From vendetti at stanford.edu  Wed Nov  1 15:36:56 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 1 Nov 2017 22:36:56 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jerven Bolleman
In-Reply-To: <364DECC0-8E99-4E51-86CA-D372F4B9ECE0@stanford.edu>
References: <59f6daed5b116_70b23fba1689c1a4126e2@ncbo-prd-app-09.stanford.edu.mail>
 <916368C5-D688-4A35-BF58-3FCA592B365E@stanford.edu>
 <CAHM_hUO5V86ix1fpZWEmCmraE2SFiGahqtOYgyXmuwLEQ5_9Ug@mail.gmail.com>
 <364DECC0-8E99-4E51-86CA-D372F4B9ECE0@stanford.edu>
Message-ID: <568FF6D5-4A32-4DF8-852A-E3372A8AD67F@stanford.edu>

Hi Jerven,

I deployed a fix to our production environment. You should be able to successfully create an account with your ?.swiss? email address now. Let us know if you experience issues.

Kind regards,
Jennifer


On Oct 31, 2017, at 2:48 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Jerven,

Thank you for the clarification. I reproduced the problem here. The application code is rejecting email addresses with top-level domains longer than 4 characters (as you suspected). I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal_web_ui/issues/66

? and will work on getting a fix out.

Kind regards,
Jennifer


On Oct 30, 2017, at 12:22 PM, Jerven Bolleman <me at jerven.eu<mailto:me at jerven.eu>> wrote:

Hi Jennifer,

Yes, on that page and when using the contact form.
Just when using my official address ending in sib.swiss
jerven.bolleman at sib.swiss<mailto:jerven.bolleman at sib.swiss>.
me at jerven.eu<mailto:me at jerven.eu> works
i.e. I suspect an issue with the e-mail validation service not expecting long TLDs

Regards,
Jerven

 <image.png>

On Mon, Oct 30, 2017 at 7:50 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jerven,

Just to clarify, you?re filling out the form on this page:

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

? and getting an error message? Could you send us a screenshot? I tried creating a new account just now using that form and I wasn?t able to reproduce the error here.

Thanks,
Jennifer



On Oct 30, 2017, at 12:55 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jerven Bolleman

Email: me at jerven.eu<mailto:me at jerven.eu>

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

Feedback:

I can't register as I keep on getting an error for please enter an e-mail address with the mail address jerven.bolleman at sib.swiss<mailto:jerven.bolleman at sib.swiss>.

This also affects this help form

Regards,
Jerven Bolleman

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--
Jerven Bolleman
me at jerven.eu<mailto:me at jerven.eu>

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From spencer.c.knight at gmail.com  Thu Nov  2 10:42:43 2017
From: spencer.c.knight at gmail.com (Spencer Knight)
Date: Thu, 2 Nov 2017 10:42:43 -0700
Subject: [bioontology-support] Bioportal bioontology services down
Message-ID: <CAPqVBQ4KvVL4UdwM+38NfY5_4SFr=2Bm5-BwUu2BgKG7y5=Spw@mail.gmail.com>

Hello,

It appears that the server is down for all Bioontology tech services
(online ontology library, annotator, etc.). Any idea as to when you
anticipate that this will be up and running again?

Thanks and Best,
Spencer

-- 
Spencer C. Knight, Ph.D.
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From vendetti at stanford.edu  Thu Nov  2 11:20:32 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 2 Nov 2017 18:20:32 +0000
Subject: [bioontology-support] Bioportal bioontology services down
In-Reply-To: <CAPqVBQ4KvVL4UdwM+38NfY5_4SFr=2Bm5-BwUu2BgKG7y5=Spw@mail.gmail.com>
References: <CAPqVBQ4KvVL4UdwM+38NfY5_4SFr=2Bm5-BwUu2BgKG7y5=Spw@mail.gmail.com>
Message-ID: <5AC02E36-DE88-463C-A649-028D9F11794A@stanford.edu>

Hello Spencer,

We had an outage this morning, but everything is back up. Apologies that you experienced issues.

Kind regards,
Jennifer


> On Nov 2, 2017, at 10:42 AM, Spencer Knight <spencer.c.knight at gmail.com> wrote:
> 
> Hello,
> 
> It appears that the server is down for all Bioontology tech services (online ontology library, annotator, etc.). Any idea as to when you anticipate that this will be up and running again?
> 
> Thanks and Best,
> Spencer
> 
> -- 
> Spencer C. Knight, Ph.D.
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



From jasim.waheed at rwth-aachen.de  Fri Nov  3 08:59:16 2017
From: jasim.waheed at rwth-aachen.de (Waheed Ansari, Jasim)
Date: Fri, 3 Nov 2017 15:59:16 +0000
Subject: [bioontology-support] Is Bioportal recommender's REST API down
Message-ID: <9bbbaf8568144fe8b8d842e03eb98944@rwth-aachen.de>

Hi,

I am using Bioportal recommender REST API for my thesis work, I just encountered "Internal Server Error" while accessing the HTTP
http://data.bioontology.org/recommender?input=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20and%20the%20eye


If it is the server issue, I would like to know by when can it be resolved?

Thanks and regards,
Jasim Waheed
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From vendetti at stanford.edu  Fri Nov  3 09:45:13 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 3 Nov 2017 16:45:13 +0000
Subject: [bioontology-support] Is Bioportal recommender's REST API down
In-Reply-To: <9bbbaf8568144fe8b8d842e03eb98944@rwth-aachen.de>
References: <9bbbaf8568144fe8b8d842e03eb98944@rwth-aachen.de>
Message-ID: <8F7E61B6-149B-491C-9BF5-E4407A8E5D25@stanford.edu>

Hi Jasim,

Apologies for the inconvenience. The recommender endpoint has been restored.

Kind regards,
Jennifer



On Nov 3, 2017, at 8:59 AM, Waheed Ansari, Jasim <jasim.waheed at rwth-aachen.de<mailto:jasim.waheed at rwth-aachen.de>> wrote:

Hi,

I am using Bioportal recommender REST API for my thesis work, I just encountered "Internal Server Error" while accessing the HTTP
http://data.bioontology.org/recommender?input=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20and%20the%20eye

If it is the server issue, I would like to know by when can it be resolved?

Thanks and regards,
Jasim Waheed
<bioportal_issue.png>_______________________________________________
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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 chaitanya at lumiata.com  Fri Nov  3 13:23:37 2017
From: chaitanya at lumiata.com (Chaitanya Churi)
Date: Fri, 3 Nov 2017 13:23:37 -0700
Subject: [bioontology-support] Virtual Appliance request
Message-ID: <EDE3419E-9784-4644-905C-BB3F5F90DB87@lumiata.com>

Hello,

I was interested in the NCBO Virtual appliance to be able to run the Bioontology Annotator service on a local or virtual machine. 
The instructions recommend that we contact support to initiate this request. Is this something you could help us with?

Appreciate your help.

Chaitanya




Dr. Chaitanya Churi
Senior Data Scientist
chaitanya at lumiata.com <mailto:chaitanya at lumiata.com>
www.lumiata.com <http://www.lumiata.com/>
Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

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From ian.w.harrison at gmail.com  Mon Nov  6 05:11:38 2017
From: ian.w.harrison at gmail.com (Ian Harrison)
Date: Mon, 6 Nov 2017 14:11:38 +0100
Subject: [bioontology-support] Looking for BioPortal VMWare Virtual Appliance
Message-ID: <0ea18995-5295-1507-a835-7916b4c4eb0e@gmail.com>

Hi


I'd like to setup BioPortal inside our firewall for use with locally 
produced ontologies. Can I get a VMWare distribution


Thanks


Ian

-- 
Ian Harrison                Email: ian.w.harrison at gmail.com
Tel: +33 (0)6 85 79 20 50 (France) +44 (0)7580 618125 (UK)


From jgraybeal at stanford.edu  Mon Nov  6 18:24:01 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 7 Nov 2017 02:24:01 +0000
Subject: [bioontology-support] Looking for BioPortal VMWare Virtual
 Appliance
In-Reply-To: <0ea18995-5295-1507-a835-7916b4c4eb0e@gmail.com>
References: <0ea18995-5295-1507-a835-7916b4c4eb0e@gmail.com>
Message-ID: <3D37EAF8-C11D-4B72-BEA7-BAE64F1EBF5C@stanford.edu>

Hello Ian,

Thanks for your interest in the virtual appliance, I will be happy to help you with your request.

For our record keeping please give us the following information:
- your BioPortal user name -- if you need one go to http://bioportal.bioontology.org/accounts/new
- a one to two sentence description of your project
- why you want to use the VA rather than the public instance. For example, do you want to host
  non-biomedical or proprietary ontologies, or annotate private data? Do you have performance concerns?

We usually respond within a business day upon receiving this information.

