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>

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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: <CD6631D2-926B-4DC7-B389-9ED5560C922D@stanford.edu>

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 <bioontology-support-bounces at lists.stanford.edu> on behalf of "support at bioontology.org" <support at bioontology.org>
Date: Friday, May 1, 2020 at 9:51 AM
To: "support at bioontology.org" <support at bioontology.org>, "justin.levens at uky.edu" <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.
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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: <B8E6CF3F-407B-4E75-B3EF-F095F66A6C95@stanford.edu>

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<mailto:support at bioontology.org> wrote:


Name: jlevens

Email: justin.levens at uky.edu<mailto:justin.levens at uky.edu>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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



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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: <OF0A00F187.B117233C-ON0025855B.000CEDD2-0025855B.000D2C40@notes.na.collabserv.com>
References: <OFA371DB05.D8A0740C-ON0025855A.0080DBCF-0025855A.0081F1D4@LocalDomain>
 <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>
 <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
 <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
 <OF0A00F187.B117233C-ON0025855B.000CEDD2-0025855B.000D2C40@notes.na.collabserv.com>
Message-ID: <BCE686CF-2AD0-469C-82EE-24E1F9925980@stanford.edu>

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 <chinghua at us.ibm.com>
Date: Thursday, April 30, 2020 at 7:24 PM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Cc: "bioontology-support at lists.stanford.edu" <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:

#<Net::HTTPConflict:0x00007fc4288004a0>
#<Net::HTTPCreated:0x00007fc426903750>
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:

#<Net::HTTPConflict:0x00007ffd700145a8>
#<Net::HTTPBadRequest:0x00007ffd7083f9d0>
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 <vendetti at stanford.edu>
To: Ching-Hua Chen <chinghua at us.ibm.com>
Cc: "bioontology-support at lists.stanford.edu" <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 <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> 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<mailto: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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
To: Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>>
Cc: "bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>" <bioontology-support at lists.stanford.edu<mailto: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 <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> 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:

<Image.67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu.png>



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?:

<Image.9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu.png>


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






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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: <BCE686CF-2AD0-469C-82EE-24E1F9925980@stanford.edu>
References: <BCE686CF-2AD0-469C-82EE-24E1F9925980@stanford.edu>,
 <OFA371DB05.D8A0740C-ON0025855A.0080DBCF-0025855A.0081F1D4@LocalDomain>
 <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>
 <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
 <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
 <OF0A00F187.B117233C-ON0025855B.000CEDD2-0025855B.000D2C40@notes.na.collabserv.com>
Message-ID: <OF02F28B33.0547FC34-ON0025855B.007536A9-0025855B.00754AD2@notes.na.collabserv.com>

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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: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
Message-ID: <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>


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  <https://slack-redir.net/link?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FBAO%2Fclasses%2Fhttp%253A%252F%252Fwww.bioassayontology.org%252Fbao%2523BAO_0003048%3Fapikey%3D3f58b9d8-8896-4db0-8bc4-815c42d3df5b&v=3>";
> HttpHeaders headers = new HttpHeaders();
> headers.set("Accept", "text/html,application/json");
> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
> HttpEntity entity = new HttpEntity(headers);
> HttpEntity<String> 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
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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: <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
Message-ID: <D83575AD-893F-486A-B93B-3E05F2DFF9D4@stanford.edu>

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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://slack-redir.net/link?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FBAO%2Fclasses%2Fhttp%253A%252F%252Fwww.bioassayontology.org%252Fbao%2523BAO_0003048%3Fapikey%3D3f58b9d8-8896-4db0-8bc4-815c42d3df5b&v=3>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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: <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://slack-redir.net/link?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FBAO%2Fclasses%2Fhttp%253A%252F%252Fwww.bioassayontology.org%252Fbao%2523BAO_0003048%3Fapikey%3D3f58b9d8-8896-4db0-8bc4-815c42d3df5b&v=3>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto: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



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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: <a42296b4-9bd8-60cc-455f-df65b94208dc@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <a42296b4-9bd8-60cc-455f-df65b94208dc@med.miami.edu>
Message-ID: <E79319E0-234F-4C1B-A5EC-F60DB9FC534A@stanford.edu>

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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C53e49736eda14831535c08d7f0687cbe%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637242203900794797&sdata=QGPd%2By%2Fr%2FflNc31Zz8antU1zXEcMFn5GrBRBNJOCerk%3D&reserved=0>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto: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



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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: <a42296b4-9bd8-60cc-455f-df65b94208dc@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <a42296b4-9bd8-60cc-455f-df65b94208dc@med.miami.edu>
Message-ID: <CBA525C9-132C-4CFB-B53A-9AC4E436312A@stanford.edu>

