Retrieve bioSamples from NCBI using url API

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4.5 years ago

mounim1024 • 0

Hello everyone,

I was wondering and looking around in thr internet if there's any way to retrieve biosamples meta data using the url API, In fact, i need this for a script that will be implemented in django, I used the same method to retrieve bioProject metadata and it worked perfectly ( i just dynamically combined the link outils.ncbi.nlm.nih.gov/entrez/outils/eftech.fcgi + the name of database + the accession numbera), which returns an XML.

This method doesn't work for bioSamples because the developers of Entrez used a "historyId" attribute instead of the accession number for retrieving data from using the link !

I would like to get your help or guidance for any path that might be helpfull

Thanks

api sequence • 1.0k views

ADD COMMENT • link updated 4.5 years ago by GenoMax 147k • written 4.5 years ago by mounim1024 • 0

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Not clear what exactly you are looking to get. Can you provide an example?

ADD REPLY • link 4.5 years ago by GenoMax 147k

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In the case that this is a problem of conversion of the "historyID" to NCBI accession number for making the API request : you can try using biomaRt in R in which you can interchange between different identifiers. A post related to this : C: Map Protein Accession Number to Uniprot identifier in R

ADD REPLY • link 4.5 years ago by manaswwm ▴ 550

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