John


On Nov 6, 2017, at 5:11 AM, Ian Harrison <ian.w.harrison at gmail.com<mailto:ian.w.harrison at gmail.com>> wrote:

Hi


I'd like to setup BioPortal inside our firewall for use with locally produced ontologies. Can I get a VMWare distribution


Thanks


Ian

--
Ian Harrison                Email: ian.w.harrison at gmail.com<mailto:ian.w.harrison at gmail.com>
Tel: +33 (0)6 85 79 20 50 (France) +44 (0)7580 618125 (UK)

_______________________________________________
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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

========================
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 chaitanya at lumiata.com  Tue Nov  7 12:00:27 2017
From: chaitanya at lumiata.com (Chaitanya Churi)
Date: Tue, 7 Nov 2017 12:00:27 -0800
Subject: [bioontology-support] Help with bioontology virtual machine
Message-ID: <57947F5B-3227-41A5-A970-0093E4C5056B@lumiata.com>

Hi,
I?m working with the virtual machine installation of the bioontology portal (specifically the third Release Candidate (Version 2.5 Release Candidate 3)). 

I?m querying the annotator endpoint and I?m having trouble with the output. 

If I query the regular bioportal api at http://data.bioontology.org/annotator <http://data.bioontology.org/annotator>, I get the output I care about with all the annotations, but if I query my local instance like so http://192.168.1.132/annotator
with the same exact API call, I get back only a list of semantic types and no annotations. Is the output format for this version different? Is there updated documentation for this?

Appreciate your help.

Thanks

Chaitanya



Dr. Chaitanya Churi
Senior Data Scientist
chaitanya at lumiata.com <mailto:chaitanya at lumiata.com>
www.lumiata.com <http://www.lumiata.com/>
Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

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From alexander.li at regeneron.com  Thu Nov  9 06:29:22 2017
From: alexander.li at regeneron.com (Alexander Li)
Date: Thu, 9 Nov 2017 14:29:22 +0000
Subject: [bioontology-support] NCBO API key
Message-ID: <5D27C883-6FCB-43ED-B5FE-FFFA49649F63@regeneron.com>

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From support at bioontology.org  Thu Nov  9 07:57:50 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 09 Nov 2017 07:57:50 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Murat YAKAR
Message-ID: <5a047afead587_631c3f93a693760444024@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Nov  9 11:01:16 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 9 Nov 2017 19:01:16 +0000
Subject: [bioontology-support] NCBO API key
In-Reply-To: <5D27C883-6FCB-43ED-B5FE-FFFA49649F63@regeneron.com>
References: <5D27C883-6FCB-43ED-B5FE-FFFA49649F63@regeneron.com>
Message-ID: <590F8888-5054-449F-861F-3158B4664D45@stanford.edu>

Hello Alexander,

Instructions for getting an API key are available on our wiki:

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

Kind regards,
Jennifer



On Nov 9, 2017, at 6:29 AM, Alexander Li <alexander.li at regeneron.com<mailto:alexander.li at regeneron.com>> wrote:

Hello,

I?m interested in accessing the mappings between two onotologies hosted on the NCBO BioPortal (EFO, SNOMED CT).  To do this I am using the API, specifically the R scripts provided in the sample code git repository (https://github.com/ncbo/ncbo_rest_sample_code).

I am new to using API?s but it looks like an ANP key is required to access this mapping.  Can you advise on how to obtain such a key?

Thank you,
Alex

Alexander Li, PhD
Associate Manager, Analytical Genetics
Regeneron Genetics Center
Office: 914.847.1174


________________________________
* ******************************************************************* This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ******************************************************************* *

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From vendetti at stanford.edu  Thu Nov  9 11:35:47 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 9 Nov 2017 19:35:47 +0000
Subject: [bioontology-support] Help with bioontology virtual machine
In-Reply-To: <57947F5B-3227-41A5-A970-0093E4C5056B@lumiata.com>
References: <57947F5B-3227-41A5-A970-0093E4C5056B@lumiata.com>
Message-ID: <066499E8-5995-475F-80C8-69FFA3651CE9@stanford.edu>

Hello Dr. Churi,

I?m wondering if you could provide us with more information.

- What ontologies have you loaded into the Virtual Appliance? If you?ve loaded any, they would be listed on the ontology browse page (Tools -> Ontology Browser).

- Are you able to see any results from the Annotator in the user interface of your appliance?

We spun up a test instance of the appliance here, loaded 4 ontologies (NCIT, RADLEX, GO, and STY), and tried reproducing this problem. The annotator service worked as expected.

Kind regards,
Jennifer


On Nov 7, 2017, at 12:00 PM, Chaitanya Churi <chaitanya at lumiata.com<mailto:chaitanya at lumiata.com>> wrote:

Hi,
I?m working with the virtual machine installation of the bioontology portal (specifically the third Release Candidate (Version 2.5 Release Candidate 3)).

I?m querying the annotator endpoint and I?m having trouble with the output.

If I query the regular bioportal api at http://data.bioontology.org/annotator, I get the output I care about with all the annotations, but if I query my local instance like so http://192.168.1.132/annotator
with the same exact API call, I get back only a list of semantic types and no annotations. Is the output format for this version different? Is there updated documentation for this?

Appreciate your help.

Thanks

Chaitanya


[https://lh5.googleusercontent.com/iYAOors3sipDiaMVVlLOYryK-aMZXrJJlQ3adHayqmU0RPdOKD9MheNofOXdpiVpvCF2j2iEYXjgU7UrTuuKDW6yuU-_KCnECSksLBGM-3v1ulPSPI-Gju23TB102leR3bqI1Cfc]

Dr. Chaitanya Churi
Senior Data Scientist
chaitanya at lumiata.com<mailto:chaitanya at lumiata.com>
www.lumiata.com<http://www.lumiata.com/>

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

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From jean.charlet at upmc.fr  Sun Nov 12 13:17:43 2017
From: jean.charlet at upmc.fr (Charlet Jean)
Date: Sun, 12 Nov 2017 22:17:43 +0100
Subject: [bioontology-support] ALS Ontology upload
Message-ID: <2FA0CD8A-4F12-4C16-A235-E421EC34D023@upmc.fr>

I just upload an ontology of amyotrophic lateral sclerosis (social module).

As for another one of my team (ontopsychia) , I would like that this ontology can be browsed but not download (because, it?s an alpha version).

In my memories, I had to send you an email.

Thank you to confirm me this.

Best regards,
Jean Charlet

           ,,,,
          (o-o)
--------oOO-(_)-OOo------------------------------------------o0O-OOo----
      Jean Charlet                          M?l : Jean.Charlet at upmc.fr
    INSERM UMR_S 1142                        T?l : +33/0 1 44 27 91 09
15, rue de l'?cole de M?decine              URL : http://www.limics.fr/
  75006 Paris, France 
                 Assistance publique - H?pitaux de Paris
               LIMICS - Univ. Paris VI - Univ. Paris XIII
----------o0O-OOo------------------------------------------oOO-( )-OOo--
                                                             (o-o)
                                                              ````


From helena.lodenius at medisapiens.fi  Wed Nov 15 00:53:36 2017
From: helena.lodenius at medisapiens.fi (Helena Lodenius)
Date: Wed, 15 Nov 2017 10:53:36 +0200
Subject: [bioontology-support] NCBO Virtual Appliance 2.4 search issue
Message-ID: <CAHUa=RLkn7xDpe3tXyW7tZO8qiNK098zR-+O7vWw1Xk=2txWgA@mail.gmail.com>

Hi,

we are having trouble with our installation of the NCBO Virtual Appliance
version 2.4, that it cannot search for compound word terms, e.g. adrenal
cortical adenoma. When trying to search for them, the API returns an
internal server error message. An example API call:

http://
<server-address>:8080/search?q=Adrenal%20cortical%20adenoma*&ontologies=SNOMEDCT&objecttypes=class&include=prefLabel&display_links=no&no_context=true&pagesize=10&apikey=1234

Though these API calls do work:
http://
<server-address>:8080/search?q=Adrenal*&ontologies=SNOMEDCT&objecttypes=class&include=prefLabel&display_links=no&no_context=true&pagesize=10&apikey=1234

http://
<server-address>:8080/search?q=Adrenal%20*&ontologies=SNOMEDCT&objecttypes=class&include=prefLabel&display_links=no&no_context=true&pagesize=10&apikey=1234

The compound word call does work in our 2.2 NCBO Virtual Appliance version.
Is there a some kind of configuration problem in the application, and would
you have any advice on how to fix the issue?

