a base namespace identifier, never instantiated
Plant-Associated Microbe Gene Ontology Interest Group
Protein ANalysis THrough Evolutionary Relationships Classification System
distance matrix built from a Musa TropGENE_Diversity_Matrix object
Identifiers for consensus sequence in IPK Crop EST (Cr-EST) database (e.g HY01A10).
A comprehensive K-12 information resource for experimentation and modeling through interoperation with exisitng datasources and warehousing other key data.
The Institute for Genomic Research, TIGR Gene Index.
The Metabolic Encyclopedia of metabolic and other pathways.
The University of Minnesota Biocatalysis/Biodegradation Database.
Name of donor for Arabidopsis stock donated to the Nottingham Arabidopsis Stock Centre (e.g. Plieth)
Identifier from Maize Genome Database. (e.g. MaizeDBID:12008)
Clusters of Orthologous Groups of Proteins
The Swiss Institute of Bioinformatics database of Enzymes.
AgBase resource for functional analysis of agricultural plant and animal gene products
Proteome Inc.; represents GO annotations created in 2001 for NCBI and extracted into GOA from EntrezGene
Arex use GFP reporter constructs for measuring expression level of Arabidopsis transcription factors in different root tissues. Examples: '_591.1.2.1','591_1_14','470-3-1'
Unique identifiers for SOL Genomics Network unigenes
Project and associated database to sort EST's into sets (clusters), based upon strong DNA sequence homology. In general, the goal of EST clustering is to define a specific cluster for each transcript in a tissue or genome. "UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location". Source of all EST and gene clustering data in eGenome
MultiFun, a cellfunction assignment schema
A somewhat generic prefix for namespaces that are not identifiers for any given database. This could be a namespace for keywords, for eexample
Database of CGIAR-mandated crops germplasm
The name given to a stock donated to the Nottingham Arabidopsis Stock Centre (e.g. Shakdara )
Gramene: A Comparative Mapping Resource for Grains.
Journal / book references in the Arabidopsis world.
A namespace describing a Saccharomyces Chromosome Identifier (e.g. I, IX, MIT)
Identifiers for consensus sequence in IPK Crop EST (Cr-EST) database (e.g cl1ct1cn1g00). A consensus sequence is an alignment of EST sequences.
Information relative to the Musa Germplasm Information System (http://mgis.inibap.org)
Database of rice mutant data maintained at NIAS
Tetrahymena Genome Database Literature Reference Identifier.
The protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide
A namespace for Antirrhinum Allele names according to DragonDB
iHOP protein or gene symbol identifier namespace (e.g. iHOPsymbol:32484)
EntrezGene succeeds LocusLink. Any previously valid LocusLink ID is now a valid EntrezGene ID. There will be no new LocusLink IDs.
The Unique identifier for Arabidopsis, which is an acronym or abbreviation for the gene name (e.g. aux1)
Compugen Gene Ontology Gene Association Data.
Bacillus subtilis Genome Sequence Project.
Gene from Schizosaccharomyces pombe genes.
Identifier for genetic elements in MIPS Medicago database (e.g.AC123547_15_51.1)
National Microbial Pathogen Data Resource
Semantic Type Unique Identifier in the Unified Medical Language System (UMLS)
A phylogenomic database for plant comparative genomics
SIMAP is a pre-calculated all-against-all SImilarity MAtrix of Proteins (http://mips.gsf.de/proj/simap/). Each protein is part of a dataset which represents either a genome or a protein collection like UniProt.
RefSeq (Nucleic Acid); Identifiers that are used to link to RefSeq records
International Nucleotide Sequence Database Collaboration, comprising EMBL-EBI International Nucleotide Sequence Data Library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
An identifier representing a genetic map in the DragonDB (Atnirrhinum majus - Snapdragon) Database
TRANSFAC database of eukaryotic transcription factors
The Institute for Genomic Research, Genome Properties
Centre for Plant Energy Biology University of Western Australia 35 Stirling Highway Crawley, WA, AUSTRALIA 6009
A namespace for keywords; one keyword only
Webservice about Alignments from bielefeld university bioinformatics server
EchoBASE post-genomic database for Escherichia coli
Identifier for Clones in MIPS Arabidopsis database (MAtDB) (e.g.M7J2)
Webservice about RNA from bielefeld university bioinformatics server.
