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queryHitPathways API is restricted to human #1

Closed teheavy closed 8 years ago

teheavy commented 8 years ago

Hi,

I'm a developer who is trying to get Arabidopsis thaliana pathways from queryHitPathways API, but I'm not sure when will be this API open to other species.

Thanks!

fabregat commented 8 years ago

Hi,

I recommend you to have a look at the developer guide (http://www.reactome.org/pages/documentation/developer-guide/) where you can find the RESTful API (http://www.reactome.org/pages/documentation/developer-guide/restful-service/) where the queryHitPathways is but also to Analysis Service (http://www.reactome.org/pages/documentation/developer-guide/analysis-service/) which API is http://www.reactome.org/AnalysisService/

If you use the analysis service, please be sure that you don't use the projection methods so you will get the results in your species of interest. Finally, and taking into account your requirements, I also recommend you to use protein accessions rather than gene names.

Thank you for your interest in Reactome!

teheavy commented 8 years ago

Hi fabregat,

Thanks for the help! I've tried to use the analysis service to get query hits, however, it seems all the ones I tried on Arabidopsis does not give me any result.

AGI: AT1G68020 Uniprot: Q94AH8 http://www.reactome.org:80/AnalysisService/identifier/Q94AH8?pageSize=20&page=1&sortBy=ENTITIES_PVALUE&order=ASC&resource=UNIPROT

AGI: AT4G18780 Uniprot: Q8LPK5

and a different plant species Uniprot: Q0JKD0

But it works with Plant Reactome (although there's something wrong with search function) http://plantreactome.gramene.org/content/query?q=AT1G68020&species=Arabidopsis+thaliana&cluster=true

So I'm thinking that maybe Reactome database is not connected to Plant Reactome, is that right?

Thanks, Fred

fabregat commented 8 years ago

You're right.

They are two different projects (even though they share the code).

You also have an AnalysisService in Plant Reactome

http://plantreactome.gramene.org/AnalysisService/

Please note that you can use the "identifiers" method to submit all your protein identifiers and then get the list of most significant pathways there.

Thank you for your interest in Reactome.

Best regards,

preecej commented 8 years ago

Fred,

Plant Reactome developer here. It is true that some API functions (like queryHitPathways) are still restricted to H.sapiens results, even in the Plant Reactome. I'm working on removing that restriction now. I'll keep you updated.

teheavy commented 8 years ago

Great! Thank you guys! I used Analysis Service from Plant Reactome and got the solution I wanted!

teheavy commented 8 years ago

Oh, sorry, one more question. Since I'm currently using analysis service to get query result and export pathway using the BioPax level 3 format, I'm wondering if the service can also return an SBGN diagram?

Thanks! Fred

preecej commented 8 years ago

You could download any pathway in SBML...

http://plantreactome.gramene.org/ReactomeRESTfulAPI/RESTfulWS/sbmlExporter/6788019

...and then convert to SBGN using an external tool.

On 03/25/2016 09:22 AM, teheavy wrote:

Oh, sorry, one more question. Since I'm currently using analysis service to get query result and export pathway using the BioPax level 3 data, I'm wondering if the service can also return a SBGN diagram?

Thanks! Fred

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teheavy commented 8 years ago

Thanks! I found tools that can convert files from BioPAX to SBGN.