Best regards,
Helena Lodenius


-- 

Helena Lodenius, M.Sc. (Genetics)
Senior Data Curator
helena.lodenius at medisapiens.fi

MediSapiens Ltd
Mikonkatu 17 C
00100 Helsinki
Finland
Phone: +358 45 847 8878

MediSapiens Inc.
One Broadway
Cambridge, MA 02142
USA
Phone: (781) 519-1801

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From alexgarciac at gmail.com  Wed Nov 15 10:38:01 2017
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Wed, 15 Nov 2017 19:38:01 +0100
Subject: [bioontology-support] anotator
In-Reply-To: <B057FEAF-C46E-4017-9857-9C112AB21363@stanford.edu>
References: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
 <B057FEAF-C46E-4017-9857-9C112AB21363@stanford.edu>
Message-ID: <CALAe=OJfZyPVTxw6kwnFtHG84Vy_Wfvvssh20H4VqonOQieHXw@mail.gmail.com>

Hi John, "In general, the only technical evaluation I've seen has shown
BioPortal first or second (if I recall correctly) in terms of speed and
completeness of annotation. " could u point me to the actual
document/paper/reference with this evaluation?



On Sat, Sep 30, 2017 at 12:32 AM, John Graybeal <jgraybeal at stanford.edu>
wrote:

> Hi Alexander,
>
> A quick answer, sorry I don't have all the research data at hand but
> perhaps you can use Google Scholar to find more precise information if you
> need it.
>
> Since we consider BioPortal to be the biggest source of Biomedical
> Ontologies, we definitely consider our annotator the best service for
> annotations against a large and diverse number of ontologies. (And
> therefore, also the most reliable service in that category. :->)
>
> The article "Semantic annotation in biomedicine: the current landscape"
>  in Journal of Biomedical Semantics (https://jbiomedsem.
> biomedcentral.com/articles/10.1186/s13326-017-0153-x) has a survey of
> many, if not all, of the existing semantic annotation technologies. NCBO
> Bioportal appears in Tables 1 and 3 (scroll the table left on screen).
> While quite dated in some respects (BioPortal has over 500 BioMedical
> ontologies, and it is open source, available on GitHub) there is a lot of
> useful information here. I know there are some pipeline annotators that
> leverage BioPortal services to provide their own annotation capabilities,
> but can not offer the details off-hand, sorry.
>
> In general, the only technical evaluation I've seen has shown BioPortal
> first or second (if I recall correctly) in terms of speed and completeness
> of annotation. Of course, without specific evaluation criteria and
> comparisons, it is all but impossible to have a meaningful rebuttal to the
> observation "something else is better". Certainly there are features
> available with some other annotators that Bioportal does not provide, so
> there can be tradeoffs depending on specific needs. Conversely, among many
> other features, BioPortal supports both free text (paragraphs of content),
> and the ability to annotate the largest matching strings. These often are
> not available in other annotators.
>
> With regard to reliability, the most common concern raised about BioPortal
> is that it is not consistently responsive, especially for people with
> long-running and large-scale annotation processes and similar complex
> queries. Our monitoring services show the annotation service is up over
> 99.5% of the time, but it is definitely challenged by repeatedly annotating
> pages or more of text against all 500+ ontologies 15 times per second (per
> requestor), whether your text, or someone else's. We regularly get requests
> for the Virtual Appliance so that people can set up their own annotation
> pipeline, with only the ontologies they are interested in, and handling
> queries as fast as they can send them. That is an example of a more
> reliable service, but not a public one.
>
> Perhaps this information will be sufficient to help you, or will bring
> forward other comments from the user list.
>
> john
>
>
> On Sep 27, 2017, at 6:59 AM, Alexander Garcia Castro <
> alexgarciac at gmail.com> wrote:
>
> Hi all. I am using the NCBO annotator and I like it. In a paper I just
> submitted the reviewer is saying that there are other NER tools that are
> better. this may be true but when processing the whole of PMC over a web
> service against all biomedical ontologies or a big portion of them then...
> is there anything as reliable as bioportal annotator? could some one help
> me out with some reference that justifies the choice of  the ncbo
> annotator? I am using it because I dont know if there is a web service that
> is as reliable when processing lots of texts and also that works against
> all of biomedical ontologies -in my case it is pretty much a choice due to
> the need to reuse other peoples infrastructure because I would not be able
> to process it on my own.
>
> also, there are lots of other NER tools but why was this one specifically
> selected for the NCBO NER service? as oppose to using another NER tool for
> the NCBO annotator.
>
> cheers.
>
> --
> Alexander Garcia
> https://www.researchgate.net/profile/Alexander_Garcia
> http://www.usefilm.com/photographer/75943.html
> http://www.linkedin.com/in/alexgarciac
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632
>
>
>


-- 
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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From jgraybeal at stanford.edu  Wed Nov 15 11:27:53 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 15 Nov 2017 19:27:53 +0000
Subject: [bioontology-support] anotator
In-Reply-To: <CALAe=OJfZyPVTxw6kwnFtHG84Vy_Wfvvssh20H4VqonOQieHXw@mail.gmail.com>
References: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
 <B057FEAF-C46E-4017-9857-9C112AB21363@stanford.edu>
 <CALAe=OJfZyPVTxw6kwnFtHG84Vy_Wfvvssh20H4VqonOQieHXw@mail.gmail.com>
Message-ID: <07C43A1F-54BE-4755-9CDB-601B50B95905@stanford.edu>

could u point me to the actual document/paper/reference with this evaluation?

I can't, because I didn't capture that particular reference and it would take me too long to rediscover it.

A quick search on Google ("biomedical annotations comparison ncbo") yields a number of possible comparisons, Google scholar might narrow the field further. In particular this link is tolerably recent and tolerably complete: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116040

And the proceedings paper that Clement previously referenced on this list can be found at http://ceur-ws.org/Vol-1866/paper_62.pdf; it contains a number of references to previous evaluations.

John


On Nov 15, 2017, at 10:38 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

Hi John, "In general, the only technical evaluation I've seen has shown BioPortal first or second (if I recall correctly) in terms of speed and completeness of annotation. " could u point me to the actual document/paper/reference with this evaluation?



On Sat, Sep 30, 2017 at 12:32 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Hi Alexander,

A quick answer, sorry I don't have all the research data at hand but perhaps you can use Google Scholar to find more precise information if you need it.

Since we consider BioPortal to be the biggest source of Biomedical Ontologies, we definitely consider our annotator the best service for annotations against a large and diverse number of ontologies. (And therefore, also the most reliable service in that category. :->)

The article "Semantic annotation in biomedicine: the current landscape"  in Journal of Biomedical Semantics (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0153-x) has a survey of many, if not all, of the existing semantic annotation technologies. NCBO Bioportal appears in Tables 1 and 3 (scroll the table left on screen). While quite dated in some respects (BioPortal has over 500 BioMedical ontologies, and it is open source, available on GitHub) there is a lot of useful information here. I know there are some pipeline annotators that leverage BioPortal services to provide their own annotation capabilities, but can not offer the details off-hand, sorry.

In general, the only technical evaluation I've seen has shown BioPortal first or second (if I recall correctly) in terms of speed and completeness of annotation. Of course, without specific evaluation criteria and comparisons, it is all but impossible to have a meaningful rebuttal to the observation "something else is better". Certainly there are features available with some other annotators that Bioportal does not provide, so there can be tradeoffs depending on specific needs. Conversely, among many other features, BioPortal supports both free text (paragraphs of content), and the ability to annotate the largest matching strings. These often are not available in other annotators.

With regard to reliability, the most common concern raised about BioPortal is that it is not consistently responsive, especially for people with long-running and large-scale annotation processes and similar complex queries. Our monitoring services show the annotation service is up over 99.5% of the time, but it is definitely challenged by repeatedly annotating pages or more of text against all 500+ ontologies 15 times per second (per requestor), whether your text, or someone else's. We regularly get requests for the Virtual Appliance so that people can set up their own annotation pipeline, with only the ontologies they are interested in, and handling queries as fast as they can send them. That is an example of a more reliable service, but not a public one.

Perhaps this information will be sufficient to help you, or will bring forward other comments from the user list.

john


On Sep 27, 2017, at 6:59 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

Hi all. I am using the NCBO annotator and I like it. In a paper I just submitted the reviewer is saying that there are other NER tools that are better. this may be true but when processing the whole of PMC over a web service against all biomedical ontologies or a big portion of them then... is there anything as reliable as bioportal annotator? could some one help me out with some reference that justifies the choice of  the ncbo annotator? I am using it because I dont know if there is a web service that is as reliable when processing lots of texts and also that works against all of biomedical ontologies -in my case it is pretty much a choice due to the need to reuse other peoples infrastructure because I would not be able to process it on my own.

also, there are lots of other NER tools but why was this one specifically selected for the NCBO NER service? as oppose to using another NER tool for the NCBO annotator.

cheers.