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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C53e49736eda14831535c08d7f0687cbe%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637242203900794797&sdata=QGPd%2By%2Fr%2FflNc31Zz8antU1zXEcMFn5GrBRBNJOCerk%3D&reserved=0>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto: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



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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: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
Message-ID: <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>

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 <br />
> Host: 127.0.0.1 <br />
> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu <br />
> Authorization: apikey token=<key> <br />
> Accept: text/html,application/json <br />


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 <jpt55 at med.miami.edu 
>> <mailto:jpt55 at med.miami.edu>> 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  <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C53e49736eda14831535c08d7f0687cbe%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637242203900794797&sdata=QGPd%2By%2Fr%2FflNc31Zz8antU1zXEcMFn5GrBRBNJOCerk%3D&reserved=0>";
>>> HttpHeaders headers = new HttpHeaders();
>>> headers.set("Accept", "text/html,application/json");
>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
>>> HttpEntity entity = new HttpEntity(headers);
>>> HttpEntity<String> 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 
>> <mailto: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

  

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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: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
Message-ID: <a42296b4-9bd8-60cc-455f-df65b94208dc@med.miami.edu>


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 <jpt55 at med.miami.edu 
>> <mailto:jpt55 at med.miami.edu>> 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  <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C53e49736eda14831535c08d7f0687cbe%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637242203900794797&sdata=QGPd%2By%2Fr%2FflNc31Zz8antU1zXEcMFn5GrBRBNJOCerk%3D&reserved=0>";
>>> HttpHeaders headers = new HttpHeaders();
>>> headers.set("Accept", "text/html,application/json");
>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
>>> HttpEntity entity = new HttpEntity(headers);
>>> HttpEntity<String> 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 
>> <mailto: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
>
>
>
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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: <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.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<http://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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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 <br />
Host: 127.0.0.1 <br />
User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu> <br />
Authorization: apikey token=<key> <br />
Accept: text/html,application/json <br />



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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C53e49736eda14831535c08d7f0687cbe%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637242203900794797&sdata=QGPd%2By%2Fr%2FflNc31Zz8antU1zXEcMFn5GrBRBNJOCerk%3D&reserved=0>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto: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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>
 <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu>
Message-ID: <d09e31b6-54dc-4da4-b107-840eed2e54b9@med.miami.edu>

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 
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fwww.bioassayontology.org%2F&data=02%7C01%7Cjpt55%40med.miami.edu%7C61153ed13b224512e74a08d7f13116da%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243065457872994&sdata=WOsgf3SV2aiigbiillts8kh4HkDn7AD1k7Qi%2Bp4fDCM%3D&reserved=0>%2Fbao%23BAO_0003048' 
> is not a valid IRI"],"status":400}]
>
> Thanks,
>
> Misha
>
>
>
>> On May 4, 2020, at 1:46 PM, John Turner <jpt55 at med.miami.edu 
>> <mailto:jpt55 at med.miami.edu>> 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 <br />
>>> Host: 127.0.0.1 <br />
>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu <br />
>>> Authorization: apikey token=<key> <br />
>>> Accept: text/html,application/json <br />
>>
>>
>>
>> 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 <jpt55 at med.miami.edu 
>>>> <mailto:jpt55 at med.miami.edu>> 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  <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C61153ed13b224512e74a08d7f13116da%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243065457882991&sdata=a9LD8agx6bOxqPKlGe%2Fh2jSIuIFxH%2BDJ0HA2s7vBgaI%3D&reserved=0>";
>>>>> HttpHeaders headers = new HttpHeaders();
>>>>> headers.set("Accept", "text/html,application/json");
>>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
>>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
>>>>> HttpEntity entity = new HttpEntity(headers);
>>>>> HttpEntity<String> 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 
>>>> <mailto: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 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
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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: <d09e31b6-54dc-4da4-b107-840eed2e54b9@med.miami.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>
 <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu>
 <d09e31b6-54dc-4da4-b107-840eed2e54b9@med.miami.edu>
Message-ID: <E9ADCC39-1B15-4AC7-AFD8-50E86593917B@stanford.edu>

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<String> 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<mailto:jpt55 at med.miami.edu>");
    headers.set("Authorization", "apikey token=" + API_KEY);
    RestTemplate restTemplate = new RestTemplate();
    HttpEntity<String> entity = new HttpEntity<String>("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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fwww.bioassayontology.org%2F&data=02%7C01%7Cjpt55%40med.miami.edu%7C61153ed13b224512e74a08d7f13116da%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243065457872994&sdata=WOsgf3SV2aiigbiillts8kh4HkDn7AD1k7Qi%2Bp4fDCM%3D&reserved=0>%2Fbao%23BAO_0003048' is not a valid IRI"],"status":400}]

