Ranked retrieval of Computational Biology models

BMC Bioinformatics

Table 3 Semantic index

URI		qualifier		content
	bqbiol_is	bqbiol_isVersionOf	bqmodel_is
urn:miriam:obo.chebi. CHEBI:27732	BIOMD0000000241	BIOMD0000000241		caffeine chebi 27732 chebi home advanced search browse ontology periodic ... moleculeschebimain caffeine chebi 116485 central nervous system stimulant caffeine ryanodine receptor modulator mutagen 1,3,7-trimethyl-3,7 dihydro-1 h-purine-2,6 iuphar 1,3,7-trimethylxanthine dion msdchem d00528 kegg drug [..]
urn:miriam:kegg. compound:C07481	BIOMD0000000241		BIOMD0000000241	kegg compound c07481 entry c07481 compound name caffeine 1,3,7-trimethylxanthine formula c8h10n4o2 mass 194.0804 structure remark d00528 comment source coffea arabica tax 13443 xanthines reaction r07920 r07921 27732 knapsack c00001492 [..]
urn:miriam:kegg. compound:C00385	BIOMD0000000015			kegg compound c00385 name xanthine formula c5h4n4o2 mass 152.0334 ko00230 purine metabolism caffeine metabolism [...]
urn:miriam:kegg. compound:C00048		BIOMD0000000221 BIOMD0000000222 BIOMD0000000219 BIOMD0000000218		kegg compound c00048 entry c00048 glyoxylate glyoxylic acid formula c2h2o3 mass 74.0004 structure reaction r00013 r00364 purine metabolism path ko00232 caffeine metabolism glycine serine null_1 threonine metabolism [...]
. . .				. . .

The semantic index is used to connect each existing URI in the database to the models in which it occurs. Thus, each column contains a set of IDs identifying a bio-model in C_M. We additionally store how the URI is connected to the annotated model constituent (through the qualifier column). For each URI, the content, i. e. textual representation, that had been extracted from the ontology term corresponding to the URI, is normalised and indexed as well. A query can then be enriched by further related URIs (see also Figure 2, Ontology Query), resulting in an expanded query.

ISSN: 1471-2105