--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

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

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





--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac


========================
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  Wed Nov 15 15:55:22 2017
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 15 Nov 2017 15:55:22 -0800
Subject: [bioontology-support] [BioPortal] Feedback from jonlapointe
Message-ID: <5a0cd3ea50e61_3f9c3f83dc5628c87886d@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Nov 15 16:14:50 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 Nov 2017 00:14:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from jonlapointe
In-Reply-To: <5a0cd3ea50e61_3f9c3f83dc5628c87886d@ncbo-prd-app-08.stanford.edu.mail>
References: <5a0cd3ea50e61_3f9c3f83dc5628c87886d@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <7FF35EB4-5FBD-4387-8D0E-C5B124A2D429@stanford.edu>

Hi Jonathan,

Yes, there appears to have been a problem with the Ontology Browse page. It?s back up now - please let us know if you have further issues.

Kind regards,
Jennifer


On Nov 15, 2017, at 3:55 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: jonlapointe

Email: jonathan.lapointe at jl3.ca<mailto:jonathan.lapointe at jl3.ca>

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

Feedback:

Hi, it seems like I can't search ontologies today. Is there a problem with the site ?

Thanks,
Jonathan

_______________________________________________
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 Nov 16 12:55:09 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 16 Nov 2017 12:55:09 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Fred Trotter
Message-ID: <5a0dfb2da9214_1f373fc5b6d34f4496519@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Nov 16 14:33:15 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 Nov 2017 22:33:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Fred Trotter
In-Reply-To: <5a0dfb2da9214_1f373fc5b6d34f4496519@ncbo-prd-app-08.stanford.edu.mail>
References: <5a0dfb2da9214_1f373fc5b6d34f4496519@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <A2EEF10D-65A9-4102-BBCE-2BC496A0D105@stanford.edu>

Hi Fred,


On Nov 16, 2017, at 12:55 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Fred Trotter

Email: fred.trotter at gmail.com<mailto:fred.trotter at gmail.com>

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

Feedback:

Hi, your HCPCS ontology says that it has 5000+ classes
http://bioportal.bioontology.org/ontologies/HCPCS

But when you click "Classes" there is nothing there.

That cannot be right.

HCPCS is one of a small handful of ontologies in BioPortal with a ?flat? model, meaning that the ontology has no (or very little) hierarchy. For flat ontologies we offer a search box, rather than a tree for navigating terms. On the classes page for HCPCS [1], you can start typing in the ?Jump To:? text box in the upper left portion of the page.  BioPortal will then display a dropdown list of terms using autocomplete functionality based on the characters you type. You can select a class from the list and BioPortal will display the details in the right-hand side of the page. The classes are also available via our REST API [2].


Also, the "license" section of HCPCS code is set to be the same as UMLS. And indeed, HCPCS is available through UMLS. But it is also available directly from CMS under much less restrictive licensing. (UMLS licensing can require you to view to accept sub-licenses, which is onerous if all you want is HCPCS, etc)

https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo/index.html

I love the service, it is clearly the best of its kind. It would be cool if these bugs could be fixed.

I looked at the link you reference above, but it?s not obvious to me what formats they offer. I could only find a PDF document. BioPortal accepts ontology uploads in OWL, OBO, and SKOS format.

UMLS ontologies are a special case for us. We import them programmatically with a Python script that converts from UMLS Metathesaurus format to an RDF TTL file that's consumable by our application. If you?re aware of a version of HCPCS from CMS in a format that we currently handle, we could look at retrieving it from them and updating the license information.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies/HCPCS/?p=classes
[2] http://data.bioontology.org/ontologies/HCPCS/classes
[3] https://github.com/ncbo/umls2rdf



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From benjamin_gyori at hms.harvard.edu  Mon Nov 20 07:32:18 2017
From: benjamin_gyori at hms.harvard.edu (Benjamin Gyori)
Date: Mon, 20 Nov 2017 10:32:18 -0500
Subject: [bioontology-support] OBO upload, class browser issue
Message-ID: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>

Dear BioPortal developers,

I am trying to upload an ontology called Bioentities in OBO format. The
ontology contains around ~450 terms, with each term having a (1) name (2)
list of synonym strings (3) list of mappings to external ontologies (4)
list of isa / partof / inverse_isa / has_part relationships to other terms
in the same ontology and also external ontologies.

I have uploaded the OBO file, but found that even after it was parsed and
indexed, the "Classes" page returned "Problem retrieving classes". Could
you help determine how I need to modify the OBO file to work with the class
browser? I am attaching a small sample of the overall ontology for
reference. The ontology is uploaded at
http://bioportal.bioontology.org/ontologies/BE, but is currently set to
private - I can share it if it helps find the issue.

Thank you for your help!

Best regards,
Ben

---
Benjamin M. Gyori, PhD
Research Associate in Therapeutic Science
Laboratory of Systems Pharmacology
Harvard Medical School
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From vendetti at stanford.edu  Mon Nov 20 11:03:39 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 20 Nov 2017 19:03:39 +0000
Subject: [bioontology-support] OBO upload, class browser issue
In-Reply-To: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>
References: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>
Message-ID: <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu>

Hi Ben,


On Nov 20, 2017, at 7:32 AM, Benjamin Gyori <benjamin_gyori at hms.harvard.edu<mailto:benjamin_gyori at hms.harvard.edu>> wrote:

Dear BioPortal developers,

I am trying to upload an ontology called Bioentities in OBO format. The ontology contains around ~450 terms, with each term having a (1) name (2) list of synonym strings (3) list of mappings to external ontologies (4) list of isa / partof / inverse_isa / has_part relationships to other terms in the same ontology and also external ontologies.

I have uploaded the OBO file, but found that even after it was parsed and indexed, the "Classes" page returned "Problem retrieving classes". Could you help determine how I need to modify the OBO file to work with the class browser? I am attaching a small sample of the overall ontology for reference. The ontology is uploaded at http://bioportal.bioontology.org/ontologies/BE, but is currently set to private - I can share it if it helps find the issue.


There?s no need to change the visibility from private to public. We have admin privileges / full access to your ontology content.

In order to construct / display a term hierarchy, the BioPortal UI first accesses our REST API?s roots endpoint to retrieve the root-level terms. It appears that the roots endpoint for the OBO file you uploaded today is returning an empty set:

http://data.bioontology.org/ontologies/BE/classes/roots

This is the underlying reason the classes page results in a 404 error. I noticed that all of the terms in your ontology have an isa / subclass relationship to "ONT:PROTEIN-FAMILY?. However, ONT:PROTEIN-FAMILY isn?t explicitly defined in the ontology, nor are there any import statements among the document header tags pointing to the external ontology where it?s defined. Probably BioPortal should be able to infer that ONT:PROTEIN-FAMILY is a root term in your ontology, even though ONT:PROTEIN-FAMILY isn't explicitly defined. I will need to enter an issue in our tracker for this and investigate.

In the mean time, if you have an urgent need to view the classes page in BioPortal, I think you would need to submit a version of your ontology to us where that term is either explicitly defined in the ontology source file, or an import statement is added for the external ontology in which the term is defined. If you decide to go that route, feel free to send something to us privately, and we could test it out in our staging environment first.

Kind regards,
Jennifer

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From benjamin_gyori at hms.harvard.edu  Mon Nov 20 20:19:55 2017
From: benjamin_gyori at hms.harvard.edu (Benjamin Gyori)
Date: Mon, 20 Nov 2017 23:19:55 -0500
Subject: [bioontology-support] OBO upload, class browser issue
In-Reply-To: <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu>
References: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>
 <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu>
Message-ID: <CAAjm4XPFtNHBP+1qDWEMFBRqMMfeHE5C2A9fDwit=BjPhT1f_w@mail.gmail.com>

Hi Jennifer,

Thank you, that's really helpful! I modified the root node to be part of
the BE ontology, and now the classes are loaded correctly. I also really
like the visualization on some of the other ontologies and would like to
make it work for this one. But for some reason I get this blank view when I
click on the Visualization tab:
[image: Inline image 1]
Could you help figure out what I need to change to make visualization work?

Another question I had is about mapping to outside ontologies. In this
ontology xrefs, inverse_is_a and has_part relationships often link to
outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc.
What is the preferred way to add links to such outside ontologies in the
OBO file I upload? Currently, I encode them as, for instance "has_part:
HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could
be linked out to the given outside resources via the web interface.

Thank you again for your help!

