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[bioontology-support] ***2nd Request*** JSON file sent to actual file, not dumped to screen

Paul R Alexander palexander at stanford.edu
Tue Nov 19 10:04:37 PST 2013


Mona,

Did you mean HTTP Client rather than HTML Client? Any HTTP client should make an HTTP request, and then you would be able to read the body of the HTTP response as a string. You can see a Java example for working with the Annotator here:
https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/AnnotateText.java

Paul


On Nov 19, 2013, at 9:57 AM, Mona Salem <monasalem123 at gmail.com> wrote:

> Hello Ray and all
> I am a java developer and wish to call the NCBO annotator with a simple HTML
> Client call, from my Java program.  (See earlier email below.) 
> I want the results to go to a filename.json or fname.xml, not dumped to the
> screen.  Is this possible? I want to work with files not screen dumps.  
> 
> Or will I need to use the AnnotatorClient.java and all the Java classes in
> the following link?  
> 
> https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=b
> rowse&path=%2Ftrunk%2FJava%2FAnnotator%2Fsrc%2FAnnotatorClient.java&revision
> =48&view=markup
> 
> 
> I am using Eclipse.  What version of Maven is best:  the standard or the IAM
> (aka Q)?
> 
> Thanks for all your help
> Mona Salem
> 
> -----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: Friday, November 15, 2013 12:08 PM
> To: bioontology-support at lists.stanford.edu
> Subject: bioontology-support Digest, Vol 67, Issue 24
> 
> Send bioontology-support mailing list submissions to
> 	bioontology-support at lists.stanford.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> or, via email, send a message with subject or body 'help' to
> 	bioontology-support-request at lists.stanford.edu
> 
> You can reach the person managing the list at
> 	bioontology-support-owner at lists.stanford.edu
> 
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of bioontology-support digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: bioontology-support Digest, Vol 67,	Issue 23 (Mona Salem)
>   2. I need the json file output sent to an actual	file, not to
>      the screen (Mona Salem)
>   3. Bioportal down? (James Malone)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 14 Nov 2013 15:47:56 -0800
> From: "Mona Salem" <monasalem123 at gmail.com>
> To: <bioontology-support at lists.stanford.edu>
> Cc: 'Ray Fergerson' <ray.fergerson at stanford.edu>
> Subject: Re: [bioontology-support] bioontology-support Digest, Vol 67,
> 	Issue 23
> Message-ID: <001501cee193$f32148d0$d963da70$@com>
> Content-Type: text/plain;	charset="US-ASCII"
> 
> Hello
> I need help in retrieving results.
> 
> Using the following call:
> http://data.bioontology.org/annotator?apikey=4ea81d74-8960-4525-810b-fa1baab
> 576ff&text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%
> 20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20
> and%20the%20eye.&max_level=0&ontologies=NCIT
> 
> How can I get the json file sent to an actual file, and not dumped to the
> screen?  I wish to capture the preferred names (for the project I am working
> on).  
> 
> Thanks
> Mona
> 
>> To: Beck, Tim (Dr.)
>> Cc: support at bioontology.org
>> Subject: Re: [bioontology-support] Form widget problem
>> 
>> Tim,
>> 
>> This is a (hopefully) temporary problem with HPO. We are reprocessing 
>> the ontology today.
>> 
>> Also, Trish is no longer with NCBO. You can continue to email the 
>> support list to get assistance.
>> 
>> Paul
>> 
>> 
>> On Oct 25, 2013, at 4:21 AM, Beck, Tim (Dr.) <tb143 at leicester.ac.uk>
>> wrote:
>> 
>>> Hi BioPortal team, hi Trish,
>>> 
>>> The "Term-selection field on a form" widget works fine for other
>> ontologies I'm interested in, however I'm not seeing any terms from 
>> the Human Phenotype Ontology when I attempt to list terms from all 
>> ontologies
>> (class="bp_form_complete-all-uri") or specifically HPO.
>>> 
>>> Also, the "Form Autocomplete" demo on your website doesn't seem to be
>> working: http://bioportal.bioontology.org/ontologies/HP/?p=widgets
>>> 
>>> Is this a temporary problem with HPO?
>>> 
>>> Thanks for your help.
>>> 
>>> Regards,
>>> Tim
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 12 Nov 2013 21:49:14 +0300
> From: Mark Gerard <mark.gerard at clinovo.com>
> To: bioontology-support at lists.stanford.edu
> Subject: [bioontology-support] Extracting parent child relationships
> 	using	the web service
> Message-ID:
> 	<CALbVH61Jj7BAbUBz5OLEuwXvj5aYM7KD3fB_+iHUMR7iN9Lo6A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all -
> 
> I have been trying to get the hierarchical information as displayed on the
> web interface @"http://bioportal.bioontology.org/" when a term is searched
> in a given ontology -
> 
> This is what I intend to achieve =>
> https://trac.clinovo.com/clincapture/attachment/ticket/741/howTo.jpg
> 
> Context:
> 
> Given the information returned by the web service, we intend to
> programmatic-ally build this hierarchy (really, display the fields as shown
> in the screen shot above) in another system (open source application =>
