# bioontol.schema
# ldap schema for bio-ontologies - vocabulary trees
# version 0.1, 1jun02, 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


## use ldap standard name attr
## use standard name attribute
#attributetype ( Name-attr-oid  
#	NAME ( 'nm' 'Name' 'Term' )
#	DESC 'Name of term'
#	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 ( id2-oid 
  NAME 'id2'
	DESC 'secondary id'
	EQUALITY caseExactMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Synonym-oid  
	NAME ( 'syn' 'synonym' )
	DESC 'Synonym of term'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

## use standard description attribute
attributetype ( Description-attr-oid  
	NAME ( 'des' )
	DESC 'Description'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

attributetype ( Desreference-attr-oid
	NAME ( 'desref' )
	DESC 'Description reference'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 )

## in gnomap schema
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 ) 

##?? GN is in some other schema !
#attributetype ( GN-oid SUP dbxref 
#	NAME ( 'GN' 'gene-xref' )
#	DESC 'gene cross-reference'  ) 

attributetype ( AL-oid  SUP dbxref
	NAME ( 'AL' 'allele-xref'  )
	DESC 'allele cross-reference'  ) 
attributetype ( TR-oid  SUP dbxref
	NAME ( 'TR' 'transcript-xref'  )
	DESC 'transcript cross-reference'  ) 
attributetype ( TRE-oid  SUP dbxref
	NAME ( 'TRE' 'reporter-xref'  )
	DESC 'reporter cross-reference'  ) 
attributetype ( LSK-oid  SUP dbxref
	NAME ( 'LSK' 'stock-xref'  )
	DESC 'stock cross-reference'  ) 

## other attributes
## association == gene+ links -- these are sub-objects rather than attributes?!
## dbxref == ? not links?
## synonym
## reference
## comment

## is-a, part-of, derived-from, other parent-child relations


## 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
	) 
	
## vocabular sections such as 'body parts', 'dna features' 
## - is this attribute or object ?
## one reason for this is term IDs may be unique only for a section

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

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 )


## 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 ( Bio-Ontology-oid NAME 'Bio-Ontology'
	DESC 'Bio-Ontology or Controlled Vocubulary'
	SUP top 
  MUST ( name $ id ) 
	MAY ( description $ url $ web $ content ) 
	)

objectclass ( Section-oid 
	NAME ( 'sec' 'Section' )
	DESC 'Section of ontology'
	SUP Bio-Ontology
	MAY (  category ) 
	)
	
attributetype ( TermRelation-oid  
	NAME ( 'relation'  )
	DESC 'parent-child relationship of terms'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 

attributetype ( ParentTerm-oid  
	NAME ( 'par' 'parent'  )
	DESC 'parent-child relationship of terms'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 
	
attributetype ( ChildTerm-oid  
	NAME ( 'kid' 'child'  )
	DESC 'parent-child relationship of terms'
	EQUALITY caseIgnoreMatch
	SUBSTR caseIgnoreSubstringsMatch
	SYNTAX 1.3.6.1.4.1.1466.115.121.1.15 ) 


objectclass ( Term-oid NAME 'Term'
	DESC 'Term'
	SUP Section 
	MAY (  des $ desref $ dbxref  $ parent  )
	)
 
objectclass ( Term-association-oid NAME 'Term-association'
	DESC 'Objects associated with term'
	SUP Term  
	MAY (  dbxref  )
	)

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