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Representation of Proteins with Posttranslational Modifications in the HL7 SPL Standard

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Methods in Pharmacology and Toxicology

Part of the book series: Methods in Pharmacology and Toxicology

Abstract

The Health Level Seven (HL7) Structured Product Labeling (SPL) is an ANSI-accredited data exchange standard, which was adopted by the US Food and Drug Administration (FDA) for the exchange of health and regulatory product and facility data. We describe an extension of this standard for exchanging structural characteristics of substances used as ingredients in medicinal products, particularly in biopharmaceuticals. The chapter covers basics of the abstract SPL data model, its specialization for substances, and its further specialization for proteins with posttranslational modifications. The standard utilizes the XML syntax framework, which allows combining specialized substance-related standards, such as the IUPAC International Chemical Identifier (InChI), with coded terminologies and quantitative parameters important for substance identification. The key elements of the data model for substances are structural units connected in a specified manner or related to each other as mixtures. Small molecules are represented by chemical structures and are uniquely defined using InChI. Macromolecules are represented in two different ways depending on whether they were synthesized in a template-driven chemical/biochemical process (e.g., proteins synthesized on ribosomes) or in a non-template-driven process (e.g., synthetic polymers). In the case of proteins, the arrangement of repeating units is described using the conventional amino acid letter notation. In the case of synthetic polymers, the explicit chemical structures of repeating units are provided. Finally, layers of modifications to the chains are described consistently by substituting the standard structural repeating units with special structural units whose structures are provided in the same XML document. The InChI canonicalization algorithm and the InChI atom numbering schema are used to ensure that the relationships between structural units are represented canonically. Bridging “bioinformatical” and “chemoinformatical” approaches in this way allows describing structures of very complex biochemical objects such as proteins with posttranslational modifications.

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This publication targets the scientific chemoinformatics community only and should not be regarded as a guidance for industry.

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Authors and Affiliations

  1. U.S. Food and Drug Administration, Silver Spring, MD, USA

    Yulia Borodina

  2. Pragmatic Data, LLC, Indianapolis, IN, USA

    Gunther Schadow

Authors
  1. Yulia Borodina
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  2. Gunther Schadow
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Correspondence to Yulia Borodina .

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Borodina, Y., Schadow, G. (2018). Representation of Proteins with Posttranslational Modifications in the HL7 SPL Standard. In: Methods in Pharmacology and Toxicology. Humana Press. https://doi.org/10.1007/7653_2018_31

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  • DOI: https://doi.org/10.1007/7653_2018_31

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  • Publisher Name: Humana Press

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