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.

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

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:

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+)

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"])

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(!)

• DIMEdb Home Page
• DIMEdb Help Page

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