Integrating systems biology models and biomedical ontologies

BMC Systems Biology

Table 2 List of examples for querying the BioModels knowledge base

Query	Query string	# results
Contradictory defined entities	Nothing	4,899
Models which represent a process involving sugar	model-of some (has-part some (has-function some (realized-by only (has-participant some sugar))))	54
Parts of BIOMD0000000015 that represent processes involving sugar	part-of some BIOMD0000000015 and represents some (has-function some (realized-by only (has-participant some sugar)))	29
Model entities that represent the cell cycle	represents some (has-part some (has-function some (realized-by only 'cell cycle')))	14
Model entities that represent mutagenic central nervous system drugs in the gastrointestinal systems	represents some (has-part some ('has role' some 'central nervous system drug' and 'has role' some mutagen and part-of some 'Gastrointestinal system')	2
Model entities that represent catalytic activity involving sugar in the endocrine pancreas	represents some (has-function some (realized-by only (realizes some 'catalytic activity' and has-participant some (sugar and contained-in some (part-of some 'Endocrine pancreas')))))	4

List of examples for querying the BioModels (release 18) knowledge base. The results of these queries are based on automated reasoning (i.e., deductive inference). Every result listed in the table is the result of a formal proof that is based on the constraints formalized in the SBML Harvester software, the annotation assertions of models in BioModels and the knowledge contained in biomedical ontologies.
If an answer to any of the queries is incorrect, then this inaccuracy must be the consequence of either an incorrect assertion in a biomedical ontology, an inappropriate use of SBML model elements, an incorrect model, a faulty model annotation or a mistake in our assumptions about SBML's ontological commitment.
Quantifying these cases and correcting the underlying problems requires a manual analysis of the models and their annotations, and we intend to collaborate with the BioModels Database curators on identifying and correcting possibly incorrect model annotations. The SBML Harvester software can further provide the means to verify models before inclusion in the BioModels Database.

ISSN: 1752-0509