From h.s.liyanage at surrey.ac.uk Thu Nov 1 03:05:48 2018 From: h.s.liyanage at surrey.ac.uk (h.s.liyanage at surrey.ac.uk) Date: Thu, 1 Nov 2018 10:05:48 +0000 Subject: [bioontology-support] Pregnancy Ontology In-Reply-To: References: Message-ID: Dear Jennifer, That?s brilliant! Many thanks for promptly resolving this issue. Best regards, Harshana From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] Sent: 31 October 2018 22:20 To: Liyanage, Harshana Dr (Sch of Biosci & Med) Cc: support at bioontology.org Subject: Re: [bioontology-support] Pregnancy Ontology Hello Harshana, Apologies that the initial attempt to upload your ontology failed. I deleted and recreated your ontology in our system, and uploaded the attached OWL file. Your ontology data is accessible now [1]. You can use the add button at the top of the Submissions table to upload new versions. Kind regards, Jennifer [1] http://bioportal.bioontology.org/ontologies/PREGONTO On Oct 31, 2018, at 5:00 AM, h.s.liyanage at surrey.ac.uk wrote: Dear BioPortal Team, I have created an ontology titled ?Pregnancy Ontology? on BioPortal at the following address. https://bioportal.bioontology.org/ontologies/PREGONTO My initial ontology upload failed during the creation of the ontology page and I have not been able to upload any OWL files since then. The issue is that there is no place to upload the ontology in this particular page (I have not come across this issue in the other ontology pages I have created). Could you please associate the attached OWL file with this ontology and enable uploading of future updates of the OWL file. Alternatively, I would be happy to recreate the ontology page on BioPortal if you are able to delete the current page. My use name on BioPortal is: harshanal Thank you. Best regards, Harshana Harshana Liyanage (Dr) Research Fellow Department of Clinical and Experimental Medicine Faculty of Health and Medical Sciences Room 07 PGM 02, Leggett Building, Daphne Jackson Road University of Surrey Tel: +44 (0) 1483 68 3836 Email: h.s.liyanage at surrey.ac.uk Web: surrey.ac.uk Follow the University of Surrey Surrey Winter Statistics School (SWISS 2019) - 14-18th January 2019 ? Book Now! _______________________________________________ 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 megapode32559 at gmail.com Tue Nov 6 00:26:23 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Tue, 6 Nov 2018 16:26:23 +0800 Subject: [bioontology-support] Keeping track of the text corresponding to the annotated ontology classes? Message-ID: Hi, It seems that the annotator endpoint only returns the relevant classes, but does not return the corresponding text. Is there a way to return the corresponding text along with the relevant classes? Thanks. http://data.bioontology.org/documentation#nav_annotator -- Best wishes, Michael From megapode32559 at gmail.com Tue Nov 6 01:01:03 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Tue, 6 Nov 2018 17:01:03 +0800 Subject: [bioontology-support] Why class search may return wrong class URL? Message-ID: Hi, http://bioportal.bioontology.org/search?q=postpartum%20depression&ontologies=&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=true&categories= In the above search page, I see the URL which does not seem to work. Would you please let me know what is wrong with it? Thanks. http://purl.obolibrary.org/obo/DOID_9478 -- Best wishes, Michael From jgraybeal at stanford.edu Tue Nov 6 09:49:56 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 6 Nov 2018 17:49:56 +0000 Subject: [bioontology-support] Why class search may return wrong class URL? In-Reply-To: References: Message-ID: <5A68F4EF-2DBB-462F-B9D3-EFB87E68B814@stanford.edu> Hi Michael, I just tried the Purl and the BioPortal link to the class above it on that page. For me both are working now, though the class page took quite a while (I think it's a big tree of resources). I know the Purl server was down very briefly this morning, that might have been when you tried it. Please try it again and let us know if you are still having trouble. john On Nov 6, 2018, at 2:01 AM, Michael Liu > wrote: Hi, http://bioportal.bioontology.org/search?q=postpartum%20depression&ontologies=&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=true&categories= In the above search page, I see the URL which does not seem to work. Would you please let me know what is wrong with it? Thanks. http://purl.obolibrary.org/obo/DOID_9478 -- Best wishes, Michael _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed Nov 7 11:42:08 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 7 Nov 2018 19:42:08 +0000 Subject: [bioontology-support] Keeping track of the text corresponding to the annotated ontology classes? In-Reply-To: References: Message-ID: <3EA0DF4E-105C-4D02-8543-FAFAE0BA5BB3@stanford.edu> Hi Michael, Thank you for contacting us. The annotator service does return the annotated string for each class along with the start and end index of where the string occurred in the text (in the ?annotations? list): http://data.bioontology.org/annotator?text=Lung%20cancer%20occurs%20in%20non-smokers&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false [cid:E07F55C1-B460-4E6C-8CD1-3F0E8CEFFDCF at stanford.edu] Were you looking for a different output? Thanks! Michael On Nov 6, 2018, at 12:26 AM, Michael Liu > wrote: Hi, It seems that the annotator endpoint only returns the relevant classes, but does not return the corresponding text. Is there a way to return the corresponding text along with the relevant classes? Thanks. http://data.bioontology.org/documentation#nav_annotator -- Best wishes, Michael _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-11-07 at 11.40.14 AM.png Type: image/png Size: 649854 bytes Desc: Screen Shot 2018-11-07 at 11.40.14 AM.png URL: From support at bioontology.org Fri Nov 9 02:44:07 2018 From: support at bioontology.org (support at bioontology.org) Date: Fri, 09 Nov 2018 02:44:07 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Jane Lomax Message-ID: <5be564f7786f7_22382ab8c8dff3805372@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From john.zobolas at ntnu.no Fri Nov 9 05:57:21 2018 From: john.zobolas at ntnu.no (John Zobolas) Date: Fri, 9 Nov 2018 13:57:21 +0000 Subject: [bioontology-support] Questions regarding the REST API Message-ID: <1541771841693.45184@ntnu.no> Hi, I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things: 1. ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma) which almost always (as far as I can tell) is false. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:false ones? 2. Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!) 3. I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym, will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type). 4. The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr 5. If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right? 6. Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string? 7. I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does. 8. Is there a way to get results by id? Something like: /searchByID/id=URLid (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,...}? 9. Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty! ?BR, John. ?------------------ John Zobolas PhD Student Department of Biology, Faculty of Natural Sciences, NTNU Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri Nov 9 10:44:28 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 9 Nov 2018 18:44:28 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Jane Lomax In-Reply-To: <5be564f7786f7_22382ab8c8dff3805372@ncbo-prd-app-09.stanford.edu.mail> References: <5be564f7786f7_22382ab8c8dff3805372@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Jane, Apologies for that glitch. I reprocessed NCIT in our system and the CSV file is now downloadable. Kind regards, Jennifer On Nov 9, 2018, at 2:44 AM, support at bioontology.org wrote: Name: Jane Lomax Email: jane at scibite.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FNCIT Feedback: Hi - I'm getting a 500 error for the CSV file for NCIT ontology: http://data.bioontology.org/ontologies/NCIT/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv Error message: { -"errors": [ "Cannot read latest submission upload file: /srv/ncbo/repository/NCIT/69/NCIT.csv.gz" ], "status": 500 } thanks Jane _______________________________________________ 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 Fri Nov 9 15:46:10 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 9 Nov 2018 23:46:10 +0000 Subject: [bioontology-support] Questions regarding the REST API In-Reply-To: <1541771841693.45184@ntnu.no> References: <1541771841693.45184@ntnu.no> Message-ID: Hi John, Thanks for contacting us. See my answers inline below. On Nov 9, 2018, at 5:57 AM, John Zobolas > wrote: Hi, I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things: 1. ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma) which almost always (as far as I can tell) isfalse. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:falseones? The results are by default filtered on obsolete:false. There is a parameter called also_search_obsolete={true|false} if you want a more granular control over this flag. 1. Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!) Both paramours work, but the correct one to use is display_context={true|false}, which is the one advertised in our documentation. 1. I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym, will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type). You can create ontologies/groups programmatically using your own API key via a POST call, but you cannot delete anything from the system. That function is limited to admins only. 1. The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr Yes, the errors should all have a uniform response. If you notice otherwise, that would probably constitute a bug. Let us know if you find an error that deviates from this format. { * - "errors": [ * "You must provide a valid `acronym` to retrieve an ontology" ], * "status": 404 } { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } 1. If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right? Correct. These two endpoints appear to have a slightly different handling of the empty fields. The classes endpoint displays empty lists, where as the search endpoint just drops the empty attributes from the response. Example: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 http://data.bioontology.org/search?q=CALR%20NM_004343.3:c.1092_1143del52&ontologies=NCIT&require_exact_match=true 1. Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string? You can try calling the search endpoint without passing in a search string and limiting the results to a specific ontology. You need to pass a ?special? parameter called ?ontology_types=ONTOLOGY? in order for the queriless search to work: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY This will give you ALL results stored in our search index for the ontology NCIT. This isn?t the ?advertised? method of getting all classes, rather a ?workaround? that let?s you execute a search call without passing a query string. 1. I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does. Again, correct! The @id represents the class ID as defined in the original source ontology. The same class can be reused in multiple ontologies. The ?unique? ID of a class in BioPortal is a combination of the @id and the ontology acronym, as in: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 1. Is there a way to get results by id? Something like: /searchByID/id=URLid (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,?}? Yes, you can pass the URL-encoded full ID in the ?q? parameter to the /search endpoint: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true You cannot search by multiple IDs. 1. Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty! If you want to limit results to a given class within a given ontology(ies), just add the ?ontologies=?BAO,DOID? to the query: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO,DOID http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO Hope this helps! Feel free to reach out if you have further questions. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- ?BR, John. ?------------------ John Zobolas PhD Student Department of Biology, Faculty of Natural Sciences, NTNU Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From megapode32559 at gmail.com Sat Nov 10 19:51:23 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Sat, 10 Nov 2018 21:51:23 -0600 Subject: [bioontology-support] How a tree is determined from a DAG? Message-ID: Hi, I see some class has more than one superclasses, which means that the class hierarchy should be a directed acyclic graph (DAG) instead of a tree. But the panel on the left shows a tree structure. Is there tree draw by using only the first subClassOf property of each class? Thanks. https://bioportal.bioontology.org/ontologies/EFO/?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_64746 -- Best wishes, Michael From john.zobolas at ntnu.no Sun Nov 11 12:18:19 2018 From: john.zobolas at ntnu.no (John Zobolas) Date: Sun, 11 Nov 2018 20:18:19 +0000 Subject: [bioontology-support] Questions regarding the REST API In-Reply-To: References: <1541771841693.45184@ntnu.no>, Message-ID: <1541967499734.46992@ntnu.no> Hi Michael, Thanks so much for the answers and very helpful indeed! Please see inline for further discussion/clarification on some of those. BR, John. ________________________________ From: Michael Dorf Sent: Saturday, November 10, 2018 12:46 AM To: John Zobolas Cc: support at bioontology.org Subject: Re: [bioontology-support] Questions regarding the REST API Hi John, Thanks for contacting us. See my answers inline below. On Nov 9, 2018, at 5:57 AM, John Zobolas > wrote: Hi, I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things: 1. ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma) which almost always (as far as I can tell) isfalse. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:falseones? The results are by default filtered on obsolete:false. There is a parameter called also_search_obsolete={true|false} if you want a more granular control over this flag. 1. Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!) Both paramours work, but the correct one to use is display_context={true|false}, which is the one advertised in our documentation. 1. I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym, will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type). You can create ontologies/groups programmatically using your own API key via a POST call, but you cannot delete anything from the system. That function is limited to admins only. 1. The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr Yes, the errors should all have a uniform response. If you notice otherwise, that would probably constitute a bug. Let us know if you find an error that deviates from this format. { * - "errors": [ * "You must provide a valid `acronym` to retrieve an ontology" ], * "status": 404 } { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } 1. If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right? Correct. These two endpoints appear to have a slightly different handling of the empty fields. The classes endpoint displays empty lists, where as the search endpoint just drops the empty attributes from the response. Example: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 http://data.bioontology.org/search?q=CALR%20NM_004343.3:c.1092_1143del52&ontologies=NCIT&require_exact_match=true 1. Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string? You can try calling the search endpoint without passing in a search string and limiting the results to a specific ontology. You need to pass a ?special? parameter called ?ontology_types=ONTOLOGY? in order for the queriless search to work: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY This will give you ALL results stored in our search index for the ontology NCIT. This isn?t the ?advertised? method of getting all classes, rather a ?workaround? that let?s you execute a search call without passing a query string. Really helpful!!! I noticed also that when you do: http://data.bioontology.org/ontologies/NCIT/classes/ you get a total count of 144695 classes, while the query http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY returns 140329 as a total count and the difference must be that the first has the obsolete terms as well, right? Because if I do: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY&also_search_obsolete=true, then I get 144695! Is there a specific ordering on the returned results on the query: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY? Are the results ordered by prefLabel or @id for example?(doesn't seem to be the case) Also, does this query return all classes in all ontologies in BioPortal: http://data.bioontology.org/search?ontologies=&ontology_types=ONTOLOGY ? And if so, what ordering is applied to the results? 1. I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does. Again, correct! The @id represents the class ID as defined in the original source ontology. The same class can be reused in multiple ontologies. The ?unique? ID of a class in BioPortal is a combination of the @id and the ontology acronym, as in: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 Useful to know! 1. Is there a way to get results by id? Something like: /searchByID/id=URLid (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,?}? Yes, you can pass the URL-encoded full ID in the ?q? parameter to the /search endpoint: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true Actually I kinda though that the `search?q=something` searched for `something` in the prefLabel and synonyms only! (but it seems this is not the case, since it searchs for a match with the @id as well :) Which other fields does it look for a match? Also I noticed that the `something` must always be URL encoded (otherwise you get no results). Do you think that the `ontologies=GO,BAO` part should be also (for the comma mostly)? Do you know if there is an id I can request that has more than 50 matches (a class that is included in more than 50 ontologies)? This would mean that I would have a second page of results (since the default pagesize is 50). You cannot search by multiple IDs. 1. Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty! If you want to limit results to a given class within a given ontology(ies), just add the ?ontologies=?BAO,DOID? to the query: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO,DOID Here, is there a preferential sorting happening for these results (first BAO entry and then DOID for example? - though I see you get them the other way around) http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO Hope this helps! Feel free to reach out if you have further questions. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- ?BR, John. ?------------------ John Zobolas PhD Student Department of Biology, Faculty of Natural Sciences, NTNU Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Mon Nov 12 03:58:01 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 12 Nov 2018 03:58:01 -0800 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be Message-ID: <5be96ac99ee8f_4692ab575a4341853291@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Nov 12 12:35:39 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 12 Nov 2018 20:35:39 +0000 Subject: [bioontology-support] How a tree is determined from a DAG? In-Reply-To: References: Message-ID: <2FB23240-FD8D-4138-9EBC-01C9D3498B37@stanford.edu> Hello Michael, Apologies, but I?m not sure I understand what you?re looking for. BioPortal accepts ontologies in a handful of different formats. We use a tree to depict the class structure. The properties used to display the tree structure depend on the ontology format. subClassOf is used for OWL ontologies, ?broader" for SKOS vocabularies, and ?part_of?, ?contains?, and ?develops from? for OBO ontologies. The class you mention below appears in two places in the tree because it has two subClassOf declarations in the ontology source file. Kind regards, Jennifer > On Nov 10, 2018, at 7:51 PM, Michael Liu wrote: > > Hi, > > I see some class has more than one superclasses, which means that the > class hierarchy should be a directed acyclic graph (DAG) instead of a > tree. But the panel on the left shows a tree structure. Is there tree > draw by using only the first subClassOf property of each class? > Thanks. > > https://bioportal.bioontology.org/ontologies/EFO/?