diff --git a/.gitignore b/.gitignore index 9f66589..d3b864a 100644 --- a/.gitignore +++ b/.gitignore @@ -114,3 +114,4 @@ site/ Chinook.sqlite chroma.sqlite3 notebooks +chatbgc_env diff --git a/README.md b/README.md index d907b67..d2e80fc 100644 --- a/README.md +++ b/README.md @@ -16,10 +16,46 @@

-Ask questions about biosynthetic gene clusters in your genome dataset via LLMs using Retrieval-Augmented Generation. +Ask questions about BGCs in your genome dataset generated by [`BGCFlow`](https://github.com/NBChub/bgcflow) using Large Language Models (LLMs). -* Free software: MIT -* Documentation: +This python package utilizes vector-based Retrieval-Augmented Generation (RAG) to translate natural language (English) to SQL Queries and is trained to query information from `antiSMASH` and other genome mining tools included in the [`BGCFlow`](https://github.com/NBChub/bgcflow) pipelines. + +![RAG](chatbgc/assets/3_RAG.png) + +## Quickstart +For a quick use of `chatBGC`, you will need an [OpenAI API Key](https://platform.openai.com/api-keys) and the DuckDB database of your `BGCFlow` run (generated using `bgcflow build database`). See [BGCFlow Wiki](https://github.com/NBChub/bgcflow/wiki/04-Building-and-Serving-OLAP-Database) for more details on creating the database. + +```bash +# Setup API Key +OPENAI_API_KEY="" + +# Create new folder to set up duckdb and vector database +mkdir chatbgc +cd chatbgc + +# Copy the database build using BGCFlow to this directory +BGCFLOW_DIR="" +PROJECT_NAME="" +ANTISMASH_VERSION="7.1.0" # change this to the correct antiSMASH version used in your BGCFlow run. Only supports version 7.1.0 or above +cp $BGCFLOW_DIR/data/processed/$PROJECT_NAME/dbt/antiSMASH_7.1.0/dbt_bgcflow.duckdb dbt_bgcflow.duckdb -n + +# Create python environment and install ChatBGC +python3 -m venv chatbgc_env +source chatbgc_env/bin/activate +python3 -m pip install --upgrade pip +pip install git+https://github.com/NBChub/chatBGC.git + +# Setup variable environment / secrets +touch .env +echo "export OPENAI_API_KEY=$OPENAI_API_KEY" > .env +source .env + +# Train ChatBGC (Do it once) +chatbgc train --llm_type openai_chat --model gpt-4o dbt_bgcflow.duckdb + +# Run ChatBGC +chatbgc run --llm_type openai_chat --model gpt-4o dbt_bgcflow.duckdb +``` ## Configuration @@ -106,8 +142,9 @@ chatbgc run chatbgc run --llm_type openai_chat ``` -## Development guide (TO DO) -- Create duckdb schema +## Notes +* Free software: MIT +* Documentation: ## Credits diff --git a/chatbgc/__init__.py b/chatbgc/__init__.py index 8b10b72..a5eb596 100644 --- a/chatbgc/__init__.py +++ b/chatbgc/__init__.py @@ -2,4 +2,4 @@ __author__ = """Matin Nuhamunada""" __email__ = "matinnu@biosustain.dtu.dk" -__version__ = "0.1.3" +__version__ = "0.2.0" diff --git a/chatbgc/assets/3_RAG.png b/chatbgc/assets/3_RAG.png new file mode 100644 index 0000000..f802adb Binary files /dev/null and b/chatbgc/assets/3_RAG.png differ diff --git a/chatbgc/cli.py b/chatbgc/cli.py index 8b3d7c9..1f5bd0f 100644 --- a/chatbgc/cli.py +++ b/chatbgc/cli.py @@ -58,7 +58,7 @@ def train( self, duckdb_path, model="llama3", - training_folder=str((Path(__file__).parent / "data").resolve()), + training_folder=str((Path(__file__).parent / "data/").resolve()), llm_type="ollama", ): """ diff --git a/chatbgc/data/antismash.md b/chatbgc/data/antismash/antismash_docs.md similarity index 100% rename from chatbgc/data/antismash.md rename to chatbgc/data/antismash/antismash_docs.md diff --git a/chatbgc/data/glossary.md b/chatbgc/data/antismash/antismash_glossary.md similarity index 100% rename from chatbgc/data/glossary.md rename to chatbgc/data/antismash/antismash_glossary.md diff --git a/chatbgc/data/antismash/antismash_tables.md b/chatbgc/data/antismash/antismash_tables.md new file mode 100644 index 0000000..c9f6f6d --- /dev/null +++ b/chatbgc/data/antismash/antismash_tables.md @@ -0,0 +1,598 @@ +# AntiSMASH DuckDB Database Documentation +This documentation describes the table in the duckDB antiSMASH database. +It covers the structure and purpose of each table and column in the database schema, making it easier to understand and use the database for querying and analysis. + +## Table: antismash.as_domain_profiles +This table stores information about domain profiles. +A functional secondary metabolite domain profile predicted by antiSMASH. + +- **as_domain_profile_id**: Identifier for the