From vendetti at stanford.edu  Thu May  2 16:43:52 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 2 May 2019 23:43:52 +0000
Subject: [bioontology-support] [External] [BioPortal] Feedback from
 fergusonch
In-Reply-To: <5B767879-2D31-4C91-AFA7-87D1E7E1D068@bah.com>
References: <697544E5-A874-4001-AEA4-F6EBC477E9F5@bah.com>
 <FC04F3DA-09EE-419D-A6D4-D0C4B470125A@stanford.edu>
 <5B767879-2D31-4C91-AFA7-87D1E7E1D068@bah.com>
Message-ID: <1800B114-4233-461E-AF81-85FFBBA7D5B6@stanford.edu>

Hi Chris,


On Apr 29, 2019, at 1:26 PM, Ferguson, Christopher [USA] <Ferguson_Christopher at bah.com<mailto:Ferguson_Christopher at bah.com>> wrote:

Hi Jennifer,

Thank you again. I did try resubmitting an OWL file into another test and had it load fine. I?m not sure what the problem was with my earliest attempted submissions, but I?ll be sure to convert from TTL to OWL prior to submission in the future. One thing I did notice though is that the annotation properties are duplicated (PATEpiTest Ontology), is that because I provided the URIs for the respective properties during the submission process? (i.e. I entered http://www.w3.org/2000/01/rdf-schema#label for Preferred Label and now see ?Preferred Name? and ?Label? in the Class viewer)


There?s a post in our mailing list archive that I believe answers your question:

http://ncbo-support.2288202.n4.nabble.com/Re-bioontology-support-SNOMED-ttl-file-tp4656300.html

If you still have questions after looking it over, feel free to follow up with us.

Kind regards,
Jennifer

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From mdorf at stanford.edu  Mon May  6 16:54:21 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 6 May 2019 23:54:21 +0000
Subject: [bioontology-support] Help Loading my ontology to the
In-Reply-To: <9DFB6B02-2E58-4B0C-97AF-34FD28155CF0@stanford.edu>
References: <CAGO0_kkOaJoHwHZ-G6tQAWb2XY+A2OoEcMPLu0NSgLZ3fyCVEg@mail.gmail.com>
 <55ACAE58-864B-4D50-8DC3-2D074881F521@stanford.edu>
 <CAGO0_kn9=QdyMqcbCBp+8qsGzM=oCHNQ1ZtJ1sDY9r-W6xoLWQ@mail.gmail.com>
 <F4AADBE2-BD0B-4F54-A727-32A93A4A39D6@stanford.edu>
 <CAGO0_kki5c0=+21VDT4m_C8MRCW0DVrjUoMfLy7sK+7p9nMoNQ@mail.gmail.com>
 <9DFB6B02-2E58-4B0C-97AF-34FD28155CF0@stanford.edu>
Message-ID: <3012DC59-EE21-4C76-878B-E6113879475B@stanford.edu>

Hi Dan,

As requested, I?ve converted NEO from a view of SNOMEDCT into a standalone ontology. The ontology has been re-processed and is now available for viewing:

http://bioportal.bioontology.org/ontologies/NEO

Please let us know if you require further assistance.

Thanks,

Michael




On May 3, 2019, at 4:46 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Dan,

Apologies for the delayed response. We?ve been in the process of importing a large number of UMLS ontologies into our system, which has required us to hold off on making changes to existing ontologies.

I?m out of the office next week, but my colleague Michael has kindly offered to make the modification you requested below. I?ve entered an issue in our tracker to that effect:

https://github.com/ncbo/bioportal-project/issues/116

Best regards,
Jennifer



On Apr 30, 2019, at 3:52 PM, Daniel Hier <dbhier at dbhier.com<mailto:dbhier at dbhier.com>> wrote:

Thank you again.  I pasted the definition into Web Protege.  I am pretty far along in rebuilding my ontology.  I feel I know more now and am using Protege correctly.  My prior attempts were a mix of different IRIs.  Now everything looks consistent and professional.
Is there any way for me to change my NEO ontology from "ontology view" back to "ontology"?  Thanks again for all of your expert help!  I will try to get a descriptive paper  published in NEUROINFORMATICS as a data project and I will cite the BIOPORTAL as the repository.

Dan

On Mon, Apr 29, 2019 at 6:20 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Dan,


On Apr 28, 2019, at 7:14 AM, Daniel Hier <dbhier at dbhier.com<mailto:dbhier at dbhier.com>> wrote:

Thank you for helping me with my ontology NEO (neurological examination ontology).  I have decided to rebuild it from scratch in PROTEGE and my partial version with 400 classes and it will now load properly.  I will finish it with 650 classes.  I particularly like the download feature of CSV file--that is a very nice feature that I will use when I post-process my file.

Thanks again for your help.  There must have been subtle errors in my original ontology.  I am about 60% done rebuilding it.


OK - thanks for letting us know that you?ve made additional uploads.

Nonetheless, I did want to track down why your previous submissions were failing. The problem occurred fairly deep in our stack in some code where we use a 3rd party library to load / parse ontologies. Normally this library produces helpful error messages, but in this particular case, we weren?t getting any indication of failure, so it took some digging around and testing before i was able to isolate the issue.

It turns out there?s a syntax error on line 1033 of your ontology (shown in bold below):

<!-- http://webprotege.stanford.edu/R95MZmrikwqzrjl7N1cShdN -->

<owl:Class rdf:about="http://webprotege.stanford.edu/R95MZmrikwqzrjl7N1cShdN">
  <rdfs:subClassOf rdf:resource="http://webprotege.stanford.edu/RCAfDthAKPwhOppuDOBzZo2"/>
  <webprotege:R8JlHtLpsj8hW18voM8qfVy>&lt;apraxic gait&gt;&lt;Bruns apraxia&gt;&lt;magnetic gait&gt;&lt;frontal gait&gt;|</webprotege:R8JlHtLpsj8hW18voM8qfVy>
  <webprotege:R9erWLcZm8MU17huk4CFMwy>|30767006|</webprotege:R9erWLcZm8MU17huk4CFMwy>
  <BbHRvdgdu3Y4vbyVxXTwfu:UMLS>C1510417</BbHRvdgdu3Y4vbyVxXTwfu:UMLS>
  <rdfs:label>gait apraxia</rdfs:label>
  <skos:definition rdf:resource="apraxia for walking, accompanied by inability to make skilled walking movements with the legs.gait apraxia; unexplained by weakness, sensory loss, or incoordination (n.d.) Farlex Partner Medical Dictionary. (2012). [Retrieved April 21 2016 from http://medical-dictionary.thefreedictionary.com/gait+apraxia]"/>
</owl:Class>

? where a skos:definition has an opening tag, but no closing tag. I added an end tag, i.e.:

 <skos:definition>apraxia for walking, accompanied by inability to make skilled walking movements with the legs.gait apraxia; unexplained by weakness, sensory loss, or incoordination (n.d.) Farlex Partner Medical Dictionary. (2012). [Retrieved April 21 2016 from http://medical-dictionary.thefreedictionary.com/gait+apraxia]</skos:definition>

... and tested uploading this fixed version of your ontology in our staging environment, and it succeeded.

I?m wondering - did you hand edit your ontology file before you submitted it to BioPortal? Or, did you simply upload the file that you exported from WebProtege? If it?s the latter, I recommend notifying the Protege team that your ontology was exported without an end tag for that particular skos definition.

Kind regards,
Jennifer



--
Daniel B Hier MD


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From mdorf at stanford.edu  Mon May  6 20:09:31 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 7 May 2019 03:09:31 +0000
Subject: [bioontology-support] I've uploaded an ontology (Adherence
	and	Integrated Care in Spanish) to Bioportal but I can't
	retrieve	the classes to visualize them.
In-Reply-To: <584AAA93-86B3-4AD9-9F66-96FF41003FC1@juntadeandalucia.es>
References: <0B60ABDC-5519-46B9-B8EA-4D62BC460037@juntadeandalucia.es>
 <86DCB185-15E5-4179-9354-58D325A1B820@stanford.edu>
 <ED757B02-219C-46E7-9BAE-FBDB398FCA2D@juntadeandalucia.es>
 <BE725166-C802-48E6-96A8-FD439178C9FF@stanford.edu>
 <584AAA93-86B3-4AD9-9F66-96FF41003FC1@juntadeandalucia.es>
Message-ID: <136EB984-365F-4D5E-B9B4-E902A2598B1E@stanford.edu>

Hi Carlos,

Your ontology has been re-processed and is now available at:

http://bioportal.bioontology.org/ontologies/ADHER_INTCARE_SP?p=classes

Let us know if you run into any other issues.

