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Questions tagged [bioservices]

A Python package to access biological web services programmatically (e.g. KEGG, BioModels, UniProt).

From the the website:

BioServices is a Python package that provides access to many Bioinformatics Web Services (e.g., UniProt) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols).

The primary goal of BioServices is to use Python as a glue language to provide a programmatic access to Biological Web Services. By doing so, elaboration of new applications that combine several Web Services should be fostered.

One of the main philosophy of BioServices is to make use of the existing REST or SOAP/WSDL Web Services and therefore existing databases, not to re-invent new databases.

The first release of BioServices provides a wrapping to more than 18 Web Services (more if we consider BioMart and PSICQUIC portals that link to many other Web Services).

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How to parse a Uniprot Dat file to retrieve GO in python?

I have tried BioPython SeqIO and other parsers but couldn't find any good tool to parse DAT files. https://omics.pnl.gov/software/uniprot-dat-file-parser I have tried this one but they don't provide any gene annotations…
Muhammad Zeeshan
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Using Python Multiprocessing Module to Download Models from the BioModels Database

I'm trying to use python multiprocessing module to speed up some computations. The first step is acquiring a number of models from the BioModels database. There is an API for this called BioServices which can be downloaded with pip install…
CiaranWelsh
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Python 3.4 Bioservices installation

I'm trying to install the bioservices : 1.2.5 on my Windows 7 with Python 3.4 installed. The path has the scripts included but I still continue to have the syntax error when trying to use 'pip install'. I tried to install 'bioservices' using: sudo…
user3602771
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How to programmatically map GI numbers directly to HGNC gene names?

I have a collection of ~2000 GI numbers that I need to map to HGNC (aka HUGO) gene names. I will have to do a similar mapping repeatedly in the future, as part of a data analysis pipeline, so I will like to do this mapping programmatically (as…
kjo
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How can I turn this list of strings into a dataframe in pandas

Ok so essentially I extracted a large list of values from a database online using the bioservices package. What I want to do if turn this list of strings into a dataframe using pandas that I can then further format. this is my extracted list of…
Inan Khan
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How to avoid a NameError when defining a class?

I am writing a class: from bioservices import KEGGParser class Retrieve_Data(): def __init__(self): def hugo2kegg(self,gene_name,organism): s=KEGGParser() kegg_gene_entry = s.get(organism+':'+gene_name) …
CiaranWelsh
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