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

Eamonn Maguire eamonnmag at gmail.com
Thu Dec 19 03:06:45 PST 2013


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,

Eamonn

On 19 Dec 2013, at 09:28, Eamonn Maguire <eamonnmag at gmail.com> 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. 
> 
> Thanks,
> 
> Eamonn
> 
> 
> On 18 Dec 2013, at 18:03, Paul R Alexander <palexander at stanford.edu> wrote:
> 
>> 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.
>> 
>> Paul
>> 
>> 
>> On Dec 17, 2013, at 2:56 PM, Eamonn Maguire <eamonnmag at gmail.com> 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: Ray Fergerson
>>> Sent: 17/12/2013 22:46
>>> To: Eamonn Maguire
>>> Cc: support at bioontology.org; ISA Team
>>> Subject: RE: [bioontology-support] Please don't change current REST services
>>> 
>>> 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
>>>  
>>> 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: 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: support at bioontology.org Support
>>> Cc: 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",
>>> o    "prevPage": null
>>> },
>>> ·         -
>>> "collection": [
>>> o    -
>>> {
>>> §  "prefLabel": "Melanoma",
>>> §  "@id": "http://purl.bioontology.org/ontology/MDR/10053571",
>>> §  "@type": "http://www.w3.org/2002/07/owl#Class",
>>> §  -
>>> "links": {
>>> §  "self":"http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMDR%2F10053571",
>>> §  "ontology": "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
>>>  
>>> 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
>>>  
>>>  
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
> 

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