From support at bioontology.org  Wed Aug  1 08:46:21 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 01 Aug 2018 08:46:21 -0700
Subject: [bioontology-support] [BioPortal] Feedback from cloudcray
Message-ID: <5b61d5cdf09a7_7feb3facd0144224115c0@ncbo-prd-app-08.stanford.edu.mail>

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From markampa at pennmedicine.upenn.edu  Wed Aug  1 05:38:09 2018
From: markampa at pennmedicine.upenn.edu (Miller, Mark)
Date: Wed, 1 Aug 2018 12:38:09 +0000
Subject: [bioontology-support] bulk download of mapping data?
In-Reply-To: <87C00012-5FB1-46F8-9301-FCBFC334C288@stanford.edu>
References: <BYAPR04MB40698C753F98ECBB24F45914F72A0@BYAPR04MB4069.namprd04.prod.outlook.com>
 <87C00012-5FB1-46F8-9301-FCBFC334C288@stanford.edu>
Message-ID: <BYAPR04MB4069EA37FD719423F9D085DEF72D0@BYAPR04MB4069.namprd04.prod.outlook.com>

Thanks, Jennifer.  I understand.

I modified the python label-fetching example https://github.com/ncbo/ncbo_rest_sample_code/blob/master/python/python3/get_labels.py to get mappings.  I also wrote an R script that gets terms from the search API.  I?m thinking of ways to make them more efficient, but in the absence of that, there may be times when I send queries that require a lot of paging.

-Mark

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, July 30, 2018 12:09 PM
To: Miller, Mark <markampa at pennmedicine.upenn.edu>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] bulk download of mapping data?

Hello Mark,



On Jul 27, 2018, at 12:45 PM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

I?m user markampa

I would like to download a large number of your high-quality term mappings.  I think I see how to do it thought the API, but would prefer downloading a static file or retrieving the mappings with a SPARQL query.


The open SPARQL endpoint is a beta service that we published a number of years ago, but haven?t had the resources to maintain. The data is entirely out of date. Current ontology data is only available via our REST API.

Apologies that we also don?t make the mappings available as static files.

If you let me know what mappings you?re trying to retrieve, I can help with which API calls to use.

Kind regards,
Jennifer





I see https://www.bioontology.org/wiki/SPARQL_BioPortal but can?t seem to get the sample queries to work.

I created a query file like this

mark at office:~/apache-jena-3.8.0/bin$<mailto:mark at office:~/apache-jena-3.8.0/bin$> cat > ~/bpmap.rq
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs>>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#<http://www.w3.org/2000/01/rdf-schema>>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#<http://www.w3.org/2004/02/skos/core>>
SELECT
*
WHERE {
        ?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
        ?mapping map:source ?source .
    }

And submitted it with Jena?s remote query command like this, but got an error.

mark at office:~/apache-jena-3.8.0/bin$<mailto:mark at office:~/apache-jena-3.8.0/bin$> ./rsparql --service 'http://sparql.bioontology.org/mappings/sparql/?apikey=9cf735c3-a44a-404f-8b2f-c49d48b2b8b2' --query  ~/bpmap.rq
HTTP Exeception
HttpException: 500 HTTP 500 error making the query: INTERNAL SERVER ERROR
        at org.apache.jena.sparql.engine.http.HttpQuery.rewrap(HttpQuery.java:370)
        at org.apache.jena.sparql.engine.http.HttpQuery.execGet(HttpQuery.java:336)
        at org.apache.jena.sparql.engine.http.HttpQuery.exec(HttpQuery.java:288)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(QueryEngineHTTP.java:352)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(QueryEngineHTTP.java:344)
        at org.apache.jena.sparql.util.QueryExecUtils.doSelectQuery(QueryExecUtils.java:196)
        at org.apache.jena.sparql.util.QueryExecUtils.executeQuery(QueryExecUtils.java:79)
        at arq.rsparql.exec(rsparql.java:76)
        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
        at arq.rsparql.main(rsparql.java:44)
mark at office:~/apache-jena-3.8.0/bin$<mailto:mark at office:~/apache-jena-3.8.0/bin$>
_______________________________________________
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From dr.jzhou at gmail.com  Wed Aug  1 14:07:07 2018
From: dr.jzhou at gmail.com (Jackie Jia Zhou)
Date: Wed, 1 Aug 2018 16:07:07 -0500
Subject: [bioontology-support] Download SNOMED CT
Message-ID: <CAKvRNXuApZvVyf6UJhNF6qukKYfNbC-sRE09_m_deDbVVH11kQ@mail.gmail.com>

Dear BioPortal support,

I have a question regarding SNOMED CT on BioPortal. I wonder how I can
download the newest version SNOMED CT data from BioPortal, as I don't see a
'Download' button any where on the SNOMED CT page?

I am specifically interested in the SNOMED CT disease terms, how can I get
all those terms?

Thank you for your help,

- Jackie
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From vendetti at stanford.edu  Thu Aug  2 10:49:27 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 2 Aug 2018 17:49:27 +0000
Subject: [bioontology-support] Download SNOMED CT
In-Reply-To: <CAKvRNXuApZvVyf6UJhNF6qukKYfNbC-sRE09_m_deDbVVH11kQ@mail.gmail.com>
References: <CAKvRNXuApZvVyf6UJhNF6qukKYfNbC-sRE09_m_deDbVVH11kQ@mail.gmail.com>
Message-ID: <1972EC60-77D5-438E-A7AB-12807A2556A9@stanford.edu>

Hello Jackie,


On Aug 1, 2018, at 2:07 PM, Jackie Jia Zhou <dr.jzhou at gmail.com<mailto:dr.jzhou at gmail.com>> wrote:

I have a question regarding SNOMED CT on BioPortal. I wonder how I can download the newest version SNOMED CT data from BioPortal, as I don't see a 'Download' button any where on the SNOMED CT page?


Due to licensing restrictions, we?re unable to offer downloads of the SNOMEDCT ontology source file from our public website. If you?re a current UMLS license holder [1], please contact our technical program manager John Graybeal (cc'ed) offline for possible download options.

Alternatively, you can access SNOMEDCT data via our REST API, which doesn?t require a license. The API is documented here:

http://data.bioontology.org/documentation

If you decide to use the API, you?ll need to get an API key:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key



I am specifically interested in the SNOMED CT disease terms, how can I get all those terms?


Here?s an example of a REST call that would retrieve the ?Disease" class from SNOMEDCT:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/64572001>?apikey=your_api_key_here

You can use the hypermedia links in the reply to explore things like parents, children, descendants, etc.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/databases/umls.html#license_request

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From vendetti at stanford.edu  Thu Aug  2 15:11:51 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 2 Aug 2018 22:11:51 +0000
Subject: [bioontology-support] [BioPortal] Feedback from cloudcray
In-Reply-To: <5b61d5cdf09a7_7feb3facd0144224115c0@ncbo-prd-app-08.stanford.edu.mail>
References: <5b61d5cdf09a7_7feb3facd0144224115c0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <B0611C03-E54A-4D22-837D-15C3D1E134A6@stanford.edu>

Hello,


On Aug 1, 2018, at 8:46 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


On the Class Endpoint, the synonym property is consistently returning only one result. However, when using the search API, I can see multiple synonyms:

Search request (6 synonyms):
http://data.bioontology.org/search?q=99213

Class request (1 synonym):
http://data.bioontology.org/ontologies/CPT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCPT%2F99213

Is this a bug? Or is there a parameter I need to set to return multiple synonyms/"altLabels"?



No, there isn?t a parameter you need to set to get multiple return values for synonyms.

I manually reindexed the CPT ontology and flushed our application caches to rule out a problem with indexing on the latest version. The indexing completed successfully, but I still see the same behavior you describe above.

My colleague that implemented the search functionality in BioPortal is better equipped to track down what?s happening, although he?s out on vacation at the moment. I?ve entered an issue in our tracker:

https://github.com/ncbo/ontologies_api/issues/51

Apologies that we may not be able to get you an answer until he returns.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Thu Aug  2 15:26:44 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 2 Aug 2018 22:26:44 +0000
Subject: [bioontology-support] bulk download of mapping data?
In-Reply-To: <BYAPR04MB4069EA37FD719423F9D085DEF72D0@BYAPR04MB4069.namprd04.prod.outlook.com>
References: <BYAPR04MB40698C753F98ECBB24F45914F72A0@BYAPR04MB4069.namprd04.prod.outlook.com>
 <87C00012-5FB1-46F8-9301-FCBFC334C288@stanford.edu>
 <BYAPR04MB4069EA37FD719423F9D085DEF72D0@BYAPR04MB4069.namprd04.prod.outlook.com>
Message-ID: <B3B7445D-CA1D-4C93-AD3C-375A68E78496@stanford.edu>

Hi Mark,


On Aug 1, 2018, at 5:38 AM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

Thanks, Jennifer.  I understand.

I modified the python label-fetching example https://github.com/ncbo/ncbo_rest_sample_code/blob/master/python/python3/get_labels.py to get mappings.  I also wrote an R script that gets terms from the search API.


If you?re so inclined, we welcome pull requests for additions to our sample code repository.


I?m thinking of ways to make them more efficient, but in the absence of that, there may be times when I send queries that require a lot of paging.


You?re not the only person that?s requested mappings as static file downloads. I?ve entered an issue in our tracker for this topic:

https://github.com/ncbo/bioportal-project/issues/84

? in the event you wanted to +1 it, and/or add any comments.

