From support at bioontology.org Fri May 1 06:25:55 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 01 May 2020 06:25:55 -0700 Subject: [bioontology-support] [BioPortal] Feedback from jlevens Message-ID: <5eac2363b132d_5497228cccc549f1@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri May 1 11:12:59 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 1 May 2020 18:12:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from jlevens In-Reply-To: <5eac2363b132d_5497228cccc549f1@ncbo-prd-app-09.stanford.edu.mail> References: <5eac2363b132d_5497228cccc549f1@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Justin, We import MedDRA into BioPortal from the National Library of Medicine?s UMLS Metathesaurus. They do releases twice per year in May and November. I looked at their forthcoming releases page, and it does mention MedDRA as one of the updated sources in the 2020AA distribution: https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/forthcoming_releases.html ? though, it doesn?t specify the exact version. I assume it would be the latest V23.0, since the last distribution (2019AB) contained 22.0: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/metadata.html Once they make the 2020AA distribution available, it generally takes us 2 or 3 days to do the full import / upload / processing of contained ontologies. The 2019AA release was made available May 6th of last year, so I would expect they will be doing the 2020AA release shortly. You could always contact their customer support team if you need an exact date: https://www.nlm.nih.gov/research/umls/support.html Kind regards, Jennifer From: bioontology-support on behalf of "support at bioontology.org" Date: Friday, May 1, 2020 at 9:51 AM To: "support at bioontology.org" , "justin.levens at uky.edu" Subject: [bioontology-support] [BioPortal] Feedback from jlevens Name: jlevens Email: justin.levens at uky.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA Feedback: Hello, who is responsible for updating the MedDRA ontology? The newest version of the MedDRA ontology was release very recently (V23.0) and I was wondering how to get this version implemented into BioPortal. Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri May 1 11:19:27 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 1 May 2020 18:19:27 +0000 Subject: [bioontology-support] [BioPortal] Feedback from jlevens In-Reply-To: <5eac2363b132d_5497228cccc549f1@ncbo-prd-app-09.stanford.edu.mail> References: <5eac2363b132d_5497228cccc549f1@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Justin, Thanks for this question. I have the action item (from a previous request) to contact the appropriate people to see if we can get the most current version. Usually we get it through UMLS, which will take a while longer. I'll announce what I learn via the list (and copying you). John On May 1, 2020, at 6:25 AM, support at bioontology.org wrote: Name: jlevens Email: justin.levens at uky.edu Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA Feedback: Hello, who is responsible for updating the MedDRA ontology? The newest version of the MedDRA ontology was release very recently (V23.0) and I was wondering how to get this version implemented into BioPortal. Thanks. _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Fri May 1 11:40:01 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 1 May 2020 18:40:01 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: References: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu> <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Message-ID: Hi Ching-Hua, No ? you don?t need to be concerned with the ERROR_DIFF status for MESH. This status is assigned because the system ran into some kind of problem while trying to generate a diff file between submissions. If there is only one submission of MESH in your appliance, there was no previous submission for comparison. With regard to ICD10 ? this is an ontology that we import into BioPortal from the UMLS Metathesaurus. Many of these UMLS ontologies are special cases, in the sense that we don?t support direct upload for two reasons: 1). Format ? The UMLS distribution of ontology content is in the form of a relational database. BioPortal is backed by an RDF store, so we have to do a programmatic conversion of UMLS format to RDF that we then are able to load into the RDF store. This is in contrast to OBO, OWL, and SKOS files that end users can simply upload to BioPortal and/or virtual appliance instances without any kind of intermediate process. 2). Licensing ? Some of the UMLS ontologies have licensing restrictions that prevent us from being able to distribute the RDF files that we generate. ICD10 is one of these ontologies, and likely the reason that the bioportal_ontologies_import script failed to create an upload. All of that said, there are a number of end users that have duplicated our UMLS import process in their local virtual appliance instances and have successfully uploaded UMLS ontologies. We offer documentation for how to go about doing this on our wiki: https://www.bioontology.org/wiki/Importing_UMLS_To_Virtual_Appliance Hope this information helps. Kind regards, Jennifer From: Ching-Hua Chen Date: Thursday, April 30, 2020 at 7:24 PM To: Jennifer Leigh Vendetti Cc: "bioontology-support at lists.stanford.edu" Subject: RE: [bioontology-support] Annotation GET results Hi Jennifer, I tried manually parsing the MESH ontology since it had successfully UPLOADED and this is now it's submissionStatus: 'submissionStatus': ['RDF', 'OBSOLETE', 'INDEXED_PROPERTIES', 'METRICS', 'RDF_LABELS', 'UPLOADED', 'ERROR_DIFF', 'ANNOTATOR', 'INDEXED'], It now seems to be generating annotations! However, do I need to be concerned about the "ERROR_DIFF" status? I am still not sure what to do with ICD10 since it does not seem to have been uploaded at all. Thanks, Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson ----- Original message ----- From: Ching-Hua Chen/Watson/IBM To: vendetti at stanford.edu Cc: bioontology-support at lists.stanford.edu Subject: Re: [EXTERNAL] Re: [bioontology-support] Annotation GET results Date: Thu, Apr 30, 2020 7:39 PM Thanks, Jennifer! So it turns out the the ontologies I am having trouble with do not show the status that you showed in your example, but they also do not show ERROR statuses. For one of the ontologies that is not working for me (MESH), the submissionStatus ONLY contains "UPLOADED". For another of the ontologies that is not working for me (ICD10), the entire json result returned from the API call is empty. I tried re-running the ruby script bioportal_ontologies_import for both and now noticed that in the case of MESH I see: # # The parsing log says: I, [2020-04-30T19:26:57.372106 #2135] INFO -- : ["Starting to process http://data.bioontology.org/ontologies/MESH/submissions/2"] D, [2020-04-30T19:26:57.372283 #2135] DEBUG -- : ["Pull location found, but no file in the upload file path. Retrying download."] D, [2020-04-30T19:34:31.451585 #2135] DEBUG -- : ["Download complete"] I, [2020-04-30T19:34:31.499970 #2135] INFO -- : ["Starting to process MESH/submissions/2"] I, [2020-04-30T19:34:31.623563 #2135] INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"] And in the case of ICD10 I see: # # There isn't even a repository created on the appliance, so I am surprised that when I run list_ontologies I see the ICD10 ontology listed. Any advice on how to fix the import process, which seems to have failed? Do I have to contact the ontology owners? Thank you! Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson ----- Original message ----- From: Jennifer Leigh Vendetti To: Ching-Hua Chen Cc: "bioontology-support at lists.stanford.edu" Subject: [EXTERNAL] Re: [bioontology-support] Annotation GET results Date: Thu, Apr 30, 2020 12:03 PM Hi Ching-Hua, You could use an API call like the following to examine the latest submission of a given ontology: http://data.bioontology.org/ontologies/ICD10/latest_submission?include=all In the JSON results, there should be a ?submissionStatus? name/value pair with an array of statuses, e.g.: [cid:image001.png at 01D61FAD.3E5501D0] If any of the processing steps failed, there would be status values with an ?ERROR? string, e.g.: [cid:image002.png at 01D61FAD.3E5501D0] Alternatively, you could issue API calls to get the root classes of an ontology, or all of the classes for an ontology. If the ontology failed to process correctly, you would likely see failures or empty sets when trying to access the ontology content: http://data.bioontology.org/ontologies/ICD10/classes/roots http://data.bioontology.org/ontologies/ICD10/classes Finally, you could look at the log file for a given ontology to see if there were any error during processing. Information about log file location is here: https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#Is_there_a_log_file_for_parsing.3F We also have some public documentation of the REST API that you may find helpful: http://data.bioontology.org/documentation Kind regards, Jennifer On Apr 30, 2020, at 7:59 AM, Ching-Hua Chen > wrote: Thanks, Jennifer! My apologies, the text I was actually annotating is: text_to_annotate = "Relationship among genotype, biochemical phenotype, and cognitive performance in females with phenylalanine hydroxylase deficiency: report from the Maternal Phenylketonuria Collaborative Study. OBJECTIVE To examine the relationship of phenylalanine hydroxylase ( PAH ) genotypes to biochemical phenotype and cognitive development in maternal phenylketonuria ( PKU ) . METHODOLOGY PAH gene mutations were examined in 222 hyperphenylalaninemic females enrolled in the Maternal PKU Collaborative Study ( MPKUCS ) . A total of 84 different mutations were detected , and complete genotype was obtained in 199 individuals . Based on previous knowledge about mutation-phenotype associations , 78 of the mutations could be assigned to one of four classes of severity ( severe PKU , moderate PKU , mild PKU , and mild hyperphenylalaninemia [ MHP ] ) . Then , 189 MPKUCS subjects were grouped according to the various combinations of mutation classifications . The sample sizes were large enough for statistical testing in four groups with at least one mutation that completely abolishes enzyme activity . These patients are considered functionally hemizygous . RESULTS The biochemical phenotype predicted from the genotype in functionally hemizygous patients was related significantly to the assigned phenylalanine level . Cognitive performance ( IQ ) was also significantly related to genotype . The IQ of PAH-deficient mothers with a severe PKU mutation in combination with a MHP mutation or a mild PKU mutation was 99 and 96 , respectively , whereas the IQ of PKU mothers with two severe PKU mutations or with one severe and one moderate PKU mutation was 83 and 84 , respectively . Of the patients with PKU , 92 % had been treated during childhood . Those who were untreated or treated late had lower than average IQ scores for their group of mutation combinations . Females with moderate or mild PKU who were treated early and treated for > 6 years showed IQ scores 10 points above average for their group . CONCLUSIONS The reproductive outcome in maternal phenylketonuria is dependent on prenatal metabolic control and postnatal environmental circumstances . Both factors depend on the intellectual resources of the mother with PKU . The significant relationship among genotype , biochemical phenotype , and cognitive performance observed in the present study is of importance for the development of an optimal strategy for future treatment of females with PKU who plan pregnancy" Is there a way to check the status of submitted ontologies without using the UI? (My appliance is not very responsive when I try to access it using the UI. However, when I make API calls it seems to be quite responsive. Maybe the reason I am getting empty results for some ontologies is that the request is timing out....) Should I be examining the ontology submission status? I'm not very familiar with the API yet, if you are able to provide an example API call that can return the status would be much appreciated! Best, Ching-Hua Chen Computational Health Behavior & Decision Science IBM, T.J. Watson Research Center 1101 Kitchawan Road, Yorktown Heights, NY 10598 chinghua at us.ibm.com (914) 945-2061 (o); (845) 519-7582 (m) "Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson ----- Original message ----- From: Jennifer Leigh Vendetti > To: Ching-Hua Chen > Cc: "bioontology-support at lists.stanford.edu" > Subject: [EXTERNAL] Re: [bioontology-support] Annotation GET results Date: Wed, Apr 29, 2020 7:25 PM Hello Ching-Hua, On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen > wrote: I am running the sample code "annotate_txt.py" and experiencing results that I can't understand. I modified the API call to the following, in order to specifically use the ICD10 ontology: get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate)) When I reference the public bioportal, I get non-zero results for the text_to_annotate provided. I?m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used: http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye. ? and I see an empty result set: However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance. This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening? If you?re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include ?Parsed, Indexed, Metrics, Annotator?: Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 111524 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 110174 bytes Desc: image002.png URL: From chinghua at us.ibm.com Fri May 1 14:21:08 2020 From: chinghua at us.ibm.com (Ching-Hua Chen) Date: Fri, 1 May 2020 21:21:08 +0000 Subject: [bioontology-support] Annotation GET results In-Reply-To: References: , <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu> <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu> Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.image001.png at 01D61FAD.3E5501D0.png Type: image/png Size: 111524 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.image002.png at 01D61FAD.3E5501D0.png Type: image/png Size: 110174 bytes Desc: not available URL: From jpt55 at med.miami.edu Mon May 4 10:39:25 2020 From: jpt55 at med.miami.edu (John Turner) Date: Mon, 4 May 2020 13:39:25 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: Message-ID: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. > String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; > HttpHeaders headers = new HttpHeaders(); > headers.set("Accept", "text/html,application/json"); > headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); > //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); > HttpEntity entity = new HttpEntity(headers); > HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); > ObjectMapper mapper = new ObjectMapper(); > JsonNode root = mapper.readTree(response.getBody()); > String label = root.get("prefLabel").asText(); Thanks, John Paul Turner -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon May 4 12:03:55 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 4 May 2020 19:03:55 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: Message-ID: Hi John, I am not sure that I can tell exactly what?s wrong without actually running this code. I?ve tried running it from within the existing Ontolobridge project, but I think my code is too old - for some reason, headers.set method wasn?t resolving. We have some Java sample code that you can adopt to your app: https://github.com/ncbo/ncbo_rest_sample_code/tree/master/java/src One potential issue could be that you aren?t passing the API key via the header. Here is the syntax for that: https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/ClassesSearch.java#L66 I?m not sure exactly how this translates to the Spring specific libraries, but the generic getConnection code should look like this: private HttpURLConnection getConnection(String urlToGet) throws IOException { URL url; HttpURLConnection conn; url = new URL(urlToGet); conn = (HttpURLConnection) url.openConnection(); conn.setRequestMethod("GET"); conn.setRequestProperty("Authorization", "apikey token=? + API_KEY); conn.setRequestProperty("Accept", "application/json"); return conn; } Hope this helps. Misha On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 May 4 13:19:37 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 4 May 2020 20:19:37 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: Message-ID: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Hi John T, 400 error is not a permission error, but a "bad request" error. This suggests the code that is building your request (from all those component parts) is formatting something incorrect. Can you inspect the network traffic on your side to see exactly what is being sent out? Also, since your API key got published to our support list, may we request you change the key? You can do this by accessing your profile settings in BioPortal. John G On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 4 15:27:57 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 4 May 2020 22:27:57 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Message-ID: oops, my bad (was imagining CEDAR in my mind). We will contact you offline to coordinate API key reset. john On May 4, 2020, at 1:57 PM, John Turner > wrote: Also sorry if I am blind but I don't see a button to change my key on my profile settings page. On 5/4/2020 4:19 PM, John Graybeal wrote: Hi John T, 400 error is not a permission error, but a "bad request" error. This suggests the code that is building your request (from all those component parts) is formatting something incorrect. Can you inspect the network traffic on your side to see exactly what is being sent out? Also, since your API key got published to our support list, may we request you change the key? You can do this by accessing your profile settings in BioPortal. John G On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 4 15:28:30 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 4 May 2020 22:28:30 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Message-ID: oops, my bad (was imagining CEDAR in my mind). We will contact you offline to coordinate API key reset. john On May 4, 2020, at 1:57 PM, John Turner > wrote: Also sorry if I am blind but I don't see a button to change my key on my profile settings page. On 5/4/2020 4:19 PM, John Graybeal wrote: Hi John T, 400 error is not a permission error, but a "bad request" error. This suggests the code that is building your request (from all those component parts) is formatting something incorrect. Can you inspect the network traffic on your side to see exactly what is being sent out? Also, since your API key got published to our support list, may we request you change the key? You can do this by accessing your profile settings in BioPortal. John G On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpt55 at med.miami.edu Mon May 4 13:46:53 2020 From: jpt55 at med.miami.edu (John Turner) Date: Mon, 4 May 2020 16:46:53 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Message-ID: Oops, yes I will generate a new API key and censor it in future here. Below is headers I see on a net capture to a local server URL: http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 > Connection: keep-alive
