20140518

RDF model

• Improved INSDC to RDF converter using SIO and nicer URIs.

Note for turtle: http://www.w3.org/TR/turtle/

• D.4 Changes from January 2008 Team Submission to First Public Working Draft
• Adopted SPARQL's syntax for prefixed names (see editor's draft):
• '.'s in names in all positions of a local name apart from the first or last, e.g. ex:first.name.
• digits in the first character of the PN_LOCAL lexical token, e.g. ex:7tm.
• 6.4 Escape Sequences
• reserved character escape sequences consist of a '' followed by one of ~.-!$&'()*+,;=/?#@%_ and represent the character to the right of the ''.

[141]  	PNAME_LN	  ::=  	PNAME_NS PN_LOCAL
[169]  	PN_LOCAL	  ::=  	(PN_CHARS_U | ':' | [0-9] | PLX ) ((PN_CHARS | '.' | ':' | PLX)* (PN_CHARS | ':' | PLX) )?
[167]  	PN_CHARS	  ::=  	PN_CHARS_U | '-' | [0-9] | #x00B7 | [#x0300-#x036F] | [#x203F-#x2040]

[165]  	PN_CHARS_U	  ::=  	PN_CHARS_BASE | '_'
[170]  	PLX	  ::=  	PERCENT | PN_LOCAL_ESC
[170s]	PERCENT	::=	'%' HEX HEX
[171s]	HEX	::=	[0-9] | [A-F] | [a-f]
[173]  	PN_LOCAL_ESC	  ::=  	'\' ( '_' | '~' | '.' | '-' | '!' | '$' | '&' | "'" | '(' | ')' | '*' | '+' | ',' | ';' | '=' | '/' | '?' | '#' | '@' | '%' )

[140]  	PNAME_NS	  ::=  	PN_PREFIX? ':'
[168]  	PN_PREFIX	  ::=  	PN_CHARS_BASE ((PN_CHARS|'.')* PN_CHARS)?
[164]  	PN_CHARS_BASE	  ::=  	[A-Z] | [a-z] | [#x00C0-#x00D6] | [#x00D8-#x00F6] | [#x00F8-#x02FF] | [#x0370-#x037D] | [#x037F-#x1FFF] | [#x200C-#x200D] | [#x2070-#x218F] | [#x2C00-#x2FEF] | [#x3001-#xD7FF] | [#xF900-#xFDCF] | [#xFDF0-#xFFFD] | [#x10000-#xEFFFF]

-> basically only ':', '.' and '-' are allowed in local part.

Ensembl

• Core Ensembl human genes/transcrpts are converted to RDF. (Conversion just took 20min; 26Mil triples; 3GB)
• Generated RDF is loaded into Virtuoso for SPARQL query testing. (Loading took 1min)
• Discussed how to deal with variations.

UniProt

• UniProt uses Ensembl identifiers for genes.

Identifiers.org

• Content negotiation
• Collection URIs

GFVO

• Started to re-write BioInterchange to use GFVO, SIO.
• Corrected GFVO ontology.
• Created a script to collect statistics of RDF data.