Kind regards,
Jennifer


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From support at bioontology.org  Sat Aug  4 07:01:50 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 04 Aug 2018 07:01:50 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b65b1ceb65f8_67743ff3e650c81889713@ncbo-prd-app-09.stanford.edu.mail>

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From dr.jzhou at gmail.com  Mon Aug  6 08:12:01 2018
From: dr.jzhou at gmail.com (Jackie Jia Zhou)
Date: Mon, 6 Aug 2018 10:12:01 -0500
Subject: [bioontology-support] Download SNOMED CT
In-Reply-To: <1972EC60-77D5-438E-A7AB-12807A2556A9@stanford.edu>
References: <CAKvRNXuApZvVyf6UJhNF6qukKYfNbC-sRE09_m_deDbVVH11kQ@mail.gmail.com>
 <1972EC60-77D5-438E-A7AB-12807A2556A9@stanford.edu>
Message-ID: <CAKvRNXuubSRc5d1e7uyzQqury=iNPNkzeKK6OH7xjwrY5YwCdA@mail.gmail.com>

Thank you, Jennifer!

-Jackie

On Thu, Aug 2, 2018 at 12:49 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Jackie,
>
>
> On Aug 1, 2018, at 2:07 PM, Jackie Jia Zhou <dr.jzhou at gmail.com> wrote:
>
> I have a question regarding SNOMED CT on BioPortal. I wonder how I can
> download the newest version SNOMED CT data from BioPortal, as I don't see a
> 'Download' button any where on the SNOMED CT page?
>
>
>
> Due to licensing restrictions, we?re unable to offer downloads of the
> SNOMEDCT ontology source file from our public website. If you?re a current
> UMLS license holder [1], please contact our technical program manager John
> Graybeal (cc'ed) offline for possible download options.
>
> Alternatively, you can access SNOMEDCT data via our REST API, which
> doesn?t require a license. The API is documented here:
>
> http://data.bioontology.org/documentation
>
> If you decide to use the API, you?ll need to get an API key:
>
> https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key
>
>
>
> I am specifically interested in the SNOMED CT disease terms, how can I get
> all those terms?
>
>
>
> Here?s an example of a REST call that would retrieve the ?Disease" class
> from SNOMEDCT:
>
> http://data.bioontology.org/ontologies/SNOMEDCT/classes/
> http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001
> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/64572001>
> ?apikey=your_api_key_here
>
> You can use the hypermedia links in the reply to explore things like
> parents, children, descendants, etc.
>
> Kind regards,
> Jennifer
>
> [1] https://www.nlm.nih.gov/databases/umls.html#license_request
>
>
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From vendetti at stanford.edu  Mon Aug  6 10:55:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 6 Aug 2018 17:55:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5b65b1ceb65f8_67743ff3e650c81889713@ncbo-prd-app-09.stanford.edu.mail>
References: <5b65b1ceb65f8_67743ff3e650c81889713@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <51704C3C-1E73-4F4C-9639-BF874FB50131@stanford.edu>

Hello Chen,

Ontology (and ontology view) acronyms are unique IDs in our system and are not allowed to be changed once created. If you want to use a new acronym, you?ll need to create a new ontology view entry and we can delete the old one for you.

Kind regards,
Jennifer


On Aug 4, 2018, at 7:01 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

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

Feedback:

Dear,
I was going to change the acronym of my ontology view "NEGO". (before change "NEGO", After change "NEST"). But I couldn't do it by myself. Could you help me?
P.S. I also saw an error report when submitting the view. Could you help check? Thanks.
Best, Chen

_______________________________________________
bioontology-support mailing list
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From support at bioontology.org  Thu Aug  9 08:49:00 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 09 Aug 2018 08:49:00 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Venkat
Message-ID: <5b6c626c7e825_3dca3fa89c494b3c80870@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Thu Aug  9 02:07:31 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 09 Aug 2018 02:07:31 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b6c04537c057_47d33fdca2c41cb089459@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu Aug  9 11:27:50 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 9 Aug 2018 18:27:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Venkat
In-Reply-To: <5b6c626c7e825_3dca3fa89c494b3c80870@ncbo-prd-app-09.stanford.edu.mail>
References: <5b6c626c7e825_3dca3fa89c494b3c80870@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <81DC96D8-7CF9-4181-A746-117863A71F3B@stanford.edu>

Venkat,

We do not have an example in R in our repository (examples are at https://github.com/ncbo/ncbo_rest_sample_code) that I am aware of.

However, the thread in the support list archives at http://ncbo-support.2288202.n4.nabble.com/bioontology-support-API-Example-Code-in-R-td4655378.html has quite a bit more information that may be useful.

In addition, OntoCat (described in "ontoCAT: an R package for ontology traversal and search", https://academic.oup.com/bioinformatics/article/27/17/2468/223268) is written in R and accesses BIoPortal. So you may find some useful code in that source as well.

John


On Aug 9, 2018, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Venkat

Email: gadepallivs at vcu.edu<mailto:gadepallivs at vcu.edu>

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

Feedback:

I am an R user, do you have an example of downloading data using R?
I am interested in the complete lineage of Microorganism/Prokaryote/bacteria lineage ...
Trying to convert each branch into a row, however because of cyclic network I am failing to do so.

Wondering if there is an easier way to download the network into a table format?

appreciate your inputs


_______________________________________________
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


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From jgraybeal at stanford.edu  Thu Aug  9 12:07:06 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 9 Aug 2018 19:07:06 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5b6c04537c057_47d33fdca2c41cb089459@ncbo-prd-app-09.stanford.edu.mail>
References: <5b6c04537c057_47d33fdca2c41cb089459@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <EA7A08D4-DEFB-42D2-BF60-941408646DF2@stanford.edu>

Chen,

Your ontology has been deleted (thanks Jennifer!), and we have confirmed your problem with creating a new mapping and written up a ticket on it (https://github.com/ncbo/bioportal-project/issues/85). I am not sure how quick/easy this will be to solve, but we will have a look to see.

Thanks for your input,

John


On Aug 9, 2018, at 2:07 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fncicb.nci.nih.gov<http://252Fncicb.nci.nih.gov>%252Fxml%252Fowl%252FEVS%252FThesaurus.owl%2523C25409

Feedback:

Dear,
Could you please delete the ontology view "Nutritional Epidemiological STandard" (acronym: NEGO) created by me?
Meanwhile, for classes, when I click "class mappings" --> create new mapping --> target ontology or view --> target class, target class doesn't appear. I waited for 2 hours, it still didn't work.
Could you help me? Thanks in advance.
Best, Chen

_______________________________________________
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


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From vendetti at stanford.edu  Thu Aug  9 15:25:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 9 Aug 2018 22:25:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <EA7A08D4-DEFB-42D2-BF60-941408646DF2@stanford.edu>
References: <5b6c04537c057_47d33fdca2c41cb089459@ncbo-prd-app-09.stanford.edu.mail>
 <EA7A08D4-DEFB-42D2-BF60-941408646DF2@stanford.edu>
Message-ID: <4E85B1A7-518A-4292-9FDA-A6BF3508B586@stanford.edu>

Hello Chen,

The target class search is blocked due to a mixed content error. Until we?re able to deploy a fix to our production environment, you should be able to use a workaround of modifying the protocol in the address bar of your browser from HTTPS to HTTP, i.e.:

http://bioportal.bioontology.org/ontologies/ONE?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25409<https://bioportal.bioontology.org/ontologies/ONE?p=classes&conceptid=http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409>

Jennifer


On Aug 9, 2018, at 12:07 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Chen,

Your ontology has been deleted (thanks Jennifer!), and we have confirmed your problem with creating a new mapping and written up a ticket on it (https://github.com/ncbo/bioportal-project/issues/85). I am not sure how quick/easy this will be to solve, but we will have a look to see.

Thanks for your input,

John


On Aug 9, 2018, at 2:07 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fncicb.nci.nih.gov<http://252fncicb.nci.nih.gov/>%252Fxml%252Fowl%252FEVS%252FThesaurus.owl%2523C25409

Feedback:

Dear,
Could you please delete the ontology view "Nutritional Epidemiological STandard" (acronym: NEGO) created by me?
Meanwhile, for classes, when I click "class mappings" --> create new mapping --> target ontology or view --> target class, target class doesn't appear. I waited for 2 hours, it still didn't work.
Could you help me? Thanks in advance.
Best, Chen

_______________________________________________
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


_______________________________________________
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  Fri Aug 10 02:35:51 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 10 Aug 2018 02:35:51 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>

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From Chen.Yang at UGent.be  Fri Aug 10 01:28:58 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Fri, 10 Aug 2018 08:28:58 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <4E85B1A7-518A-4292-9FDA-A6BF3508B586@stanford.edu>
References: <5b6c04537c057_47d33fdca2c41cb089459@ncbo-prd-app-09.stanford.edu.mail>
 <EA7A08D4-DEFB-42D2-BF60-941408646DF2@stanford.edu>
 <4E85B1A7-518A-4292-9FDA-A6BF3508B586@stanford.edu>
Message-ID: <18156524ac6a4d8fa3b9c56c0fe48414@xmail303.UGent.be>

Thank you Jennifer and John!
That?s quite helpful! As a beginner, I am really sure I would have other questions in the future :-P
So? looking forward to the next talk :-P
Have a good day!
Chen

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 10 August 2018 00:26
To: support at bioontology.org
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hello Chen,

The target class search is blocked due to a mixed content error. Until we?re able to deploy a fix to our production environment, you should be able to use a workaround of modifying the protocol in the address bar of your browser from HTTPS to HTTP, i.e.:

http://bioportal.bioontology.org/ontologies/ONE?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25409<https://bioportal.bioontology.org/ontologies/ONE?p=classes&conceptid=http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409>

Jennifer



On Aug 9, 2018, at 12:07 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Chen,

Your ontology has been deleted (thanks Jennifer!), and we have confirmed your problem with creating a new mapping and written up a ticket on it (https://github.com/ncbo/bioportal-project/issues/85). I am not sure how quick/easy this will be to solve, but we will have a look to see.

