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 CM. 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.

Henkel et al. BMC Bioinformatics 2010 11:423   doi:10.1186/1471-2105-11-423

Open Data