From Sina.Madani at vumc.org  Fri Sep  1 10:29:42 2017
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Fri, 1 Sep 2017 17:29:42 +0000
Subject: [bioontology-support] search by id in a subtree
In-Reply-To: <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
Message-ID: <D5CF07DD.34D68%sina.madani@vanderbilt.edu>

Hi Michael,

Thank you so much for the info. I have a couple of follow up questions:


  1.  I tried to load SNOMED.ttl into our local instance of bioportal appliance (RC2) but after a minute I got "Incomplete response received from application? in my browser. Which log file I need to look at to see what went wrong. The SNOMED.ttl file was provided to me previously and I believe it?s a product of UMLS2RDF script
  2.  When tried to add a new ontology to the appliance, in the drop down format, I saw UMLS. How does it work? Does it transform UMLS RRF files directly into the bioportal appliance? My understanding is that we need to use UMLS2RDF script externally and load the result file into the bioportal appliance.
  3.  Is there anyway to included obsolete/retired concepts in the output ttl file when using UMLS2RDF script?  If I look for SNOMED concept Dermoid Cyst of Ovary ?119424003?, even when obsolete option is checked in NCBO bioportal, no concept is returned. It would be great if we can find out the status of a SNOEMD concept (active versus inactive). It would be even better to see the additional metadata for this retired concept from ref sets like ?Possibly equivalent to? ?Benign teratoma of Ovary?.
  4.  Could you please show how to use an apikey in one of your examples below? It seems the syntax has been changed since few years ago.


Thanks !

Sina

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Thursday, August 31, 2017 at 5:38 PM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree

Hi Sina,

I am not sure which one of the two interpretations you are asking about:

1. Determine whether a term with a given id is located within a specific subtree. If that?s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=Djid4IeYolSffvWdNQN0t3ArG2gyknqpLr1mJ%2FZ%2B%2B0Y%3D&reserved=0> in a subtree of the term ?Asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=1v21JOokiz1RqMv8T%2F8c%2ByvSiVUtinbCyQ9Sqp8YqjE%3D&reserved=0>:

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fq%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002%26ontology%3DSNOMEDCT%26subtree_root_id%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=4%2BdwosGLQUm2EtM6y3hgEngHrF4iW6EqwyZwxDDO%2BdM%3D&reserved=0>

OR

2. Get ALL the descendants (direct/indirect) of a given term (?Asthma?). In this case, the call would be:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001%2Ftree&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=5egh6wZ81Ymp7SHFkAflQCM%2B0HoEsEm7rt0Q4pcV%2BJg%3D&reserved=0>

Let me know if this helps.

Thank you for keeping in touch with us!

Michael


On Aug 29, 2017, at 12:26 PM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children?

Thanks!
Sina
_______________________________________________
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From mdorf at stanford.edu  Fri Sep  1 11:33:56 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 1 Sep 2017 18:33:56 +0000
Subject: [bioontology-support] question on ontology
In-Reply-To: <tencent_21F7A4CD067044F95445EE37@qq.com>
References: <tencent_21F7A4CD067044F95445EE37@qq.com>
Message-ID: <D13B5EA2-DA4B-4406-8E2E-B380A2FB7A61@stanford.edu>

Hi ??,

Thank you for contacting us. Unfortunately, I am not able to provide answers to your questions. This support list is focused around addressing questions / issues with the BioPortal software, and/or parsing issues that arise when ontologies are submitted. You might want to consider contacting the authors of the LOINC ontology (their contact information is listed on the ontology summary page [1]), as they may have ideas about how to extend their ontology, or create a related one.

Thanks,
Michael

[1] http://bioportal.bioontology.org/ontologies/LOINC
______________________________________________


On Aug 31, 2017, at 4:58 AM, ?? <1431288072 at qq.com<mailto:1431288072 at qq.com>> wrote:

I have a question about the LOINC ontology document.  Why it has so much individuals,that is ,why not using classes only like other ontologies such as HPO.

And if I want to build a chinese loinc based the translation, what should I do? what format should I use? Looking forward any suggestions.Thanks so much.
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From mdorf at stanford.edu  Fri Sep  1 11:54:52 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 1 Sep 2017 18:54:52 +0000
Subject: [bioontology-support] search by id in a subtree
In-Reply-To: <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
 <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
Message-ID: <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>

Please see answers inline.

Thanks!

Michael


On Sep 1, 2017, at 10:29 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi Michael,

Thank you so much for the info. I have a couple of follow up questions:


  1.  I tried to load SNOMED.ttl into our local instance of bioportal appliance (RC2) but after a minute I got "Incomplete response received from application? in my browser. Which log file I need to look at to see what went wrong. The SNOMED.ttl file was provided to me previously and I believe it?s a product of UMLS2RDF script

The parsing log file should be located in the repository directory for that ontology/submission number. Usually, that structure is:

/srv/ncbo/repository/SNOMEDCT/5/parsing.log

If the submission itself has not made it through, you can check the REST server log, located in:

/srv/ncbo/ontologies_api/shared/log

My sysadmin tells me that by default that log is not enabled. You need to edit this file:

/srv/ncbo/ontologies_api/current/config/unicorn.rb

And uncomment these lines:

#stderr_path 'log/unicorn.stderr.log'
#stdout_path 'log/unicorn.stdout.log'

  1.  When tried to add a new ontology to the appliance, in the drop down format, I saw UMLS. How does it work? Does it transform UMLS RRF files directly into the bioportal appliance? My understanding is that we need to use UMLS2RDF script externally and load the result file into the bioportal appliance.

As far as I am aware, ALL UMLS ontologies in our repository are imported directly from the source in a bulk job that we run periodically via the UMLS2RDF script. I am not sure whether the appliance would be able to handle the RRF files via a straight submission.

  1.  Is there anyway to included obsolete/retired concepts in the output ttl file when using UMLS2RDF script?  If I look for SNOMED concept Dermoid Cyst of Ovary ?119424003?, even when obsolete option is checked in NCBO bioportal, no concept is returned. It would be great if we can find out the status of a SNOEMD concept (active versus inactive). It would be even better to see the additional metadata for this retired concept from ref sets like ?Possibly equivalent to? ?Benign teratoma of Ovary?.

Another developer on the team who is no longer with us had written the original UMLS2RDF script. Sorry I can?t offer much assistance with this question. If I were dealing with the same issue, I?d probably try to find the relevant lines in the python script and modify them to see if they produce the effect you are seeking:

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py

  1.  Could you please show how to use an apikey in one of your examples below? It seems the syntax has been changed since few years ago.

You can pass the API key either via the ?apikey=<yourapikey> request parameter or via the Authorization var in the headers:

Key: Authorization
Value: apikey token=<yourapikey>

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&apikey=yourapikey<http://data.bioontology.org/search?q=http://purl.bioontology.org/ontology/SNOMEDCT/707512002&ontology=SNOMEDCT&subtree_root_id=http://purl.bioontology.org/ontology/SNOMEDCT/195967001&apikey=yourapikey>


Thanks !

Sina

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Thursday, August 31, 2017 at 5:38 PM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree

Hi Sina,

I am not sure which one of the two interpretations you are asking about:

1. Determine whether a term with a given id is located within a specific subtree. If that?s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=Djid4IeYolSffvWdNQN0t3ArG2gyknqpLr1mJ%2FZ%2B%2B0Y%3D&reserved=0> in a subtree of the term ?Asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=1v21JOokiz1RqMv8T%2F8c%2ByvSiVUtinbCyQ9Sqp8YqjE%3D&reserved=0>:

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fq%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002%26ontology%3DSNOMEDCT%26subtree_root_id%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=4%2BdwosGLQUm2EtM6y3hgEngHrF4iW6EqwyZwxDDO%2BdM%3D&reserved=0>

OR

2. Get ALL the descendants (direct/indirect) of a given term (?Asthma?). In this case, the call would be:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001%2Ftree&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=5egh6wZ81Ymp7SHFkAflQCM%2B0HoEsEm7rt0Q4pcV%2BJg%3D&reserved=0>

Let me know if this helps.

Thank you for keeping in touch with us!

Michael


On Aug 29, 2017, at 12:26 PM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children?

Thanks!
Sina
_______________________________________________
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 Sep  1 15:27:59 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 1 Sep 2017 22:27:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from michelle
In-Reply-To: <59a87d6874100_62873fb74319a4f8149dc@ncbo-prd-app-09.stanford.edu.mail>
References: <59a87d6874100_62873fb74319a4f8149dc@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <967DD03F-EED6-425C-B6CD-DC3F7A15B76F@stanford.edu>

Hi Michelle,

Thank you for reporting this to us. Unfortunately, this is a known issue with the BioPortal backend parsing mechanism that is unable to correctly identify and mark root classes in SKOS ontologies. This issue is tracked here:

https://github.com/ncbo/ontologies_linked_data/issues/82

and here:

https://github.com/ncbo/bioportal-project/issues/36

The reason you are seeing search results from this ontology in CEDAR is that this bug specifically affects the root classes endpoint:

http://data.bioontology.org/ontologies/FAST-EVENT-SKOS/classes/roots (returns an empty set)

All other endpoints for the ontology, including the search, are functional:

http://data.bioontology.org/search?q=new%20deal&ontologies=FAST-EVENT-SKOS

We?ll try to prioritize fixing this issue in a timely manner. Please, check the Github links above for the latest status of our progress.

