[MOBY-l] Moby class hierarchy

[Lukas Mueller]

Hi,

On the trip home I was thinking about a class hierarchy for moby objects 
until the ibook batteries ran out. This could maybe be a basis for 
future discussion?
Since with have a class hierarchy, we don't need to specify the class in 
the quadruple anymore, so we're back to a triple. In the square brackets 
are the slots, attributes or whatever you want to call it, so that every 
object only has minimal information. The root element is Moby, and its 
children are indented etc. The Moby objects can be grouped ad hoc in 
Moby_lists. Sorry for the weird format but I'm not too familiar with XDL 
or whatever the right acronym is...

Cheers
Lukas


Moby [triple]
	VirtualSequence [length]	# does not contain the complete 
sequence, only length
		Sequence [sequence]
		DNA []
			Chromosome [chromosomeNumber]
			Assembly
				BAC etc.
			SequenceFragment 	[seq]
			Polymorphism	[type {snp, indel, deletion, insertion, 
reversion} start, end, polymorphicSeq]	
			Locus [GeneModel_List]
				
			GeneModel [Sequence, orientation, Chromosome, start, end, 
SequenceFeatureAnnotation_List]
				
			Repeat []
			Domain []
			Transposon []
		RNA	[]	
			EST
			tRNA [aminoAcid]
			snRNA []
			rRNA []
			Primary Transcript []
			Mature Transcript []
		Protein []
			ProteinSecondaryStructure [type, start, end]
		Domain [start, end]
			DNADomain []
			ProteinDomain []
	Keyword [id, term]
		GOTerm [id, term]
	Ontology
		GOOntology [GOTerm,
	Annotation [evidence]
		SequencFeatureAnnotation [start, end, SequenceFeatureOntologyId]
		GOAnnotation [GOTerm]
		
	SequenceAlignment
		Multiple
			ClustalW [SeqList, {parameters}]
		Pairwise
	SequenceMatch
		BLAST
			NCBI-BLAST [seq (query), Seq_List (matched), {match_parameters}
			WU-BLAST
		FASTA
	ExpressionAnalysis
		# Jason?
	Pathway	[pathwayName]
	Genefamily [genefamilyName]
	Species [speciesCommonName, speciesScientificName, NCBITaxonID]
	Experiment [experimentName, experimentType, experimentDescription, 
experimentData, experimentResult]
	Publication [title, journal, Individuals_List, year, Institution]
	WebResource
	Individual [firstName, lastName, email, Institution]
	Institution [name, address]
	Alias
	Description
	Moby_List [Moby+]