Thanks,

Michael

On Apr 29, 2019, at 10:19 PM, Carlos Luis Parra Calder?n <carlos.parra.sspa at juntadeandalucia.es<mailto:carlos.parra.sspa at juntadeandalucia.es>> wrote:

Hi Jennifer.

Ok. We wait for your solution.

Thanks.

Carlos.

Carlos Luis Parra Calder?n

Jefe de Secci?n de Innovaci?n Tecnol?gica
Hospital Universitario Virgen del Roc?o
Servicio Andaluz de Salud
Consejer?a de Salud
Avda. Manuel Siurot S/N - 41013 Sevilla<x-apple-data-detectors://1/0>
Tel:    +34 955 01 36 62<tel:+34%20955%2001%2036%2062> - (31 36 62)
M?vil: +34 697 95 48 64<tel:+34%20697%2095%2048%2064> - (75 48 64)
www.huvr.es<http://www.huvr.es/>
carlos.parra.sspa at juntadeandalucia.es<mailto:carlos.parra.sspa at juntadeandalucia.es>
skype: carlos.luis.parra

Director del Grupo de Investigaci?n e Innovaci?n en Inform?tica Biom?dica, Ingenier?a biom?dica y Econom?a de la Salud.
Instituto de Biomedicina de Sevilla
www.ibis-sevilla.es/<http://www.ibis-sevilla.es/>

Asistente Honorario.
Escuela T?cnica Superior de Ingenier?a Inform?tica.
Universidad de Sevilla.
_________________________________________________________________________________________________

Head of Technological Innovation
Virgen del Roc?o University Hospital

Head of Research and Innovation in Biomedical Informatics, Biomedical Engineering & Health Economy,
Institute of Biomedicine of Seville

Honorary assistant
School Computer Science
University of Seville
________________________________________

El 30 abr 2019, a las 1:33, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> escribi?:

Hello Carlos,

Yes, you?re correct. We?re going to look at your ontology and try to figure out why it?s not loading in BioPortal. We should be able to start investigating tomorrow.

Kind regards,
Jennifer


On Apr 29, 2019, at 3:20 PM, Carlos Luis Parra Calder?n <carlos.parra.sspa at juntadeandalucia.es<mailto:carlos.parra.sspa at juntadeandalucia.es>> wrote:

Dear Jennifer.

Thank you very much for your support and commitment!!

I understand that you are going to try to diagnose and try to solve the problem?

All the best.

Carlos.

Carlos Luis Parra Calder?n

Jefe de Secci?n de Innovaci?n Tecnol?gica
Hospital Universitario Virgen del Roc?o
Servicio Andaluz de Salud
Consejer?a de Salud
Avda. Manuel Siurot S/N - 41013 Sevilla<x-apple-data-detectors://1/0>
Tel:    +34 955 01 36 62<tel:+34%20955%2001%2036%2062> - (31 36 62)
M?vil: +34 697 95 48 64<tel:+34%20697%2095%2048%2064> - (75 48 64)
www.huvr.es<http://www.huvr.es/>
carlos.parra.sspa at juntadeandalucia.es<mailto:carlos.parra.sspa at juntadeandalucia.es>
skype: carlos.luis.parra

Director del Grupo de Investigaci?n e Innovaci?n en Inform?tica Biom?dica, Ingenier?a biom?dica y Econom?a de la Salud.
Instituto de Biomedicina de Sevilla
www.ibis-sevilla.es/<http://www.ibis-sevilla.es/>

Asistente Honorario.
Escuela T?cnica Superior de Ingenier?a Inform?tica.
Universidad de Sevilla.
_________________________________________________________________________________________________

Head of Technological Innovation
Virgen del Roc?o University Hospital

Head of Research and Innovation in Biomedical Informatics, Biomedical Engineering & Health Economy,
Institute of Biomedicine of Seville

Honorary assistant
School Computer Science
University of Seville
________________________________________

El 29 abr 2019, a las 17:55, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> escribi?:

Apologies that you?re having difficulty loading your ontology in BioPortal. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/112

? so that we can have a look.

_______________________________________________
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 shyamanm.jayasundara at student.montana.edu  Tue May  7 06:21:18 2019
From: shyamanm.jayasundara at student.montana.edu (Jayasundara, Shyaman)
Date: Tue, 7 May 2019 13:21:18 +0000
Subject: [bioontology-support] Requesting NCBO - VMWare Virtual Appliance
Message-ID: <DM6PR02MB5961899D378D9CE26C07DA72DE310@DM6PR02MB5961.namprd02.prod.outlook.com>

Hello NCBO support,

I am a research student at Montana State University and I'm trying to use NCBO ontology recommender scores for a project. Since I am retrieving scores for a large abstract database, it consumes a lot of time. Therefore I want to install this locally. The project is related to Research Domain Criteria (RDoC)<https://www.nimh.nih.gov/research/research-funded-by-nimh/rdoc/index.shtml> and research articles classification according to RDoC construct categories. Therefore I hope to gain access to the VMWare Virtual Appliance.

Sincerely,
Shyaman

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From support at bioontology.org  Wed May  8 06:15:18 2019
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 08 May 2019 06:15:18 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Vaibhav
Message-ID: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail>

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From filipowj at tchpc.tcd.ie  Thu May  9 04:29:01 2019
From: filipowj at tchpc.tcd.ie (filipowj at tchpc.tcd.ie)
Date: Thu, 09 May 2019 11:29:01 +0000
Subject: [bioontology-support] OWL Ontology
Message-ID: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie>

Hi there,

I work for Trinity College Dublin and looking to submit new ontology to the BioPortal.
I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal.
I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value.
So I add them as annotation to the class in protege.
Once .owl file is submitted to BioPortal I can see them as new properties on Details Section
but when I use API Get call they're not visible like they were never parsed.

Here is the call:
http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey (http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=ce36656e-7615-400a-ac5c-2f1ea4b39908)

cui and notation are included but there are not showing up.

My ontology is created with Protege, please find attached the screenshots.
I'd appreciate your suggestions.

Best Regards,
Juliusz Filipowski
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From mdorf at stanford.edu  Thu May  9 13:48:08 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 9 May 2019 20:48:08 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Vaibhav
In-Reply-To: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail>
References: <5cd2d6664e770_61e22af7275c1a40877b@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <9366E929-182C-4072-9178-01ADCFDB6D5B@stanford.edu>

Hi Vaibhav,

Thank you for contacting us. I?ve tried the links you sent, and they all resolve fine on my end. Does the problem still exist on yours? We?ve been working on a fresh import of UMLS ontologies from the National Library of Medicine over the last few days. Our work may have caused a brief downtime that you?ve experienced.

Please let us know if this is still an issue.

Thanks,

Michael



On May 8, 2019, at 6:15 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Vaibhav

Email: vaibhav.joy at gmail.com<mailto:vaibhav.joy at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FSNOMEDCT%252F175050003%26jump_to_nav%3Dtrue

Feedback:

This API is return error message "The input class id '175050003' is not a valid IRI".
http://data.bioontology.org/ontologies/SNOMEDCT/classes/175050003/children

Also, it is not showing on the website for the following URL
http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=175050003

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

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From mdorf at stanford.edu  Thu May  9 14:00:49 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 9 May 2019 21:00:49 +0000
Subject: [bioontology-support] OWL Ontology
In-Reply-To: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie>
References: <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie>
Message-ID: <B5FC6792-B1DF-4005-A31D-67E6FC55C595@stanford.edu>

Hi Juliusz,

Thank you for contacting us. The ontology TESTJF that your call below is referring to isn?t the same as the one you are referring to in your screenshots. TESTJF contains only two classes and none of the annotations that you mentioned (see screenshots). Is it possible that you uploaded a wrong ontology?

Michael

[cid:DD280B99-1FA4-42F9-BA65-EEF63DEFBC4D at stanford.edu]
[cid:4B80A9F1-3790-422E-81DD-F3486F24A077 at stanford.edu]



On May 9, 2019, at 4:29 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:

Hi there,

I work for Trinity College Dublin and looking to submit new ontology to the BioPortal.
I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal.
I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value.
So I add them as annotation to the class in protege.
Once .owl file is submitted to BioPortal I can see them as new properties on Details Section
but when I use API Get call they're not visible like they were never parsed.