Thank you,

Michael


On Aug 31, 2017, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

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

Feedback:

submitted FAST-EVENT-SKOS which per its publisher is a SKOS file (http://experimental.worldcat.org/fast/). It has over 15,000 individuals. When I go to Classes tab in BioPortal, I get "problem retrieving classes". When I use FAST-EVENT-SKOS in CEDAR to constrain values of a field, I can search for terms. And when I populate the template, I see a dropdown of terms. But in both cases only about 20 terms (out of ~15,000) appear. I've shared the CEDAR template, called "test", with CEDAR dev team group

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From support at bioontology.org  Tue Sep  5 09:01:49 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 05 Sep 2017 09:01:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from William Lau
Message-ID: <59aeca6dcbdaf_57883f85f82fa7e8248f9@ncbo-prd-app-09.stanford.edu.mail>

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From malobaid at oakland.edu  Tue Sep  5 09:49:41 2017
From: malobaid at oakland.edu (Mazen Alobaidi)
Date: Tue, 5 Sep 2017 12:49:41 -0400
Subject: [bioontology-support] ontologies filter
Message-ID: <CAG9cnoBBJv0KkDFC=NkDR2Oabty9FQhBmFkjUSQiXkUc185msg@mail.gmail.com>

Hi,
I'm using rest call as below, but I want to restricted it with only using
MESH.  How I can do this?

http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye
.

if used the filter ontology  I get the below error in rest call using Java

java.io.FileNotFoundException:
http://data.bioontology.org/annotator?ontologies=MESH&longest_only=false&exclude_numbers=false&whole_word_only=false&exclude_synonyms=false&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which%2Bare+found+predominantly+in+skin+but+also+in+the+bowel+and+the%2Beye
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown
Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown
Source)
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From vendetti at stanford.edu  Tue Sep  5 10:23:29 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 5 Sep 2017 17:23:29 +0000
Subject: [bioontology-support] [BioPortal] Feedback from William Lau
In-Reply-To: <59aeca6dcbdaf_57883f85f82fa7e8248f9@ncbo-prd-app-09.stanford.edu.mail>
References: <59aeca6dcbdaf_57883f85f82fa7e8248f9@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <0612EC27-CCD7-40E0-8D98-06F317F8EE59@stanford.edu>

Hello William,

Apologies, but I?m not able to reproduce that behavior at the moment. Issuing the same REST call on my end shows 582 results:


[cid:C5424A95-59F0-44F1-8A6B-963AA6E9098A at hsd1.ca.comcast.net]


Are you still experiencing this issue?

Kind regards,
Jennifer



On Sep 5, 2017, at 9:01 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: William Lau

Email: william.lau at nih.gov<mailto:william.lau at nih.gov>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMESH%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FMESH%252FC565039

Feedback:

For the REST API search feature, seems like there is a problem with specifying the ontologies to search against:
http://data.bioontology.org/search?q=melanoma&ontologies=NCIT

It used to work, but now complains about: The ontologies parameter `[NCIT]` includes non-existent acronyms. Notice that acronyms are case sensitive.

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From vendetti at stanford.edu  Tue Sep  5 10:34:36 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 5 Sep 2017 17:34:36 +0000
Subject: [bioontology-support] ontologies filter
In-Reply-To: <CAG9cnoBBJv0KkDFC=NkDR2Oabty9FQhBmFkjUSQiXkUc185msg@mail.gmail.com>
References: <CAG9cnoBBJv0KkDFC=NkDR2Oabty9FQhBmFkjUSQiXkUc185msg@mail.gmail.com>
Message-ID: <736C6DAB-4284-4D8C-B6F2-2DBAB9AC0DBA@stanford.edu>

Hello Mazen,

On Sep 5, 2017, at 9:49 AM, Mazen Alobaidi <malobaid at oakland.edu<mailto:malobaid at oakland.edu>> wrote:

Hi,
I'm using rest call as below, but I want to restricted it with only using MESH.  How I can do this?

http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.


To restrict search to a particular ontology, you use the ?ontologies? parameter, as documented here:

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




if used the filter ontology  I get the below error in rest call using Java

java.io.FileNotFoundException: http://data.bioontology.org/annotator?ontologies=MESH&longest_only=false&exclude_numbers=false&whole_word_only=false&exclude_synonyms=false&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which%2Bare+found+predominantly+in+skin+but+also+in+the+bowel+and+the%2Beye
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)


Without seeing your Java code, it?s difficult to say what?s going wrong. You used the ?ontologies? parameter correctly (i.e. ontologies=MESH). Also, entering the above URL in a browser correctly returns results from the annotator endpoint. So, the URL doesn?t appear to be malformed in any way.

A Java error like this was reported on our mailing list previously. You may want to read the post in the archive and see if the suggested solution works for you:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-java-io-FileNotFoundException-http-data-bioontology-org-ontologies-NCIT-classes-9-td4652641.html

Kind regards,
Jennifer

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From lauwill at mail.nih.gov  Tue Sep  5 10:35:46 2017
From: lauwill at mail.nih.gov (Lau, William (NIH/CIT) [E])
Date: Tue, 5 Sep 2017 17:35:46 +0000
Subject: [bioontology-support] [BioPortal] Feedback from William Lau
In-Reply-To: <0612EC27-CCD7-40E0-8D98-06F317F8EE59@stanford.edu>
References: <59aeca6dcbdaf_57883f85f82fa7e8248f9@ncbo-prd-app-09.stanford.edu.mail>
 <0612EC27-CCD7-40E0-8D98-06F317F8EE59@stanford.edu>
Message-ID: <DM5PR09MB1819C11387A5DE6F470B6FE584960@DM5PR09MB1819.namprd09.prod.outlook.com>

Thanks for your response. I just tried the same call again and it works now.

Thanks,
William

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 05, 2017 1:23 PM
To: support at bioontology.org
Cc: Lau, William (NIH/CIT) [E] <lauwill at mail.nih.gov>
Subject: Re: [bioontology-support] [BioPortal] Feedback from William Lau

Hello William,

Apologies, but I?m not able to reproduce that behavior at the moment. Issuing the same REST call on my end shows 582 results:


[cid:image001.png at 01D3264B.E07B3550]


Are you still experiencing this issue?

Kind regards,
Jennifer



On Sep 5, 2017, at 9:01 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: William Lau
Email: william.lau at nih.gov<mailto:william.lau at nih.gov>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMESH%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FMESH%252FC565039

Feedback:
For the REST API search feature, seems like there is a problem with specifying the ontologies to search against:
http://data.bioontology.org/search?q=melanoma&ontologies=NCIT
It used to work, but now complains about: The ontologies parameter `[NCIT]` includes non-existent acronyms. Notice that acronyms are case sensitive.

_______________________________________________
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 Sina.Madani at vumc.org  Wed Sep  6 08:24:47 2017
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Wed, 6 Sep 2017 15:24:47 +0000
Subject: [bioontology-support] search by id in a subtree
In-Reply-To: <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
 <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
 <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>
Message-ID: <103B3C18EAB4F444A941714214A04B81592E1386@ITS-HCWNEM105.ds.vanderbilt.edu>

Hi Michael,

I was able to upload RxNorm and LOINC (downloaded from NCBO site) into our local instance without any error. However, it seems processing doesn?t start automatically. The instruction for manual processing is not working either. http://localinstnace/admin page also doesn?t show the uploaded ontologies so that I can trigger ?process? from the drop down selected action. The UI under each ontology submission shows ?uploaded?.
Which log file I need to look at to pin point the issue? Attached are the parsing log files from the 2 repositories and ncbo_cron log scheduler.

Thanks!

Sina

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Friday, September 01, 2017 2:55 PM
To: Madani, Sina
Cc: support at bioontology.org
Subject: Re: [bioontology-support] search by id in a subtree

Please see answers inline.

Thanks!

Michael


On Sep 1, 2017, at 10:29 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi Michael,

Thank you so much for the info. I have a couple of follow up questions:


  1.  I tried to load SNOMED.ttl into our local instance of bioportal appliance (RC2) but after a minute I got "Incomplete response received from application? in my browser. Which log file I need to look at to see what went wrong. The SNOMED.ttl file was provided to me previously and I believe it?s a product of UMLS2RDF script
The parsing log file should be located in the repository directory for that ontology/submission number. Usually, that structure is:

/srv/ncbo/repository/SNOMEDCT/5/parsing.log

If the submission itself has not made it through, you can check the REST server log, located in:

/srv/ncbo/ontologies_api/shared/log

My sysadmin tells me that by default that log is not enabled. You need to edit this file:

/srv/ncbo/ontologies_api/current/config/unicorn.rb

And uncomment these lines:

#stderr_path 'log/unicorn.stderr.log'
#stdout_path 'log/unicorn.stdout.log'

  1.  When tried to add a new ontology to the appliance, in the drop down format, I saw UMLS. How does it work? Does it transform UMLS RRF files directly into the bioportal appliance? My understanding is that we need to use UMLS2RDF script externally and load the result file into the bioportal appliance.
As far as I am aware, ALL UMLS ontologies in our repository are imported directly from the source in a bulk job that we run periodically via the UMLS2RDF script. I am not sure whether the appliance would be able to handle the RRF files via a straight submission.