> clincapture) which is using bio-portal as the end point for medical coding.
> 
> What I have done so for:
> 
> 1. I am able to use the old "http://rest.bioontology.org" (I am yet to get
> acquainted with the new web service) to extract the coded term for a given
> verbatim term entered by the user in our system
> 
> 2. I have tried to work with the view extraction service but it seems to me
> that it only returns one subclass of the concept (the immediate sub class)
> - I am looking for the entire hierarchy
> 
> 3. I have also tinkered with the RDF term service but it would appear that
> the generated xml does not have the entire hierarchy - It would seem that
> the returned xml cannot allow me to walk back to the root element (as
> depicted on the UX)
> 
> I know I am missing something or have probably not looked somewhere, can
> anyone give me some leads as to how I can retrieve the information in the
> tree view (With the hierarchy)? I will really appreciate the help!
> 
> Mark
> 
> --
> *Mark Gerard*
> Software Developer
> *mark.gerard at clinovo.com <sophie.mccallum at clinovo.com>*
>  *Cell*: (256) 794323934
> *Tel*: (256) 794323934
> *www.clinovo.com <http://www.clinovo.com>*
> 
> [image: Clinovo] <http://www.clinovo.com/>
> [image: Facebook] <http://www.facebook.com/clinovo> [image:
> Linkedin]<http://www.linkedin.com/company/890144?trk=NUS_CMPY_TWIT>
> [image: Twitter] <http://twitter.com/Clinovo>
>  *Confidentiality Notice: Unless expressly stated otherwise, this message
> is confidential and may be privileged. It is intended for the addressee(s)
> only. Access to this e-mail by anyone else is unauthorized. If you are not
> an addressee, please inform the sender immediately.*
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> ------------------------------
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
> End of bioontology-support Digest, Vol 67, Issue 23
> ***************************************************
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 14 Nov 2013 15:50:15 -0800
> From: "Mona Salem" <monasalem123 at gmail.com>
> To: <bioontology-support at lists.stanford.edu>
> Cc: 'Ray Fergerson' <ray.fergerson at stanford.edu>
> Subject: [bioontology-support] I need the json file output sent to an
> 	actual	file, not to the screen
> Message-ID: <001601cee194$453c4430$cfb4cc90$@com>
> Content-Type: text/plain;	charset="US-ASCII"
> 
> 
> Hello
> I need help in retrieving results.
> 
> Using the following call:
> http://data.bioontology.org/annotator?apikey=4ea81d74-8960-4525-810b-fa1baab
> 576ff&text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%
> 20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20
> and%20the%20eye.&max_level=0&ontologies=NCIT
> 
> How can I get the json file sent to an actual file, and not dumped to the
> screen?  I wish to capture the preferred names (for the project I am working
> on).  
> 
> Thanks
> Mona
> 
> -----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, November 12, 2013 12:08 PM
> To: bioontology-support at lists.stanford.edu
> Subject: bioontology-support Digest, Vol 67, Issue 23
> 
> Send bioontology-support mailing list submissions to
> 	bioontology-support at lists.stanford.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> or, via email, send a message with subject or body 'help' to
> 	bioontology-support-request at lists.stanford.edu
> 
> You can reach the person managing the list at
> 	bioontology-support-owner at lists.stanford.edu
> 
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of bioontology-support digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Form widget problem (Beck, Tim  (Dr.))
>   2. Extracting parent child relationships using	the web service
>      (Mark Gerard)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 12 Nov 2013 12:16:09 +0000
> From: "Beck, Tim  (Dr.)" <tb143 at leicester.ac.uk>
> To: Ray Fergerson <ray.fergerson at stanford.edu>
> Cc: "support at bioontology.org" <support at bioontology.org>
> Subject: Re: [bioontology-support] Form widget problem
> Message-ID: <7365B4E6-7B0B-46C9-948A-67725FE7FFC9 at mail.cfs.le.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
> 
> Thanks Ray.
> 
> Regarding the form widget again: I get the same values for both the
> "a_bioportal_concept_id" and "a_bioportal_full_id" attributes.
> 
> For example, from
> http://bioportal.bioontology.org/ontologies/MESH/?p=widgets if I type the
> term "Neoplasms" into the "Example 3" box I get: 
> 
> <input id="c_bioportal_concept_id" type="hidden"
> value="http://purl.bioontology.org/ontology/MSH/D009369">
> <input id="c_bioportal_full_id" type="hidden"
> value="http://purl.bioontology.org/ontology/MSH/D009369">
> 
> However, I would expect the concept id to have a value of "D009369".
> 
> This duplication of values also seems to occur for the other ontologies I'm
> interested in.
> 
> Is this a fault or have I misunderstood what the concept id relates to?
> 
> Thanks for your help.
> 
> Regards,
> Tim
> 
> 
> On 1 Nov 2013, at 18:57, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> 
>> This appears to be working now.
>> 
