[ensembl-dev] Few queries regarding Ensembl Rest API Endpoints

[Jorge Batista da Rocha]

Hi Jaya! 

Thanks for getting in touch! Sorry for the delay, I’ll address the Qs as best I can, but will check in with our dev teams too. 

1.) As far as I know, when the request requires species, it is possible to use non-scientific names from here: https://github.com/Ensembl/ensembl-rest/wiki/Parameters#species there is a json file there with species alias info http://rest.ensembl.org/info/species.json 

2.) I do not think it is possible to get around the size limit as this protects the API service for all users. There may be other workarounds - like our mysql access https://www.ensembl.org/info/data/mysql.html . That would be more suitable for large sizes of data. 

And as for training- yes of course - Ensembl Outreach has a REST API workshop as part of our offerings, https://training.ensembl.org/hosting 

Please drop us a message at helpdesk at ensembl.org <mailto:helpdesk at ensembl.org> to get in contact about training workshops and we’ll take it from there. 

Cheers
Jorge (Ensembl Outreach)


Dr Jorge Batista da Rocha
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)

> On 13 Dec 2024, at 23:01, Jaya Sravani Sirigineedi <jsirigin at charlotte.edu> wrote:
> 
> Hello,
> 
> I am Jaya Sravani Sirigineedi, a part-time software developer working on the Integrated Genome Browser(IGB) by Bioviz.org under the supervision of Dr. Ann Loraine. Currently, we are exploring the Ensembl Rest API endpoints to integrate them into IGB. We plan to provide a dynamic search for the users where they can enter a non-scientific genome name and we provide suggestions based on that, once the user selects one of the suggestions we get all the genome data from Ensembl and load them into IGB to visualize them. 
> While investigating the APIs, we encountered a few questions and would greatly appreciate your guidance. Here is the list of questions:
> 
> Genome Search Functionality with Non-Scientific Names: There is one API that's available to do a search using the non-scientific name (https://rest.ensembl.org/documentation/info/taxonomy_name) that is present in Ensembl and we have observed there is no prefix search i.e., if I search for hum instead of human it doesn't return any results. We are wondering if any APIs are available to do this kind of search.
> Handling API Size Limits: For a few APIs, such as this API (https://rest.ensembl.org/sequence/region/human/X:1..156040895?content-type=application/json) that returns the sequence of a specified region and this one (https://rest.ensembl.org/overlap/region/human/1:0-26170921?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon) that returns the features overlapped over the specified region, we observed that size limits restrict the amount of data retrieved. Since we aim to load entire chromosomes, is there a way to bypass or increase these limits, perhaps via an API key or another method?
> Additionally, we would like to inquire if it would be possible to arrange a workshop, meeting, or session where we could discuss these questions in more detail and learn how to make the best use of the Ensembl APIs for our project. We are flexible and can adjust to your schedule.
> 
> Thank you for your time and assistance. Please let us know if you need any more information.
> 
> Looking forward to your response.
> 
> Thanks & Regards
> Jaya Sravani Sirigineedi
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