Cellular Network Knowledge Base (CNKB)

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== INTRODUCTION ==
== INTRODUCTION ==
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The Cellular Network Knowledge Base (CNKB) maintains the B-Cell Interactome and stores protein-protein and protein-dna interactions from several public databases. It stores sequence info, interaction type, GO annotation, cellular and molecular phenotype context for the interaction, algorithm or experimental procedure for inferring the interaction, and homology relationships across multiple species. One CNKB table is available for querying via a geWorkbench plugin and for visualizing interactions in geWorkbench Cytoscape module, but the number of tables accessed by geWorkbench needs to be extended in order to provide more information to the user.
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The Cellular Network Knowledge Base (CNKB) maintains the B-cell Interactome and stores protein-protein and protein-dna interactions from several public databases. It stores sequence info, interaction type, GO annotation, cellular and molecular phenotype context for the interaction, algorithm or experimental procedure for inferring the interaction, and homology relationships across multiple species. One CNKB table is available for querying via a geWorkbench plugin and for visualizing interactions in geWorkbench Cytoscape module, but the number of tables accessed by geWorkbench needs to be extended in order to provide more information to the user.
== REQUIREMENTS ==
== REQUIREMENTS ==

Latest revision as of 21:54, 30 October 2010

INTRODUCTION

The Cellular Network Knowledge Base (CNKB) maintains the B-cell Interactome and stores protein-protein and protein-dna interactions from several public databases. It stores sequence info, interaction type, GO annotation, cellular and molecular phenotype context for the interaction, algorithm or experimental procedure for inferring the interaction, and homology relationships across multiple species. One CNKB table is available for querying via a geWorkbench plugin and for visualizing interactions in geWorkbench Cytoscape module, but the number of tables accessed by geWorkbench needs to be extended in order to provide more information to the user.

REQUIREMENTS

  • make the database schema compatible with the BioPAX ontology requirements
    • import data in BioPAX markup
    • export data in BioPAX markup
  • associate all pathologies referenced in the database with their appropriate histology ICD9/ICD10 codes
  • the cellular component of a particular interaction should be linked to one or more Gene Ontology terms, parent & child nodes
  • each interaction should be associated with one or more Gene Ontology molecular functions
  • store microarray annotation data for widely-used Illumina chip platforms
  • store runtime information (command-line string) for programs such as ARACNE or MINDY

MAPPING BioPAX CLASSES TO CNKB TABLES/COLUMNS

CNKB Table
CNKB Column
BioPAX Class
BioPAX Property
Comment
cellular_componentnameCellularLocationVocabularycellularLocationshould reference a term in the GO Cellular Component Ontology
dbxrefdb_sourceXrefdba reference to the PSI-MI Ontology database citation (CV)
detectionshortlabelExperimentalFormVocabularyN/Aa reference to the PSI-MI Ontology interaction detection method (CV)
interaction_dbxrefinteraction_idN/AN/AFK pointer to "id" in pairwise_interaction table, internal identifier
interaction_dbxrefdbxref_idN/AN/AFK pointer to "id" in dbxref table, internal identifier
interaction_dbxrefvaluePublicationXrefN/AThis column contains PubMed identifiers
interaction_modulatorN/AInteraction.Control.Modulationparticipanta control interaction in which a physical entity modulates a catalysis interaction
interaction_pathwaypairwise_idPathwaypathwayComponentan interaction associated with a specific pathway
interaction_pathwaypathway_idPathwaypathwayComponenta pathway can be a component of another pathway
interaction_typeinteraction_typeInteractioninteractionTypeshould reference the PSI-MI ontology interaction type
interactorshort_namePhysicalEntity.ProteinN/Aa physical entity consisting of a sequence of amino acids (ex. EGFR)
pairwise_interactionms_id1Xrefidentrez id: defines external cross-references to entities in external databases
pairwise_interactionms_id2Xrefidentrez id: defines external cross-references to entities in external databases
pairwise_interactiongene1MolecularInteractionparticipant"MolecularInteraction" is default class for representing molecular interactions
pairwise_interactiongene2MolecularInteraction participant"MolecularInteraction" is default class for representing molecular interactions
pairwise_interactionconfidence_valueEvidencecondifenceconfidence in the containing instance, usually a statistical measure
pairwise_interactionis_modulatedN/AN/Aif set to 'Y', indicates that this interaction should have a corresponding entry in the 'interaction_modulator' table
pairwise_interactioninteraction_typeInteractioninteractionTypethis is actually a FK pointer to the CV term in the "interaction_type" table
pairwise_interactiontaxonomyControlledVocabularyterm"term", a BioPAX DataProperty, signifies the external controlled vocabulary term
pairwise_interactionsourceXrefdb"db", a BioPAX DataProperty, signifies the name of the external database
pathwayshort_nameEntity.PathwayN/AA set or series of interactions forming a network which biologists have found useful to group together for organizational, historic, or other reasons. It is possible to define a pathway without specifying the interactions within it (treated like a "black box").
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