Thanks,

Misha



On May 4, 2020, at 1:46 PM, John Turner <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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 <br />
Host: 127.0.0.1 <br />
User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu> <br />
Authorization: apikey token=<key> <br />
Accept: text/html,application/json <br />



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 <jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>> 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<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7C61153ed13b224512e74a08d7f13116da%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243065457882991&sdata=a9LD8agx6bOxqPKlGe%2Fh2jSIuIFxH%2BDJ0HA2s7vBgaI%3D&reserved=0>";
HttpHeaders headers = new HttpHeaders();
headers.set("Accept", "text/html,application/json");
headers.set("User-Agent", "Ontolobridge; Contact jpt55 at med.miami.edu<mailto:jpt55 at med.miami.edu>");
//headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
HttpEntity entity = new HttpEntity(headers);
HttpEntity<String> 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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7Cjpt55%40med.miami.edu%7C61153ed13b224512e74a08d7f13116da%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243065457882991&sdata=TlmpRkh3iMNq%2FT5yLlfCCoI1KWM3irce4NYAi%2BjZnAk%3D&reserved=0>

========================
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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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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: <E9ADCC39-1B15-4AC7-AFD8-50E86593917B@stanford.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>
 <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu>
 <d09e31b6-54dc-4da4-b107-840eed2e54b9@med.miami.edu>
 <E9ADCC39-1B15-4AC7-AFD8-50E86593917B@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<String> 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 <mailto:jpt55 at med.miami.edu>");
>      headers.set("Authorization","apikey token=" +API_KEY);
>      RestTemplate restTemplate =new RestTemplate();
>      HttpEntity<String> entity =new HttpEntity<String>("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 <jpt55 at med.miami.edu 
>> <mailto:jpt55 at med.miami.edu>> 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 
>>> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fwww.bioassayontology.org%2F&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514350317&sdata=vfn1LkKieUd53FTcGC9b7B5GZ0%2BhVIwTboezkDo1PA4%3D&reserved=0>%2Fbao%23BAO_0003048' 
>>> is not a valid IRI"],"status":400}]
>>>
>>> Thanks,
>>>
>>> Misha
>>>
>>>
>>>
>>>> On May 4, 2020, at 1:46 PM, John Turner <jpt55 at med.miami.edu 
>>>> <mailto:jpt55 at med.miami.edu>> 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 <br />
>>>>> Host: 127.0.0.1 <br />
>>>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu 
>>>>> <mailto:jpt55 at med.miami.edu> <br />
>>>>> Authorization: apikey token=<key> <br />
>>>>> Accept: text/html,application/json <br />
>>>>
>>>>
>>>>
>>>> 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 <jpt55 at med.miami.edu 
>>>>>> <mailto:jpt55 at med.miami.edu>> 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  <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514350317&sdata=n3f330hM6bI%2Bhs6WT5P%2Bwhed8moMrdH52WkPrdfMEQ4%3D&reserved=0>";
>>>>>>> HttpHeaders headers = new HttpHeaders();
>>>>>>> headers.set("Accept", "text/html,application/json");
>>>>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
>>>>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
>>>>>>> HttpEntity entity = new HttpEntity(headers);
>>>>>>> HttpEntity<String> 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 
>>>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>>>>>> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514360314&sdata=adGS%2BLFJgW511IVTrC9XS9JJill1OuwyZXCr08OQRz8%3D&reserved=0>
>>>>>
>>>>> ========================
>>>>> 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 
>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>>>> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514360314&sdata=adGS%2BLFJgW511IVTrC9XS9JJill1OuwyZXCr08OQRz8%3D&reserved=0>
>>>
>
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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: <E9ADCC39-1B15-4AC7-AFD8-50E86593917B@stanford.edu>
References: <b399ff5c-4198-bd33-1941-a017c3917058@med.miami.edu>
 <f1fd9065-9a14-7c8c-11d1-767f971a9995@med.miami.edu>
 <8856A8BC-57D9-4871-A121-FDCF56078F7B@stanford.edu>
 <d520063a-0e62-1a15-0585-5936d48611c7@med.miami.edu>
 <26E4D49D-1114-431F-9D6B-F49A07EE0D7E@stanford.edu>
 <d09e31b6-54dc-4da4-b107-840eed2e54b9@med.miami.edu>
 <E9ADCC39-1B15-4AC7-AFD8-50E86593917B@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<String> 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 <mailto:jpt55 at med.miami.edu>");
>      headers.set("Authorization","apikey token=" +API_KEY);
>      RestTemplate restTemplate =new RestTemplate();
>      HttpEntity<String> entity =new HttpEntity<String>("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 <jpt55 at med.miami.edu 
>> <mailto:jpt55 at med.miami.edu>> 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 
>>> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fwww.bioassayontology.org%2F&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514350317&sdata=vfn1LkKieUd53FTcGC9b7B5GZ0%2BhVIwTboezkDo1PA4%3D&reserved=0>%2Fbao%23BAO_0003048' 
>>> is not a valid IRI"],"status":400}]
>>>
>>> Thanks,
>>>
>>> Misha
>>>
>>>
>>>
>>>> On May 4, 2020, at 1:46 PM, John Turner <jpt55 at med.miami.edu 
>>>> <mailto:jpt55 at med.miami.edu>> 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 <br />
>>>>> Host: 127.0.0.1 <br />
>>>>> User-Agent: Ontolobridge; Contact jpt55 at med.miami.edu 
>>>>> <mailto:jpt55 at med.miami.edu> <br />
>>>>> Authorization: apikey token=<key> <br />
>>>>> Accept: text/html,application/json <br />
>>>>
>>>>
>>>>
>>>> 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 <jpt55 at med.miami.edu 
>>>>>> <mailto:jpt55 at med.miami.edu>> 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  <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslack-redir.net%2Flink%3Furl%3Dhttp%253A%252F%252Fdata.bioontology.org%252Fontologies%252FBAO%252Fclasses%252Fhttp%25253A%25252F%25252Fwww.bioassayontology.org%25252Fbao%252523BAO_0003048%253Fapikey%253D3f58b9d8-8896-4db0-8bc4-815c42d3df5b%26v%3D3&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514350317&sdata=n3f330hM6bI%2Bhs6WT5P%2Bwhed8moMrdH52WkPrdfMEQ4%3D&reserved=0>";
>>>>>>> HttpHeaders headers = new HttpHeaders();
>>>>>>> headers.set("Accept", "text/html,application/json");
>>>>>>> headers.set("User-Agent", "Ontolobridge; Contactjpt55 at med.miami.edu  <mailto:jpt55 at med.miami.edu>");
>>>>>>> //headers.set("Cookie","JSESSIONID=EC9EBA70B831429B74F7D2BF1F7E0A10");RestTemplate restTemplate = new RestTemplate();
>>>>>>> HttpEntity entity = new HttpEntity(headers);
>>>>>>> HttpEntity<String> 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 
>>>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>>>>>> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514360314&sdata=adGS%2BLFJgW511IVTrC9XS9JJill1OuwyZXCr08OQRz8%3D&reserved=0>
>>>>>
>>>>> ========================
>>>>> 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 
>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>>>> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7Cjpt55%40med.miami.edu%7Ce509b9157afa433eba7108d7f15696a0%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637243226514360314&sdata=adGS%2BLFJgW511IVTrC9XS9JJill1OuwyZXCr08OQRz8%3D&reserved=0>
>>>
>
-- 