Here is the call:
http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey<http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=ce36656e-7615-400a-ac5c-2f1ea4b39908>

cui and notation are included but there are not showing up.

My ontology is created with Protege, please find attached the screenshots.
I'd appreciate your suggestions.

Best Regards,
Juliusz Filipowski



<Screenshot 2019-05-09 at 12.26.40 (2).png><Screenshot 2019-05-09 at 12.26.33 (2).png>_______________________________________________
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 hpan at rti.org  Thu May  9 14:29:13 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Thu, 9 May 2019 21:29:13 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>,
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
Message-ID: <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael


On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john



On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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 May  9 16:52:13 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 9 May 2019 23:52:13 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
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 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
Message-ID: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael



On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael


On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john



On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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 hpan at rti.org  Thu May  9 17:29:37 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Fri, 10 May 2019 00:29:37 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
Message-ID: <SN6PR07MB56452ED754410232FFE0D34CD60C0@SN6PR07MB5645.namprd07.prod.outlook.com>

Thank you, Michael! I apologize for mixing up the formats. Yes, it makes sense.

Best regards,
Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

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


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

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From hpan at rti.org  Fri May 10 04:25:19 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Fri, 10 May 2019 11:25:19 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
Message-ID: <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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  Fri May 10 11:50:54 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 10 May 2019 18:50:54 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
 <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
Message-ID: <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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 hpan at rti.org  Fri May 10 11:54:38 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Fri, 10 May 2019 18:54:38 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
 <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
Message-ID: <SN6PR07MB5645EFEE2561CCAE3327A959D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>

It works on my end as well!

I appreciate your help, Michael!

Have a great weekend!

Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael


On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael





On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael




On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>






On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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 hpan at rti.org  Fri May 10 13:41:42 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Fri, 10 May 2019 20:41:42 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
 <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
Message-ID: <SN6PR07MB56459D3EB4C763AA585C8F93D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>

Hi Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael


On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael





On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael




On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>






On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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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https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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  Fri May 10 13:59:44 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 10 May 2019 20:59:44 +0000
Subject: [bioontology-support] OWL Ontology
In-Reply-To: <5dafd28c86c39aa8523d807b8820e2c8@tchpc.tcd.ie>
References: <B5FC6792-B1DF-4005-A31D-67E6FC55C595@stanford.edu>
 <55544f35f51d1be0bc8e0cf8c02f2eda@tchpc.tcd.ie>
 <5dafd28c86c39aa8523d807b8820e2c8@tchpc.tcd.ie>
Message-ID: <3BD73393-5010-4CE1-B431-4CD0EA154516@stanford.edu>

Hi Juliusz,

Thanks for getting back to us. Before I proceed with my specific comments on your ontology, please note that the BioPortal support is mainly focused on issues related to using the BioPortal system as well as the BioPortal REST APIs. For questions related to ontology development, I would suggest posting your query on the Protege support list [1], which tends to be monitored by a larger community of ontology experts.  My background is in software development, so I?m not very good at recommending ways of defining your ontology structure.

That said, I?ve compared the class in your ontology that you were referring to, ?Maxillary sinus?, with a couple of classes from other UMLS ontologies that define the properties ?notation? and ?cui?. The difference appears to be in the namespace that is used for the ?notation?:


Your class:
http://data.bioontology.org/ontologies/ICD-O-3-T/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCDN-O-3-T%2FC31.0?display=all<http://data.bioontology.org/ontologies/ICD-O-3-T/classes/http://purl.bioontology.org/ontology/CDN-O-3-T/C31.0?display=all>

http://purl.bioontology.org/ontology/CDN-O-3-T/notation": [

  *   "C001"

]

SNOMEDCT:
http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006?display=all<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/410607006?display=all>

http://www.w3.org/2004/02/skos/core#notation": [

  *   "410607006"

]

ICD10:
http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FK70-K77.9?display=all<http://data.bioontology.org/ontologies/ICD10/classes/http://purl.bioontology.org/ontology/ICD10/K70-K77.9?display=all>

http://www.w3.org/2004/02/skos/core#notation": [

  *   "K70-K77.9?

]

Try using the namespace http://www.w3.org/2004/02/skos/core for your ?notation? property. Once in place, we should be able to recognize it and process it correctly for our search index.

As far as the property ?cui?, it doesn?t appear to exist in any of the classes that you referred to in your ontology, so I can?t comment on whether it?s defined properly.

Thanks,

Michael

[1] https://protege.stanford.edu/support.php


On May 10, 2019, at 1:26 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:

Hi Michael,

Many thanks for your email.
I'm sorry for confusion there I used TESTJF for testing and tried uploading different versions.
Please take a look at my correct ontology: ICD-O-3-T and screenshots attached

I've added notation through the annotations to class Lip and it's visible in the description but via API call
it is attached to properties and not to an actual attribute?

In an essence I'm not sure how to add attributes: notation and cui.

I appreciate your help.

Juliusz Filipowski

May 9, 2019 10:45 PM, "Michael Dorf" <mdorf at stanford.edu<mailto:mdorf at stanford.edu?to=%22Michael%20Dorf%22%20%3Cmdorf at stanford.edu%3E>> wrote:
Hi Juliusz,
Thank you for contacting us. The ontology TESTJF that your call below is referring to isn?t the same as the one you are referring to in your screenshots. TESTJF contains only two classes and none of the annotations that you mentioned (see screenshots). Is it possible that you uploaded a wrong ontology?
Michael
<PastedGraphic-1.png>
<PastedGraphic-2.png>


On May 9, 2019, at 4:29 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:
Hi there,

I work for Trinity College Dublin and looking to submit new ontology to the BioPortal.
I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal.
I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value.
So I add them as annotation to the class in protege.
Once .owl file is submitted to BioPortal I can see them as new properties on Details Section
but when I use API Get call they're not visible like they were never parsed.

Here is the call:
http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey<http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=ce36656e-7615-400a-ac5c-2f1ea4b39908>

cui and notation are included but there are not showing up.

My ontology is created with Protege, please find attached the screenshots.
I'd appreciate your suggestions.

Best Regards,
Juliusz Filipowski



<Screenshot 2019-05-09 at 12.26.40 (2).png><Screenshot 2019-05-09 at 12.26.33 (2).png>_______________________________________________
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<Screenshot 2019-05-10 at 09.17.46.png><Screenshot 2019-05-10 at 09.18.16.png>

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From hpan at rti.org  Fri May 10 14:59:51 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Fri, 10 May 2019 21:59:51 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <SN6PR07MB56459D3EB4C763AA585C8F93D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <19214E17-2F26-45E6-8BFF-F172A57361CD@stanford.edu>
 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
 <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
 <SN6PR07MB56459D3EB4C763AA585C8F93D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
Message-ID: <SN6PR07MB5645B47FB535627A0718D058D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>

Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes

Thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org>
Sent: Friday, May 10, 2019 4:42 PM
To: Michael Dorf <mdorf at stanford.edu>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>; support at bioontology.org; Pan, Huaqin (Helen) <hpan at rti.org>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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 jgraybeal at stanford.edu  Fri May 10 16:53:55 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 10 May 2019 23:53:55 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <SN6PR07MB5645B47FB535627A0718D058D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <3650B17B-FEAF-4232-8EFC-E3C3310CACAA@stanford.edu>
 <SN6PR07MB564522EB51F18A2D2F9AF864D63D0@SN6PR07MB5645.namprd07.prod.outlook.com>
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 <SN6PR07MB5645B47FB535627A0718D058D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
Message-ID: <A74E9B99-756D-4E79-9DA5-54604145F005@stanford.edu>

Helen,

I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing?

It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?).

However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache.

John



On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes

Thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Friday, May 10, 2019 4:42 PM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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

_______________________________________________
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 mdorf at stanford.edu  Fri May 10 17:20:12 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Sat, 11 May 2019 00:20:12 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <A74E9B99-756D-4E79-9DA5-54604145F005@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
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Message-ID: <E2ECBD5D-16C7-4495-8347-1CB7F41C038F@stanford.edu>

Hi Helen,

Both ontologies appear properly on my end as well. The LungMap ontology now has a single root class, ?respiratory system?, hope that?s as intended.  As John said, it does take a bit of time for the results of the processing to propagate through our various architecture layers. Feel free to contact us if the issue still persists.

Thanks,

Michael


On May 10, 2019, at 4:53 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Helen,

I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing?