> Host: 127.0.0.1
> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu
> Authorization: apikey token=
> Accept: text/html,application/json
On 5/4/2020 4:19 PM, John Graybeal wrote: > Hi John T, > > 400 error is not a permission error, but a "bad request" error. This > suggests the code that is building your request (from all those > component parts) is formatting something incorrect. Can you inspect > the network traffic on your side to see exactly what is being sent out? > > Also, since your API key got published to our support list, may we > request you change the key? ?You can do this by accessing your profile > settings in BioPortal. > > John G > >> On May 4, 2020, at 10:39 AM, John Turner > > wrote: >> >> >> I am trying to figure out why I am getting 400 errors whenever I make >> requests to the API. I have taken the url used in the below code and >> it works perfectly in my browser. >>> String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; >>> HttpHeaders headers = new HttpHeaders(); >>> headers.set("Accept", "text/html,application/json"); >>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); >>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); >>> HttpEntity entity = new HttpEntity(headers); >>> HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); >>> ObjectMapper mapper = new ObjectMapper(); >>> JsonNode root = mapper.readTree(response.getBody()); >>> String label = root.get("prefLabel").asText(); >> Thanks, >> John Paul Turner >> _______________________________________________ >> 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 ?| ORCID ?0000-0001-6875-5360 > > > -- John Paul Turner PhD Candidate Stephan Schurer Lab Molecular and Cellular Pharmacology University of Miami Miller School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpt55 at med.miami.edu Mon May 4 13:57:03 2020 From: jpt55 at med.miami.edu (John Turner) Date: Mon, 4 May 2020 16:57:03 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Message-ID: Also sorry if I am blind but I don't see a button to change my key on my profile settings page. On 5/4/2020 4:19 PM, John Graybeal wrote: > Hi John T, > > 400 error is not a permission error, but a "bad request" error. This > suggests the code that is building your request (from all those > component parts) is formatting something incorrect. Can you inspect > the network traffic on your side to see exactly what is being sent out? > > Also, since your API key got published to our support list, may we > request you change the key? ?You can do this by accessing your profile > settings in BioPortal. > > John G > >> On May 4, 2020, at 10:39 AM, John Turner > > wrote: >> >> >> I am trying to figure out why I am getting 400 errors whenever I make >> requests to the API. I have taken the url used in the below code and >> it works perfectly in my browser. >>> String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; >>> HttpHeaders headers = new HttpHeaders(); >>> headers.set("Accept", "text/html,application/json"); >>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); >>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); >>> HttpEntity entity = new HttpEntity(headers); >>> HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); >>> ObjectMapper mapper = new ObjectMapper(); >>> JsonNode root = mapper.readTree(response.getBody()); >>> String label = root.get("prefLabel").asText(); >> Thanks, >> John Paul Turner >> _______________________________________________ >> 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 ?| ORCID ?0000-0001-6875-5360 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue May 5 13:15:36 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 5 May 2020 20:15:36 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> Message-ID: <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> Hi John, I am able to reproduce this on my end. I am still investigating the cause of the error, which is: Exception in thread "main" org.springframework.web.client.HttpClientErrorException$BadRequest: 400 Bad Request: [{"errors":["The input class id 'http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048' is not a valid IRI"],"status":400}] Thanks, Misha On May 4, 2020, at 1:46 PM, John Turner > wrote: Oops, yes I will generate a new API key and censor it in future here. Below is headers I see on a net capture to a local server URL: http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 Connection: keep-alive
Host: 127.0.0.1
User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu
Authorization: apikey token=
Accept: text/html,application/json
On 5/4/2020 4:19 PM, John Graybeal wrote: Hi John T, 400 error is not a permission error, but a "bad request" error. This suggests the code that is building your request (from all those component parts) is formatting something incorrect. Can you inspect the network traffic on your side to see exactly what is being sent out? Also, since your API key got published to our support list, may we request you change the key? You can do this by accessing your profile settings in BioPortal. John G On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -- John Paul Turner PhD Candidate Stephan Schurer Lab Molecular and Cellular Pharmacology University of Miami Miller School of Medicine _______________________________________________ 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 jpt55 at med.miami.edu Tue May 5 16:49:08 2020 From: jpt55 at med.miami.edu (John Turner) Date: Tue, 5 May 2020 19:49:08 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> Message-ID: Thank you Misha, I have no had time to test the api key yet but will get back to you tomorrow John Paul Turner On 5/5/2020 4:15 PM, Michael Dorf wrote: > Hi John, > > I am able to reproduce this on my end. I am still investigating the > cause of the error, which is: > > Exception in thread "main" > org.springframework.web.client.HttpClientErrorException$BadRequest: > 400 Bad Request: [{"errors":["The input class id > 'http%3A%2F%2Fwww.bioassayontology.org > %2Fbao%23BAO_0003048' > is not a valid IRI"],"status":400}] > > Thanks, > > Misha > > > >> On May 4, 2020, at 1:46 PM, John Turner > > wrote: >> >> Oops, yes I will generate a new API key and censor it in future here. >> Below is headers I see on a net capture to a local server >> >> URL: >> http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 >> >>> Connection: keep-alive
>>> Host: 127.0.0.1
>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu
>>> Authorization: apikey token=
>>> Accept: text/html,application/json
>> >> >> >> On 5/4/2020 4:19 PM, John Graybeal wrote: >>> Hi John T, >>> >>> 400 error is not a permission error, but a "bad request" error. This >>> suggests the code that is building your request (from all those >>> component parts) is formatting something incorrect. Can you inspect >>> the network traffic on your side to see exactly what is being sent out? >>> >>> Also, since your API key got published to our support list, may we >>> request you change the key? ?You can do this by accessing your >>> profile settings in BioPortal. >>> >>> John G >>> >>>> On May 4, 2020, at 10:39 AM, John Turner >>> > wrote: >>>> >>>> >>>> I am trying to figure out why I am getting 400 errors whenever I >>>> make requests to the API. I have taken the url used in the below >>>> code and it works perfectly in my browser. >>>>> String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; >>>>> HttpHeaders headers = new HttpHeaders(); >>>>> headers.set("Accept", "text/html,application/json"); >>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); >>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); >>>>> HttpEntity entity = new HttpEntity(headers); >>>>> HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); >>>>> ObjectMapper mapper = new ObjectMapper(); >>>>> JsonNode root = mapper.readTree(response.getBody()); >>>>> String label = root.get("prefLabel").asText(); >>>> Thanks, >>>> John Paul Turner >>>> _______________________________________________ >>>> 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 ?| ORCID ?0000-0001-6875-5360 >>> >>> >>> >> -- >> >> >> John Paul Turner >> >> PhD Candidate >> >> Stephan Schurer Lab >> >> Molecular and Cellular Pharmacology >> >> University of Miami Miller School of Medicine >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue May 5 17:43:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Wed, 6 May 2020 00:43:59 +0000 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> Message-ID: Hi John, It took me a bit to set up a Spring based project, and run it (it?s been a while since I?ve done it), but I?ve finally managed to get your code to work. The gist is that Spring is a bit less forgiving to the URL-encoded strings than the Standard Java HttpURLConnection. For Spring RestTemplate to work with this API request (one that includes a URL-encoded fragment) you need to use their own UriComponentsBuilder to construct the URL before passing it on to RestTemplate.exchange, instead of a String based URL. Here is a working example: private static HttpEntity queryViaSpring(String baseURL, String classID) { HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); headers.set("Authorization", "apikey token=" + API_KEY); RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity("parameters", headers); UriComponentsBuilder builder = UriComponentsBuilder.fromHttpUrl(baseURL).path(classID); UriComponents components = builder.build(true); URI uri = components.toUri(); return restTemplate.exchange(uri, HttpMethod.GET, entity, String.class); } I?m also attaching the full Java class I wrote, which includes both Spring and non-Spring working examples. Hope this helps. Misha On May 5, 2020, at 4:49 PM, John Turner > wrote: Thank you Misha, I have no had time to test the api key yet but will get back to you tomorrow John Paul Turner On 5/5/2020 4:15 PM, Michael Dorf wrote: Hi John, I am able to reproduce this on my end. I am still investigating the cause of the error, which is: Exception in thread "main" org.springframework.web.client.HttpClientErrorException$BadRequest: 400 Bad Request: [{"errors":["The input class id 'http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048' is not a valid IRI"],"status":400}] Thanks, Misha On May 4, 2020, at 1:46 PM, John Turner > wrote: Oops, yes I will generate a new API key and censor it in future here. Below is headers I see on a net capture to a local server URL: http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 Connection: keep-alive
Host: 127.0.0.1
User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu
Authorization: apikey token=
Accept: text/html,application/json
On 5/4/2020 4:19 PM, John Graybeal wrote: Hi John T, 400 error is not a permission error, but a "bad request" error. This suggests the code that is building your request (from all those component parts) is formatting something incorrect. Can you inspect the network traffic on your side to see exactly what is being sent out? Also, since your API key got published to our support list, may we request you change the key? You can do this by accessing your profile settings in BioPortal. John G On May 4, 2020, at 10:39 AM, John Turner > wrote: I am trying to figure out why I am getting 400 errors whenever I make requests to the API. I have taken the url used in the below code and it works perfectly in my browser. String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b"; HttpHeaders headers = new HttpHeaders(); headers.set("Accept", "text/html,application/json"); headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu"); //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); HttpEntity entity = new HttpEntity(headers); HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); ObjectMapper mapper = new ObjectMapper(); JsonNode root = mapper.readTree(response.getBody()); String label = root.get("prefLabel").asText(); Thanks, John Paul Turner _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -- John Paul Turner PhD Candidate Stephan Schurer Lab Molecular and Cellular Pharmacology University of Miami Miller School of Medicine _______________________________________________ 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: NcboApiTest.java Type: application/octet-stream Size: 3615 bytes Desc: NcboApiTest.java URL: From jpt55 at med.miami.edu Tue May 5 17:47:22 2020 From: jpt55 at med.miami.edu (John Turner) Date: Tue, 5 May 2020 20:47:22 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> Message-ID: <239d1c1d-bdbe-c8dc-e831-34d809c55acd@med.miami.edu> Ok, thanks for this help. I will test this tomorrow. On 5/5/2020 8:43 PM, Michael Dorf wrote: > Hi John, > > It took me a bit to set up a Spring based project, and run it (it?s > been a while since I?ve done it), but I?ve finally managed to get your > code to work. The gist is that Spring is a bit less forgiving to the > URL-encoded strings than the Standard Java?HttpURLConnection. For > Spring RestTemplate to work with this API request (one that includes a > URL-encoded fragment) you need to use their own?UriComponentsBuilder > to construct the URL before passing it on to RestTemplate.exchange, > instead of a String based URL. > > Here is a working example: > > private static HttpEntity queryViaSpring(String baseURL, String classID) { > HttpHeaders headers =new HttpHeaders(); > headers.set("Accept","application/json"); > headers.set("User-Agent","Ontolobridge; Contact jpt55 at med.miami.edu "); > headers.set("Authorization","apikey token=" +API_KEY); > RestTemplate restTemplate =new RestTemplate(); > HttpEntity entity =new HttpEntity("parameters", headers); > UriComponentsBuilder builder = UriComponentsBuilder.fromHttpUrl(baseURL).path(classID); > UriComponents components = builder.build(true); > URI uri = components.toUri(); > return restTemplate.exchange(uri, HttpMethod.GET, entity, String.class); > } > > I?m also attaching the full Java class I wrote, which includes both > Spring and non-Spring working examples. > > Hope this helps. > > Misha > > > > >> On May 5, 2020, at 4:49 PM, John Turner > > wrote: >> >> Thank you Misha, >> >> I have no had time to test the api key yet but will get back to you >> tomorrow >> >> John Paul Turner >> >> On 5/5/2020 4:15 PM, Michael Dorf wrote: >>> Hi John, >>> >>> I am able to reproduce this on my end. I am still investigating the >>> cause of the error, which is: >>> >>> Exception in thread "main" >>> org.springframework.web.client.HttpClientErrorException$BadRequest: >>> 400 Bad Request: [{"errors":["The input class id >>> 'http%3A%2F%2Fwww.bioassayontology.org >>> %2Fbao%23BAO_0003048' >>> is not a valid IRI"],"status":400}] >>> >>> Thanks, >>> >>> Misha >>> >>> >>> >>>> On May 4, 2020, at 1:46 PM, John Turner >>> > wrote: >>>> >>>> Oops, yes I will generate a new API key and censor it in future >>>> here. Below is headers I see on a net capture to a local server >>>> >>>> URL: >>>> http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 >>>> >>>>> Connection: keep-alive
>>>>> Host: 127.0.0.1
>>>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu >>>>>
>>>>> Authorization: apikey token=
>>>>> Accept: text/html,application/json
