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[bioontology-support] Please don't change current REST services

Ray Fergerson ray.fergerson at stanford.edu
Tue Dec 17 14:46:34 PST 2013


Eamonn,



You can just ask for the next page. If you have 1000 items and the page
size is 500 this is just one extra call. Which call specifically is giving
you problems?



The way to specify pages is at the top of the documentation at:



http://data.bioontology.org/documentation



Ray



From: Eamonn Maguire [mailto:eamonnmag at gmail.com]
Sent: Tuesday, December 17, 2013 8:31 AM
To: Ray Fergerson
Cc: support at bioontology.org; ISA Team
Subject: Re: [bioontology-support] Please don't change current REST
services



Hi Ray,



We're working on porting all our code over to the new version of bioportal
(I can refer you to the Java code if you’d like it for other users so they
don’t have to do it themselves).



I have a question. I may have a few more by the time I finish. One is to
do with paging. How do I remove paging. There is a limit to the calls of
500 items per page. However, I have some examples, e.g. dose where the
number of results is quite large, nearing 1000. Is there a way of skipping
the paging altogether?



Thanks,



Eamonn



On 7 Nov 2013, at 00:10, Ray Fergerson <ray.fergerson at stanford.edu> wrote:





Eamonn,



Sorry for the delay in getting back to you. The idea here would be to
group all of the preferred name lookups into a single call and retrieve
them all at once using the “batch” call. Please see the documentation for
how to do this.



 <http://data.bioontology.org/documentation#nav_batch>
http://data.bioontology.org/documentation#nav_batch



We may (probably will) later have a scheme for specifying which properties
of a class you want to retrieve on all calls. This feature only exists on
certain calls at the moment, including the batch call.



Ray



From:  <mailto:bioontology-support-bounces at lists.stanford.edu>
bioontology-support-bounces at lists.stanford.edu [
<mailto:bioontology-support-bounces at lists.stanford.edu>
mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Eamonn
Maguire
Sent: Friday, October 25, 2013 4:28 AM
To:  <mailto:support at bioontology.org> support at bioontology.org Support
Cc:  <mailto:isatools at googlegroups.com> isatools at googlegroups.com
Subject: [bioontology-support] Please don't change current REST services



Hi all,



First of all, we use bioportal REST services across numerous tools,
including OntoMaton and ISAcreator, ISAconfigurator etc. This move to the
SPARQL results really messes things up for whilst providing an extra
number of calls to get the same information we get with one call at
present. For example:



This call to search on melanoma gives me this.



{

·         "page": 1,

·         "pageCount": 45,

·         "prevPage": null,

·         "nextPage": 2,

·         -

"links": {

o    "nextPage":  <http://data.bioontology.org/search?q=melanoma&page=2>
"http://data.bioontology.org/search?q=melanoma&page=2",

o    "prevPage": null

},

·         -

"collection": [

o    -

{

§  "prefLabel": "Melanoma",

§  "@id":  <http://purl.bioontology.org/ontology/MDR/10053571>
"http://purl.bioontology.org/ontology/MDR/10053571",

§  "@type":  <http://www.w3.org/2002/07/owl#Class>
"http://www.w3.org/2002/07/owl#Class",

§  -

"links": {

§  "self":
<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.b
ioontology.org%2Fontology%2FMDR%2F10053571>
"http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.b
ioontology.org%2Fontology%2FMDR%2F10053571",

§  "ontology":  <http://data.bioontology.org/ontologies/MEDDRA>
"http://data.bioontology.org/ontologies/MEDDRA”,

§  
.



Now, if I want to find out which ontology this term came from, I have to
do another search to this  <http://data.bioontology.org/ontologies/MEDDRA>
http://data.bioontology.org/ontologies/MEDDRA



I have to perform 2 calls to just get the name of the ontology it came
from. It requires 2 calls for each term and places extra burden on both
your servers and slows down our applications.



Is there some way you could you make it easier to get this information
from the original call please?



Many thanks,



Eamonn



--

Eamonn Maguire





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