The SEED; The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices
The InterPro database of protein domains and motifs.
The Institute for Genomic Research, Comprehensive Microbial Resource.
Identifier for Contigs in MIPS Medicago database (e.g.mth2-26n6)
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
Operations and datatypes for retreiving microarray data from BASE2 databases.
Identifier for genetic elements in MIPS Maize database (e.g.CG:temp36:AC145389.6-RB)
Neighbour joining tree built from a TropGENE_Distance_Matrix object
The combination of SWISS-PROT and TrEMBL; includes TrEMBLnew.
Identifier for Contigs in MIPS Arabidopsis database (MAtDB) (e.g.chromosome 2)
Canonical from Maize Genome Database. (e.g. MaizeDB:apb1)
UniProt Archive; a non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office
PRINTS compendium of protein fingerprints
namespace relative to the data contained in OryzaTagLine. (http://urgi.infobiogen.fr/OryzaTagLine/)
Identifiers for a EST cluster in IPK Crop EST (Cr-EST) database (e.g 1).
The Institute for Genomic Research, Trypanosoma brucei database.
Arabidopsis Genome Initiative (TAIR, TIGR, MIPS)
Namespace for debugging client-server communication.
SUBA is a sub-cellular protein localization database for Arabidopsis thaliana. A sub-cellular localization call describes the pinpointing of a protein to a specific subcellular component within the cell. The following information is associated with a call: id: unique key for call (for DB lookup) location: the sub-cellular location as a GO id type: the type of evidence as a GO evidence code source: publication id of the source (for predictors, this points to the paper where the predictor was first described). DISCLAIMER: Abusing namespaces in this way is a horrible violation of all that I hold sacred. I do not endorse it, I'm just following orders.
Natural variant of Arabidopsis (e.g. Ler) stored at the Nottingham Arabidopsis Stock Centre
LIFEdb, a database for the integration and dissemination of functional data
Proteomics Standards Initiative Molecular Interaction methods namespace
Temporary reference for unpublished papers.
any planet partner institution like MIPS, NASC,...
Gramene: A Comparative Mapping Resource for Grains
ProtLocDB is a a Protein Localisation Database hosted at the Scottish Crop Research Institute that contains sequence information, BLAST results and the subcellular localisations of numerous partial plant cDNA-GFP fusions expressed from a Tobacco Mosaic Virus vector. This namespace is used for images from this database (examples: B_000001_A, C_000036_FP)
Gene Ontology Annotation at EBI annotations from InterPro to GO mapping.
The Pharmacogenetics and Pharmacogenomics Knowledge Base
Complete disjunctive tables for diversity analysis : accessions per row, alleles in column, coded in 0/1 with 2 columns per allele (one for presence, one for absence)
GenProtEC E. coli genome and proteome database.
Schematikon protein structural motif database, structure segment ID
Unique number given to all Arabidopsis inserts (e.g. salk:000001)
Arabidopsis module of the OryGenesDB database
UniProtKB/Swiss-Prot, a curated protein sequence database which provides a high level of annotation and a minimal level of redundancy
A type of Arabidopsis seed as defined by the Arabidopsis Stock Centre (e.g. Gene Trap)
Database of studies made as recorded by ICIS
Oryza sativa module of the OryGenesDB database
A number given by a donor for Arabidopsis stock donated to the Nottingham Arabidopsis Stock Centre (e.g. BFM2)
description for MyTestingNamespace_11254519980312
NCBI PubChem database of chemical structures
Identifier for Contigs in MIPS Rice Japonicus database (e.g.chromosome 2)
Splice variant identifier from the Arabidopsis Genome Initiative.
Getz command line query tool from SRS package.