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_64746 > > -- > Best wishes, > Michael > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From vendetti at stanford.edu Mon Nov 12 12:50:38 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 12 Nov 2018 20:50:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be In-Reply-To: <5be96ac99ee8f_4692ab575a4341853291@ncbo-prd-app-08.stanford.edu.mail> References: <5be96ac99ee8f_4692ab575a4341853291@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hello Chen, On Nov 12, 2018, at 3:58 AM, support at bioontology.org wrote: I have a question. BioPortal is a nice API. we can search classes. However, there are a lot of individuals also in BioPotal. However, they cannot be searched. is it a pity? Yes, you?re correct. The search functionality only deals with classes. We don?t have any plans in the near future to modify the code base to include instances. I know it?s not exactly what you?re looking for, but you might be interested to know that there are a couple of REST endpoints that allow you to view instances either at the class or ontology level. They are documented here: http://data.bioontology.org/documentation#Instance Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From megapode32559 at gmail.com Mon Nov 12 14:29:29 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Mon, 12 Nov 2018 16:29:29 -0600 Subject: [bioontology-support] How a tree is determined from a DAG? In-Reply-To: <2FB23240-FD8D-4138-9EBC-01C9D3498B37@stanford.edu> References: <2FB23240-FD8D-4138-9EBC-01C9D3498B37@stanford.edu> Message-ID: Hi Jennifer, OK. By checking under both the parents, I see that "Autosomal dominant Charcot-Marie-Tooth disease type 2" appears in two places in the webportal. But when I search "Autosomal dominant Charcot-Marie-Tooth disease type 2", it only jumps to one of them. Is there a way to show all the matches when a class name is searched? > The class you mention below appears in two places in the tree because it has two subClassOf declarations in the ontology source file. -- Best wishes, Michael From megapode32559 at gmail.com Mon Nov 12 15:11:35 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Mon, 12 Nov 2018 17:11:35 -0600 Subject: [bioontology-support] Errors in NIFSTD In-Reply-To: References: Message-ID: Hi, I see things like "List" in NIFSTD. Is it an error? Thanks. http://bioportal.bioontology.org/ontologies/NIFSTD/?p=classes&conceptid=http%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23List -- Best wishes, Michael From megapode32559 at gmail.com Mon Nov 12 15:44:01 2018 From: megapode32559 at gmail.com (Michael Liu) Date: Mon, 12 Nov 2018 17:44:01 -0600 Subject: [bioontology-support] How a tree is determined from a DAG? In-Reply-To: References: <2FB23240-FD8D-4138-9EBC-01C9D3498B37@stanford.edu> Message-ID: Note that some other ontology viewer seems to deal with this multi-parent presentation problem better. See the following example. https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0018623 On Mon, Nov 12, 2018 at 4:29 PM Michael Liu wrote: > > Hi Jennifer, > > OK. By checking under both the parents, I see that "Autosomal dominant > Charcot-Marie-Tooth disease type 2" appears in two places in the > webportal. But when I search "Autosomal dominant Charcot-Marie-Tooth > disease type 2", it only jumps to one of them. Is there a way to show > all the matches when a class name is searched? > > > The class you mention below appears in two places in the tree because it has two subClassOf declarations in the ontology source file. > > -- > Best wishes, > Michael -- Best wishes, Michael From mdorf at stanford.edu Mon Nov 12 16:51:40 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 13 Nov 2018 00:51:40 +0000 Subject: [bioontology-support] Questions regarding the REST API In-Reply-To: <1541967499734.46992@ntnu.no> References: <1541771841693.45184@ntnu.no> <1541967499734.46992@ntnu.no> Message-ID: <4B31DE59-BE46-4CCF-8E84-348A27ED7879@stanford.edu> Hi John, Really helpful!!! I noticed also that when you do: http://data.bioontology.org/ontologies/NCIT/classes/ you get a total count of 144695 classes, while the query http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY returns 140329 as a total count and the difference must be that the first has the obsolete terms as well, right? Because if I do: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY&also_search_obsolete=true, then I get 144695! At the moment, the pagination counts aren?t always reported correctly. Sometime ago, we?ve implemented a system that prevents expensive COUNT queries going live against our 4store backend. These queries used to really bog down our servers, often resulting in downtime. The COUNT queries used to be executed on paged REST services, such as search. So, in order to determine the correct number of pages for a given call, our system used to first execute a COUNT query, storing the result in the output. The new system would pre-cache these counts, so when a paged service call is made, the count would be retrieved from a static repository. Unfortunately, there appears to be a bug in this process that triggers the different numbers you are seeing. There is an issue in our Github repository that tracks our progress on fixing this problem: https://github.com/ncbo/ontologies_linked_data/issues/88 It's best to simply use an iterator to go through ALL pages of available results until you hit an empty collection instead of relying on the reported totalCount. Is there a specific ordering on the returned results on the query: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY? Are the results ordered by prefLabel or @id for example?(doesn't seem to be the case) That?s a good question! Normally, the results are sorted by the match rank and ontology rank (see more on that below) respectively. In this case, however, there is neither a search string, nor multiple ontologies to rank against. So, there really isn?t any deterministic order in this case. Also, does this query return all classes in all ontologies in BioPortal: http://data.bioontology.org/search?ontologies=&ontology_types=ONTOLOGY ? And if so, what ordering is applied to the results? Yes, that should return results for all publicly available ontologies. Sort order (or lack of thereof) is the same. Actually I kinda though that the `search?q=something` searched for `something` in the prefLabel and synonyms only! (but it seems this is not the case, since it searchs for a match with the @id as well :) Which other fields does it look for a match? These are the fields being searched in their order of rank priority: id prefLabelExact (match on the full pref label) prefLabel (match on partial pref label) synonymExact (match on the full synonym(s)) synonym (match on the partial synonym(s)) notation (last fragment of id) cui (for UMLS ontologies) semantic_types Also I noticed that the `something` must always be URL encoded (otherwise you get no results). Do you think that the `ontologies=GO,BAO` part should be also (for the comma mostly)? Not strictly necessary, but it?s definitely an option: ontologies=NCIT%2CGO Do you know if there is an id I can request that has more than 50 matches (a class that is included in more than 50 ontologies)? This would mean that I would have a second page of results (since the default pagesize is 50). Sure: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000002&require_exact_match=true BTW, you can control the number of results per page by passing "pagesize=10? parameter. Here, is there a preferential sorting happening for these results (first BAO entry and then DOID for example? - though I see you get them the other way around) http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO We have an algorithm that ranks ontologies, based on a variety of flags. The latest rankings can be found here: https://gist.github.com/mdorf/cea96433cf4bf7dd94d109c8e06e29c0 "BAO"=>{:bioportalScore=>0.648, :umlsScore=>0.0}, "DOID"=>{:bioportalScore=>0.711, :umlsScore=>0.0}, As you can see, DOID is ranked higher, therefore it appears before the BAO result. Thanks again for your great questions! Michael On Nov 11, 2018, at 12:18 PM, John Zobolas > wrote: Hi Michael, Thanks so much for the answers and very helpful indeed! Please see inline for further discussion/clarification on some of those. BR, John. ________________________________ From: Michael Dorf > Sent: Saturday, November 10, 2018 12:46 AM To: John Zobolas Cc: support at bioontology.org Subject: Re: [bioontology-support] Questions regarding the REST API Hi John, Thanks for contacting us. See my answers inline below. On Nov 9, 2018, at 5:57 AM, John Zobolas > wrote: Hi, I am developing a module that's uses your API to get results back from different ontologies and I want to ask a few things: 1. ?I see that when I search for a string, in the results there is a property obsolete (e.g. http://data.bioontology.org/search?q=melanoma) which almost always (as far as I can tell) isfalse. Can I ever find it to be true (meaning that that entry is not used any more so I will have to prune that result)? Or you automatically filter the results to show only obsolete:falseones? The results are by default filtered on obsolete:false. There is a parameter called also_search_obsolete={true|false} if you want a more granular control over this flag. 1. Is the URL parameter no_contexts=true equal to display_context=false (I accidentally discovered that they work the same but the first one is not mentioned in the documentation, so I should probably use the later!) Both paramours work, but the correct one to use is display_context={true|false}, which is the one advertised in our documentation. 