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CREATE UNIQUE INDEX md5s_md5 ON md5s (md5);
CREATE INDEX md5_protein_id ON md5_protein (id);
CREATE INDEX md5_protein_md5 ON md5_protein (md5);
CREATE INDEX md5_protein_function ON md5_protein (function);
CREATE INDEX md5_protein_organism ON md5_protein (organism);
CREATE INDEX md5_protein_source ON md5_protein (source);
CREATE INDEX md5_ontology_id ON md5_ontology (id);
CREATE INDEX md5_ontology_md5 ON md5_ontology (md5);
CREATE INDEX md5_ontology_function ON md5_ontology (function);
CREATE INDEX md5_ontology_source ON md5_ontology (source);
CREATE INDEX md5_rna_id ON md5_rna (id);
CREATE INDEX md5_rna_md5 ON md5_rna (md5);
CREATE INDEX md5_rna_function ON md5_rna (function);
CREATE INDEX md5_rna_organism ON md5_rna (organism);
CREATE INDEX md5_rna_tax_rank ON md5_rna (tax_rank);
CREATE INDEX md5_rna_source ON md5_rna (source);
CREATE INDEX md5_organism_unique_md5 ON md5_organism_unique (md5);
CREATE INDEX md5_organism_unique_source ON md5_organism_unique (source);
CREATE INDEX aliases_protein_id on aliases_protein (id);
CREATE INDEX functions_name ON functions (name);
CREATE INDEX contigs_id ON contigs (name);
CREATE INDEX contigs_organism ON contigs (organism);
CREATE INDEX contigs_length ON contigs (length);
CREATE INDEX id2contig_id ON id2contig (id);
CREATE INDEX id2contig_contig ON id2contig (contig);
CREATE INDEX organisms_ncbi_name ON organisms_ncbi (name);
CREATE INDEX organisms_ncbi_tax_id ON organisms_ncbi (ncbi_tax_id);
CREATE INDEX ontology_seed_id ON ontology_seed (id);
CREATE INDEX ontology_kegg_id ON ontology_kegg (id);
CREATE INDEX ontology_eggnog_id ON ontology_eggnog (id);
CREATE INDEX ontology_eggnog_type ON ontology_eggnog (type);
CREATE INDEX ontologies_id ON ontologies (id);
CREATE INDEX ontologies_type ON ontologies (source);
CREATE INDEX sources_name ON sources (name);
CREATE INDEX sources_type ON sources (type);
# load ontologies table
INSERT INTO ontologies (level1,level2,level3,level4,id,type) SELECT level1,level2,level3,level4,id,'KO' FROM ontology_kegg;
INSERT INTO ontologies (level1,level2,level3,level4,id,type) SELECT level1,level2,level3,level4,id,'Subsystems' FROM ontology_seed;
INSERT INTO ontologies (level1,level2,level3,id,type) SELECT level1,level2,level3,id,type FROM ontology_eggnog;
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