The Institute for Genomic Research, Arabidopsis thaliana database
Identifier for Clones in MIPS Maize database (e.g.ZMMBBc0404B14r)
Namespace for the Affymetrix identification code for each set of probe pairs on the GeneChip. This probe set ID represents a set of probes (25-mer) designed to represent a gene (e.g. 245612_at)
Gene Ontology Annotation at EBI annotations from keyword mapping.
SUBA is a sub-cellular protein localization database for Arabidopsis thaliana. A sub-cellular localization prediction describes the pinpointing of a protein to a specific subcellular component within the cell by a prediction algorithm. The following information is associated with a prediction: id: unique key for prediction call (for DB lookup) location: the sub-cellular location as a GO id predictor: name of the prediction algorithm that made the call score: confidence score associated with the prediction (if available) DISCLAIMER: Abusing namespaces in this way is a horrible violation of all that I hold sacred. I do not endorse it, I'm just following orders.
Computer-annotated protein sequence database containing the
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
Identifier for Gene Calls of the International Medicago Genome Annotation (e.g.AC123547_15_51.1)
Namespace for Sun Grid Engine (SGE) status flags.
Identifier for Elements in MIPS Rice Japonicus database (e.g.9629.m05123)
LOCSVMPSI: subcellular localization for eukayotic proteins based on SVM and PSI-BLAST
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. (http://mged.sourceforge.net/ontologies/)
An Identifier for an experiment stored in Nottingham Arabidopsis Stock Centre's microarray database. The suffix is the same as the experiment ID (e.g. NASCARRAYS-343)
An identifier representing an author in the DragonDB database
String Unique Identifier in the Unified Medical Language System (UMLS)
A namespace to represent any publication identifier. Examples of entities that are covered by this namespace include: - PubMed ID - ISBN - ISI identifier - any other publication id
TRAnscript Integrated Table, an integrated database of transcripts expressed in human skeletal muscle
The EcoGene Database of Escherichia coli Sequence and Function
A collection of stocks at the Nottingham Arabidopsis Stoc Centre (e.g. SALK)
PSORT protein subcellular localization databases and prediction tools for bacteria
Concept Identifier in the Unified Medical Language System (UMLS)
Chemical Entities of Biological Interest
The IUPHAR Compendium of Receptor Characterization and Classification.
Identifier from Plant Ontology. (e.g. flower)
Database of automatically annotated genomic data.
The Institute for Genomic Research, TIGRFAMs HMM collection.
Identifier from Plant Ontology Database. (e.g. PO:1234567)
Kyoto Encyclopedia of Genes and Genomes.
The Institute for Genomic Research, Plasmodium falciparum database.
Simple Modular Architecture Research Tool
Database of Rice Gene Expression data maintained at NIAS
Proteomics Standards Initiative protein modification ontology
Database of rice mutant data maintained at IRRI
An identifier representing an NCBI (GenBank) Accession number, including the version suffix (e.g. J00522.1)
Database of Arabidopsis Gene Expression data maintained at NIAS
NCBI PubChem database of bioassay records
A namespace to be used when you have an ID, but you don't know what namespace it belongs to.
BRENDA, The Comprehensive Enzyme Information System
ProDom protein domain families automatically generated from Swiss-Prot and TrEMBL
iHOP analyzed abstract identifier namespace
An identifier representing an NCBI (GenBank) Accession number, without a version (e.g. J00522)
EST from the Solanaceae Genomics Network database (e.g. SGN-E:333157)
Search SNPs with potential phenotypic effect.
AGRIS_TFFamilyName is obtained from AGRIS AtTFDB database, which contains comprehensive collection of Arabidopsis Transcription Factors (TFs) classified into TF families identified based on the presence of conserved domains and directly from published literature through manual curation process.
RESID Database of Protein Modifications.
An accession number from Pathbase (European mutant mouse pathology database)
description for MyTestingNamespace_11253757326251
Gene Ontology Annotation at EBI annotations from HAMAP to GO mapping.