John Paul Turner

PhD Candidate

Stephan Schurer Lab

Molecular and Cellular Pharmacology

University of Miami Miller School of Medicine

  

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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: <CAOaXRCfB=8sa5=zCcp83yhYSfRFpT95=aG--Zcv-x7ehjbBeRA@mail.gmail.com>

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]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

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.
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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>

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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: <CAOaXRCfB=8sa5=zCcp83yhYSfRFpT95=aG--Zcv-x7ehjbBeRA@mail.gmail.com>
References: <CAOaXRCfB=8sa5=zCcp83yhYSfRFpT95=aG--Zcv-x7ehjbBeRA@mail.gmail.com>
Message-ID: <AECAA93B-5633-4831-B555-F3FCEC5E73D2@stanford.edu>

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://<your virtual appliance hostname>/ontologies/NCIT/submissions/<submission id>/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 <your 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<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On May 7, 2020, at 8:02 AM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> 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<mailto:rakesh at pieriandx.com>

[pierian-logo-trans-light-background]<http://www.pieriandx.com/>   [linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/>  [twitter_circle-512] <https://twitter.com/pieriandx>

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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On May 6, 2020, at 8:40 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Maribel

Email: mluna at riversidemedgroup.com<mailto:mluna at riversidemedgroup.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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>

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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: <BB22F84D-B8E8-4DB8-A0D8-43254D48ECC6@stanford.edu>

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<mailto:support at bioontology.org> wrote:


