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Coordinate Systems

The DAS registration server uses coordinate systems to describe the data that is made available by a DAS source. This information is important for the DAS clients, to deal with data correctly, as they often can accept data served in multiple coordinate systems.

The coordinate systems are described by four fields: Authority, (assembly) Version, Type, and Organism. The assembly version is important for genome assemblies, but not really applicable for other datasets like UniProt sequences, therefore this field is optional.

Authority

 The name of an authority/institution that defines the accession codes of a coordinate system or that provides a gene-build. In the latter case this field also contains the version number of the assembly. Currently the following authority names are supported (for assembly authorities we added the assembly version):
  • AaegL_1
  • AgamP_3
  • ARMA
  • BDGP
  • BDGP_4.3
  • BGI_2005-01
  • BROADD_1
  • BROADD_2
  • BROADE_1
  • BROADO_3
  • BROADO_5
  • BROADS_1
  • Btau_
  • Btau__2.0
  • Btau__3.1
  • BUSHBABY_1
  • CASP
  • CAT
  • cavPor
  • CEL_130
  • CEL_160
  • CHIMP_1
  • CHIMP_2.1
  • COMMON_SHREW_1
  • CSAV_2.0
  • dipOrd
  • EMBL
  • EMBL
  • EMDB
  • Ensembl
  • Entrez
  • EquCab
  • FUGU_4
  • GENCODE_2.2
  • GUINEAPIG
  • Havana
  • HEDGEHOG
  • HIV
  • HUGO_ID
  • IPI
  • IPI_ID
  • IRGSP_4.0
  • JGI_2
  • JGI_4.1
  • KEGG
  • MEDAKA_1
  • MGI
  • MGI_Symbol
  • micMur
  • MICROBAT_1
  • MMUL__1
  • MOZ2a
  • NASC29
  • NCBI_34
  • NCBI_35
  • NCBI_36
  • NCBI m_34
  • NCBI m_35
  • NCBIM_36
  • NCBIM_37
  • OANA_5
  • PDBresnum
  • Pfam
  • pika
  • PPYG
  • proCap
  • pteVam
  • RABBIT
  • RGSC_3.4
  • SGD_1
  • SGD_1.01
  • SGD_32
  • SQUIRREL
  • TAIR_6
  • TAIR_7
  • tarSyr
  • TENREC
  • TETRAODON
  • TETRAODON_7
  • TIGR
  • TIGR_5
  • TREESHREW
  • turTru
  • UniParc
  • UniProt
  • vicPac
  • WASHUC_1
  • WASHUC_2
  • WB_170
  • WS
  • WS_180
  • ZFISH_6
  • ZFISH_7
  • Zv_4
  • Zv_5

Type

 A type or category of the coordinate system. This refers to the "physical dimension" of the annotated data. Currently the following categories are available:
  • Chromosome
  • Clone
  • Contig
  • Gene_ID
  • Protein Sequence
  • Protein Structure
  • Scaffold
  • Supercontig
  • Volume Map

Organism

 The organism the data refers to. Not every DAS source is organism specific, therefore this field is optional.

Listing of all coordinate systems

Using the fields described above, currently the following coordinate systems are provided.
[show in separate window]