>>>> >>>> >>>> >>>> On 5/4/2020 4:19 PM, John Graybeal wrote: >>>>> Hi John T, >>>>> >>>>> 400 error is not a permission error, but a "bad request" error. >>>>> This suggests the code that is building your request (from all >>>>> those component parts) is formatting something incorrect. Can you >>>>> inspect the network traffic on your side to see exactly what is >>>>> being sent out? >>>>> >>>>> Also, since your API key got published to our support list, may we >>>>> request you change the key? ?You can do this by accessing your >>>>> profile settings in BioPortal. >>>>> >>>>> John G >>>>> >>>>>> On May 4, 2020, at 10:39 AM, John Turner >>>>> > wrote: >>>>>> >>>>>> >>>>>> I am trying to figure out why I am getting 400 errors whenever I >>>>>> make requests to the API. I have taken the url used in the below >>>>>> code and it works perfectly in my browser. >>>>>>> String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; >>>>>>> HttpHeaders headers = new HttpHeaders(); >>>>>>> headers.set("Accept", "text/html,application/json"); >>>>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); >>>>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); >>>>>>> HttpEntity entity = new HttpEntity(headers); >>>>>>> HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); >>>>>>> ObjectMapper mapper = new ObjectMapper(); >>>>>>> JsonNode root = mapper.readTree(response.getBody()); >>>>>>> String label = root.get("prefLabel").asText(); >>>>>> Thanks, >>>>>> John Paul Turner >>>>>> _______________________________________________ >>>>>> 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 ?| ORCID ?0000-0001-6875-5360 >>>>> >>>>> >>>>> >>>> -- >>>> >>>> >>>> John Paul Turner >>>> >>>> PhD Candidate >>>> >>>> Stephan Schurer Lab >>>> >>>> Molecular and Cellular Pharmacology >>>> >>>> University of Miami Miller School of Medicine >>>> >>>> >>>> _______________________________________________ >>>> 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 jpt55 at med.miami.edu Wed May 6 05:40:48 2020 From: jpt55 at med.miami.edu (John Turner) Date: Wed, 6 May 2020 08:40:48 -0400 Subject: [bioontology-support] 400 bad requests using Java rest requests. In-Reply-To: References: <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu> <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu> Message-ID: <0c14ec07-4247-1540-0d63-720f20229171@med.miami.edu> This appears to be working, thank you John Paul Turner On 5/5/2020 8:43 PM, Michael Dorf wrote: > Hi John, > > It took me a bit to set up a Spring based project, and run it (it?s > been a while since I?ve done it), but I?ve finally managed to get your > code to work. The gist is that Spring is a bit less forgiving to the > URL-encoded strings than the Standard Java?HttpURLConnection. For > Spring RestTemplate to work with this API request (one that includes a > URL-encoded fragment) you need to use their own?UriComponentsBuilder > to construct the URL before passing it on to RestTemplate.exchange, > instead of a String based URL. > > Here is a working example: > > private static HttpEntity queryViaSpring(String baseURL, String classID) { > HttpHeaders headers =new HttpHeaders(); > headers.set("Accept","application/json"); > headers.set("User-Agent","Ontolobridge; Contact jpt55 at med.miami.edu "); > headers.set("Authorization","apikey token=" +API_KEY); > RestTemplate restTemplate =new RestTemplate(); > HttpEntity entity =new HttpEntity("parameters", headers); > UriComponentsBuilder builder = UriComponentsBuilder.fromHttpUrl(baseURL).path(classID); > UriComponents components = builder.build(true); > URI uri = components.toUri(); > return restTemplate.exchange(uri, HttpMethod.GET, entity, String.class); > } > > I?m also attaching the full Java class I wrote, which includes both > Spring and non-Spring working examples. > > Hope this helps. > > Misha > > > > >> On May 5, 2020, at 4:49 PM, John Turner > > wrote: >> >> Thank you Misha, >> >> I have no had time to test the api key yet but will get back to you >> tomorrow >> >> John Paul Turner >> >> On 5/5/2020 4:15 PM, Michael Dorf wrote: >>> Hi John, >>> >>> I am able to reproduce this on my end. I am still investigating the >>> cause of the error, which is: >>> >>> Exception in thread "main" >>> org.springframework.web.client.HttpClientErrorException$BadRequest: >>> 400 Bad Request: [{"errors":["The input class id >>> 'http%3A%2F%2Fwww.bioassayontology.org >>> %2Fbao%23BAO_0003048' >>> is not a valid IRI"],"status":400}] >>> >>> Thanks, >>> >>> Misha >>> >>> >>> >>>> On May 4, 2020, at 1:46 PM, John Turner >>> > wrote: >>>> >>>> Oops, yes I will generate a new API key and censor it in future >>>> here. Below is headers I see on a net capture to a local server >>>> >>>> URL: >>>> http::/127.0.0.1/test/BAO/classes/http%3A%2F%2Fwww_bioassayontology_org%2Fbao%23BAO_0003048 >>>> >>>>> Connection: keep-alive
>>>>> Host: 127.0.0.1
>>>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu >>>>>
>>>>> Authorization: apikey token=
>>>>> Accept: text/html,application/json
>>>> >>>> >>>> >>>> On 5/4/2020 4:19 PM, John Graybeal wrote: >>>>> Hi John T, >>>>> >>>>> 400 error is not a permission error, but a "bad request" error. >>>>> This suggests the code that is building your request (from all >>>>> those component parts) is formatting something incorrect. Can you >>>>> inspect the network traffic on your side to see exactly what is >>>>> being sent out? >>>>> >>>>> Also, since your API key got published to our support list, may we >>>>> request you change the key? ?You can do this by accessing your >>>>> profile settings in BioPortal. >>>>> >>>>> John G >>>>> >>>>>> On May 4, 2020, at 10:39 AM, John Turner >>>>> > wrote: >>>>>> >>>>>> >>>>>> I am trying to figure out why I am getting 400 errors whenever I >>>>>> make requests to the API. I have taken the url used in the below >>>>>> code and it works perfectly in my browser. >>>>>>> String bioportalAPI = "http://data.bioontology.org/ontologies/BAO/classes/http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0003048?apikey=3f58b9d8-8896-4db0-8bc4-815c42d3df5b "; >>>>>>> HttpHeaders headers = new HttpHeaders(); >>>>>>> headers.set("Accept", "text/html,application/json"); >>>>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu "); >>>>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate(); >>>>>>> HttpEntity entity = new HttpEntity(headers); >>>>>>> HttpEntity response = restTemplate.exchange(bioportalAPI, HttpMethod.GET, entity, String.class); >>>>>>> ObjectMapper mapper = new ObjectMapper(); >>>>>>> JsonNode root = mapper.readTree(response.getBody()); >>>>>>> String label = root.get("prefLabel").asText(); >>>>>> Thanks, >>>>>> John Paul Turner >>>>>> _______________________________________________ >>>>>> 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 ?| ORCID ?0000-0001-6875-5360 >>>>> >>>>> >>>>> >>>> -- >>>> >>>> >>>> John Paul Turner >>>> >>>> PhD Candidate >>>> >>>> Stephan Schurer Lab >>>> >>>> Molecular and Cellular Pharmacology >>>> >>>> University of Miami Miller School of Medicine >>>> >>>> >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>>> >>> > -- John Paul Turner PhD Candidate Stephan Schurer Lab Molecular and Cellular Pharmacology University of Miami Miller School of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From rakesh at pieriandx.com Thu May 7 08:02:42 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Thu, 7 May 2020 10:02:42 -0500 Subject: [bioontology-support] Issue Message-ID: Hello, We've installed a local version of BioPortal v2.5 and have successfully loaded a few ontologies. We're however having trouble with the property field for the NCI Thesaurus wherein we'd like the Synonyms and Definition loaded correctly. I have tried the following as the property to map these to but the parser throws an error: Thesaurus:P90 Thesaurus:P97 I have also tried the full URL: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 and got the same error message. How do we set these properties correctly? Thanks, Rakesh -- *Rakesh Nagarajan* Founder, President, and Chief Technology & Visionary Officer m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 6 08:40:42 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 06 May 2020 08:40:42 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Maribel Message-ID: <5eb2da7ae90da_3aaf28d71904607e@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu May 7 15:42:25 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 7 May 2020 22:42:25 +0000 Subject: [bioontology-support] Issue In-Reply-To: References: Message-ID: Hi Rakesh, Thank you for the email. Using the full URL of the property is the correct way to set the prefLabel/synonym/definition property. I?ve checked our own version of NCIT, and the same properties (P108 for prefLabel, P90 for synonym, and P97 for definition) are being used: [cid:A5FB61F0-D9CB-4BD7-A8D7-FB40E8A96CDF] The corresponding rest service call asserts this: http://data.bioontology.org/ontologies/NCIT/classes?display=prefLabel,synonym,definition,properties You can see that the values of the corresponding properties match with their selected counterparts. Normally, when you modify any of these fields via the UI, the re-processing of the ontology is automatically triggered. Is your version of NCIT the same as ours? (20.04d) The errors you included give me no indication of the real problem. I?d need to see the entire log/stack trace to get better clues on what?s causing this. Try the following: 1. Go to http:///ontologies/NCIT/submissions//edit and enter the properties for Preferred Name, Synonym, and Definition into their respective fields. Click on Save Submission. 2. Watch the parsing log to make sure the ontology is getting re-processed. 3. If the re-processing isn?t triggered automatically, use go to /admin, select the ontology inside the table and choose ?Apply to Selected Rows: Process?. 4. Clear the caches from the Admin tool => Site Administration Tab => Cache Management. We have recently published a new set of documents for administering and running an NCBO Virtual Appliance. You?ll find good troubleshooting tips there: https://ontoportal.github.io/administration/ https://ontoportal.github.io/administration/management/reference_ncbo-cron/ https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/ Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 7, 2020, at 8:02 AM, Rakesh Nagarajan > wrote: Hello, We've installed a local version of BioPortal v2.5 and have successfully loaded a few ontologies. We're however having trouble with the property field for the NCI Thesaurus wherein we'd like the Synonyms and Definition loaded correctly. I have tried the following as the property to map these to but the parser throws an error: Thesaurus:P90 Thesaurus:P97 I have also tried the full URL: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 and got the same error message. How do we set these properties correctly? Thanks, Rakesh -- Rakesh Nagarajan Founder, President, and Chief Technology & Visionary Officer m: 314-504-5620 e: rakesh at pieriandx.com [pierian-logo-trans-light-background] [linkedin_circle-512] [twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. _______________________________________________ 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 2020-05-07 at 10.51.34 AM.png Type: image/png Size: 185738 bytes Desc: Screen Shot 2020-05-07 at 10.51.34 AM.png URL: From mdorf at stanford.edu Thu May 7 16:35:15 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 7 May 2020 23:35:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Maribel In-Reply-To: <5eb2da7ae90da_3aaf28d71904607e@ncbo-prd-app-09.stanford.edu.mail> References: <5eb2da7ae90da_3aaf28d71904607e@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <31E8FD36-25E9-48F0-9354-8BC5B4DE2985@stanford.edu> Hi Maribel, Thank you for the email. Unfortunately, we don?t offer support for the contents of individual ontologies. Your best best is to write to the person designated as the contact for this ontology. You can find the CPT contact details here: http://bioportal.bioontology.org/ontologies/CPT?p=summary As an aside, soon BioPortal will be removing CPT from its hosted content at the request of the ontology providers. We will send out an announcement soon, but current users of this content will need to find other sources for their work. Sincerely, ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 6, 2020, at 8:40 AM, support at bioontology.org wrote: Name: Maribel Email: mluna at riversidemedgroup.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F17108%26jump_to_nav%3Dtrue Feedback: Hello, wanted more information regarding two codes. _______________________________________________ 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 May 7 10:52:44 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 07 May 2020 10:52:44 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Elizabeth Anderson Message-ID: <5eb44aec334d7_a1127506dc82724@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri May 8 12:15:14 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 8 May 2020 19:15:14 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Elizabeth Anderson In-Reply-To: <5eb44aec334d7_a1127506dc82724@ncbo-prd-app-09.stanford.edu.mail> References: <5eb44aec334d7_a1127506dc82724@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Elizabeth, Thanks for your email. Please see my answers inline in BLUE. Michael On May 7, 2020, at 10:52 AM, support at bioontology.org wrote: Name: Elizabeth Anderson Email: e13cook at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Ffeedback%3Flocation%3Dhttps%25253A%25252F%25252Fbioportal.bioontology.org%25252F Feedback: Dear BioPortal, My team and I are working on a web application that accesses the Annotator function of BioPortal programmatically through REST API. As we were working on this, we had a few questions about the process. Firstly, we have a question about annotating phrases vs. single words. Our app takes a list of words/phrases and sends them to be annotated, but if we want to annotate a phrase (that has spaces in it), we can't get back an annotation. Does the annotator just have functionality for single words at this point, or can it annotate phrases? The Annotator annotates on term preferred labels and synonyms rather than single words vs phrases. If the label consists of a phrase, it will annotate on it against the corresponding phrase in the text. There is a parameter ?longest_only=true/false? you can pass to retain only the longest annotations for a given phrase. For example, in the text: "Melanoma is a malignant tumor" If a term with a prefLabel ?Malignant Tumor? is found and the longest_only=true, the Annotator will discard all other matches on individual words, such as ?Tumor?. If longest_only=false, ALL matches on both the phrases and individual words will be included. Secondly, we have a question about the "text" parameter of the Annotator API call. During our testing, we found that when we use special characters in the POST call, we get back errors from the annotator. Does the annotator handle special characters over the REST API? I don?t know of any specific issues with handling unicode characters in the Annotator. Here is a sample query that returns annotations for at least some of the (English) terms within the text: http://data.bioontology.org/annotator?text=Melanoma%20is%20??%20?????%20???????%20???????%20???????%20???????%20??????%20bad%20?????????%20disease%20???????%20??????%20???????%20??????...%20???????%20??????%20???????%20??????%20??%20????%20???????%20????%20???%20???????%20??????%20?????????%20||%20??%20?????%20||%20???????%E3%80%80?????%20??????%E3%80%80?????