  1.  Is there anyway to included obsolete/retired concepts in the output ttl file when using UMLS2RDF script?  If I look for SNOMED concept Dermoid Cyst of Ovary ?119424003?, even when obsolete option is checked in NCBO bioportal, no concept is returned. It would be great if we can find out the status of a SNOEMD concept (active versus inactive). It would be even better to see the additional metadata for this retired concept from ref sets like ?Possibly equivalent to? ?Benign teratoma of Ovary?.
Another developer on the team who is no longer with us had written the original UMLS2RDF script. Sorry I can?t offer much assistance with this question. If I were dealing with the same issue, I?d probably try to find the relevant lines in the python script and modify them to see if they produce the effect you are seeking:

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fumls2rdf%2Fblob%2Fmaster%2Fumls2rdf.py&data=02%7C01%7CSina.Madani%40vumc.org%7C8189b294e8d048e596de08d4f16af0e5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398888992007829&sdata=49D2ZZ7sFUng7EfshrXwh3is0xnC6XlTiVFFzgrhnBE%3D&reserved=0>

  1.  Could you please show how to use an apikey in one of your examples below? It seems the syntax has been changed since few years ago.
You can pass the API key either via the ?apikey=<yourapikey> request parameter or via the Authorization var in the headers:

Key: Authorization
Value: apikey token=<yourapikey>

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&apikey=yourapikey<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fq%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002%26ontology%3DSNOMEDCT%26subtree_root_id%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001%26apikey%3Dyourapikey&data=02%7C01%7CSina.Madani%40vumc.org%7C8189b294e8d048e596de08d4f16af0e5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398888992007829&sdata=pBWp7V7W3XRRv%2FJ16%2BlXBv9kvPKe%2BV0h586hpE0wJJk%3D&reserved=0>



Thanks !

Sina

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Thursday, August 31, 2017 at 5:38 PM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree

Hi Sina,

I am not sure which one of the two interpretations you are asking about:

1. Determine whether a term with a given id is located within a specific subtree. If that?s the case, yes, you should be able to do this. Here is an example that searches for the term "Uncomplicated moderate persistent asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/707512002<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=Djid4IeYolSffvWdNQN0t3ArG2gyknqpLr1mJ%2FZ%2B%2B0Y%3D&reserved=0> in a subtree of the term ?Asthma?, id = http://purl.bioontology.org/ontology/SNOMEDCT/195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=1v21JOokiz1RqMv8T%2F8c%2ByvSiVUtinbCyQ9Sqp8YqjE%3D&reserved=0>:

http://data.bioontology.org/search?q=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002&ontology=SNOMEDCT&subtree_root_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fq%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F707512002%26ontology%3DSNOMEDCT%26subtree_root_id%3Dhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=4%2BdwosGLQUm2EtM6y3hgEngHrF4iW6EqwyZwxDDO%2BdM%3D&reserved=0>

OR

2. Get ALL the descendants (direct/indirect) of a given term (?Asthma?). In this case, the call would be:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001/tree<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F195967001%2Ftree&data=02%7C01%7CSina.Madani%40vumc.org%7C2644df805915449cfd4708d4f0b8a267%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398123172117321&sdata=5egh6wZ81Ymp7SHFkAflQCM%2B0HoEsEm7rt0Q4pcV%2BJg%3D&reserved=0>

Let me know if this helps.

Thank you for keeping in touch with us!

Michael


On Aug 29, 2017, at 12:26 PM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

Would it be possible to use Restful services to search by id under a given subtree (like SNOMED Asthma) for all direct and indirect children?

Thanks!
Sina
_______________________________________________
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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7CSina.Madani%40vumc.org%7C8189b294e8d048e596de08d4f16af0e5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636398888992007829&sdata=xZAKEhPsT3R9RoDKhNXIMy1BMTkErQLZ%2Bh3CMH0lefI%3D&reserved=0>

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From pouchard at bnl.gov  Wed Sep  6 07:57:57 2017
From: pouchard at bnl.gov (Pouchard, Line)
Date: Wed, 6 Sep 2017 14:57:57 +0000
Subject: [bioontology-support] Enabling cron job in VA
Message-ID: <46F1E5E6-5762-463C-A7F6-64586D48254C@bnl.gov>

Dear all:

Can you please send directions on how to enable a cron job for automatic update of ontologies in the Virtual Appliance?

Line

?
Line Pouchard
Computational Science Initiative
Brookhaven National Laboratory
Building 725, room 2-189
PO Box 5000
Upton, New York, 11973-5000
ORCID:0000-0002-2120-6521
Phone 631 344-4626
Cell 865 405-5120
http://www.bnl.gov/compsci

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From vendetti at stanford.edu  Wed Sep  6 10:34:03 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 6 Sep 2017 17:34:03 +0000
Subject: [bioontology-support] Enabling cron job in VA
In-Reply-To: <46F1E5E6-5762-463C-A7F6-64586D48254C@bnl.gov>
References: <46F1E5E6-5762-463C-A7F6-64586D48254C@bnl.gov>
Message-ID: <D0162880-2A04-4FEB-8168-BBE3A9FE7E53@stanford.edu>

Hello Line,


On Sep 6, 2017, at 7:57 AM, Pouchard, Line <pouchard at bnl.gov<mailto:pouchard at bnl.gov>> wrote:

Dear all:

Can you please send directions on how to enable a cron job for automatic update of ontologies in the Virtual Appliance?


I?m not sure I understand exactly what you?re asking. The BioPortal Virtual Appliance comes with a project called ncbo_cron that contains a background task that checks the ontology parsing queue for new ontologies every 5 minutes. If you add a new ontology submission, the parsing process should begin within 5 minutes. The ncbo_cron background task is automatically launched when you install the Virtual Appliance, so there shouldn?t be any additional steps necessary on your part.

Or, perhaps you?re referring to the desire to enter a URL for an ontology that?s checked nightly for new submissions? If so, this is something you configure yourself when you add a new ontology submission. On any ontology summary page, you can click the "Add submission" link, and enter such a pull URL in the Location section of the resulting form:


[cid:BC9811AA-3FF7-4FA6-957A-20843FCC571F at hsd1.ca.comcast.net]


Choose the ?Load from URL? radio button, and enter the URL that points to your ontology source file. Once you?ve filled out this form and click the ?Add submission? button, the Virtual Appliance will pull the initial version of your ontology from that URL, and it will also begin checking on a nightly basis for new versions. If a new version is detected, it will automatically get downloaded/processed.

Hope that helps.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Wed Sep  6 12:51:42 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 6 Sep 2017 19:51:42 +0000
Subject: [bioontology-support] Virtual Appliance ontology loading
 questions [WAS: search by id in a subtree]
In-Reply-To: <103B3C18EAB4F444A941714214A04B81592E1386@ITS-HCWNEM105.ds.vanderbilt.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
 <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
 <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>
 <103B3C18EAB4F444A941714214A04B81592E1386@ITS-HCWNEM105.ds.vanderbilt.edu>
Message-ID: <DD6742C8-FD3E-4DDD-86F4-18030B3C61C5@stanford.edu>

Hello Sina,


On Sep 6, 2017, at 8:24 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

I was able to upload RxNorm and LOINC (downloaded from NCBO site) into our local instance without any error. However, it seems processing doesn?t start automatically.


I looked at the contents of the scheduler.log file you sent and saw two sections indicating that RxNorm and LOINC processing was initiated:

LOINC parsing:

I, [2017-09-05T07:56:58.495982 #3285]  INFO -- : Starting ontology process queue check
I, [2017-09-05T07:57:07.410794 #3285]  INFO -- : Logging parsing output to /srv/ncbo/repository/LOINC/1/parsing.log
I, [2017-09-05T07:57:07.418516 #3285]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/LOINC/submissions/1"]
I, [2017-09-05T07:57:07.860300 #3285]  INFO -- : ["Starting to process LOINC/submissions/1"]
I, [2017-09-05T07:57:08.862298 #3285]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse?]

RXNORM parsing:

I, [2017-09-05T09:56:48.083438 #4033]  INFO -- : Starting ontology process queue check
I, [2017-09-05T09:56:51.196790 #4033]  INFO -- : Logging parsing output to /srv/ncbo/repository/RXNORM/1/parsing.log
I, [2017-09-05T09:56:51.203966 #4033]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/RXNORM/submissions/1"]
I, [2017-09-05T09:56:51.732885 #4033]  INFO -- : ["Starting to process RXNORM/submissions/1"]
I, [2017-09-05T09:56:52.791871 #4033]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse?]

Note that the ncbo_cron process checks the ontology parsing queue every 5 minutes, so there may be a small delay between when you create a new ontology submission and the time when parsing begins. The line that says ?skipping OWLAPI parse? simply means that a UMLS TTL file was detected and it wasn?t necessary to feed this particular ontology file through the OWL API. The OWL API is 3rd party software that we use internally to parse all ontologies submitted to BioPortal, with the exception of the set of UMLS ontologies that we import twice per year from the National Library of Medicine.


The instruction for manual processing is not working either. http://localinstnace/admin page also doesn?t show the uploaded ontologies so that I can trigger ?process? from the drop down selected action.


The contents of the Admin page are created from an ontology report that?s generated on a nightly basis, which is why you don?t see your new submissions there.

What happens when you issue a REST API call to retrieve the classes for LOINC or RxNorm? Are you seeing any data? Example query:

http://{ip_address_of_your_appliance}:8080/ontologies/LOINC/classes


The UI under each ontology submission shows ?uploaded?.


If you see that the REST endpoint is returning data, but the UI still only shows the Uploaded status, you may need to clear the caches. There are buttons to clear the caches on the Admin page (you can click all 4 to clear all of the various application caches). Note that only users with administrative privileges can access the Admin page that you refer to above. After clearing the caches, when you return to any ontology summary page, you should also refresh the browser page using the key combination to clear the cache memory (e.g., Apple + R on a Mac).

