ORE Ontology GEM Implementation

Table of Contents

Data Structure Approaches

		In-memory Processing
Triple Store Data Structure	In-memory Data Structure	Direct access at loaded position	Direct access URI as ID (pre-loaded)	Iteration foward	Iteration backward	Append after last loaded	Append after global last	Insert after loaded item	Insert before loaded item	Insert after loaded position	Insert before loaded position	Delete loaded item	Delete from loaded position	Fetch one by global position	Fetch one by URI	Fetch range	Fetch next range	Persist one at global position	Persist one by URI	Persist range	List size	Issues	ORE Compliance	Comments
doubly linked list
	doubly linked list	NO	SLOW	FAST	FAST	FAST	FAST	FAST	FAST	NO	NO	FAST	NO	NO	FAST	SLOW	SLOW	NO	FAST	SLOW	NO
	convert to array on fetch	FAST	SLOW	FAST	FAST	FAST	FAST	FAST	FAST	FAST	FAST	FAST	FAST	NO	FAST	SLOW	SLOW	NO	FAST	SLOW	NO
	convert to hash (key=proxy URI) on fetch	NO	FAST	FAST	FAST	FAST	FAST	FAST	FAST	NO	NO	FAST	NO	NO	FAST	SLOW	SLOW	NO	FAST	SLOW	NO
doubly linked list + order index
	doubly linked list	SLOW	SLOW	FAST	FAST	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	FAST	SLOW	SLOW	SLOW	FAST	SLOW	FAST
	convert to array on fetch	FAST	SLOW	FAST	FAST	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	FAST	SLOW	SLOW	SLOW	FAST	SLOW	FAST
	convert to hash (key=proxy URI) on fetch	SLOW	FAST	FAST	FAST	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	SLOW	FAST	SLOW	SLOW	SLOW	FAST	SLOW	FAST

NOTE: All operations are available by adding order index to each proxy for the list as a triple in the triplestore, but most operations that change the list become very slow as it requires updates to all items after the effected item. Delete could be made fast be allowing for missing index values, but then list size becomes a slow operation.

List Header Info

Lists with headers will hold the following information.

		example value types
key	description of value	doubly linked	doubly linked + order	array	hash
first	pointer to first item in list	URI of first proxy	URI of first proxy	URI of first proxy	URI of first proxy
last	pointer to last item in list	URI of last proxy	URI of last proxy	URI of last proxy	URI of last proxy
count	count of all items in list	X	X	X	X
first_loaded	pointer to first item in loaded range of items	item	item	array[0]	URI of first loaded proxy
current	pointer to current item	item	item	int cpos	URI of current proxy
last_loaded	pointer to last item in loaded range of items	item	item	array[size of array]	URI of last loaded proxy
count_loaded	count of items in currently loaded range	X	=position of last - position of first	size of array	size of hash
resume_token	pointer to item after last_loaded	URI of proxy	URI of proxy	URI of proxy	URI of proxy
loaded_items	pointer to loaded items	use first_loaded	use first_loaded	array	hash

List Item Info

		example value types
key	description of value	doubly linked	doubly linked + order	array	hash	Comments
uri	URI of proxy for this item	URI of this proxy	URI of this proxy	URI of this proxy	URI of this proxy	This is the hash key for loaded_items when the list is implemented as a hash.
prev	pointer to previous item in list	URI of prev proxy	URI of prev proxy	= p - 1	URI of prev proxy
next	pointer to next item in list	URI of next proxy	URI of next proxy	= p + 1	URI of next proxy
prev_loaded	pointer to previous item in loaded range of items	prev item	prev item	= pl - 1	URI of prev proxy
next_loaded	pointer to next item in loaded range of items	next item	next item	= pl + 1	URI of next proxy
proxyFor	URI of list item being aggregated	URI	URI	URI	URI
proxyIn	URI of list aggregation	URI of aggregation	URI of aggregation	URI of aggregation	URI of aggregation
proxyIn_loaded	pointer to List Header	header	header	header	header
position (p)	position in full list	X	p	p	X
position_loaded (pl)	position in loaded range of items	X	pl	pl	X

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ORE Ontology GEM Implementation

Data Structure Approaches

List Header Info

List Item Info