Information about chemicals

This tutorial explains how to use a few of the VHP4Safety services to aggregate information about a chemical of interest.

Let’s start with the compound with the name “aflatoxin B1”.

Name to Structure

The first task we have is to establish a chemical identity of what we mean with “aflatoxin B1”. That is, what is the chemical structure. This common task is the starting point of most cheminformatics workflows: the resolve the chemical structure from a chemical name. That is, a name to structure conversion.

There are many solutions available, including the main chemical compounds databases like PubChem and ChemSpider. Because we want to use a common VHP4Safety language (a controlled vocabulary or glossary), we can also use a VHP4Safety solution for this task.

For this, we have set up a service to link specific chemical structures to names and external databases, the VHP4Safety Wikibase.

Step 1

Visit the compound wiki and use the search box to find “aflatoxin B1”. The resulting page should look something like this:

Step 2

On this page we can find chemical information and links to other database. Information we can find include:

• the SMILES: a line notation to describe the chemical structure (using a chemical graph approach)

• the mass

• the InChI and InChIKey: the global, unique identifier of this compound

Write down the SMILES, which we are going to use in the next section.

Second, we find external identifiers and links to resources with more information about this compound. For example, for this compound we find a link to the ToxBank Wiki (doi:10.1002/minf.201200114) where the SEURAT-1 cluster projects collected information about compounds in their discussion to reach their Gold Compound collection.

Other information we can find:

• the Wikidata Q identifier: a link to Wikidata

• the PubChem CID: a link to PubChem

• xenobiotic metabolism pathway: a link to a WikiPathways describing experimental knowledge about the compound metabolism

Visualize a Structure

With the SMILES you got from the compound wiki, you can now visualize this with the CDK Depict service.

Step 3

Copy/paste the SMILES into the text box and wait for CDK Depict to make a 2D depiction:

Note that you can change the depiction style/properties. For example, you can choose to not abbreviate long chains:

Or to show the CIP R/S labels:

External databases

Back in the wikibase, we can find links to other databases. The compound wiki provides links to the following databases. For each we can list the chemical compounds that have links to those resources:

• ToxBank: general toxicology info (all ToxBank compounds)

• WikiPathways: compound metabolism (all WikiPathways compounds)

Step 4

Visit WikiPathways and check the human metabolism of “aflatoxin B1”. The resulting page should look like this:

These resources can provide important information, but for new compounds you mean also need computationally predicted properties. The platform support this. The following section uses the SOMBIE tool, that predicts site-of-metabolism properties, starting with the SMILES we get from the compound wiki.

Identifier Mapping

The compound wiki also lists a PubChem Compound Identifier (“cid”). The BridgeDb webservice can convert this to identifiers from other database.

Step 5

The BridgeDb Webservice has an API call where you can request other identifiers (“xrefs”) for a PubChem CID identifier with the following URL pattern: https://bridgedb.cloud.vhp4safety.nl/Human/xrefs/Cpc/186907

Click the link and check in what other databases information is provided for “aflatoxin B1”. The output should look something like this:

C00000546    KNApSAcK
CHEBI:2504   ChEBI
C06800       KEGG Compound
DTXSID00873175       EPA CompTox
186907       PubChem-compound
OQIQSTLJSLGHID-WNWIJWBNSA-N  InChIKey
CHEMBL1697694        ChEMBL compound
DTXSID9020035        EPA CompTox
1162-65-8    CAS
162470       Chemspider
Q4689278     Wikidata
HMDB0006552  HMDB
2504 ChEBI
HMDB06552    HMDB

Metabolite prediction

… SOMBIE todo