%20of%20the%20skin&ontologies=NCIT,SNOMEDCT&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false For reference, here is the POST call (we are writing a Shiny App in R): postBody I haven?t received any attachments or additional text with this message. Can you please resend it? Also, please include the exact text you were annotating with, your full request with parameters, and any error messages you have received. _______________________________________________ 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 rakesh at pieriandx.com Fri May 8 13:06:35 2020 From: rakesh at pieriandx.com (Rakesh Nagarajan) Date: Fri, 8 May 2020 15:06:35 -0500 Subject: [bioontology-support] Issue In-Reply-To: References: Message-ID: Michael, Thanks! The issue was that I had to create a brand new submission. Editing the prior submission with the new property URLs and reuploading the same file threw the error but creating a new submission with the same information loaded successfully. Thanks again for your help and the additional links! Have a great weekend. Rakesh On Thu, May 7, 2020 at 5:42 PM Michael Dorf wrote: > Hi Rakesh, > > Thank you for the email. Using the full URL of the property is the correct > way to set the prefLabel/synonym/definition property. I?ve checked our own > version of NCIT, and the same properties (P108 for prefLabel, P90 for > synonym, and P97 for definition) are being used: > > > > The corresponding rest service call asserts this: > > > http://data.bioontology.org/ontologies/NCIT/classes?display=prefLabel,synonym,definition,properties > > You can see that the values of the corresponding properties match with > their selected counterparts. Normally, when you modify any of these fields > via the UI, the re-processing of the ontology is automatically triggered. > > Is your version of NCIT the same as ours? (20.04d) > > The errors you included give me no indication of the real problem. I?d > need to see the entire log/stack trace to get better clues on what?s > causing this. Try the following: > > 1. Go to http:// hostname>/ontologies/NCIT/submissions//edit and enter the > properties for Preferred Name, Synonym, and Definition into their > respective fields. Click on Save Submission. > 2. Watch the parsing log to make sure the ontology is getting re-processed. > 3. If the re-processing isn?t triggered automatically, use go to virtual appliance hostname>/admin, select the ontology inside the table and > choose ?Apply to Selected Rows: Process?. > 4. Clear the caches from the Admin tool => Site Administration Tab => > Cache Management. > > We have recently published a new set of documents for administering and > running an NCBO Virtual Appliance. You?ll find good troubleshooting tips > there: > > https://ontoportal.github.io/administration/ > https://ontoportal.github.io/administration/management/reference_ncbo-cron/ > > https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/ > > Thanks, > > Michael > > > > ---------------------------------------------------- > Michael Dorf > Chief Software Architect > The National Center for Biomedical Ontology > Stanford Biomedical Informatics Research > mdorf at stanford.edu > O: 650-723-0357 > M: 650-995-4374 > ---------------------------------------------------- > > On May 7, 2020, at 8:02 AM, Rakesh Nagarajan wrote: > > Hello, > We've installed a local version of BioPortal v2.5 and have > successfully loaded a few ontologies. We're however having trouble with the > property field for the NCI Thesaurus wherein we'd like the Synonyms and > Definition loaded correctly. I have tried the following as the property to > map these to but the parser throws an error: > > Thesaurus:P90 > Thesaurus:P97 > > I have also tried the full URL: > > http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97 > http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 > > and got the same error message. How do we set these properties correctly? > > Thanks, > Rakesh > > > -- > > *Rakesh Nagarajan* > > Founder, President, and Chief Technology & Visionary Officer > > m: 314-504-5620 > e: rakesh at pieriandx.com > > [image: pierian-logo-trans-light-background] > [image: linkedin_circle-512] > [image: twitter_circle-512] > > > Wisdom in Every Report? > > CONFIDENTIALITY NOTICE: This message and any attachments are solely for > the use of the intended recipient and may contain privileged, confidential > or other legally protected information. If you are not the intended > recipient, please destroy all copies without reading or disclosing their > contents and notify the sender of the error by reply email. > > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -- *Rakesh Nagarajan* Founder, President, and Chief Technology & Visionary Officer m: 314-504-5620 e: rakesh at pieriandx.com [image: pierian-logo-trans-light-background] [image: linkedin_circle-512] [image: twitter_circle-512] Wisdom in Every Report? CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-07 at 10.51.34 AM.png Type: image/png Size: 185738 bytes Desc: not available URL: From support at bioontology.org Mon May 11 09:49:49 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 11 May 2020 09:49:49 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Zhiliang Hu Message-ID: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From elie.arnaud at mnhn.fr Mon May 11 03:39:43 2020 From: elie.arnaud at mnhn.fr (Elie ARNAUD) Date: Mon, 11 May 2020 12:39:43 +0200 (CEST) Subject: [bioontology-support] BioOntology API access through R Message-ID: <1725171884.671783.1589193583669.JavaMail.zimbra@mnhn.fr> Hello BioOntology team, allow me to introduce us: me and Yvan Le Bras (in copy) are part of the french National Data Hub (PNDB: [ http://www.patrinat.fr/fr/pole-national-de-donnees-de-biodiversite-pndb-6256 | http://www.patrinat.fr/fr/pole-national-de-donnees-de-biodiversite-pndb-6256 ] ). Yvan is our team leader while I am involved as a developper. One of our mission consists in writing metadata for research projects led by french institutions. Within this mission, we came to work on a metadata filling tool, helping the user to fetch the more information as possible, in the most automated way (MetaShARK: [ https://github.com/earnaud/MetaShARK-v2 | https://github.com/earnaud/MetaShARK-v2 ] ). This tool has one particularity: it is developped with R language. Also, we are planning to integrate semantic annotation within this tool. The great features of the BioPortal Annotator (and its whole API access) greatly interests us. However, there is no more than an example script of how to retrieve data from you portal with R. To solve this, and since we would need the best features to have a successful and comfortable development, I am beginning to work on a convenience R package wrapping the requests to your API within R functions. Since I am not the proper author of this work, I have obviously many questions to ask to you, mainly about intellectual rights: - do you give me the proper authorization to work on this package? (yes, this one is basic but I must ask it) - which people/organization shall I cite concerning the API work? These people are to be named for license purposes. - since I develop this package with git version controlling system, I will end up by uploading it online. Would you prefer a public release? private shared repository? or even another platform (such as Gitlab)? I wish all of the BioPortal team to stay safe and healthy, Elie Arnaud Ing?nieur Donn?es et M?tadonn?es UMS Patrinat / PNDB -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 11 10:38:59 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 May 2020 17:38:59 +0000 Subject: [bioontology-support] BioOntology API access through R In-Reply-To: <1725171884.671783.1589193583669.JavaMail.zimbra@mnhn.fr> References: <1725171884.671783.1589193583669.JavaMail.zimbra@mnhn.fr> Message-ID: <10584F91-F466-4C82-975F-2BF08CBFD336@stanford.edu> Hello Elie, Thank you for your inquiry. I will reply to your inquiry directly later today?it's an exciting project and there are several interesting topics that we'd be happy to talk to you about! John On May 11, 2020, at 3:39 AM, Elie ARNAUD > wrote: Hello BioOntology team, allow me to introduce us: me and Yvan Le Bras (in copy) are part of the french National Data Hub (PNDB: http://www.patrinat.fr/fr/pole-national-de-donnees-de-biodiversite-pndb-6256). Yvan is our team leader while I am involved as a developper. One of our mission consists in writing metadata for research projects led by french institutions. Within this mission, we came to work on a metadata filling tool, helping the user to fetch the more information as possible, in the most automated way (MetaShARK: https://github.com/earnaud/MetaShARK-v2). This tool has one particularity: it is developped with R language. Also, we are planning to integrate semantic annotation within this tool. The great features of the BioPortal Annotator (and its whole API access) greatly interests us. However, there is no more than an example script of how to retrieve data from you portal with R. To solve this, and since we would need the best features to have a successful and comfortable development, I am beginning to work on a convenience R package wrapping the requests to your API within R functions. Since I am not the proper author of this work, I have obviously many questions to ask to you, mainly about intellectual rights: - do you give me the proper authorization to work on this package? (yes, this one is basic but I must ask it) - which people/organization shall I cite concerning the API work? These people are to be named for license purposes. - since I develop this package with git version controlling system, I will end up by uploading it online. Would you prefer a public release? private shared repository? or even another platform (such as Gitlab)? I wish all of the BioPortal team to stay safe and healthy, Elie Arnaud Ing?nieur Donn?es et M?tadonn?es UMS Patrinat / PNDB _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 11 14:20:22 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 May 2020 21:20:22 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zhiliang Hu In-Reply-To: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Zhiliang, There is such a link, but it is not a purl link, it is an API call. Replace 'bioportal' with 'data' and append '/download', so for your example: http://data.bioontology.org/ontologies/VT/download The ontology has to be downloadable and accessible to you (you must provide your API key). John On May 11, 2020, at 9:49 AM, support at bioontology.org wrote: Name: Zhiliang Hu Email: zhu at iastate.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FVT%3Fp%3Dclasses%26conceptid%3Droot Feedback: Is there a way to get a stable purl link to download the latest version of an ontology, such as vt, to be used by wget? (http://bioportal.bioontology.org/ontologies/VT?p=classes&conceptid=root) Thanks, Zhiliang ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhu at iastate.edu Mon May 11 14:18:36 2020 From: zhu at iastate.edu (Hu, Zhiliang [AN S]) Date: Mon, 11 May 2020 21:18:36 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zhiliang Hu In-Reply-To: <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu> References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu> Message-ID: Thank you Jennifer, API will be good. Could you advice how can I get an API.key? I have an account on http://bioportal.bioontology.org/ but don't seem find the way as the DOC says. Zhiliang On May 11, 2020, at 02:35 PM, Jennifer Leigh Vendetti > wrote: Hello Zhiliang, On May 11, 2020, at 9:49 AM, support at bioontology.org wrote: Name: Zhiliang Hu Email: zhu at iastate.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FVT%3Fp%3Dclasses%26conceptid%3Droot Feedback: Is there a way to get a stable purl link to download the latest version of an ontology, such as vt, to be used by wget? (http://bioportal.bioontology.org/ontologies/VT?p=classes&conceptid=root) BioPortal doesn?t offer PURLs for the download locations of ontology source files. However, the /download endpoint in the REST API will always point to the latest download for any given ontology. For example, issuing this call: http://data.bioontology.org/ontologies/VT/download ? will result in the download of version 10.3 (the latest version) of the Vertebrate Trait Ontology. Also of note is that ontology acronyms are unmodifiable in the BioPortal system. So, as long as VT isn?t deleted altogether from BioPortal, the above URL will always work. Our REST API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon May 11 14:44:24 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 11 May 2020 21:44:24 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zhiliang Hu In-Reply-To: References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu> Message-ID: Zhiliang, I'm not sure what docs you are referring to, but I notice the help page at https://bioportal.bioontology.org/help#Getting_an_API_key (text below) isn't quite complete. The final step is: Once logged in, click on your name in the upper right corner, then choose Account Settings from that menu. You will see your key there. I also include the link to the API documentation, which has more information about how to specify your API key when making an API call. John Programming with the BioPortal API Documentation about how to use the BioPortal REST API to access information is available here: http://data.bioontology.org/documentation Getting an API key Use of the BioPortal REST API requires an API key. To retrieve your API key, log into your account on the BioPortal website. If you don't have an account, you'll need to create one. Your API key will be listed in plain text on your account page. On May 11, 2020, at 2:18 PM, Hu, Zhiliang [AN S] > wrote: Thank you Jennifer, API will be good. Could you advice how can I get an API.key? I have an account on http://bioportal.bioontology.org/ but don't seem find the way as the DOC says. Zhiliang On May 11, 2020, at 02:35 PM, Jennifer Leigh Vendetti > wrote: Hello Zhiliang, On May 11, 2020, at 9:49 AM, support at bioontology.org wrote: Name: Zhiliang Hu Email: zhu at iastate.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FVT%3Fp%3Dclasses%26conceptid%3Droot Feedback: Is there a way to get a stable purl link to download the latest version of an ontology, such as vt, to be used by wget? (http://bioportal.bioontology.org/ontologies/VT?p=classes&conceptid=root) BioPortal doesn?t offer PURLs for the download locations of ontology source files. However, the /download endpoint in the REST API will always point to the latest download for any given ontology. For example, issuing this call: http://data.bioontology.org/ontologies/VT/download ? will result in the download of version 10.3 (the latest version) of the Vertebrate Trait Ontology. Also of note is that ontology acronyms are unmodifiable in the BioPortal system. So, as long as VT isn?t deleted altogether from BioPortal, the above URL will always work. Our REST API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhu at iastate.edu Mon May 11 15:27:28 2020 From: zhu at iastate.edu (Hu, Zhiliang [AN S]) Date: Mon, 11 May 2020 22:27:28 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Zhiliang Hu In-Reply-To: References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail> <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu> Message-ID: <8D1F4ED4-3268-4497-810F-E5DDA76A86E9@iastate.edu> Hi John, This is exactly what I need. (I was referring to your REST API DOC (http://data.bioontology.org/documentation) Jennifer pointed to. Thank you, Zhiliang On May 11, 2020, at 04:44 PM, John Graybeal > wrote: Zhiliang, I'm not sure what docs you are referring to, but I notice the help page at https://bioportal.bioontology.org/help#Getting_an_API_key (text below) isn't quite complete. The final step is: Once logged in, click on your name in the upper right corner, then choose Account Settings from that menu. You will see your key there. I also include the link to the API documentation, which has more information about how to specify your API key when making an API call. John Programming with the BioPortal API Documentation about how to use the BioPortal REST API to access information is available here: http://data.bioontology.org/documentation Getting an API key Use of the BioPortal REST API requires an API key. To retrieve your API key, log into your account on the BioPortal website. If you don't have an account, you'll need to create one. Your API key will be listed in plain text on your account page. On May 11, 2020, at 2:18 PM, Hu, Zhiliang [AN S] > wrote: Thank you Jennifer, API will be good. Could you advice how can I get an API.key? I have an account on http://bioportal.bioontology.org/ but don't seem find the way as the DOC says. Zhiliang On May 11, 2020, at 02:35 PM, Jennifer Leigh Vendetti > wrote: Hello Zhiliang, On May 11, 2020, at 9:49 AM, support at bioontology.org wrote: Name: Zhiliang Hu Email: zhu at iastate.edu Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FVT%3Fp%3Dclasses%26conceptid%3Droot Feedback: Is there a way to get a stable purl link to download the latest version of an ontology, such as vt, to be used by wget? (http://bioportal.bioontology.org/ontologies/VT?p=classes&conceptid=root) BioPortal doesn?t offer PURLs for the download locations of ontology source files. However, the /download endpoint in the REST API will always point to the latest download for any given ontology. For example, issuing this call: http://data.bioontology.org/ontologies/VT/download ? will result in the download of version 10.3 (the latest version) of the Vertebrate Trait Ontology. Also of note is that ontology acronyms are unmodifiable in the BioPortal system. So, as long as VT isn?t deleted altogether from BioPortal, the above URL will always work. Our REST API is documented here: http://data.bioontology.org/documentation Kind regards, Jennifer _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 13 09:13:37 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 13 May 2020 09:13:37 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Katie Durnen, MD Message-ID: <5ebc1cb1ec22f_685f20fa1e84401c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 13 10:36:12 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 13 May 2020 17:36:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Katie Durnen, MD In-Reply-To: <5ebc1cb1ec22f_685f20fa1e84401c@ncbo-prd-app-09.stanford.edu.mail> References: <5ebc1cb1ec22f_685f20fa1e84401c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Katie, Thanks for this Feedback. Unfortunately we are going to be removing the CPT shortly, per the request of its owners. So we will not be updating these codes further. John On May 13, 2020, at 9:13 AM, support at bioontology.org wrote: Name: Katie Durnen, MD Email: durnenmd at atallamd.