1. I was looking at the documentation in the available media types section, and I was wondering that if I send an HTTP request with method DELETE to a URL like http://data.bioontology.org/groups/:acronym or http://data.bioontology.org/ontologies/:acronym, will I be actually deleting that specific group/ontology? I mean do I even have the privileges to do that or is something that only an `admin` could do (because in the documentation it is not specified who can do what for every HTTP verb and media type). You can create ontologies/groups programmatically using your own API key via a POST call, but you cannot delete anything from the system. That function is limited to admins only. 1. The format of error responses is always the same no matter what query I use in your provided REST service (an object with errors and status properties, the first having an array of Strings as a value and the second the status code/number as a value)??? E.g. what I will get when I hit: http://data.bioontology.org/ontologies/GOfr Yes, the errors should all have a uniform response. If you notice otherwise, that would probably constitute a bug. Let us know if you find an error that deviates from this format. { * - "errors": [ * "You must provide a valid `acronym` to retrieve an ontology" ], * "status": 404 } { * - "errors": [ * "The search query must be provided via /search?q=[&page=&pagesize=]" ], * "status": 400 } 1. If I have the acronym of an ontology, I can access (all) the classes: (e.g. http://data.bioontology.org/ontologies/MCCL/classes). The first result in the previous query has the prefLabel:FetalCellLine. So, if I query the: http://data.bioontology.org/search?q=FetalCellLine&ontologies=MCCL I get this one result and whatever property was empty in the 'classes query' result (e.g. definition:[ ]), it's not shown in the later query, right? Correct. These two endpoints appear to have a slightly different handling of the empty fields. The classes endpoint displays empty lists, where as the search endpoint just drops the empty attributes from the response. Example: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 http://data.bioontology.org/search?q=CALR%20NM_004343.3:c.1092_1143del52&ontologies=NCIT&require_exact_match=true 1. Is there a way to get all the results from an ontology (paginated of course) through a query different than the one like /ontologies/:acronym/classes and have the results pruned (no empty properties) as when you query by search string? You can try calling the search endpoint without passing in a search string and limiting the results to a specific ontology. You need to pass a ?special? parameter called ?ontology_types=ONTOLOGY? in order for the queriless search to work: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY This will give you ALL results stored in our search index for the ontology NCIT. This isn?t the ?advertised? method of getting all classes, rather a ?workaround? that let?s you execute a search call without passing a query string. Really helpful!!! I noticed also that when you do: http://data.bioontology.org/ontologies/NCIT/classes/ you get a total count of 144695 classes, while the query http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY returns 140329 as a total count and the difference must be that the first has the obsolete terms as well, right? Because if I do: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY&also_search_obsolete=true, then I get 144695! Is there a specific ordering on the returned results on the query: http://data.bioontology.org/search?ontologies=NCIT&ontology_types=ONTOLOGY? Are the results ordered by prefLabel or @id for example?(doesn't seem to be the case) Also, does this query return all classes in all ontologies in BioPortal: http://data.bioontology.org/search?ontologies=&ontology_types=ONTOLOGY ? And if so, what ordering is applied to the results? 1. I have noticed that the @id in the results is not a unique id, right? For example, there are many results with this id: http://purl.obolibrary.org/obo/DOID_1909, belonging to different ontologies - and the difference between them is small, for example one result does not provide the definition while the other does. Again, correct! The @id represents the class ID as defined in the original source ontology. The same class can be reused in multiple ontologies. The ?unique? ID of a class in BioPortal is a combination of the @id and the ontology acronym, as in: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C129834 Useful to know! 1. Is there a way to get results by id? Something like: /searchByID/id=URLid (according to (7) this could result in more than 1 result) or /searchByID/ids={URLid1,URLid2,URLid3,?}? Yes, you can pass the URL-encoded full ID in the ?q? parameter to the /search endpoint: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true Actually I kinda though that the `search?q=something` searched for `something` in the prefLabel and synonyms only! (but it seems this is not the case, since it searchs for a match with the @id as well :) Which other fields does it look for a match? Also I noticed that the `something` must always be URL encoded (otherwise you get no results). Do you think that the `ontologies=GO,BAO` part should be also (for the comma mostly)? Do you know if there is an id I can request that has more than 50 matches (a class that is included in more than 50 ontologies)? This would mean that I would have a second page of results (since the default pagesize is 50). You cannot search by multiple IDs. 1. Is there a way to get results by a combination of id+ontology acronym? Something like /searchByIDAndOntology/id=URL&ontology=OntologyAcronym? Actually, if you merge the 2 last questions, what I am asking is this query: /searchByIDAndOntology/id=[list of URLids]&ontologies=[list of ontologies]? The nearest I found in the documentation was the query with the subtree_root_id which needs the search string (so I can't use it in my case). Also, this could cover the (6) if the list of ids is empty! If you want to limit results to a given class within a given ontology(ies), just add the ?ontologies=?BAO,DOID? to the query: http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO,DOID Here, is there a preferential sorting happening for these results (first BAO entry and then DOID for example? - though I see you get them the other way around) http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909&require_exact_match=true&ontologies=BAO Hope this helps! Feel free to reach out if you have further questions. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- ?BR, John. ?------------------ John Zobolas PhD Student Department of Biology, Faculty of Natural Sciences, NTNU Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Nov 12 17:09:05 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 13 Nov 2018 01:09:05 +0000 Subject: [bioontology-support] How a tree is determined from a DAG? In-Reply-To: References: <2FB23240-FD8D-4138-9EBC-01C9D3498B37@stanford.edu> Message-ID: <6ED45DCB-85E5-4701-A971-7DA84D1D7001@stanford.edu> Hi Michael, > On Nov 12, 2018, at 2:29 PM, Michael Liu wrote: > > OK. By checking under both the parents, I see that "Autosomal dominant > Charcot-Marie-Tooth disease type 2" appears in two places in the > webportal. But when I search "Autosomal dominant Charcot-Marie-Tooth > disease type 2", it only jumps to one of them. Is there a way to show > all the matches when a class name is searched? Unfortunately, it doesn?t appear that the tree in the presentation layer was developed to operate in this manner. Only one occurrence of the class is selected, regardless of how many times it appears. Apologies also that I can?t think of an immediate workaround in the current application to get the view that you want. I saw your subsequent email with a screen shot from another application. I?ll get started on entering a feature request in our tracker. Kind regards, Jennifer From jean.charlet at upmc.fr Thu Nov 15 07:20:19 2018 From: jean.charlet at upmc.fr (Charlet Jean) Date: Thu, 15 Nov 2018 16:20:19 +0100 Subject: [bioontology-support] Ontology visible but not downloadable In-Reply-To: References: Message-ID: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> Hello Jennifer, As usual (with me :-)), is it possible to set a flag on a new ontology of my team, http://bioportal.bioontology.org/ontologies/ONTOPARON/, to prevent the file from being downloadable ? As for the others (ONTOPSYCHIA), I think that my colleagues doctors will agree to open the full access later. Kinds regards, Jean. ,,,, (o-o) --------oOO-(_)-OOo------------------------------------------o0O-OOo---- Jean Charlet M?l : Jean.Charlet at upmc.fr INSERM UMR_S 1142 T?l : +33/0 1 44 27 91 09 15, rue de l'?cole de M?decine URL : http://www.limics.fr/ 75006 Paris, France Assistance publique - H?pitaux de Paris LIMICS - Univ. Paris VI - Univ. Paris XIII ----------o0O-OOo------------------------------------------oOO-( )-OOo-- (o-o) ```` -------------- next part -------------- An HTML attachment was scrubbed... URL: From JLLoomis at mintz.com Thu Nov 15 11:16:38 2018 From: JLLoomis at mintz.com (Loomis, John) Date: Thu, 15 Nov 2018 19:16:38 +0000 Subject: [bioontology-support] article inquiry 15 November Message-ID: <45433c0f2d894bdeafe51ed0f625dc53@MINTZMBX02.MINTZ.com> Hello, I was trying to figure out how to access: CPT Assistant Nov 98:29, Mar 99:10, Oct 99:3, Jun 02:11, Jul 05:1, May 08:5, May 12:5, Sep 13:3. cited here: http://bioportal.bioontology.org/ontologies/CPT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F88273 under the article: Molecular cytogenetics; chromosomal in situ hybridization, analyze 10-30 cells (eg, for microdeletions) Are you able to help? Thanks, John Loomis Research Services Coordinator Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. One Financial Center, Boston, MA 02111 +1.617.348.1779 JLLoomis at mintz.com | Mintz.com [mintz.com] ________________________________ STATEMENT OF CONFIDENTIALITY: The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain confidential or privileged information. If you are not the intended recipient, or the person responsible for delivering the e-mail to the intended recipient, be advised you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Please notify Mintz, Levin, Cohn, Ferris, Glovsky and Popeo immediately at either (617) 542-6000 or at DirectorofIT at Mintz.com, and destroy all copies of this message and any attachments. You will be reimbursed for reasonable costs incurred in notifying us. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Nov 15 11:56:14 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 15 Nov 2018 19:56:14 +0000 Subject: [bioontology-support] article inquiry 15 November In-Reply-To: <45433c0f2d894bdeafe51ed0f625dc53@MINTZMBX02.MINTZ.com> References: <45433c0f2d894bdeafe51ed0f625dc53@MINTZMBX02.MINTZ.com> Message-ID: Hi John, We import CPT from the National Library of Medicine?s UMLS Metathesaurus [1]. According to their documentation [2], these citations are "Reference to CPT Assistant Newsletter articles?. I googled CPT Assistant, and it appears to be a paid newsletter from the AMA [3]. If you?re a subscriber to the newsletter, perhaps they have a support list where you could ask how to access theses particular articles. Kind regards, Jennifer [1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/ [2] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/metarepresentation.html [3] https://commerce.ama-assn.org/store/catalog/productDetail.jsp?product_id=prod1170021&navAction=push On Nov 15, 2018, at 11:16 AM, Loomis, John > wrote: Hello, I was trying to figure out how to access: CPT Assistant Nov 98:29, Mar 99:10, Oct 99:3, Jun 02:11, Jul 05:1, May 08:5, May 12:5, Sep 13:3. cited here: http://bioportal.bioontology.org/ontologies/CPT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F88273 under the article: Molecular cytogenetics; chromosomal in situ hybridization, analyze 10-30 cells (eg, for microdeletions) Are you able to help? Thanks, John Loomis Research Services Coordinator Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. One Financial Center, Boston, MA 02111 +1.617.348.1779 JLLoomis at mintz.com | Mintz.com [mintz.com] ________________________________ STATEMENT OF CONFIDENTIALITY: The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain confidential or privileged information. If you are not the intended recipient, or the person responsible for delivering the e-mail to the intended recipient, be advised you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Please notify Mintz, Levin, Cohn, Ferris, Glovsky and Popeo immediately at either (617) 542-6000 or at DirectorofIT at Mintz.com, and destroy all copies of this message and any attachments. You will be reimbursed for reasonable costs incurred in notifying us. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu Nov 15 16:43:14 2018 From: support at bioontology.org (support at bioontology.org) Date: Thu, 15 Nov 2018 16:43:14 -0800 Subject: [bioontology-support] [BioPortal] Feedback from suzi aleksander Message-ID: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Nov 15 17:17:39 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 16 Nov 2018 01:17:39 +0000 Subject: [bioontology-support] Ontology visible but not downloadable In-Reply-To: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> References: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> Message-ID: <3CEF9867-D2E5-4F9C-9D39-5BAAB4AE905A@stanford.edu> Hello Jean, On Nov 15, 2018, at 7:20 AM, Charlet Jean > wrote: As usual (with me :-)), is it possible to set a flag on a new ontology of my team, http://bioportal.bioontology.org/ontologies/ONTOPARON/, to prevent the file from being downloadable ? I?ve added the necessary flag in our system to remove the download link for ONTOPARON. You may have to refresh the page to see the change. On a related note, I noticed that the latest upload failed to finish parsing in our system. I?m looking into it. Best, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From himanso.sahni at nih.gov Thu Nov 15 17:30:09 2018 From: himanso.sahni at nih.gov (Sahni, Himanso (NIH/NCI) [C]) Date: Fri, 16 Nov 2018 01:30:09 +0000 Subject: [bioontology-support] REST API key Message-ID: Hello I work on the NCI GDC https://gdc.cancer.gov/ project and would like to utilize the Bioportal?s REST API to query the NCI thesaurus (NCIT), UMLS & ICD10 vocabularies. What is the process of requesting the apikey ? thanks Himanso Sahni (Contractor) GDC Technical Lead Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. P.O. Box B, Frederick, MD 21702 Office: 240 276 5233 Physical address: 9605 Medical Center Drive, Suite 280, Rockville, MD 20852 himanso.sahni at nih.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Nov 15 17:39:59 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 16 Nov 2018 01:39:59 +0000 Subject: [bioontology-support] REST API key In-Reply-To: References: Message-ID: <1FF4F35E-8BCE-4118-8E53-18CB6B5F9CA1@stanford.edu> Hello Himanso, We have instructions for getting an API key on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer On Nov 15, 2018, at 5:30 PM, Sahni, Himanso (NIH/NCI) [C] > wrote: Hello I work on the NCI GDC https://gdc.cancer.gov/ project and would like to utilize the Bioportal?s REST API to query the NCI thesaurus (NCIT), UMLS & ICD10 vocabularies. What is the process of requesting the apikey ? thanks Himanso Sahni (Contractor) GDC Technical Lead Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. P.O. Box B, Frederick, MD 21702 Office: 240 276 5233 Physical address: 9605 Medical Center Drive, Suite 280, Rockville, MD 20852 himanso.sahni at nih.gov _______________________________________________ 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 himanso.sahni at nih.gov Thu Nov 15 17:57:45 2018 From: himanso.sahni at nih.gov (Sahni, Himanso (NIH/NCI) [C]) Date: Fri, 16 Nov 2018 01:57:45 +0000 Subject: [bioontology-support] REST API key In-Reply-To: <1FF4F35E-8BCE-4118-8E53-18CB6B5F9CA1@stanford.edu> References: <1FF4F35E-8BCE-4118-8E53-18CB6B5F9CA1@stanford.edu> Message-ID: Thanks for the prompt reply. Just realized I already had registered back in 2015 ? Himanso Sahni (Contractor) GDC Technical Lead Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. P.O. Box B, Frederick, MD 21702 Office: 240 276 5233 Physical address: 9605 Medical Center Drive, Suite 280, Rockville, MD 20852 himanso.sahni at nih.gov From: Jennifer Leigh Vendetti Date: Thursday, November 15, 2018 at 8:40 PM To: "Sahni, Himanso (NIH/NCI) [C]" Cc: "support at bioontology.org" Subject: Re: [bioontology-support] REST API key Hello Himanso, We have instructions for getting an API key on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Kind regards, Jennifer On Nov 15, 2018, at 5:30 PM, Sahni, Himanso (NIH/NCI) [C] > wrote: Hello I work on the NCI GDC https://gdc.cancer.gov/ project and would like to utilize the Bioportal?s REST API to query the NCI thesaurus (NCIT), UMLS & ICD10 vocabularies. What is the process of requesting the apikey ? thanks Himanso Sahni (Contractor) GDC Technical Lead Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. P.O. Box B, Frederick, MD 21702 Office: 240 276 5233 Physical address: 9605 Medical Center Drive, Suite 280, Rockville, MD 20852 himanso.sahni at nih.gov _______________________________________________ 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 jean.charlet at upmc.fr Fri Nov 16 00:27:23 2018 From: jean.charlet at upmc.fr (Charlet Jean) Date: Fri, 16 Nov 2018 09:27:23 +0100 Subject: [bioontology-support] Ontology visible but not downloadable In-Reply-To: <3CEF9867-D2E5-4F9C-9D39-5BAAB4AE905A@stanford.edu> References: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> <3CEF9867-D2E5-4F9C-9D39-5BAAB4AE905A@stanford.edu> Message-ID: <5520EA73-1DE4-4DBD-8ED3-6903F5F6CBDA@upmc.fr> Thank you. The new version is the same as the previous one (I think) except that it is exported from Prot?g? with the ? reasonings ? made and the record of some axioms. Perhaps this action is responsible of the problem Best Jean. > Le 16 nov. 2018 ? 02:17, Jennifer Leigh Vendetti a ?crit : > > Hello Jean, > > >> On Nov 15, 2018, at 7:20 AM, Charlet Jean wrote: >> >> As usual (with me :-)), is it possible to set a flag on a new ontology of my team, http://bioportal.bioontology.org/ontologies/ONTOPARON/, to prevent the file from being downloadable ? > > > I?ve added the necessary flag in our system to remove the download link for ONTOPARON. You may have to refresh the page to see the change. > > On a related note, I noticed that the latest upload failed to finish parsing in our system. I?m looking into it. > > Best, > Jennifer > ,,,, (o-o) --------oOO-(_)-OOo------------------------------------------o0O-OOo---- Jean Charlet M?l : Jean.Charlet at upmc.fr INSERM UMR_S 1142 T?l : +33/0 1 44 27 91 09 15, rue de l'?cole de M?decine URL : http://www.limics.fr/ 75006 Paris, France Assistance publique - H?pitaux de Paris LIMICS - Univ. Paris VI - Univ. Paris XIII ----------o0O-OOo------------------------------------------oOO-( )-OOo-- (o-o) ```` From vendetti at stanford.edu Fri Nov 16 12:33:40 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 16 Nov 2018 20:33:40 +0000 Subject: [bioontology-support] Ontology visible but not downloadable In-Reply-To: <5520EA73-1DE4-4DBD-8ED3-6903F5F6CBDA@upmc.fr> References: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> <3CEF9867-D2E5-4F9C-9D39-5BAAB4AE905A@stanford.edu> <5520EA73-1DE4-4DBD-8ED3-6903F5F6CBDA@upmc.fr> Message-ID: <4EC25DB0-7BC4-4C17-BC1B-A511466628B5@stanford.edu> Hello Jean, The problem was on our end with one of our production machines. I?ve reprocessed your ontology, which is fully available in BioPortal now (minus the download link). Best, Jennifer On Nov 16, 2018, at 12:27 AM, Charlet Jean > wrote: Thank you. The new version is the same as the previous one (I think) except that it is exported from Prot?g? with the ? reasonings ? made and the record of some axioms. Perhaps this action is responsible of the problem Best Jean. Le 16 nov. 2018 ? 02:17, Jennifer Leigh Vendetti > a ?crit : Hello Jean, On Nov 15, 2018, at 7:20 AM, Charlet Jean > wrote: As usual (with me :-)), is it possible to set a flag on a new ontology of my team, http://bioportal.bioontology.org/ontologies/ONTOPARON/, to prevent the file from being downloadable ? I?ve added the necessary flag in our system to remove the download link for ONTOPARON. You may have to refresh the page to see the change. On a related note, I noticed that the latest upload failed to finish parsing in our system. I?m looking into it. Best, Jennifer ,,,, (o-o) --------oOO-(_)-OOo------------------------------------------o0O-OOo---- Jean Charlet M?l : Jean.Charlet at upmc.fr INSERM UMR_S 1142 T?l : +33/0 1 44 27 91 09 15, rue de l'?cole de M?decine URL : http://www.limics.fr/ 75006 Paris, France Assistance publique - H?pitaux de Paris LIMICS - Univ. Paris VI - Univ. Paris XIII ----------o0O-OOo------------------------------------------oOO-( )-OOo-- (o-o) ```` -------------- next part -------------- An HTML attachment was scrubbed... URL: From jean.charlet at upmc.fr Fri Nov 16 14:20:53 2018 From: jean.charlet at upmc.fr (Charlet Jean) Date: Fri, 16 Nov 2018 23:20:53 +0100 Subject: [bioontology-support] Ontology visible but not downloadable In-Reply-To: <4EC25DB0-7BC4-4C17-BC1B-A511466628B5@stanford.edu> References: <8E660F25-DF47-45FC-87A7-495F2CA3A9DF@upmc.fr> <3CEF9867-D2E5-4F9C-9D39-5BAAB4AE905A@stanford.edu> <5520EA73-1DE4-4DBD-8ED3-6903F5F6CBDA@upmc.fr> <4EC25DB0-7BC4-4C17-BC1B-A511466628B5@stanford.edu> Message-ID: <6FBC4E98-9C01-4255-83DC-8B9616382657@upmc.fr> Thanks a lot. Best, Jean. > Le 16 nov. 2018 ? 