Thanks for your input,

John


On Aug 9, 2018, at 2:07 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fncicb.nci.nih.gov<http://252fncicb.nci.nih.gov/>%252Fxml%252Fowl%252FEVS%252FThesaurus.owl%2523C25409

Feedback:
Dear,
Could you please delete the ontology view "Nutritional Epidemiological STandard" (acronym: NEGO) created by me?
Meanwhile, for classes, when I click "class mappings" --> create new mapping --> target ontology or view --> target class, target class doesn't appear. I waited for 2 hours, it still didn't work.
Could you help me? Thanks in advance.
Best, Chen

_______________________________________________
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

_______________________________________________
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  Fri Aug 10 10:08:31 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 10 Aug 2018 10:08:31 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Melanie Courtot
Message-ID: <5b6dc68f9afde_43563f9a334c635c61245@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Aug 10 11:07:42 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 10 Aug 2018 18:07:42 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Melanie Courtot
In-Reply-To: <5b6dc68f9afde_43563f9a334c635c61245@ncbo-prd-app-09.stanford.edu.mail>
References: <5b6dc68f9afde_43563f9a334c635c61245@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <B2259284-1668-42BB-8642-E5D0AA5521B3@stanford.edu>

Hi Melanie,

We changed the status of the ontology to ?retired?. Is that a sufficient resolution?

Kind regards,
Jennifer



On Aug 10, 2018, at 10:08 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Melanie Courtot

Email: mcourtot at ebi.ac.uk<mailto:mcourtot at ebi.ac.uk>

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

Feedback:

Hi,

The AERO has been deprecated for quite a long time. Would it be possible to either remove it from BioPortal, or at leat clearly indicate its obsolete status?

Thanks,
Melanie

_______________________________________________
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 pep1 at fliegerjunge.com  Fri Aug 10 13:55:17 2018
From: pep1 at fliegerjunge.com (Joe Bedder)
Date: Fri, 10 Aug 2018 15:55:17 -0500
Subject: [bioontology-support] API key request
Message-ID: <201808102055.w7AKnnHl017256@mx0a-00000d03.pphosted.com>

Hi

How can we request an API key ?  Personal use.

Thank you
Joe Bedder


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From vendetti at stanford.edu  Fri Aug 10 18:02:28 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 11 Aug 2018 01:02:28 +0000
Subject: [bioontology-support] API key request
In-Reply-To: <201808102055.w7AKnnHl017256@mx0a-00000d03.pphosted.com>
References: <201808102055.w7AKnnHl017256@mx0a-00000d03.pphosted.com>
Message-ID: <6F8AEF2A-BF4A-4CE2-A8E6-8730CA8A458E@stanford.edu>

Hello Joe,

There are instructions on our wiki for this:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

Kind regards,
Jennifer



On Aug 10, 2018, at 1:55 PM, Joe Bedder <pep1 at fliegerjunge.com<mailto:pep1 at fliegerjunge.com>> wrote:

Hi

How can we request an API key ?  Personal use.

Thank you
Joe Bedder


_______________________________________________
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 vendetti at stanford.edu  Fri Aug 10 18:09:27 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 11 Aug 2018 01:09:27 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer



On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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 Chen.Yang at UGent.be  Sat Aug 11 02:45:07 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Sat, 11 Aug 2018 09:45:07 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
 <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
Message-ID: <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class ?Administration? (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) into ONE.
I want to indicate the ?Administration? is the same as the ?Administration? in NCIT.
In a word, those two ?Administration? classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,
Chen


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 11 August 2018 03:09
To: support at bioontology.org
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer




On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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  Sun Aug 12 22:05:42 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 13 Aug 2018 05:05:42 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
 <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
 <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>
Message-ID: <6AB4C29D-AEE8-4F1A-A014-065ABC1816B3@stanford.edu>

Chen, a quick note to consider. Because the identifiers are the same, the concepts are already considered the same, and BioPortal will automatically create a mapping between the two entries.

This does not respond directly to your question, or and it does not prevent you from creating your own mapping. I just wanted to explain how BioPortal treats this situation.

John

On Aug 11, 2018, at 2:45 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class ?Administration? (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) into ONE.
I want to indicate the ?Administration? is the same as the ?Administration? in NCIT.
In a word, those two ?Administration? classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,
Chen


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 11 August 2018 03:09
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer




On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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


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From Chen.Yang at UGent.be  Mon Aug 13 00:12:16 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Mon, 13 Aug 2018 07:12:16 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <6AB4C29D-AEE8-4F1A-A014-065ABC1816B3@stanford.edu>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
 <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
 <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>
 <6AB4C29D-AEE8-4F1A-A014-065ABC1816B3@stanford.edu>
Message-ID: <fb109434e2d947429e59e198ab9b4d60@xmail303.UGent.be>

Hi John, thanks. However, there is no mapping automatically created by BioPortal. Chen

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: 13 August 2018 07:06
To: Chen Yang <Chen.Yang at UGent.be>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Chen, a quick note to consider. Because the identifiers are the same, the concepts are already considered the same, and BioPortal will automatically create a mapping between the two entries.

This does not respond directly to your question, or and it does not prevent you from creating your own mapping. I just wanted to explain how BioPortal treats this situation.

John

On Aug 11, 2018, at 2:45 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class ?Administration? (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) into ONE.
I want to indicate the ?Administration? is the same as the ?Administration? in NCIT.
In a word, those two ?Administration? classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,
Chen


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 11 August 2018 03:09
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer





On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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

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From vendetti at stanford.edu  Mon Aug 13 11:42:10 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 13 Aug 2018 18:42:10 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <fb109434e2d947429e59e198ab9b4d60@xmail303.UGent.be>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
 <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
 <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>
 <6AB4C29D-AEE8-4F1A-A014-065ABC1816B3@stanford.edu>
 <fb109434e2d947429e59e198ab9b4d60@xmail303.UGent.be>
Message-ID: <D4A0EC6E-8AAD-49FD-B8A2-28124B57B827@stanford.edu>

Hello Chen,

BioPortal did generate the mapping that John mentioned below. You can see that mapping by selecting the Administration class in the ONE ontology, then clicking the Class Mappings link on the right-hand side. I?ve included a screenshot below of the LOOM and SAME_URI mappings that were generated for that term in the NCIT ontology:

[cid:B5EDCB4A-DF35-4D9D-A636-96B947E36CFA at stanford.edu]

What?s not clear to me is why the ontology-level mappings pane is empty (i.e., the tab that you navigate to by clicking the top-level ?Mappings? link):


[cid:A38B3AD5-2EA1-4265-8D65-01D60AEB71CC at stanford.edu]


The same issue was reported for another ontology in BioPortal a couple of weeks ago. We have an existing issue in our tracker for this, so I?ve added a comment indicating that it?s happening with the ONE ontology:

https://github.com/ncbo/ontologies_api/issues/50

Apologies for this inconvenience.

Kind regards,
Jennifer



On Aug 13, 2018, at 12:12 AM, Chen Yang <chen.yang at ugent.be<mailto:chen.yang at ugent.be>> wrote:

Hi John, thanks. However, there is no mapping automatically created by BioPortal. Chen

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: 13 August 2018 07:06
To: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Chen, a quick note to consider. Because the identifiers are the same, the concepts are already considered the same, and BioPortal will automatically create a mapping between the two entries.

This does not respond directly to your question, or and it does not prevent you from creating your own mapping. I just wanted to explain how BioPortal treats this situation.

John

On Aug 11, 2018, at 2:45 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class ?Administration? (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) into ONE.
I want to indicate the ?Administration? is the same as the ?Administration? in NCIT.
In a word, those two ?Administration? classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,
Chen


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 11 August 2018 03:09
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer





On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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

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From Chen.Yang at UGent.be  Mon Aug 13 15:59:52 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Mon, 13 Aug 2018 22:59:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <D4A0EC6E-8AAD-49FD-B8A2-28124B57B827@stanford.edu>
References: <5b6d5c77a4bdb_31763f81495336bc2842f@ncbo-prd-app-08.stanford.edu.mail>
 <89E31583-A0D9-4E54-AF50-7FFBFACBCEFD@stanford.edu>
 <f7b8104b83b641ac9841a27107dba2c2@xmail303.UGent.be>
 <6AB4C29D-AEE8-4F1A-A014-065ABC1816B3@stanford.edu>
 <fb109434e2d947429e59e198ab9b4d60@xmail303.UGent.be>
 <D4A0EC6E-8AAD-49FD-B8A2-28124B57B827@stanford.edu>
Message-ID: <87ca975eb9ef4655a77a5339a03d2421@xmail303.UGent.be>

Dear Jennifer and John,
I am really sorry for what I said before. Yes, BioPortal did mappings automatically.
Could you please inform me once you solve the issue? It is also possible that I uploaded an file with errors, but I am not able to detect by myself.
I would be more than happy to hear from you, it would be a good opportunity for me to improve my understanding of ontology.
Thank you in advance.
Best regards,
Chen

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 13 August 2018 20:42
To: Chen Yang <Chen.Yang at UGent.be>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hello Chen,

BioPortal did generate the mapping that John mentioned below. You can see that mapping by selecting the Administration class in the ONE ontology, then clicking the Class Mappings link on the right-hand side. I?ve included a screenshot below of the LOOM and SAME_URI mappings that were generated for that term in the NCIT ontology:

[cid:image001.png at 01D43368.E178E940]

What?s not clear to me is why the ontology-level mappings pane is empty (i.e., the tab that you navigate to by clicking the top-level ?Mappings? link):


[cid:image002.png at 01D43368.E178E940]


The same issue was reported for another ontology in BioPortal a couple of weeks ago. We have an existing issue in our tracker for this, so I?ve added a comment indicating that it?s happening with the ONE ontology:

https://github.com/ncbo/ontologies_api/issues/50

Apologies for this inconvenience.

