PPLRE Organism Table
The PPLRE Organism Table is a PPLRE Table identifies all Organism Species and Strains relevant to the PPLRE Project. I.e. all known Bacteria and Archaea.
Attributes + Descriptions:
|
Attribute Name |
Description |
|
OrganismID |
The primary key. An integer that identifies a unique Organism. Also a foreign key to the OrganismNCBI table (see NCBI). |
|
OrganismDefault NameID |
The organism’s default name that will be commonly used by within the project. A foreign key to the OrganismName table. Values will match those in PSORTdb (organism). |
|
DomainID |
Identifies the organism’s tree-of-life domain. A foreign key to the OrganismDomain table. Sample values: 2(Bacteria) and 2157(Archaea). |
|
PhylumID |
Identifies the organism’s tree-of-life phylum. A foreign key to the OrganismPhylum table. In the near term, this attribute may only play a role during the generation of human reports. |
|
ClassID |
Identifies the Class of the organism. A foreign key to the OrganismClass table. In the near term, this attribute may only play a role during the generation of human reports. |
|
GramStain |
Identifies the Gram Stain of the organism, it is from the “Bacteria” domain. Values: 1(positive), -1(negative), and NULL (e.g. for Archaea). |
|
Sequenced (future) |
Identifies whether the organism has been sequenced. Values: true/false. |
Rows
~64,119 or greater
Source:
- NCBIOrganismTreeNode and NCBIOrganismName table (butinclude only organisms from the Archaea and Bacteria domains).
- Bacteria Gram information will be retrieved from thegram_stain field in PSORTdb http://psort.org/genomes/genomes.pl
Uses:
- To facilitate the insertionof future results into PSORTdb
- To facilitate the creation of human readable reports,where an actual organism name is preferred over an identification number.
Example:
|
Organism ID |
OrganismDefault Name ID |
Domain ID |
PhylumID |
ClassID |
Genus |
Gram Stain |
|
287 |
7177(Pseudomonas aeruginosa) |
2(Bacteria) |
1(Proteo-bacteria) |
2(Gamma Proteobacteria) |
1(Pseudomonas) |
-1 |
|
1423 |
36701(Bacillus subtilis) |
2(Bacteria) |
2(Firmicutes) |
1(Bacilli) |
2(Bacillus) |
1 |
|
2180 |
2157(Archaea) |
3(Eury-archaeota) |
3(Methano-bacteria) |
1(Methano thermus) |
NULL |
|
|
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