authority (+version) type organism string representation
ARMA Chromosome Dasypus novemcinctus ARMA,Chromosome,Dasypus novemcinctus
AaegL_1 Supercontig Aedes aegypti AaegL_1,Supercontig,Aedes aegypti
AaegL_1 Chromosome Aedes aegypti AaegL_1,Chromosome,Aedes aegypti
AgamP_3 Scaffold Anopheles gambiae AgamP_3,Scaffold,Anopheles gambiae
AgamP_3 Chromosome Anopheles gambiae AgamP_3,Chromosome,Anopheles gambiae
BDGP Chromosome Drosophila melanogaster BDGP,Chromosome,Drosophila melanogaster
BDGP_4.3 Chromosome Drosophila melanogaster BDGP_4.3,Chromosome,Drosophila melanogaster
BGI_2005-01 Chromosome Oryza sativa indica BGI_2005-01,Chromosome,Oryza sativa indica
BROADD_2 Chromosome Canis familiaris BROADD_2,Chromosome,Canis familiaris
BROADD_1 Chromosome Canis familiaris BROADD_1,Chromosome,Canis familiaris
BROADE_1 Chromosome Loxodonta africana BROADE_1,Chromosome,Loxodonta africana
BROADO_3 Chromosome Monodelphis domestica BROADO_3,Chromosome,Monodelphis domestica
BROADO_5 Chromosome Monodelphis domestica BROADO_5,Chromosome,Monodelphis domestica
BROADS_1 Chromosome Gasterosteus aculeatus BROADS_1,Chromosome,Gasterosteus aculeatus
BUSHBABY_1 Chromosome Otolemur garnettii BUSHBABY_1,Chromosome,Otolemur garnettii
Btau_ Chromosome Bos taurus Btau_,Chromosome,Bos taurus
Btau__3.1 Chromosome Bos taurus Btau__3.1,Chromosome,Bos taurus
Btau__2.0 Chromosome Bos taurus Btau__2.0,Chromosome,Bos taurus
CASP Protein Structure CASP,Protein Structure
CAT Chromosome Felis catus CAT,Chromosome,Felis catus
CEL_130 Chromosome Caenorhabditis elegans CEL_130,Chromosome,Caenorhabditis elegans
CEL_160 Chromosome Caenorhabditis elegans CEL_160,Chromosome,Caenorhabditis elegans
CHIMP_2.1 Chromosome Pan troglodytes CHIMP_2.1,Chromosome,Pan troglodytes
CHIMP_1 Chromosome Pan troglodytes CHIMP_1,Chromosome,Pan troglodytes
COMMON_SHREW_1 Chromosome Sorex araneus COMMON_SHREW_1,Chromosome,Sorex araneus
CSAV_2.0 Chromosome Ciona savignyi CSAV_2.0,Chromosome,Ciona savignyi
EMBL Clone Danio rerio EMBL,Clone,Danio rerio
EMBL Clone Mus musculus EMBL,Clone,Mus musculus
EMBL Clone Sus scrofa EMBL,Clone,Sus scrofa
EMBL Clone Canis familiaris EMBL,Clone,Canis familiaris
EMBL Clone Homo sapiens EMBL,Clone,Homo sapiens
EMBL Clone EMBL,Clone
EMDB Volume Map EMDB,Volume Map
Ensembl Gene_ID Mus musculus Ensembl,Gene_ID,Mus musculus
Ensembl Gene_ID Rattus norvegicus Ensembl,Gene_ID,Rattus norvegicus
Ensembl Protein Sequence Fugu rubripes Ensembl,Protein Sequence,Fugu rubripes
Ensembl Gene_ID Homo sapiens Ensembl,Gene_ID,Homo sapiens
Ensembl Gene_ID Ensembl,Gene_ID
Ensembl Protein Sequence Ensembl,Protein Sequence
Ensembl Protein Sequence Homo sapiens Ensembl,Protein Sequence,Homo sapiens
Ensembl Protein Sequence Rattus norvegicus Ensembl,Protein Sequence,Rattus norvegicus
Entrez Gene_ID Homo sapiens Entrez,Gene_ID,Homo sapiens
Entrez Gene_ID Entrez,Gene_ID
EquCab Chromosome EquCab,Chromosome
FUGU_4 Chromosome Fugu rubripes FUGU_4,Chromosome,Fugu rubripes
GENCODE_2.2 Protein Sequence Homo sapiens GENCODE_2.2,Protein Sequence,Homo sapiens
GUINEAPIG Chromosome GUINEAPIG,Chromosome
HEDGEHOG Chromosome Erinaceus europaeus HEDGEHOG,Chromosome,Erinaceus europaeus
HIV Chromosome HIV-1, strain HXB2 HIV,Chromosome,HIV-1, strain HXB2
HUGO_ID Gene_ID HUGO_ID,Gene_ID
Havana Protein Sequence Homo sapiens Havana,Protein Sequence,Homo sapiens
IPI_ID Protein Sequence IPI_ID,Protein Sequence
IPI Protein Sequence IPI,Protein Sequence
IRGSP_4.0 Chromosome Oryza sativa japonica IRGSP_4.0,Chromosome,Oryza sativa japonica
JGI_2 Chromosome Ciona intestinalis JGI_2,Chromosome,Ciona intestinalis
JGI_4.1 Chromosome Xenopus tropicalis JGI_4.1,Chromosome,Xenopus tropicalis
KEGG Chromosome KEGG,Chromosome
MEDAKA_1 Chromosome Oryzias Latipes MEDAKA_1,Chromosome,Oryzias Latipes
MGI_Symbol Gene_ID Mus musculus MGI_Symbol,Gene_ID,Mus musculus
