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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 download coloured KEGG PATHWAY maps in python

I have a list of enzymes (EC numbers, "df" from the code) that I want to highlight in KEGG PATHWAY maps. I would like to make a python script that automatically saves the highlighted maps. So far I could only make urls from which I manually download…
Pol Torrent
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How to access a KEGG entry without specifying the organism using bioservices?

I try to access KEGG via bioservices to get certain information about a list of genes. Problem is that I do not know beforehand to which organism the individual genes belong; in my list can be a lot of genes that all belong to different organisms.…
Cleb
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Exception handling and continuing with a for loop in python

I have the following code: import Bio from bioservices import KEGGParser, UniProt, QuickGO #start a new method of my custom 'Retrieve_Data' class def locate_common_GO(self,list_of_genes,GO_term): #initialize variables and classes q =…
CiaranWelsh
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How to solve "ECitMatch() got multiple values for argument 'bdata'"?

I am new to use bioservices Python package. Now I am going to use that to retrieve PMIDs for two citations, given the specified information and this is the code I have tried: from bioservices import EUtils s =…
Zoey
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xmltodict: ExpatError: syntax error: line 1, column 0, getting xml from QuickGO

I'm finding myself a bit confused by the error I get from the following from future.standard_library import install_aliases install_aliases() from urllib.request import urlopen import xmltodict oboxml =…
Jeff S.
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SSL errors for all pip commands

I'm trying to begin using Python 3.6 on a Windows 10 Enterprise but whenever I try to use pip to install necessary packages I always get a similar SSL error. pip install requests gives the following error: Collecting requests Retrying…
user90823745
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How to retrieve all ChEBI IDs for a given KEGG compound?

Let's say I want to map a KEGG ID to a ChEBI ID using bioservices, I can do: from bioservices import * kegg_con = KEGG() kegg_entry = kegg_con.parse(kegg_con.get('C00033')) print(kegg_entry['DBLINKS']['ChEBI'].split()) This will return [u'15366',…
Cleb
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If statement and writing to file

I am using the KEGG API to download genomic data and writing it to a file. There are 26 files total and some of of them contain the the dictionary 'COMPOUND'. I would like to assign these to CompData and write them to the output file. I tried…
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PTM data from bioservices uniprot

I want to retrieve Post-translational modifications (PTMs) data from Uniprot via bioservices, I am using following script: from bioservices import uniprot u = uniprot.UniProt() ptm = u.search("P38903", frmt="xls", include=True,…
user3698773
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Bioinformatic retrieval of GO terms and comparison against a user specified term

I have the following function (that belongs to a class): import Bio from bioservices import KEGGParser, UniProt, QuickGO def locate_common_GO(self,list_of_genes,GO_term): #initialize variables and classes q = QuickGO() a =…
CiaranWelsh
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Python package: Bioservices, error using UniChem() command

I was following the tutorial on the webpage: http://pythonhosted.org/bioservices/compound_tutorial.html Everything worked well until I reached the following command: uni = UniChem() and then I received the error message: Traceback (most recent call…
joel38237
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Chem.RDKFingerprint did not match C++ signature for some SMILES, but okay for others

I'm working on trying to use ligands that are referenced in UniProt with the same ligand in PDB entries. For many ligands (e.g. FAD), the three-letter code is the same in both UniProt and PDB entries, but for some there is a slight difference. For…
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I want to put the output of this print(d) function into a pandas dataframe

I am working with the bioservices package in python and I want to take the output of this function and put it into a dataframe using pandas from bioservices import UniProt u = UniProt(verbose=False) d =…
Inan Khan
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How to interconvert InChI and InChIKey?

I would like to retrieve IDs from several databases using InChI as an input, e.g. InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1 One can use unichem from bioservices for this, however, these functions all require the…
Cleb
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How to retrieve InChI key for KEGG compound?

I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this. One could do it via ChEBI like this: from bioservices import * kegg_con = KEGG() kegg_entry =…
Cleb
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