Chemicals

In order to uniquely identify chemicals, we use InChI keys as the primary way of identifying chemicals.

Source

We rely on PubChem for information about chemistry as well as user inputs.

How will the information accessed?

We will be accessing PubChem from within the MBDB by making calls to their REST API (opens in a new tab).

Why InChI keys?

There's a number of advantages to using InChi keys.

Only the chemical structure needs to be known

InChi keys are directly derived from an InChI string which in turn is derived from the chemical structure. This means that even for chemicals that are not deposited anywhere, we are still able to generate the same unique identifier that it will eventually get when deposited to PubChem or similar resource.

Searching across different isotope version of the same chemical

Even after being turned into InChI keys, it's still possible to identify that the only difference between two chemical is their isotopic composition. This is very useful if one wants to search for all records that contain a certain molecule, regardless of isotope. This feature would be very difficult to create otherwise.

Efficient searching

InChI keys has the advantage of being very well suited for being efficiently searched and stored in databases, it's part of how they were designed.

I can't find my chemical, what should I do?

You can add your own chemical
here (opens in a new tab). Note that you have to be logged in to create a new vocabulary item, and that it will be available to everyone.

Furthermore, as we use InChI keys, you need to know the chemical structure. Based on the structure, the InChI string can be generated, which in turn can be converted to an InChI key. Most chemical software should be able to fo this.

Fields available

id

The id prefix is inchikey:.

Description: The id of the chemical in the form of an inchikey:XLYOFNOQVPJJNP-UHFFFAOYSA-N"
Required: yes
Type: string (keyword)

title

Description: The systematic name of the chemical
Required: yes
Type: object (Title)
Contains: see Vocabulary title

additional_identifiers:

Description: Unique and persistent identifier from an external source; options of sources are CAS number (cas:), ChEMBL ID(chembl:), Pubchem Compound ID (pccid:), and Pubchem Substance ID (pcsid:)
Required: no
Type: array of string

molecular_weight

Description: The molecular weight of the chemical
Required: yes
Type: object (Molecular weight)
Contains: See Molecular weight

chemical_formula:

Description: The chemical formula (e.g H2O) of the chemical
Required: yes
Type: string (fulltext)