tasks.md

OpenBEL API

• Validation
  • BEL 2 only
• Autocomplete
  • BEL 2 only
• Import / Export functionality only supports BEL 2.0. An error will be returned if a document's BEL version is != 2.0.

bel.rb

• Language conversion command in bel.rb (e.g. "bel langconvert") to convert from BEL 1.0 to 2.0.
  • Can we use bel.rb's evidence model for the substrate?

BEL Script

• Support BEL version in document properties header.
• Move "Evidence" to "Support". Particularly important for mapping to Evidence model.

(William) BEL Nanopub JSON (BNJ, pronounced "binge") / JGF

• BNJ naming, binge pronounciation
• Evidence -> Nanopub
• Summary Text -> Support (/William)

Punchlist

• Report semantic success/failure for BEL Expression parser.
• Error messages for version1 and version2 semantics.

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BEL/BEL Script Parser

• Syntactic validation of BEL expressions (ASTs)
• BEL, version 1.0.
  • Represent language semantics (functions, relationships, encoding, signatures, etc.)
  • Syntax validation
  • Semantic validation
• BEL, version 2.0.
  • Represent language semantics (functions, relationships, encoding, signatures, etc.)
  • Syntax validation
  • Semantic validation
• BEL Script, version 1.1
  • Syntax validation (document level)
  • Add document property for BEL version (e.g. SET Document BELVersion = "2.0.0")
  • Add URI support for BEL namespace and annotation.
  • Revisit supporting annotation domain (e.g. Anatomy) that comprise multiple datasets (e.g. MESH, UBERON).
    • Conversation with Natalie: http://wiki.openbel.org/display/~abargnesi/Resolving+annotations+and+namespaces+by+type+URI
  • BEL Script parser with adapters for BEL versions 1.0 and 2.0.

XBEL

• New schema for XBEL; support BEL, version 2.0.
  • Add document property for BEL version (e.g. <bel:version>2.0.0</bel:version>)
  • Add URI support for BEL namespace and annotation.
  • Revisit supporting annotation domain (e.g. Anatomy) that comprise multiple datasets (e.g. MESH, UBERON).
    • Conversation with Natalie: http://wiki.openbel.org/display/~abargnesi/Resolving+annotations+and+namespaces+by+type+URI
• Rewrite XBEL translator within bel.rb.
• Parse XBEL for BEL, version 2.0, for AST

JGF

• Review BEL JGF format for conformity.
• Support specifying BEL language in graph metadata
• Add document property for BEL version (e.g. <bel:version>2.0.0</bel:version>)
• Add URI support for BEL namespace and annotation.
• Revisit supporting annotation domain (e.g. Anatomy) that comprise multiple datasets (e.g. MESH, UBERON).
  • Conversation with Natalie: http://wiki.openbel.org/display/~abargnesi/Resolving+annotations+and+namespaces+by+type+URI

RDF

• Review RDF representation for BEL 1.0
• Design and document RDF representation for BEL 2.0
• Implement AST to RDF conversion

API

• Review/document nanopublication (BEL evidence) resulting from processing BEL 2.0
• OpenBEL API autocomplete, syntax, semantic, and component analysis
• Automatable deployment solution for installing

Upgrade content

• Upgrade tools for BEL 1.0 to BEL 2.0 (e.g., activities, locations, etc.)
• Command-line tool (e.g. bel ugprade in bel.rb).
• Upgrade content on import into OpenBEL API from BEL, version 1.0 to version 2.0.
• Upgrade BEL/XBEL documents (corpora, abstracts, etc.)

Vocabulary

• Upgrade BEL terminology throughout (including nanopublications, BEL knowledge networks (BKNs), etc.)

Documentation

• OpenBEL API documentation
• Language specification and documentation
• Provide Integration test documentation
• Provide full user documentation on new features & functionality available in BEL 2.0

Process

• Work closely with PMP and Fraunhofer to test the updated functionality & features

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• [prototype] Implement BEL structural parsers, producing AST.
• [prototype] Implement BEL line parser.
  • normalize new lines
  • line continuator
  • apply BEL structural parsers
• [prototype] Implement BEL Script line parser.
  • normalize new lines
  • line continuator
• [prototype] Implement BEL Script record parsers, producing AST.
• [prototype] Define BEL version 1.0.
  • function types
  • relationship types
  • modification types
  • amino acids
• [prototype] Implement BEL structural validation rules (condition, error messages).
  • [error] Incomplete parameter at column N.
  • [error] Incomplete term at column N.
  • [error] Missing relationship at column N.
• [prototype] Implement BEL version 1.0 syntax validation rules (condition, error messages).
  • [error] Invalid function type.
  • [error] Invalid relationship type.
  • [error] Invalid modification.
  • [error] Invalid amino acid.
• [prototype] Implement BEL version 2.0 syntax validation rules (condition, error messages).
  • [error]
  • [warning]
• [prototype] Implement BEL Script version 1.0 syntax validation rules (condition, error messages).
  • [error] SET DOCUMENT record is invalid.
  • [error] SET DOCUMENT records must occur at the top of the document.
  • [error] DEFINE ANNOTATION record is invalid.
  • [error] DEFINE NAMESPACE record is invalid.
  • [error] DEFINE records must occur at the top of the document after all SET DOCUMENT records.
  • [error] SET record is invalid.
  • [error] Annotation "{NAME}" has not been defined using a DEFINE ANNOTATION record.
  • [error] BEL statement is invalid.
  • [warning] The document does not set a Name property. Try SET DOCUMENT Name = "Document Name".
  • [warning] The document does not set a Version property. Try SET DOCUMENT Version = "Document Version".