MGI Gene_ID Mus musculus MGI,Gene_ID,Mus musculus
MICROBAT_1 Chromosome Myotis lucifugus MICROBAT_1,Chromosome,Myotis lucifugus
MMUL__1 Chromosome Macaca mulatta MMUL__1,Chromosome,Macaca mulatta
MOZ2a Chromosome MOZ2a,Chromosome
NASC29 Chromosome Arabidopsis thaliana NASC29,Chromosome,Arabidopsis thaliana
NCBI_35 Chromosome Homo sapiens NCBI_35,Chromosome,Homo sapiens
NCBI_36 Clone Homo sapiens NCBI_36,Clone,Homo sapiens
NCBI_36 Contig Homo sapiens NCBI_36,Contig,Homo sapiens
NCBI_35 Clone Homo sapiens NCBI_35,Clone,Homo sapiens
NCBI_36 Chromosome Homo sapiens NCBI_36,Chromosome,Homo sapiens
NCBI_34 Chromosome Homo sapiens NCBI_34,Chromosome,Homo sapiens
NCBI_35 Contig Homo sapiens NCBI_35,Contig,Homo sapiens
NCBI_35 Protein Sequence Homo sapiens NCBI_35,Protein Sequence,Homo sapiens
NCBI m_34 Chromosome Mus musculus NCBI m_34,Chromosome,Mus musculus
NCBI m_34 Contig Mus musculus NCBI m_34,Contig,Mus musculus
NCBI m_35 Chromosome Mus musculus NCBI m_35,Chromosome,Mus musculus
NCBI m_35 Contig Mus musculus NCBI m_35,Contig,Mus musculus
NCBIM_36 Chromosome Mus musculus NCBIM_36,Chromosome,Mus musculus
NCBIM_37 Chromosome Mus musculus NCBIM_37,Chromosome,Mus musculus
OANA_5 Chromosome Ornithorhynchus anatinus OANA_5,Chromosome,Ornithorhynchus anatinus
PDBresnum Protein Structure PDBresnum,Protein Structure
PPYG Chromosome PPYG,Chromosome
Pfam Protein Sequence Pfam,Protein Sequence
RABBIT Chromosome Oryctolagus cuniculus RABBIT,Chromosome,Oryctolagus cuniculus
RGSC_3.4 Chromosome Rattus norvegicus RGSC_3.4,Chromosome,Rattus norvegicus
SGD_32 Gene_ID Saccharomyces cerevisiae SGD_32,Gene_ID,Saccharomyces cerevisiae
SGD_1.01 Chromosome Saccharomyces cerevisiae SGD_1.01,Chromosome,Saccharomyces cerevisiae
SGD_32 Chromosome Saccharomyces cerevisiae SGD_32,Chromosome,Saccharomyces cerevisiae
SGD_1 Chromosome Saccharomyces cerevisiae SGD_1,Chromosome,Saccharomyces cerevisiae
SQUIRREL Chromosome Spermophilus tridecemlineatus SQUIRREL,Chromosome,Spermophilus tridecemlineatus
TAIR_6 Chromosome Arabidopsis thaliana TAIR_6,Chromosome,Arabidopsis thaliana
TAIR_7 Chromosome Arabidopsis thaliana TAIR_7,Chromosome,Arabidopsis thaliana
TENREC Chromosome Echinops telfairi TENREC,Chromosome,Echinops telfairi
TETRAODON Chromosome Tetraodon nigroviridis TETRAODON,Chromosome,Tetraodon nigroviridis
TETRAODON_7 Chromosome Tetraodon nigroviridis TETRAODON_7,Chromosome,Tetraodon nigroviridis
TIGR_5 Chromosome Oryza sativa japonica TIGR_5,Chromosome,Oryza sativa japonica
TIGR Gene_ID Arabidopsis thaliana TIGR,Gene_ID,Arabidopsis thaliana
TREESHREW Chromosome Tupaia belangeri TREESHREW,Chromosome,Tupaia belangeri
UniParc Protein Sequence UniParc,Protein Sequence
UniProt Protein Sequence UniProt,Protein Sequence
WASHUC_1 Chromosome Gallus gallus WASHUC_1,Chromosome,Gallus gallus
WASHUC_2 Chromosome Gallus gallus WASHUC_2,Chromosome,Gallus gallus
WB_170 Chromosome Caenorhabditis elegans WB_170,Chromosome,Caenorhabditis elegans
WS Chromosome Caenorhabditis elegans WS,Chromosome,Caenorhabditis elegans
WS_180 Chromosome Caenorhabditis elegans WS_180,Chromosome,Caenorhabditis elegans
ZFISH_7 Chromosome Danio rerio ZFISH_7,Chromosome,Danio rerio
ZFISH_6 Chromosome Danio rerio ZFISH_6,Chromosome,Danio rerio
ZFISH_6 Scaffold Danio rerio ZFISH_6,Scaffold,Danio rerio
ZFISH_7 Scaffold Danio rerio ZFISH_7,Scaffold,Danio rerio
Zv_5 Scaffold Danio rerio Zv_5,Scaffold,Danio rerio
Zv_5 Chromosome Danio rerio Zv_5,Chromosome,Danio rerio
Zv_4 Chromosome Danio rerio Zv_4,Chromosome,Danio rerio
cavPor Chromosome cavPor,Chromosome
dipOrd Chromosome dipOrd,Chromosome
micMur Chromosome micMur,Chromosome
pika Chromosome pika,Chromosome
proCap Chromosome proCap,Chromosome
pteVam Chromosome pteVam,Chromosome
tarSyr Chromosome tarSyr,Chromosome
turTru Chromosome turTru,Chromosome
vicPac Chromosome vicPac,Chromosome