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FCPT%252F97607%26jump_to_nav%3Dtrue Feedback: The Current Procedural Terminology "classes" page has not been updated since 2019. There are some 2020 updates to the codes, especially in Surgery. _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Fri May 15 03:54:17 2020 From: support at bioontology.org (support at bioontology.org) Date: Fri, 15 May 2020 03:54:17 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman Message-ID: <5ebe74d95891e_2a07250071084487@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Fri May 15 07:22:48 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Fri, 15 May 2020 14:22:48 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: <5ebe74d95891e_2a07250071084487@ncbo-prd-app-09.stanford.edu.mail> References: <5ebe74d95891e_2a07250071084487@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and at http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John [cid:E28F7E70-184F-40F0-9F20-E9A630F0CC47 at attlocal.net] On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology, http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-15 at 7.04.36 AM.png Type: image/png Size: 261431 bytes Desc: Screen Shot 2020-05-15 at 7.04.36 AM.png URL: From support at bioontology.org Mon May 18 05:15:35 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 18 May 2020 05:15:35 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Martin Hofmann-Apitius Message-ID: <5ec27c67531e1_607d258bc98712c5@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon May 18 09:45:32 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 18 May 2020 16:45:32 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Martin Hofmann-Apitius In-Reply-To: <5ec27c67531e1_607d258bc98712c5@ncbo-prd-app-09.stanford.edu.mail> References: <5ec27c67531e1_607d258bc98712c5@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <0EBE8611-7318-4E74-8A96-BBE63A1D6DFB@stanford.edu> Hello Martin, I?ve added akodamullil and maestro as administrators to the list of requested ontologies below. They may need to refresh their browsers to see the change. They should be able to use the add / edit buttons at the top of the Submission table to upload new versions, and/or edit ontology metadata. Let us know if you run into any issues. Kind regards, Jennifer On May 18, 2020, at 5:15 AM, support at bioontology.org wrote: Name: Martin Hofmann-Apitius Email: martin.hofmann-apitius at scai.fraunhofer.de Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Dear Colleagues, I need your help. Former PhD students have uploaded their ontology work to BioPortal, however, they are not any longer in our team and pursue their career in other areas (e.g. in industry). We need to update some of our ontologies (we are actually doing that in collaborations, e.g. with FDA and NCBI) and therefore we would need the credentials to add new versions to the ontologies uploaded by our team years ago. Please find below the list of ontologies we would need to get access to (as owners): List of ontologies of our department that we need to have access to: 1. https://bioportal.bioontology.org/ontologies/ADO (Owner: Ashutosh Malhotra) 2. https://bioportal.bioontology.org/ontologies/MSO (Owner: Ashutosh Malhotra) 3. https://bioportal.bioontology.org/ontologies/PDON (Owner: Erfan Younesi) 4. https://bioportal.bioontology.org/ontologies/CTO (Owner: Erfan Younesi) 5. https://bioportal.bioontology.org/ontologies/PTS (Owner: Erfan Younesi) 6. https://bioportal.bioontology.org/ontologies/BRCT (Owner: Erfan Younesi) 7. https://bioportal.bioontology.org/ontologies/PLIO (Owner: Erfan Younesi) 8. https://bioportal.bioontology.org/ontologies/HUPSON (Owner: Michaela Guendel) Neither Ashu Malhotra, nor Erfan Younesi nor Michi Grendel are in our Department any more. Instead, we would like to add the following members of my team as administrators to the above mentioned ontologies: - Alpha Tom Kodamullil (username: akodamullil) - Sumit Madan (username: maestro) Would be great if you could enable us to take care of our ontologies. best wishes Martin _______________________________________________ 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 martin.hofmann-apitius at scai.fraunhofer.de Mon May 18 09:57:02 2020 From: martin.hofmann-apitius at scai.fraunhofer.de (Martin Hofmann-Apitius) Date: Mon, 18 May 2020 18:57:02 +0200 (CEST) Subject: [bioontology-support] [BioPortal] Feedback from Martin Hofmann-Apitius In-Reply-To: <0EBE8611-7318-4E74-8A96-BBE63A1D6DFB@stanford.edu> References: <0EBE8611-7318-4E74-8A96-BBE63A1D6DFB@stanford.edu> Message-ID: <1950703239.338767.1589821022780.JavaMail.zimbra@zimbra> Thank you so much! Best wishes Martin Von meinem iPhone gesendet > Am 18.05.2020 um 18:45 schrieb Jennifer Leigh Vendetti : > > ? Hello Martin, > > I?ve added akodamullil and maestro as administrators to the list of requested ontologies below. They may need to refresh their browsers to see the change. > > They should be able to use the add / edit buttons at the top of the Submission table to upload new versions, and/or edit ontology metadata. > > Let us know if you run into any issues. > > Kind regards, > Jennifer > > > >> On May 18, 2020, at 5:15 AM, support at bioontology.org wrote: >> >> Name: Martin Hofmann-Apitius >> >> Email: martin.hofmann-apitius at scai.fraunhofer.de >> >> Location: https%3A%2F%2Fbioportal.bioontology.org%2F >> >> >> Feedback: >> >> Dear Colleagues, >> >> I need your help. Former PhD students have uploaded their ontology work to BioPortal, however, they are not any longer in our team and pursue their career in other areas (e.g. in industry). We need to update some of our ontologies (we are actually doing that in collaborations, e.g. with FDA and NCBI) and therefore we would need the credentials to add new versions to the ontologies uploaded by our team years ago. Please find below the list of ontologies we would need to get access to (as owners): >> >> List of ontologies of our department that we need to have access to: >> 1. https://bioportal.bioontology.org/ontologies/ADO (Owner: Ashutosh Malhotra) >> 2. https://bioportal.bioontology.org/ontologies/MSO (Owner: Ashutosh Malhotra) >> 3. https://bioportal.bioontology.org/ontologies/PDON (Owner: Erfan Younesi) >> 4. https://bioportal.bioontology.org/ontologies/CTO (Owner: Erfan Younesi) >> 5. https://bioportal.bioontology.org/ontologies/PTS (Owner: Erfan Younesi) >> 6. https://bioportal.bioontology.org/ontologies/BRCT (Owner: Erfan Younesi) >> 7. https://bioportal.bioontology.org/ontologies/PLIO (Owner: Erfan Younesi) >> 8. https://bioportal.bioontology.org/ontologies/HUPSON (Owner: Michaela Guendel) >> >> Neither Ashu Malhotra, nor Erfan Younesi nor Michi Grendel are in our Department any more. Instead, we would like to add the following members of my team as administrators to the above mentioned ontologies: >> - Alpha Tom Kodamullil (username: akodamullil) >> - Sumit Madan (username: maestro) >> >> Would be great if you could enable us to take care of our ontologies. >> >> best wishes >> >> Martin >> >> >> _______________________________________________ >> 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 May 18 15:45:12 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 18 May 2020 22:45:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> References: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> Message-ID: <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> Hello Karin, I downloaded your ontology source file and noticed this line at the bottom: "### Generated by the OWL API (version 4.1.3) https://github.com/owlcs/owlapi? I?m curious to know if you developed this ontology using the Protege ontology editor? Sometimes if I?m trying to determine whether BioPortal will successfully load an ontology, I attempt to load it into Protege first. Both tools use the OWL API internally for loading and parsing OWL ontologies. I have Protege 5.5.0 installed on my Mac (Catalina OS) and tried to open the afo.ttl file. I let Protege sit for a couple of hours, but it seems to hang while trying to load one of the imports (see screen shot below). Just curious if anyone on your team has successfully loaded your ontology in Protege? Or, if not, is there some other tool you?re using to develop / maintain this ontology? Kind regards, Jennifer [cid:823B78A5-6FF3-45CC-ADD4-81225E8A0C90 at stanford.edu] On May 15, 2020, at 7:45 AM, Karin Colsman > wrote: Thanks, John, that is excellent news! The ontology that we are looking to publish is this one: http://purl.allotrope.org/voc/afo/REC/2020/03/afo.ttl Could you please have a look if it is compatible? We don?t have skos:Concept etc. ? it?s an Owl ontology with skos annotations. We will be looking to replace an older version: http://bioportal.bioontology.org/ontologies/AFO Kind regards Karin Colsman From: John Graybeal > Sent: Friday, May 15, 2020 15:23 To: NCBO User Support > Cc: Karin Colsman > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and athttp://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology,http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-18 at 3.27.20 PM.png Type: image/png Size: 413265 bytes Desc: Screen Shot 2020-05-18 at 3.27.20 PM.png URL: From karin.colsman.contractor at osthus.com Mon May 18 22:19:58 2020 From: karin.colsman.contractor at osthus.com (Karin Colsman) Date: Tue, 19 May 2020 05:19:58 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> References: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> Message-ID: <0240e6e66e7b4cfda5a810bcf4659ebd@osthus.com> Hi Jennifer, thanks for testing! The ontology is developed in modules, assembled by SPARQL construct and then run through the OWL API for normalization. I?d expect the developers to test in Prot?g? too ? maybe the server/internet was faster when they tested. I have taken a look at the imports and they sum up to ca. 1.5 MB, which is not acceptable. I have a meeting with the ontology developers today and will raise the issue there. Kind regards Karin From: Jennifer Leigh Vendetti Sent: Monday, May 18, 2020 23:45 To: Karin Colsman Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Hello Karin, I downloaded your ontology source file and noticed this line at the bottom: "### Generated by the OWL API (version 4.1.3) https://github.com/owlcs/owlapi? I?m curious to know if you developed this ontology using the Protege ontology editor? Sometimes if I?m trying to determine whether BioPortal will successfully load an ontology, I attempt to load it into Protege first. Both tools use the OWL API internally for loading and parsing OWL ontologies. I have Protege 5.5.0 installed on my Mac (Catalina OS) and tried to open the afo.ttl file. I let Protege sit for a couple of hours, but it seems to hang while trying to load one of the imports (see screen shot below). Just curious if anyone on your team has successfully loaded your ontology in Protege? Or, if not, is there some other tool you?re using to develop / maintain this ontology? Kind regards, Jennifer [cid:image001.png at 01D62DA5.839915F0] On May 15, 2020, at 7:45 AM, Karin Colsman > wrote: Thanks, John, that is excellent news! The ontology that we are looking to publish is this one: http://purl.allotrope.org/voc/afo/REC/2020/03/afo.ttl Could you please have a look if it is compatible? We don?t have skos:Concept etc. ? it?s an Owl ontology with skos annotations. We will be looking to replace an older version: http://bioportal.bioontology.org/ontologies/AFO Kind regards Karin Colsman From: John Graybeal > Sent: Friday, May 15, 2020 15:23 To: NCBO User Support > Cc: Karin Colsman > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and athttp://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology,http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 339016 bytes Desc: image001.png URL: From karin.colsman.contractor at osthus.com Tue May 19 03:44:19 2020 From: karin.colsman.contractor at osthus.com (Karin Colsman) Date: Tue, 19 May 2020 10:44:19 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> References: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> Message-ID: Hi Jennifer, I apologize ? I gave you the wrong link. We have a better artifact at http://purl.allotrope.org/voc/afo/merged/REC/2020/03/merged.ttl which does not require any imports. I have just registered a new account for us (DG_Allotrope_AFO). Could you please give that account permission to upload new versions to http://bioportal.bioontology.org/ontologies/AFO ? I could then do some testing myself and take up less of your time. The existing account (WEspejo_Osthus) was a personal acount by one of our employees who has left the company. Thank you and kind regards Karin Colsman From: Jennifer Leigh Vendetti Sent: Monday, May 18, 2020 23:45 To: Karin Colsman Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Hello Karin, I downloaded your ontology source file and noticed this line at the bottom: "### Generated by the OWL API (version 4.1.3) https://github.com/owlcs/owlapi? I?m curious to know if you developed this ontology using the Protege ontology editor? Sometimes if I?m trying to determine whether BioPortal will successfully load an ontology, I attempt to load it into Protege first. Both tools use the OWL API internally for loading and parsing OWL ontologies. I have Protege 5.5.0 installed on my Mac (Catalina OS) and tried to open the afo.ttl file. I let Protege sit for a couple of hours, but it seems to hang while trying to load one of the imports (see screen shot below). Just curious if anyone on your team has successfully loaded your ontology in Protege? Or, if not, is there some other tool you?re using to develop / maintain this ontology? Kind regards, Jennifer [cid:image001.png at 01D62DD2.D2F03CF0] On May 15, 2020, at 7:45 AM, Karin Colsman > wrote: Thanks, John, that is excellent news! The ontology that we are looking to publish is this one: http://purl.allotrope.org/voc/afo/REC/2020/03/afo.ttl Could you please have a look if it is compatible? We don?t have skos:Concept etc. ? it?s an Owl ontology with skos annotations. We will be looking to replace an older version: http://bioportal.bioontology.org/ontologies/AFO Kind regards Karin Colsman From: John Graybeal > Sent: Friday, May 15, 2020 15:23 To: NCBO User Support > Cc: Karin Colsman > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and athttp://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology,http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 339016 bytes Desc: image001.png URL: From vendetti at stanford.edu Tue May 19 07:08:12 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Tue, 19 May 2020 14:08:12 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: References: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> Message-ID: Hi Karin, Sure, no problem. I gave your new account administrative access to AFO. You may need to refresh your browser to see the change. Let us know if you need further assistance. Kind regards, Jennifer On May 19, 2020, at 3:44 AM, Karin Colsman > wrote: Hi Jennifer, I apologize ? I gave you the wrong link. We have a better artifact at http://purl.allotrope.org/voc/afo/merged/REC/2020/03/merged.ttl which does not require any imports. I have just registered a new account for us (DG_Allotrope_AFO). Could you please give that account permission to upload new versions to http://bioportal.bioontology.org/ontologies/AFO ? I could then do some testing myself and take up less of your time. The existing account (WEspejo_Osthus) was a personal acount by one of our employees who has left the company. Thank you and kind regards Karin Colsman From: Jennifer Leigh Vendetti > Sent: Monday, May 18, 2020 23:45 To: Karin Colsman > Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Hello Karin, I downloaded your ontology source file and noticed this line at the bottom: "### Generated by the OWL API (version 4.1.3) https://github.com/owlcs/owlapi? I?m curious to know if you developed this ontology using the Protege ontology editor? Sometimes if I?m trying to determine whether BioPortal will successfully load an ontology, I attempt to load it into Protege first. Both tools use the OWL API internally for loading and parsing OWL ontologies. I have Protege 5.5.0 installed on my Mac (Catalina OS) and tried to open the afo.ttl file. I let Protege sit for a couple of hours, but it seems to hang while trying to load one of the imports (see screen shot below). Just curious if anyone on your team has successfully loaded your ontology in Protege? Or, if not, is there some other tool you?re using to develop / maintain this ontology? Kind regards, Jennifer On May 15, 2020, at 7:45 AM, Karin Colsman > wrote: Thanks, John, that is excellent news! The ontology that we are looking to publish is this one: http://purl.allotrope.org/voc/afo/REC/2020/03/afo.ttl Could you please have a look if it is compatible? We don?t have skos:Concept etc. ? it?s an Owl ontology with skos annotations. We will be looking to replace an older version: http://bioportal.bioontology.org/ontologies/AFO Kind regards Karin Colsman From: John Graybeal > Sent: Friday, May 15, 2020 15:23 To: NCBO User Support > Cc: Karin Colsman > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and athttp://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology,http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexgarciac at gmail.com Tue May 19 13:37:57 2020 From: alexgarciac at gmail.com (Alexander Garcia Castro) Date: Tue, 19 May 2020 22:37:57 +0200 Subject: [bioontology-support] vector types Message-ID: Hi, anyone knows about an ontology for vector types? for instance, Base Vector Component Source Vector Microbial Expression Vector Plant Expression Vector Special Application Vector Best. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue May 19 14:38:10 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 19 May 2020 21:38:10 +0000 Subject: [bioontology-support] vector types In-Reply-To: References: Message-ID: <5BACCBF4-F34E-4D9C-B916-6E9818B9D388@stanford.edu> Hello Alexander, Did you try the BioPortal Recommender (https://bioportal.bioontology.org/recommender)? In case not: I entered those five keywords and got three hits with good scores: NCIT, OCHV, and SNOMEDCT. You can adjust the weighting of the categories (in the Advanced section) to match your own needs. If there is a good one that is not listed there, maybe someone can submit it! John On May 19, 2020, at 1:37 PM, Alexander Garcia Castro > wrote: Hi, anyone knows about an ontology for vector types? for instance, Base Vector Component Source Vector Microbial Expression Vector Plant Expression Vector Special Application Vector Best. -- Alexander Garcia https://www.researchgate.net/profile/Alexander_Garcia http://www.usefilm.com/photographer/75943.html http://www.linkedin.com/in/alexgarciac _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Thu May 21 01:01:15 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 21 May 2020 01:01:15 -0700 Subject: [bioontology-support] [BioPortal] Feedback from PaulNSchofield Message-ID: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at pps.slac_mgt Thu May 21 01:01:23 2020 From: MAILER-DAEMON at pps.slac_mgt (Mail Delivery Subsystem) Date: Thu, 21 May 2020 01:01:23 -0700 Subject: [bioontology-support] Returned mail: see transcript for details Message-ID: <202005210801.04L81NI5016630@mx0a-00000d04.pphosted.com> The original message was received at Thu, 21 May 2020 01:01:17 -0700 from m0102888.ppops.net [127.0.0.1] ----- The following addresses had permanent fatal errors ----- (reason: 550 mole.bio.cam.ac.uk is no longer in use; please try @cam.ac.uk instead) ----- Transcript of session follows ----- ... while talking to mx.cam.ac.uk.: >>> DATA <<< 550 mole.bio.cam.ac.uk is no longer in use; please try @cam.ac.uk instead 550 5.1.1 ... User unknown <<< 503-All RCPT commands were rejected with this error: <<< 503-mole.bio.cam.ac.uk is no longer in use; please try @cam.ac.uk instead <<< 503 Valid RCPT command must precede DATA -------------- next part -------------- An embedded message was scrubbed... From: support at bioontology.org Subject: [BioPortal] Feedback from PaulNSchofield Date: Thu, 21 May 2020 01:01:15 -0700 Size: 3817 URL: From vendetti at stanford.edu Thu May 21 08:36:01 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 21 May 2020 15:36:01 +0000 Subject: [bioontology-support] [BioPortal] Feedback from PaulNSchofield In-Reply-To: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Hi Paul, On May 21, 2020, at 1:01 AM, support at bioontology.org wrote: Dear Bioportal, We have been uploading a new version of the MPATH ontology to our git recently and the final verson was uploaded yesterday. At the moment there are some conflicting dates on Bioportal and the most recent version is not showing. So on the list of ontologies (http://bioportal.bioontology.org/ontologies) the last upload is dated 21.5, on the MPATH summary page its listed as 18.5 (http://bioportal.bioontology.org/ontologies/MPATH/?p=summary). From what I can see the version available is that one from 18.5. We did probably do a premature commit on the 18th, but are concerned that for some reason the new version is not parsing. We have checked it in Protege and it does seem to parse fine. Any guidance gratefully accepted! Best wishes, Paul I took a look at MPATH in our system this morning. BioPortal picked up the version that you uploaded yesterday and it?s fully parsed now without issue. The version is listed as ?2020-05-19?, which was set using the data-version from the source file: data-version: 2020-05-19 With regard to the Browse page for viewing all ontologies, this is what I see: [cid:B61169F6-6A73-4A95-A231-A69D10C331DF at lan] I think the mismatch that you saw yesterday may have been due to cached page content. As far as I can tell at the moment, the upload dates are now consistent across pages. Kind regards, Jennifer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-05-21 08.21.20.png Type: image/png Size: 422341 bytes Desc: Screenshot 2020-05-21 08.21.20.png URL: From karin.colsman.contractor at osthus.com Thu May 21 23:04:17 2020 From: karin.colsman.contractor at osthus.com (Karin Colsman) Date: Fri, 22 May 2020 06:04:17 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Karin Colsman In-Reply-To: References: <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu> <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu> Message-ID: <6875ff1f1c244334bca76575b95e2cfb@osthus.com> It?s uploaded and working fine. Thanks for all your help! From: Jennifer Leigh Vendetti Sent: Tuesday, May 19, 2020 15:08 To: Karin Colsman Cc: support at bioontology.org; Amnon Ptashek ; Matthew Fox Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Hi Karin, Sure, no problem. I gave your new account administrative access to AFO. You may need to refresh your browser to see the change. Let us know if you need further assistance. Kind regards, Jennifer On May 19, 2020, at 3:44 AM, Karin Colsman > wrote: Hi Jennifer, I apologize ? I gave you the wrong link. We have a better artifact at http://purl.allotrope.org/voc/afo/merged/REC/2020/03/merged.ttl which does not require any imports. I have just registered a new account for us (DG_Allotrope_AFO). Could you please give that account permission to upload new versions to http://bioportal.bioontology.org/ontologies/AFO ? I could then do some testing myself and take up less of your time. The existing account (WEspejo_Osthus) was a personal acount by one of our employees who has left the company. Thank you and kind regards Karin Colsman From: Jennifer Leigh Vendetti > Sent: Monday, May 18, 2020 23:45 To: Karin Colsman > Cc: support at bioontology.org Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Hello Karin, I downloaded your ontology source file and noticed this line at the bottom: "### Generated by the OWL API (version 4.1.3) https://github.com/owlcs/owlapi? I?m curious to know if you developed this ontology using the Protege ontology editor? Sometimes if I?m trying to determine whether BioPortal will successfully load an ontology, I attempt to load it into Protege first. Both tools use the OWL API internally for loading and parsing OWL ontologies. I have Protege 5.5.0 installed on my Mac (Catalina OS) and tried to open the afo.ttl file. I let Protege sit for a couple of hours, but it seems to hang while trying to load one of the imports (see screen shot below). Just curious if anyone on your team has successfully loaded your ontology in Protege? Or, if not, is there some other tool you?re using to develop / maintain this ontology? Kind regards, Jennifer On May 15, 2020, at 7:45 AM, Karin Colsman > wrote: Thanks, John, that is excellent news! The ontology that we are looking to publish is this one: http://purl.allotrope.org/voc/afo/REC/2020/03/afo.ttl Could you please have a look if it is compatible? We don?t have skos:Concept etc. ? it?s an Owl ontology with skos annotations. We will be looking to replace an older version: http://bioportal.bioontology.org/ontologies/AFO Kind regards Karin Colsman From: John Graybeal > Sent: Friday, May 15, 2020 15:23 To: NCBO User Support > Cc: Karin Colsman > Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman Karin, We would be delighted to have your content in BioPortal. BioPortal supports SKOS and SKOS annotations, if the SKOS file follows some common SKOS practices. You can see this displayed in the PLOS Thesaurus page, as in the example shown below (and athttp://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%239501). The information about the necessary practices is found at https://www.bioontology.org/wiki/SKOSSupport. If you need more customized support, please don't hesitate to contact me directly. John On May 15, 2020, at 3:54 AM, support at bioontology.org wrote: Name: Karin Colsman Email: karin.colsman.contractor at osthus.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: Dear support team, we are looking to upload a skos-based ontology (Allotrope Foundation Ontology,http://purl.allotrope.org/) to your portal. Would it be possible to support skos-based annotations, so that we won't have to maintain a fork/duplicate all the annotations? Kind regards Karin Colsman _______________________________________________ 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 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From leylajael at gmail.com Mon May 25 06:48:15 2020 From: leylajael at gmail.com (=?UTF-8?Q?Leyla_Jael_Garc=C3=ADa_Castro?=) Date: Mon, 25 May 2020 15:48:15 +0200 Subject: [bioontology-support] GO ontology, children is-a and part-of In-Reply-To: References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> Message-ID: Dear all, Does the current Gene Ontology release at BioPortal coincide with the latest version? I find differences with what is listed on the QuickGO website, I am trying to understand where those differences come from. For instance, term GO:0003258 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003258 in Bioportal lists GO.0006357 as one of its parents (subClassOf). However, according to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0003258 that is-a relation was removed on 2012-08-06 (see Change Log section). Why does Bioportal still includes this relation? Also, I found a difference between the website and the API. On the website I found GO:0000981 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000981 to be a subClassOf GO:0003700 only. When I use the API to query the children of GO:0006357 http://data.bioontology.org/ontologies/GO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0006357/children the term GO:0000981 is listed there. According to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0000981, GO:0000981 part_of GO:0006357 but there is no is_a relation between the two of them. Are terms related via part_of reported as children by the API? Kind regards, -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue May 26 12:59:34 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 26 May 2020 19:59:34 +0000 Subject: [bioontology-support] GO ontology, children is-a and part-of In-Reply-To: References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu> Hi Leyla, Thanks for your email. Our copy of Gene Ontology is set to be updated nightly from the following URL: http://purl.obolibrary.org/obo/go.obo Our nightly pull mechanism checks the URL for the presence of a new file, and, if found, automatically downloads it and creates a new ontology submission on our end. The version inside the remote file currently reads: format-version: 1.2 data-version: releases/2020-05-02 ?which matches the one we have in our system. We use OWL API to process our ontologies, including those in OBO format. A good test of how OWL API processes an ontology would be to open the file in the Protege ontology editor. According to the screenshot below, Protege treats GO:0006357 as the superclass of the term GO:0006357: [cid:7A7C754A-AEBD-4362-9D3A-A5B3AF4CB188] Looking at GO:0000981, the same SubClass Of relationship is observed. So it does appear that the ?part of? relationship is treated as the "SubClass Of". [cid:5CF85BFF-3BC1-4D79-9138-2900792610CB] Unfortunately, as a software engineer, I am not an ontology development expert to offer a more thorough reasoning as to how each of these relationships is being evaluated. I am hoping that perhaps someone on this list can provide a more in-depth coverage of this use case. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 25, 2020, at 6:48 AM, Leyla Jael Garc?a Castro > wrote: Dear all, Does the current Gene Ontology release at BioPortal coincide with the latest version? I find differences with what is listed on the QuickGO website, I am trying to understand where those differences come from. For instance, term GO:0003258 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003258 in Bioportal lists GO.0006357 as one of its parents (subClassOf). However, according to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0003258 that is-a relation was removed on 2012-08-06 (see Change Log section). Why does Bioportal still includes this relation? Also, I found a difference between the website and the API. On the website I found GO:0000981 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000981 to be a subClassOf GO:0003700 only. When I use the API to query the children of GO:0006357 http://data.bioontology.org/ontologies/GO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0006357/children the term GO:0000981 is listed there. According to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0000981, GO:0000981 part_of GO:0006357 but there is no is_a relation between the two of them. Are terms related via part_of reported as children by the API? Kind regards, _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-26 at 12.39.15 PM.png Type: image/png Size: 842397 bytes Desc: Screen Shot 2020-05-26 at 12.39.15 PM.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-26 at 12.48.24 PM.png Type: image/png Size: 442818 bytes Desc: Screen Shot 2020-05-26 at 12.48.24 PM.png URL: From moefinger at deerfield.com Tue May 26 12:38:34 2020 From: moefinger at deerfield.com (Matthew Oefinger) Date: Tue, 26 May 2020 19:38:34 +0000 Subject: [bioontology-support] API key Message-ID: Hi, I am interested in using your API. How to I acquire an API key? Thank you, Matt This e-mail message is intended for the use of its intended recipient and may contain proprietary, confidential and/or privileged information. If you are not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this e-mail, its contents and any attachment(s), in whole or in part, is strictly prohibited without the prior written consent of Deerfield Management Company, L.P. If you have received this e-mail in error or are not the intended recipient, you are not authorized to use the information in this message in any way. Please do not read, copy, forward or store this message unless you are an intended recipient of it. Please notify the sender immediately by return e-mail, delete this e-mail and any attachment(s) and destroy all copies. Any unauthorized use is strictly prohibited. If you reply to this message, Deerfield Management Company, L.P. may collect personal information about you in accordance with our Privacy Policy. For additional information on our privacy practices, please click here. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 27 01:40:29 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 27 May 2020 01:40:29 -0700 Subject: [bioontology-support] [BioPortal] Feedback from dattah Message-ID: <5ece277d852a1_550e1def75047797@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 27 04:51:35 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 27 May 2020 04:51:35 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Sakina Message-ID: <5ece54473e08c_6876298bc9448467@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 27 11:16:36 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 27 May 2020 18:16:36 +0000 Subject: [bioontology-support] [BioPortal] Feedback from dattah In-Reply-To: <5ece277d852a1_550e1def75047797@ncbo-prd-app-09.stanford.edu.mail> References: <5ece277d852a1_550e1def75047797@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello, I suggest you try the SIFR repository, http://bioportal.lirmm.fr/ontologies. It contains a number of French terminologies related to biomedicine. John On May 27, 2020, at 1:40 AM, support at bioontology.org wrote: Name: dattah Email: dele.attah at avenirbiz.