domain profile. +- **name**: Name of the domain profile. +- **description**: Description of the domain profile. +- **DATABASE**: Database associated with the domain profile. +- **TYPE**: Type of the domain profile. + +## Table: antismash.as_domain_subtypes +This table stores information about domain subtypes. +Possible subtypes of domains predicted by antiSMASH, e.g. TransAT-KS. + +- **subtype**: Identifier for the domain subtype. +- **description**: Description of the domain subtype. + +## Table: antismash.bgc_categories +This table stores information about BGC categories. +Biosynthetic gene cluster categories according to MIBiG spec. + +- **category**: Identifier for the BGC category. Values could be pks, nrps, ripp, terpene, saccharide, alkaloid, or other. +- **description**: Description of the BGC category. The following are the categories and its description: 'pks' is 'Polyketide', 'nrps' is 'Nonribosomal peptide', 'ripp' is 'Ribosomally synthesized and post-translationally modified peptide', 'terpene' is 'Terpene', 'saccharide' is'Saccharide', 'alkaloid' is 'Alkaloid', and 'other' is 'Other'. + +## Table: antismash.candidate_types +This table stores information about candidate types. +Candidate cluster types as used by antiSMASH. + +- **candidate_type_id**: Identifier for the candidate type. +- **description**: Description of the candidate type. Can be 'chemical hybrid', 'interleaved', 'neighbouring', or 'single'. + +## Table: antismash.clusterblast_algorithms +This table stores information about clusterblast algorithms. +Available *ClusterBlast algorithms. + +- **algorithm_id**: Identifier for the algorithm. +- **name**: Name of the algorithm. Value could be 'clusterblast','knownclusterblast', or 'subclusterblast'. + + +## Table: antismash.comparippson_mibig_references +This table stores references to MIBIG entries used in comparative analysis. + +- **comparippson_mibig_id**: Identifier for the MIBIG reference. +- **accession**: Accession number of the MIBIG entry. +- **name**: Name of the MIBIG entry. +- **product**: Product associated with the MIBIG entry. +- **compound**: Compound associated with the MIBIG entry. + +## Table: antismash.filenames +This table stores information about filenames associated with assemblies. +Tracking a number of interesting filenames for an assembly id. + +- **assembly_id**: Identifier for the assembly. +- **base_filename**: Base filename for the assembly. + +## Table: antismash.functional_classes +This table stores information about functional classes. +An index of possible functional classes. + +- **functional_class_id**: Identifier for the functional class. +- **name**: Name of the functional class. Values for basic functional classes are 'biosynthetic', 'regulator', 'transporter', or 'other'. Advanced classes are 'bgc_seed' and 'biosynthetic_smcog', which are the child of parent class 'biosynthetic'. +- **parent_id**: Identifier for the parent functional class, if applicable. + +## Table: antismash.gene_ontologies +This table stores information about gene ontologies. + +- **go_id**: Identifier for the gene ontology. +- **identifier**: Unique identifier for the gene ontology. +- **description**: Description of the gene ontology. + +## Table: antismash.module_domain_functions +This table stores information about functions associated with module domains in table antismash.modules. + +- **function_id**: Identifier for the function. +- **FUNCTION**: Description of the function. Values could be 'starter','loader', 'carrier_protein', 'modification', 'finalisation', or 'other'. + +## Table: antismash.pfams +This table stores information about Pfam entries. +pfam domain metadata. + +- **pfam_id**: Identifier for the Pfam entry. +- **name**: Name of the Pfam entry. +- **description**: Description of the Pfam entry. +- **trusted_cutoff**: Trusted cutoff value for the Pfam entry. + +## Table: antismash.profiles +This table stores information about HMM profiles. +HMM profiles used during cluster detection. + +- **name**: Name of the profile. +- **description**: Description of the profile. +- **cutoff**: Cutoff value for the profile. +- **filename**: Filename associated with the profile. + +## Table: antismash.regulators +This table stores information about regulators, part of the antiSMASH TFBS (transcription factor binding site) finder feature. + +- **regulator_id**: Identifier for the regulator. +- **name**: Name of the regulator. +- **description**: Description of the regulator. + +## Table: antismash.regulator_confidence +This table stores information about regulator confidence levels, part of the antiSMASH TFBS (transcription factor binding site) finder feature. + +- **confidence_id**: Identifier for the confidence level. +- **name**: Name of the confidence level. Can be 'weak', 'medium', or 'strong'. +- **strength**: Strength of the confidence level. + +## Table: antismash.resfams +This table stores information about Resfam entries. + +- **resfam_id**: Identifier for the Resfam entry. +- **accession**: Accession number of the Resfam entry. +- **name**: Name of the Resfam entry. +- **description**: Description of the Resfam entry. + +## Table: antismash.sampling_sites +This table stores information about sampling sites. +A site where a biological sample was taken. + +- **site_id**: Identifier for the sampling site. + +## Table: antismash.substrates +This table stores information about substrates. + +- **substrate_id**: Identifier for the substrate. +- **name**: Name of the substrate. +- **description**: Description of the substrate. + +## Table: antismash.t2pks_products +This table stores information about T2PKS products. + +- **product_type**: Type of the product. +- **product_function**: Function of the product. + +## Table: antismash.t2pks_profiles +This table stores information about T2PKS profiles. + +- **profile_id**: Identifier for the profile. +- **name**: Name of the profile. +- **description**: Description of the profile. + +## Table: antismash.taxa +This table stores NCBI taxonomic classification information. + +- **tax_id**: Identifier for the taxonomic entry. +- **ncbi_taxid**: NCBI taxonomic identifier. +- **superkingdom**: Superkingdom classification. +- **kingdom**: Kingdom classification. +- **phylum**: Phylum classification. +- **class**: Class classification. +- **taxonomic_order**: Order classification. +- **family**: Family classification. +- **genus**: Genus classification. +- **species**: Species classification. +- **strain**: Strain classification. +- **name**: Name of the taxonomic entry. + +## Table: antismash.tigrfams +This table stores information about TIGRFAM entries. +tigrfam domain metadata. + +- **tigrfam_id**: Identifier for the TIGRFAM entry. +- **name**: Name of the TIGRFAM entry. +- **description**: Description of the TIGRFAM entry. +- **trusted_cutoff**: Trusted cutoff value for the TIGRFAM entry. + +## Table: antismash.bgc_types +This table stores information about BGC types. +Biosynthetic gene cluster types. + +- **bgc_type_id**: Identifier for the BGC type. +- **term**: Term associated with the BGC type. +- **description**: Description of the BGC type. +- **category**: Category associated with the BGC type. + +## Table: antismash.monomers +This table stores information about monomers. + +- **monomer_id**: Identifier for the monomer. +- **substrate_id**: Identifier for the substrate associated with the monomer. +- **name**: Name of the monomer. +- **description**: Description of the monomer. + +## Table: antismash.rel_as_domain_to_subtype +This table stores relationships between domain subtypes and domains. +Relationships between a specific aSDomain and subtypes. + +- **as_domain_id**: Identifier for the domain. +- **subtype**: Identifier for the subtype. + +## Table: antismash.samples +This table stores information about samples. +A biological sample. + +- **sample_id**: Identifier for the sample. +- **habitat**: Habitat where the sample was collected. +- **TIME**: Time when the sample was collected. +- **site_id**: Identifier for the sampling site. + +## Table: antismash.smcogs +This table stores information about SMCOG entries. +Secondary Metabolite specific Clusters of Orthologous Groups (smCoGs). + +- **smcog_id**: Identifier for the SMCOG entry. +- **name**: Name of the SMCOG entry. +- **description**: Description of the SMCOG entry. +- **functional_class_id**: Identifier for the functional class associated with the SMCOG entry. + +## Table: antismash.bgc_rules +This table stores information about BGC rules. +The detection rule used for a specific BGC type. + +- **bgc_rule_id**: Identifier for the BGC rule. +- **RULE**: Description of the rule. +- **bgc_type_id**: Identifier for the BGC type associated with the