DrugBank Release Notes

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This export was originally created on Jan 1 2020, and contained invalid XML in the complete database XML file. This issue was corrected on Jan 3.

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This release includes a change to the XML data and schema:

• The DrugBank accession number for salts (now termed product ingredients) can now point to a drug (active moiety) entry.
• Drug products from the EMA (European Medical Association) are now included in the export.

Some of the structures in the previous release were invalid, this has been corrected in 5.0.11.

This release includes a new dataset, Structure External Links. The structure external links datasets are CSV files which include structure information in the form of InChI/InChI Key/SMILES as well as identifiers for other drug-structure resources (such as ChEBI, ChEMBL, etc.). Included in each dataset is also the PubChem Compound ID (CID) and the particular PubChem Substance ID (SID) for the given DrugBank record.

This release also includes an update to the PubChem SIDs based on the latest deposition.

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Fixes

• fixes missing header in the full database xml file

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Fixes

• This release fixes a bug in the Target Sequences exports (FASTA format). Specifically, there were some missing DrugBank IDs for protein/gene sequences in the FASTA headers. If you are using version 5.0.0 to 5.0.2, please upgrade to this version as soon as possible.
• This version also includes a fix for duplicate drug-drug interactions. Each drug pair will now only include a single drug interaction description.

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This version brings our XML release format in line with the information that can be found on the www.drugbank.ca website.

If you plan on using DrugBank data commercially, please contact us at info@omx.io.

Current XML Schema Changes

Replaced Elements

This version introduces a new reference-list-type element type which includes structured data describing references to textbooks, web pages, and articles (typically from PubMed).

<xs:complexType name="article-type">
    <xs:sequence>
        <xs:element name="pubmed-id" type="xs:string"/>
        <xs:element name="citation" type="xs:string"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="textbook-type">
    <xs:sequence>
        <xs:element name="isbn" type="xs:string"/>
        <xs:element name="citation" type="xs:string"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="link-type">
    <xs:sequence>
        <xs:element name="title" type="xs:string"/>
        <xs:element name="url" type="xs:anyURI"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="article-list-type">
    <xs:sequence>
        <xs:element maxOccurs="unbounded" minOccurs="0" name="article" type="article-type"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="textbook-list-type">
    <xs:sequence>
        <xs:element maxOccurs="unbounded" minOccurs="0" name="textbook" type="textbook-type"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="link-list-type">
    <xs:sequence>
        <xs:element maxOccurs="unbounded" minOccurs="0" name="link" type="link-type"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="reference-list-type">
    <xs:sequence>
        <xs:element maxOccurs="1" minOccurs="1" name="articles" type="article-list-type">
            <xs:annotation>
                <xs:documentation>Articles are typically PubMed references, although there are some references which do not have a PubMed ID.</xs:documentation>
            </xs:annotation>
        </xs:element>
        <xs:element maxOccurs="1" minOccurs="1" name="textbooks" type="textbook-list-type"/>
        <xs:element maxOccurs="1" minOccurs="1" name="links" type="link-list-type"/>
    </xs:sequence>
</xs:complexType>

• <drug> elements now use reference-list-type elements for <general-references>
• <target> elements now use reference-list-type element for <references>

Additional Elements

• <pathway> elements now include a category element containing the name of the SMPDB category for that pathway.
• <drug> elements now include the following new elements:
  • <unii>: the unii associated with the drug
  • <average-mass>: the average-mass of small-molecule drugs
  • <monoisotopic-mass>: the monoisotopic mass of small-molecule drugs
  • <state>: one of solid, liquid, or gas
  • <pdb-entries>: a list of <pdb-entry> elements, each containing a pdb identifier for the drug
  • <fda-label>: a URI pointing to a copy of the FDA label for the drug
  • <msds>: a URI pointing to a copy of the material safety data sheet for the drug
• <drug-salt> elements now include the following new elements:
  • <unii>: the unii associated with the drug salt
  • <average-mass>: the average-mass of the drug salt
  • <monoisotopic-mass>: the monoisotopic mass of the drug salt
• <product> elements now include the following new elements
  • <labeller>: The name of the product labeller
• <manufacturer> elements now include the following new elements
  • <url>: a URL representing the manufacturer
• <patent> elements now include the following new elements:
  • <pediatric-extension>: a boolean indicating whether a pediatric exclusivity extension applies to the patent
• <external-identifiers> elements now include new identifiers. The <resource> element can now include the following new values:
  • ChEMBL
  • Therapeutic Targets database