It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?).

However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache.

John



On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes

Thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Friday, May 10, 2019 4:42 PM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael




On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael



On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>





On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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

_______________________________________________
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 hpan at rti.org  Sat May 11 05:46:47 2019
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Sat, 11 May 2019 12:46:47 +0000
Subject: [bioontology-support] metadata treeview error message
In-Reply-To: <E2ECBD5D-16C7-4495-8347-1CB7F41C038F@stanford.edu>
References: <SN6PR07MB5645F7B68BF66DBD2957F2E5D64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <BYAPR02MB4519586A842FDF91D59416A1DA4B0@BYAPR02MB4519.namprd02.prod.outlook.com>
 <SN6PR07MB5645A974D224DA00D34E9D3BD64B0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <D7686267-E0E8-4AD2-AEDB-911358F552FD@stanford.edu>
 <SN6PR07MB564526B013CDB8AE487D4DE6D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <E44EEF72-25F8-4B46-B048-4FC022912B22@stanford.edu>
 <SN6PR07MB56453DBB6CDB6052732D8E79D6440@SN6PR07MB5645.namprd07.prod.outlook.com>
 <FCDC37B9-441D-424D-B977-B4F02E246288@stanford.edu>
 <SN6PR07MB5645ED3C53E630FCDE3EA86BD6470@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645CC75807812736CFB7385D62E0@SN6PR07MB5645.namprd07.prod.outlook.com>
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 <SN6PR07MB5645B4C44931A8ACBED89777D63F0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645E710C189A37F117F6A67D6330@SN6PR07MB5645.namprd07.prod.outlook.com>
 <392D926C-8241-4A27-933F-0BE891825A20@stanford.edu>
 <SN6PR07MB56452352F135624BCB8ABE40D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <A3893C0A-0A69-4CCB-9A44-2E352BED65E7@stanford.edu>
 <SN6PR07MB56459D3EB4C763AA585C8F93D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <SN6PR07MB5645B47FB535627A0718D058D60C0@SN6PR07MB5645.namprd07.prod.outlook.com>
 <A74E9B99-756D-4E79-9DA5-54604145F005@stanford.edu>
 <E2ECBD5D-16C7-4495-8347-1CB7F41C038F@stanford.edu>
Message-ID: <SN6PR07MB56453D95B4B3DEA9B1D35A42D60D0@SN6PR07MB5645.namprd07.prod.outlook.com>

Hi John and Michael,

I just did another upload of mouse obo file, and indeed it was able to reload successfully. I will try clear cache if I run into any errors.

Yes, the single root class is what I wanted. Thanks again for your help!

Best regards,
Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Friday, May 10, 2019 8:20 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: support at bioontology.org; John Graybeal <jgraybeal at stanford.edu>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Both ontologies appear properly on my end as well. The LungMap ontology now has a single root class, ?respiratory system?, hope that?s as intended.  As John said, it does take a bit of time for the results of the processing to propagate through our various architecture layers. Feel free to contact us if the issue still persists.

Thanks,

Michael



On May 10, 2019, at 4:53 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Helen,

I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing?

It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?).

However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache.

John




On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes

Thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Friday, May 10, 2019 4:42 PM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Prot?g? doesn?t display the hierarchical structure for the ?part_of?, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don?t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

I?ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn?t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn?t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn?t display the hierarchical structure for ?part-of?. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I?ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael





On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
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] metadata treeview error message

Hi Michael,

It?s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Sorry, but I don?t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael




On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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] metadata treeview error message

Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I?ve re-processed your ontology, and it?s now visible in BioPortal.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I uploaded an ontology file a few days ago and it hasn?t been parsed yet. Usually it doesn?t take this long. Would you please take a look ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi Jennifer,

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

I appreciate your help!

Helen

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use ?subClassOf".
2). For OBO ontologies we use ?part_of?, ?contains?, and ?develops from?.
3). For SKOS ontologies we use ?broader?.

There is no standard property built into the OWL language for representing "part of? relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They?ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive ?subclass_of? property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of ?subclass_of? and ?part_of?, but I am having trouble display the ?part_of? relations in a tree view.

I am available for a phone call or web conference if that?s helpful.

I appreciate your help!

Helen
919-434-4665


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer




<image001.png>






On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John,

I think this question is for your team ?

I uploaded an ontology file with properties of ?subclass?, ?part_of?, and ?treeview?. Currently only the ?subclass? displays as tree view. How do I make the ?part_of? relation also display in tree view at BioPortal? I added the ?treeview? properties for both  ?subclass? and ?part_of?.

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

Best wishes.

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: Re: [bioontology-support] metadata treeview error message

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.


Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message ?The prefix "metadata" for element "metadata:treeView" is not bound? when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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

_______________________________________________
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

_______________________________________________
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  Fri May 10 11:10:41 2019
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 10 May 2019 11:10:41 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Joab
Message-ID: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail>

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From c.cruschi at elif.it  Mon May 13 03:16:20 2019
From: c.cruschi at elif.it (Claudio Cruschi)
Date: Mon, 13 May 2019 12:16:20 +0200
Subject: [bioontology-support] technical support for bioportal_web_UI
Message-ID: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it>

Hi,

I'm writing because I have some problems with the web ui bioportal rails 
application (the latest github version of the master branch) in the 
virtual appliance.

I copied the web app to the rails/releases/<current_datetime> directory, 
I created the "current" symbolic link to this folder, I created all the 
other symbolic links to the shared folder and restarted all services 
with the bprestart command. But when I open the browser to the IP 
address of the appliance, the following error is returned to me:


  "We're sorry, but something went wrong.

Web application could not be started by the Phusion Passenger 
application server."


Could you give me a step by step procedures to deploy and run bioportal 
web ui in the virtual machine?

Regards

Claudio C.




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From alex.skrenchuk at stanford.edu  Mon May 13 12:26:31 2019
From: alex.skrenchuk at stanford.edu (Alex Skrenchuk)
Date: Mon, 13 May 2019 19:26:31 +0000
Subject: [bioontology-support] technical support for bioportal_web_UI
In-Reply-To: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it>
References: <6eadead4-f963-ad1a-2264-0b28ce0de80d@elif.it>
Message-ID: <B310367F-9223-4019-B70E-CC253E92243A@stanford.edu>

Hi Claudio

Ontoportal Virtual Appliance v2.5 is not configured appropriately to run latest version of bioportal web ui.
We will be releasing a new version of the appliance that runs latest version of Bioportal stack in the next few weeks.

-Alex

From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of Claudio Cruschi <c.cruschi at elif.it>
Date: Monday, May 13, 2019 at 9:21 AM
To: "support at bioontology.org" <support at bioontology.org>
Subject: [bioontology-support] technical support for bioportal_web_UI

Hi,

I'm writing because I have some problems with the web ui bioportal rails application (the latest github version of the master branch) in the virtual appliance.

I copied the web app to the rails/releases/<current_datetime> directory, I created the "current" symbolic link to this folder, I created all the other symbolic links to the shared folder and restarted all services with the bprestart command. But when I open the browser to the IP address of the appliance, the following error is returned to me:



"We're sorry, but something went wrong.

Web application could not be started by the Phusion Passenger application server."



Could you give me a step by step procedures to deploy and run bioportal web ui in the virtual machine?

Regards

Claudio C.



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From jonquet at lirmm.fr  Mon May 13 14:39:00 2019
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Mon, 13 May 2019 14:39:00 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Joab
In-Reply-To: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail>
References: <5cd5bea1e7ffb_5e1a2ad1e0e573ec88534@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <FEFBE0F2-C2FF-4428-881B-F51474177D76@lirmm.fr>

Dear Chen, 

Could you specify your question a bit more? 
1. Are you interested in ontologies in other languages in BioPortal? 
2. Somewhere else? 
3. Interested in ontologies that have been explicitly translated or in multilingual ontologies (providing labels in different languages)?
4. Are you interested in mappings btw ontologies in different languages?
5. Other ;)

Best
Clement Jonquet

> Le 10 mai 2019 ? 11:10, support at bioontology.org a ?crit :
> 
> Name: Joab
> 
> Email: chen.joab at gmail.com
> 
> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fmappings
> 
> 
> Feedback:
> 
> Hi,
> 
> Are there ontologies that are translated and not in english? ie. French, German etc.
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Thu May 16 06:31:20 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 16 May 2019 06:31:20 -0700
Subject: [bioontology-support] [BioPortal] Feedback from William Van Woensel
Message-ID: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu May 16 08:09:41 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 May 2019 15:09:41 +0000
Subject: [bioontology-support] [BioPortal] Feedback from William Van
 Woensel
In-Reply-To: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail>
References: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <DD2D42A7-ADE8-4974-ACCB-119E7E79D276@stanford.edu>

Hi William,

Could you please include a URL for one of the pages where you see this error? The BioPortal application does use some older 3rd party JavaScript plug-ins that we haven?t had the resources to look into replacing yet. It?s unclear to me if you?re referring to one of those pages.