rule. + +## Table: antismash.isolates +This table stores information about isolates. +A single biological isolate, sample or strain. + +- **isolate_id**: Identifier for the isolate. +- **sample_id**: Identifier for the sample associated with the isolate. + +## Table: antismash.genomes +This table stores information about genomes. +Information on a genome. + +- **genome_id**: Identifier for the genome. +- **tax_id**: Identifier for the taxonomic entry associated with the genome. +- **bio_project**: BioProject associated with the genome. +- **bio_sample**: BioSample associated with the genome. +- **isolate_id**: Identifier for the isolate associated with the genome. +- **assembly_id**: Identifier for the assembly associated with the genome. + +## Table: antismash.dna_sequences +This table stores information about DNA sequences. + +- **dna**: DNA sequence. +- **md5**: MD5 checksum of the DNA sequence. +- **accession**: Accession number for the DNA sequence. +- **definition**: Definition of the DNA sequence. +- **contig_type**: Type of the contig. +- **chromosome_type**: Type of the chromosome. +- **record_number**: Record number for the DNA sequence. +- **VERSION**: Version of the DNA sequence. +- **genome_id**: Identifier for the genome associated with the DNA sequence. + +## Table: antismash.regions +This table stores information about regions in the DNA sequences containing Biosynthetic Gene Clusters as predicted by antiSMASH. People commonly refers to region when mentioning a BGC. +A region of interest as predicted by antiSMASH. + +- **region_id**: Identifier for the region. +- **accession**: Accession number for the DNA sequence associated with the region. +- **region_number**: Number of the region. +- **LOCATION**: Location of the region. +- **start_pos**: Start position of the region. +- **end_pos**: End position of the region. +- **contig_edge**: Indicates if the region is at the contig edge. +- **best_mibig_hit_acc**: Best MIBIG hit accession number. +- **best_mibig_hit_description**: Best MIBIG hit description. +- **best_mibig_hit_similarity**: Best MIBIG hit similarity. + +## Table: antismash.rel_regions_types +This table stores relationships between regions and BGC types. + +- **region_id**: Identifier for the region. +- **bgc_type_id**: Identifier for the BGC type. + +## Table: antismash.tta_codons +This table stores information about TTA codons. This codon are quite rare in GC-rich organism such as Streptomyces. While genes involved in primary metabolism almost exclusively use CTC codons to code for Leu, key genes in secondary metabolism and cell differentiation often contain TTA codons. +A TTA codon record. + +- **tta_codon_id**: Identifier for the TTA codon. +- **seq_id**: Identifier for the DNA sequence. +- **LOCATION**: Location of the TTA codon in the DNA sequence. + +## Table: antismash.binding_sites +This table stores information about binding sites of regulators, part of the antiSMASH TFBS (transcription factor binding site) finder feature. + +- **binding_site_id**: Identifier for the binding site. +- **regulator_id**: Identifier for the regulator. +- **region_id**: Identifier for the region. +- **score**: Score of the binding site. +- **START**: Start position of the binding site. +- **confidence_id**: Identifier for the confidence level. + +## Table: antismash.candidates +This table stores information about candidates cluster. +A candidate cluster as predicted by antiSMASH. + +- **candidate_id**: Identifier for the candidate. +- **region_id**: Identifier for the region. +- **LOCATION**: Location of the candidate in the region. +- **candidate_type_id**: Identifier for the candidate type. +- **smiles**: SMILES notation for the candidate. +- **polymer**: Polymer information for the candidate. + +## Table: antismash.cdss +This table stores information about coding sequences (CDSs). +A CDS record. + +- **cds_id**: Identifier for the CDS. +- **functional_class_id**: Identifier for the functional class associated with the CDS. +- **locus_tag**: Locus tag of the CDS. +- **name**: Name of the CDS. +- **product**: Product encoded by the CDS. +- **protein_id**: Protein identifier for the CDS. +- **TRANSLATION**: Translation of the CDS. +- **LOCATION**: Location of the CDS in the region. +- **region_id**: Identifier for the region. + +## Table: antismash.clusterblast_hits +This table stores information