From: tcofoegbu Date: Tue, 4 Aug 2015 09:54:10 +0000 (+0100) Subject: JAL-1788 updated biojson docs X-Git-Tag: Release_2_10_0~554 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=04d6cd653e4c94d919b196530a30f66f39bf9d4e;hp=c394157681d10261bd6f7883b19eaf88d6784609;p=jalview.git JAL-1788 updated biojson docs --- diff --git a/examples/biojson-doc/biojson_uml.png b/examples/biojson-doc/biojson_uml.png new file mode 100644 index 0000000..8a8a971 Binary files /dev/null and b/examples/biojson-doc/biojson_uml.png differ diff --git a/examples/biojson-doc/index.html b/examples/biojson-doc/index.html index 7c82aaf..ba607f4 100755 --- a/examples/biojson-doc/index.html +++ b/examples/biojson-doc/index.html @@ -1,18 +1,354 @@ - Docson Example + BioJSON Format Documentation + +

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

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Navigation Tips

When the mouse is hovered over the elements in the main content section, traversable elements become highlighted and clickable.
Click the âobjectâ button or plus â+â link to expand an object
Click the minus âââ to collapse an object
Click the parenthesis â{}â 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

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Main Content

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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

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BioJSON UML Diagram

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