>> Ray
>> 
>> -----Original Message-----
>> From: bioontology-support-bounces at lists.stanford.edu
>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of 
>> Paul R Alexander
>> Sent: Monday, October 28, 2013 11:15 AM
>> To: Beck, Tim (Dr.)
>> Cc: support at bioontology.org
>> Subject: Re: [bioontology-support] Form widget problem
>> 
>> Tim,
>> 
>> This is a (hopefully) temporary problem with HPO. We are reprocessing 
>> the ontology today.
>> 
>> Also, Trish is no longer with NCBO. You can continue to email the 
>> support list to get assistance.
>> 
>> Paul
>> 
>> 
>> On Oct 25, 2013, at 4:21 AM, Beck, Tim (Dr.) <tb143 at leicester.ac.uk>
>> wrote:
>> 
>>> Hi BioPortal team, hi Trish,
>>> 
>>> The "Term-selection field on a form" widget works fine for other
>> ontologies I'm interested in, however I'm not seeing any terms from 
>> the Human Phenotype Ontology when I attempt to list terms from all 
>> ontologies
>> (class="bp_form_complete-all-uri") or specifically HPO.
>>> 
>>> Also, the "Form Autocomplete" demo on your website doesn't seem to be
>> working: http://bioportal.bioontology.org/ontologies/HP/?p=widgets
>>> 
>>> Is this a temporary problem with HPO?
>>> 
>>> Thanks for your help.
>>> 
>>> Regards,
>>> Tim
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 12 Nov 2013 21:49:14 +0300
> From: Mark Gerard <mark.gerard at clinovo.com>
> To: bioontology-support at lists.stanford.edu
> Subject: [bioontology-support] Extracting parent child relationships
> 	using	the web service
> Message-ID:
> 	<CALbVH61Jj7BAbUBz5OLEuwXvj5aYM7KD3fB_+iHUMR7iN9Lo6A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all -
> 
> I have been trying to get the hierarchical information as displayed on the
> web interface @"http://bioportal.bioontology.org/" when a term is searched
> in a given ontology -
> 
> This is what I intend to achieve =>
> https://trac.clinovo.com/clincapture/attachment/ticket/741/howTo.jpg
> 
> Context:
> 
> Given the information returned by the web service, we intend to
> programmatic-ally build this hierarchy (really, display the fields as shown
> in the screen shot above) in another system (open source application =>
> clincapture) which is using bio-portal as the end point for medical coding.
> 
> What I have done so for:
> 
> 1. I am able to use the old "http://rest.bioontology.org" (I am yet to get
> acquainted with the new web service) to extract the coded term for a given
> verbatim term entered by the user in our system
> 
> 2. I have tried to work with the view extraction service but it seems to me
> that it only returns one subclass of the concept (the immediate sub class)
> - I am looking for the entire hierarchy
> 
> 3. I have also tinkered with the RDF term service but it would appear that
> the generated xml does not have the entire hierarchy - It would seem that
> the returned xml cannot allow me to walk back to the root element (as
> depicted on the UX)
> 
> I know I am missing something or have probably not looked somewhere, can
> anyone give me some leads as to how I can retrieve the information in the
> tree view (With the hierarchy)? I will really appreciate the help!
> 
> Mark
> 
> --
> *Mark Gerard*
> Software Developer
> *mark.gerard at clinovo.com <sophie.mccallum at clinovo.com>*
>  *Cell*: (256) 794323934
> *Tel*: (256) 794323934
> *www.clinovo.com <http://www.clinovo.com>*
> 
> [image: Clinovo] <http://www.clinovo.com/>
> [image: Facebook] <http://www.facebook.com/clinovo> [image:
> Linkedin]<http://www.linkedin.com/company/890144?trk=NUS_CMPY_TWIT>
> [image: Twitter] <http://twitter.com/Clinovo>
>  *Confidentiality Notice: Unless expressly stated otherwise, this message
> is confidential and may be privileged. It is intended for the addressee(s)
> only. Access to this e-mail by anyone else is unauthorized. If you are not
> an addressee, please inform the sender immediately.*
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131
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> 
> ------------------------------
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
> End of bioontology-support Digest, Vol 67, Issue 23
> ***************************************************
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 15 Nov 2013 13:16:52 +0000
> From: James Malone <malone at ebi.ac.uk>
> To: "support at bioontology.org Support" <support at bioontology.org>
> Subject: [bioontology-support] Bioportal down?
> Message-ID: <52861EC4.8020901 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Widgets aren't responding and I can't get to any ontology...
> 
> James
> 
> --
> Blog: http://drjamesmalone.blogspot.co.uk/
> Twitter: https://twitter.com/jamesmalone
> 
> European Bioinformatics Institute (EMBL-EBI) European Molecular Biology
> Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United
> Kingdom
> Tel: + 44 (0) 1223 494 676
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
> End of bioontology-support Digest, Vol 67, Issue 24
> ***************************************************
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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