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- Docson Example
+ BioJSON Format Documentation
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BioJSON Format
+The BioJSON Format was introduced in Jalview 2.9 to serve as a standard format for representing/exchanging Bioinformatics Alignment data in JSON. This is the first version of the specification and we welcome all feedbacks on how to make BioJSON better, sustainable and widely adopted worldwide.
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+This page describes the data available in BioJSON format, the main content section was created with Docson - a resource which uses a JSON schema to generate a beautified and an interactive documentation.
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Advantages of JSON/BioJSON
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JSON is very popular and available in almost all programming languages
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Integrates seamlessly with the HTTP rest architecture
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Very light weight, self describing and easy to understand
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Handles linked data very efficiently
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Navigation Tips
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When the mouse is hovered over the elements in the main content section, traversable elements become highlighted and clickable.
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Click the âobjectâ button or plus â+â link to expand an object
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Click the minus âââ to collapse an object
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Click the parenthesis â{}â link to view the JSON schema which provides a more technical description of the data
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When you expand an object the following information becomes visible: The variables in the object, their data types and the description of each variable. This exactly corresponds to how it appears in BioJSON
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Main Content
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Brief definition of key terms
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Residue - This is a single unit of a Nucleic acid (RNA, DNA) or Amino acid (Protein).
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Sequence - A Sequence contains an array of residues with basic details about it (i.e name, start/end positions, database source, etc)
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Alignment - An alignment consists of an array of individual Sequences organised together, one above each other
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Group - Sections of an alignment or Sequence can be coupled together to form a group
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Annotation - Annotation provides various kinds of information for what is known about a sequence(Sequence Annotation), or a collection of sequences in the alignment (Alignment Annotation)
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Feature - Used to store data of known properties for sections of a sequence or alignment
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