Kind regards,
Jennifer




On Aug 13, 2018, at 12:12 AM, Chen Yang <chen.yang at ugent.be<mailto:chen.yang at ugent.be>> wrote:

Hi John, thanks. However, there is no mapping automatically created by BioPortal. Chen

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: 13 August 2018 07:06
To: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Chen, a quick note to consider. Because the identifiers are the same, the concepts are already considered the same, and BioPortal will automatically create a mapping between the two entries.

This does not respond directly to your question, or and it does not prevent you from creating your own mapping. I just wanted to explain how BioPortal treats this situation.

John

On Aug 11, 2018, at 2:45 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class ?Administration? (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) into ONE.
I want to indicate the ?Administration? is the same as the ?Administration? in NCIT.
In a word, those two ?Administration? classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,
Chen


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 11 August 2018 03:09
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Hello Chen,

Could you please tell us which two classes you?re trying to create a mapping between? I assume you?re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,
Jennifer






On Aug 10, 2018, at 2:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

_______________________________________________
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

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From support at bioontology.org  Tue Aug 14 03:52:23 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 14 Aug 2018 03:52:23 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Pat Hudson
Message-ID: <5b72b467a2367_72163fc4361d204c8308a@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Aug 14 10:11:12 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 14 Aug 2018 17:11:12 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Pat Hudson
In-Reply-To: <5b72b467a2367_72163fc4361d204c8308a@ncbo-prd-app-08.stanford.edu.mail>
References: <5b72b467a2367_72163fc4361d204c8308a@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <CB864F6F-25C6-4E1E-A67F-97F30E115575@stanford.edu>

Hello Pat,

We import the CPT ontology into BioPortal from the National Library of Medicine?s UMLS [1]. According to their documentation, ?SIB? is an abbreviation for "has sibling relationship in a Metathesaurus source vocabulary? [2]:

[cid:1A4A938B-0A01-4B1A-9644-3600A67CCED4 at stanford.edu]

If you need a more detailed explanation, I suggest contacting either UMLS customer service [3], or the ontology maintainer (their contact information is listed on the summary page for CPT).

[1] https://www.nlm.nih.gov/research/umls/
[2] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html
[3] https://www.nlm.nih.gov/research/umls/support.html


On Aug 14, 2018, at 3:52 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Pat Hudson

Email: p-hudson at sbcglobal.net<mailto:p-hudson at sbcglobal.net>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D51500

Feedback:

What does the category "Inverse of SIB" stand for?

_______________________________________________
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  Wed Aug 15 13:02:49 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 15 Aug 2018 13:02:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
Message-ID: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Aug 15 13:10:51 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 15 Aug 2018 20:10:51 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>

Hi Karen,

I don?t follow exactly what you?re asking. The ontology is listed in our Ontology Browser page (screen shot below). Do you mean that it should also be designated as part of the ?OBO_Foundry? group?

Jennifer



[cid:A9C75130-8A97-4FD8-A5B1-A06B3AEEC3FE at stanford.edu]



On Aug 15, 2018, at 1:02 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Karen Yook

Email: karen at wormbase.org<mailto:karen at wormbase.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%3Ffilter%3DOBO_Foundry

Feedback:

I'm wondering why the C. elegans phenotype ontology isn't listed in the library of ontologies. It seems like it should be. Is this a matter of file naming?

https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary

_______________________________________________
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 karen at wormbase.org  Wed Aug 15 13:15:43 2018
From: karen at wormbase.org (Karen Yook)
Date: Wed, 15 Aug 2018 13:15:43 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
 <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
Message-ID: <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>

Ah, that must be it.  Also I was searching for the original name of the
ontology, that being Worm Phenotype Ontology, which is not found. I do not
know when the name changed or if that ever gets used anymore.
Thanks for your reply.

Karen


~~~~
Karen Yook

Curator
WormBase Caltech
Tel: 415.306.4150
e-mail: kyook at caltech.edu
e-mail: karen at wormbase.org
skype name: wbkaren


On Wed, Aug 15, 2018 at 1:10 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Karen,
>
> I don?t follow exactly what you?re asking. The ontology is listed in our
> Ontology Browser page (screen shot below). Do you mean that it should also
> be designated as part of the ?OBO_Foundry? group?
>
> Jennifer
>
>
>
>
>
>
> On Aug 15, 2018, at 1:02 PM, support at bioontology.org wrote:
>
> Name: Karen Yook
>
> Email: karen at wormbase.org <karen at wormbase.org>
>
> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%3Ffilter%3DOBO_Foundry
>
>
>
> *Feedback:*
>
> I'm wondering why the C. elegans phenotype ontology isn't listed in the
> library of ontologies. It seems like it should be. Is this a matter of file
> naming?
>
> https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary
>
> _______________________________________________
> 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  Wed Aug 15 13:56:36 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 15 Aug 2018 20:56:36 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
 <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
 <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>
Message-ID: <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>

I added the ontology to the OBO_Foundry group, so you should be able to use that filter now on the Ontology Browser page.

You mentioned that you think some of the ontology metadata like the name is out of date? We could ping the contact person and ask them to update this information. Do you know if Gary Schindelman is still the maintainer?

Jennifer



[cid:DED64042-9010-4DC2-89C4-E294EB2D9A06 at stanford.edu]



On Aug 15, 2018, at 1:15 PM, Karen Yook <karen at wormbase.org<mailto:karen at wormbase.org>> wrote:

Ah, that must be it.  Also I was searching for the original name of the ontology, that being Worm Phenotype Ontology, which is not found. I do not know when the name changed or if that ever gets used anymore.
Thanks for your reply.

Karen


~~~~
Karen Yook

Curator
WormBase Caltech
Tel: 415.306.4150
e-mail: kyook at caltech.edu<mailto:kyook at caltech.edu>
e-mail: karen at wormbase.org<mailto:karen at wormbase.org>
skype name: wbkaren


On Wed, Aug 15, 2018 at 1:10 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Karen,

I don?t follow exactly what you?re asking. The ontology is listed in our Ontology Browser page (screen shot below). Do you mean that it should also be designated as part of the ?OBO_Foundry? group?

Jennifer



<Screenshot 2018-08-15 13.08.10.png>



On Aug 15, 2018, at 1:02 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Karen Yook

Email: karen at wormbase.org<mailto:karen at wormbase.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%3Ffilter%3DOBO_Foundry

Feedback:

I'm wondering why the C. elegans phenotype ontology isn't listed in the library of ontologies. It seems like it should be. Is this a matter of file naming?

https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary

_______________________________________________
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


<Screen Shot 2018-08-15 at 1.13.31 PM.png>

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From karen at wormbase.org  Wed Aug 15 14:21:33 2018
From: karen at wormbase.org (Karen Yook)
Date: Wed, 15 Aug 2018 14:21:33 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
 <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
 <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>
 <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>
Message-ID: <B37E5C97-EE7D-4479-BA23-3B9ABFCAFB36@wormbase.org>

Hi Jennifer, 

I don?t think the metadata is out of date, it?s more me that is out of date. The ontology from the beginning was called the Worm Phenotype Ontology, WPO, for short. I?m not sure when it was updated to C elegant fir the purpose of distribution on the NCBO.  I?ve added Gary Schindelman to the thread in case he has any comments. 

Regardless, thanks for adding it to the OBO_foundry list. Gary please let us know if that is ok or not. 

