 19:27:06 +0200 Subject: [bioontology-support] =?utf-8?q?=5Bbioportal-announce=5D_Research?= =?utf-8?q?_engineer_position_in_Montpellier=2C_France_-_Web_architect_?= =?utf-8?q?=E2=80=93_Semantic_web_technologies_=E2=80=93_Text_and_data_min?= =?utf-8?q?ing?= Message-ID: <6AD25A29-F837-4356-9D2B-2072351B2F76@lirmm.fr> Dear all, We have a job opening in Montpellier, France to work on semantic web technologies, ontology managment and text mining workflows? at LIRMM (University of Montpellier & CNRS Informatics Research lab). The position is for 1 year with possible extensions. ******** A key aspect in addressing semantic interoperability is the use of terminologies, vocabularies and ontologies as a common denominator to structure data and make them interoperable. In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories: (i) the SIFR BioPortal (http://bioportal.lirmm.fr ) which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data; (ii) AgroPortal (http://agroportal.lirmm.fr ) a reference repository for semantic resources in agronomy, agriculture, food, plant sciences and biodiversity. These platforms allow us to tackle scientific problems in natural language processing, semantic annotation, ontology engineering, while being driven by concrete use cases with impacts in biomedicine and agronomy. In the context of the ANR PractiKPharma and VisaTM projects, we are seeking a motivated, curious and interested research engineer and web developer to take hands on the platforms and prototypes developed. Your role will be both to support the current platforms and investigate technical decisions to enable the development of new features in relation to text and data mining. Within PractiKPharma, your role will consist in enhancing the SIFR Annotator to facilitate its use to annotate clinical data (in collaboration with HEGP and LORIA). Within the VisaTM project, your role will be to enable interoperation of both AgroProtal and BioPortal with the text and data mining infrastructure developed in the OpenMinTeD project (in collaboration with INRA and INIST). You will work with a small team (4 persons) at LIRMM in both a national and international context. Further extension of the proposed 12-month-contract are possible. ******** See http://www.lirmm.fr/~jonquet/positions/2018_PractiKPharma-VisaTM_IGR_position.pdf Regards ------------------------------------------------------------------------------------------- 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: -------------- next part -------------- _______________________________________________ bioportal-announce mailing list bioportal-announce at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioportal-announce From support at bioontology.org Thu Sep 27 16:47:52 2018 From: support at bioontology.org (support at bioontology.org) Date: Thu, 27 Sep 2018 16:47:52 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Chris Message-ID: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Sep 27 16:55:42 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 27 Sep 2018 23:55:42 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Chris In-Reply-To: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail> References: <5bad6c28ef982_37582ad167b795a4124c5@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <1655EE7F-1DA1-4783-B15E-006CCAAAD7CE@stanford.edu> Hi Chris, I think this message from our mailing list archive may address your question: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Jaime-Parra-MD-phD-tp4655505p4655508.html If not, feel free to follow up again. Kind regards, Jennifer On Sep 27, 2018, at 4:47 PM, support at bioontology.org wrote: Name: Chris Email: cvolzer3 at gmail.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Droot Feedback: What does "inverse of SIB" mean? Thanks! _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Sep 27 18:10:52 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 28 Sep 2018 01:10:52 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh In-Reply-To: <2032047650.1906847.1537846277280@mail.yahoo.com> References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> <2032047650.1906847.1537846277280@mail.yahoo.com> Message-ID: <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu> Hello Dr. El-Sappagh, The error that occurs in our log file is this: "Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002? There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn?t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore: http://www.co-ode.org/ontologies/ont.owl#DDO_0000002 After making this modification, I believe our system will be able to parse the ontology. Kind regards, Jennifer > On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh wrote: > > Dear Dr. Jennifer, > Thank you for your