Best,
Ben

On Mon, Nov 20, 2017 at 2:03 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Ben,
>
>
> On Nov 20, 2017, at 7:32 AM, Benjamin Gyori <benjamin_gyori at hms.harvard.ed
> u> wrote:
>
> Dear BioPortal developers,
>
> I am trying to upload an ontology called Bioentities in OBO format. The
> ontology contains around ~450 terms, with each term having a (1) name (2)
> list of synonym strings (3) list of mappings to external ontologies (4)
> list of isa / partof / inverse_isa / has_part relationships to other terms
> in the same ontology and also external ontologies.
>
> I have uploaded the OBO file, but found that even after it was parsed and
> indexed, the "Classes" page returned "Problem retrieving classes". Could
> you help determine how I need to modify the OBO file to work with the class
> browser? I am attaching a small sample of the overall ontology for
> reference. The ontology is uploaded at http://bioportal.bioontolog
> y.org/ontologies/BE
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_BE&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=ix4fLnHrlpV6PLWEgZQBUFTXOiAxDUULFR7mFwfMybU&m=7pTgI3Cg7CSmF0ySLrQpJmaS69W8XcIPkIKthgrcypo&s=XphzNGPyzCDZKwW5OjMqs54jiJh_A-iINam9RwvLK0Y&e=>,
> but is currently set to private - I can share it if it helps find the issue.
>
>
>
> There?s no need to change the visibility from private to public. We have
> admin privileges / full access to your ontology content.
>
> In order to construct / display a term hierarchy, the BioPortal UI first
> accesses our REST API?s roots endpoint to retrieve the root-level terms. It
> appears that the roots endpoint for the OBO file you uploaded today is
> returning an empty set:
>
> http://data.bioontology.org/ontologies/BE/classes/roots
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_ontologies_BE_classes_roots&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=ix4fLnHrlpV6PLWEgZQBUFTXOiAxDUULFR7mFwfMybU&m=7pTgI3Cg7CSmF0ySLrQpJmaS69W8XcIPkIKthgrcypo&s=6y0988TqAoLirDVYydol3UynCYMYbNVI6z7yYxZcnGc&e=>
>
> This is the underlying reason the classes page results in a 404 error. I
> noticed that all of the terms in your ontology have an isa / subclass
> relationship to "ONT:PROTEIN-FAMILY?. However, ONT:PROTEIN-FAMILY isn?t
> explicitly defined in the ontology, nor are there any import statements
> among the document header tags pointing to the external ontology where it?s
> defined. Probably BioPortal should be able to infer that ONT:PROTEIN-FAMILY
> is a root term in your ontology, even though ONT:PROTEIN-FAMILY isn't
> explicitly defined. I will need to enter an issue in our tracker for this
> and investigate.
>
> In the mean time, if you have an urgent need to view the classes page in
> BioPortal, I think you would need to submit a version of your ontology to
> us where that term is either explicitly defined in the ontology source
> file, or an import statement is added for the external ontology in which
> the term is defined. If you decide to go that route, feel free to send
> something to us privately, and we could test it out in our staging
> environment first.
>
> Kind regards,
> Jennifer
>
>
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From Aaron.Zhang at jax.org  Tue Nov 21 08:16:56 2017
From: Aaron.Zhang at jax.org (Aaron Zhang)
Date: Tue, 21 Nov 2017 16:16:56 +0000
Subject: [bioontology-support] Search with API
Message-ID: <68227CC2-C3F8-4FF9-A5E3-8FC096988C80@jax.org>

Dear Sir/Madam,

I am trying to use the REST API that you provide to search for ontologies that have a class name that is the same to my query.

For example, if I search ?valproic acid? through the browser (Class Search), I get matches in 26 ontologies, the names of which are what I hope to get;

[cid:image001.png at 01D362BA.3DD93300]
however, if I run the search through API with the following paramaters, I got 100,361 results. I am confused what is the dramatic difference; how can I get a REST response that more closely reassembles the browser search?

API response: {"page":1,"pageCount":20073,"totalCount":100361,"prevPage":null,"nextPage":2, ?

Response response = given()
        .request().with()
            .param("apikey", api_key)
            .param("include", "prefLabel")
            .param("page", pageNumber)
            .param("pagesize", 5)
            .param("include_views", false)
            .param("display_context", false)
            .param("display_links", false)
            .param("ontology", "CHEBI")
            .param("roots_only", true)
        .expect()
            .statusCode(200)
        .get("search?q=" + term);


I appreciate your help.
Best,
Aaron


---

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From mdorf at stanford.edu  Tue Nov 21 13:23:48 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 21 Nov 2017 21:23:48 +0000
Subject: [bioontology-support] bioontology-support post from
 aaron.zhang@jax.org requires approval
In-Reply-To: <mailman.32060.1511281034.3205.bioontology-support@lists.stanford.edu>
References: <mailman.32060.1511281034.3205.bioontology-support@lists.stanford.edu>
Message-ID: <8AF17654-0D5F-4C90-9846-49EE3710FB37@stanford.edu>

Hi Aaron,

Thank you for your inquiry. The difference in the number of matches that you see is mostly attributed to the way our user interface presents the results. It makes a call to our /search endpoint but does some additional processing that groups the results by each ontology. A link on the bottom of each search result allows you to view the additional results (Ex: 26 more from this ontology). The REST endpoint does not perform any groupings. It presents the ALL results, ordered by their respective search ranks.

I did notice a discrepancy that between our API and documentation in the example that you presented. Namely, the parameter ?roots_only? appears to be deprecated, and the search does not take it into account. CHEBI specifically, contains only three root classes:

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

Thus, even if the ?roots_only? parameter was working you, wouldn?t get any hits on the query ?valproic acid?. I will look into both updating our documentation as well as a possibility of re-introducing the ?roots_only? parameter in our future releases. I?ve created this issue in our Github tracking system, so you can keep track of our progress on resolving it: https://github.com/ncbo/ontologies_api/issues/40

Thanks again!

Michael


Dear Sir/Madam,

I am trying to use the REST API that you provide to search for ontologies that have a class name that is the same to my query.

For example, if I search ?valproic acid? through the browser (Class Search), I get matches in 26 ontologies, the names of which are what I hope to get;

<image001.png>
however, if I run the search through API with the following paramaters, I got 100,361 results. I am confused what is the dramatic difference; how can I get a REST response that more closely reassembles the browser search?

API response: {"page":1,"pageCount":20073,"totalCount":100361,"prevPage":null,"nextPage":2, ?

Response response = given()
        .request().with()
            .param("apikey", api_key)
            .param("include", "prefLabel")
            .param("page", pageNumber)
            .param("pagesize", 5)
            .param("include_views", false)
            .param("display_context", false)
            .param("display_links", false)
            .param("ontology", "CHEBI")
            .param("roots_only", true)
        .expect()
            .statusCode(200)
        .get("search?q=" + term);


I appreciate your help.
Best,
Aaron


---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


From: bioontology-support-request at lists.stanford.edu<mailto:bioontology-support-request at lists.stanford.edu>
Subject: confirm 379e086c8e7158b1da434a380722b7e178aa2e9e
Date: November 21, 2017 at 8:17:14 AM PST


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From J.Bard at ed.ac.uk  Wed Nov 22 01:35:49 2017
From: J.Bard at ed.ac.uk (BARD Jonathan)
Date: Wed, 22 Nov 2017 09:35:49 +0000
Subject: [bioontology-support] ontology loading problem
Message-ID: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven?t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



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From Richard.Baldock at igmm.ed.ac.uk  Wed Nov 22 01:46:16 2017
From: Richard.Baldock at igmm.ed.ac.uk (Richard Baldock)
Date: Wed, 22 Nov 2017 09:46:16 +0000
Subject: [bioontology-support] ontology loading problem
In-Reply-To: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
References: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
Message-ID: <E7F0C2A0-802A-4EB4-BA48-5E3F2C2AD5A1@igmm.ed.ac.uk>

Dear Jonathan,

I haven?t changed anything ?out there?. I have an internal copy and it is the case I have to switch off one of the checks that OBO-Edit does but I can?t remember the details. I can try to download the file and see if it will load here. Here being at home of course I am fully out of the HGU, desk cleared, room empty and my shed full of junk!

Cheers

Richard.

Professor Richard Baldock
Biomedical Systems Analysis

******* Please note changed telephone numbers ********
?

Richard.Baldock at igmm.ed.ac.uk
MRC Human Genetics Unit 			Tel(direct): +44-131-6518661
MRC IGMM						Tel(mbl):    +44-779-3977030
University of Edinburgh				Tel(sb):      +44-131-6518500
Crewe Road						Fax:           +44-131-6518800
Edinburgh, EH4 2XU, UK.