Cheers,
Karen

> On Aug 15, 2018, at 13:56, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
> 
> I added the ontology to the OBO_Foundry group, so you should be able to use that filter now on the Ontology Browser page.
> 
> You mentioned that you think some of the ontology metadata like the name is out of date? We could ping the contact person and ask them to update this information. Do you know if Gary Schindelman is still the maintainer?
> 
> Jennifer
> 
> 
> 
> <Screenshot 2018-08-15 13.55.51.png>
> 
> 
> 
>> On Aug 15, 2018, at 1:15 PM, Karen Yook <karen at wormbase.org> wrote:
>> 
>> Ah, that must be it.  Also I was searching for the original name of the ontology, that being Worm Phenotype Ontology, which is not found. I do not know when the name changed or if that ever gets used anymore. 
>> Thanks for your reply.  
>> 
>> Karen 
>> 
>> 
>> ~~~~
>> Karen Yook
>> 
>> Curator 
>> WormBase Caltech
>> Tel: 415.306.4150
>> e-mail: kyook at caltech.edu
>> e-mail: karen at wormbase.org
>> skype name: wbkaren
>> 
>> 
>>> On Wed, Aug 15, 2018 at 1:10 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
>>> Hi Karen,
>>> 
>>> I don?t follow exactly what you?re asking. The ontology is listed in our Ontology Browser page (screen shot below). Do you mean that it should also be designated as part of the ?OBO_Foundry? group?
>>> 
>>> Jennifer
>>> 
>>> 
>>> 
>>> <Screenshot 2018-08-15 13.08.10.png>
>>> 
>>> 
>>> 
>>>> On Aug 15, 2018, at 1:02 PM, support at bioontology.org wrote:
>>>> 
>>>> Name: Karen Yook 
>>>> 
>>>> Email: karen at wormbase.org
>>>> 
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%3Ffilter%3DOBO_Foundry
>>>> 
>>>> 
>>>> Feedback:
>>>> 
>>>> I'm wondering why the C. elegans phenotype ontology isn't listed in the library of ontologies. It seems like it should be. Is this a matter of file naming?
>>>> 
>>>> https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary
>>>> 
>>>> 
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>> 
>> <Screen Shot 2018-08-15 at 1.13.31 PM.png>
> 
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From vendetti at stanford.edu  Wed Aug 15 15:55:16 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 15 Aug 2018 22:55:16 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
 <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
 <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>
 <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>
Message-ID: <EB4A46C2-E877-4207-AD14-293CB651C865@stanford.edu>

Hi Karen,

I made a mistake in my replies to you. There is apparently a difference between OBO Foundry and OBO library ontologies. There?s a set of 10 OBO Foundry ontologies, which can be seen on the OBO Foundry website (http://www.obofoundry.org/) shaded in blue:

[cid:98E254C6-BF21-4F66-BA0E-AD5348CDFD8E at stanford.edu]



All other ontologies on their website (shaded in white) are OBO library ontologies. BioPortal?s OBO_Foundry group is only supposed to contain the set of 10 OBO Foundry ontologies, so I will need to undo the addition of WB-PHENOTYPE to that group. When you?re using the Ontology Browser page and looking for an OBO ontology that?s not one of the 10 OBO Foundry ontologies, please instead use the ?OBO? filter in the Format box:

[cid:EE3F89DC-9FDA-4B5C-9F01-28D210928E5C at stanford.edu]

Apologies for the confusion.

Jennifer





On Aug 15, 2018, at 1:56 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

I added the ontology to the OBO_Foundry group, so you should be able to use that filter now on the Ontology Browser page.

You mentioned that you think some of the ontology metadata like the name is out of date? We could ping the contact person and ask them to update this information. Do you know if Gary Schindelman is still the maintainer?

Jennifer



<Screenshot 2018-08-15 13.55.51.png>



On Aug 15, 2018, at 1:15 PM, Karen Yook <karen at wormbase.org<mailto:karen at wormbase.org>> wrote:

Ah, that must be it.  Also I was searching for the original name of the ontology, that being Worm Phenotype Ontology, which is not found. I do not know when the name changed or if that ever gets used anymore.
Thanks for your reply.