Name: Elizabeth Anderson

Email: e13cook at gmail.com<mailto:e13cook at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Ffeedback%3Flocation%3Dhttps%25253A%25252F%25252Fbioportal.bioontology.org<http://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<http://data.bioontology.org/annotator?text=Melanoma%20is%20%E0%B2%AC%E0%B2%BE%20%E0%B2%87%E0%B2%B2%E0%B3%8D%E0%B2%B2%E0%B2%BF%20%E0%B2%B8%E0%B2%82%E0%B2%AD%E0%B2%B5%E0%B2%BF%E0%B2%B8%E0%B3%81%20%E0%B2%87%E0%B2%82%E0%B2%A6%E0%B3%86%E0%B2%A8%E0%B3%8D%E0%B2%A8%20%E0%B2%B9%E0%B3%83%E0%B2%A6%E0%B2%AF%E0%B2%A6%E0%B2%B2%E0%B2%BF%20%E0%B2%A8%E0%B2%BF%E0%B2%A4%E0%B3%8D%E0%B2%AF%E0%B2%B5%E0%B3%82%20%E0%B2%85%E0%B2%B5%E0%B2%A4%E0%B2%B0%E0%B2%BF%E0%B2%AA%20bad%20%E0%B2%B8%E0%B2%A4%E0%B3%8D%E0%B2%AF%E0%B2%BE%E0%B2%B5%E0%B2%A4%E0%B2%BE%E0%B2%B0%20disease%20%E0%B2%AE%E0%B2%A3%E0%B3%8D%E0%B2%A3%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%AE%E0%B2%B0%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%AE%E0%B2%BF%E0%B2%97%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%95%E0%B2%97%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B3%80...%20%E0%B2%AE%E0%B2%A3%E0%B3%8D%E0%B2%A3%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%AE%E0%B2%B0%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%AE%E0%B2%BF%E0%B2%97%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%95%E0%B2%97%E0%B2%B5%E0%B2%BE%E0%B2%97%E0%B2%BF%20%E0%B2%AD%E0%B2%B5%20%E0%B2%AD%E0%B2%B5%E0%B2%A6%E0%B2%BF%20%E0%B2%AD%E0%B2%A4%E0%B2%BF%E0%B2%B8%E0%B2%BF%E0%B2%B9%E0%B3%87%20%E0%B2%AD%E0%B2%B5%E0%B2%A4%E0%B2%BF%20%E0%B2%A6%E0%B3%82%E0%B2%B0%20%E0%B2%A8%E0%B2%BF%E0%B2%A4%E0%B3%8D%E0%B2%AF%E0%B2%B5%E0%B3%82%20%E0%B2%85%E0%B2%B5%E0%B2%A4%E0%B2%B0%E0%B2%BF%E0%B2%AA%20%E0%B2%B8%E0%B2%A4%E0%B3%8D%E0%B2%AF%E0%B2%BE%E0%B2%B5%E0%B2%A4%E0%B2%BE%E0%B2%B0%20%7C%7C%20%E0%B2%AC%E0%B2%BE%20%E0%B2%87%E0%B2%B2%E0%B3%8D%E0%B2%B2%E0%B2%BF%20%7C%7C%20%E3%81%84%E3%82%8D%E3%81%AF%E3%81%AB%E3%81%BB%E3%81%B8%E3%81%A9%E3%80%80%E3%81%A1%E3%82%8A%E3%81%AC%E3%82%8B%E3%82%92%20%E3%82%8F%E3%81%8C%E3%82%88%E3%81%9F%E3%82%8C%E3%81%9E%E3%80%80%E3%81%A4%E3%81%AD%E3%81%AA%E3%82%89%E3%82%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<mailto:bioontology-support at lists.stanford.edu>
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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: <AECAA93B-5633-4831-B555-F3FCEC5E73D2@stanford.edu>
References: <CAOaXRCfB=8sa5=zCcp83yhYSfRFpT95=aG--Zcv-x7ehjbBeRA@mail.gmail.com>
 <AECAA93B-5633-4831-B555-F3FCEC5E73D2@stanford.edu>
Message-ID: <CAOaXRCc85YVEO3_G5O0rtbc4aD0H03OW3BixyZFWx+0n+gRxoQ@mail.gmail.com>

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 <mdorf at stanford.edu> 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://<your virtual appliance
> hostname>/ontologies/NCIT/submissions/<submission id>/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 <your
> 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 <rakesh at pieriandx.com> 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] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> 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]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

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.
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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>

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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 
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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 <elie.arnaud at mnhn.fr<mailto:elie.arnaud at mnhn.fr>> 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<mailto: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



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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: <C6EC5670-59B1-4E31-9DF9-380D93CBDF9E@stanford.edu>

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<mailto:support at bioontology.org> wrote:


Name: Zhiliang Hu

Email: zhu at iastate.edu<mailto:zhu at iastate.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://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



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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: <D34C6631-75FD-41D2-B071-964E0CE8876C@iastate.edu>

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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Zhiliang,


On May 11, 2020, at 9:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Zhiliang Hu

Email: zhu at iastate.edu<mailto:zhu at iastate.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://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


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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: <D34C6631-75FD-41D2-B071-964E0CE8876C@iastate.edu>
References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail>
 <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu>
 <D34C6631-75FD-41D2-B071-964E0CE8876C@iastate.edu>
Message-ID: <F9BE3159-0EAC-4571-85B4-054E9F1DC417@stanford.edu>

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<http://bioportal.bioontology.org/>. If you don't have an account, you'll need to create one<http://bioportal.bioontology.org/accounts/new>.

