@DatabaseTarget(name = "BIOBASE TRANSFAC", description = "A manually curated database of transcription factors", version = "",
sb.append("<p>").append(target.description()).append("</p>"); sb.append("<h2>Target versions of <a href=\"").append(target.url()).append("\">").append(target.name()).append("</a></h2>"); sb.append("<ul>"); for (String version : target.version()) { sb.append("<li type=circle>").append(version).append("</li>");
.getAnnotation(DatabaseTarget.class); if (dbAnnotation != null) { String name = dbAnnotation.name().trim(); String description = dbAnnotation .description().trim(); String url = dbAnnotation.url().trim();
@DatabaseTarget(name = "BIOBASE TRANSPATH", description = "A manually curated database of pathways", version = "",
@DatabaseTarget(name = "GlycomeDB", description = "A carbohydrate structure metadatabase", version = "", url = "http://www.glycome-db.org") @Authors(authors = {"Jan Taubert"}, emails = {"jantaubert at users.sourceforge.net"}) @Custodians(custodians = {"Victor Lesk"}, emails = {"v.lesk at imperial.ac.uk"})
@DatabaseTarget(name = "Arabidopsis Hormone Database (AHD)", description = "A systematic and comprehensive view of morphological phenotypes regulated by plant hormones.", version = "",
@DatabaseTarget(name = "TAIR", description = "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana ", version = "10",
@DatabaseTarget(name = "GlycomeDB", description = "A carbohydrate structure metadatabase", version = "", url = "http://www.glycome-db.org") @Authors(authors = {"Jan Taubert", "Victor Lesk"}, emails = {"jantaubert at users.sourceforge.net", "v.lesk at imperial.ac.uk"}) @Custodians(custodians = {"Victor Lesk"}, emails = {"v.lesk at imperial.ac.uk"})
@DatabaseTarget(name = "BioCyc", description = "BioCyc databases", version = "BioPax version 2", url = "http://www.biocyc.org") @DataURL(name = "BioCyc databases", description = "Place biopax-level2.owl or similar file in data folder with no directory structure", urls = { "" }) public class Parser extends ONDEXParser {
@DatabaseTarget(name = "AraCyc", description = "The AraCyc database", version = "Release 6, October 14, 209", url = "http://www.genome.jp/kegg") @DataURL(name = "AraCyc databases", description = "URL on application to AraCyc all files in data folder with no directory structure",
@DatabaseTarget(name = "BCSDB", description = "Bacterial Carbohydrate Structure DataBase", version = "pre-release BCSDB-3 gamma version", url = "http://www.glyco.ac.ru/bcsdb3") @Custodians(custodians = {"Victor Lesk"}, emails = {"v.lesk at imperial.ac.uk"}) @Status(description = "declared on 28/07/2010", status = StatusType.DISCONTINUED)
@DatabaseTarget(name = "BRENDA", description = "Brenda enzymatics database", version = "BRENDA release online since 2nd July 2010", url = "http://www.brenda-enzymes.info/") @Custodians(custodians = {"Jan Taubert"}, emails = {"jan.taubert at rothamsted.ac.uk"}) @Status(description = "tested on 28/07/2010", status = StatusType.STABLE)
@DatabaseTarget(name = "geneontology-external2go-ec2go", description = "the ec component of the external2go set of mappings in the geneontology", version = "2012/06/19", url = "http://www.geneontology.org/external2go/") @DataURL(name = "ec2go", description = "external2go mapping file", urls = "http://www.geneontology.org/external2go/ec2go") @DataSourceRequired(ids = MetaData.cvGO)
@DatabaseTarget(name = "phytozome", description = "Phytozome is a joint project of JGI and CIG to facilitate comparative genomic studies amongst green plants. This Phytozome parser creates Chromosome, Scaffold, Gene, CDS and Protein concepts.", version = "9.0", url = "http://phytozome.net/") @DataURL(name = "Phytozome annotation directory", description = "This parser requires as input the annotation directory of a specific species. Do not change the file names. It parses the GFF3, peptide FASTA, CDS FASTA and Synonyms TXT file inside of the annotation directory. It was tested on Arabidopsis, rice, poplar and brachypodium.",
@DatabaseTarget(name = "EXPASY ENZYME", description = "EXPASY ENZYME database", version = "2012/11/28", url = "http://www.expasy.ch/") @DataURL(name = "enzclass and enzyme files", description = "enzclass and enzyme, all txt and dat files in directory files", urls = {"ftp://ftp.expasy.org/databases/enzyme"}) @DataSourceRequired(ids = {
@DatabaseTarget(name = "BRENDA", description = "The BRENDA enzyme database", version = "July 2009", url = "http://www.brenda-enzymes.org") @DataURL(name = "brenda zip and exception file", description = "brenda zip file and an exceptions file for data file inconsistancies", urls = {"http://www.brenda-enzymes.org/brenda_download/brenda_dl_0905.zip", "https://ondex.svn.sourceforge.net/svnroot/ondex/trunk/ondex-parent/modules/enzymatics/data/brenda/exception.txt"}) @DataSourceRequired(ids = {