Karen


~~~~
Karen Yook

Curator
WormBase Caltech
Tel: 415.306.4150
e-mail: kyook at caltech.edu<mailto:kyook at caltech.edu>
e-mail: karen at wormbase.org<mailto:karen at wormbase.org>
skype name: wbkaren


On Wed, Aug 15, 2018 at 1:10 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Karen,

I don?t follow exactly what you?re asking. The ontology is listed in our Ontology Browser page (screen shot below). Do you mean that it should also be designated as part of the ?OBO_Foundry? group?

Jennifer



<Screenshot 2018-08-15 13.08.10.png>



On Aug 15, 2018, at 1:02 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Karen Yook

Email: karen at wormbase.org<mailto:karen at wormbase.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%3Ffilter%3DOBO_Foundry

Feedback:

I'm wondering why the C. elegans phenotype ontology isn't listed in the library of ontologies. It seems like it should be. Is this a matter of file naming?

https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary

_______________________________________________
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


<Screen Shot 2018-08-15 at 1.13.31 PM.png>

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

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From garys at caltech.edu  Thu Aug 16 11:08:16 2018
From: garys at caltech.edu (Schindelman, Gary C.)
Date: Thu, 16 Aug 2018 18:08:16 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Karen Yook
In-Reply-To: <B37E5C97-EE7D-4479-BA23-3B9ABFCAFB36@wormbase.org>
References: <5b7486e98b9e6_2a23fa769bc6d1c6274@ncbo-prd-app-09.stanford.edu.mail>
 <565BD2BC-C17C-40F8-856C-095683BC99D5@stanford.edu>
 <CAF4a_bONShk4F1YLrfJn5wwtZVAuzOi8FsxfSChJ=LtB2w-ZAw@mail.gmail.com>
 <9EE79BE7-92E6-4B06-8E76-6BCFEC9041F7@stanford.edu>
 <B37E5C97-EE7D-4479-BA23-3B9ABFCAFB36@wormbase.org>
Message-ID: <146D28EF-C33B-4E7F-A674-5FA05ECAA315@caltech.edu>

Sure, No worries
On Aug 15, 2018, at 2:21 PM, Karen Yook <karen at wormbase.org<mailto:karen at wormbase.org>> wrote:

OBO_foundry list.

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From wynner at mail.nih.gov  Thu Aug 16 16:35:15 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Thu, 16 Aug 2018 23:35:15 +0000
Subject: [bioontology-support] searching by synonyms
Message-ID: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

Thanks,
Rob
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From mussavi at uvic.ca  Thu Aug 16 16:51:10 2018
From: mussavi at uvic.ca (mussavi)
Date: Thu, 16 Aug 2018 16:51:10 -0700
Subject: [bioontology-support] Request for NCBO VMWare Virtual Appliance
Message-ID: <14292f037c770264c0cb6d34688b1841@uvic.ca>

Hello 

I am a Health Information Science PhD Candidate at University of
Victoria, British Columbia. As part of my studies, I need to work on
annotating clinical text, but given the security and privacy limitations
of utilizing services that are not hosted in Canada, I need to implement
a local version. 

I appreciate your help with providing the download link for the NCBO
Virtual Appliance. 

Thanks 

Ali Mussavi
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From vendetti at stanford.edu  Thu Aug 16 16:56:31 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 Aug 2018 23:56:31 +0000
Subject: [bioontology-support] searching by synonyms
In-Reply-To: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>
References: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>
Message-ID: <CA25F169-D15A-4E05-B60C-BA7178E3C896@stanford.edu>

Hi Rob,

Apologies, but I?m not sure I followed your question.

We do have a search endpoint in the REST API for searching by ontology properties. It?s documented here:

http://data.bioontology.org/documentation#nav_prop_search

Is this what you meant?

Kind regards,
Jennifer



On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

Thanks,
Rob
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Fri Aug 17 07:15:22 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 17 Aug 2018 07:15:22 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Zachary Lutterbie
Message-ID: <5b76d87a1b6b9_55ed3fbc6ca304f489357@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Fri Aug 17 11:34:27 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 17 Aug 2018 11:34:27 -0700
Subject: [bioontology-support] [BioPortal] Feedback from cloudcray
Message-ID: <5b771533e3b02_7f773fa0ecfc149086757@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Aug 17 12:15:01 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 17 Aug 2018 19:15:01 +0000
Subject: [bioontology-support] [BioPortal] Feedback from cloudcray
In-Reply-To: <5b771533e3b02_7f773fa0ecfc149086757@ncbo-prd-app-08.stanford.edu.mail>
References: <5b771533e3b02_7f773fa0ecfc149086757@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <4CB23406-E668-4DAB-A825-220F9AF6D28D@stanford.edu>

Hello,

When you make requests via the API, we only return a subset of available attributes for performance reasons. You can override this behavior using the ?include" parameter, documented in the General Usage section of the REST API documentation:

http://data.bioontology.org/documentation#nav_usage

For example, I modified the REST API call you listed below to use ?include=all? (return all attributes):

http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2FC0086511?include=all<http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http://purl.bioontology.org/ontology/MEDLINEPLUS/C0086511?include=all>

? and the properties you mentioned are returned (in the properties array):

[cid:B63DAB60-0CC9-486E-A53A-777AF10D9755 at stanford.edu]



Jennifer



On Aug 17, 2018, at 11:34 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: cloudcray

Email: cloud at patientprice.com<mailto:cloud at patientprice.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMEDLINEPLUS%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FMEDLINEPLUS%252FC1148523%26jump_to_nav%3Dtrue

Feedback:

While using the MedlinePlus Topic ontology, I noticed a discrepancy between the data available in the UI vs the API

Certain properties aren't available on the API, but are visible in the UI, such as "MP HEALTH TOPIC URL" and "MP OTHER LANGUAGE URL". It is important to have access to these properties to properly cite the original source of the information.

Please let me know if there's another way to access this data via API - thank you!

UI URL:

http://bioportal.bioontology.org/ontologies/MEDLINEPLUS/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2FC1148523&jump_to_nav=true#details

API Request URL:

http://data.bioontology.org/ontologies/MEDLINEPLUS/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDLINEPLUS%2FC0086511

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From vendetti at stanford.edu  Fri Aug 17 16:50:38 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 17 Aug 2018 23:50:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Zachary
	Lutterbie
In-Reply-To: <5b76d87a1b6b9_55ed3fbc6ca304f489357@ncbo-prd-app-08.stanford.edu.mail>
References: <5b76d87a1b6b9_55ed3fbc6ca304f489357@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <C635236E-6E39-4959-A3A4-1EA59C041E46@stanford.edu>

Hello Zachary,

We import CPT into BioPortal from the National Library of Medicine?s UMLS [1]. Due to licensing restrictions, we aren?t able to offer a download link on our site for the ontology source file. If you?re a current UMLS license holder, please contact our technical program manager John Graybeal (cc?ed) to discuss obtaining a copy privately. If you don?t have a UMLS license, they are free of charge and straightforward to obtain [2].

As part of our import process, we do generate a CSV version of the ontology that could be imported into Excel. It contains all properties for each class, not just preferred names and synonyms. You could perhaps use it as a starting point and remove any columns you don?t need.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/
[2] https://uts.nlm.nih.gov//license.html



On Aug 17, 2018, at 7:15 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Zachary Lutterbie

Email: zlutterbie at ppghealthcare.com<mailto:zlutterbie at ppghealthcare.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%252F99215%26jump_to_nav%3Dtrue

Feedback:

Hello. I am a data analyst with PPG Healthcare in Fort Worth, TX, and I use your amazing site for CPT Descriptions to give our team more thorough details when analyzing our data. Currently I update the CPT Mapping one-by-one, and was curious is there was an export into Excel giving the Preferred Name and Synonyms. It would be a tremendous help to my team. Thank you in advance for reviewing the possibility of such a table.

_______________________________________________
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From wynner at mail.nih.gov  Sat Aug 18 12:52:05 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Sat, 18 Aug 2018 19:52:05 +0000
Subject: [bioontology-support] searching by synonyms
In-Reply-To: <CA25F169-D15A-4E05-B60C-BA7178E3C896@stanford.edu>
References: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>
 <CA25F169-D15A-4E05-B60C-BA7178E3C896@stanford.edu>
Message-ID: <BL0PR0901MB2449FFB6124E64486CF6791AFB3C0@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi Jennifer,

Yes.  I took a look at the documentation and have tried the following calls using my key.  Neither seem to return what I?m looking for, so maybe I?m doing something wrong.

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT/search?q=Malignant

I?d like to restrict my search to just synonyms, and have classes returned that match the search value (a contains or exact match).

Can this be done through BioPortal instead?  If I go to the Advanced Search there is an option to select all properties, but is there a way to search by a single property?

Thanks!
Rob

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, August 16, 2018 7:57 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov>
Cc: support at bioontology.org; De Coronado, Sherri (NIH/NCI) [E] <decorons at mail.nih.gov>
Subject: Re: [bioontology-support] searching by synonyms

Hi Rob,

Apologies, but I?m not sure I followed your question.

We do have a search endpoint in the REST API for searching by ontology properties. It?s documented here:

http://data.bioontology.org/documentation#nav_prop_search

Is this what you meant?

Kind regards,
Jennifer




On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

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

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From zlutterbie at ppghealthcare.com  Mon Aug 20 09:14:53 2018
From: zlutterbie at ppghealthcare.com (Zachary Lutterbie)
Date: Mon, 20 Aug 2018 16:14:53 +0000
Subject: [bioontology-support] CPT Descriptions and Analysis
Message-ID: <CY1PR11MB0425B64B95560803CBA5FBC3C1320@CY1PR11MB0425.namprd11.prod.outlook.com>

I have recently signed up for a UMLS license in order to map our analytics with the most up to date and descriptive details. I have downloaded the 2018AA Full Release file, however I cannot find any portion that has CPT and descriptors as I can find on BioPortal's website. Can you please point me to the file where I can create a lookup based off of CPT codes?

Thank you very much in advance.
Zack Lutterbie

Zachary Lutterbie
Data Analyst

[1452612211259_PPG]
3017 W. 7th St., Suite 200,
Fort Worth, TX 76107
O: 817-725-7900 Ext 1262
C: 940-230-6949
zlutterbie at ppghealthcare.com<mailto:zlutterbie at ppghealthcare.com>

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From rachel.robinson at statesprospective.com  Mon Aug 20 04:05:45 2018
From: rachel.robinson at statesprospective.com (Rachel Robinson)
Date: Mon, 20 Aug 2018 16:35:45 +0530
Subject: [bioontology-support] API
Message-ID: <068901d43875$d8868290$899387b0$@statesprospective.com>

 

 

Hi,

 

Good Day to You!

Could you please let me know your response regarding my previous email. We
will provide you with a few samples for your review.

Target Industry :_______________

Target Geography: ____________

Target Job Titles : ______________

Regards

Rachel - Marketing Manager

 

From: Rachel Robinson [mailto:rachel.robinson at statesprospective.com] 
Sent: 17 August 2018 19:29
To: 'support at bioontology.org'
Subject: API
Importance: High

 

Hi,

 

I found your company profile in "API Directory''. We are dealing with the
database of potential clients/customer related to your industry. Would you
be interested to acquiring the professionals list like "CEO, CFO, Managers,
Directors, Distributors, Suppliers, Resellers, purchasers and other
professionals" as per your requirements. Our list will help you to enlarge
your marketing supply across the globe.

 

Our list includes: Company Name, Contact Name, Job Title, Phone Number, Fax
Number, Email Address, Company address SIC Code and many more as per your
requirements from your industry.

 

Please provide your target as show below, so I can get back to you with more
relevant information on those particular lists.

 

Target Industry :__________________________ (Any Industry)

Target Geography :_______________________ (Worldwide)

Target Job Titles :_________________________ (Any Titles)

 

 

Looking forward to hearing from you!

 

Best Regards,

Rachel Robinson 

Marketing Manager

 