Kind regards,
Jennifer

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From pouchard at bnl.gov  Wed Sep  6 13:53:08 2017
From: pouchard at bnl.gov (Pouchard, Line)
Date: Wed, 6 Sep 2017 20:53:08 +0000
Subject: [bioontology-support] Enabling cron job in VA
In-Reply-To: <D0162880-2A04-4FEB-8168-BBE3A9FE7E53@stanford.edu>
References: <46F1E5E6-5762-463C-A7F6-64586D48254C@bnl.gov>
 <D0162880-2A04-4FEB-8168-BBE3A9FE7E53@stanford.edu>
Message-ID: <32B551F1-C2BA-4E64-BB78-BE397B0C3E41@bnl.gov>

Jennifer:

thank you.  This helps.
Line

?
Line Pouchard
Computational Science Initiative
Brookhaven National Laboratory
Building 725, room 2-189
PO Box 5000
Upton, New York, 11973-5000
ORCID:0000-0002-2120-6521
Phone 631 344-4626
Cell 865 405-5120
http://www.bnl.gov/compsci


From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Wednesday, September 6, 2017 at 1:34 PM
To: "Pouchard, Line" <pouchard at bnl.gov>
Cc: "support at bioontology.org" <support at bioontology.org>, John Graybeal <jgraybeal at stanford.edu>
Subject: Re: [bioontology-support] Enabling cron job in VA

Hello Line,


On Sep 6, 2017, at 7:57 AM, Pouchard, Line <pouchard at bnl.gov<mailto:pouchard at bnl.gov>> wrote:

Dear all:

Can you please send directions on how to enable a cron job for automatic update of ontologies in the Virtual Appliance?


I?m not sure I understand exactly what you?re asking. The BioPortal Virtual Appliance comes with a project called ncbo_cron that contains a background task that checks the ontology parsing queue for new ontologies every 5 minutes. If you add a new ontology submission, the parsing process should begin within 5 minutes. The ncbo_cron background task is automatically launched when you install the Virtual Appliance, so there shouldn?t be any additional steps necessary on your part.

Or, perhaps you?re referring to the desire to enter a URL for an ontology that?s checked nightly for new submissions? If so, this is something you configure yourself when you add a new ontology submission. On any ontology summary page, you can click the "Add submission" link, and enter such a pull URL in the Location section of the resulting form:


[cid:image001.png at 01D32730.9DCABF60]


Choose the ?Load from URL? radio button, and enter the URL that points to your ontology source file. Once you?ve filled out this form and click the ?Add submission? button, the Virtual Appliance will pull the initial version of your ontology from that URL, and it will also begin checking on a nightly basis for new versions. If a new version is detected, it will automatically get downloaded/processed.

Hope that helps.

Kind regards,
Jennifer

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From Sina.Madani at vumc.org  Thu Sep  7 10:06:33 2017
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Thu, 7 Sep 2017 17:06:33 +0000
Subject: [bioontology-support] Virtual Appliance ontology loading
 questions [WAS: search by id in a subtree]
In-Reply-To: <DD6742C8-FD3E-4DDD-86F4-18030B3C61C5@stanford.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
 <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
 <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>
 <103B3C18EAB4F444A941714214A04B81592E1386@ITS-HCWNEM105.ds.vanderbilt.edu>
 <DD6742C8-FD3E-4DDD-86F4-18030B3C61C5@stanford.edu>
Message-ID: <103B3C18EAB4F444A941714214A04B81592E1C0F@ITS-HCWNEM105.ds.vanderbilt.edu>

Thank you very much Jennifer for the explanation.
It turned out the Audio module of the Virtual machine was causing the instance to pause and go into hibernation. After I disabled that module the appliance started parsing ontologies immediately.
I tested loading and parsing LOINC and RxNorm so far and everything seems fine. However, both terminology names are showing as ?unknown? under submission section. I only filled out the mandatory fields though.
Also, I guess the current UMLS2RDF does not include obsolete concepts so there is no function in the API to query for the status of a given concepts. Is that right? Do you have any suggestion/workaround for us?

Thanks!
Sina

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Wednesday, September 06, 2017 3:52 PM
To: Madani, Sina
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Virtual Appliance ontology loading questions [WAS: search by id in a subtree]

Hello Sina,


On Sep 6, 2017, at 8:24 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

I was able to upload RxNorm and LOINC (downloaded from NCBO site) into our local instance without any error. However, it seems processing doesn?t start automatically.


I looked at the contents of the scheduler.log file you sent and saw two sections indicating that RxNorm and LOINC processing was initiated:

LOINC parsing:

I, [2017-09-05T07:56:58.495982 #3285]  INFO -- : Starting ontology process queue check
I, [2017-09-05T07:57:07.410794 #3285]  INFO -- : Logging parsing output to /srv/ncbo/repository/LOINC/1/parsing.log
I, [2017-09-05T07:57:07.418516 #3285]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/LOINC/submissions/1<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FLOINC%2Fsubmissions%2F1&data=02%7C01%7CSina.Madani%40vumc.org%7C54ca8d4842914805a6bd08d4f560b636%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636403243106615828&sdata=F7xCr0uwPUIhDIS9f5QWdj7XarsgUIG5vGguArST6Dk%3D&reserved=0>"]
I, [2017-09-05T07:57:07.860300 #3285]  INFO -- : ["Starting to process LOINC/submissions/1"]
I, [2017-09-05T07:57:08.862298 #3285]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse?]

RXNORM parsing:

I, [2017-09-05T09:56:48.083438 #4033]  INFO -- : Starting ontology process queue check
I, [2017-09-05T09:56:51.196790 #4033]  INFO -- : Logging parsing output to /srv/ncbo/repository/RXNORM/1/parsing.log
I, [2017-09-05T09:56:51.203966 #4033]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/RXNORM/submissions/1<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FRXNORM%2Fsubmissions%2F1&data=02%7C01%7CSina.Madani%40vumc.org%7C54ca8d4842914805a6bd08d4f560b636%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636403243106615828&sdata=fguNqeQDKplR1hpdtKBZXpqtZHIB3%2FkkhCcRACEiFfw%3D&reserved=0>"]
I, [2017-09-05T09:56:51.732885 #4033]  INFO -- : ["Starting to process RXNORM/submissions/1"]
I, [2017-09-05T09:56:52.791871 #4033]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse?]

Note that the ncbo_cron process checks the ontology parsing queue every 5 minutes, so there may be a small delay between when you create a new ontology submission and the time when parsing begins. The line that says ?skipping OWLAPI parse? simply means that a UMLS TTL file was detected and it wasn?t necessary to feed this particular ontology file through the OWL API. The OWL API is 3rd party software that we use internally to parse all ontologies submitted to BioPortal, with the exception of the set of UMLS ontologies that we import twice per year from the National Library of Medicine.



The instruction for manual processing is not working either. http://localinstnace/admin page also doesn?t show the uploaded ontologies so that I can trigger ?process? from the drop down selected action.


The contents of the Admin page are created from an ontology report that?s generated on a nightly basis, which is why you don?t see your new submissions there.

What happens when you issue a REST API call to retrieve the classes for LOINC or RxNorm? Are you seeing any data? Example query:

http://{ip_address_of_your_appliance}:8080/ontologies/LOINC/classes<http://%7bip_address_of_your_appliance%7d:8080/ontologies/LOINC/classes>



The UI under each ontology submission shows ?uploaded?.


If you see that the REST endpoint is returning data, but the UI still only shows the Uploaded status, you may need to clear the caches. There are buttons to clear the caches on the Admin page (you can click all 4 to clear all of the various application caches). Note that only users with administrative privileges can access the Admin page that you refer to above. After clearing the caches, when you return to any ontology summary page, you should also refresh the browser page using the key combination to clear the cache memory (e.g., Apple + R on a Mac).

Kind regards,
Jennifer

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From vendetti at stanford.edu  Thu Sep  7 11:35:14 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 7 Sep 2017 18:35:14 +0000
Subject: [bioontology-support] Virtual Appliance ontology loading
 questions [WAS: search by id in a subtree]
In-Reply-To: <103B3C18EAB4F444A941714214A04B81592E1C0F@ITS-HCWNEM105.ds.vanderbilt.edu>
References: <D5CB2A1F.34C0D%sina.madani@vanderbilt.edu>
 <0CE320FB-BFF3-45A4-A337-6031345FCCA9@stanford.edu>
 <D5CF07DD.34D68%sina.madani@vanderbilt.edu>
 <3DAC0952-315B-4386-99C5-F329B0B1BBF7@stanford.edu>
 <103B3C18EAB4F444A941714214A04B81592E1386@ITS-HCWNEM105.ds.vanderbilt.edu>
 <DD6742C8-FD3E-4DDD-86F4-18030B3C61C5@stanford.edu>
 <103B3C18EAB4F444A941714214A04B81592E1C0F@ITS-HCWNEM105.ds.vanderbilt.edu>
Message-ID: <16B43B92-9723-4BBA-BAE3-8948F105312A@stanford.edu>

Hello Sina,


On Sep 7, 2017, at 10:06 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Thank you very much Jennifer for the explanation.
It turned out the Audio module of the Virtual machine was causing the instance to pause and go into hibernation. After I disabled that module the appliance started parsing ontologies immediately.
I tested loading and parsing LOINC and RxNorm so far and everything seems fine. However, both terminology names are showing as ?unknown? under submission section. I only filled out the mandatory fields though.


If you want the UI to display a version number, you can go to any ontology summary page, click the ?Edit submission information? link, enter a value in the ?VERSION? field, and click the Save submission button.



Also, I guess the current UMLS2RDF does not include obsolete concepts so there is no function in the API to query for the status of a given concepts. Is that right? Do you have any suggestion/workaround for us?


I?m not sure I?m following your question. Could you give me an example of a concept you know to be obsolete that isn?t being displayed in BioPortal?

Also, if you issue a REST call against the classes endpoint using the ?include=all? parameter, the API will show whether or not a concept is obsolete, as well as a list of all properties with their values. Here?s an example of a REST call to retrieve the ?Surveys? class from LOINC:

http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FMTHU000004?include=all<http://data.bioontology.org/ontologies/LOINC/classes/http://purl.bioontology.org/ontology/LNC/MTHU000004?include=all>

? and a screen shot of the result:


[cid:DE7C4F51-302F-4AB6-9353-D9198C23CF0F at stanford.edu]

Is the information you?re looking for contained in this result?

