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

Paul R Alexander palexander at stanford.edu
Wed Dec 18 09:57:30 PST 2013


No worries about the emails, we love getting feedback and are still looking at ways to improve the API, especially from a developer’s perspective.

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.

2. To get around making two calls to get the latest submission, we typically just make one call to the /submissions endpoint (http://data.bioontology.org/submissions). This has the latest submissions for all ontologies. Views can be included by passing include_views=true.

3. It’s not clear to me what URI you are referring to here, but again if it’s available on the submission then it would come back with the call from item 2. We have tried to design the system so that you typically don’t need to know submission ids, so it would be good to know what you are running up against here.

Please let me know if you have other questions.

Paul



On Dec 18, 2013, at 6:58 AM, Eamonn Maguire <eamonnmag at gmail.com> wrote:

> Hello again,
> 
> Apologies for all the emails. This is as a direct result of us implementing the calls to the new services in these few days.
> 
> I have some more points/issues.
> 
> 
> 1. 'include' parameter behaviour in Search
> 
> Removing links from include list doesn't remove all list terms. e.g. include=definition,synonym,prefLabel gives me everything for this URL http://data.bioontology.org/search?q=dose&ontologies=EFO&include=definition,synonym,prefLabel&apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42
> 
> Removing the definition does work however. http://data.bioontology.org/search?q=dose&ontologies=EFO&include=prefLabel&apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42
> 
> 2. latest submission/version id not available from ontologies view. I'd rather not have to do 2 calls for every ontology.
> 
> 3. No URI information available from http://data.bioontology.org/ontologies
> 
> If the latest version (or submission id) and uri could be added to the results, that would be great. Having to do an additional call for every ontology for the version is a bit time consuming, and not having the URI for an ontology at all increases the number of downstream queries required for our RDF/OWL converters.
> 
> Many thanks,
> 
> Eamonn
> 
> On 17 Dec 2013, at 22:56, 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
> 
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