# gnomap2.schema
# ldap schema for euGenes gnomap data
# version 0.2, 3jan01, d.gilbert
 

## ldap Syntax Object Identifiers
#binary: 1.3.6.1.4.1.1466.115.121.1.5
#integer:1.3.6.1.4.1.1466.115.121.1.27
#directory string: 1.3.6.1.4.1.1466.115.121.1.15 
#printable string: 1.3.6.1.4.1.1466.115.121.1.44
#numeric string: 1.3.6.1.4.1.1466.115.121.1.36
#octet string: 1.3.6.1.4.1.1466.115.121.1.40

attributetype ( Species-attr-oid  
	NAME ( 'spp' 'Species' )
	DESC 'Species'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Chromosome-attr-oid  
	NAME ( 'chr' 'Chromosome' )
	DESC 'Chromosome'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Feature-attr-oid  
	NAME ( 'ft' 'Feature' )
	DESC 'Chromosome feature'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Location-oid  
	NAME ( 'loc' 'Location' )
	DESC 'Chromosome feature physical (base) location'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

attributetype ( Loc-start-oid  
	NAME ( 'start' 'Location-start' )
	DESC 'start base number of feature'
	EQUALITY integerMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.27
	) 

attributetype ( Loc-stop-oid  
	NAME ( 'stop' 'Location-stop' )
	DESC 'last base number of feature'
	EQUALITY integerMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.27
	) 

# strand should be an enum ( '+', '-', '0' )
attributetype ( Strand-oid  
	NAME ( 'strand'   )
	DESC 'dna strand (forward,reverse)'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 
	) 

attributetype ( Map-location-oid  
	NAME ( 'map' 'map-location' )
	DESC 'Chromosome feature genetic, cytologic location'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

attributetype ( Dbxref-oid  
	NAME ( 'dbxref'  )
	DESC 'Database cross-reference'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

#? this should be any of D/E/G feature /key=value
attributetype ( note-oid  
	NAME ( 'note'  )
	DESC 'Feature note'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

## should be numeric value
attributetype ( Count-oid  
	NAME ( 'count' )
	DESC 'count of items'
	EQUALITY integerMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.27
	) 
	
#? change name to avoid confusion w/ sequence ?
attributetype ( Bases-oid  
	NAME ( 'bases' 'base-count' )
	DESC 'count of bases'
	SUP Count
	) 

attributetype ( NA-sequence-attr-oid  
	NAME ( 'na' 'nucleic-acid' )
	DESC 'sequence of nucleic acid data'
	EQUALITY caseIgnoreMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15
	) 

attributetype ( Binary-NA-sequence-attr-oid  
	NAME ( 'bna' 'binary-nucleic-acid' )
	DESC 'binary coded sequence of nucleic acid data'
	SUP nucleic-acid
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.5
	) 

attributetype ( AA-sequence-attr-oid  
	NAME ( 'aa' 'amino-acid' )
	DESC 'sequence of amino acid data'
	EQUALITY caseIgnoreMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15
	) 

attributetype ( Binary-AA-sequence-attr-oid  
	NAME ( 'baa' 'binary-amino-acid' )
	DESC 'binary coded sequence of amino acid data'
	SUP amino-acid
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.5
	) 


attributetype ( content-oid  
	NAME ( 'con' 'content' )
	DESC 'data content types'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

#attributetype ( category-oid NAME 'category'
#	DESC 'category of group'
#	EQUALITY caseIgnoreMatch
#	SUBSTR caseIgnoreSubstringsMatch
#	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

## in biomirror-catalog-spec.schema
#attributetype ( format-oid 
#	NAME ( 'fmt' 'format' )
#	DESC 'data format'
#	EQUALITY caseIgnoreMatch
#	SUBSTR caseIgnoreSubstringsMatch
#	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

## in biomirror-catalog-spec.schema
#attributetype ( id-oid NAME 'id'
#	DESC 'object id'
#	EQUALITY caseExactMatch
#	SUBSTR caseIgnoreSubstringsMatch
#	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15
#	SINGLE-VALUE )

attributetype ( urc-oid 
	NAME ( 'urc' 'url-component' )
	DESC 'cgi key parameter to url'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

## replace with core labeledURI attr
#attributetype ( url-oid NAME 'url'
#	DESC 'universal resource locator'
#	SUP labeledURI
#	EQUALITY caseIgnoreMatch
#	SUBSTR caseIgnoreSubstringsMatch )
#
#attributetype ( web-oid NAME 'web'
#	DESC 'web page' SUP labeledURI )

## in biomirror-catalog-spec.schema
#attributetype ( taxonomy-oid NAME 'taxonomy'
#	DESC 'taxonomic or phylogenetic classification'
#	EQUALITY caseIgnoreMatch
#	SUBSTR caseIgnoreSubstringsMatch
#	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Service-oid  
	NAME ( 'srv' 'service' )
	DESC 'bioinformatics service'
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15  )

#attributetype ( Group-bc-oid  
#	NAME ( 'bc' 'bioComponent' )
#	DESC 'bioinformatics domain component'
#	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15
#	SINGLE-VALUE )
	
	
## in biomirror-catalog-spec.schema
#objectclass ( bcObject-oid NAME 'bcObject'
#	DESC 'bioinformatics component object'
#	SUP top AUXILIARY MUST bc 
#	)

objectclass ( Bioinformatics-Service-oid NAME 'Bioinformatics-Service'
	DESC 'bioinformatics service'
	SUP top AUXILIARY MUST srv 
	MAY ( mail $ url $ web $ content )
	)

objectclass ( Genome-map-oid NAME 'Genome-map'
	DESC 'Genome map'
	SUP top 
	MUST ( id )
	MAY (  name $ description $ spp $ content $ format $ url $ urc $ web )
	)

objectclass ( Species-oid NAME 'Species'
	DESC 'Species held in map'
	SUP Genome-map 
	MAY (  bases  $ chr )
	)

objectclass ( Chromosome-oid NAME 'Chromosome'
	DESC 'Chromosomes held in species map'
	SUP Species 
	MAY (  bases $ loc $ start $ stop $ strand $ map )
	)

## optional ascii or binary attribute ?
objectclass ( NA-Sequence-oid NAME 'NA-sequence'
	DESC 'Nucleic acid sequence from chromosome in species map'
	SUP Chromosome 
	MUST ( na )
	MAY ( bna )
	)
	
objectclass ( AA-Sequence-oid NAME 'AA-sequence'
	DESC 'Amino acid sequence from chromosome in species map'
	SUP Chromosome 
	MUST ( aa )
	MAY ( baa )
	)

objectclass ( Feature-summary-oid NAME 'Feature-summary'
	DESC 'Feature summary in chromosome in species map'
	SUP Chromosome 
	MAY (  ft $ count  )
	)

## Feature-list == Feature-summary, but wrapper for any list of features, w/ count
objectclass ( Feature-list-oid NAME 'Feature-list'
	DESC 'Feature list from chromosome in species map'
	SUP Chromosome 
	MAY (  ft $ count  )
	)

objectclass ( Feature-oid NAME 'Feature'
	DESC 'Feature in chromosome in species map'
	SUP Feature-summary 
	MAY ( dbxref $ note )
	)