Kind regards,
Jennifer

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From support at bioontology.org  Thu Sep  7 13:03:42 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 07 Sep 2017 13:03:42 -0700
Subject: [bioontology-support] [BioPortal] Feedback from marcibowen
Message-ID: <59b1a61eba26a_6ebc3f98b90592e065913@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Sep  7 15:12:52 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 7 Sep 2017 22:12:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from marcibowen
In-Reply-To: <59b1a61eba26a_6ebc3f98b90592e065913@ncbo-prd-app-09.stanford.edu.mail>
References: <59b1a61eba26a_6ebc3f98b90592e065913@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <2F5D6664-EB4C-45DB-ABFA-F9F4A1C30C34@stanford.edu>

Apologies Marci, but I?m not sure what you?re asking. Could you send the REST API call that you?re using? Also, what property are you referring to when you say ?code??

Kind regards,
Jennifer


On Sep 7, 2017, at 1:03 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: marcibowen

Email: marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>

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

Feedback:

When using the api when I submit 'seizure" I only get 50 SNOMED Codes, but when I go to the web portal (http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=root) I get 325 SNOMED codes. How do I fix the api to return 325 SNOMED codes.

Thanks,
Marci Bowen

_______________________________________________
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  Thu Sep  7 18:14:53 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 8 Sep 2017 01:14:53 +0000
Subject: [bioontology-support] [BioPortal] Feedback from marcibowen
In-Reply-To: <BF8A5D24-6E90-4F42-BC31-DE1704670588@duke.edu>
References: <59b1a61eba26a_6ebc3f98b90592e065913@ncbo-prd-app-09.stanford.edu.mail>
 <2F5D6664-EB4C-45DB-ABFA-F9F4A1C30C34@stanford.edu>
 <BF8A5D24-6E90-4F42-BC31-DE1704670588@duke.edu>
Message-ID: <911F91AE-5621-4D42-B6B7-CD1BEDAC084C@stanford.edu>

Hello Marci,

Unfortunately, the screen shot came through very small and is unreadable.

Just to clarify, if I issue this REST call in a browser:

http://data.bioontology.org/search?q=seizure&ontology=SNOMEDCT

The search endpoint returns 925 matches:

[cid:73F808FA-7779-48B3-90C5-BB686411439F at stanford.edu]

I?m guessing you?re referring to the first item in the result set - the term with preferred name ?Seizure? and cui ?C0036572?? I?m also guessing that you want the list of values for the ?Definitional manifestation of? property? I don?t know of a way to get this data via the search endpoint. The only way I?m aware of to retrieve that data is via the classes endpoint. The call looks like this:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F91175000?include=all<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/91175000?include=all>

The portion of the URL after /classes/ is the URL encoded version of the BioPortal class ID for the Seizure class. To follow is a partial screen shot showing that this call will return the list of values for the desired property:

[cid:91B19BDE-55F0-4EEE-BCE0-A4C341080C16 at stanford.edu]



Kind regards,
Jennifer



On Sep 7, 2017, at 3:27 PM, Marci Bowen <marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>> wrote:

The rest api is

free_text = 'seizure'
url = 'http://data.bioontology.org/search?q='
headers = {'Authorization': 'apikey token=a9b1cb5e-9729-40ac-bd13-5596f66ca5a8'}

This is a screen shot of what I am trying to do.
<BioPortal Web Search.png>
On Sep 7, 2017, at 6:12 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Apologies Marci, but I?m not sure what you?re asking. Could you send the REST API call that you?re using? Also, what property are you referring to when you say ?code??

Kind regards,
Jennifer


On Sep 7, 2017, at 1:03 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: marcibowen

Email: marcia.bowen at duke.edu<mailto:marcia.bowen at duke.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=_XpVTJrtr0X0leljtIDRlyodLng6oKbmgmLrhWmENRA&m=428p5FlqrR4aafurPbUzonUx6xH0tl4bDJj0I1zcE3w&s=kNWdD6O4doZTMQd4OW8X-8u65NUkAtTMUeLwScFMRIo&e=>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

When using the api when I submit 'seizure" I only get 50 SNOMED Codes, but when I go to the web portal (http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=root<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_SNOMEDCT-3Fp-3Dclasses-26conceptid-3Droot&d=DwMGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=_XpVTJrtr0X0leljtIDRlyodLng6oKbmgmLrhWmENRA&m=428p5FlqrR4aafurPbUzonUx6xH0tl4bDJj0I1zcE3w&s=9m8TkKKBhityx-fTxZSma3UJZQSgUb5QreOid6st62A&e=>) I get 325 SNOMED codes. How do I fix the api to return 325 SNOMED codes.

Thanks,
Marci Bowen

_______________________________________________
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 mpourrezashahri at montana.edu  Fri Sep  8 16:50:10 2017
From: mpourrezashahri at montana.edu (Pourreza Shahri, Morteza)
Date: Fri, 8 Sep 2017 23:50:10 +0000
Subject: [bioontology-support] NCBO Virtual Appliance Request
Message-ID: <DM5PR02MB2330761D31567F900344685BA6950@DM5PR02MB2330.namprd02.prod.outlook.com>

Dear Support team,


I am Morteza Pourreza Shahri, PhD student in computer science at Montana State University under supervision of Dr. Indika Kahanda (CC'd). We are working on extracting ontology terms from the text. Since there are millions of files, running NCBO in offline mode would be a better solution for our work.


I was wondering if you could provide us with the NCBO Virtual Appliance, so we would be able to run it offline.


Sincerely,

Morteza Pourreza Shahri

PhD Student

Gianforte School of Computing

Montana State University

Bozeman, MT, USA
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From owkata at gmail.com  Sun Sep 10 23:10:01 2017
From: owkata at gmail.com (=?utf-8?Q?=E7=8E=8B=E5=AE=81?=)
Date: Mon, 11 Sep 2017 14:10:01 +0800
Subject: [bioontology-support] I want to try the VMWare Virtual Appliance
Message-ID: <59b628ba.c9896b0a.927d.2863@mx.google.com>

Hi, boss

I want to try the VMWare Virtual Appliance, how can I get it?
Thank you!

BR

Ning

??? Windows 10 ?????

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From jgraybeal at stanford.edu  Mon Sep 11 13:29:25 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 11 Sep 2017 20:29:25 +0000
Subject: [bioontology-support] I want to try the VMWare Virtual Appliance
In-Reply-To: <59b628ba.c9896b0a.927d.2863@mx.google.com>
References: <59b628ba.c9896b0a.927d.2863@mx.google.com>
Message-ID: <4E1932B4-4862-4999-AB2E-10E53B6CECB2@stanford.edu>

Hello,

Thank you 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 Sep 10, 2017, at 11:10 PM, ?? <owkata at gmail.com<mailto:owkata at gmail.com>> wrote:

Hi, boss

I want to try the VMWare Virtual Appliance, how can I get it?
Thank you!

BR

Ning

??? Windows 10 ???<https://go.microsoft.com/fwlink/?LinkId=550986>??

_______________________________________________
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 jonquet at lirmm.fr  Mon Sep 11 18:39:41 2017
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Mon, 11 Sep 2017 18:39:41 -0700
Subject: [bioontology-support] Open 18-month postdoc position on ontology
	repository (agronomy) and ontology alignment in Montpellier, France
Message-ID: <039001d32b68$022db760$06892620$@lirmm.fr>

Dear BioPortal community, 

If you like to work on the NCBO technology with us, check this out ;)

Clement

 

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

 

The 3 French Labex  <http://www.lirmm.fr/numev/> NUMEV,
<http://www.agropolis-fondation.fr/fr/communaute-scientifique-de-montpellier
/un-reseau-scientifique-de-premier-rang-mondial/labex-agro.html> AGRO and
<http://www.labex-cemeb.org/> CEMEB within the context of the AgroPortal
project ( <http://agroportal.lirmm.fr> http://agroportal.lirmm.fr) which
builds an ontology repository for agronomy are offering a 1.5-year postdoc
position starting early 2018 in Montpellier, to work on agronomical
ontologies and their alignments as well as take part in the international
GACS initiative (http://www.agrisemantics.org/gacs/). 

 

Abstract: 

Standards vocabularies and ontologies are key elements to achieve data
interoperability. The AgroPortal project (http://agroportal.lirmm.fr
<http://agroportal.lirmm.fr/> ) develops and supports a reference ontology
repository for agronomy, plant sciences, biodiversity and nutrition. We have
already designed and implemented an advanced prototype offering
ontology-based services that hosts 64 ontologies or vocabularies including
some reference resources in the domain: Agrovoc, NAL thesaurus, Crop
Ontology, etc. One of the challenges when dealing with multiple ontologies
is to determine their overlap and align them.

We are offering a postdoc position to investigate and develop ontology
mapping capabilities for AgroPortal ontologies and participate into the
international Global Agricultural Concept Scheme (GACS) project. With the
experience and technology developed with the YAM++ application (LIRMM's
ontology alignment matcher - http://yamplusplus.lirmm.fr
<http://yamplusplus.lirmm.fr/> ), we will make AgroPortal a state-of-the-art
platform for mapping extraction, generation, validation, evaluation, storage
and retrieval by adopting a complete semantic web and linked open data
approach and engaging the community for curation. We will first focus on the
ontologies of the Montpellier community (agronomy, food, biodiversity) and
then join the GACS project(integration of Agrovoc, NAL Thesaurus & CAB
Thesaurus) of the RDA AgriSemantics working group (http://agrisemantics.org
<http://agrisemantics.org/> ).