On 22 Nov 2017, at 09:35, BARD Jonathan <J.Bard at ed.ac.uk> wrote:

> I have had 4 emails (below) about my ontologies not loading 
> 
> These should all be stable as they haven?t been touched by me for a few years
> 
> Is the problem at your end?
> 
> Jonathan
> 
> --------------------------------------------
> 
> Professor Jonathan Bard
> 
> Balliol College, Oxford - graduate advisor
> Dept. Physiology, Anatomy & Genetics
>    Oxford - visiting member
> 45 Charlbury Road, OX2 6UX UK
> T= 44/0 1865 315185, M = 07741477720
> 
> BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo. 
> 
> BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo. 
> 
> BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo. 
> 
> BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo. 
> 
> 
> 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

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From vendetti at stanford.edu  Wed Nov 22 12:24:16 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 22 Nov 2017 20:24:16 +0000
Subject: [bioontology-support] ontology loading problem
In-Reply-To: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
References: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
Message-ID: <DECC9E5F-E8E9-4FF8-B6F1-43A3F45EF143@stanford.edu>

Hello Jonathan,

All of the URLs you listed below are part of a SourceForge site where the root seems to have been removed and results in a 404 error:

http://obo.cvs.sourceforge.net/

I noticed these are all OBO ontologies, so I looked on the OBO Foundry website and was able to find this updated download URL for the Anatomical Entity Ontology:

http://purl.obolibrary.org/obo/aeo.owl

The other 3 ontologies are marked as obsolete on the OBO Foundry website, so I was unable to find alternative download URLs. If you?d like, I could modify these entries in BioPortal to stop checking the SourceForge URLs on a daily basis for new versions. This would prevent BioPortal from sending you email about load failures. The ontologies are otherwise fine and displaying as normal in the BioPortal application.

Kind regards,
Jennifer


On Nov 22, 2017, at 1:35 AM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven?t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
_______________________________________________
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  Wed Nov 22 12:52:07 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 22 Nov 2017 20:52:07 +0000
Subject: [bioontology-support] OBO upload, class browser issue
In-Reply-To: <CAAjm4XPFtNHBP+1qDWEMFBRqMMfeHE5C2A9fDwit=BjPhT1f_w@mail.gmail.com>
References: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>
 <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu>
 <CAAjm4XPFtNHBP+1qDWEMFBRqMMfeHE5C2A9fDwit=BjPhT1f_w@mail.gmail.com>
Message-ID: <D052F98D-AC94-4A3E-87E1-E834F92E77FF@stanford.edu>

Hi Ben,


On Nov 20, 2017, at 8:19 PM, Benjamin Gyori <benjamin_gyori at hms.harvard.edu<mailto:benjamin_gyori at hms.harvard.edu>> wrote:

I modified the root node to be part of the BE ontology, and now the classes are loaded correctly.


OK, good to hear.


I also really like the visualization on some of the other ontologies and would like to make it work for this one. But for some reason I get this blank view when I click on the Visualization tab: Could you help figure out what I need to change to make visualization work?


The visualization software you?re referring to is 3rd party, developed by the University of Victoria for BioPortal a few years ago. There?s a known issue that?s cropped up where the software doesn?t work over HTTPS [1]. As of yet, we haven?t been able to secure the resources to take over development and maintenance of their code. There?s a simple workaround in the mean time though. If you modify the URL in the address bar to use HTTP, you?ll be able to see the visualizations:


[cid:2200C37A-6487-49C2-8BD0-D5A2F8011ABC at stanford.edu]




Another question I had is about mapping to outside ontologies. In this ontology xrefs, inverse_is_a and has_part relationships often link to outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc. What is the preferred way to add links to such outside ontologies in the OBO file I upload? Currently, I encode them as, for instance "has_part: HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could be linked out to the given outside resources via the web interface.

If I understood your question correctly, we don?t offer this kind of functionality. The mappings we generate are between ontology classes from the set of ontologies that exist in BioPortal. I did a quick search and the ontologies you mentioned above don?t appear to have been uploaded into our application, although they could be if they are published in a format we can handle.

I vaguely recall a research group that may have customized a virtual appliance instance of BioPortal to handle external mappings. Let me see if I can track that information down.

Kind regards,
Jennifer

[1] https://github.com/ncbo/biomixer/issues/2


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From J.Bard at ed.ac.uk  Wed Nov 22 13:25:30 2017
From: J.Bard at ed.ac.uk (BARD Jonathan)
Date: Wed, 22 Nov 2017 21:25:30 +0000
Subject: [bioontology-support] ontology loading problem
In-Reply-To: <DECC9E5F-E8E9-4FF8-B6F1-43A3F45EF143@stanford.edu>
References: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
 <DECC9E5F-E8E9-4FF8-B6F1-43A3F45EF143@stanford.edu>
Message-ID: <5EC51B83-4C16-44A7-9726-46F13B399C25@ed.ac.uk>

Jennifer

You are right - the last 3 are out of date and, as far as I am concerned, be lost

Thanks for updating the AEO which may still be useful

Regards

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720





On 22 Nov 2017, at 20:24, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jonathan,

All of the URLs you listed below are part of a SourceForge site where the root seems to have been removed and results in a 404 error:

http://obo.cvs.sourceforge.net/

I noticed these are all OBO ontologies, so I looked on the OBO Foundry website and was able to find this updated download URL for the Anatomical Entity Ontology:

http://purl.obolibrary.org/obo/aeo.owl

The other 3 ontologies are marked as obsolete on the OBO Foundry website, so I was unable to find alternative download URLs. If you?d like, I could modify these entries in BioPortal to stop checking the SourceForge URLs on a daily basis for new versions. This would prevent BioPortal from sending you email about load failures. The ontologies are otherwise fine and displaying as normal in the BioPortal application.

Kind regards,
Jennifer


On Nov 22, 2017, at 1:35 AM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven?t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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From jgraybeal at stanford.edu  Wed Nov 22 18:54:11 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 23 Nov 2017 02:54:11 +0000
Subject: [bioontology-support] OBO upload, class browser issue
In-Reply-To: <D052F98D-AC94-4A3E-87E1-E834F92E77FF@stanford.edu>
References: <CAAjm4XO+Z1NHCmcfeZaBbhdi5+KHiPKvw2JwHCp1j51z01HsJw@mail.gmail.com>
 <496666FC-0D7B-4B16-88AE-0FC4A7B0C5F9@stanford.edu>
 <CAAjm4XPFtNHBP+1qDWEMFBRqMMfeHE5C2A9fDwit=BjPhT1f_w@mail.gmail.com>
 <D052F98D-AC94-4A3E-87E1-E834F92E77FF@stanford.edu>
Message-ID: <2FB582DB-C79C-4868-A87A-87635602E4E5@stanford.edu>

The AgroPortal group, led by Clement Jonquet, has customized a virtual appliance instance of BioPortal to handle external mappings. Unfortunately, it appears to incur a significant performance hit, that has prevented us from doing the same with BioPortal, at least without a lot of work.

Another question I had is about mapping to outside ontologies. In this ontology xrefs, inverse_is_a and has_part relationships often link to outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc. What is the preferred way to add links to such outside ontologies in the OBO file I upload? Currently, I encode them as, for instance "has_part: HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could be linked out to the given outside resources via the web interface.

When you say 'outside ontologies', do you mean outside OBO or outside BioPortal? We should be able to process mappings to other terms in BioPortal (NCIT for example).

With regard to OBO references to terms of ontologies in BioPortal, I am not sure how BioPortal processes the CURIE format for those mappings. (Perhaps a full IRI would be better?)  I'll see if we can dig up any additional answers in that regard. (There might be some information in the OBO support lists also.)

John


On Nov 22, 2017, at 12:52 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Ben,


On Nov 20, 2017, at 8:19 PM, Benjamin Gyori <benjamin_gyori at hms.harvard.edu<mailto:benjamin_gyori at hms.harvard.edu>> wrote:

I modified the root node to be part of the BE ontology, and now the classes are loaded correctly.


OK, good to hear.


I also really like the visualization on some of the other ontologies and would like to make it work for this one. But for some reason I get this blank view when I click on the Visualization tab: Could you help figure out what I need to change to make visualization work?


The visualization software you?re referring to is 3rd party, developed by the University of Victoria for BioPortal a few years ago. There?s a known issue that?s cropped up where the software doesn?t work over HTTPS [1]. As of yet, we haven?t been able to secure the resources to take over development and maintenance of their code. There?s a simple workaround in the mean time though. If you modify the URL in the address bar to use HTTP, you?ll be able to see the visualizations:


<Screenshot 2017-11-22 12.42.07.png>




Another question I had is about mapping to outside ontologies. In this ontology xrefs, inverse_is_a and has_part relationships often link to outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc. What is the preferred way to add links to such outside ontologies in the OBO file I upload? Currently, I encode them as, for instance "has_part: HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could be linked out to the given outside resources via the web interface.

If I understood your question correctly, we don?t offer this kind of functionality. The mappings we generate are between ontology classes from the set of ontologies that exist in BioPortal. I did a quick search and the ontologies you mentioned above don?t appear to have been uploaded into our application, although they could be if they are published in a format we can handle.

I vaguely recall a research group that may have customized a virtual appliance instance of BioPortal to handle external mappings. Let me see if I can track that information down.

