Table 1 Knowledge Sources within the Library of Knowledge Integration (LOKI)

BioGRID

http://thebiogrid.org

[8]

BioGRID is a repository with genetic and protein interaction data from model organisms and humans used by Biofilter for linking position and region data to interaction information.

NCBI dbSNP

http://www.ncbi.nlm.nih.gov/snp

A database of SNPs and multiple small-scale variations including insertions, deletions, microsatellites and non-polymorphic variants. This resource includes a complete list of known human SNPs and their base pair positions relative to the human reference genome. Biofilter uses the data of dbSNP in two ways: connecting SNP identifiers (RS numbers) of dbSNP to genomic positions and connecting retired identifiers to current identifiers.

NCBI gene

http://www.ncbi.nlm.nih.gov/gene

Entrez is a search engine that allows researchers to search many discrete health sciences databases at the NCBI. The database provides an extensive list of known human genes, their beginning and ending base pair positions, and many alternate names and cross-referenced database identifiers. This data is used in two ways within Biofilter: to connect gene symbols to their genomic regions, and to connect equivalent gene symbols and identifiers to each other.

Gene ontology

http://www.geneontology.org

[9]

The Gene Ontology database defines terms representing gene product properties, such as cellular components, molecular function, and biological processes, within a hierarchical tree of ontology groups and related proteins.

MINT

http://mint.bio.uniroma2.it/mint/Welcome.do

[10]

The Molecular Interaction database contains experimentally verified protein-protein interactions from the scientific literature, which are used in Biofilter for linking position and region data to interacting protein pairs.

NetPath

http://www.netpath.org

[11]

The NetPath database consists of curated human signaling pathways which are used by Biofilter.

OregAnno

http://www.oreganno.org/oregano

[12]

The Open REGulatory ANNOtation database is used by Biofilter for curation information about known regulatory elements from the scientific literature.

Pfam

http://pfam.sanger.ac.uk

[13]

The Pfam database is a large collection of protein families. The annotation of data respective to proteins within Biofilter is based on the information from Pfam.

PharmGKB

http://www.pharmgkb.org

[14]

Biofilture currently uses this database for pathway based data, future releases of Biofilter will also include drug-related data of gene-drug associations and pharmacological association study results.

Reactome

http://www.reactome.org/ReactomeGWT/entrypoint.html

[15]

Biofilter uses the information contained in Reactome to establish pathway and network relationships between genes.

UCSC genome browser

http://genome.ucsc.edu

[16]

This source provides access to a growing database of genomic sequence and annotations for a wide variety of organisms, currently we use the UCSC for location information for evolutionary conserved regions (ECRs) for Biofilter and to acess OregAnno’s regulatory region data.

NHGRI GWAS catalog

http://www.genome.gov/gwastudies/

[17]

A catalog of published GWAS SNP-trait associations with p-values < 1.0 × 10–5, for studies with at least 100,000 SNPs assayed