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.
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.
Advantages of JSON/BioJSON
- JSON is very popular and available in almost all programming languages
- Integrates seamlessly with the HTTP rest architecture
- Very light weight, self describing and easy to understand
- Handles linked data very efficiently
Navigation Tips
- When the mouse is hovered over the elements in the main content section, traversable elements become highlighted and clickable.
- Click the “object” button or plus “+” link to expand an object
- Click the minus “—” to collapse an object
- Click the parenthesis “{}” link to view the JSON schema which provides a more technical description of the data
- 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
Main Content
Brief definition of key terms
- Residue - This is a single unit of a Nucleic acid (RNA, DNA) or Amino acid (Protein).
- Sequence - A Sequence contains an array of residues with basic details about it (i.e name, start/end positions, database source, etc)
- Alignment - An alignment consists of an array of individual Sequences organised together, one above each other
- Group - Sections of an alignment or Sequence can be coupled together to form a group
- 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)
- Feature - Used to store data of known properties for sections of a sequence or alignment
BioJSON UML Diagram
