Cellular Network Knowledge Base (CNKB)
From Informatics
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_component | name | CellularLocationVocabulary | cellularLocation | should reference a term in the GO Cellular Component Ontology |
dbxref | db_source | Xref | db | a reference to the PSI-MI Ontology database citation (CV) |
detection | shortlabel | ExperimentalFormVocabulary | N/A | a reference to the PSI-MI Ontology interaction detection method (CV) |
interaction_dbxref | interaction_id | N/A | N/A | FK pointer to "id" in pairwise_interaction table, internal identifier |
interaction_dbxref | dbxref_id | N/A | N/A | FK pointer to "id" in dbxref table, internal identifier |
interaction_dbxref | value | PublicationXref | N/A | This column contains PubMed identifiers |
interaction_modulator | N/A | Interaction.Control.Modulation | participant | a control interaction in which a physical entity modulates a catalysis interaction |
interaction_pathway | pairwise_id | Pathway | pathwayComponent | an interaction associated with a specific pathway |
interaction_pathway | pathway_id | Pathway | pathwayComponent | a pathway can be a component of another pathway |
interaction_type | interaction_type | Interaction | interactionType | should reference the PSI-MI ontology interaction type |
interactor | short_name | PhysicalEntity.Protein | N/A | a physical entity consisting of a sequence of amino acids (ex. EGFR) |
pairwise_interaction | ms_id1 | Xref | id | entrez id: defines external cross-references to entities in external databases |
pairwise_interaction | ms_id2 | Xref | id | entrez id: defines external cross-references to entities in external databases |
pairwise_interaction | gene1 | MolecularInteraction | participant | "MolecularInteraction" is default class for representing molecular interactions |
pairwise_interaction | gene2 | MolecularInteraction | participant | "MolecularInteraction" is default class for representing molecular interactions |
pairwise_interaction | confidence_value | Evidence | condifence | confidence in the containing instance, usually a statistical measure |
pairwise_interaction | is_modulated | N/A | N/A | if set to 'Y', indicates that this interaction should have a corresponding entry in the 'interaction_modulator' table |
pairwise_interaction | interaction_type | Interaction | interactionType | this is actually a FK pointer to the CV term in the "interaction_type" table |
pairwise_interaction | taxonomy | ControlledVocabulary | term | "term", a BioPAX DataProperty, signifies the external controlled vocabulary term |
pairwise_interaction | source | Xref | db | "db", a BioPAX DataProperty, signifies the name of the external database |
pathway | short_name | Entity.Pathway | N/A | A 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"). |