kind reply. > Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link: > > http://bioportal.bioontology.org/ontologies/FASTO > > Thank you for your support. > > Best Regards. > > > .......................................................... > Shaker El-Sappagh, PhD. > Post-Doctoral Fellow > UWB Wireless Communications Research Center, > Department of Information and Communication Engineering, > Inha University, Incheon, South Korea. > Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. > > > On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti wrote: > > > Hello Dr. El-Sappagh, > > It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive: > > http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html > > Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system. > > Kind regards, > Jennifer > > > >> On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote: >> >> Name: Shaker El-Sappagh >> >> Email: Shaker_elsapagh at yahoo.com >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO >> >> >> Feedback: >> >> Please, I have uploaded my FASTO ontology. It has not worked yet. >> >> Best regards . >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > From shaker_elsapagh at yahoo.com Thu Sep 27 19:05:16 2018 From: shaker_elsapagh at yahoo.com (Shaker El-Sappagh) Date: Fri, 28 Sep 2018 02:05:16 +0000 (UTC) Subject: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh In-Reply-To: <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu> References: <5ba9078f11d9e_35342ad4cfc60ca4145dd@ncbo-prd-app-08.stanford.edu.mail> <1F8C98B2-87A0-4B02-A377-BEA8300AB317@stanford.edu> <2032047650.1906847.1537846277280@mail.yahoo.com> <8C96CBB4-D54F-4A2E-9F0C-89ADDB8E0E96@stanford.edu> Message-ID: <404437831.1297530.1538100316184@mail.yahoo.com> Dear Dr. Jennifer,Thank you for your kind reply. I have changed the URL and uploaded the zip file for the ontology. Thank you for your support.Best Regards. .......................................................... Shaker El-Sappagh, PhD. Post-Doctoral FellowUWB Wireless Communications Research Center, Department of Information and Communication Engineering, Inha University, Incheon, South Korea.Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. On Friday, September 28, 2018, 10:11:02 AM GMT+9, Jennifer Leigh Vendetti wrote: Hello Dr. El-Sappagh, The error that occurs in our log file is this: "Illegal Element Name (Element Is Not A QName): http://www.co-ode.org/ontologies/ont.owl#DDO:0000002? There are 3 occurrences in the FASTO.owl source file of the above URI, where the colon character isn?t allowed in the end fragment (DDO:0000002). The URI will need to be modified to remove the colon character, e.g., you could replace it with an underscore: http://www.co-ode.org/ontologies/ont.owl#DDO_0000002 After making this modification, I believe our system will be able to parse the ontology. Kind regards, Jennifer > On Sep 24, 2018, at 8:31 PM, Shaker El-Sappagh wrote: > > Dear Dr. Jennifer, > Thank you for your kind reply. > Please, I have uploaded my ontology as it is required.You can find the FASTO ontology at this link: > > http://bioportal.bioontology.org/ontologies/FASTO > > Thank you for your support. > > Best Regards. > > > .......................................................... > Shaker El-Sappagh, PhD. > Post-Doctoral Fellow > UWB Wireless Communications Research Center, > Department of Information and Communication Engineering, > Inha University, Incheon, South Korea. > Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. > > > On Tuesday, September 25, 2018, 3:35:12 AM GMT+9, Jennifer Leigh Vendetti wrote: > > > Hello Dr. El-Sappagh, > > It appears you?ve submitted multiple ontology files inside of a RAR file. We don?t support RAR files. Instead, you?ll need to repackage your ontology files inside of a ZIP file. We also have some requirements about how the ZIP file is named so that BioPortal can figure out which of the files is your main ontology file. The naming convention is described in this post in our mailing list archive: > > http://ncbo-support.2288202.n4.nabble.com/bioontology-support-How-to-handle-imported-ontologies-on-bioportal-tp4654202p4654212.html > > Let us know once you?ve resubmitted in the proper format, and we?ll have another look at whether the ontology parsed in our system. > > Kind regards, > Jennifer > > > >> On Sep 24, 2018, at 8:49 AM, support at bioontology.org wrote: >> >> Name: Shaker El-Sappagh >> >> Email: Shaker_elsapagh at yahoo.com >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FFASTO >> >> >> Feedback: >> >> Please, I have uploaded my FASTO ontology. It has not worked yet. >> >> Best regards . >> >> >> _______________________________________________ >> 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: