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Old 07-16-2010, 05:52 AM   #1
svl
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Default pathways API KEGG

Hi all,

First a general question:
Does anyone know of a good biological pathway database comparison? Is KEGG an extensive one, or are all those databases for a specific type of pathways?

And the more detailed one:
Basically what I want is, in an automated fashion, for a list of genes (ENSG###) -> get all pathways in which the transcripts/proteins of a gene play a role.

The closest I have come so far is by using the Ensembl perl api and KEGG perl API:
  1. Ensembl API: make gene object with Ensembl id ( ENSG#### )
  2. Ensembl API: get the unigene id ( using $gene->get_all_DBLinks )
  3. KEGG API: retrieve pathways ($serv->KeggGetPathwaysByGenes )
So far, so good, it works, but there aren't many genes in my lists with an annotated pathway (around 10%)...making me wonder whether KEGG is a good resource for listing all possible pathways annotated.

Does anyone know a better workflow for this?

Thanks,
Stef

Last edited by svl; 07-16-2010 at 07:45 AM.
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Old 07-24-2010, 04:46 AM   #2
BioSlayer
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Another resource that can be accessed via an API is WikiPathways http://www.wikipathways.org/index.ph...ays_Webservice.

I will say try to integrate the information collected from different sources all together for you to get to see a wholesome picture. Other pathway resources out there are WIT and PathDB as I remember but I am not really sure if they do have an API to their interface...
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Old 08-01-2010, 08:01 AM   #3
svl
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Thanks for the help, BioSlayer, I've decided to just download txt DBs with the pathway information as using the API could get really slow for the hundreds of genes I would like to query the DB with... I have different scripts for KEGG and Reactome pathways now, will have a look at your suggestions as well.

-Stef
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Old 02-09-2011, 04:44 PM   #4
sneha
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Hi guyz,
I want to know how the Kegg API works if I want to automate a list of genes from P.aeruginosa organism and obtain the metabolic pathways the resulting proteins are involved in. Thanks.
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Old 02-10-2011, 12:31 AM   #5
svl
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Hi Sneha,

Here's the documentation of the api:
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

There is example code for perl, ruby, python and java.

/Stef
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Old 02-10-2011, 02:37 PM   #6
sneha
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Thanks svl for the link. When I am downloading SOAP Lite , MIME-Base64, LWP and URI , and running the example scripts, it is not working as it says it cannot locate the module and stuff. Is there any other way that I can go about it? Thanks.
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