mongo_schema

MongoDB schema

EGRIN 2.0 uses MongoDB as its backend. By convention, the databases are named using an organism three-letter short code code followed by _db, e.g. the E. coli database is called eco_db. For a list of available databases, please consult our Available Databases.

If you have assembled the database on your local machine, MongoDB typically stores its data in /data/db/.

Please note that the ASSEMBLE scripts backup the database flat files (BSON) to a user specified target directory automatically.

Collections

###ensemble_info { _id: ObjectId, run_id: int, run_name: text, start_time: timestamp, finish_time: timestamp, num_iterations: int, organism: text, species: text, num_rows: int, rows: [row_id], num_columns: int, cols: [col_id], num_clusters: int, git_sha: text, added_to_ensemble: timestamp }

###row_info { _id: ObjectId, row_id: int, egrin2_row_name: text, additional_info...(depends on annotations supplied) }

###col_info { _id: ObjectId, col_id: int, egrin2_col_name: text, additional_info [{ name: text, value: text, unit: text }] }

###bicluster_info { _id: ObjectId, run_id: int, cluster: int, rows: [row_id], columns: [col_id], residual: decimal, }

###motif_info: { cluster_id: ObjectId, gre_id: text, motif_num: int, seqtype: text, evalue: decimal, meme_motif_site: [{ row_id: int, reverse: boolean, scaffoldId: text, start: int, pvalue: decimal }], pwm: [{ row: int, a: decimal, c: decimal, g: decimal, t: decimal }] }

###fimo { _id: ObjectId, cluster_id:, ObjectId, motif_num, int, scaffoldId: text, start: int, stop: int, strand: boolean, score: decimal, p-value: decimal, in_coding_rgn: boolean }

###gene_expression { _id: ObjectId, row_id: int, col_id: int, raw_expression: decimal, standardized_expression: decimal }

###genome { _id: ObjectId, scaffoldId: int, NCBI_RefSeq: text, NCBI_taxonomyId: text }

###row_row { _id: ObjectId, row_ids: [ int ], counts: int, weight: decimal, backbone_pval: decimal }

###col_resample { _id: ObjectId, n_rows: int, col_id: int, resamples: int, lowest_raw: [ decimal ], lowest_standardized: [ decimal ], }

###corem { _id: ObjectId, corem_id: int rows: [int], cols: [{ col_id: int, pval: decimal }], edges: [text] density: decimal, weighted_density: decimal }