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] <zhu at iastate.edu<mailto:zhu at iastate.edu>> 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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Zhiliang,


On May 11, 2020, at 9:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Zhiliang Hu

Email: zhu at iastate.edu<mailto:zhu at iastate.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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



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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: <F9BE3159-0EAC-4571-85B4-054E9F1DC417@stanford.edu>
References: <5eb9822d42fd5_59b2058c1c5740@ncbo-prd-app-09.stanford.edu.mail>
 <7FC2E875-1BCC-44F1-A484-143202D027AB@stanford.edu>
 <D34C6631-75FD-41D2-B071-964E0CE8876C@iastate.edu>
 <F9BE3159-0EAC-4571-85B4-054E9F1DC417@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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> 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<http://bioportal.bioontology.org/>. If you don't have an account, you'll need to create one<http://bioportal.bioontology.org/accounts/new>.

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] <zhu at iastate.edu<mailto:zhu at iastate.edu>> 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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Zhiliang,


On May 11, 2020, at 9:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Zhiliang Hu

Email: zhu at iastate.edu<mailto:zhu at iastate.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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




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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>

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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: <D1A9C9F6-EA60-4B81-9708-F800C26227CA@stanford.edu>

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<mailto:support at bioontology.org> wrote:


Name: Katie Durnen, MD

Email: durnenmd at atallamd.com<mailto:durnenmd at atallamd.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://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<mailto: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



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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>

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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: <B77EDDC4-A43F-47D5-A3CA-70610A8F6312@stanford.edu>

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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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<mailto:support at bioontology.org> wrote:


Name: Karin Colsman

Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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



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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>

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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<mailto:support at bioontology.org> wrote:


Name: Martin Hofmann-Apitius

Email: martin.hofmann-apitius at scai.fraunhofer.de<mailto:martin.hofmann-apitius at scai.fraunhofer.de>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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 <vendetti at 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
> 
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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: <E6276EEA-882E-4787-9336-1E44113E552A@stanford.edu>
 <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 <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Friday, May 15, 2020 15:23
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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

<image001.png>




On May 15, 2020, at 3:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Karin Colsman
Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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




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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: <E6276EEA-882E-4787-9336-1E44113E552A@stanford.edu>
 <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 <vendetti at stanford.edu>
Sent: Monday, May 18, 2020 23:45
To: Karin Colsman <karin.colsman.contractor at osthus.com>
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 <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Friday, May 15, 2020 15:23
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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

<image001.png>





On May 15, 2020, at 3:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Karin Colsman
Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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




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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: <E6276EEA-882E-4787-9336-1E44113E552A@stanford.edu>
 <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu>
 <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu>
Message-ID: <a41ebffb9b41472ab5b91bd11dddbddb@osthus.com>

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 <vendetti at stanford.edu>
Sent: Monday, May 18, 2020 23:45
To: Karin Colsman <karin.colsman.contractor at osthus.com>
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 <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Friday, May 15, 2020 15:23
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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

<image001.png>





On May 15, 2020, at 3:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Karin Colsman
Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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




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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: <a41ebffb9b41472ab5b91bd11dddbddb@osthus.com>
References: <E6276EEA-882E-4787-9336-1E44113E552A@stanford.edu>
 <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu>
 <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu>
 <a41ebffb9b41472ab5b91bd11dddbddb@osthus.com>
Message-ID: <EC50F038-53E2-4AA6-BE8B-B8F3172093C8@stanford.edu>

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 <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Monday, May 18, 2020 23:45
To: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
Cc: support at bioontology.org<mailto: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


<image001.png>





On May 15, 2020, at 7:45 AM, Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Friday, May 15, 2020 15:23
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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

<image001.png>





On May 15, 2020, at 3:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Karin Colsman
Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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





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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: <CALAe=OK94Xxbmgyh9BkBtT5MNeYsfp9tcaAQcyhSMA0G-Gj59g@mail.gmail.com>

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
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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: <CALAe=OK94Xxbmgyh9BkBtT5MNeYsfp9tcaAQcyhSMA0G-Gj59g@mail.gmail.com>
References: <CALAe=OK94Xxbmgyh9BkBtT5MNeYsfp9tcaAQcyhSMA0G-Gj59g@mail.gmail.com>
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 <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> 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<mailto: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



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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>

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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 -----
<ps at mole.bio.cam.ac.uk>
    (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 <ps at mole.bio.cam.ac.uk>... 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
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From: support at bioontology.org
Subject: [BioPortal] Feedback from PaulNSchofield
Date: Thu, 21 May 2020 01:01:15 -0700
Size: 3817
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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: <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>