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From support at bioontology.org  Mon Aug 20 03:13:03 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 20 Aug 2018 03:13:03 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Sat Aug 18 08:49:22 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 18 Aug 2018 08:49:22 -0700
Subject: [bioontology-support] [BioPortal] Feedback from HanfeiBaoOnt
Message-ID: <5b7840021084a_36993f829faf2754470ec@ncbo-prd-app-08.stanford.edu.mail>

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From mdorf at stanford.edu  Mon Aug 20 15:45:21 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 20 Aug 2018 22:45:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

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

Feedback:

Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal. http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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 wynner at mail.nih.gov  Tue Aug 21 09:46:29 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Tue, 21 Aug 2018 16:46:29 +0000
Subject: [bioontology-support] Request for Virtual Appliance
Message-ID: <BL0PR0901MB24492F8B4598632029ADB953FB310@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi all,

I am with the NIH/NCI Enterprise Vocabulary Services project.  Would like to request an NCBO Virtual Appliance for my local machine/VMWare for exploration.  Can definitely follow-up with username and key if needed.

Many thanks,
Rob

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From mdorf at stanford.edu  Tue Aug 21 14:43:34 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 21 Aug 2018 21:43:34 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
 <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
Message-ID: <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>

Hi Chen,

I?ve gotten some more insight on why your ontology isn?t processing correctly in BioPortal.

http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.

Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.

The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:

Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal. http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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

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From Chen.Yang at UGent.be  Tue Aug 21 15:00:25 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Tue, 21 Aug 2018 22:00:25 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
 <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
 <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
Message-ID: <7bddd38125034ee9a31850142840ec0a@xmail303.UGent.be>

Hi Michael,
Thanks a lot! I will add a letter and submit again!
Thank you so much for your explanation!
Best regards,
Chen




From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 21 August 2018 23:44
To: support at bioontology.org
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hi Chen,

I?ve gotten some more insight on why your ontology isn?t processing correctly in BioPortal.
http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:
Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal. http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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

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From mdorf at stanford.edu  Thu Aug 23 14:34:18 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 23 Aug 2018 21:34:18 +0000
Subject: [bioontology-support] [BioPortal] Feedback from HanfeiBaoOnt
In-Reply-To: <5b7840021084a_36993f829faf2754470ec@ncbo-prd-app-08.stanford.edu.mail>
References: <5b7840021084a_36993f829faf2754470ec@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <BA65D971-6CEB-4884-9095-C551DBB218A4@stanford.edu>

Hi Hanfei,

Thanks for contacting us. On our end, it doesn?t look like your ontology has been created. Did you intend this ontology to be a view of another ontology? If not, just ignore the checkbox ?This ontology is a view of:?; it should be unchecked by default. Try re-submitting your ontology once again, perhaps there was a momentary issue on our end at the time of your original submission.

If it still doesn?t work, let me know, and we?ll try to submit it internally.

Thanks!

Michael

On Aug 18, 2018, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: HanfeiBaoOnt

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

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

Dear colleagues,

I have post a new ontology "HIVGenetics***.owl", yesterday and it showed:"We're sorry but something has gone wrong. We have been notified of this error."
When I am searching the new ontology today, it seems that the new ontology does not exist, Perhaps because I made some mistakes when did it(for example the item "view Of...").

I would like to ask your instructions to finish the work.

Thank you,

Sincerely yours

Hanfei Bao

_______________________________________________
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 Chen.Yang at UGent.be  Fri Aug 24 07:49:03 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Fri, 24 Aug 2018 14:49:03 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
 <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
 <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
Message-ID: <a53e6328786e4ba482eb3bc3377e117e@xmail303.UGent.be>

Hi Michael,
I modified my ontology and uploaded again (e.g. 00073 --> ne00073). It seemed ok after uploading on 22/08, however, it is finally marked as error rdf today.
Best,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 21 August 2018 23:44
To: support at bioontology.org
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hi Chen,

I?ve gotten some more insight on why your ontology isn?t processing correctly in BioPortal.
http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:
Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal. http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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>
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From mdorf at stanford.edu  Fri Aug 24 15:56:30 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 24 Aug 2018 22:56:30 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <a53e6328786e4ba482eb3bc3377e117e@xmail303.UGent.be>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
 <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
 <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
 <a53e6328786e4ba482eb3bc3377e117e@xmail303.UGent.be>
Message-ID: <0A6004B9-3DE4-44FE-B487-B51EF1240453@stanford.edu>

Hi Chen,

Thank you for working with us on this issue. I?ve checked your updated NEST.owl file, and it still has a number of declarations such as:

    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00057"/>
    </Declaration>
    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00061"/>
    </Declaration>

The best thing for you to do before uploading a new submission to BioPortal is to open your updated file in Protege client and do ?File => Save as? => RDF/XML Syntax?. If the ontology is not parsing correctly, you will see a dialog with a list of errors:

[cid:5BC99FE5-5143-412C-989D-4B0056F1903B at stanford.edu]

If you still see any of these errors in Protege, that means that BioPortal will not be able to successfully process this ontology. Once these errors have been displayed, you can click on the little red triangle (!) icon in the top right corner of the Protege client to see the exact messages from the log. This will help you narrow down the declarations that still need to be fixed.

I hope this helps in getting your errors straightened out.

Thanks!

Michael


On Aug 24, 2018, at 7:49 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Michael,
I modified my ontology and uploaded again (e.g. 00073 --> ne00073). It seemed ok after uploading on 22/08, however, it is finally marked as error rdf today.
Best,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 21 August 2018 23:44
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hi Chen,

I?ve gotten some more insight on why your ontology isn?t processing correctly in BioPortal.
http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:
Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal.http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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

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From Chen.Yang at UGent.be  Fri Aug 24 16:00:23 2018
From: Chen.Yang at UGent.be (Chen Yang)
Date: Fri, 24 Aug 2018 23:00:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <0A6004B9-3DE4-44FE-B487-B51EF1240453@stanford.edu>
References: <5b7a942f8f19a_19d23f85bc09888831688@ncbo-prd-app-09.stanford.edu.mail>
 <ACEFDC45-CD7A-49BA-8AC8-06571CB98FDD@stanford.edu>
 <E0559A21-64E1-453B-A469-22584A2EF25B@stanford.edu>
 <a53e6328786e4ba482eb3bc3377e117e@xmail303.UGent.be>
 <0A6004B9-3DE4-44FE-B487-B51EF1240453@stanford.edu>
Message-ID: <05184d8bdd764b8b9ab231021d2d63c5@xmail303.UGent.be>

Hi Michael,
Thanks a lot. I will follow what you suggested. Thanks again.
Best regards,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 25 August 2018 00:57
To: Chen Yang <Chen.Yang at UGent.be>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hi Chen,

Thank you for working with us on this issue. I?ve checked your updated NEST.owl file, and it still has a number of declarations such as:

    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00057"/>
    </Declaration>
    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00061"/>
    </Declaration>

The best thing for you to do before uploading a new submission to BioPortal is to open your updated file in Protege client and do ?File => Save as? => RDF/XML Syntax?. If the ontology is not parsing correctly, you will see a dialog with a list of errors:

[cid:image001.png at 01D43C0E.FFD93260]

If you still see any of these errors in Protege, that means that BioPortal will not be able to successfully process this ontology. Once these errors have been displayed, you can click on the little red triangle (!) icon in the top right corner of the Protege client to see the exact messages from the log. This will help you narrow down the declarations that still need to be fixed.

I hope this helps in getting your errors straightened out.

Thanks!

Michael



On Aug 24, 2018, at 7:49 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Michael,
I modified my ontology and uploaded again (e.g. 00073 --> ne00073). It seemed ok after uploading on 22/08, however, it is finally marked as error rdf today.
Best,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 21 August 2018 23:44
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Hi Chen,

I?ve gotten some more insight on why your ontology isn?t processing correctly in BioPortal.
http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I?ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I?ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven?t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I?ll try to keep you posted on what further I find out.

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 Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:
Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal.http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
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

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From rachel.robinson at statesprospective.com  Tue Aug 28 06:25:11 2018
From: rachel.robinson at statesprospective.com (Rachel Robinson)
Date: Tue, 28 Aug 2018 18:55:11 +0530
Subject: [bioontology-support] API
Message-ID: <0eab01d43ed2$8ee31cd0$aca95670$@statesprospective.com>

 

 

Hi,

 

Good Day to You!

Could you please let me know your response regarding my previous email. We
will provide you with a few samples for your review.

Target Industry :_______________

Target Geography: ____________

Target Job Titles : ______________

Regards

Rachel - Marketing Manager

 

From: Rachel Robinson [mailto:rachel.robinson at statesprospective.com] 
Sent: 17 August 2018 19:29
To: 'support at bioontology.org'
Subject: API
Importance: High

 

Hi,

 

I found your company profile in "API Directory''. We are dealing with the
database of potential clients/customer related to your industry. Would you
be interested to acquiring the professionals list like "CEO, CFO, Managers,
Directors, Distributors, Suppliers, Resellers, purchasers and other
professionals" as per your requirements. Our list will help you to enlarge
your marketing supply across the globe.

 

Our list includes: Company Name, Contact Name, Job Title, Phone Number, Fax
Number, Email Address, Company address SIC Code and many more as per your
requirements from your industry.

 

Please provide your target as show below, so I can get back to you with more
relevant information on those particular lists.

 

Target Industry :__________________________ (Any Industry)

Target Geography :_______________________ (Worldwide)

Target Job Titles :_________________________ (Any Titles)

 

 

Looking forward to hearing from you!

 

Best Regards,

Rachel Robinson 

Marketing Manager

 

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From Ross.W.Filice at gunet.georgetown.edu  Tue Aug 28 12:02:17 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Tue, 28 Aug 2018 15:02:17 -0400
Subject: [bioontology-support] programmatic class mappings
