PPLRE OrganismProteinLocalization Table

• The PPLRE OrganismProteinLocalization Table is a PPLRE Table that will contain the both the curated OPL() relations, and the relations predicted by PPLRE.

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Metadata

Attribute Name	Description
PPLID	An integer that identifies a unique localization of an organism’s protein. The primary key of the table. (i.e. multiple localizations for a protein will have multiple entries).
OrganismID	An identifier to the organism in the relationship. A foreign key to the Organism. (n.b. the NCBI taxonomy id)
ProteinID	An identifier to the protein in the relationship. A foreign key to the Protein table.
LocalizationID	A foreign key to the Localization table that identifies the localization region in the relationship.
PassageID	A foreign key to the DocumentParagraph table. The value identifies the region of text that contains the suggestion of the relationship.
MethodUsed	Denotes whether the relationship is an experimental discovery (i.e. in a published article), or is a suggested relationship due to similarity to another protein (BLAST homology), or predicted (by PSORT-b or PA-SUB). Valid values: “Experiment, Similarity, Other”. For the first phase of the project this will likely contain only examples of “Experiment”.
Likelihood	A number that indicates the expected truth of a predicted relationship. Valid values: [1.0-true, 0.0-false]. Has value 1.0 for records where MethodUsed=Experimental.

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Statistics

• Rows: will grow from 500+ to several thousand as the project progresses.

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Source

1. OrganismProteinLocalizationPseudomona(see table definition below)
2. OrganismProteinLocalizationArchaea(see table definition below)
3. OrganismProteinLocalizationEPSORTdb (see table definition below)
4. PPLRE predictions. (future)
5. PA-SUB homology based predictions.(future)

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Intended Use

• Train phase: contains the examples.
• Test phase: also contains the system output.

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Example

PPLID	Orga nismID	Prot einID	Locali zationID	Text RegionID	Source	Likeli hood
1	562	19,749	3	4,729	Curated_Experiment	n/a
2	37924	737,163	4	23,182	Curated_Homology	n/a
3	2180	81,724	1	58,208	Curated_Experiment	n/a
4	2180	79,173	2	74,290	Predicted_PPLRE	0.9
…	…	…	…	…	…	…