Hi Paul,


On May 21, 2020, at 1:01 AM, support at bioontology.org<mailto: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

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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: <EC50F038-53E2-4AA6-BE8B-B8F3172093C8@stanford.edu>
References: <E6276EEA-882E-4787-9336-1E44113E552A@stanford.edu>
 <13DD06CC-25D6-40E0-986E-FDDF078373DE@stanford.edu>
 <2D221771-CF1C-42B3-8328-8F51F5C755FC@stanford.edu>
 <a41ebffb9b41472ab5b91bd11dddbddb@osthus.com>
 <EC50F038-53E2-4AA6-BE8B-B8F3172093C8@stanford.edu>
Message-ID: <6875ff1f1c244334bca76575b95e2cfb@osthus.com>

It?s uploaded and working fine. Thanks for all your help!


From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Tuesday, May 19, 2020 15:08
To: Karin Colsman <karin.colsman.contractor at osthus.com>
Cc: support at bioontology.org; Amnon Ptashek <amnon.ptashek at allotrope.org>; Matthew Fox <matthew.fox at allotrope.org>
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 <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Monday, May 18, 2020 23:45
To: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
Cc: support at bioontology.org<mailto: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


<image001.png>







On May 15, 2020, at 7:45 AM, Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Friday, May 15, 2020 15:23
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>>
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<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=http://localhost/plosthes.2017-1#9501>).

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

<image001.png>






On May 15, 2020, at 3:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Karin Colsman
Email: karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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





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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: <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail>
 <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
Message-ID: <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>

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,
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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: <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>
References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail>
 <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
 <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>
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<mailto: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<mailto: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<https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http://purl.obolibrary.org/obo/GO_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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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: <BN8PR01MB5362A7D1236CFCFB34C68ACBB7B00@BN8PR01MB5362.prod.exchangelabs.com>

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<https://deerfield.com/privacy-policy>. Thank you.
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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>

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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>

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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: <AC0C599C-A33F-4225-9E77-C0023E0EB214@stanford.edu>

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<mailto:support at bioontology.org> wrote:


Name: dattah

Email: dele.attah at avenirbiz.com<mailto:dele.attah at avenirbiz.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FOMIM%3Fp%3Dclasses

Feedback:

dele.attah at avenirbiz.com<mailto: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<mailto: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



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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: <A75091F5-A1AB-4BA1-8668-7EC66AEF6DC0@stanford.edu>
 <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 <iletisim at setint.com.tr<mailto:iletisim at setint.com.tr>> 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<mailto:sezgin.sezer at setint.com.tr> Web Sitesi : www.setint.com.tr<http://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



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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<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On May 27, 2020, at 4:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Sakina

Email: sakina302 at gmail.com<mailto:sakina302 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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: <D4DA6371-2516-4440-BF63-C789FB876A42@stanford.edu>

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 <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> 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<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On May 27, 2020, at 4:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Sakina

Email: sakina302 at gmail.com<mailto:sakina302 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto: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



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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>

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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<mailto:redcap at vumc.org>) for support with this issue.

John



On May 27, 2020, at 8:34 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: omarial

Email: obaydullah.marial at health.nsw.gov.au<mailto:obaydullah.marial at health.nsw.gov.au>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto: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



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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: <BN8PR12MB2865BAC1946521CF1E7D0FD0A28E0@BN8PR12MB2865.namprd12.prod.outlook.com>

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<https://projectredcap.org/>)
Vanderbilt Institute for Clinical and Translational Research (VICTR)

From: Harris, Paul <paul.a.harris at vumc.org>
Sent: Thursday, May 28, 2020 6:43 AM
To: John Graybeal <jgraybeal at stanford.edu>; support at bioontology.org
Cc: obaydullah.marial at health.nsw.gov.au; REDCap <redcap at vumc.org>
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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Wednesday, May 27, 2020 at 11:37 PM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "obaydullah.marial at health.nsw.gov.au<mailto:obaydullah.marial at health.nsw.gov.au>" <obaydullah.marial at health.nsw.gov.au<mailto: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<mailto:redcap at vumc.org>) for support with this issue.

John



On May 27, 2020, at 8:34 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: omarial
Email: obaydullah.marial at health.nsw.gov.au<mailto:obaydullah.marial at health.nsw.gov.au>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7Credcap%40vumc.org%7C98a91627f25a4825284308d802fc4b10%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637262629906465311&sdata=0znAYASHqNybku12TY3RULcO6xH38lI%2Fu6AOqUAdgZw%3D&reserved=0>%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<mailto: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.]
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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 <jgraybeal at stanford.edu>
Date: Wednesday, May 27, 2020 at 11:37 PM
To: "support at bioontology.org" <support at bioontology.org>
Cc: "obaydullah.marial at health.nsw.gov.au" <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<mailto:redcap at vumc.org>) for support with this issue.