about clusterblast hits. +ClusterBlast hit storage, also for Sub- and KnownClusterblast. + +- **clusterblast_hit_id**: Identifier for the clusterblast hit. +- **region_id**: Identifier for the region. +- **rank**: Rank of the clusterblast hit. +- **acc**: Accession number of the clusterblast hit. +- **description**: Description of the clusterblast hit. +- **similarity**: Similarity of the clusterblast hit. +- **algorithm_id**: Identifier for the algorithm used. + +## Table: antismash.comparippson_asdb_references +This table stores references to ASDB entries used in comparative analysis. + +- **comparippson_asdb_id**: Identifier for the ASDB reference. +- **cds_id**: Identifier for the CDS. +- **product**: Product associated with the ASDB reference. + +## Table: antismash.comparippson_hits +This table stores information about comparippson hits. +CompaRiPPson hits storage for both MIBiG and aS-DB. + +- **comparippson_hit_id**: Identifier for the comparippson hit. +- **cds_id**: Identifier for the CDS. +- **similarity**: Similarity of the comparippson hit. +- **region_id**: Identifier for the region. +- **comparippson_mibig_id**: Identifier for the MIBIG reference. +- **comparippson_asdb_id**: Identifier for the ASDB reference. + +## Table: antismash.genes +This table stores information about genes. +A gene record. + +- **gene_id**: Identifier for the gene. +- **locus_tag**: Locus tag of the gene. +- **LOCATION**: Location of the gene in the region. +- **region_id**: Identifier for the region. + +## Table: antismash.modules +This table stores information about modules. +An NRPS/PKS module with multiple child domains, the loaded substrate and resulting modified monomer. + +- **module_id**: Identifier for the module. +- **LOCATION**: Location of the module. +- **TYPE**: Type of the module. +- **trans_at**: Indicates if the module is trans-AT. +- **complete**: Indicates if the module is complete. +- **iterative**: Indicates if the module is iterative. +- **multi_gene**: Indicates if the module is multi-gene. +- **region_id**: Identifier for the region. + +## Table: antismash.pfam_domains +This table stores information about Pfam domains. +A PFAM domain prediction. + +- **pfam_domain_id**: Identifier for the Pfam domain. +- **DATABASE**: Database associated with the Pfam domain. +- **detection**: Detection method for the Pfam domain. +- **score**: Score of the Pfam domain. +- **evalue**: E-value of the Pfam domain. +- **TRANSLATION**: Translation of the Pfam domain. +- **pfam_id**: Identifier for the Pfam entry. +- **LOCATION**: Location of the Pfam domain. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.pfam_go_entries +This table stores relationships between Pfam domains and gene ontologies. + +- **pfam_domain_id**: Identifier for the Pfam domain. +- **go_id**: Identifier for the gene ontology. + +## Table: antismash.profile_hits +This table stores information about profile hits. + +- **profile_hit_id**: Identifier for the profile hit. +- **cds_id**: Identifier for the CDS. +- **name**: Name of the profile. +- **evalue**: E-value of the profile hit. +- **bitscore**: Bit score of the profile hit. +- **seeds**: Number of seeds for the profile hit. + +## Table: antismash.protoclusters +This table stores information about protoclusters. +A protocluster as predicted by antiSMASH. + +- **protocluster_id**: Identifier for the protocluster. +- **region_id**: Identifier for the region. +- **LOCATION**: Location of the protocluster. +- **bgc_type_id**: Identifier for the BGC type. + +## Table: antismash.rel_candidates_modules +This table stores relationships between candidates and modules. +Many to many relation for compounds to modules. + +- **candidate_id**: Identifier for the candidate. +- **module_id**: Identifier for the module. + +## Table: antismash.rel_candidates_protoclusters +This table stores relationships between candidates and protoclusters. +Many to many relation for candidates to protoclusters + +- **candidate_id**: Identifier for the candidate. +- **protocluster_id**: Identifier for the protocluster. + +## Table: antismash.rel_candidates_types +This table stores relationships between candidates and BGC types. +Many to many relation for candidates and bgc_types. + +- **candidate_id**: Identifier for the candidate. +- **bgc_type_id**: Identifier for the BGC type. + +## Table: antismash.rel_cds_candidates +This table stores relationships between CDSs and candidates. +Many to many relation for CDSs to candidates. + +- **candidate_id**: Identifier for the candidate. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.rel_cds_protoclusters +This table stores relationships between CDSs and protoclusters. +Many to many relation for CDSs to protoclusters. + +- **protocluster_id**: Identifier for the protocluster. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.rel_modules_monomers +This table stores relationships between modules and monomers. +Many to many relation for modules to substrates and monomers. + +- **module_id**: Identifier for the module. +- **substrate**: Identifier for the substrate. +- **monomer**: Identifier for the monomer. + +## Table: antismash.resfam_domains +This table stores information about Resfam domains. + +- **resfam_domain_id**: Identifier for the Resfam domain. +- **score**: Score of the Resfam domain. +- **evalue**: E-value of the Resfam domain. +- **resfam_id**: Identifier for the Resfam entry. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.ripps +This table stores information about RiPPs (Ribosomally synthesized and Post-translationally modified Peptides). +A (predicted) ribosomally preduced peptide compound. + +- **protocluster_id**: Identifier for the protocluster. +- **peptide_sequence**: Peptide sequence of the RiPP. +- **molecular_weight**: Molecular weight of the RiPP. +- **monoisotopic_mass**: Monoisotopic mass of the RiPP. +- **alternative_weights**: Alternative weights of the RiPP. +- **bridges**: Number of bridges in the RiPP. +- **CLASS**: Class of the RiPP. +- **subclass**: Subclass of the RiPP. +- **score**: Score of the RiPP. +- **locus_tag**: Locus tag associated with the RiPP. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.smcog_hits +This table stores information about SMCOG hits. +Metadata about an smCoG hit. + +- **smcog_id**: Identifier for the SMCOG entry. +- **cds_id**: Identifier for the CDS. +- **score**: Score of the SMCOG hit. +- **evalue**: E-value of the SMCOG hit. +- **image_path**: Path to the image associated with the SMCOG hit. + +## Table: antismash.t2pks +This table stores information about T2PKS (Type II Polyketide Synthases). +Predicted compound details for a Type II PKS. + +- **t2pks_id**: Identifier for the T2PKS. +- **protocluster_id**: Identifier for the protocluster. + +## Table: antismash.t2pks_cds_domain +This table stores information about T2PKS CDS domains. + +- **domain_id**: Identifier for the domain. +- **t2pks_id**: Identifier for the T2PKS. +- **cds_id**: Identifier for the CDS. +- **profile_id**: Identifier for the profile. +- **protein_type**: Type of the protein. +- **protein_function**: Function of the protein. +- **evalue**: E-value of the domain. +- **bitscore**: Bit score of the domain. + +## Table: antismash.t2pks_product_classes +This table stores relationships between T2PKS and product classes. + +- **t2pks_id**: Identifier for the T2PKS. +- **product_class**: Product class associated with the T2PKS. + +## Table: antismash.t2pks_starters +This table stores information about T2PKS starters. +A Type II PKS-specific starter domain. + +- **domain_id**: Identifier for the domain. +- **t2pks_id**: Identifier for the T2PKS. +- **name**: Name of the starter. +- **evalue**: E-value of the starter. +- **bitscore**: Bit score of the starter. + +## Table: antismash.t2pks_starter_elongation +This table stores information about T2PKS starter elongation combinations. + +- **combo_id**: Identifier for the combination. +- **domain_id**: Identifier for the domain. +- **elongation**: Elongation value. +- **weight**: Weight of the elongation combination. + +## Table: antismash.tigrfam_domains +This table stores information about TIGRFAM domains. +A TIGRFAM domain prediction. + +- **tigrfam_domain_id**: Identifier for the TIGRFAM domain. +- **DATABASE**: Database associated with the TIGRFAM domain. +- **detection**: Detection method for the TIGRFAM domain. +- **score**: Score of the TIGRFAM domain. +- **evalue**: E-value of the TIGRFAM domain. +- **TRANSLATION**: Translation of the TIGRFAM domain. +- **tigrfam_id**: Identifier for the TIGRFAM entry. +- **LOCATION**: Location of the TIGRFAM domain. +- **cds_id**: Identifier for the CDS. + +## Table: antismash.as_domains +This table stores information about domains. +A