Kind regards,
Jennifer


On May 16, 2019, at 6:31 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: William Van Woensel

Email: william.van.woensel at gmail.com<mailto:william.van.woensel at gmail.com>

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

Feedback:

Hi,

It looks like there's an issue with loading JavaScript on the webpages - I'm seeing a lot of errors such as :

"Blocked loading mixed active content ?http://code.jquery.com/.."

This is due to the fact that you're website is hosted on HTTPS but it's trying to load resources from HTTP. It should be easy to fix this.

Thanks,

William

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

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From support at bioontology.org  Thu May 16 13:37:12 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 16 May 2019 13:37:12 -0700
Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero
Message-ID: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu May 16 16:21:25 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 May 2019 23:21:25 +0000
Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero
In-Reply-To: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>
References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu>

Hi Sean,

Due to CPT licensing restrictions, we?re not able to offer downloads of the ontology data in any format.

I?m not sure I followed exactly what you?d like to do. We have a REST API that could help with efficiently retrieving preferred names, e.g.:


[cid:B5292DF1-A834-4A8D-83EE-38F34574A6C4 at stanford.edu]

The API is documented here:

http://data.bioontology.org/documentation

Kind regards,
Jennifer



On May 16, 2019, at 1:37 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: sean.guerrero

Email: sean.guerrero at hoag.org<mailto:sean.guerrero at hoag.org>

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%252F11056%26jump_to_nav%3Dtrue

Feedback:

Hello,

I'm looking at the Current Procedural Terminology section under the "Classes" tab. I'm looking for a way to pull the Preferred Name of the CPT codes I am searching for. Is there an excel file that I can use to reference?

-Sean

_______________________________________________
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 Sean.Guerrero at Hoag.org  Thu May 16 17:31:37 2019
From: Sean.Guerrero at Hoag.org (Guerrero, Sean)
Date: Fri, 17 May 2019 00:31:37 +0000
Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero
In-Reply-To: <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu>
References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>
 <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu>
Message-ID: <MN2PR03MB48628DAB5109B938CA4D9D80970B0@MN2PR03MB4862.namprd03.prod.outlook.com>

Hi Jennifer,

Thanks for the quick response!
I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below:

It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names?

[cid:image001.png at 01D50C0D.35029ED0]

24546
24565
24566
24575
24579
24586


Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<http://www.hoagorthopedicinstitute.com/>

[cid:image001.png at 01D27580.6E6F5760]

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, May 16, 2019 4:21 PM
To: support at bioontology.org
Cc: Guerrero, Sean <Sean.Guerrero at Hoag.org>
Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from sean.guerrero

Hi Sean,

Due to CPT licensing restrictions, we?re not able to offer downloads of the ontology data in any format.

I?m not sure I followed exactly what you?d like to do. We have a REST API that could help with efficiently retrieving preferred names, e.g.:


[cid:image003.png at 01D50C0D.35029ED0]

The API is documented here:

http://data.bioontology.org/documentation<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=A6N22i7fnfeSiQaLf0OENzo3wokz9yJLtS2I9PreK0A&s=pRxoxqpw5ZsRB41CYtIVN4Pnmw1ghWgRtSlfvuxe_pg&e=>

Kind regards,
Jennifer




On May 16, 2019, at 1:37 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: sean.guerrero
Email: sean.guerrero at hoag.org<mailto:sean.guerrero at hoag.org>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=A6N22i7fnfeSiQaLf0OENzo3wokz9yJLtS2I9PreK0A&s=9u3ZuTlA8LmKOfrYhVAM_LDSIqT8XUs9_vsTPhNhkWI&e=>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__252Fpurl.bioontology.org&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=A6N22i7fnfeSiQaLf0OENzo3wokz9yJLtS2I9PreK0A&s=DM33TZtgeWdIdZTPsJ-cyfOc4c7ZxtdvBHKI7a_VMr4&e=>%252Fontology%252FCPT%252F11056%26jump_to_nav%3Dtrue

Feedback:
Hello,
I'm looking at the Current Procedural Terminology section under the "Classes" tab. I'm looking for a way to pull the Preferred Name of the CPT codes I am searching for. Is there an excel file that I can use to reference?
-Sean

_______________________________________________
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 May 17 17:13:23 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 18 May 2019 00:13:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from William Van
 Woensel
In-Reply-To: <004501d50cba$a3e630c0$ebb29240$@gmail.com>
References: <5cdd6628235e0_7ee22ad9df4ba0a85901c@ncbo-prd-app-08.stanford.edu.mail>
 <DD2D42A7-ADE8-4974-ACCB-119E7E79D276@stanford.edu>
 <004501d50cba$a3e630c0$ebb29240$@gmail.com>
Message-ID: <6296F66A-10E6-420B-AB0B-3EC6E3857DFE@stanford.edu>

Hi William,


On May 17, 2019, at 7:13 AM, William Van Woensel <william.vanwoensel at gmail.com<mailto:william.vanwoensel at gmail.com>> wrote:

See for instance:

https://bioportal.bioontology.org/ontologies/DOID/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_4#visualization<https://bioportal.bioontology.org/ontologies/DOID/?p=classes&conceptid=http://purl.obolibrary.org/obo/DOID_4#visualization>


Thanks for the link. We?re aware of this occurrence. The mixed content errors are originating from biomixer [1] - a 3rd party application for visualizing ontologies that was developed by the University of Victoria and contributed to BioPortal. They no longer maintain the application, and as I mentioned below, we?ve so far lacked the resources to take over the code base. There are several issues with the software, which we track in the GitHub repository [2].

For the moment, if you want to use the software, you can change the protocol in the address bar of your browser to http and you?ll be able to see the visualizations. Apologies for the inconvenience.

Kind regards,
Jennifer

[1] https://github.com/ncbo/biomixer
[2] https://github.com/ncbo/biomixer/issues


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From vendetti at stanford.edu  Fri May 17 17:39:38 2019
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 18 May 2019 00:39:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero
In-Reply-To: <MN2PR03MB48628DAB5109B938CA4D9D80970B0@MN2PR03MB4862.namprd03.prod.outlook.com>
References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>
 <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu>
 <MN2PR03MB48628DAB5109B938CA4D9D80970B0@MN2PR03MB4862.namprd03.prod.outlook.com>
Message-ID: <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu>

Hi Sean,

The web-based BioPortal application doesn?t have a table that lists CPT codes and preferred names. We just display the ontology classes as a navigable tree structure.

I?m not sure if using the REST API is a possibility for you. You can pass multiple terms to the search endpoint, e.g., the following URL uses all the CPT codes you listed below (see the q={?} portion):

http://data.bioontology.org/search?q={24546%2024565%2024566%2024575%2024579%2024586}&ontologies=CPT&include=prefLabel&display_links=false&display_context=false<http://data.bioontology.org/search?q=%7B24546%2024565%2024566%2024575%2024579%2024586%7D&ontologies=CPT&include=prefLabel&display_links=false&display_context=false>

If you enter that URL in a browser window, you can see a list of the preferred names for those codes. Screen shot below. FYI - you need an API key to use the REST API (instructions for getting one are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key).

We also provide examples in a GitHub repository for using the API programmatically: https://github.com/ncbo/ncbo_rest_sample_code. It?s possible to write a short script that would retrieve this data.

Hope that information helps.

Kind regards,
Jennifer

[cid:A72B13FE-2EB4-4BAD-8159-77088307DAAA at stanford.edu]




On May 16, 2019, at 5:31 PM, Guerrero, Sean <Sean.Guerrero at Hoag.org<mailto:Sean.Guerrero at Hoag.org>> wrote:

Hi Jennifer,

Thanks for the quick response!
I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below:

It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names?