 

More detail here: 

http://www.lirmm.fr/sifr/positions/2017_InterLabex-Lingua_postdoc_position.p
df 

or 

http://www.lirmm.fr/sifr/positions/2017_InterLabex-Lingua_postdoc_position.h
tml

 

Please, consider transferring  the job description in your labs and
networks.

 

Best regards

Clement 

 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

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From support at bioontology.org  Tue Sep 12 08:49:37 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 12 Sep 2017 08:49:37 -0700
Subject: [bioontology-support] [BioPortal] Feedback from michelle
Message-ID: <59b80211c8f31_23b53f8977434e4c8025c@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Sep 12 11:09:47 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 12 Sep 2017 18:09:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from michelle
In-Reply-To: <59b80211c8f31_23b53f8977434e4c8025c@ncbo-prd-app-09.stanford.edu.mail>
References: <59b80211c8f31_23b53f8977434e4c8025c@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <ACA830C0-C540-4890-AD2B-676701430F7A@stanford.edu>

Hi Michelle,


On Sep 12, 2017, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

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

Feedback:

When you change an ontology's visibility from Private to Public, how long should it take to be able to use that ontology in CEDAR to create templates?
I submitted the ontology FISH-AST as a Private ontology. A few minutes ago I changed the ontology's visibility to Public. I cannot find the ontology when searching from the CEDAR template creator. I tried logging out of CEDAR and back in, and also tried creating a new template (rather than adding a field to existing template), and still can't see this ontology.



When you change an ontology from private to public in BioPortal, it takes effect immediately.

I spoke with the CEDAR team and they mentioned that they cache the list of ontology names from BioPortal, but that the cache is updated every 5 minutes. So, there shouldn?t be more than a few minutes of delay before you can use your ontology and associated terms in CEDAR. I also worked with someone on the CEDAR team to see if we could see your ontology in the template creator, and the FISH-AST ontology and terms were showing up here.

Are you still experiencing issues?

Kind regards,
Jennifer

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From futo at stanford.edu  Tue Sep 12 11:18:01 2017
From: futo at stanford.edu (Michelle Futornick)
Date: Tue, 12 Sep 2017 18:18:01 +0000
Subject: [bioontology-support] [BioPortal] Feedback from michelle
In-Reply-To: <ACA830C0-C540-4890-AD2B-676701430F7A@stanford.edu>
References: <59b80211c8f31_23b53f8977434e4c8025c@ncbo-prd-app-09.stanford.edu.mail>,
 <ACA830C0-C540-4890-AD2B-676701430F7A@stanford.edu>
Message-ID: <MWHPR02MB2560E2B3C405DFA5ED451359BF690@MWHPR02MB2560.namprd02.prod.outlook.com>

Thanks Jennifer, I can see it now. I must have been checking before the 5-minute refresh. This is good information to have, thank you!

Michelle


________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Tuesday, September 12, 2017 11:09 AM
To: support at bioontology.org
Cc: Michelle Futornick; martin.oconnor at stanford.edu
Subject: Re: [bioontology-support] [BioPortal] Feedback from michelle

Hi Michelle,


On Sep 12, 2017, at 8:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

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

Feedback:

When you change an ontology's visibility from Private to Public, how long should it take to be able to use that ontology in CEDAR to create templates?
I submitted the ontology FISH-AST as a Private ontology. A few minutes ago I changed the ontology's visibility to Public. I cannot find the ontology when searching from the CEDAR template creator. I tried logging out of CEDAR and back in, and also tried creating a new template (rather than adding a field to existing template), and still can't see this ontology.



When you change an ontology from private to public in BioPortal, it takes effect immediately.

I spoke with the CEDAR team and they mentioned that they cache the list of ontology names from BioPortal, but that the cache is updated every 5 minutes. So, there shouldn?t be more than a few minutes of delay before you can use your ontology and associated terms in CEDAR. I also worked with someone on the CEDAR team to see if we could see your ontology in the template creator, and the FISH-AST ontology and terms were showing up here.

Are you still experiencing issues?

Kind regards,
Jennifer

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From wei_luo_99 at hotmail.com  Tue Sep 12 11:22:08 2017
From: wei_luo_99 at hotmail.com (Wei Luo)
Date: Tue, 12 Sep 2017 18:22:08 +0000
Subject: [bioontology-support] NCBO REST Sample Code errors
Message-ID: <BLUPR15MB0146BE1740DDEFD941AAF80DC2690@BLUPR15MB0146.namprd15.prod.outlook.com>

Hi,


I ran your 5 example codes in java using eclipse. Two of them had exception errors. I downloaded your 3 jar files to my computer and set the build path. I have attached the error log files. Please take a look.


Thanks, Wei
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From vendetti at stanford.edu  Tue Sep 12 12:08:06 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 12 Sep 2017 19:08:06 +0000
Subject: [bioontology-support] NCBO REST Sample Code errors
In-Reply-To: <BLUPR15MB0146BE1740DDEFD941AAF80DC2690@BLUPR15MB0146.namprd15.prod.outlook.com>
References: <BLUPR15MB0146BE1740DDEFD941AAF80DC2690@BLUPR15MB0146.namprd15.prod.outlook.com>
Message-ID: <39BC61A5-4085-4901-8F6E-954EB9C35CCF@stanford.edu>

Hello Wei,

Thanks for letting us know. I?ve entered a couple of issues in our tracker:

https://github.com/ncbo/ncbo_rest_sample_code/issues

? and will look into them.

Kind regards,
Jennifer


On Sep 12, 2017, at 11:22 AM, Wei Luo <wei_luo_99 at hotmail.com<mailto:wei_luo_99 at hotmail.com>> wrote:

Hi,

I ran your 5 example codes in java using eclipse. Two of them had exception errors. I downloaded your 3 jar files to my computer and set the build path. I have attached the error log files. Please take a look.

Thanks, Wei
<annotator><CreateMapping.log>_______________________________________________
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 mark.frisse at Vanderbilt.Edu  Tue Sep 12 15:31:09 2017
From: mark.frisse at Vanderbilt.Edu (Frisse, Mark E)
Date: Tue, 12 Sep 2017 22:31:09 +0000
Subject: [bioontology-support] dead links
Message-ID: <6D1555B4-BE89-4E10-8979-4B510ED92B9F@vanderbilt.edu>

Bragging about your site here.
Some links do not appear to be right

https://www.bioontology.org/community/publications


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From vendetti at stanford.edu  Tue Sep 12 15:38:42 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 12 Sep 2017 22:38:42 +0000
Subject: [bioontology-support] dead links
In-Reply-To: <6D1555B4-BE89-4E10-8979-4B510ED92B9F@vanderbilt.edu>
References: <6D1555B4-BE89-4E10-8979-4B510ED92B9F@vanderbilt.edu>
Message-ID: <CFCD2DB5-F69B-4344-9820-6AE4E2B275DC@stanford.edu>

Hello Mark,


On Sep 12, 2017, at 3:31 PM, Frisse, Mark E <mark.frisse at Vanderbilt.Edu<mailto:mark.frisse at Vanderbilt.Edu>> wrote:

Bragging about your site here.
Some links do not appear to be right

https://www.bioontology.org/community/publications


Could you please clarify on what page you found this link? I navigated to https://www.bioontology.org/, hovered over ?Community" in the top navigation menu, and selected the ?Forum, Blog, & Publications? menu item, which seems to work fine.

You can find the publications page here:

 https://www.bioontology.org/publications

Kind regards,
Jennifer


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From support at bioontology.org  Tue Sep 19 06:02:39 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 19 Sep 2017 06:02:39 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Elena
Message-ID: <59c1156f33654_647e3fd3f4505e8066b2@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Tue Sep 19 07:42:49 2017
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 19 Sep 2017 07:42:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Mark Arking
Message-ID: <59c12ce991d20_db13fc57dca5abc659fb@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Sep 19 13:31:05 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 19 Sep 2017 20:31:05 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Elena
In-Reply-To: <59c1156f33654_647e3fd3f4505e8066b2@ncbo-prd-app-09.stanford.edu.mail>
References: <59c1156f33654_647e3fd3f4505e8066b2@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <FC025494-E40E-489C-95C7-B8DD4069293C@stanford.edu>

Hello Elena,

I don?t know what you mean by ?disconnected?. I checked our system and found a valid user account associated with your email address. Your account name is ?erumyantseva?. What sort of problem are you having?

Kind regards,
Jennifer



On Sep 19, 2017, at 6:02 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Elena

Email: elena.rumyantseva at oracle.com<mailto:elena.rumyantseva at oracle.com>

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

Feedback:

Dear all, it seems like my account have been disconnected. Is there any reason this might have happen?

Thank you,
Elena

_______________________________________________
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 elena.rumyantseva at oracle.com  Tue Sep 19 13:34:24 2017
From: elena.rumyantseva at oracle.com (Elena Rumyantseva)
Date: Tue, 19 Sep 2017 13:34:24 -0700 (PDT)
Subject: [bioontology-support] [BioPortal] Feedback from Elena
In-Reply-To: <FC025494-E40E-489C-95C7-B8DD4069293C@stanford.edu>
References: <59c1156f33654_647e3fd3f4505e8066b2@ncbo-prd-app-09.stanford.edu.mail>
 <FC025494-E40E-489C-95C7-B8DD4069293C@stanford.edu>
Message-ID: <53d7dee0-c744-4309-be0c-1deeca9922bc@default>

Hi Jennifer,

?

You are absolutely right, I used my email as a login information, and thereby was not able to access neither the password recovery or login into my account. Thank you so much for checking and pointing this out.

?

Have a great rest of your day!

Elena 

?

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu] 
Sent: Tuesday, September 19, 2017 4:31 PM
To: support at bioontology.org
Cc: Elena Rumyantseva <elena.rumyantseva at oracle.com>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Elena

?

Hello Elena, 

?

I don?t know what you mean by ?disconnected?. I checked our system and found a valid user account associated with your email address. Your account name is ?erumyantseva?. What sort of problem are you having?

?

Kind regards,

Jennifer

?

?

?

On Sep 19, 2017, at 6:02 AM, HYPERLINK "mailto:support at bioontology.org"support at bioontology.org wrote:

?

Name: Elena 

Email: HYPERLINK "mailto:elena.rumyantseva at oracle.com"elena.rumyantseva at oracle.com 

Location: https%3A%2F%HYPERLINK "https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=RoP1YumCXCgaWHvlZYR8PQcxBKCX5YTpkKY057SbK10&r=zd_gw5MXaz8T9JwNXubKrMetNs_5bfduzS-5pUt81tM&m=F8sThsBa09ih5aCrL7yxr3X_5sSgUArLRkp3-nzx38A&s=brUgGKLXAziUSyZarCaGqasU4JrHDVNNUXjFIqsbprU&e="2Fbioportal.bioontology.org%2Flogin 


Feedback: 

Dear all, it seems like my account have been disconnected. Is there any reason this might have happen?

Thank you, 
Elena

?

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

?
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From vendetti at stanford.edu  Tue Sep 19 15:54:58 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 19 Sep 2017 22:54:58 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Mark Arking
In-Reply-To: <59c12ce991d20_db13fc57dca5abc659fb@ncbo-prd-app-09.stanford.edu.mail>
References: <59c12ce991d20_db13fc57dca5abc659fb@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <913E4CAB-5435-475B-9399-FAE45DF5B2BC@stanford.edu>

Hi Mark,

We import MEDDRA into BioPortal from the UMLS. Due to licensing restrictions, we don?t offer a download link on our site. If you happen to have a UMLS license and provide us with your license number, we can facilitate getting you a copy privately.

If you don?t already have a UMLS license, they are free, and you can sign up here:

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

Kind regards,
Jennifer



On Sep 19, 2017, at 7:42 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Mark Arking

Email: mark.arking at fda.hhs.gov<mailto:mark.arking at fda.hhs.gov>

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

Feedback:

Would it be possible to get a copy of the MedDra in OWL/RDF format?

_______________________________________________
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 mhartung at cit-ec.uni-bielefeld.de  Wed Sep 20 02:13:41 2017
From: mhartung at cit-ec.uni-bielefeld.de (Matthias Hartung)
Date: Wed, 20 Sep 2017 11:13:41 +0200
Subject: [bioontology-support] Submission of SCIO ontology
Message-ID: <b5fdae0f-b541-f074-cd51-b04a408b6824@cit-ec.uni-bielefeld.de>

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
Phone:  +49 521 106 12223
Fax:    +49 521 106 6560

Office: 2.310

Inspiration 1 / Zehlendorfer Damm 201
33619 Bielefeld
Germany

From vendetti at stanford.edu  Wed Sep 20 07:58:11 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 20 Sep 2017 14:58:11 +0000
Subject: [bioontology-support] Submission of SCIO ontology
In-Reply-To: <b5fdae0f-b541-f074-cd51-b04a408b6824@cit-ec.uni-bielefeld.de>
References: <b5fdae0f-b541-f074-cd51-b04a408b6824@cit-ec.uni-bielefeld.de>
Message-ID: <61DE15CB-5955-4EEB-81EA-E40C42AAF198@stanford.edu>

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

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From mhartung at cit-ec.uni-bielefeld.de  Wed Sep 20 08:20:00 2017
From: mhartung at cit-ec.uni-bielefeld.de (Matthias Hartung)
Date: Wed, 20 Sep 2017 17:20:00 +0200
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: <decec1da-7b19-3f70-8cd7-97da97d6837e@cit-ec.uni-bielefeld.de>

Dear Jennifer,

thank you very much for your quick support. We highly appreciate this.

Best regards,

Matthias




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 Mark.Arking at fda.hhs.gov  Wed Sep 20 08:05:53 2017
From: Mark.Arking at fda.hhs.gov (Arking, Mark *)
Date: Wed, 20 Sep 2017 15:05:53 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Mark Arking
In-Reply-To: <913E4CAB-5435-475B-9399-FAE45DF5B2BC@stanford.edu>
References: <59c12ce991d20_db13fc57dca5abc659fb@ncbo-prd-app-09.stanford.edu.mail>
 <913E4CAB-5435-475B-9399-FAE45DF5B2BC@stanford.edu>
Message-ID: <353D25840C950D4F9060434FE87F9FEDA2C847@FDSWP09439.fda.gov>

Jennifer-

Thank you so much.  Attached is our UMLS license (Jonathan Chu cc?ed).  Please let me know if you need additional information.

Respectfully,

Mark Arking
240.441.6275

[cid:image001.png at 01D331FB.4DD58EB0]

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 19, 2017 6:55 PM
To: NCBO User Support
Cc: Arking, Mark *
Subject: Re: [bioontology-support] [BioPortal] Feedback from Mark Arking

Hi Mark,

We import MEDDRA into BioPortal from the UMLS. Due to licensing restrictions, we don?t offer a download link on our site. If you happen to have a UMLS license and provide us with your license number, we can facilitate getting you a copy privately.

If you don?t already have a UMLS license, they are free, and you can sign up here:

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

Kind regards,
Jennifer



On Sep 19, 2017, at 7:42 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Mark Arking
Email: mark.arking at fda.hhs.gov<mailto:mark.arking at fda.hhs.gov>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMEDDRA%3Fp%3Dclasses

Feedback:
Would it be possible to get a copy of the MedDra in OWL/RDF format?

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

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From support at bioontology.org  Wed Sep 20 23:58:13 2017
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 20 Sep 2017 23:58:13 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Srilatha
Message-ID: <59c36305ceb13_5b883f9defa5ac18948@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Thu Sep 21 01:41:51 2017
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 21 Sep 2017 01:41:51 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Viv Junker
Message-ID: <59c37b4fb372c_1aac3fe334650458162de@ncbo-prd-app-09.stanford.edu.mail>

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From christian.kamann at student.uni-luebeck.de  Thu Sep 21 03:31:49 2017
From: christian.kamann at student.uni-luebeck.de (Christian Kamann)
Date: Thu, 21 Sep 2017 10:31:49 +0000
Subject: [bioontology-support] ICD10 Ontology
Message-ID: <17CE01CB-3ED4-4048-820F-5141C29B2B32@student.uni-luebeck.de>

Dear NCBO team,

I'm currently working on my master thesis in medical informatics and I was looking for an ICD-10 ontology to use it as a unifying ontology in order to map different data sources to it. I found this one on your page while I used Google:https://bioportal.bioontology.org/ontologies/ICD10. But unfortunately I don?t see a possibility to download it as an OWL- or TTL-File. Does such a file of the ontology exists and would it be possible to grant me access to it?

Greetings from the University of L?beck (Germany)
Christian Kamann
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From jgraybeal at stanford.edu  Thu Sep 21 09:41:11 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 21 Sep 2017 16:41:11 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Viv Junker
In-Reply-To: <59c37b4fb372c_1aac3fe334650458162de@ncbo-prd-app-09.stanford.edu.mail>
References: <59c37b4fb372c_1aac3fe334650458162de@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <74A6E926-E086-4EA1-95E1-3AA0C7AD19CB@stanford.edu>

Viv,

I think the question of why OntoMaton doesn't list the entries may be one for the OntoMaton developers. I am not aware of any change on our end that would cause that, at least in the last few years. If we have any experts on that here we will try to get their input as well.

To answer your second question about the links, we would have to see what the links look like that you have used. There might be any number of reasons for them to be invalid, but examples are needed to evaluation the situation.

John


On Sep 21, 2017, at 4:41 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Viv Junker

Email: v.junker at sheffield.ac.uk<mailto:v.junker at sheffield.ac.uk>

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

Feedback:

During my role as a curator in Win Hide's lab at Sheffield University, I have been using NIFSTD ontology for curation of disease types, tissues and cell types.
I have used your ontologies via use of OntoMaton which has normally listed your entries in the drop down menu.
There are no longer links to your database in this platform, and I's like to ask why?
Also, having already used NIFSTD within our Repository, I've checked the links added and they are no longer valid.
I'd greatly appreciate a reply to know what has happened.
With thanks, Viv

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

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


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From vendetti at stanford.edu  Thu Sep 21 12:13:49 2017
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 21 Sep 2017 19:13:49 +0000
Subject: [bioontology-support] ICD10 Ontology
In-Reply-To: <17CE01CB-3ED4-4048-820F-5141C29B2B32@student.uni-luebeck.de>
References: <17CE01CB-3ED4-4048-820F-5141C29B2B32@student.uni-luebeck.de>
Message-ID: <21125BBD-C747-488D-B6F8-CEC3E7AE60BC@stanford.edu>

Hello Christian,

We import ICD-10 into BioPortal from the UMLS. Due to licensing restrictions, we can?t post a download link on our site. If you have a UMLS license, please send us the license number and we can provide you with a TTL file privately. If you don?t already have a license, they are free and you can sign up for one here:

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

Kind regards,
Jennifer



On Sep 21, 2017, at 3:31 AM, Christian Kamann <christian.kamann at student.uni-luebeck.de<mailto:christian.kamann at student.uni-luebeck.de>> wrote:

Dear NCBO team,

I'm currently working on my master thesis in medical informatics and I was looking for an ICD-10 ontology to use it as a unifying ontology in order to map different data sources to it. I found this one on your page while I used Google:https://bioportal.bioontology.org/ontologies/ICD10. But unfortunately I don?t see a possibility to download it as an OWL- or TTL-File. Does such a file of the ontology exists and would it be possible to grant me access to it?

Greetings from the University of L?beck (Germany)
Christian Kamann
_______________________________________________
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 alexgarciac at gmail.com  Wed Sep 27 06:59:08 2017
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Wed, 27 Sep 2017 15:59:08 +0200
Subject: [bioontology-support] anotator
Message-ID: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>

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
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From jonquet at lirmm.fr  Wed Sep 27 07:03:56 2017
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Wed, 27 Sep 2017 07:03:56 -0700
Subject: [bioontology-support] anotator
In-Reply-To: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
References: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
Message-ID: <023101d33799$76db16b0$64914410$@lirmm.fr>

Hi Alexander, 

Check out the archive of this mailing list and if yu don?t find your responses come back to me.

 

Clement

 

De : bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Alexander Garcia Castro
Envoy? : mercredi 27 septembre 2017 06:59
? : NCBO User Support <support at bioontology.org>
Objet : [bioontology-support] anotator

 

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

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From c.chung at med.miami.edu  Fri Sep 29 10:18:41 2017
From: c.chung at med.miami.edu (Chung, Caty Elizabeth)
Date: Fri, 29 Sep 2017 17:18:41 +0000
Subject: [bioontology-support] [BioPortal]:  BAO
In-Reply-To: <59ce7e4d928b4_2c723f8155382fdc10a1@ncbo-prd-app-08.stanford.edu.mail>
References: <59ce7e4d928b4_2c723f8155382fdc10a1@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <BN6PR07MB3507E7AE24E5F2E88EBA8734B97E0@BN6PR07MB3507.namprd07.prod.outlook.com>

Hello,


I just wanted to add a screenshot of the issue.  We checked the BAO files and checked in Protege, and we think it is the NCBO BioPortal display for the following BioAssay Ontology version in:

https://bioportal.bioontology.org/ontologies/BAO?p=classes


Caty





________________________________
From: support at bioontology.org <support at bioontology.org>
Sent: Friday, September 29, 2017 1:09 PM
To: support at bioontology.org; Chung, Caty Elizabeth
Subject: [BioPortal] Feedback from Caty Chung


Name: Caty Chung

Email: c.chung at miami.edu

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

Feedback:

NCBO BioPortal is not displaying some of the labels, which can be expanded and display.
On Protege, we do not seem to see any problem.

https://bioportal.bioontology.org/ontologies/BAO?p=classes
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From support at bioontology.org  Fri Sep 29 10:09:33 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 29 Sep 2017 10:09:33 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung
Message-ID: <59ce7e4d928b4_2c723f8155382fdc10a1@ncbo-prd-app-08.stanford.edu.mail>

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From sageh at stanford.edu  Fri Sep 29 12:14:43 2017
From: sageh at stanford.edu (Sage Thery Hellerstedt)
Date: Fri, 29 Sep 2017 19:14:43 +0000
Subject: [bioontology-support] APO URL error clarification
Message-ID: <MWHPR02MB25576C66626E52ED71568128CF7E0@MWHPR02MB2557.namprd02.prod.outlook.com>

Hi BioPortal Team,


We received the following error message at the Saccharomyces Genome Database about the APO (on 9/26):




?BioPortal failed to load Ascomycete Phenotype Ontology (APO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo.


Please verify the URL you provided for daily loading of your ontology:

  1.  Make sure you are signed in to BioPortal.
  2.  Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/APO.
  3.  Click the "Edit submission information" link.
  4.  In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area.

If you need further assistance, please contact us<mailto:support at bioontology.org> via the BioPortal support mailing list.?



The above URL appears active for me, could you please clarify if there is a problem with it?


Additionally, we are having difficulty accessing the ?edit submission information? for the APO as the person who used to do this is no longer with the group. Could you direct me how to make an account with editing privileges or is there is an existing account/email address on file we could access?


Thanks for your help.


Best regards,

Sage Hellerstedt


Biocuration Assistant

Saccharomyces Genome Database
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From mdorf at stanford.edu  Fri Sep 29 14:53:08 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 29 Sep 2017 21:53:08 +0000
Subject: [bioontology-support] APO URL error clarification
In-Reply-To: <MWHPR02MB25576C66626E52ED71568128CF7E0@MWHPR02MB2557.namprd02.prod.outlook.com>
References: <MWHPR02MB25576C66626E52ED71568128CF7E0@MWHPR02MB2557.namprd02.prod.outlook.com>
Message-ID: <55828B58-9502-4161-841D-9CD41C401977@stanford.edu>

Hi Sage,

I?ve checked APO ontology and was able to create a new submission successfully, loaded from the URL you provided. I would ignore this error message for now, as it may have been a result of some momentary downtime on yours or our end.

Feel free to contact us if you this message persists or you encounter any other issues.

Thanks,

Michael



On Sep 29, 2017, at 12:14 PM, Sage Thery Hellerstedt <sageh at stanford.edu<mailto:sageh at stanford.edu>> wrote:

Hi BioPortal Team,

We received the following error message at the Saccharomyces Genome Database about the APO (on 9/26):




?BioPortal failed to load Ascomycete Phenotype Ontology (APO) from URL: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo.

Please verify the URL you provided for daily loading of your ontology:

  1.  Make sure you are signed in to BioPortal.
  2.  Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/APO.
  3.  Click the "Edit submission information" link.
  4.  In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area.

If you need further assistance, please contact us<mailto:support at bioontology.org> via the BioPortal support mailing list.?


The above URL appears active for me, could you please clarify if there is a problem with it?

Additionally, we are having difficulty accessing the ?edit submission information? for the APO as the person who used to do this is no longer with the group. Could you direct me how to make an account with editing privileges or is there is an existing account/email address on file we could access?

Thanks for your help.

Best regards,
Sage Hellerstedt

Biocuration Assistant

Saccharomyces Genome Database
_______________________________________________
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 Sep 29 15:24:12 2017
From: mdorf at stanford.edu (Michael Dorf)
Date: Fri, 29 Sep 2017 22:24:12 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Caty Chung
In-Reply-To: <59ce7e4d928b4_2c723f8155382fdc10a1@ncbo-prd-app-08.stanford.edu.mail>
References: <59ce7e4d928b4_2c723f8155382fdc10a1@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <5F60C423-F869-4095-8A4B-DEC603DDA83E@stanford.edu>

Hi Caty,

Thank you for reporting this issue to us. I?ve re-processed the BioAssay ontology, but the issue still persisted. The empty labels in a tree appear because the actual preferred labels have not been set in the ontology during the processing. This is a bug that we?ll need some time to investigate further. I?ve created an issue in our Github repository which you can use to track our progress on this item:

https://github.com/ncbo/bioportal-project/issues/52

We?ll also keep you posted once the issue is resolved.

Thanks!

Michael


On Sep 29, 2017, at 10:09 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Caty Chung

Email: c.chung at miami.edu<mailto:c.chung at miami.edu>

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

Feedback:

NCBO BioPortal is not displaying some of the labels, which can be expanded and display.
On Protege, we do not seem to see any problem.

https://bioportal.bioontology.org/ontologies/BAO?p=classes

_______________________________________________
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 Sep 29 15:32:55 2017
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 29 Sep 2017 22:32:55 +0000
Subject: [bioontology-support] anotator
In-Reply-To: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
References: <CALAe=O+_Mj3j7PU3xd9qVZM7Z8t0vSpScDf+gCYGeD3sVjAb8w@mail.gmail.com>
Message-ID: <B057FEAF-C46E-4017-9857-9C112AB21363@stanford.edu>

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


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From jonquet.lirmm at gmail.com  Fri Sep 29 20:55:23 2017
From: jonquet.lirmm at gmail.com (Clement Jonquet)
Date: Fri, 29 Sep 2017 20:55:23 -0700
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: <C80910A8-9C5A-4715-80AF-600074D40998@gmail.com>

Hi Alexander

Quick response, I am on the go. 

You can also check 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015610/
And previous message I have sent on that mailing list. 

We recently evaluated also the NCBO Annotator in the CLEF eHealth 2017 campaign. Check the proceedings. 

Roughly: 
Annotator generally has good precision (especially if good ontologies cover well a domain e.g diseases) because of its huge dictionary but not so good recall because of poor NLP implemented. 
Check out also historical 2009-2010 papers for this. 

The CLEF eHealth lessons are : NCBO Annotator or the SIFR Annotator are among the best dictionary based Annotators. But we all loose the game against supervised machine learning methods. 
What justify their existence (among other things ) is the fact that in the health domain it's often very hard to get preannotated training data. 

Something the community always loved about the NCBO Annotator is that it's available out of the shelf as a web service. This was one of the killer idea. 

If you are interested in annotating clinical data or scoring your annotations, check out the NCBO Annotator+ on the SIFR BioPortal. We have added NegEx/ConText here and scoring. It's under submission for publication. 

Hope it helps. 

Clement Jonquet 
Assistant Professor, Univ of Montpellier, Visiting  scholar at Stanford univ. 

> Le 29 sept. 2017 ? 15:32, John Graybeal <jgraybeal at stanford.edu> a ?crit :
> 
> 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
> 
> 
> _______________________________________________
> 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  Fri Sep 29 08:37:30 2017
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 29 Sep 2017 08:37:30 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Yuosef
Message-ID: <59ce68badfcac_75993f82a0f8b79c2191c@ncbo-prd-app-09.stanford.edu.mail>

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