@Status( status = StatusType.STABLE ) public class RDFExporterPlugin extends ONDEXExport
@Status(description = "parses a very limited set of interpro", status = StatusType.EXPERIMENTAL) public class Parser extends ONDEXParser
@Status(description = "Changed to DISCONTINUED (by Christian) as there is no export file or directory.", status = StatusType.DISCONTINUED) public class Statistics extends ONDEXExport
@Status(description = "Untested formally", status = StatusType.EXPERIMENTAL) @DatabaseTarget(name = "BIOBASE TRANSFAC", description = "A manually curated database of transcription factors",
@Status(description = "Untested formally", status = StatusType.EXPERIMENTAL) @DatabaseTarget(name = "BIOBASE TRANSPATH", description = "A manually curated database of pathways",
@Status(status = StatusType.STABLE, description = "Tested December 2013 (Jacek Grzebyta)") public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Status(status=StatusType.EXPERIMENTAL) public class Export extends ONDEXExport {
@Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Authors(authors = { "Jan Taubert" }, emails = { "jantaubert at users.sourceforge.net" }) @Custodians(custodians = { "Jan Taubert" }, emails = { "jantaubert at users.sourceforge.net" }) @Status(status = StatusType.STABLE, description = "Tested October 2012 (Jan Taubert)") public class Parser extends ONDEXParser {
@Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Status(status = StatusType.EXPERIMENTAL) public class NT2ProteinBLASTxAlignmentMapping extends ONDEXMapping {
@Status(description = "Tested December 2013 (Artem Lysenko)", status = StatusType.STABLE) @Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Status(description = "Tested July 2010 (Jan Taubert)", status = StatusType.STABLE) @Authors(authors = {"Matthew Pocock", "Jan Taubert"}, emails = {"drdozer at users.sourceforge.net", "jantaubert at users.sourceforge.net"}) @Custodians(custodians = {"Jan Taubert"}, emails = {"jantaubert at users.sourceforge.net"})
@Status(description = "Parses Arabidopsis CDS and proteins, to be used with TAIR release 2010. Tested August 2013 (Artem Lysenko)", status = StatusType.STABLE) @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 ",
@Status(description = "Tested December 2013 (Artem Lysenko)", status = StatusType.STABLE) @Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Status(description = "not tested yet", status = StatusType.EXPERIMENTAL) @DataSourceRequired(ids = { net.sourceforge.ondex.parser.ec.MetaData.DS_EC})
@Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport implements ArgumentNames {
@Status(description = "Tested with AraCyc, LycoCyc, HumanCyc and Reactome by Jan Taubert (January 2013)", status = StatusType.STABLE) @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 = { "" })
@Status(description = "Tested November 2013 for Arabidopsis, Rice, Poplar, Brachypodium in Phytozome 9.1 (Keywan Hassani-Pak)", status = StatusType.STABLE) @Authors(authors = {"Keywan Hassani-Pak"}, emails = {"keywan at users.sourceforge.net"}) @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/")