<image001.png>

24546
24565
24566
24575
24579
24586


Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<http://www.hoagorthopedicinstitute.com/>

<image002.png>

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From Sean.Guerrero at Hoag.org  Mon May 20 09:57:17 2019
From: Sean.Guerrero at Hoag.org (Guerrero, Sean)
Date: Mon, 20 May 2019 16:57:17 +0000
Subject: [bioontology-support] [BioPortal] Feedback from sean.guerrero
In-Reply-To: <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu>
References: <5cddc9f8ae34b_4b1c2acd382d8478203f1@ncbo-prd-app-08.stanford.edu.mail>
 <302EDFE3-43E0-4D09-9002-2AD15C798CE5@stanford.edu>
 <MN2PR03MB48628DAB5109B938CA4D9D80970B0@MN2PR03MB4862.namprd03.prod.outlook.com>
 <8719B4FD-6CC9-4402-B9FC-4818E2E2B2A3@stanford.edu>
Message-ID: <BYAPR03MB4855BAAF959FA1FBF7504CBC97060@BYAPR03MB4855.namprd03.prod.outlook.com>

This is perfect, Jennifer. Thank you so much!

Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<http://www.hoagorthopedicinstitute.com/>

[cid:image001.png at 01D27580.6E6F5760]

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Friday, May 17, 2019 5:40 PM
To: Guerrero, Sean <Sean.Guerrero at Hoag.org>
Cc: support at bioontology.org
Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from sean.guerrero

Hi Sean,

The web-based BioPortal application doesn?t have a table that lists CPT codes and preferred names. We just display the ontology classes as a navigable tree structure.

I?m not sure if using the REST API is a possibility for you. You can pass multiple terms to the search endpoint, e.g., the following URL uses all the CPT codes you listed below (see the q={?} portion):

http://data.bioontology.org/search?q={24546%2024565%2024566%2024575%2024579%2024586}&ontologies=CPT&include=prefLabel&display_links=false&display_context=false<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_search-3Fq-3D-257B24546-252024565-252024566-252024575-252024579-252024586-257D-26ontologies-3DCPT-26include-3DprefLabel-26display-5Flinks-3Dfalse-26display-5Fcontext-3Dfalse&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=qLz4M2PWtVGbWSWWOHNUj_7e00eXYLhVtH6Qos7r4fQ&e=>

If you enter that URL in a browser window, you can see a list of the preferred names for those codes. Screen shot below. FYI - you need an API key to use the REST API (instructions for getting one are here: https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FHelp-23Getting-5Fan-5FAPI-5Fkey&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=B0vvK3Hsz2YaG8dnowJARtKwMGNG49yRpddV-dc01yw&e=>).

We also provide examples in a GitHub repository for using the API programmatically: https://github.com/ncbo/ncbo_rest_sample_code<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=USW8G7Nf1SQZHPX23pslXxFgtBA_HaK9TjbAQcCgNJI&e=>. It?s possible to write a short script that would retrieve this data.

Hope that information helps.

Kind regards,
Jennifer

[cid:image002.png at 01D50EF2.676A4570]





On May 16, 2019, at 5:31 PM, Guerrero, Sean <Sean.Guerrero at Hoag.org<mailto:Sean.Guerrero at Hoag.org>> wrote:

Hi Jennifer,

Thanks for the quick response!
I have a batch of CPT codes and would like to pull the descriptions under the Preferred Name field. Example below:

It doesn?t look like there?s a way to pull a batch of these and the only way to do it would be to copy and paste the CPT codes, one by one. Is this correct? Is their a table of some sort on your website with all CPT codes and preferred names?

<image001.png>

24546
24565
24566
24575
24579
24586


Sean A. Guerrero, MHA
Manager of Business Intelligence, Strategic Analytics and Reporting
Hoag Orthopedic Institute
949/727-5066
 Sean.Guerrero at hoag.org<mailto:Sean.Guerrero at hoag.org> | www.HoagOrthopedicInstitute.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hoagorthopedicinstitute.com_&d=DwMGaQ&c=Jm96lXPlqWoEzygepMnfdIX7sQ1vW_jjEr7ngDjW5HA&r=Z1TFBcoCAjLuZXPJ_jaoYWXoaJw6f3_8FpK1NdAKgao&m=lvd60UBrr0l_taOoyHe_UbBUzeHCLBdQVFR61dxQLgk&s=3z7yXcEbTLnShYj-xaJqpfiZonoON0IzRX9IrJQoZPQ&e=>

<image002.png>


----------------------------------------------------------------------
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From support at bioontology.org  Thu May 23 08:51:03 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 23 May 2019 08:51:03 -0700
Subject: [bioontology-support] [BioPortal] Feedback from John Nguyen
Message-ID: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail>

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From ias41 at cam.ac.uk  Wed May 22 07:21:24 2019
From: ias41 at cam.ac.uk (Ines Smit)
Date: Wed, 22 May 2019 15:21:24 +0100
Subject: [bioontology-support] getting 'classified as' information via API
Message-ID: <cef293f6420b0e5117c02123b4f80653@cam.ac.uk>

Hello BioPortal team,

On the page of the MedDRA term 'Blood pressure Lowered' on the interface 
(https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10024982), 
there is the information 'Classified as: Blood pressure decreased'.
This redirects to the term 'Blood pressure decreased'. This latter 
concept is the Preferred Term (PT) and the former is the Lower Level 
Term (LLT) in MedDRA. The PT has the ID 10005734.

How can I get that relationship via the API?

When I search the LLT (10024982) I get the concept but it doesn't 
include the ID or name of the PT (10005734).
I'm using 
'http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA'

I would like to find the PT (Blood pressure decreased - 10005734) upon 
submitting the LLT (Blood pressure lowered - 10024982).

I also tried the Annotate service with the hierarchy parameter but it 
loosk like the LLT>PT is not included as a level in the hierarchy, as it 
jumps straight from the LLT to the higher level terms.

Thank you,
Ines

From jgraybeal at stanford.edu  Thu May 23 19:59:15 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 May 2019 02:59:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from John Nguyen
In-Reply-To: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail>
References: <5ce6c1674583_71192ae4670ca94c6f@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D8109FB6-4B9F-4A02-9DAD-7614BCC98214@stanford.edu>

Hello John,

With apologies, our widgets have an issue right now that we have not had time to troubleshoot. This is documented in the ticket https://github.com/ncbo/bioportal_web_ui/issues/79; I am adding your detailed information to that ticket.

We have just a few urgent priorities which we need to complete, and we will have a look at this as soon as we can thereafter.

John



On May 23, 2019, at 8:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: John Nguyen

Email: jnguyen at ipro.us<mailto:jnguyen at ipro.us>

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

Feedback:

Hi, I'm trying to implement the NCBO web widget form autocomplete for a company's project. I follow the directions on the wiki but ran this error in the javascript console.

jQuery(...).bioportal_autocomplete is not a function.

I went on the form_complete.js code and found on line 273 that it seems I have to include a script that I assumed you guys had called public/javascripts/JqueryPlugins/autocomplete/crossdomain_autocomplete.js
I was wondering if this script was suppose to be included with the form_complete.js and if so I was wondering how I can access it?

_______________________________________________
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 May 23 20:11:29 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 May 2019 03:11:29 +0000
Subject: [bioontology-support] getting 'classified as' information via
	API
In-Reply-To: <cef293f6420b0e5117c02123b4f80653@cam.ac.uk>
References: <cef293f6420b0e5117c02123b4f80653@cam.ac.uk>
Message-ID: <F2DE7DBF-6D1B-4730-BEF6-9254794DBE06@stanford.edu>

Hello Ines,

I believe you can get what you want by adding "include=properties" to your query, as in

http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA&include=properties

This will include all the annotation properties, one of which is 'classified_as'. (You may wish to append ',notation' to the above so that you can see the concept for which the properties apply, when there is more than one concept returned by the search.)

John

On May 22, 2019, at 7:21 AM, Ines Smit <ias41 at cam.ac.uk<mailto:ias41 at cam.ac.uk>> wrote:

Hello BioPortal team,

On the page of the MedDRA term 'Blood pressure Lowered' on the interface (https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10024982), there is the information 'Classified as: Blood pressure decreased'.
This redirects to the term 'Blood pressure decreased'. This latter concept is the Preferred Term (PT) and the former is the Lower Level Term (LLT) in MedDRA. The PT has the ID 10005734.

How can I get that relationship via the API?

When I search the LLT (10024982) I get the concept but it doesn't include the ID or name of the PT (10005734).
I'm using 'http://data.bioontology.org/search?q=10024982&ontologies=MEDDRA'

I would like to find the PT (Blood pressure decreased - 10005734) upon submitting the LLT (Blood pressure lowered - 10024982).

