Table 1:

Parameters of the System, as Apply to the Query and the Answers

Parameter Name	Description	Options
Semantic relationship	Type of relationship between drug and gene required for retrieval.	Predications, sentence-level co-occurrence, document-level co-occurrence
Food and Drug Administration (FDA) filter	Accept drugs that appear on a list of FDA-approved drugs. The list was obtained from the FDA website (FDA.gov) and normalized using SemRep_UTH.	Yes or No
Clinical trials (CT) filter	Accept drugs found in the “intervention” field from ClinicalTrials.gov, normalized using SemRep_UTH.	Yes or No
Phase filter	Accept drugs either passing the FDA filter (marketed) or the CT filter for trials with a phase of, at most, x (phases 1–3).	Phase 1,1/2, 2, 3, or Marketed
National Cancer Institute (NCI) thesaurus filter	Return drugs that appear in the Pharmacological Substance branch of the NCI thesaurus hierarchy.	Yes or No
Frequency filter	Minimum number of extracted relationships (predication or co-occurrence) required before the drug is returned.	One to Many (eg, 5)
Predication filter	For predications, retrieve only drugs that occur in relationships with the target gene of predicate type x.	INHIBITS, INTERACTS_WITH, COEXISTS_WITH
Semantic type filter	Semantic types of drugs to retain.	aapp, antb, clnd, horm, imft, nnon, opco, orch, phsu

aapp, amino acid, peptide, or protein; antb, antibiotic; clnd, clinical drug; horm, hormone; imft, immunologic factor; nnon, nucleic acid, nucleoside, or nucleotide; opco, organophosphorus compound; orch, organic chemical; phsu, pharmaceutical substance.