Table 1.

Data Types and Sources accessible by current annotation modules.

Data source, access method	Data provider, data location	Type of annotation used by FACT
Ensembl, Perl API access to local or remote database	European Bioinformatics Institute and Wellcome Trust Sanger Institute (GB) [8], http://www.ensembl.org	Ensembl ID, Gene Symbol, Gene Name, Chromosomal Location, Homologues Genes, Interpro Domains, RefSeq Accession Number, Affymetrix ID
euGenes, local database	University of Indiana (USA) [10], ftp://iubio.bio.indiana.edu/eugenes/	euGene ID, Gene Symbol, Gene Name, GDB ID, OMIM ID, Genomic Localization, GeneOntology Terms, Protein Accession Numbers
Image Consortium, local database	Lawrence Livermore National Laboratory (USA) [28], ftp://image.llnl.gov/image/imagene/	Clone Image ID
Biological Biochemical Image Database, HTTP parser and HTTP request	National Institute of Aging, NIH (USA) [11], http://bbid.grc.nia.nih.gov/cgi-bin/pathwaysearch.pl	Pathway Name and Image-link
GeneOntology, local database	GeneOntology Consortium [2], http://www.geneontology.org/GO.current.annotations.shtml	ID and Name of GO-Term (Biological Process, Molecular Function, Cellular Localization)
Cancer Genome Anatomy Project, local database	National Cancer Institute, NIH (USA) [29], ftp://ftp1.nci.nih.gov/pub/CGAP	Biocarta name, Biocarta short name, KEGG Pathway Name, KEGG Pathway ID, PFAM ID
LocusLink / EntrezGene, local database	NCBI/NIH (USA) [30], ftp://ftp.ncbi.nih.gov/refseq/LocusLink / ftp://ftp.ncbi.nih.gov/gene	A. LocusLink ID, Gene Symbol, Gene Name, Genomic Localization, GeneOntology Terms, OMIM ID B. Key references (PubMed links)
Mouse Genome Database, local database	Jackson Laboratory (USA) [31], ftp://ftp.informatics.jax.org	MGI ID / Gene Symbol
Internal CloneBase, local database	Deutsches Krebsforschungs zentrum, Div. Molecular Genetics (D)	General Information on available Clones
CpG, local database	University of California Santa Cruz (USA), ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/cpgIsland.txt.gz	Calculated relative CpG content of genomic region
STRING, local database	EMBL (D) [12], http://string.embl.de (medium or better confidence)	Protein interaction data (computed and imported from other databases)
Affymetrix CEL files	Affymetrix Inc. / FACT, http://www.affymetrix.com	Use of Affymetrix probe IDs
Reactome, local database and HTTP request	European Bioinformatics Institute (GB) [3], http://www.reactome.org/download	Pathway information