RefSeq (Protein); Identifiers that are used to link to RefSeq records
Identifier for Elements in MIPS Arabidopsis database (MAtDB) (e.g.At1g01800)
Pfam: Protein families database of alignments and HMMs.
table of allele frequency for a pool of accessions, ordered by type of markers and locus
RAPID is the 'RIKEN Arabidopsis Phenome Information Database', a searchable site of phenotypic data in transposon-insertional mutants. This namespace is for their line codes (like 13-0753-1).
Wormpep, database of proteins of C. elegans.
SDSC functional genomics ID as used by PlantsP (http://plantsp.sdsc.edu) and related dbases PlantsT and PlantsUBQ. IDs are unique across these three dbases.
National Center for Biotechnology Information, Bethesda.
Integrated Microbial Genomes, The JGI's IMG website for genome annotation
The Institute for Genomic Research, Plasmodium falciparum database
Identifier for Clones in MIPS Medicago database (e.g.mth2-26n6)
Prosite. Database of protein families and domains.
DictyBase (Dictyostelium discoideum) locus
The Institute for Genomic Research, EGAD database
Adult Mouse Anatomical Dictionary; part of mouse Gene Expression Database
Schematikon protein structural motif database, ID for particular subset of PDB
BioCASe network of specimen providers central database
The NSF 2010 Project on Essential Gene Functions in Arabidopsis Seed Development. This project deals with genes that give a seed phenotype when disrupted by mutation. See http://www.seedgenes.org.
Any one of a series of two or more different genes that occupy the same position (locus) on a chromosome (e.g. cer5-1)
An agent that induces/increases the frequency of mutations in Arabidopsis (e.g. EMS)
A generic namespace to hold the common name of a gene from any organism. This is slightly more useful than the Global_Keyword namespace that is more commonly used for this case.
Nottingham Arabidopsis Stock Centre Seeds Database
Rubber Tree module of the TropGENE database
Database of rice mutant data maintained at IRFGC
A namespace to represent any entity within the Gene Ontology
An identifier representing a Universal Resource Locator (idenifiers within the W3C's URL specification)
UniProtKB-TrEMBL, a computer-annotated protein sequence database supplementing UniProtKB and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in UniProtKB/Swiss-Prot
Virus Database at University College London
The name for a slide stored in Nottingham Arabidopsis Stock Centre's microarray database (e.g. Ulm_1-5_4days-305nm_Rep2_ATH1)
Identifiers for a clone library in IPK Crop EST (Cr-EST) database (e.g HY).
Sugarcane module of the TropGENE database
Identifier for Contigs in MIPS Maize database (e.g.ZMMBBc0063A01)
Schematikon protein structural motif database, structure motif ID
Database of rice germplasm data maintained at the IRRI Genetic Resources Center (GRC).
SGN external genomic clone read identifier, e.g. LE_HBa0031A19_SP6_139417
A namespace for Antirrhinum Sequence Identifiers according to DragonDB
The name for an experiment stored in Nottingham Arabidopsis Stock Centre's microarray database (e.g. UV-B response of Arabidopsis)
Gene Ontology Annotation at EBI annotations from EC mapping.
Identifiers for EST sequences in IPK Crop EST (Cr-EST) database (e.g HY01A10V).
Namespace used for testing BioMOBY services.
Identifier from Gene Ontology Database. (e.g. GO:1234)
Database of rice (DNA sequences) maintained at CAAS.
Digital Object Identifier, a unique identifier for a document, usually for a published paper, but can be for books, etc.
A namepace representing records in the dbSNP database (database of Single Nucleotide Polymorphisms) at the NCBI.
locus-linked allele in the TropGENE database
Insertion line identifier used by atidb.org @ John Innes Centre for their Gene Traps mutants (example: GT.114525)
Namespace for the BLAST Like Alignment Tool (BLAT).
NCBI PubChem database of chemical substances
The Vertebrate Genome Annotation database
position of loci on a map in the TropGENE database
High-quality Automated and Manual Annotation of microbial Proteomes
description for MyTestingNamespace_11254519980291
A namespace describing a Saccharomyces Open Reading Frame Identifier