functional domain on a gene as predicted by antiSMASH. + +- **as_domain_id**: Identifier for the domain. +- **detection**: Detection method for the domain. +- **score**: Score of the domain. +- **evalue**: E-value of the domain. +- **TRANSLATION**: Translation of the domain. +- **pks_signature**: PKS signature of the domain. +- **minowa**: Minowa score of the domain. This score predicts the specificity of adenylation domains in nonribosomal peptide synthetases (NRPS). +- **nrps_predictor**: NRPS predictor score. +- **stachelhaus**: Stachelhaus score. This score predicts the specificity of adenylation domains in nonribosomal peptide synthetases (NRPS). +- **consensus**: Consensus sequence of the domain. +- **kr_activity**: Indicates if the domain has (keto reductase) KR activity. +- **kr_stereochemistry**: Stereochemistry of the (keto reductase) KR activity. +- **as_domain_profile_id**: Identifier for the domain profile. +- **LOCATION**: Location of the domain. +- **cds_id**: Identifier for the CDS. +- **module_id**: Identifier for the module. +- **function_id**: Identifier for the function. +- **follows**: Indicates if the domain follows another domain. + +## Table: antismash.cluster_compare_hits +This table stores information about cluster comparison hits. +ClusterCompare hit storage. + +- **hit_id**: Identifier for the cluster comparison hit. +- **region_id**: Identifier for the region. +- **protocluster_id**: Identifier for the protocluster. +- **reference_accession**: Reference accession number. +- **description**: Description of the cluster comparison hit. +- **score**: Score of the cluster comparison hit. +- **identity_metric**: Identity metric of the cluster comparison hit. +- **order_metric**: Order metric of the cluster comparison hit. +- **components_metric**: Components metric of the cluster comparison hit. + +## Table: antismash.rel_as_domains_substrates +This table stores relationships between AS domains and substrates. +Many to many relation for as_domains to substrate. + +- **as_domain_id**: Identifier for the AS domain. +- **substrate_id**: Identifier for the substrate. +- **position_in_domain**: Position of the substrate in the domain. + +## Table: antismash.sequence_gc_content +This view stores GC content information for sequences. + +- **accession**: Accession number for the DNA sequence. +- **gc_content**: GC content percentage of the DNA sequence. + +## Table: antismash.sequence_lengths +This view stores sequence length information. + +- **accession**: Accession number for the DNA sequence. +- **seq_length**: Length of the DNA sequence. diff --git a/chatbgc/data/antismash/question_sql_pair.json b/chatbgc/data/antismash/question_sql_pair.json new file mode 100644 index 0000000..6081ff0 --- /dev/null +++ b/chatbgc/data/antismash/question_sql_pair.json @@ -0,0 +1,258 @@ +[ + { + "id":0, + "question":"What are the different domain profiles available in the antiSMASH database?", + "sql":"SELECT * FROM antismash.as_domain_profiles;", + "answer":"The database contains 58 different domain profiles including Beta-eliminating lyase, various Condensation domains, Glycopeptide-specific NRPS domain, Heterocyclization domain, Epimerization domain, multiple Methyl transferase domains, Adenylation domains, Aminotransferase classes, Ketosynthase domain, Ketoreductase domain, Enoylreductase domain, Dehydrogenase domains, Acyltransferase domain, NRPS COM domains, Polyketide cyclase domains, PKS docking domains, Co-enzyme A ligase domain, Acyl-carrier protein domains, Male sterility protein, branching domain, Formylation domain, FkbH-like domain, GNAT domain, Halogenase domain, Pyran synthase domain, Fungal nonreducing product template domain, NRPS domains, and Phosphatidylglycerol lysyltransferase domain.", + "category":"General Information", + "difficulty":"Easy" + }, + { + "id":1, + "question":"List all antiSMASH BGC categories and their descriptions.", + "sql":"SELECT * FROM antismash.bgc_categories;", + "answer":"There are seven BGC categories, including Polyketide (pks), Nonribosomal peptide (nrps), Ribosomally synthesized and post-translationally modified peptide (ripp), Terpene (terpene), Saccharide (saccharide), Alkaloid (alkaloid) and Other (other)", + "category":"General Information", + "difficulty":"Easy" + }, + { + "id":2, + "question":"What are antiSMASH candidate types and their