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Taxonomy   Taxonomy information about the organism that was the source of the molecule | |
| EBI Taxonomy A:10, R:2, T:ETAXI, I:188000 | Taxonomy classification of organism set up by Swissprot at EBI based on NCBI taxonomy |
| EBI Taxonomy Synonyms A:3, R:1, T:ETAXI_SYNONYMS, I:12300 | Synonyms of organism names for the Swissprot, EBI taxonomy classification |
| Taxonomy of Molecule A:35, R:3, T:MOLECULE_SOURCE, I:33300 | The PDBe organism and taxonomy information together with source and host organism details and crossreferences to the Swissprot and NCBI taxonomies. The assignment has to be done on the molecule (and not entry or chain) level, since in special cases, more than 1 organism may be used as the source of the entry, while all the chains that correspond to the same molecules will have the same taxonomy |
| NCBI Taxonomy A:6, R:9, T:NCBI, I:188000 | The common NCBI taxonomy classification (http://www.ncbi.nlm.nih.gov/Taxonomy/) |
| NCBI Synonyms A:3, R:1, T:NCBI_SYNONYMS, I:240000 | Synonyms of organism names for the NCBI taxonomy classification |
:String, 
:Integer, 
:Number, 
:Date, 
:Unknown
The attribute is a part of the name of an instance
The attribute is a part of the reference key of an instance
The attribute is not supposed to be visible and used for queries
The attribute is supposed to be used in summary reports (lists) for the entity
:Optional, 
:Many
=Reverse relation of the entity that the relation refers to
=Entity that this relation establishes an association (reverse entity)
The relation is the containment relation of the entity
The relation is associated with an external entity from a different mart The relation is not supposed to be visible and used for queries|
EBI Taxonomy  Taxonomy classification of organism set up by Swissprot at EBI based on NCBI taxonomy Reference attributes:Tax Id - Naming attributes:Full Name | |
Tax Id C:TAX_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Full Name C:FULL_NAME, S:306, A:22.0 | The swissprot full name |
Annotation Source C:ANNOTATION_SOURCE, S:30, A:4.0 | The source of the taxonomy information |
Complete Genome Flag C:COMPLETE_GENOME_FLAG, S:1, A:1.0 | (internal) |
Hidden C:HIDDEN, S:3, A:2.0 | (internal) |
Left Number C:LEFT_NUMBER, S:15, A:4.0 | A more effecient alternative representation of the taxonomy tree |
Parent Id C:PARENT_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) of the parent node (family,genus etc) in the taxonomy tree |
Rank C:RANK, S:20, A:7.0 | The rank of the node in the taxonomy tree (species, family, genus, kingdom etc) |
Right Number C:RIGHT_NUMBER, S:15, A:4.0 | A more effecient alternative representation of the taxonomy tree |
Scientific Name C:SCIENTIFIC_NAME, S:100, A:21.0 | The scientific name of the taxonomy node |
derived from related | The NCBI taxonomy from where this was derived |
has related | Synonyms of the taxonomy |
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EBI Taxonomy Synonyms Synonyms of organism names for the Swissprot, EBI taxonomy classification Reference attributes:Tax Id,Name Class,Name Txt - Naming attributes:Name Txt | |
Name Txt C:NAME_TXT, S:100, A:16.0 | The synonym of the organism |
Name Class C:NAME_CLASS, S:30, A:16.0 | The type of synonym |
Tax Id C:TAX_ID, S:10, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
of related | The taxonomy that this is synonym of |
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Taxonomy of Molecule The PDBe organism and taxonomy information together with source and host organism details and crossreferences to the Swissprot and NCBI taxonomies.
