2.4. Manipulating compound identifiers

Application: retrieving information about a compound

This section uses BioServices to demonstrate the interest of combining several services together within a single framework using the Python language as a glue language

2.4.1. Retrieve a compound identifier from KEGG, ChEBI and ChEMBL

Let us look at a compound called Geldanamycin that inhibits Hsp90. Let us search for information about that compound in several databases and manipulate the different identifiers.

First, let us retrieve information on KEGG database:

>>> from bioservices import KEGG
>>> k = KEGG(verbose=False)

KEGG compounds have links to other databases. It is not systematic but the ChEBI database is often referenced. So we will want to convert the KEGG identifer to a ChEBI identifier. Later, we can convert a ChEBI to a ChEMBL identifier using another Web Service such as UniChem.

We can get a mapping dictionary from the KEGG compound to ChEBI as follows:

>>> map_kegg_chebi = k.conv("chebi", "compound")
>>> len(map_kegg_chebi) 
15845

>>> print(k.find("compound", "geldanamycin"))
cpd:C11222  Geldanamycin
cpd:C15823  Progeldanamycin

Let us look at the first one (KEGG id cpd:C11222). We can get lots of information from KEGG already by using:

>>> print(k.get("C11222"))

Form which, there is a link to other databases in particular ChEBI (ChEBI:5292). We could use the mapping dictionary created above:

>>> map_kegg_chebi['cpd:C11222']
'chebi:5292'

Unfortunately, there is no mapping function from KEGG to ChEMBL in KEGG Web Service. There was a mapping function in bioservices.unichem servive that was dropped in 2022. We can still use another service. In order to convert KEGG gene names into uniprot gene name, we can also use the UniProt web service from BioServices as follows:

>>> from bioservices import UniProt
>>> u = UniProt()
>>> u.mapping(fr='UniProtKB_AC-ID', to='KEGGD', query="ZAP70_HUMAN")
{'ZAP70_HUMAN':  'hsa:7535'}