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The excitement of modern biological research is that we all agree that, at least at some level, we are all exploring aspects of the same thing.

To some of the blind men the elephant feels like a column, to some like a snake, to others like a wall. Biological science is very much like the parable of the blind men and elephant. Biomedical information is a vast interconnected web of data which crosses many domains of discourse with very different ways of viewing the world. Here the data model attempts to achieve a number of goals. The other major area of the specification is biological sequence data and its associated information. Despite its importance, the bibliographic specification will not be discussed further here, since it does not present ideas which may be novel to the reader. Unlike biological data, this data is relatively well understood, so we hope that the bibliographic specification can be quite complete and stable.

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We have followed the American National Standard for Bibliographic References (ANSI Z39.29-1977) and consulted with the US Patent Office and professional librarians to ensure complete and accurate representation of citation information. It is clear that this class of information is central to all scientific fields within and outside of molecular biology so we expect these definitions to be widely useful. There are two major areas for which data objects have been defined. They are also described in the section on the appropriate module. Selected ASN.1 definitions are inserted into the body of the text as necessary. This section provides an overview of all modules.

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Each module section begins with a description of the elements, followed by the full ASN.1 definition of the module. Some of these are described in the section on the module and some with more extensive interfaces are described in additional sections. Each C++ class has at a minimum, functions to: create it, write it to an ASN.1 stream, read it from an ASN.1 stream, and destroy it. Each ASN.1 defined object has a matching C++ language class.

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The data specification sections are arranged by ASN.1 module with detailed discussions of data objects defined in each and the software functions available to operate on those objects. A much fuller description of ASN.1 and the NCBI software tools which use it appears in later chapters. Enough explanation will be given here to allow the reader to examine the data definitions. For this reason we have chosen to describe our data in Abstract Syntax Notation 1 (ASN., 8825). However, we also wish to embrace the intellectual rigor imposed by describing our data within a formal system and in a machine readable and checkable way. Since we expect that computer technologies will continue to develop at a rapid rate, NCBI has made considerable investment of time and energy to ensure that our data and software tools are not too tightly bound to any particular computer platform or database technology. In the following sections we will present the unifying ideas, then examine each area of the model in more detail. Specialized objects are defined which are appropriate within a domain. It is designed to provide a few unifying concepts which cross a wide range of domains, providing a path between the domains. The NCBI sequence databases and software tools are designed around a particular model of biological sequence data. The Data Model section outlines the NCBI model for biotechnology information, which is centered on the concept of a biological sequence as a simple, linear coordinate system.Īssociating Annotations With Locations On Biological SequencesĬollections of Related Biological Sequences The following is an outline of the topics presented in this chapter: Francis OuelletteĬhapter 2 - The NCBI Data Model Chapter Outline Another good source of information about the NCBI data model is:Ī Practical Guide to the Analysis of Genes and ProteinsĮdited by Andreas D. ASN.1 type names and the corresponding C++ class or data member names are used almost interchangeably throughout the chapter. This chapter describes the NCBI Biological Sequence Data Model, with emphasis on the ASN.1 files and C++ API. Biological Sequence Data Model Introduction