John




On May 27, 2020, at 8:34 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: omarial
Email: obaydullah.marial at health.nsw.gov.au<mailto:obaydullah.marial at health.nsw.gov.au>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7Cpaul.a.harris%40vumc.org%7Ca569b802411e4a04bbc608d802c0d132%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637262374463993056&sdata=UASdoiMdVKIXGl7FB4aQVGKj4p%2B7RG3X%2FaC92S%2FSxmg%3D&reserved=0>%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<mailto: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.]
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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: <CAGFJoxeqpfmRgvPL5Z26jiP+X4dMOAH-VNqv_EvCXuf_YY1ySw@mail.gmail.com>

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
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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>
 <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
 <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>
 <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu>
Message-ID: <CACLxDV7AGkaWraeUwLEKm3WLKFGQfb6CVHWA-peCsSah-_w_mA@mail.gmail.com>

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 <mdorf at stanford.edu> 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
> <https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http://purl.obolibrary.org/obo/GO_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
>
>
>
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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: <CACLxDV7AGkaWraeUwLEKm3WLKFGQfb6CVHWA-peCsSah-_w_mA@mail.gmail.com>
References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail>
 <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
 <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>
 <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu>
 <CACLxDV7AGkaWraeUwLEKm3WLKFGQfb6CVHWA-peCsSah-_w_mA@mail.gmail.com>
Message-ID: <E6AB2ADE-4EC3-4F92-900F-DC96117C6A47@stanford.edu>

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<mailto: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 <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> 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:

<Screen Shot 2020-05-26 at 12.39.15 PM.png>

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".

<Screen Shot 2020-05-26 at 12.48.24 PM.png>
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<mailto: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<mailto: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<https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http://purl.obolibrary.org/obo/GO_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,


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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: <CAGFJoxeqpfmRgvPL5Z26jiP+X4dMOAH-VNqv_EvCXuf_YY1ySw@mail.gmail.com>
References: <CAGFJoxeqpfmRgvPL5Z26jiP+X4dMOAH-VNqv_EvCXuf_YY1ySw@mail.gmail.com>
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 <vk396 at njit.edu> 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
> 
> <Untitled.png>_______________________________________________
> 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>

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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<mailto:redcap at vumc.org>) for support with this issue.

Michael


On May 28, 2020, at 10:50 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nicholas Mondinos

Email: Nick.Mondinos at health.wa.gov.au<mailto:Nick.Mondinos at health.wa.gov.au>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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

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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 <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> 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<mailto:redcap at vumc.org>) for support with this issue.

Michael


On May 28, 2020, at 10:50 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nicholas Mondinos

Email: Nick.Mondinos at health.wa.gov.au<mailto:Nick.Mondinos at health.wa.gov.au>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://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<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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: <BN8PR01MB5362A7D1236CFCFB34C68ACBB7B00@BN8PR01MB5362.prod.exchangelabs.com>
References: <BN8PR01MB5362A7D1236CFCFB34C68ACBB7B00@BN8PR01MB5362.prod.exchangelabs.com>
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 <moefinger at deerfield.com<mailto:moefinger at deerfield.com>> 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<https://deerfield.com/privacy-policy>. Thank you. _______________________________________________
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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: <E6AB2ADE-4EC3-4F92-900F-DC96117C6A47@stanford.edu>
References: <5ec6354b91675_56031d9274462522@ncbo-prd-app-08.stanford.edu.mail>
 <E6A747B3-C8DC-49D0-B2AB-5A606CCF1FF6@stanford.edu>
 <CACLxDV5r7rveRN_Nebg95c5vzk+w+i7YfOPZ7v-HYrTdg5GY9Q@mail.gmail.com>
 <7693F2DF-1E65-4BF0-8384-5C0671A58ACB@stanford.edu>
 <CACLxDV7AGkaWraeUwLEKm3WLKFGQfb6CVHWA-peCsSah-_w_mA@mail.gmail.com>
 <E6AB2ADE-4EC3-4F92-900F-DC96117C6A47@stanford.edu>
Message-ID: <CACLxDV5G_FMZ4hfj03z+tETijEpwQFEF4ePKCu5HjHNJ9Koe_Q@mail.gmail.com>

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 <mdorf at stanford.edu> 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 <mdorf at stanford.edu> 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:
>>
>> <Screen Shot 2020-05-26 at 12.39.15 PM.png>
>>
>> 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".
>>
>> <Screen Shot 2020-05-26 at 12.48.24 PM.png>
>> 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
>> <https://bioportal.bioontology.org/ontologies/GO/?p=classes&conceptid=http://purl.obolibrary.org/obo/GO_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
>>
>>
>>
>
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