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

Ray Fergerson ray.fergerson at
Thu Dec 19 11:54:58 PST 2013


We don’t currently have the notion of a score for the annotations. It
wasn’t terribly obvious that the previous scores were of much general
value so we didn’t regenerate them for the new API. Because of the way
that the annotation is done, we don’t actually have information about the
“quality” of the match itself. The system just does exact string matches.
If you are interested in scoring based on prefName vs. synonym then you
can easily construct such a scheme yourself since we provide the data.


From: Paul R Alexander [mailto:palexander at]
Sent: Thursday, December 19, 2013 10:51 AM
To: Eamonn Maguire
Cc: Ray Fergerson; ISA Team; support at
Subject: Re: [bioontology-support] Please don't change current REST

I’ll let Ray handle the question about the score because I’m not entirely
sure what the plans are there.

We are working on ways to make more of the class information available
when annotating without suffering performance degradation. Hopefully this
will make it into a release early in 2014.


On Dec 19, 2013, at 3:06 AM, Eamonn Maguire <eamonnmag at> wrote:

Some notes on the annotator api:

Score is missing from results now. SYN (synonym) and PREF (preferred) is
the only thing available. Is score now gone from your comparison or are
you just not showing it?

'prefLabel' would be useful in the annotated class information otherwise
no way of knowing the actual ontology term that can be used for annotation
without additional queries. I have to do an additional query for each
result Item just to find out it’s string representation.

Thanks as always,


On 19 Dec 2013, at 09:28, Eamonn Maguire <eamonnmag at> wrote:

Great, thanks Paul.

1. I’m assuming here that you mean the links and context still appear. You
can turn these off by adding &no_links=true&no_context=true. We didn’t
document these options because we weren’t sure if people would need them,
but it does help in slimming down large responses quite a bit.

This is great. The one thing we’d need that appears in the links section
is the Ontology the term comes from. Would it be possible for you to move
this to a higher level so that the whole links section can be skipped if
we’re just doing a term search?

I’m working on the ontology tree traversal code now so I’ll probably have
more questions by the end of the day.



On 18 Dec 2013, at 18:03, Paul R Alexander <palexander at>

I think we could examine raising the page size limit. We would need some
time to evaluate the ramifications, though. I’ve added an issue for us to
look into this.

The paging is not done by slicing the results, at least not in code. It’s
done at the database level, so the underlying system there may do some
optimizations when subsequent requests that differ only in the offset are
made. We could examine doing something like you suggest with pre-fetching
subsequent pages.


On Dec 17, 2013, at 2:56 PM, Eamonn Maguire <eamonnmag at> wrote:

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:  <mailto:ray.fergerson at> Ray Fergerson
Sent: 17/12/2013 22:46
To:  <mailto:eamonnmag at> Eamonn Maguire
Cc:  <mailto:support at> support at;
<mailto:isatools at> ISA Team
Subject: RE: [bioontology-support] Please don't change current REST


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: <mailto:eamonnmag at>
eamonnmag at]
Sent: Tuesday, December 17, 2013 8:31 AM
To: Ray Fergerson
Cc:  <mailto:support at> 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 <
<mailto:ray.fergerson at> 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 this.


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

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

bioontology-support mailing list
bioontology-support at

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