I also tried the Annotate service with the hierarchy parameter but it loosk like the LLT>PT is not included as a level in the hierarchy, as it jumps straight from the LLT to the higher level terms.

Thank you,
Ines
_______________________________________________
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  Thu May 23 12:37:13 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 23 May 2019 12:37:13 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples
Message-ID: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Sat May 25 04:45:36 2019
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 25 May 2019 04:45:36 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf
Message-ID: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Mon May 27 21:52:59 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 28 May 2019 04:52:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples
In-Reply-To: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail>
References: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <BF8B04DE-8109-4BAD-B67D-E970946F2970@stanford.edu>

Jeff,

Thank you for this report. We have not assessed this deeply enough to find out what is causing this problem, though I believe you are correct that the link for the property should go to p=properties.

I created ticket https://github.com/ncbo/bioportal-project/issues/118 to track this problem; not sure how quickly we'll be able to address it. Please let us know if it will be impacting you significantly in the near term.

John

On May 23, 2019, at 12:37 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jeffrey Staples

Email: jeffrey.staples at regeneron.com<mailto:jeffrey.staples at regeneron.com>

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

Feedback:

I am encountering an IRI issue that may because by improper URL forwarding for ontology properties. For example, LOINC property "member_of" as the IRI "http://purl.bioontology.org/ontology/LNC/member_of", which forwards to "http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=member_of". This page says "The page you are looking for wasn't found. Please try again." However, if I change the forwarded URL to "http://bioportal.bioontology.org/ontologies/LOINC?p=properties&conceptid=member_of" then I get what I believe to be the correct page. I don't if correcting the URL forwarding will fix IRI problem, but I thought you would want to know in the case that it does cause a problem for others.

Best,

Jeff

_______________________________________________
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  Mon May 27 22:22:09 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 28 May 2019 05:22:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Manuel T.
 Schrempf
In-Reply-To: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail>
References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu>

Manuel,

Thank you for this report. We have entered it as https://github.com/ncbo/bioportal-project/issues/119, and will be examining it in more detail soon.

I note that all of the top-level classes in FMA have been defined as owl#Thing in BioPortal, so I believe this is a design decision made by the original developers of the ontology representation (that is, not a bug). If you would like to be more explicit about why you see it as wrong, that may help us assess the situation more clearly.

Thank you for your time to share this with us.

John

On May 25, 2019, at 4:45 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Manuel T. Schrempf

Email: e0920136 at student.tuwien.ac.at<mailto:e0920136 at student.tuwien.ac.at>

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

Feedback:

Hello Bioporal,
in your FMA 5.0.0 CSV file the following entry is wrong:

http://purl.org/sig/ont/fma/fma85802,FMA attribute entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

since the parent "http://www.w3.org/2002/07/owl#Thing" does not contain a valid FMA id. I guess some other errors are in other anatomy datasets too, since my automatic parsing threw some errors. I will just exclude this anatomy from my parsing and hope future releases will have the errors fixed.

Best,
Manuel T. Schrempf

_______________________________________________
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 e0920136 at student.tuwien.ac.at  Mon May 27 23:08:13 2019
From: e0920136 at student.tuwien.ac.at (Manuel T. Schrempf)
Date: Tue, 28 May 2019 08:08:13 +0200
Subject: [bioontology-support] [BioPortal] Feedback from Manuel T.
 Schrempf
In-Reply-To: <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu>
References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail>
 <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu>
Message-ID: <a604b784-95c0-b72a-9ecb-f394df6387df@student.tuwien.ac.at>

Hello John,

just that owl#Thing has no ID as (FMAxxxxxx), I parse the FMA CSV with a 
bash script and remove reduntant information, meaning everything except 
the pure integer number, since the rest is not needed for a unique 
identifacion by an ID on a database. 
"http://www.w3.org/2002/07/owl#Thing" has no FMA ID, that is why I 
reported the issue.

Best,
Manuel

On 28.05.19 07:22, John Graybeal wrote:
> Manuel,
>
> Thank you for this report. We have entered it as 
> https://github.com/ncbo/bioportal-project/issues/119, and will be 
> examining it in more detail soon.
>
> I note that all of the top-level classes in FMA have been defined as 
> owl#Thing in BioPortal, so I believe this is a design decision made by 
> the original developers of the ontology representation (that is, not a 
> bug). If you would like to be more explicit about why you see it as 
> wrong, that may help us assess the situation more clearly.
>
> Thank you for your time to share this with us.
>
> John
>
>> On May 25, 2019, at 4:45 AM, support at bioontology.org 
>> <mailto:support at bioontology.org> wrote:
>>
>> Name: Manuel T. Schrempf
>>
>> Email: e0920136 at student.tuwien.ac.at 
>> <mailto:e0920136 at student.tuwien.ac.at>
>>
>> Location: http%3A%2F%2Fbioportal.bioontology.org 
>> <http://2Fbioportal.bioontology.org>%2Fontologies%2FFMA
>>
>>
>> *Feedback:*
>>
>> Hello Bioporal,
>> in your FMA 5.0.0 CSV file the following entry is wrong:
>>
>> http://purl.org/sig/ont/fma/fma85802,FMA attribute 
>> entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
>>
>> since the parent "http://www.w3.org/2002/07/owl#Thing" does not 
>> contain a valid FMA id. I guess some other errors are in other 
>> anatomy datasets too, since my automatic parsing threw some errors. I 
>> will just exclude this anatomy from my parsing and hope future 
>> releases will have the errors fixed.
>>
>> Best,
>> Manuel T. Schrempf
>>
>>
>> _______________________________________________
>> 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 swt at stanford.edu  Tue May 28 10:32:23 2019
From: swt at stanford.edu (Samson Tu)
Date: Tue, 28 May 2019 17:32:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Manuel T.
 Schrempf
In-Reply-To: <a604b784-95c0-b72a-9ecb-f394df6387df@student.tuwien.ac.at>
References: <5ce92ae04a495_7f312ad0df1ee5d0106f0@ncbo-prd-app-08.stanford.edu.mail>
 <00A035F3-5C84-4654-85F8-0AB568D5205B@stanford.edu>
 <a604b784-95c0-b72a-9ecb-f394df6387df@student.tuwien.ac.at>
Message-ID: <99B7E352-06AE-4CA9-B108-A19D9D929DED@stanford.edu>

Hi,

By definition, every top-level entity in an OWL ontology has owl#Thing as a parent. It?s not a design decision on the part of FMA developers. 

It?s a design decision on the part of Bioportal CSV-output developers whether to generate an entry for this definitional parent-child relationship. Given that decision, users of the CSV output have to live with the consequences either way.

With best regards,
Samson


> On May 27, 2019, at 11:08 PM, Manuel T. Schrempf <e0920136 at student.tuwien.ac.at> wrote:
> 
> Hello John,
> 
> just that owl#Thing has no ID as (FMAxxxxxx), I parse the FMA CSV with a bash script and remove reduntant information, meaning everything except the pure integer number, since the rest is not needed for a unique identifacion by an ID on a database. "http://www.w3.org/2002/07/owl#Thing" <http://www.w3.org/2002/07/owl#Thing> has no FMA         ID, that is why I reported the issue.
> 
> Best,
> Manuel
> 
> On 28.05.19 07:22, John Graybeal wrote:
>> Manuel,
>> 
>> Thank you for this report. We have entered it as https://github.com/ncbo/bioportal-project/issues/119 <https://github.com/ncbo/bioportal-project/issues/119>, and will be examining it in more detail soon.
>> 
>> I note that all of the top-level classes in FMA have been defined as owl#Thing in BioPortal, so I believe this is a design decision made by the original developers of the ontology representation (that is, not a bug). If you would like to be more explicit about why you see it as wrong, that may help us assess the situation more clearly. 
>> 
>> Thank you for your time to share this with us.
>> 
>> John
>> 
>>> On May 25, 2019, at 4:45 AM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>>> 
>>> Name: Manuel T. Schrempf
>>> 
>>> Email: e0920136 at student.tuwien.ac.at <mailto:e0920136 at student.tuwien.ac.at>
>>> Location: http%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies%2FFMA
>>> 
>>> 
>>> Feedback:
>>> 
>>> Hello Bioporal, 
>>> in your FMA 5.0.0 CSV file the following entry is wrong:
>>> 
>>> http://purl.org/sig/ont/fma/fma85802,FMA <http://purl.org/sig/ont/fma/fma85802,FMA> attribute entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802 <http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
>>> 
>>> since the parent "http://www.w3.org/2002/07/owl#Thing <http://www.w3.org/2002/07/owl#Thing>" does not contain a valid FMA id. I guess some other errors are in other anatomy datasets too, since my automatic parsing threw some errors. I will just exclude this anatomy from my parsing and hope future releases will have the errors fixed.
>>> 
>>> Best, 
>>> Manuel T. Schrempf
>>> 
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support <https://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
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From julius.pasion at corteva.com  Tue May 28 11:26:02 2019
From: julius.pasion at corteva.com (Pasion, Julius)
Date: Tue, 28 May 2019 18:26:02 +0000
Subject: [bioontology-support] Homepage not working?
Message-ID: <DM6PR17MB3194CB8097D8698FC6EB7160F51E0@DM6PR17MB3194.namprd17.prod.outlook.com>

