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

Eamonn Maguire eamonnmag at
Tue Dec 17 14:56:46 PST 2013

  Well the problem is the speed (500 take a long time to load) and not
being able to make it completely parallel since I'll need the first call to
know how many pages to retrieve.

Also, how are you implementing the paging? Are you doing the query each
time then slicing the results according to the page size and requested page
number (to create an offset)? Or are results cached in some way to enable
pre-emptive speed ups of subsequent calls?

In summary, one call would be better for us, especially if implementation
is as I described in the former.
From: Ray Fergerson <ray.fergerson at>
Sent: 17/12/2013 22:46
To: Eamonn Maguire <eamonnmag at>
Cc: support at; ISA Team <isatools at>
Subject: RE: [bioontology-support] Please don't change current REST services


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:


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

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?



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


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

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.


*From:* bioontology-support-bounces at [
mailto:bioontology-support-bounces at<bioontology-support-bounces at>
] *On Behalf Of *Eamonn Maguire
*Sent:* Friday, October 25, 2013 4:28 AM
*To:* support at Support
*Cc:* isatools at
*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

This call to search on *melanoma* gives me this.


·         *"**page**"*: 1,

·         *"**pageCount**"*: 45,

·         *"**prevPage**"*: null,

·         *"**nextPage**"*: 2,

·         -

*"**links**"*: {

o    *"**nextPage**"*: "
" <>,

o    *"**prevPage**"*: null


·         -

*"**collection**"*: [

o    -


§  *"**prefLabel**"*: "Melanoma",

§  *"**@id**"*:

§  *"**@type**"*:

§  -

*"**links**"*: {

§  *"**self**"*:"

§  *"**ontology**"*:

§  *….*

Now, if I want to find out which ontology this term came from, I have to do
another search to this

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 Maguire
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