The assignment has to be done on the molecule (and not entry or chain) level, since in special cases, more than 1 organism
may be used as the source of the entry, while all the chains that correspond to the same molecules will have the same taxonomy Reference attributes:Molecule Source Id - Naming attributes:Accession Code,Ncbi Tax Id | |
Molecule Source Id C:MOLECULE_SOURCE_ID, S:10, A:4.0 | The database identifier of the Molecule Source |
Accession Code C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
Systematic Name C:SYSTEMATIC_NAME, S:80, A:1.0 | (obsolete) |
Atcc C:ATCC, S:80, A:2.0 | American Type Culture Collection tissue culture number (http://www.atcc.org). |
Cell Id C:CELL_ID, S:80, A:2.0 | (future use) |
Cell Line C:CELL_LINE, S:80, A:2.0 | A specific line of cells used as the expression system |
Cellular Location C:CELL_LOCATION, S:80, A:2.0 | Identifies the location inside (or outside) the cell. |
Cell Type C:CELL_TYPE, S:80, A:2.0 | Cell type (i.e. ENDOTHELIAL) |
Details C:DETAILS, S:4000, A:4.0 | A description of special aspects of the entity |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Fragment C:FRAGMENT, S:2000, A:1.0 | |
Gene C:GENE, S:80, A:2.0 | Specific gene which expressed the molecule. |
Host Culture Collection C:HOST_CULTURE_COLLECTION, S:2000, A:1.0 | (future use) |
Host Vector C:HOST_VECTOR, S:80, A:2.0 | (future use) |
Host Vector Type C:HOST_VECTOR_TYPE, S:80, A:2.0 | (future use) |
Molecule Engineered C:MOLECULE_ENGINEERED, S:1, A:1.0 | Indicates whether the component is engineered. |
Molecule Id C:MOLECULE_ID, S:0, A:4.0 | The database identifier of the Molecule |
Molecule Source Type C:MOLECULE_SOURCE_TYPE, S:10, A:4.0 | The type of the molecule_source: N: natural, details of the source from which the entity was obtained, in those cases where the entity was isolated directly from a natural tissue. G: genetically maninupated, details of the source from which the entity was obtained, in those cases where the source was a genetically manipulated one. The following are treated separately: Items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). |
Molecule Type C:MOLECULE_TYPE, S:10, A:4.0 | Molecule type: P: Polymer molecule S: Polymer segment M: Non-polymer W: Water group The only type of molecule associates with a source are Polymer molecules |
Mutation String C:MUTATION_STRING, S:40, A:1.0 | Details about an entity mutation. |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the NCBI or Swissprot-EBI taxonomy tree |
Organ C:ORGAN, S:80, A:2.0 | Specific organ which expressed the molecule. |
Organelle C:ORGANELLE, S:80, A:2.0 | Organized structure within cell (i.e. MITOCHONDRIA) |
PDB Common Name C:PDB_COMMON_NAME, S:700, A:4.0 | Common name of the organism from which the biological polymer entity was isolated (as in the PDB). |
PDB Scientific Name C:PDB_SCIENTIFIC_NAME, S:700, A:2.0 | Scientific name of the organism of the natural source (as in the PDB) |
PDB Strain C:PDB_STRAIN, S:700, A:1.0 | The strain of the organism from which the entity was isolated (obsolete) |
Plasmid C:PLASMID, S:80, A:3.0 | The name of the plasmid that contained the gene and produced the entity in the host organism. |
Plasmid Details C:PLASMID_DETAILS, S:4000, A:1.0 | Details about the plasmid. |
Secretion C:SECRETION, S:80, A:2.0 | Identifies the secretion from which the molecule was isolated. |
Strain C:STRAIN, S:2000, A:3.0 | The strain of the organism from which the entity was isolated. |
Synthetic C:SYNTHETIC, S:1, A:1.0 | |
Tissue C:TISSUE, S:255, A:1.0 | The tissue of the organism from which the entity was isolated. (future use) |
Tissue Fraction C:TISSUE_FRACTION, S:2000, A:1.0 | The sub-cellular fraction of the tissue of the natural organism from which the gene was obtained (i.e. mitochondria,nucleus,membrane) (future use) |
Variant C:VARIANT, S:2000, A:2.0 | Identifies the organism variant for natural sources or the variant of the organism used as the expression system. |
Source Tissue C:SOURCE_TISSUE, S:0, A:1.0 | The tissue of the natural organism from which the gene was obtained. (ie heart,liver,eye lens) |
of related | The entry where this molecule source was used |
of related | The molecules that have this source |
organism related | The organism that was used as source |
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NCBI Taxonomy The common NCBI taxonomy classification (http://www.ncbi.nlm.nih.gov/Taxonomy/) Reference attributes:Tax Id - Naming attributes:Rank | |
Tax Id C:TAX_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Rank C:RANK, S:20, A:7.0 | The rank of the node in the taxonomy tree (species, family, genus, kingdom etc) |
Hidden C:HIDDEN, S:3, A:2.0 | (internal) |
Parent Id C:PARENT_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) of the parent node (family,genus etc) in the taxonomy tree |
Preferred Common Name C:PREFERRED_COMMON_NAME, S:100, A:2.0 | The common name of the taxonomy node |
Scientific Name C:SCIENTIFIC_NAME, S:100, A:21.0 | The scientific name of the taxonomy node |
used related | The molecules that this organism was used as source |
relates related | The EBI taxonomies derived from this taxonomy |
has related | Synonyms of the taxonomy |
belong related | |
belong related | Reverse relation:of organism of Reverse entity:CATH Protein Structure Classification - Relation attributes:Tax Id |
belong related | |
belong related | |
belong related | |
belong related | Reverse relation:of organism of Reverse entity:SCOP Structural Classification of Proteins - Relation attributes:Tax Id |
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NCBI Synonyms Synonyms of organism names for the NCBI taxonomy classification Reference attributes:Tax Id,Name Class,Name Txt - Naming attributes:Name Txt | |
Name Txt C:NAME_TXT, S:100, A:22.0 | The synonym of the organism |
Name Class C:NAME_CLASS, S:100, A:14.0 | The type of synonym |
Tax Id C:TAX_ID, S:10, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
of related | The taxonomy that this is synonym of |
Entity Details: A=Number of attributes of the Entity
R=Number of relations of the Entity
T=Name of the database table
I=Approximation of the number of instances of the entity