Dear NCBO,


I have set up an EC2 instance using AWS, and set up an Application Load Balancer to redirect HTTP80 to HTTPS443, and forward to the instance. However, my homepage is always returning an invalid response. When I try to access the homepage, the url is the same except ":80" is added to the end of the url. Even weirder is that if I type in other parts of the website like "domain.com/help" or "domain.com/search", I am able to see the website (although in some of those pages, I get errors from the website itself). Would you be able to help with this issue? I get a 500: internal server error whenever I try to access the homepage.



My current pipeline is:

*         Route53 url is input by client

*         redirect to ALB

*         redirects 80 to 443 (w/SSL)

*         forwards to target group on port 80

*         EC2 instance



Any help is appreciated thank you!

Sincerely,

Julius

*



This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail,in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html
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From jgraybeal at stanford.edu  Tue May 28 19:23:07 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 29 May 2019 02:23:07 +0000
Subject: [bioontology-support] Homepage not working?
In-Reply-To: <DM6PR17MB3194CB8097D8698FC6EB7160F51E0@DM6PR17MB3194.namprd17.prod.outlook.com>
References: <DM6PR17MB3194CB8097D8698FC6EB7160F51E0@DM6PR17MB3194.namprd17.prod.outlook.com>
Message-ID: <A290496B-C9E2-4891-947F-BFD68847F93E@stanford.edu>

Hi Julius,

I'm sorry, but I think your question is simply about handling redirects, and is outside the scope of this list, which is specifically about BioPortal and OntoPortal software and virtual appliance issues. You may want to look in or post to a more general-purpose site like StackExchange or Quora?

I will touch base with you offline to discuss possible Virtual Appliance related topics.

John

On May 28, 2019, at 11:26 AM, Pasion, Julius <julius.pasion at corteva.com<mailto:julius.pasion at corteva.com>> wrote:

Dear NCBO,


I have set up an EC2 instance using AWS, and set up an Application Load Balancer to redirect HTTP80 to HTTPS443, and forward to the instance. However, my homepage is always returning an invalid response. When I try to access the homepage, the url is the same except ":80" is added to the end of the url. Even weirder is that if I type in other parts of the website like "domain.com/help<http://domain.com/help>" or "domain.com/search<http://domain.com/search>", I am able to see the website (although in some of those pages, I get errors from the website itself). Would you be able to help with this issue? I get a 500: internal server error whenever I try to access the homepage.



My current pipeline is:

?         Route53 url is input by client

?         redirect to ALB

?         redirects 80 to 443 (w/SSL)

?         forwards to target group on port 80

?         EC2 instance



Any help is appreciated thank you!

Sincerely,

Julius

?




This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail,in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html<http://www.dupont.com/corp/email_disclaimer.html>_______________________________________________
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  Wed May 29 10:06:17 2019
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 29 May 2019 17:06:17 +0000
Subject: [bioontology-support] commercial use license
In-Reply-To: <6cc2617a-c86d-4bfc-98cc-5faf6f730e33@Spark>
References: <0d8970a2-284d-4a0f-8a35-34aa7e540147@Spark>
 <6cc2617a-c86d-4bfc-98cc-5faf6f730e33@Spark>
Message-ID: <D9B203F0-5732-4AAB-A17A-74AD0B076C47@stanford.edu>

Hi Tom,

Thanks for your question, I hope you don't mind my using it as an opportunity for a general answer.

The majority of the ontologies in the BioPortal resource  can be downloaded directly, either via the UI or API. Their license terms, if any, are specified in the metadata field shown in the summary page for the ontology.  (There is even a tool to support populating your own OntoPortal instance with these ontologies, but I think that isn't your use case.)

Some licenses?mostly for UMLS ontologies but also some others?do not allow us to make the download directly available. In those few cases where the UMLS license or a private agreement allows it, we will make an individual ontology available in response to a direct request, under the circumstances you describe.

We recommend to users who want to work with UMLS content, and who have licenses to do so, build the necessary pipeline to convert the UMLS content to ontology form. Many users use the umls2rdf pipeline available in the NCBO repository (https://github.com/ncbo/umls2rdf); there are other similar software repositories in GitHub but I am not familiar with them.

If you do not want to do that development itself, I expect you could contract with us to set up the software on your behalf. (Please note, I haven't thought that all the way through; contact me offline if you want to discuss it further.)

I hope this synopsis helps you consider how you would like to proceed. Please don't hesitate to contact me if you wish to ask any other questions.

John

On May 29, 2019, at 4:41 AM, Tom Nygren <tom.nygren at kirontech.com<mailto:tom.nygren at kirontech.com>> wrote:

Hi there,

We are a Cambridge (UK) based health insurance analytics company.

We would be interested in incorporating some of your data for use in our analytics.

If we meet the licensing requirements with the original providers of the ontology, do you offer any kind of commercial license that would allow us to use the ontologies themselves?

Thanks and regards

Tom

---

Tom Nygren
COO
Kirontech
+44 7771 268 566

========================
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 mdorf at stanford.edu  Wed May 29 14:50:28 2019
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 29 May 2019 21:50:28 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Staples
In-Reply-To: <BF8B04DE-8109-4BAD-B67D-E970946F2970@stanford.edu>
References: <5ce6f669884cf_7bfd2b19f48787948467b@ncbo-prd-app-08.stanford.edu.mail>
 <BF8B04DE-8109-4BAD-B67D-E970946F2970@stanford.edu>
Message-ID: <A6C737BA-DB81-4850-9266-32D974AE3BBE@stanford.edu>

Hi Jeff,

Unfortunately, BioPortal UI doesn?t offer the same support for individual property URLs, as it does for ontology classes. You can access the entire property tree via the http://bioportal.bioontology.org/ontologies/LOINC?p=properties link, but the same link cannot be used to access individual properties. If you do require access to individual properties, your best bet is to use our REST services. Here are a couple of links that may be of note:

http://data.bioontology.org/ontologies/LOINC/properties
http://data.bioontology.org/ontologies/LOINC/properties/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2Fanalyzes?include=all<http://data.bioontology.org/ontologies/LOINC/properties/http://purl.bioontology.org/ontology/LNC/analyzes?include=all>

Hope this helps!

Michael

On May 27, 2019, at 9:52 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Jeff,

Thank you for this report. We have not assessed this deeply enough to find out what is causing this problem, though I believe you are correct that the link for the property should go to p=properties.

I created ticket https://github.com/ncbo/bioportal-project/issues/118 to track this problem; not sure how quickly we'll be able to address it. Please let us know if it will be impacting you significantly in the near term.

John

On May 23, 2019, at 12:37 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jeffrey Staples

Email: jeffrey.staples at regeneron.com<mailto:jeffrey.staples at regeneron.com>

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

Feedback:

I am encountering an IRI issue that may because by improper URL forwarding for ontology properties. For example, LOINC property "member_of" as the IRI "http://purl.bioontology.org/ontology/LNC/member_of", which forwards to "http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=member_of". This page says "The page you are looking for wasn't found. Please try again." However, if I change the forwarded URL to "http://bioportal.bioontology.org/ontologies/LOINC?p=properties&conceptid=member_of" then I get what I believe to be the correct page. I don't if correcting the URL forwarding will fix IRI problem, but I thought you would want to know in the case that it does cause a problem for others.

Best,

Jeff

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========================
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  Thu May 30 18:20:30 2019
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 30 May 2019 18:20:30 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Fred Trotter
Message-ID: <5cf0815ec1778_49622b0491c0c9b460481@ncbo-prd-app-08.stanford.edu.mail>

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