21:33, Jennifer Leigh Vendetti a ?crit : > > Hello Jean, > > The problem was on our end with one of our production machines. I?ve reprocessed your ontology, which is fully available in BioPortal now (minus the download link). > > Best, > Jennifer > > > >> On Nov 16, 2018, at 12:27 AM, Charlet Jean wrote: >> >> Thank you. The new version is the same as the previous one (I think) except that it is exported from Prot?g? with the ? reasonings ? made and the record of some axioms. Perhaps this action is responsible of the problem >> >> Best >> Jean. >> >>> Le 16 nov. 2018 ? 02:17, Jennifer Leigh Vendetti a ?crit : >>> >>> Hello Jean, >>> >>> >>>> On Nov 15, 2018, at 7:20 AM, Charlet Jean wrote: >>>> >>>> As usual (with me :-)), is it possible to set a flag on a new ontology of my team, http://bioportal.bioontology.org/ontologies/ONTOPARON/, to prevent the file from being downloadable ? >>> >>> >>> I?ve added the necessary flag in our system to remove the download link for ONTOPARON. You may have to refresh the page to see the change. >>> >>> On a related note, I noticed that the latest upload failed to finish parsing in our system. I?m looking into it. >>> >>> Best, >>> Jennifer >>> >> >> ,,,, >> (o-o) >> --------oOO-(_)-OOo------------------------------------------o0O-OOo---- >> Jean Charlet M?l : Jean.Charlet at upmc.fr >> INSERM UMR_S 1142 T?l : +33/0 1 44 27 91 09 >> 15, rue de l'?cole de M?decine URL : http://www.limics.fr/ >> 75006 Paris, France >> Assistance publique - H?pitaux de Paris >> LIMICS - Univ. Paris VI - Univ. Paris XIII >> ----------o0O-OOo------------------------------------------oOO-( )-OOo-- >> (o-o) >> ```` > ,,,, (o-o) --------oOO-(_)-OOo------------------------------------------o0O-OOo---- Jean Charlet M?l : Jean.Charlet at upmc.fr INSERM UMR_S 1142 T?l : +33/0 1 44 27 91 09 15, rue de l'?cole de M?decine URL : http://www.limics.fr/ 75006 Paris, France Assistance publique - H?pitaux de Paris LIMICS - Univ. Paris VI - Univ. Paris XIII ----------o0O-OOo------------------------------------------oOO-( )-OOo-- (o-o) ```` From vendetti at stanford.edu Fri Nov 16 16:24:38 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Sat, 17 Nov 2018 00:24:38 +0000 Subject: [bioontology-support] [BioPortal] Feedback from suzi aleksander In-Reply-To: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail> References: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> Hi Suzi, On Nov 15, 2018, at 4:43 PM, support at bioontology.org wrote: Hi, I'm looking at https://bioportal.bioontology.org/ontologies/GO, and would like to inform you that GO has had about 10 official releases since the version you last listed (BioPortal lists January 2018; compare to http://release.geneontology.org/). It's possible you missed the handover from Stanford to LBNL, and your site is not automatically updating anymore. If you need help/clarifications locating the current versions please contact us on GitHub: https://github.com/geneontology/helpdesk/issues. Thanks for alerting us to that. There appears to have been a problem with our process that checks for / loads new versions of GO on a nightly basis. I think I?ve corrected the problem, but will need to double check after the nightly process kicks off tonight. I?ll follow up to let you know how it?s proceeding. BioPortal is currently configured to load new versions of the OBO file from: http://purl.obolibrary.org/obo/go.obo. According to your documentation, that appears to be the correct URL. I notice you referenced an issue tracker above for getting help with GO. I?m wondering if the metadata we list for GO on the ontology summary page (http://bioportal.bioontology.org/ontologies/GO) is correct, i.e., the description, contact person, etc.? (Also, running FF 60.0.1 on Sierra 10.12.6, and I have to use the Web Developer tools to shrink your grey footer in order to type anything in this box- the footer overlaps this field.) I?m wondering if I could get more specifics from you here. I assume you?re referring to the feedback dialog that?s launched from Support -> Submit Feedback in the main menu bar? As far as I?m aware, this dialog has no footer: [cid:94B74565-0E78-438B-B179-7FF30AD9964E at stanford.edu] Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-11-16 16.22.19.png Type: image/png Size: 137537 bytes Desc: Screenshot 2018-11-16 16.22.19.png URL: From support at bioontology.org Mon Nov 19 07:12:32 2018 From: support at bioontology.org (support at bioontology.org) Date: Mon, 19 Nov 2018 07:12:32 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Christopher FOSTER Message-ID: <5bf2d2e0c1820_139a2ab6deb06cdc392f9@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Nov 19 11:20:47 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 19 Nov 2018 19:20:47 +0000 Subject: [bioontology-support] [BioPortal] Feedback from suzi aleksander In-Reply-To: <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> References: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail> <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> Message-ID: Hi Suzi, BioPortal is picking up new versions of GO again. Let us know if you see anything that looks amiss. Kind regards, Jennifer On Nov 16, 2018, at 4:24 PM, Jennifer Leigh Vendetti > wrote: Hi Suzi, On Nov 15, 2018, at 4:43 PM, support at bioontology.org wrote: Hi, I'm looking at https://bioportal.bioontology.org/ontologies/GO, and would like to inform you that GO has had about 10 official releases since the version you last listed (BioPortal lists January 2018; compare to http://release.geneontology.org/). It's possible you missed the handover from Stanford to LBNL, and your site is not automatically updating anymore. If you need help/clarifications locating the current versions please contact us on GitHub: https://github.com/geneontology/helpdesk/issues. Thanks for alerting us to that. There appears to have been a problem with our process that checks for / loads new versions of GO on a nightly basis. I think I?ve corrected the problem, but will need to double check after the nightly process kicks off tonight. I?ll follow up to let you know how it?s proceeding. BioPortal is currently configured to load new versions of the OBO file from: http://purl.obolibrary.org/obo/go.obo. According to your documentation, that appears to be the correct URL. I notice you referenced an issue tracker above for getting help with GO. I?m wondering if the metadata we list for GO on the ontology summary page (http://bioportal.bioontology.org/ontologies/GO) is correct, i.e., the description, contact person, etc.? (Also, running FF 60.0.1 on Sierra 10.12.6, and I have to use the Web Developer tools to shrink your grey footer in order to type anything in this box- the footer overlaps this field.) I?m wondering if I could get more specifics from you here. I assume you?re referring to the feedback dialog that?s launched from Support -> Submit Feedback in the main menu bar? As far as I?m aware, this dialog has no footer: Kind regards, Jennifer _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Nov 19 12:17:49 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 19 Nov 2018 20:17:49 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Christopher FOSTER In-Reply-To: <5bf2d2e0c1820_139a2ab6deb06cdc392f9@ncbo-prd-app-08.stanford.edu.mail> References: <5bf2d2e0c1820_139a2ab6deb06cdc392f9@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Chris, You can find the SNOMED CT codes for strings by searching the "Jump to" box in the ontologies classes page, in this case http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=root The resulting page (http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F444604002) lists the various codes associated with this term; I expect the 'notation' is the field you want. Unfortunately we do not keep the earlier SNOMED versions in BioPortal, so we can not help you with that request. John On Nov 19, 2018, at 7:12 AM, support at bioontology.org wrote: Name: Christopher FOSTER Email: chris.foster at hcahealthcare.co.uk Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSCTSPA Feedback: Please let me know the SNOMED v3/4 code and the SNOMED CT code for ""MIXED DUCTAL/LOBULAR CARCINOMA OF BREAST"" Many thanks - Chris Foster _______________________________________________ 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 suzia at stanford.edu Mon Nov 19 16:59:04 2018 From: suzia at stanford.edu (Suzi Aleksander) Date: Tue, 20 Nov 2018 00:59:04 +0000 Subject: [bioontology-support] [BioPortal] Feedback from suzi aleksander In-Reply-To: <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> References: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail>, <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> Message-ID: Hi Jennifer, Yes, http://purl.obolibrary.org/obo/go.obo is the right URL. There should just have been a new release on the 15th of this month. Our contact info on that page isn't correct- GO isn't run by EBI, but EBI has their own group that does GO annotations (GOA)- so the confusion is common. Can you put the GitHub tracker there? We're switching email systems and I'm not confident emails will be caught with our current setup. The GitHub tracker is the best place to contact us for now. For the footer issue, I've attached a screenshot. Seems like using the "contact us" under Support in the footer leads to the issue; the Support dropdown/popup window is fine. I'm slightly over 100% zoom, looks like reducing that to 80% allows me to submit (but then I can't read what I typed). And I'm viewing on my MBP, not an attached monitor. Thanks for getting back to me on this Suzi ________________________________ From: Jennifer Leigh Vendetti Sent: Friday, November 16, 2018 4:24 PM To: support at bioontology.org Cc: Suzi Aleksander Subject: Re: [bioontology-support] [BioPortal] Feedback from suzi aleksander Hi Suzi, On Nov 15, 2018, at 4:43 PM, support at bioontology.org wrote: Hi, I'm looking at https://bioportal.bioontology.org/ontologies/GO, and would like to inform you that GO has had about 10 official releases since the version you last listed (BioPortal lists January 2018; compare to http://release.geneontology.org/). It's possible you missed the handover from Stanford to LBNL, and your site is not automatically updating anymore. If you need help/clarifications locating the current versions please contact us on GitHub: https://github.com/geneontology/helpdesk/issues. Thanks for alerting us to that. There appears to have been a problem with our process that checks for / loads new versions of GO on a nightly basis. I think I?ve corrected the problem, but will need to double check after the nightly process kicks off tonight. I?ll follow up to let you know how it?s proceeding. BioPortal is currently configured to load new versions of the OBO file from: http://purl.obolibrary.org/obo/go.obo. According to your documentation, that appears to be the correct URL. I notice you referenced an issue tracker above for getting help with GO. I?m wondering if the metadata we list for GO on the ontology summary page (http://bioportal.bioontology.org/ontologies/GO) is correct, i.e., the description, contact person, etc.? (Also, running FF 60.0.1 on Sierra 10.12.6, and I have to use the Web Developer tools to shrink your grey footer in order to type anything in this box- the footer overlaps this field.) I?m wondering if I could get more specifics from you here. I assume you?re referring to the feedback dialog that?s launched from Support -> Submit Feedback in the main menu bar? As far as I?m aware, this dialog has no footer: [cid:94B74565-0E78-438B-B179-7FF30AD9964E at stanford.edu] Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2018-11-16 16.22.19.png Type: image/png Size: 137537 bytes Desc: Screenshot 2018-11-16 16.22.19.