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FOMIM%3Fp%3Dclasses Feedback: dele.attah at avenirbiz.com Hi, we are currently implementing a healthcare system in Kinshasa, Democratic Republic of Congo. We have a requirement for lists of diseases, medical procedures, pharmacy information in French. Do you have a French language version of the website. Please supply the URL. If you know of any other source of this information could you please share. Thank you. Dele Attah _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 27 12:35:10 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Wed, 27 May 2020 19:35:10 +0000 Subject: [bioontology-support] your email to BioPortal support In-Reply-To: <4d53bed3-d6e4-ee04-a193-88cb5653908f@setint.com.tr> References: <4d53bed3-d6e4-ee04-a193-88cb5653908f@setint.com.tr> Message-ID: <03B334EF-82AA-47E3-88C7-FB69F1639804@stanford.edu> Hello, I'm sorry, it appears we don't have any C++ examples for using the API, and we don't have time to put one together right now. Possibly someone on the list could chime in with an example like this. References that may be useful include: - Our existing sample code: https://github.com/ncbo/ncbo_rest_sample_code - Our documentation on the API: http://data.bioontology.org/documentation - In particular, our overview of the different types of API calls: http://data.bioontology.org/documentation#nav_media_types John On May 27, 2020, at 12:22 PM, SETINT - ileti?im > wrote: Are you looking for a C++ example of API code to ask BioPortal about disease symptoms, like 'sniffle' or 'cough'? yes 27.05.2020 21:12 tarihinde John Graybeal yazd?: Hello, We received your question on the BioPortal support list, but I wanted to email you directly to make sure I understood your request. We don't have anyone who speaks Turkish on our staff, but I'm including a Google-generated translation in case that helps. (If you reply in Turkish, or another language, I can translate back to English on my side.) You wrote: Feedback: Hi Please you send code Code : C++ webworm sample : Symptom : snuffle What c++ web form api code. Thank you Are you looking for a C++ example of API code to ask BioPortal about disease symptoms, like 'sniffle' or 'cough'? I ask because I am sure you will be disappointed in the answer. BioPortal may give you matches for the term, but its content does not include any good way to map the terms back to diseases that might cause them. If you send me your use case, I may be able to give you better advice. We do have example code in several languages in our GitHub repository (https://github.com/ncbo/ncbo_rest_sample_code), but C# is as close to C++ as we seem to have. John ================== Merhaba, Sorunuzu BioPortal destek listesinde ald?k, ancak iste?inizi anlad???mdan emin olmak i?in size do?rudan e-posta g?ndermek istedim. Personelimizde T?rk?e konu?an kimsemiz yok, ancak yard?mc? olmas? durumunda Google taraf?ndan olu?turulan bir ?eviri ekliyorum. (T?rk?e veya ba?ka bir dilde yan?t verirseniz, yan?mda tekrar ?ngilizce'ye ?evirebilirim.) Sen yazd?n: Feedback: Hi Please you send code Code : C++ webworm sample : Symptom : snuffle What c++ web form api code. Thank you BioPortal'a 'koklama' veya '?ks?r?k' gibi hastal?k belirtileri hakk?nda soru soracak bir C ++ API kodu ?rne?i mi ar?yorsunuz? Soruyorum ??nk? cevapta hayal k?r?kl???na u?rayaca??n?zdan eminim. BioPortal terim i?in e?le?meler verebilir, ancak i?eri?i terimleri kendilerine neden olabilecek hastal?klarla e?le?tirmek i?in iyi bir yol i?ermez. Bana kullan?m durumunuzu g?nderirseniz, size daha iyi tavsiye verebilirim. GitHub depomuzda birka? dilde ?rnek kodumuz var (https://github.com/ncbo/ncbo_rest_sample_code), ancak C #, g?r?nd??? gibi C ++ 'a yak?n. John -- Sezgin SEZER Koordinat?r SETINT AI Robotic Sistem E?itim ve Dan??manl?k San.Tic.A.?. ________________________________ D?zce ?niversitesi Organ Gazi Mahallesi Teknopark Cad. Teknopark No:1 ?? Kap? No: 1 Merkez - D?zce Posta kodu : 81620 Sabit Tel : 0380 222 22 16 - GSM : 0552 593 34 66 E-Posta : sezgin.sezer at setint.com.tr Web Sitesi : www.setint.com.tr YASAL UYARI : Bu e-posta mesaj? ki?iye ?zel olup, gizli bilgiler i?eriyor. E?er bu e-posta mesaj? size yanl??l?kla ula?m?ssa, i?eri?ini hi?bir ?ekilde kullanmay?n?z ve ekli dosyalar? a?may?n?z. Bu durumda l?tfen e-posta mesaj?n? kullan?c?ya hemen geri g?nderiniz. Ve t?m kopyalar?n? mesaj kutunuzdan siliniz. Bu e-posta mesaj?, hi?bir ?ekilde, herhangi bir ama? i?in ?o?alt?lamaz, yay?nlanamaz ve para kar??l??? sat?lamaz. Bu e-posta mesaj? vir?slere kar?? anti-vir?s sistemleri taraf?ndan taranm??t?r. Ancak yollay?c?, bu e-posta mesaj?n?n- virus koruma sistemleri ile kontrol ediliyor olsa bile - virus i?ermedi?ini garanti etmez ve meydana gelebilecek zararlardan do?acak hi?bir sorumlulu?u kabul etmez. The information transmittedis intended only for the person or entity to which it is addressed and may contain confidential or privileged material. Any review, retransmission or otheruse of, or taking of any action in rellance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please notify the sender and delete the material from your computer. ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Wed May 27 17:09:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 28 May 2020 00:09:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sakina In-Reply-To: <5ece54473e08c_6876298bc9448467@ncbo-prd-app-09.stanford.edu.mail> References: <5ece54473e08c_6876298bc9448467@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <0E035C09-24D5-4BB3-ACE7-43158F9C58A4@stanford.edu> Hi Sakina, Thank you for your question. I am sorry to say, but we have not maintained the Resource Index application as regularly as our other tools, such as Ontology Annotator or Ontology Recommender. I?m not aware of a particular reason for this, other than we?re a small team and providing this functionality hasn?t hit the top of our priority list. With limited resources available, we must be highly selective of the tasks we undertake. Unfortunately, the Resource Index has not been one of those tasks. This may change in the future, but for now the Resource Index remains functional at its five-year-old snapshot. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 27, 2020, at 4:51 AM, support at bioontology.org wrote: Name: Sakina Email: sakina302 at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fresource_index Feedback: Hi, I would like to know when was this web-interface last updated? Thanks and regards! Sakina _______________________________________________ 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 Wed May 27 19:59:15 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 28 May 2020 02:59:15 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Sakina In-Reply-To: <0E035C09-24D5-4BB3-ACE7-43158F9C58A4@stanford.edu> References: <5ece54473e08c_6876298bc9448467@ncbo-prd-app-09.stanford.edu.mail> <0E035C09-24D5-4BB3-ACE7-43158F9C58A4@stanford.edu> Message-ID: I can add to Michael's description here, for the BioPortal community's awareness. The Resource Index proved an expensive service to maintain. We found that the Resource Index was particularly difficult to update for data systems, which change their APIs often without maintaining the previous API. (The work to keep it current for PubMed was operationally challenging for another reason: the size of that resource, multiplied by the increasing size of BioPortal's own search index.) Also, the original code for the Resource Index drivers was old enough that it would have required considerable rework for all of the interfaces we maintained. As a result, it received considerably fewer visitors as time went by. Given that many systems (notably PubMed) now include semantic tagging/searching for their content, we could not justify investing time in keeping the Resource Index current. Therefore, we are likely to deprecate it in the near future. I have to admit that will be a sad moment for me As always, if any of you have a source of funding for maintaining this feature and driving it forward, we would be happy to talk to you! John On May 27, 2020, at 5:09 PM, Michael Dorf > wrote: Hi Sakina, Thank you for your question. I am sorry to say, but we have not maintained the Resource Index application as regularly as our other tools, such as Ontology Annotator or Ontology Recommender. I?m not aware of a particular reason for this, other than we?re a small team and providing this functionality hasn?t hit the top of our priority list. With limited resources available, we must be highly selective of the tasks we undertake. Unfortunately, the Resource Index has not been one of those tasks. This may change in the future, but for now the Resource Index remains functional at its five-year-old snapshot. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 27, 2020, at 4:51 AM, support at bioontology.org wrote: Name: Sakina Email: sakina302 at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fresource_index Feedback: Hi, I would like to know when was this web-interface last updated? Thanks and regards! Sakina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed May 27 20:34:01 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 27 May 2020 20:34:01 -0700 Subject: [bioontology-support] [BioPortal] Feedback from omarial Message-ID: <5ecf3129d0ebf_734f2cc7dcc424f0@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Wed May 27 21:37:19 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 28 May 2020 04:37:19 +0000 Subject: [bioontology-support] [BioPortal] Feedback from omarial In-Reply-To: <5ecf3129d0ebf_734f2cc7dcc424f0@ncbo-prd-app-09.stanford.edu.mail> References: <5ecf3129d0ebf_734f2cc7dcc424f0@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <262B41F8-0384-483F-BB92-F1D4D6AFB39F@stanford.edu> Hello Omarial, We are sorry, we are unable to troubleshoot the operation of REDCap, as we do not maintain it or know exactly what it expects in that setting. Possibly someone with REDCap experience can reply on this list. Otherwise, you may wish to contact REDCap support at VUMC (redcap at vumc.org) for support with this issue. John On May 27, 2020, at 8:34 PM, support at bioontology.org wrote: Name: omarial Email: obaydullah.marial at health.nsw.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccounts%2Fomarial Feedback: Hi, I have tried to save the API key in the EDCap. It comes with error message when I wnat to enable it. ERROR: The value entered is not a valid BioPortal API token! Please try again. _______________________________________________ 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 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From redcap at vumc.org Thu May 28 07:35:47 2020 From: redcap at vumc.org (REDCap) Date: Thu, 28 May 2020 14:35:47 +0000 Subject: [bioontology-support] [BioPortal] Feedback from omarial In-Reply-To: <1DC61C28-795C-40B4-B5D4-38DD45CEC0F0@vumc.org> References: <5ecf3129d0ebf_734f2cc7dcc424f0@ncbo-prd-app-09.stanford.edu.mail> <262B41F8-0384-483F-BB92-F1D4D6AFB39F@stanford.edu> <1DC61C28-795C-40B4-B5D4-38DD45CEC0F0@vumc.org> Message-ID: Omarial, I'm not quite sure why that part isn't working, but if you run the queries below on your REDCap MySQL database, it should fix this issue for you. replace into redcap_config (field_name, `value`) values ('bioportal_api_token', '065188de-67e2-42a9-aa7b-e2340d314cb0'); replace into redcap_config (field_name, `value`) values ('bioportal_api_url', 'https://data.bioontology.org/'); Rob Taylor REDCap Team Manager and Lead Developer (https://projectredcap.org) Vanderbilt Institute for Clinical and Translational Research (VICTR) From: Harris, Paul Sent: Thursday, May 28, 2020 6:43 AM To: John Graybeal ; support at bioontology.org Cc: obaydullah.marial at health.nsw.gov.au; REDCap Subject: Re: [bioontology-support] [BioPortal] Feedback from omarial John - thanks. Omarial - ifthere is no response from the bioontology support listserv, I'd recommend you connect with your local REDCap Administrator - or if that is your role would recommend you raise this in either the REDCap Community forum or try to attend one of our weekly technical support calls - with details on the Community forum. I've also cc-d our main support group in case they have ideas. Best wishes. Paul From: John Graybeal > Date: Wednesday, May 27, 2020 at 11:37 PM To: "support at bioontology.org" > Cc: "obaydullah.marial at health.nsw.gov.au" > Subject: Re: [bioontology-support] [BioPortal] Feedback from omarial Hello Omarial, We are sorry, we are unable to troubleshoot the operation of REDCap, as we do not maintain it or know exactly what it expects in that setting. Possibly someone with REDCap experience can reply on this list. Otherwise, you may wish to contact REDCap support at VUMC (redcap at vumc.org) for support with this issue. John On May 27, 2020, at 8:34 PM, support at bioontology.org wrote: Name: omarial Email: obaydullah.marial at health.nsw.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccounts%2Fomarial Feedback: Hi, I have tried to save the API key in the EDCap. It comes with error message when I wnat to enable it. ERROR: The value entered is not a valid BioPortal API token! Please try again. _______________________________________________ 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 | ORCID 0000-0001-6875-5360 [ WARNING : This email came from an external source. Please treat this message with additional caution.] -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul.a.harris at vumc.org Thu May 28 04:43:08 2020 From: paul.a.harris at vumc.org (Harris, Paul) Date: Thu, 28 May 2020 11:43:08 +0000 Subject: [bioontology-support] [BioPortal] Feedback from omarial In-Reply-To: <262B41F8-0384-483F-BB92-F1D4D6AFB39F@stanford.edu> References: <5ecf3129d0ebf_734f2cc7dcc424f0@ncbo-prd-app-09.stanford.edu.mail> <262B41F8-0384-483F-BB92-F1D4D6AFB39F@stanford.edu> Message-ID: <1DC61C28-795C-40B4-B5D4-38DD45CEC0F0@vumc.org> John ? thanks. Omarial ? ifthere is no response from the bioontology support listserv, I?d recommend you connect with your local REDCap Administrator - or if that is your role would recommend you raise this in either the REDCap Community forum or try to attend one of our weekly technical support calls ? with details on the Community forum. I?ve also cc-d our main support group in case they have ideas. Best wishes. Paul From: John Graybeal Date: Wednesday, May 27, 2020 at 11:37 PM To: "support at bioontology.org" Cc: "obaydullah.marial at health.nsw.gov.au" Subject: Re: [bioontology-support] [BioPortal] Feedback from omarial Hello Omarial, We are sorry, we are unable to troubleshoot the operation of REDCap, as we do not maintain it or know exactly what it expects in that setting. Possibly someone with REDCap experience can reply on this list. Otherwise, you may wish to contact REDCap support at VUMC (redcap at vumc.org) for support with this issue. John On May 27, 2020, at 8:34 PM, support at bioontology.org wrote: Name: omarial Email: obaydullah.marial at health.nsw.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2Faccounts%2Fomarial Feedback: Hi, I have tried to save the API key in the EDCap. It comes with error message when I wnat to enable it. ERROR: The value entered is not a valid BioPortal API token! Please try again. _______________________________________________ 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 | ORCID 0000-0001-6875-5360 [ WARNING : This email came from an external source. Please treat this message with additional caution.] -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Thu May 28 11:10:54 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Thu, 28 May 2020 14:10:54 -0400 Subject: [bioontology-support] Error RDF labels - CIVIO_1 Message-ID: Hi, I recently submitted an ontology to BioPortal (CIVIO_1). The submission shows "error rdf labels" as shown in the attached screenshot. This had happened once previously and I was informed that it was an error while processing the file and not with the ontology and that reprocessing it solved the problem. I hope it is the same issue this time. If not please let me know. I want to use this ontology with the Annotator. But this issue makes the annotator not show any annotations. Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Untitled.png Type: image/png Size: 27296 bytes Desc: not available URL: From leylajael at gmail.com Thu May 28 12:15:06 2020 From: leylajael at gmail.com (=?UTF-8?Q?Leyla_Jael_Garc=C3=ADa_Castro?