Kind regards,
Jennifer

[1] https://github.com/ncbo/biomixer/issues/2


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

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


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From vendetti at stanford.edu  Wed Nov 22 21:16:08 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 23 Nov 2017 05:16:08 +0000
Subject: [bioontology-support] ontology loading problem
In-Reply-To: <5EC51B83-4C16-44A7-9726-46F13B399C25@ed.ac.uk>
References: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
 <DECC9E5F-E8E9-4FF8-B6F1-43A3F45EF143@stanford.edu>
 <5EC51B83-4C16-44A7-9726-46F13B399C25@ed.ac.uk>
Message-ID: <978A7CA1-1986-44A3-AC4C-434C7831902B@stanford.edu>

Hi Jonathan,


On Nov 22, 2017, at 1:25 PM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

Jennifer

You are right - the last 3 are out of date and, as far as I am concerned, be lost


OK, thanks for the information. I removed the download URLs for those 3 ontologies and marked their status as retired.



Thanks for updating the AEO which may still be useful


AEO has been updated.

Best,
Jennifer



On 22 Nov 2017, at 20:24, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jonathan,

All of the URLs you listed below are part of a SourceForge site where the root seems to have been removed and results in a 404 error:

http://obo.cvs.sourceforge.net/

I noticed these are all OBO ontologies, so I looked on the OBO Foundry website and was able to find this updated download URL for the Anatomical Entity Ontology:

http://purl.obolibrary.org/obo/aeo.owl

The other 3 ontologies are marked as obsolete on the OBO Foundry website, so I was unable to find alternative download URLs. If you?d like, I could modify these entries in BioPortal to stop checking the SourceForge URLs on a daily basis for new versions. This would prevent BioPortal from sending you email about load failures. The ontologies are otherwise fine and displaying as normal in the BioPortal application.

Kind regards,
Jennifer


On Nov 22, 2017, at 1:35 AM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven?t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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From support at bioontology.org  Thu Nov 23 02:17:57 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 23 Nov 2017 02:17:57 -0800
Subject: [bioontology-support] [BioPortal] Feedback from
	patrick.hendrickx@wur.nl
Message-ID: <5a16a055e50f0_20ef3fd33fbafda44146a@ncbo-prd-app-08.stanford.edu.mail>

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From J.Bard at ed.ac.uk  Thu Nov 23 01:52:56 2017
From: J.Bard at ed.ac.uk (BARD Jonathan)
Date: Thu, 23 Nov 2017 09:52:56 +0000
Subject: [bioontology-support] ontology loading problem
In-Reply-To: <978A7CA1-1986-44A3-AC4C-434C7831902B@stanford.edu>
References: <F590120C-5743-4039-8172-ADD9AEC57626@ed.ac.uk>
 <DECC9E5F-E8E9-4FF8-B6F1-43A3F45EF143@stanford.edu>
 <5EC51B83-4C16-44A7-9726-46F13B399C25@ed.ac.uk>
 <978A7CA1-1986-44A3-AC4C-434C7831902B@stanford.edu>
Message-ID: <1B120FBB-A93C-4AC7-9B9A-5C299505209A@ed.ac.uk>

Jennifer

Many thanks

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720





On 23 Nov 2017, at 05:16, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Jonathan,


On Nov 22, 2017, at 1:25 PM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

Jennifer

You are right - the last 3 are out of date and, as far as I am concerned, be lost


OK, thanks for the information. I removed the download URLs for those 3 ontologies and marked their status as retired.



Thanks for updating the AEO which may still be useful


AEO has been updated.

Best,
Jennifer



On 22 Nov 2017, at 20:24, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jonathan,

All of the URLs you listed below are part of a SourceForge site where the root seems to have been removed and results in a 404 error:

http://obo.cvs.sourceforge.net/

I noticed these are all OBO ontologies, so I looked on the OBO Foundry website and was able to find this updated download URL for the Anatomical Entity Ontology:

http://purl.obolibrary.org/obo/aeo.owl

The other 3 ontologies are marked as obsolete on the OBO Foundry website, so I was unable to find alternative download URLs. If you?d like, I could modify these entries in BioPortal to stop checking the SourceForge URLs on a daily basis for new versions. This would prevent BioPortal from sending you email about load failures. The ontologies are otherwise fine and displaying as normal in the BioPortal application.

Kind regards,
Jennifer


On Nov 22, 2017, at 1:35 AM, BARD Jonathan <J.Bard at ed.ac.uk<mailto:J.Bard at ed.ac.uk>> wrote:

I have had 4 emails (below) about my ontologies not loading

These should all be stable as they haven?t been touched by me for a few years

Is the problem at your end?

Jonathan

--------------------------------------------

Professor Jonathan Bard

Balliol College, Oxford - graduate advisor
Dept. Physiology, Anatomy & Genetics
   Oxford - visiting member
45 Charlbury Road, OX2 6UX UK
T= 44/0 1865 315185, M = 07741477720

BioPortal failed to load Anatomical Entity Ontology (AEO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/aeo.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo.

BioPortal failed to load Human Developmental Anatomy Ontology, timed version (EHDA) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo.

BioPortal failed to load Minimal Anatomical Terminology (MAT) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo.



The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
_______________________________________________
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


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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From mhartung at cit-ec.uni-bielefeld.de  Fri Nov 24 08:48:50 2017
From: mhartung at cit-ec.uni-bielefeld.de (Matthias Hartung)
Date: Fri, 24 Nov 2017 17:48:50 +0100
Subject: [bioontology-support] Submission of SCIO ontology
In-Reply-To: <61DE15CB-5955-4EEB-81EA-E40C42AAF198@stanford.edu>
References: <b5fdae0f-b541-f074-cd51-b04a408b6824@cit-ec.uni-bielefeld.de>
 <61DE15CB-5955-4EEB-81EA-E40C42AAF198@stanford.edu>
Message-ID: <166ea4ea-4285-93e4-124e-4d0efceda797@cit-ec.uni-bielefeld.de>

Dear support team,

as a follow-up to our submission of the Spinal Cord Injury Ontology
(SCIO) to BioPortal, we would like to ask whether there is a possibility
to visualize the instances contained in the ontology as well (besides
classes and properties)?

Best regards,

Matthias Hartung




On 20.09.2017 16:58, Jennifer Leigh Vendetti wrote:
> Hello Matthias,
> 
> The ?Load from URL? property of your ontology submission was set to a
> directory instead of a complete path that includes the name of the
> ontology file that you want BioPortal to check nightly. I created a new
> submission of your ontology and changed the previous value
> from?http://psink.de/scio?to?http://psink.de/scio/SCIO_51.owl. Your
> ontology is now fully parsed and available in BioPortal.
> 
> If you?re interested in publishing new versions to that location, a
> suggested best practice is to use a file name without a version number,
> e.g.:
> 
> http://psink.de/scio/SCIO.owl
> 
> ? and instead indicate the version in your ontology source file via the
> owl:versionInfo property. The BioPortal software looks for this property
> at parse time and will display the value in the submission column of the
> Submissions table on the ontology summary page. This advice is optional
> though.
> 
> Kind regards,
> Jennifer
> 
> 
>> On Sep 20, 2017, at 2:13 AM, Matthias Hartung
>> <mhartung at cit-ec.uni-bielefeld.de
>> <mailto:mhartung at cit-ec.uni-bielefeld.de>> wrote:
>>
>> Dear Sir or Madam,
>>
>> we were trying to register the SCIO ontology [1] with BioPortal. The
>> submission has (apparently successfully) taken place yesterday.
>>
>> However, by now the ontology is not accessible via [2]. Instead, an
>> error is reported: "We're sorry but something has gone wrong. We have
>> been notified of this error."
>>
>> We would appreciate any support about what we can do in order to fix
>> this error. Thank you very much for your efforts.
>>
>> Best regards,
>>
>> Matthias Hartung
>>
>>
>> [1] http://psink.de/scio
>> [2] http://purl.bioontology.org/ontology/SCIO
>>
>>
>>
>>
>> -- 
>> Dr. Matthias Hartung
>> Semantic Computing Group
>> Cognitive Interaction Technology Center of Excellence (CITEC)
>> Bielefeld University
>>
>> e-Mail: mhartung at cit-ec.uni-bielefeld.de
>> <mailto:mhartung at cit-ec.uni-bielefeld.de>
>> Phone: ?+49 521 106 12223
>> Fax: ???+49 521 106 6560
>>
>> Office: 2.310
>>
>> Inspiration 1 / Zehlendorfer Damm 201
>> 33619 Bielefeld
>> Germany
>> _______________________________________________
>> 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
> 

-- 
Dr. Matthias Hartung
Semantic Computing Group
Cognitive Interaction Technology Center of Excellence (CITEC)
Bielefeld University

e-Mail: mhartung at cit-ec.uni-bielefeld.de
Phone:  +49 521 106 12223
Fax:    +49 521 106 6560

Office: 2.310

Inspiration 1 / Zehlendorfer Damm 201
33619 Bielefeld
Germany

From support at bioontology.org  Fri Nov 24 10:02:48 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 24 Nov 2017 10:02:48 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Barry Smith
Message-ID: <5a185ec834ee9_1a883fe92a69b63c1bb@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Fri Nov 24 11:09:35 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 Nov 2017 19:09:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Barry Smith
In-Reply-To: <5a185ec834ee9_1a883fe92a69b63c1bb@ncbo-prd-app-08.stanford.edu.mail>
References: <5a185ec834ee9_1a883fe92a69b63c1bb@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <MWHPR0201MB3516B420220EE35E4B07E1A5DA260@MWHPR0201MB3516.namprd02.prod.outlook.com>

Barry, visualizations no longer work with secure http protocol (https), as the original code is no longer maintained. Can you try changing the prefix of the url to http, if you haven?t already?