Message-ID: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

Hi - in an OWL submission what is the appropriate property to map classes across ontologies? I've tried owl sameAs but I don't know that it's working. Should we be using skos:exactMatch instead? Or other?

And similarly is there a way to map subclasses across ontologies?

Thanks much,
Ross

  Ross W. Filice, M.D.
  Associate Professor and Chief, Imaging Informatics
  Department of Radiology, MedStar Georgetown University Hospital
  Chief, Imaging Informatics
  MedStar Medical Group Radiology
  Clinical Informatics Scientist
  National Center for Human Factors in Healthcare, MedStar Institute for Innovation

  3800 Reservoir Road NW, CG 201
  Washington DC, 20007
  202-444-3450<tel:202-444-3450> PHONE
  202-444-4899<tel:202-444-4899> FAX
  ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>
  MedStarHealth.org

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From wynner at mail.nih.gov  Thu Aug 30 06:55:11 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Thu, 30 Aug 2018 13:55:11 +0000
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
Message-ID: <BL0PR0901MB244906603E155828F2444724FB080@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi,

There isn't a link to your OWL, but rdfs:label is usually the standard annotation to map across.  Many OWL files make use of it, and most well-known editors sometimes require it.

This all depends on what kind of imports and prefixes you're making use of.

Others could probably answer your other question better.  I'm just a bioportal user.

Rob

From: Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu>
Sent: Tuesday, August 28, 2018 3:02 PM
To: bioontology-support at lists.stanford.edu
Subject: [bioontology-support] programmatic class mappings

Hi - in an OWL submission what is the appropriate property to map classes across ontologies? I've tried owl sameAs but I don't know that it's working. Should we be using skos:exactMatch instead? Or other?

And similarly is there a way to map subclasses across ontologies?

Thanks much,
Ross

  Ross W. Filice, M.D.
  Associate Professor and Chief, Imaging Informatics
  Department of Radiology, MedStar Georgetown University Hospital
  Chief, Imaging Informatics
  MedStar Medical Group Radiology
  Clinical Informatics Scientist
  National Center for Human Factors in Healthcare, MedStar Institute for Innovation

  3800 Reservoir Road NW, CG 201
  Washington DC, 20007
  202-444-3450<tel:202-444-3450> PHONE
  202-444-4899<tel:202-444-4899> FAX
  ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>
  MedStarHealth.org

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From Ross.W.Filice at gunet.georgetown.edu  Thu Aug 30 11:02:16 2018
From: Ross.W.Filice at gunet.georgetown.edu (Filice, Ross W)
Date: Thu, 30 Aug 2018 14:02:16 -0400
Subject: [bioontology-support] new virtual appliance OVF
Message-ID: <DAE74CB00EC3AD49975BE0428640870B854DBD001E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>

Hi - I was hoping to upgrade our local instance of the virtual appliance.
Thanks,
Ross

  Ross W. Filice, M.D.
  Associate Professor and Chief, Imaging Informatics
  Department of Radiology, MedStar Georgetown University Hospital
  Chief, Imaging Informatics
  MedStar Medical Group Radiology
  Clinical Informatics Scientist
  National Center for Human Factors in Healthcare, MedStar Institute for Innovation

  3800 Reservoir Road NW, CG 201
  Washington DC, 20007
  202-444-3450<tel:202-444-3450> PHONE
  202-444-4899<tel:202-444-4899> FAX
  ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>
  MedStarHealth.org

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From jgraybeal at stanford.edu  Thu Aug 30 16:14:16 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 30 Aug 2018 23:14:16 +0000
Subject: [bioontology-support] programmatic class mappings
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
References: <DAE74CB00EC3AD49975BE0428640870B854DA8DAA7@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
Message-ID: <D9DB15C3-DDE1-4F3B-8496-70ED78987954@stanford.edu>

Hi Ross,

BIoPortal's treatment of mappings is described in https://www.bioontology.org/wiki/BioPortal_Mappings. 

Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)

But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Ontology-mapping-td4656476.html#a4656479:

>  You can also manually create mappings using our REST API:
> 
> http://data.bioontology.org/documentation#Mapping 
> 
> We have example code for programmatically creating mappings in our GitHub sample code repository:
> 
> https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java

I hope all this helps.

John


> On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu> wrote:
> 
> Hi ? in an OWL submission what is the appropriate property to map classes across ontologies? I?ve tried owl sameAs but I don?t know that it?s working. Should we be using skos:exactMatch instead? Or other?
>  
> And similarly is there a way to map subclasses across ontologies?
>  
> Thanks much,
> Ross
>  
>   Ross W. Filice, M.D.
>   Associate Professor and Chief, Imaging Informatics
>   Department of Radiology, MedStar Georgetown University Hospital
>   Chief, Imaging Informatics
>   MedStar Medical Group Radiology
>   Clinical Informatics Scientist
>   National Center for Human Factors in Healthcare, MedStar Institute for Innovation
> 
>   3800 Reservoir Road NW, CG 201
>   Washington DC, 20007
>   202-444-3450 PHONE
>   202-444-4899 FAX
>   ross.w.filice at medstar.net
>   MedStarHealth.org
>  
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



From vendetti at stanford.edu  Thu Aug 30 16:51:26 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 30 Aug 2018 23:51:26 +0000
Subject: [bioontology-support] searching by synonyms
In-Reply-To: <BL0PR0901MB2449FFB6124E64486CF6791AFB3C0@BL0PR0901MB2449.namprd09.prod.outlook.com>
References: <BL0PR0901MB244956EF1D7E3BA4DF3C1A15FB3E0@BL0PR0901MB2449.namprd09.prod.outlook.com>
 <CA25F169-D15A-4E05-B60C-BA7178E3C896@stanford.edu>
 <BL0PR0901MB2449FFB6124E64486CF6791AFB3C0@BL0PR0901MB2449.namprd09.prod.outlook.com>
Message-ID: <D89299C5-69FF-4E76-96F5-9381D9B29A02@stanford.edu>

Hi Rob,


On Aug 18, 2018, at 12:52 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi Jennifer,

Yes.  I took a look at the documentation and have tried the following calls using my key.  Neither seem to return what I?m looking for, so maybe I?m doing something wrong.

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT

http://data.bioontology.org/property_search?q=P90&ontologies=NCIT/search?q=Malignant

I?d like to restrict my search to just synonyms, and have classes returned that match the search value (a contains or exact match).


You can use the ?include? parameter to limit what?s returned by the API. That parameter is documented in the Common Parameters section of our API documentation:

http://data.bioontology.org/documentation#nav_usage

You can also set the display_links parameter to false to eliminate the hypermedia links that are returned by default.

For example (this is the /search endpoint, not the /property_search endpoint):

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&display_links=false

? the above call retrieves all classes from the NCIT ontology where the class name contains ?Malignant?. For each class in the resulting JSON, only the preferred label and synonyms are returned:


[cid:90B15C92-ED30-4239-9D4A-D0CFB90AC09F at stanford.edu]




For an exact match search, you would add the require_exact_match parameter:

http://data.bioontology.org/search?q=Malignant&ontologies=NCIT&include=prefLabel,synonym&require_exact_match=true&display_links=false

[cid:5924C97D-D5F4-479D-AD3C-B5CBA0CDD9A6 at stanford.edu]

Is this the type of search you?re trying to accomplish?

Kind regards,
Jennifer



Can this be done through BioPortal instead?  If I go to the Advanced Search there is an option to select all properties, but is there a way to search by a single property?

Thanks!
Rob

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Thursday, August 16, 2018 7:57 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; De Coronado, Sherri (NIH/NCI) [E] <decorons at mail.nih.gov<mailto:decorons at mail.nih.gov>>
Subject: Re: [bioontology-support] searching by synonyms

Hi Rob,

Apologies, but I?m not sure I followed your question.

We do have a search endpoint in the REST API for searching by ontology properties. It?s documented here:

http://data.bioontology.org/documentation#nav_prop_search

Is this what you meant?

Kind regards,
Jennifer




On Aug 16, 2018, at 4:35 PM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

How would I use BioPortal or the BioPortal RESTAPI to search by synonyms that can be found on classes?  I guess this would go for any one specific text property.  If I do this search using REST, could I specify my property?

Thanks,
Rob
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From amelie at knoesis.org  Fri Aug 31 08:47:12 2018
From: amelie at knoesis.org (Amelie Gyrard)
Date: Fri, 31 Aug 2018 11:47:12 -0400
Subject: [bioontology-support] DAO ontology maintenance on BioPortal
Message-ID: <CAMN9KBPsXT=vwHSWWvRekMs6h=9mbrUsB_cPGSyyyfLEu0wahw@mail.gmail.com>

Dear BioPortal,

We would like to improve the BioPortal DAO web page which has been
initially created by an alumni colleague (enclosed screenshot).

Is it possible to have several persons maintaining this web page?

We should provide the link to the code, see the visualization, etc.
Documentation: http://wiki.knoesis.org/index.php/DAO
Ontology code: http://knoesis.org/ontology/DAO.owl

Thanks

--
Best Regards
Dr. Am?lie Gyrard <http://wiki.knoesis.org/index.php/AmelieGyrard>
Kno.e.sis - Ohio Center of Excellence in Knowledge-enabled Computing
<http://knoesis.org/>
Wright State University, Ohio, USA
kHealth  <http://knoesis.org/projects/khealth>& Hazards SEES
<http://wiki.knoesis.org/index.php/Social_and_Physical_Sensing_Enabled_Decision_Support>
 Projects @Knoesis
Phone: (937)775-5140
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From jgraybeal at stanford.edu  Fri Aug 31 16:45:08 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 31 Aug 2018 23:45:08 +0000
Subject: [bioontology-support] new virtual appliance OVF
In-Reply-To: <DAE74CB00EC3AD49975BE0428640870B854DBD001E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
References: <DAE74CB00EC3AD49975BE0428640870B854DBD001E@PMHEXCMBV006.MEDSTAR.AD.MEDSTAR.NET>
Message-ID: <687AFFD7-A6A1-464C-9F62-3DF4A6F9FADB@stanford.edu>

Hi Ross,

I'm not sure what virtual appliance you are using. The general answer is that if you have access to the Virtual Appliance page at https://bioportal.bioontology.org/virtual_appliance (using your BioPortal login), you can download the latest versions that we have (Version 2.5 in OVF form, Version 2.4 in Amazon EC2 form).

If you need further information, please contact me offline and we can help get you there.

John

On Aug 30, 2018, at 11:02 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Hi ? I was hoping to upgrade our local instance of the virtual appliance.
Thanks,
Ross

  Ross W. Filice, M.D.
  Associate Professor and Chief, Imaging Informatics
  Department of Radiology, MedStar Georgetown University Hospital
  Chief, Imaging Informatics
  MedStar Medical Group Radiology
  Clinical Informatics Scientist
  National Center for Human Factors in Healthcare, MedStar Institute for Innovation

  3800 Reservoir Road NW, CG 201
  Washington DC, 20007
  202-444-3450<tel:202-444-3450> PHONE
  202-444-4899<tel:202-444-4899> FAX
  ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>
  MedStarHealth.org<http://medstarhealth.org/>

_______________________________________________
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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


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From vendetti at stanford.edu  Fri Aug 31 17:13:56 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 1 Sep 2018 00:13:56 +0000
Subject: [bioontology-support] DAO ontology maintenance on BioPortal
In-Reply-To: <CAMN9KBPsXT=vwHSWWvRekMs6h=9mbrUsB_cPGSyyyfLEu0wahw@mail.gmail.com>
References: <CAMN9KBPsXT=vwHSWWvRekMs6h=9mbrUsB_cPGSyyyfLEu0wahw@mail.gmail.com>
Message-ID: <AA72F643-BA14-4B63-B463-25545F98B28D@stanford.edu>

Hello Amelie,


On Aug 31, 2018, at 8:47 AM, Amelie Gyrard <amelie at knoesis.org<mailto:amelie at knoesis.org>> wrote:

We would like to improve the BioPortal DAO web page which has been initially created by an alumni colleague (enclosed screenshot).

Is it possible to have several persons maintaining this web page?


Yes, this is possible. Each person will need to create an account in BioPortal. Then you?ll need to send us the account names so that we can add them as administrators for this ontology. You can use this page to create new accounts:

http://bioportal.bioontology.org/accounts/new



We should provide the link to the code, see the visualization, etc.
Documentation: http://wiki.knoesis.org/index.php/DAO
Ontology code: http://knoesis.org/ontology/DAO.owl


This information can be added by anyone with administrative privileges. Navigate to the ontology summary page for your ontology (http://bioportal.bioontology.org/ontologies/DAO) and click the Add submission link.

Kind regards,
Jennifer

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