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bioportal.jpeg Type: image/jpeg Size: 651254 bytes Desc: bioportal.jpeg URL: From paola.roncaglia at icloud.com Tue Nov 20 09:06:48 2018 From: paola.roncaglia at icloud.com (Paola Roncaglia) Date: Tue, 20 Nov 2018 17:06:48 +0000 Subject: [bioontology-support] Old version of CL in BioPortal Message-ID: <8AFE7B4E-6932-4A01-B824-39247C6E56D8@icloud.com> Dear BioPortal staff, It looks like the version of the Cell Ontology (CL) in BioPortal is quite old compared to the actual latest release: http://bioportal.bioontology.org/ontologies/CL?p=summary says 2015-08-08 While the GitHub page for the CL project shows release files from 4 months ago: https://github.com/obophenotype/cell-ontology Could you update, please? Thanks, Paola Roncaglia -------------- next part -------------- An HTML attachment was scrubbed... URL: From supriya.davis at duke.edu Tue Nov 20 08:20:09 2018 From: supriya.davis at duke.edu (Supriya Davis) Date: Tue, 20 Nov 2018 16:20:09 +0000 Subject: [bioontology-support] Error support Message-ID: Hi, I am unable to search for SNOMED-CT terms. When I try to do a class search for a term eg 'pneumonia', then click on the 'SNOMED-CT' link, I get the attached error message. I appreciate your help! Supriya Davis MD Candidate Class of 2020 Duke University School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-11-20 at 10.50.05 AM.png Type: image/png Size: 196873 bytes Desc: Screen Shot 2018-11-20 at 10.50.05 AM.png URL: From mohamed.keshk at gmail.com Mon Nov 19 22:36:12 2018 From: mohamed.keshk at gmail.com (Mohamed Keshk) Date: Tue, 20 Nov 2018 00:36:12 -0600 Subject: [bioontology-support] Problem retrieving classes - Help Message-ID: mohamed.keshk at gmail.com Hi, I uploaded very small ontology (as a test), at: http://bioportal.bioontology.org/ontologies/PCL My problem is; I am not able to see the class hierarchy of the ontology. Whenever I select "Classes" tab, I get the error message "Problem retrieving classes". Please help... Thanks, Mohamed Keshk -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Nov 20 13:30:26 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 20 Nov 2018 21:30:26 +0000 Subject: [bioontology-support] Old version of CL in BioPortal In-Reply-To: <8AFE7B4E-6932-4A01-B824-39247C6E56D8@icloud.com> References: <8AFE7B4E-6932-4A01-B824-39247C6E56D8@icloud.com> Message-ID: <2E3EF907-A749-44DF-8161-FB214713A904@stanford.edu> Thanks Paola for this request. We update this ontology whenever it changes in the OBO Library, so the ontology itself is in fact current in BioPortal. We generally use 'unknown' as the version information for OBO Library ontologies, as they do not use versionInfo to identify their versions (instead using the newer versionIRI string). So I have changed this version information to read 'unknown'. I have also asked whether the OBO Library might change their recommendation to also include versionInfo attributes in the ontology, since that seems to me to be a dominant practice (reference https://github.com/OBOFoundry/OBOFoundry.github.io/issues/771). John On Nov 20, 2018, at 9:06 AM, Paola Roncaglia > wrote: Dear BioPortal staff, It looks like the version of the Cell Ontology (CL) in BioPortal is quite old compared to the actual latest release: http://bioportal.bioontology.org/ontologies/CL?p=summary says 2015-08-08 While the GitHub page for the CL project shows release files from 4 months ago: https://github.com/obophenotype/cell-ontology Could you update, please? Thanks, Paola Roncaglia _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Nov 20 13:31:18 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 20 Nov 2018 21:31:18 +0000 Subject: [bioontology-support] Problem retrieving classes - Help In-Reply-To: References: Message-ID: <44872915-2D68-4032-94E6-9A4DCF16692C@stanford.edu> Mohamed, sorry for this issue. Can you please try looking again? I am seeing the classes in my view, and am not sure if this was a timing issue or is still a problem. John On Nov 19, 2018, at 10:36 PM, Mohamed Keshk > wrote: mohamed.keshk at gmail.com Hi, I uploaded very small ontology (as a test), at: http://bioportal.bioontology.org/ontologies/PCL My problem is; I am not able to see the class hierarchy of the ontology. Whenever I select "Classes" tab, I get the error message "Problem retrieving classes". Please help... Thanks, Mohamed Keshk _______________________________________________ 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 mohamed.keshk at gmail.com Tue Nov 20 13:39:38 2018 From: mohamed.keshk at gmail.com (Mohamed Keshk) Date: Tue, 20 Nov 2018 15:39:38 -0600 Subject: [bioontology-support] Problem retrieving classes - Help In-Reply-To: <44872915-2D68-4032-94E6-9A4DCF16692C@stanford.edu> References: <44872915-2D68-4032-94E6-9A4DCF16692C@stanford.edu> Message-ID: Hi John, Thank you very much for your help. Yes, now it works fine, and I can see the classes too. Thanks, Mohamed On Tue, Nov 20, 2018 at 3:31 PM John Graybeal wrote: > Mohamed, sorry for this issue. Can you please try looking again? I am > seeing the classes in my view, and am not sure if this was a timing issue > or is still a problem. > > John > > On Nov 19, 2018, at 10:36 PM, Mohamed Keshk > wrote: > > mohamed.keshk at gmail.com > > Hi, > I uploaded very small ontology (as a test), at: > http://bioportal.bioontology.org/ontologies/PCL > My problem is; I am not able to see the class hierarchy of the ontology. > Whenever I select "Classes" tab, I get the error message "Problem > retrieving classes". > > Please help... > > Thanks, > Mohamed Keshk > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > ======================== > John Graybeal > Technical Program Manager > Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal > Stanford Center for Biomedical Informatics Research > 650-736-1632 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Nov 20 15:19:44 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 20 Nov 2018 23:19:44 +0000 Subject: [bioontology-support] Error support In-Reply-To: References: Message-ID: Hello Supriya, This may be a problem that we have seen before, and documented in this ticket: https://github.com/ncbo/bioportal_web_ui/issues/86 To test this, try logging out, and performing the same operation. If you no longer have the problem, then the problem is documented and is on our list to address, hopefully relatively soon. In the meantime, the workaround to find the data is to log out and visit the class again. If this does not fix the problem, let us know and we will work with you to collect additional data. John On Nov 20, 2018, at 8:20 AM, Supriya Davis > wrote: Hi, I am unable to search for SNOMED-CT terms. When I try to do a class search for a term eg 'pneumonia', then click on the 'SNOMED-CT' link, I get the attached error message. I appreciate your help! Supriya Davis MD Candidate Class of 2020 Duke University School of Medicine _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Tue Nov 20 16:01:03 2018 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Wed, 21 Nov 2018 00:01:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from suzi aleksander In-Reply-To: References: <5bee12a298bd8_6e552b024679babc406ae@ncbo-prd-app-08.stanford.edu.mail> <4376700E-E734-4422-BBB0-CADA49FB6329@stanford.edu> Message-ID: Hi Suzi, On Nov 19, 2018, at 4:59 PM, Suzi Aleksander > wrote: Yes, http://purl.obolibrary.org/obo/go.obo is the right URL. There should just have been a new release on the 15th of this month. Since the pull mechanism was corrected, BioPortal has retrieved 3 new versions of GO. I downloaded each of them and looked at the data-version attribute in the OBO files. I?m seeing: data-version: releases/2018-11-14 data-version: releases/2018-11-17 data-version: releases/2018-11-18 Does this correspond to what you expect? Is there a place on the GO website that would allow me to see your list of versions and compare it to what we have? Our contact info on that page isn't correct- GO isn't run by EBI, but EBI has their own group that does GO annotations (GOA)- so the confusion is common. Can you put the GitHub tracker there? We're switching email systems and I'm not confident emails will be caught with our current setup. The GitHub tracker is the best place to contact us for now. Thanks for the clarification. I edited the contact information to use the GitHub tracker. On a related note, we?re happy to grant privileges to GO administrators to make these sorts of edits yourselves. The steps involve creating a BioPortal account [1], and letting us know the username so that we can add you as administrators. I looked at the current permissions and see two accounts with admin privileges: rama and go at geneontology.org. Not sure if those are current. For the footer issue, I've attached a screenshot. Seems like using the "contact us" under Support in the footer leads to the issue; the Support dropdown/popup window is fine. I'm slightly over 100% zoom, looks like reducing that to 80% allows me to submit (but then I can't read what I typed). And I'm viewing on my MBP, not an attached monitor. Thanks for pointing that out. I performed a minor