=) Date: Thu, 28 May 2020 21:15:06 +0200 Subject: [bioontology-support] GO ontology, children is-a and part-of In-Reply-To: <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu> References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu> Message-ID: Hi Michael, Thanks for your reply. I checked the ontology on the different download formats that you offer, tried them on Prot?g? as suggested. I think I understand where the difference comes from. It is even clearer when I look at the RDF/XML version. Is this RDF/XML version the one used to display the information on the website and to retrieve information via the API? Kind regards, On Tue, May 26, 2020 at 9:59 PM Michael Dorf wrote: > Hi Leyla, > > Thanks for your email. Our copy of Gene Ontology is set to be updated > nightly from the following URL: > > http://purl.obolibrary.org/obo/go.obo > > Our nightly pull mechanism checks the URL for the presence of a new file, > and, if found, automatically downloads it and creates a new ontology > submission on our end. The version inside the remote file currently reads: > > format-version: 1.2 > data-version: releases/2020-05-02 > > ?which matches the one we have in our system. > > We use OWL API to process our ontologies, including those in OBO format. A > good test of how OWL API processes an ontology would be to open the file in > the Protege ontology editor. According to the screenshot below, Protege > treats GO:0006357 as the superclass of the term GO:0006357: > > > Looking at GO:0000981, the same SubClass Of relationship is observed. So > it does appear that the ?part of? relationship is treated as the "SubClass > Of". > > Unfortunately, as a software engineer, I am not an ontology development > expert to offer a more thorough reasoning as to how each of these > relationships is being evaluated. I am hoping that perhaps someone on this > list can provide a more in-depth coverage of this use case. > > Thanks, > > Michael > > > > > > ---------------------------------------------------- > Michael Dorf > Chief Software Architect > The National Center for Biomedical Ontology > Stanford Biomedical Informatics Research > mdorf at stanford.edu > O: 650-723-0357 > M: 650-995-4374 > ---------------------------------------------------- > > On May 25, 2020, at 6:48 AM, Leyla Jael Garc?a Castro > wrote: > > Dear all, > > Does the current Gene Ontology release at BioPortal coincide with the > latest version? I find differences with what is listed on the QuickGO > website, I am trying to understand where those differences come from. > > For instance, term GO:0003258 > https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003258 in > Bioportal lists GO.0006357 as one of its parents (subClassOf). However, > according to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0003258 that > is-a relation was removed on 2012-08-06 (see Change Log section). Why does > Bioportal still includes this relation? > > Also, I found a difference between the website and the API. On the website > I found GO:0000981 > https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000981 > to > be a subClassOf GO:0003700 only. When I use the API to query the children > of GO:0006357 > http://data.bioontology.org/ontologies/GO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0006357/children the > term GO:0000981 is listed there. According to QuickGO > https://www.ebi.ac.uk/QuickGO/term/GO:0000981, GO:0000981 part_of > GO:0006357 but there is no is_a relation between the two of them. Are terms > related via part_of reported as children by the API? > > Kind regards, > > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-26 at 12.39.15 PM.png Type: image/png Size: 842397 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-05-26 at 12.48.24 PM.png Type: image/png Size: 442818 bytes Desc: not available URL: From mdorf at stanford.edu Thu May 28 23:51:13 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 29 May 2020 06:51:13 +0000 Subject: [bioontology-support] GO ontology, children is-a and part-of In-Reply-To: References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu> Message-ID: Hi Leyla, That?s correct. The output of the OWL API processor is a file called ?owlapi.xrdf?, which is ultimately used to generate the RDF triples that are dumped into our triple store backend (4store). These triples are then retrieved from 4store to display the ontology class information you see on the class details page. ?owlapi.xrdf? is the file you download when clicking on the RDF/XML link for a given ontology submission. Hope this helps. Thank you again for your insightful questions. Michael On May 28, 2020, at 12:15 PM, Leyla Jael Garc?a Castro > wrote: Hi Michael, Thanks for your reply. I checked the ontology on the different download formats that you offer, tried them on Prot?g? as suggested. I think I understand where the difference comes from. It is even clearer when I look at the RDF/XML version. Is this RDF/XML version the one used to display the information on the website and to retrieve information via the API? Kind regards, On Tue, May 26, 2020 at 9:59 PM Michael Dorf > wrote: Hi Leyla, Thanks for your email. Our copy of Gene Ontology is set to be updated nightly from the following URL: http://purl.obolibrary.org/obo/go.obo Our nightly pull mechanism checks the URL for the presence of a new file, and, if found, automatically downloads it and creates a new ontology submission on our end. The version inside the remote file currently reads: format-version: 1.2 data-version: releases/2020-05-02 ?which matches the one we have in our system. We use OWL API to process our ontologies, including those in OBO format. A good test of how OWL API processes an ontology would be to open the file in the Protege ontology editor. According to the screenshot below, Protege treats GO:0006357 as the superclass of the term GO:0006357: Looking at GO:0000981, the same SubClass Of relationship is observed. So it does appear that the ?part of? relationship is treated as the "SubClass Of". Unfortunately, as a software engineer, I am not an ontology development expert to offer a more thorough reasoning as to how each of these relationships is being evaluated. I am hoping that perhaps someone on this list can provide a more in-depth coverage of this use case. Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On May 25, 2020, at 6:48 AM, Leyla Jael Garc?a Castro > wrote: Dear all, Does the current Gene Ontology release at BioPortal coincide with the latest version? I find differences with what is listed on the QuickGO website, I am trying to understand where those differences come from. For instance, term GO:0003258 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003258 in Bioportal lists GO.0006357 as one of its parents (subClassOf). However, according to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0003258 that is-a relation was removed on 2012-08-06 (see Change Log section). Why does Bioportal still includes this relation? Also, I found a difference between the website and the API. On the website I found GO:0000981 https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000981 to be a subClassOf GO:0003700 only. When I use the API to query the children of GO:0006357 http://data.bioontology.org/ontologies/GO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0006357/children the term GO:0000981 is listed there. According to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0000981, GO:0000981 part_of GO:0006357 but there is no is_a relation between the two of them. Are terms related via part_of reported as children by the API? Kind regards, _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu May 28 23:57:26 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 29 May 2020 06:57:26 +0000 Subject: [bioontology-support] Error RDF labels - CIVIO_1 In-Reply-To: References: Message-ID: <3B687E2E-89AE-40A3-948D-B963D8FB8A95@stanford.edu> Hi Vipina, Thank you for getting in touch with us. Indeed, it?s a strange issue that doesn?t appear to be widespread, but it does affect a small number of ontologies. I?ve reprocessed CIVIO_1, and it?s now fully available in BioPortal (including the Annotator). Please keep us posted if you run into any further issues. Thanks! Michael > On May 28, 2020, at 11:10 AM, Kuttichi Keloth, Vipina wrote: > > Hi, > > I recently submitted an ontology to BioPortal (CIVIO_1). The submission shows "error rdf labels" as shown in the attached screenshot. This had happened once previously and I was informed that it was an error while processing the file and not with the ontology and that reprocessing it solved the problem. > > I hope it is the same issue this time. If not please let me know. > > I want to use this ontology with the Annotator. But this issue makes the annotator not show any annotations. > > Thank you. > Vipina > > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From support at bioontology.org Thu May 28 22:50:34 2020 From: support at bioontology.org (support at bioontology.org) Date: Thu, 28 May 2020 22:50:34 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Nicholas Mondinos Message-ID: <5ed0a2aa66cc9_5bbd21271981025c@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri May 29 09:43:59 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 29 May 2020 16:43:59 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Nicholas Mondinos In-Reply-To: <5ed0a2aa66cc9_5bbd21271981025c@ncbo-prd-app-09.stanford.edu.mail> References: <5ed0a2aa66cc9_5bbd21271981025c@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <6FE9CE4D-4199-4CFD-9565-67A628E99EB5@stanford.edu> Hi Nicholas, Thank you for your email. I haven?t been alerted of any recent downtime with our search service. It appears fully operational when running a test query: http://data.bioontology.org/search?q=melanoma (you?ll need to append your BioPortal API key to the URL for it to execute correctly, &apikey=yourapikey). If I were to troubleshoot further, it would be useful to figure out what specific search API call (with the exact query and parameters) resulted in the failed response you observed. Other than that, we are unable to provide support on the operation of REDCap, as we do not maintain it or know exactly what it expects in that setting. Possibly someone with REDCap experience can reply on this list. Otherwise, you may wish to contact REDCap support at VUMC (redcap at vumc.org) for support with this issue. Michael On May 28, 2020, at 10:50 PM, support at bioontology.org wrote: Name: Nicholas Mondinos Email: Nick.Mondinos at health.wa.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hi. We use REDCap to access and search the BioPortal Ontology Services. Unfortunately the ontolgy service search is blank. I am not sure if its due to your servers been down (temporarily ?). Could you please advice if this is so. Discussions in the REDCap community page indicate this may happen but i am not sure. Many Thanks Nick M _______________________________________________ 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 May 29 09:49:55 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 29 May 2020 16:49:55 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Nicholas Mondinos In-Reply-To: <6FE9CE4D-4199-4CFD-9565-67A628E99EB5@stanford.edu> References: <5ed0a2aa66cc9_5bbd21271981025c@ncbo-prd-app-09.stanford.edu.mail> <6FE9CE4D-4199-4CFD-9565-67A628E99EB5@stanford.edu> Message-ID: <46C68141-078D-4E7C-910D-8937D534DC21@stanford.edu> Hi Nicholas, To add to my answer, I?ve checked a few other services on our end (ontologies, classes, latest_submission), and they all appear operational: http://data.bioontology.org/ontologies/ https://data.bioontology.org/ontologies/NCIT/classes https://data.bioontology.org/ontologies/NCIT/latest_submission We do experience occasional service downtimes, but again, there hasn?t been a recent one as far I know. Michael On May 29, 2020, at 9:43 AM, Michael Dorf > wrote: Hi Nicholas, Thank you for your email. I haven?t been alerted of any recent downtime with our search service. It appears fully operational when running a test query: http://data.bioontology.org/search?q=melanoma (you?ll need to append your BioPortal API key to the URL for it to execute correctly, &apikey=yourapikey). If I were to troubleshoot further, it would be useful to figure out what specific search API call (with the exact query and parameters) resulted in the failed response you observed. Other than that, we are unable to provide support on the operation of REDCap, as we do not maintain it or know exactly what it expects in that setting. Possibly someone with REDCap experience can reply on this list. Otherwise, you may wish to contact REDCap support at VUMC (redcap at vumc.org) for support with this issue. Michael On May 28, 2020, at 10:50 PM, support at bioontology.org wrote: Name: Nicholas Mondinos Email: Nick.Mondinos at health.wa.gov.au Location: https%3A%2F%2Fbioportal.bioontology.org%2F Feedback: Hi. We use REDCap to access and search the BioPortal Ontology Services. Unfortunately the ontolgy service search is blank. I am not sure if its due to your servers been down (temporarily ?). Could you please advice if this is so. Discussions in the REDCap community page indicate this may happen but i am not sure. Many Thanks Nick M _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Fri May 29 09:53:40 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Fri, 29 May 2020 16:53:40 +0000 Subject: [bioontology-support] API key In-Reply-To: References: Message-ID: <55F2D5A0-6593-4F1B-BAB0-D567FD3DB29B@stanford.edu> Hi Matthew, Thank you for contacting support. You can find instructions for getting an API key on our wiki: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key Thank you, Michael On May 26, 2020, at 12:38 PM, Matthew Oefinger > wrote: Hi, I am interested in using your API. How to I acquire an API key? Thank you, Matt This e-mail message is intended for the use of its intended recipient and may contain proprietary, confidential and/or privileged information. If you are not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this e-mail, its contents and any attachment(s), in whole or in part, is strictly prohibited without the prior written consent of Deerfield Management Company, L.P. If you have received this e-mail in error or are not the intended recipient, you are not authorized to use the information in this message in any way. Please do not read, copy, forward or store this message unless you are an intended recipient of it. Please notify the sender immediately by return e-mail, delete this e-mail and any attachment(s) and destroy all copies. Any unauthorized use is strictly prohibited. If you reply to this message, Deerfield Management Company, L.P. may collect personal information about you in accordance with our Privacy Policy. For additional information on our privacy practices, please click here. Thank you. _______________________________________________ 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 leylajael at gmail.com Fri May 29 12:45:44 2020 From: leylajael at gmail.com (=?UTF-8?Q?Leyla_Jael_Garc=C3=ADa_Castro?=) Date: Fri, 29 May 2020 21:45:44 +0200 Subject: [bioontology-support] GO ontology, children is-a and part-of In-Reply-To: References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail> <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu> Message-ID: Hi Michael, Thanks a lot! The process and differences across the formats are now clear to me. Regards, On Fri, May 29, 2020 at 8:51 AM Michael Dorf wrote: > Hi Leyla, > > That?s correct. The output of the OWL API processor is a file called > ?owlapi.xrdf?, which is ultimately used to generate the RDF triples that > are dumped into our triple store backend (4store). These triples are then > retrieved from 4store to display the ontology class information you see on > the class details page. > > ?owlapi.xrdf? is the file you download when clicking on the RDF/XML link > for a given ontology submission. > > Hope this helps. Thank you again for your insightful questions. > > Michael > > > On May 28, 2020, at 12:15 PM, Leyla Jael Garc?a Castro < > leylajael at gmail.com> wrote: > > Hi Michael, > > Thanks for your reply. > I checked the ontology on the different download formats that you offer, > tried them on Prot?g? as suggested. I think I understand where the > difference comes from. It is even clearer when I look at the RDF/XML > version. Is this RDF/XML version the one used to display the information on > the website and to retrieve information via the API? > > Kind regards, > > On Tue, May 26, 2020 at 9:59 PM Michael Dorf wrote: > >> Hi Leyla, >> >> Thanks for your email. Our copy of Gene Ontology is set to be updated >> nightly from the following URL: >> >> http://purl.obolibrary.org/obo/go.obo >> >> Our nightly pull mechanism checks the URL for the presence of a new file, >> and, if found, automatically downloads it and creates a new ontology >> submission on our end. The version inside the remote file currently reads: >> >> format-version: 1.2 >> data-version: releases/2020-05-02 >> >> ?which matches the one we have in our system. >> >> We use OWL API to process our ontologies, including those in OBO format. >> A good test of how OWL API processes an ontology would be to open the file >> in the Protege ontology editor. According to the screenshot below, Protege >> treats GO:0006357 as the superclass of the term GO:0006357: >> >> >> >> Looking at GO:0000981, the same SubClass Of relationship is observed. So >> it does appear that the ?part of? relationship is treated as the "SubClass >> Of". >> >> >> Unfortunately, as a software engineer, I am not an ontology development >> expert to offer a more thorough reasoning as to how each of these >> relationships is being evaluated. I am hoping that perhaps someone on this >> list can provide a more in-depth coverage of this use case. >> >> Thanks, >> >> Michael >> >> >> >> >> >> ---------------------------------------------------- >> Michael Dorf >> Chief Software Architect >> The National Center for Biomedical Ontology >> Stanford Biomedical Informatics Research >> mdorf at stanford.edu >> O: 650-723-0357 >> M: 650-995-4374 >> ---------------------------------------------------- >> >> On May 25, 2020, at 6:48 AM, Leyla Jael Garc?a Castro < >> leylajael at gmail.com> wrote: >> >> Dear all, >> >> Does the current Gene Ontology release at BioPortal coincide with the >> latest version? I find differences with what is listed on the QuickGO >> website, I am trying to understand where those differences come from. >> >> For instance, term GO:0003258 >> https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0003258 in >> Bioportal lists GO.0006357 as one of its parents (subClassOf). However, >> according to QuickGO https://www.ebi.ac.uk/QuickGO/term/GO:0003258 that >> is-a relation was removed on 2012-08-06 (see Change Log section). Why does >> Bioportal still includes this relation? >> >> Also, I found a difference between the website and the API. On the >> website I found GO:0000981 >> https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0000981 >> to >> be a subClassOf GO:0003700 only. When I use the API to query the children >> of GO:0006357 >> http://data.bioontology.org/ontologies/GO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0006357/children the >> term GO:0000981 is listed there. According to QuickGO >> https://www.ebi.ac.uk/QuickGO/term/GO:0000981, GO:0000981 part_of >> GO:0006357 but there is no is_a relation between the two of them. Are terms >> related via part_of reported as children by the API? >> >> Kind regards, >> >> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: