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[bioontology-support] What happened to CUI codes?

Oravec, Thomas oravect at ccf.org
Wed Oct 9 04:51:18 PDT 2013


This is the fourth request.

Thomas J Oravec | Data Coordinator
Genomics Medicine Institute
Cleveland Clinic Foundation
Tel: 216-445-4030
Email: oravect at ccf.org
 
-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
bioontology-support-request at lists.stanford.edu
Sent: Tuesday, October 08, 2013 4:25 PM
To: bioontology-support at lists.stanford.edu
Subject: bioontology-support Digest, Vol 66, Issue 17

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Today's Topics:

   1. Re: UMLS semantic types in NCBO Annotator and	SPARQL endpoint
      (Paul R Alexander)
   2. Re: UMLS semantic types in NCBO Annotator and SPARQL endpoint
      (Jael Garc?aCastro)


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

Message: 1
Date: Tue, 8 Oct 2013 13:11:26 -0700
From: Paul R Alexander <palexander at stanford.edu>
To: Jael Garc?aCastro <leyla.jael.garcia at gmail.com>
Cc: Ray Fergerson <ray.fergerson at stanford.edu>,
	"support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] UMLS semantic types in NCBO
	Annotator and	SPARQL endpoint
Message-ID: <92E2A4F6-A7E4-4A94-80C9-1FE33D93CDD1 at stanford.edu>
Content-Type: text/plain; charset="windows-1252"

Jael,

The new API code is released at data.bioontology.org, so you should
point there and not stagedata.bioontology.org (this is our testing
platform).

rest.bioontology.org is essentially deprecated as of now, so new fixes
won't end up there.

There is indeed a bug on the xml output at data.bioontology.org that is
causing the class information to not appear. This will be fixed later
today. If you need to see the output now, you can try the json
serialization. The xml will look different than the xml provided at
rest.bioontology.org, primarily because of the transition to our new
API, which is now more uniform across individual NCBO APIs.

Please let me know if you have further questions.

Paul


On Oct 8, 2013, at 1:04 PM, Jael Garc?aCastro
<leyla.jael.garcia at gmail.com> wrote:

> Dear Ryan, 
> 
> I have managed to work with the URL
http://rest.bioontology.org/obs/annotator from Java, it is working fine.
However, the problem with MeSH and the Semantic types persist here. I
get T999 as semantic type when annotating with MeSH (virtual id 1351)
while with SNOMED-CT (virtual id 1353) I do get T109 and T124. When will
it solved?
> 
> And the XML that I get in Java is different from the one that I get
from the Annotator interface, the last one seems to be incomplete.
> 
> Thanks,
> Jael
> 
> 
> On Tue, Oct 8, 2013 at 8:33 PM, Jael Garc?aCastro
<leyla.jael.garcia at gmail.com> wrote:
> Dear Ray,
> 
> I have seen that Bioportal has been migrated now to the RDF platform.
Now "serotonin" in MeSH indeed has types T109 and T124 as you mentioned
in your previous mail, great!
> 
> However, I am not getting the information I used to with NCBO
Annotator. Before the migration, I used this URL for the annotator
http://rest.bioontology.org/obs/annotator, now, I saw in the
documentation
(http://stagedata.bioontology.org/documentation#nav_annotator) that it
should be http://stagedata.bioontology.org/annotator, is that right? In
both cases I am getting an error saying that my API Key is not valid. I
already re-registered myself in case it has expired or kind of, but
still I get the same error with the new API Key. What am I doing wrong?
Any suggestions?
> 
> Using the apikey used by the annotator interface when XML format is
required
(http://data.bioontology.org/annotator?text=serotonin&max_level=0&ontolo
gies=MESH&format=xml&apikey=xxx), with the URL
http://rest.bioontology.org/obs/annotator I get a "Method Not Allowed",
while with http://stagedata.bioontology.org/annotator I get an "Internal
Server Error". What could be the problem?
> 
> I tried to get the XML from the Annotator interface and the XML now is
different from before, it has less information, is this a new response?
>
<annotationCollection><annotation><annotatedClass/><hierarchyCollection/
><annotationsCollection><annotations><from>1</from><to>9</to><matchType>
PREF</matchType><text>SEROTONIN</text></annotations></annotationsCollect
ion><mappingsCollection/></annotation></annotationCollection>
> 
> 
> Thanks so much in advance,
> Jael
> 
> 
> On Wed, Sep 25, 2013 at 3:19 AM, Ray Fergerson
<ray.fergerson at stanford.edu> wrote:
> Jael,
> 
>  
> 
> We may make the UMLS property URI?s that we generate resolvable but
this is not a high priority at the moment.
> 
>  
> 
> There does seem to be something wrong with the sematic types and MeSH.
They work fine for other ontologies (e.g. SNOMED). By the way, Serotonin
has types T109 and T124 (not T016 has stated below). These types are
returned in the XML for ?working? ontologies.
> 
>  
> 
> Whatever the problem with MeSH, we are about to replace this entire
backend system in a couple of days. Thus we are not going to look into
this problem. The new system should work correctly. If it doesn?t then
we will fix it. Stay tuned.
> 
>  
> 
> Ray
> 
>  
> 
> From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Jael Garc?aCastro
> Sent: Tuesday, September 24, 2013 12:09 PM
> To: support at bioontology.org
> Subject: [bioontology-support] UMLS semantic types in NCBO Annotator
and SPARQL endpoint
> 
>  
> 
> Hi all,
> 
> I tried DESCRIBE <http://purl.bioontology.org/ontology/MDDB/07224> at
http://sparql.bioontology.org. The description includes the UMLS
semantic type as
> 
> <http://bioportal.bioontology.org/ontologies/umls/hasSTY>
<http://bioportal.bioontology.org/ontologies/umls/sty/T121>
>  
> 
> I noticed that the URL
http://bioportal.bioontology.org/ontologies/umls/sty/T121 does not
resolve. Do you plan these UMLS semantic type URLs to be resolvable?
> 
> I also tried the NCBO Annotator
http://bioportal.bioontology.org/annotator with the term "serotonin" and
the ontology MeSH. This term is associated to the UMLS semantic type
T016. However, if I retrieve the annotation in the XML format using the
option "Format Result As", the semantic type retrieved is T999 "NCBO
BioPortal concept". I was expecting T016, is not the semantic type
reported by the annotator the UMLS one?
> 
> Thanks,
> 
> Jael
> 
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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

Message: 2
Date: Tue, 8 Oct 2013 21:25:01 +0100
From: Jael Garc?aCastro <leyla.jael.garcia at gmail.com>
To: Paul R Alexander <palexander at stanford.edu>
Cc: Ray Fergerson <ray.fergerson at stanford.edu>,
	"support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] UMLS semantic types in NCBO
	Annotator and SPARQL endpoint
Message-ID:
	
<CAD=KBZLw6zxkCJTP_cq9ay-a2==9hv_qegHGwWmNvLRjEPrc0Q at mail.gmail.com>
Content-Type: text/plain; charset="windows-1252"

Thanks Paul,

Could you please point me to the documentation about the API
data.bioontology.org? In rest.bioontology.org, the parameter for the
text
to be annotated used to be "textToAnnotate" but I saw it is now "text"
in
data.bioontology.org. I would like to check the rest of parameters to
make
sure I am using it in the proper way.

Thanks again,
Jael


On Tue, Oct 8, 2013 at 9:11 PM, Paul R Alexander
<palexander at stanford.edu>wrote:

> Jael,
>
> The new API code is released at data.bioontology.org, so you should
point
> there and not stagedata.bioontology.org (this is our testing
platform).
>
> rest.bioontology.org is essentially deprecated as of now, so new fixes
> won't end up there.
>
> There is indeed a bug on the xml output at data.bioontology.org that
is
> causing the class information to not appear. This will be fixed later
> today. If you need to see the output now, you can try the json
> serialization. The xml will look different than the xml provided at
> rest.bioontology.org, primarily because of the transition to our new
API,
> which is now more uniform across individual NCBO APIs.
>
> Please let me know if you have further questions.
>
> Paul
>
>
> On Oct 8, 2013, at 1:04 PM, Jael Garc?aCastro
<leyla.jael.garcia at gmail.com>
> wrote:
>
> Dear Ryan,
>
> I have managed to work with the URL
> http://rest.bioontology.org/obs/annotator from Java, it is working
fine.
> However, the problem with MeSH and the Semantic types persist here. I
get
> T999 as semantic type when annotating with MeSH (virtual id 1351)
while
> with SNOMED-CT (virtual id 1353) I do get T109 and T124. When will it
> solved?
>
> And the XML that I get in Java is different from the one that I get
from
> the Annotator interface, the last one seems to be incomplete.
>
> Thanks,
> Jael
>
>
> On Tue, Oct 8, 2013 at 8:33 PM, Jael Garc?aCastro <
> leyla.jael.garcia at gmail.com> wrote:
>
>> Dear Ray,
>>
>> I have seen that Bioportal has been migrated now to the RDF platform.
Now
>> "serotonin" in MeSH indeed has types T109 and T124 as you mentioned
in your
>> previous mail, great!
>>
>> However, I am not getting the information I used to with NCBO
Annotator.
>> Before the migration, I used this URL for the annotator
>> http://rest.bioontology.org/obs/annotator, now, I saw in the
>> documentation (
>> http://stagedata.bioontology.org/documentation#nav_annotator) that it
>> should be http://stagedata.bioontology.org/annotator, is that right?
In
>> both cases I am getting an error saying that my API Key is not valid.
I
>> already re-registered myself in case it has expired or kind of, but
still I
>> get the same error with the new API Key. What am I doing wrong? Any
>> suggestions?
>>
>> Using the apikey used by the annotator interface when XML format is
>> required (
>>
http://data.bioontology.org/annotator?text=serotonin&max_level=0&ontolog
ies=MESH&format=xml&apikey=xxx),
>> with the URL http://rest.bioontology.org/obs/annotator I get a
"Method
>> Not Allowed", while with http://stagedata.bioontology.org/annotator I
>> get an "Internal Server Error". What could be the problem?
>>
>> I tried to get the XML from the Annotator interface and the XML now
is
>> different from before, it has less information, is this a new
response?
>>
>>
<annotationCollection><annotation><annotatedClass/><hierarchyCollection/
><annotationsCollection><annotations><from>1</from><to>9</to><matchType>
PREF</matchType><text>SEROTONIN</text></annotations></annotationsCollect
ion><mappingsCollection/></annotation></annotationCollection>
>>
>>
>> Thanks so much in advance,
>> Jael
>>
>>
>> On Wed, Sep 25, 2013 at 3:19 AM, Ray Fergerson <
>> ray.fergerson at stanford.edu> wrote:
>>
>>> Jael,****
>>>
>>> ** **
>>>
>>> We may make the UMLS property URI?s that we generate resolvable but
this
>>> is not a high priority at the moment.****
>>>
>>> ** **
>>>
>>> There does seem to be something wrong with the sematic types and
MeSH.
>>> They work fine for other ontologies (e.g. SNOMED). By the way,
Serotonin
>>> has types T109 and T124 (not T016 has stated below). These types are
>>> returned in the XML for ?working? ontologies.****
>>>
>>> ** **
>>>
>>> Whatever the problem with MeSH, we are about to replace this entire
>>> backend system in a couple of days. Thus we are not going to look
into this
>>> problem. The new system should work correctly. If it doesn?t then we
will
>>> fix it. Stay tuned.****
>>>
>>> ** **
>>>
>>> Ray****
>>>
>>> ** **
>>>
>>> *From:* bioontology-support-bounces at lists.stanford.edu [mailto:
>>> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *Jael
>>> Garc?aCastro
>>> *Sent:* Tuesday, September 24, 2013 12:09 PM
>>> *To:* support at bioontology.org
>>> *Subject:* [bioontology-support] UMLS semantic types in NCBO
Annotator
>>> and SPARQL endpoint****
>>>
>>> ** **
>>>
>>> Hi all, ****
>>>
>>> I tried DESCRIBE <http://purl.bioontology.org/ontology/MDDB/07224>
at
>>> http://sparql.bioontology.org. The description includes the UMLS
>>> semantic type as ****
>>>
>>> <http://bioportal.bioontology.org/ontologies/umls/hasSTY>
<http://bioportal.bioontology.org/ontologies/umls/sty/T121>****
>>>
>>> ** **
>>>
>>> I noticed that the URL
>>> http://bioportal.bioontology.org/ontologies/umls/sty/T121 does not
>>> resolve. Do you plan these UMLS semantic type URLs to be
resolvable?****
>>>
>>> I also tried the NCBO Annotator
>>> http://bioportal.bioontology.org/annotator with the term "serotonin"
>>> and the ontology MeSH. This term is associated to the UMLS semantic
type
>>> T016. However, if I retrieve the annotation in the XML format using
the
>>> option "Format Result As", the semantic type retrieved is T999 "NCBO
>>> BioPortal concept". I was expecting T016, is not the semantic type
reported
>>> by the annotator the UMLS one?****
>>>
>>> Thanks,****
>>>
>>> Jael****
>>>
>>
>>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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