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link BEL/XBEL into Implementation section #5

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Oct 14, 2015
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link BEL/XBEL into Implementation section #5

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20 changes: 7 additions & 13 deletions version_1.0/ANTLR/README.adoc
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Original file line number Diff line number Diff line change
@@ -1,48 +1,42 @@
language
--------

ANTLR
~~~~~

Pulled directly from the
https://github.com/OpenBEL/openbel-framework[framework].

BELScript.g
^^^^^^^^^^^
+++++++++++

Parse grammar that emits an ANTLR Abstract Syntax Tree. Syntax warnings and errors are caught in this step.

Used by OpenBEL Framework 2.0 / 3.0. See https://github.com/OpenBEL/openbel-framework/blob/experimental/org.openbel.framework.common/src/main/java/org/openbel/framework/common/bel/parser/BELParser.java[BELParser.java].

BELScriptWalker.g
^^^^^^^^^^^^^^^^^
+++++++++++++++++

Walks the AST and transforms into BEL Java Objects (org.openbel.framework.common.model package).

Used by OpenBEL Framework 2.0 / 3.0. See https://github.com/OpenBEL/openbel-framework/blob/experimental/org.openbel.framework.common/src/main/java/org/openbel/framework/common/bel/parser/BELParser.java[BELParser.java].

BELScriptWalker_v1.g
^^^^^^^^^^^^^^^^^^^^
++++++++++++++++++++

_Not used_

BELScript_C_v1.g
^^^^^^^^^^^^^^^^
++++++++++++++++

_Not used_

BELScript_Python_v1.g
^^^^^^^^^^^^^^^^^^^^^
+++++++++++++++++++++

_Not used_

BELScript_v1.g
^^^^^^^^^^^^^^
++++++++++++++

_Not used_

BELStatement.g
^^^^^^^^^^^^^^
++++++++++++++

Parses a BEL Statement into a BELStatement Java Object (org.openbel.framework.common.model.BELStatement).

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13 changes: 5 additions & 8 deletions version_1.0/XML/README.adoc
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@@ -1,20 +1,17 @@
language
--------

XML
~~~

Pulled directly from the
https://github.com/OpenBEL/openbel-framework[framework].

xbel.xsd
^^^^^^^^
++++++++

XML schema definition for BEL documents. Used by the legacy Java BEL Framework.

http://resource.belframework.org/belframework/1.0/schema/xbel.xsd[XML Schema Document]

xbel-annotations.xsd
^^^^^^^^^^^^^^^^^^^^
++++++++++++++++++++

XML schema definition for BEL annotations used by the legacy Java BEL
Framework.

http://resource.belframework.org/belframework/1.0/schema/xbel-annotations.xsd[XML Schema Document]
35 changes: 35 additions & 0 deletions version_1.0/bel_specification_version_1.0.adoc
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Expand Up @@ -3255,6 +3255,41 @@ cat(p(HGNC:HSD11B1)) => \

The top statement represents the forward reaction and the bottom statement represents the reverse reaction.

Implementation
--------------

Formats
~~~~~~~

BEL Script (ANTLR Grammars)
^^^^^^^^^^^^^^^^^^^^^^^^^^^

BEL Script is a syntax and format for encoding BEL Statements and associated annotations as human-readable documents that can also be efficiently processed.

include::ANTLR/README.adoc[]

BEL Script (Ragel Parser)
^^^^^^^^^^^^^^^^^^^^^^^^^

The http://www.colm.net/open-source/ragel/[Ragel] parser files can be found https://github.com/OpenBEL/bel.rb/tree/master/lib/bel/ragel[here]. The http://www.colm.net/open-source/ragel/[Ragel] files can be used to create a parser in a http://www.colm.net/open-source/ragel/[Ragel]-supported language. For example to compile for Ruby you would execute +ragel -F0 -L -R bel.rl+.

XBEL
^^^^

include::XML/README.adoc[]

Tools
~~~~~

Java
^^^^

The https://github.com/OpenBEL/openbel-framework[OpenBEL Framework] implements a BEL Script and XBEL parser in the Java library https://github.com/OpenBEL/openbel-framework/tree/experimental/org.openbel.framework.common[org.openbel.framework.common].

Ruby
^^^^

The https://rubygems.org/gems/bel[bel] Ruby gem parses BEL Script and XBEL.

[glossary]
Glossary
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