John

________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of support at bioontology.org <support at bioontology.org>
Sent: Friday, November 24, 2017 10:02:48 AM
To: support at bioontology.org; phismith at buffalo.edu
Subject: [bioontology-support] [BioPortal] Feedback from Barry Smith


Name: Barry Smith

Email: phismith at buffalo.edu

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FBFO%3Fp%3Dclasses

Feedback:

visualization seems not to be working, e.g. on BFO, MFO(EM)
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From support at bioontology.org  Sun Nov 26 06:21:14 2017
From: support at bioontology.org (support at bioontology.org)
Date: Sun, 26 Nov 2017 06:21:14 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Barry Smith
Message-ID: <5a1acdda36b00_573b3ffcc31cf80467074@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Nov 27 10:23:53 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Nov 2017 18:23:53 +0000
Subject: [bioontology-support] Submission of SCIO ontology
In-Reply-To: <166ea4ea-4285-93e4-124e-4d0efceda797@cit-ec.uni-bielefeld.de>
References: <b5fdae0f-b541-f074-cd51-b04a408b6824@cit-ec.uni-bielefeld.de>
 <61DE15CB-5955-4EEB-81EA-E40C42AAF198@stanford.edu>
 <166ea4ea-4285-93e4-124e-4d0efceda797@cit-ec.uni-bielefeld.de>
Message-ID: <0492AAB4-7394-4CC1-930B-F5CB51A3FF66@stanford.edu>

Hello Matthias,

Apologies that the BioPortal user interface doesn?t have the functionality you enquired about below. Currently we only surface instance data via our REST API, i.e.:

http://data.bioontology.org/ontologies/SCIO/instances

Kind regards,
Jennifer



On Nov 24, 2017, at 8:48 AM, Matthias Hartung <mhartung at cit-ec.uni-bielefeld.de<mailto:mhartung at cit-ec.uni-bielefeld.de>> wrote:

Dear support team,

as a follow-up to our submission of the Spinal Cord Injury Ontology
(SCIO) to BioPortal, we would like to ask whether there is a possibility
to visualize the instances contained in the ontology as well (besides
classes and properties)?

Best regards,

Matthias Hartung



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From vendetti at stanford.edu  Mon Nov 27 10:39:50 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Nov 2017 18:39:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 patrick.hendrickx@wur.nl
In-Reply-To: <5a16a055e50f0_20ef3fd33fbafda44146a@ncbo-prd-app-08.stanford.edu.mail>
References: <5a16a055e50f0_20ef3fd33fbafda44146a@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <249A073D-C409-4FA5-BEAD-3FEE751333A2@stanford.edu>

Hello Patrick,

You should be able to enter your email address and account name on the following page:

https://bioportal.bioontology.org/lost_pass

? and receive password reset instructions. The account name associated with your email address is ?hendrickx7?. Is this what you were entering for the account name?

Kind regards,
Jennifer



On Nov 23, 2017, at 2:17 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: patrick.hendrickx at wur.nl<mailto:patrick.hendrickx at wur.nl>

Email: patrick.hendrickx at wur.nl<mailto:patrick.hendrickx at wur.nl>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F404%3Fpassword%3Dtrue

Feedback:

Hello Support team,

I really like to use your ontology. I'm not able to login because my accountname and password doesn't match. Then I tried to change the password (several times) but i still get the error that "the page you are looking for wasn't found. Please try again"

Could you please provide me a password.

Thanks in advance,

Patrick

_______________________________________________
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  Mon Nov 27 10:47:49 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Nov 2017 18:47:49 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Barry Smith
In-Reply-To: <5a1acdda36b00_573b3ffcc31cf80467074@ncbo-prd-app-09.stanford.edu.mail>
References: <5a1acdda36b00_573b3ffcc31cf80467074@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <4F9A5A80-FE4F-4497-99D9-B467A354A8A0@stanford.edu>

Hi Barry,

I entered the link you sent below in Chrome (Version 62.0.3202.94 (Official Build) (64-bit)), and asked to expand all 34 concepts for ?emotion process? class. The visualization worked fine for me. Are you seeing something different?

Kind regards,
Jennifer


[cid:AED918BB-A120-456E-BEA0-14E23AAFA91C at stanford.edu]






On Nov 26, 2017, at 6:21 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Barry Smith

Email: phismith at buffalo.edu<mailto:phismith at buffalo.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMFOEM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org<http://252Fpurl.obolibrary.org>%252Fobo%252FMFOEM_000001

Feedback:

I note that Visualization does not work so well on Chrome for things that work in Edge
Try, for instance, http://bioportal.bioontology.org/ontologies/MFOEM/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMFOEM_000001
and ask to have all child nodes of the lowest level term displayed
BS

_______________________________________________
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 csongor.nyulas at stanford.edu  Mon Nov 27 13:34:45 2017
From: csongor.nyulas at stanford.edu (Csongor Nyulas)
Date: Mon, 27 Nov 2017 13:34:45 -0800
Subject: [bioontology-support] =?utf-8?q?Fwd=3A_=5Bprotege-announce=5D_Joi?=
 =?utf-8?q?n_us_for_the_next_Protege_Short_Course_at_Stanford_University?=
 =?utf-8?b?LCBNYXJjaCAyOCDigJMgMzAsIDIwMTgh?=
In-Reply-To: <6ac8da39-450b-4156-2af4-ffe685c14d9d@stanford.edu>
References: <6ac8da39-450b-4156-2af4-ffe685c14d9d@stanford.edu>
Message-ID: <325c45b9-6cd9-3620-1fca-ef8e4eb717c3@stanford.edu>

I am forwarding the announcement below, as it may be of interest to the 
NCBO community.

Best,
Csongor


-------- Forwarded Message --------
Subject: 	[protege-announce] Join us for the next Protege Short Course 
at Stanford University, March 28 ? 30, 2018!
Date: 	Mon, 27 Nov 2017 12:02:49 -0800
From: 	Csongor Nyulas <csongor.nyulas at stanford.edu>
To: 	protege-announce at lists.stanford.edu



Dear all,

We are excited to announce the *next Prot?g? Short Course*, to be held 
at Stanford University, California, between *March**28?30, 2018*!

The Prot?g? Short Course is a 3-day intensive training, which provides 
an in-depth introduction to ontology engineering in the Web Ontology 
Language (OWL). We cover best practices in ontology building and the 
latest Semantic Web technologies, including OWL 2, RDF and SPARQL. We 
also cover topics such as collaborative development, and data access and 
import from different data sources.

Read more about it at:
http://protege.stanford.edu/shortcourse/201803/

If you have any questions about the Prot?g? Short Course, please email 
us at: protege-shortcourse at lists.stanford.edu

Please feel free to forward this announcement to anyone who might be 
interested in the course. Thank you!

We look forward to seeing you at the course!

Best regards,
The Prot?g? Team


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From support at bioontology.org  Thu Nov 30 08:13:07 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 30 Nov 2017 08:13:07 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Nicolas Le Novere
Message-ID: <5a202e1348671_4ea63f9742aade3095719@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Nov 30 12:23:50 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 30 Nov 2017 20:23:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Nicolas Le
	Novere
In-Reply-To: <5a202e1348671_4ea63f9742aade3095719@ncbo-prd-app-08.stanford.edu.mail>
References: <5a202e1348671_4ea63f9742aade3095719@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D067BD6A-CB45-4371-869A-F12C506BF753@stanford.edu>

Hi Nicolas,

Could you be more specific?

I?m looking at KISAO now in my browser and it seems OK:


[cid:1823532D-FDDE-427A-BC37-672E434F3180 at stanford.edu]


Kind regards,
Jennifer


On Nov 30, 2017, at 8:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nicolas Le Novere

Email: n.lenovere at gmail.com<mailto:n.lenovere at gmail.com>

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

Feedback:

Hello,

It seems the access to KiSAO is broken

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