release to our production environment today that should address the problem. Clicking on Contact Us in the footer will now display the feedback form in a dialog - same behavior as the Support -> Submit Feedback menu item (you may have to refresh the page to see the change). Kind regards, Jennifer [1] https://bioportal.bioontology.org/accounts/new -------------- next part -------------- An HTML attachment was scrubbed... URL: From amassengale at rsna.org Fri Nov 23 08:30:46 2018 From: amassengale at rsna.org (Andrew Massengale) Date: Fri, 23 Nov 2018 16:30:46 +0000 Subject: [bioontology-support] BioPortal API not working Message-ID: Hello, The BioPortal API is not working for us. It is rejecting our API keys; however, we have not changed our API keys. In fact, the entire website appears to be down. https://bioportal.bioontology.org/ Thanks, 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: From mdorf at stanford.edu Fri Nov 23 09:22:04 2018 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 23 Nov 2018 17:22:04 +0000 Subject: [bioontology-support] BioPortal API not working In-Reply-To: References: Message-ID: <4A86CD55-4AD1-4219-A976-65ADC156EDCC@stanford.edu> Hi Andrew, Apologies for the interruption. We?ve had an unscheduled server downtime this morning. At this point, all access has been restored. Please let us know if you continue experiencing issues with your API keys. Thanks, Michael On Nov 23, 2018, at 8:30 AM, Andrew Massengale > wrote: Hello, The BioPortal API is not working for us. It is rejecting our API keys; however, we have not changed our API keys. In fact, the entire website appears to be down. https://bioportal.bioontology.org/ Thanks, 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 Fri Nov 23 09:24:42 2018 From: amassengale at rsna.org (Andrew Massengale) Date: Fri, 23 Nov 2018 17:24:42 +0000 Subject: [bioontology-support] BioPortal API not working In-Reply-To: <4A86CD55-4AD1-4219-A976-65ADC156EDCC@stanford.edu> References: <4A86CD55-4AD1-4219-A976-65ADC156EDCC@stanford.edu> Message-ID: <7672A07C-7DC0-4800-B253-8F41313FF5DE@hq.rsna.org> Hi Michael, Services appear to be working for us again. Thank you for the quick response! Andrew M From: Michael Dorf Date: Friday, November 23, 2018 at 11:22 AM To: Andrew Massengale Cc: "support at bioontology.org" , Derrick Lottich Subject: Re: [bioontology-support] BioPortal API not working Hi Andrew, Apologies for the interruption. We?ve had an unscheduled server downtime this morning. At this point, all access has been restored. Please let us know if you continue experiencing issues with your API keys. Thanks, Michael On Nov 23, 2018, at 8:30 AM, Andrew Massengale > wrote: Hello, The BioPortal API is not working for us. It is rejecting our API keys; however, we have not changed our API keys. In fact, the entire website appears to be down. https://bioportal.bioontology.org/ Thanks, 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 alquaddoomi at nexus.ethz.ch Fri Nov 23 06:39:29 2018 From: alquaddoomi at nexus.ethz.ch (Al-Quaddoomi Faisal Sabah) Date: Fri, 23 Nov 2018 14:39:29 +0000 Subject: [bioontology-support] bioportal.bioontology.org looks like it's down Message-ID: <9C7BC8A0-AA76-4A6E-85E8-F90090D47083@nexus.ethz.ch> Hello, I wasn?t sure what the proper channel was to report this, but as of around 2:30pm CET it appears that https://bioportal.bioontology.org/account is throwing a 500 server error. I encountered it while following the advice from a 401 error I got while querying http://data.bioontology.org/search?q=splice_region_variant&apikey=7951121e-3c26-4db1-9f82-476d928dfbc2. (I thought my API was valid ? it was working for previous requests ? but perhaps not anymore? In any case, I can?t get to the account page to check.) On a mildly related note, is there someplace where I can get a dump of the API?s dataset so that I don?t have to query your server so much? I?m writing a variant aggregation pipeline, and during its development I?ve been running the pipeline pretty frequently. I?m hoping this isn?t putting any undue strain on your server(s), and I?d like to reduce my contribution to it if possible. Thanks, Faisal Alquaddoomi Software Developer ETH Z?rich, NEXUS, Switzerland -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri Nov 23 09:53:43 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 23 Nov 2018 17:53:43 +0000 Subject: [bioontology-support] bioportal.bioontology.org looks like it's down In-Reply-To: <9C7BC8A0-AA76-4A6E-85E8-F90090D47083@nexus.ethz.ch> References: <9C7BC8A0-AA76-4A6E-85E8-F90090D47083@nexus.ethz.ch> Message-ID: <5992759C-0EF0-4CA9-92E1-7791707CFAA8@stanford.edu> Thank you Faisal for this report. We had a system outage this morning that we just now fixed. (It's a holiday weekend here, so service may be a little slow. :->) Everything should be working now. Regarding your question, thank you for thinking of our system strain! We have noticed an additional load recently, but searching for a single item (as this query was) should not cause any problem. If you are repeatedly using the Annotator with large bodies of text, using the Recommender, downloading large ontologies via API by walking their pages, or searching within large branches, we request you self-monitor the responses (in addition to our internal 15 messages per second throttle) to avoid creating more work than the system can handle. We encourage anyone in these situations to avoid parallelizing their requests, instead waiting for one to complete before issuing the next. (Considering that a number of other people may also be making expensive requests at the same time.) We also invite people who are going to be using BioPortal extensively to install their own BioPortal Virtual Appliance [1]. Specifically to your question, I am not sure exactly what you mean by 'get a dump of the API's dataset'. There are multiple datasets served by BioPortal's API and they are all large (the ontologies have 9 million terms at this point) or very large (there are a whole lot of mappings). If you still want to pursue this, contact us with the specifics of your API calls so we can understand what you would need?while we don't have a bundle that we ship maybe we can recommend a good alternative. Hope this helps, and again appreciate your reaching out. John [1] https://www.bioontology.org/wiki/Category:NCBO_Virtual_Appliance On Nov 23, 2018, at 6:39 AM, Al-Quaddoomi Faisal Sabah > wrote: Hello, I wasn?t sure what the proper channel was to report this, but as of around 2:30pm CET it appears that https://bioportal.bioontology.org/account is throwing a 500 server error. I encountered it while following the advice from a 401 error I got while querying http://data.bioontology.org/search?q=splice_region_variant&apikey=x. (I thought my API was valid ? it was working for previous requests ? but perhaps not anymore? In any case, I can?t get to the account page to check.) On a mildly related note, is there someplace where I can get a dump of the API?s dataset so that I don?t have to query your server so much? I?m writing a variant aggregation pipeline, and during its development I?ve been running the pipeline pretty frequently. I?m hoping this isn?t putting any undue strain on your server(s), and I?d like to reduce my contribution to it if possible. Thanks, Faisal Alquaddoomi Software Developer ETH Z?rich, NEXUS, Switzerland _______________________________________________ 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 Sun Nov 25 08:43:04 2018 From: support at bioontology.org (support at bioontology.org) Date: Sun, 25 Nov 2018 08:43:04 -0800 Subject: [bioontology-support] [BioPortal] Feedback from Kristina Doing-Harris Message-ID: <5bfad1184a650_38092adc0853f660948f3@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Sun Nov 25 09:31:33 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Sun, 25 Nov 2018 17:31:33 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Kristina Doing-Harris In-Reply-To: <5bfad1184a650_38092adc0853f660948f3@ncbo-prd-app-08.stanford.edu.mail> References: <5bfad1184a650_38092adc0853f660948f3@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <28F847D6-0404-4A12-A6C8-A9BD2742C6DF@stanford.edu> Hello Kristina, Sorry for the trouble, I'm not sure exactly what caused the error but hopefully we can help you get it sorted out. I see an account name of KmDoing-Harris (note the additional hyphen) has been created. Please try logging in with that account name and your password, and see if that works for you. If not, or if you want to recreate the account without the hyphen, I expect you will either need to use a different email address (for uniqueness), or we will need to delete your first attempt. In the latter case, we may have to wait until tomorrow?I am about to lose access while travelling, and our more expert operations folks will be back in the office tomorrow. Please let us know whether the account name above seems to work for you. John On Nov 25, 2018, at 8:43 AM, support at bioontology.org wrote: Name: Kristina Doing-Harris Email: kdoingharris at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Flost_pass Feedback: Hi. I tried to make an account with account name KmDoingHarris. It said there was an error creating the account and when I try to login with the password I set, it says my username and password are not correct. Now it will not let me make the account, but it will also not let me reset the password. Can you please let me know what is happening? Thanks, Kristina _______________________________________________ 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 Nov 29 08:34:52 2018 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 29 Nov 2018 16:34:52 +0000 Subject: [bioontology-support] Fwd: Problem retrieving classes - Help In-Reply-To: References: <44872915-2D68-4032-94E6-9A4DCF16692C@stanford.edu> , Message-ID: Forwarding to support list? ________________________________ From: Mohamed Keshk Sent: Thursday, November 29, 2018 07:48 To: John Graybeal Subject: Re: [bioontology-support] Problem retrieving classes - Help Hi John, I'm experiencing an issue of not updating the ontology after uploading a new one. The browser still shows the old ontology hierarchy instead. Is there anything I'm missing to solve this problem? Here's my URL: http://bioportal.bioontology.org/ontologies/PCL Thanks, Mohamed -------------- next part -------------- An HTML attachment was scrubbed... URL: