dimedbpy: Python wrapper for the DIMEdb REST API

dimedbpy provides a quick and easy way to interact with the DIMEdb web service through Python. It provides metabolite queries by name, structure, and isotope information.

Installation

DIMEpy requires Python 3+ and is unfortunately not compatible with Python 2. If you are still using Python 2, a clever workaround is to install Python 3 and use that instead.

You can install it through pypi using pip:

pip install dimedbpy

If you want the 'bleeding edge' version, you can also install directly from this repository using git - but beware of dragons:

pip install git+https://www.github.com/AberystwythSystemsBiology/dimedbpy

Usage

Simple Search

Here's a quick example, showing how to retrieve metabolites by name. Note that name is the namespace and Sucrose is the search value:

from dimedbpy import get_metabolites

metabolites = get_metabolites("name", "Sucrose")

for metabolite in metabolites:
    print(metabolite.name)

The following namespaces are supported:

Namespace	API Translation	Descripton	Example
inchikey	"Identification Information.Name"	Compiled InChIKey	CZMRCDWAGMRECN-UGDNZRGBSA-N
name	"Identification Information.Name"	Common name	Sucrose
molecular_formula	"Identification Information.Molecular Formula"	Textual description of elemental composition	C12H22O11
smiles	"Identification Information.SMILES"	Isometric SMILES	Too long.
inchi	"Identification Information.InChI"	Unique InChI identifier	Too long.
kegg	"External Sources.KEGG Compound"	KEGG Compound Identifier	C00089
pubchem	"External Sources.PubChem"	PubChem Identifier	5988
cas	"External Sources.CAS"	CAS Registry Number	57-50-1
hmdb	"External Sources.HMDB Accession"	HMDB Accession Number	HMDB00258
chemspider	"External Sources.Chemspider"	Chemspider Identifier	5768
biocyc	"External Sources.BioCyc"	Bio/MetaCyc Identifier	SUCROSE
chebi	"External Sources.ChEBI"	ChEBI Identifier	17992

Mass Search

You can search for metabolites easily through the mass_search method.

Here's a simplified example:

import dimedbpy

metabolites = = dimedbpy.mass_search(
                    mass=420.69,
                    polarity="positive",
                    tolerance=0.25,
                    isotopic_distributions=[
                    "[M-H]1-", "[M+Cl]1-", "[M+Br]1-"
                    ]
                )

This is pretty self-explanatory.

There's a as_dataframe parameter you can use to output it as a pandas dataframe.

Note: If nothing is passed to the isotopic_distributions parameter, then sane defaults are used (Negative: [M-H]1-, [M+Cl]1-, M+Br]1 and Positive: [M+H]1+, [M+K]1+, [M+Na]1+)

Metabolite Object

As noted previously, both the get_metabolites() and mass_search() methods returns a list of Metabolite objects.

If you already know the InChIKey of the metabolite you're interested in - it is possible to instantiate a Metabolite instantly using the from_inchikey method.

from dimedbpy import Metabolite

metabolite = Metabolite.from_inchikey("DOUMFZQKYFQNTF-WUTVXBCWSA-N")

In addition to this, For ease of access Metabolite contains a _record property which represents a Python dictionary that contains all of the data about the Metabolite.

Moreover, the to_dict() class method returns a simplified dictionary representation of the aforementioned data. Through this method it is also possible to list the desired properties to obtain, for example:

from dimedbpy import Metabolite

metabolite = Metabolite.from_inchikey("DOUMFZQKYFQNTF-WUTVXBCWSA-N")

metabolite.to_dict(properties=["Name", "Synonyms", "Molecular Formula"])

Bug reporting and feature suggestions

Please report all bugs or feature suggestions to the issues tracker. Please do not email me directly.

We welcome all sorts of contribution, so please be as candid as you want(!)

Resources

• DIMEdb Home Page
• DIMEdb Help Page

License

dimedbpy is released under the terms of the permissive MIT license.