descriptions?", + "sql":"SELECT candidate_type_id, description FROM antismash.candidate_types;", + "answer":"AntiSMASH candidate types can be a Chemical hybrid, Interleaved, Neighbouring, or Single.", + "category":"General Information", + "difficulty":"Easy" + }, + { + "id":3, + "question":"What kind of functional classes are in the antiSMASH database?", + "sql":"SELECT * FROM antismash.functional_classes;", + "answer":"There are six functional classes, where the functional class Biosynthetic_smcog and Bgc_seed having parent-child relationships with 'biosynthetic' functional class.", + "category":"General Information", + "difficulty":"Easy" + }, + { + "id":4, + "question":"What is the GC content distribution of the DNA in the dataset?", + "sql":"SELECT accession, gc_content FROM antismash.sequence_gc_content WHERE accession = 'SEQ1234';", + "answer":"The GC content of the sequence with accession SEQ1234 is 45.67%.", + "category":"Sequences and Regions", + "difficulty":"Hard" + }, + { + "id":5, + "question":"Which genome has the longest DNA sequence?", + "sql":"SELECT g.*, LENGTH(d.dna) as dna_length FROM antismash.genomes g JOIN antismash.dna_sequences d ON g.genome_id = d.genome_id ORDER BY LENGTH(d.dna) DESC LIMIT 1;", + "answer":"Genome NBC_01737 has the longest DNA sequence with a length of 13942900 base pairs.", + "category":"Sequences and Regions", + "difficulty":"Medium" + }, + { + "id":6, + "question":"List all PKS regions in genome NBC_01737.", + "sql":"SELECT r.*, bt.*, g.*, rt.* FROM antismash.regions r JOIN antismash.dna_sequences d ON r.accession = d.accession JOIN antismash.genomes g ON d.genome_id = g.genome_id JOIN antismash.rel_regions_types rt ON r.region_id = rt.region_id JOIN antismash.bgc_types bt ON rt.bgc_type_id = bt.bgc_type_id WHERE g.assembly_id = 'NBC_01737' AND bt.term ILIKE '%PKS%';", + "answer": "The genome NBC_01737 contains 5 PKS regions with the following details:\n1. Region 1: Location [1505416:1546433], best hit loseolamycin A1/loseolamycin A2 with 68% similarity.\n2. Region 5: Location [5772447:5884359], best hit neoabyssomicin/abyssomicin with 28% similarity.\n3. Region 11: Location [8202310:8321183], best hit diazepinomicin with 75% similarity.\n4. Region 20: Location [11551477:11627322], best hit azinomycin B with 68% similarity.\n5. Region 21: Location [12318862:12465542], best hit BE-43547A1/A2/B1/B2/B3/C1/C2 with 30% similarity.", + "category":"Sequences and Regions", + "difficulty":"Hard" + }, + { + "id":7, + "question":"What are the available antiSMASH domain subtypes and their descriptions?", + "sql":"SELECT * FROM antismash.as_domain_subtypes;", + "answer":"The available antiSMASH domain subtypes are: Condensation_LCL, Trans-AT-KS, Iterative-KS, Condensation_Starter, Condensation_Dual, Hybrid-KS, cMT, Modular-KS, oMT, Polyketide_cyc2, Polyketide_cyc, nMT, Condensation_DCL, Cglyc, AA, Enediyne-KS, lacST, beta-OH, non-elongating-DB, ST, br, alphaMe, alphaMe-eDB, Miscellaneous, beta-D-OMe, non-elongating-beta-OH, DB, alphaMe-DB, beta-Me, beta-D-OH, exomethylene, eDB, keto, beta-OH/keto, red/shDB, beta-L-OH, and beta-OH/eDB. Descriptions are not provided for these subtypes.", + "category":"Relationships and References", + "difficulty":"Easy" + }, + { + "id":8, + "question":"Which candidates are associated with a specific module?", + "sql":"SELECT * FROM antismash.rel_candidates_modules WHERE module_id = 1;", + "answer":"Module 1 is associated with candidates such as Candidate 1 and Candidate 2.", + "category":"Relationships and References", + "difficulty":"Medium" + }, + { + "id":9, + "question":"What are the details of the protoclusters associated with a specific candidate?", + "sql":"SELECT * FROM antismash.rel_candidates_protoclusters WHERE candidate_id = 1;", + "answer":"Candidate 1 is associated with protoclusters such as Protocluster 1 and Protocluster 2.", + "category":"Relationships and References", + "difficulty":"Medium" + }, + { + "id":10, + "question":"Which domains are linked to a particular substrate?", + "sql":"SELECT * FROM antismash.rel_as_domains_substrates WHERE substrate_id = 1;", + "answer":"Substrate 1 is linked to multiple domains, including Domain A and Domain B.", + "category":"Relationships and References", + "difficulty":"Medium" + }, + { + "id":11, + "question":"What are the details of a specific gene identified by its locus tag?", + "sql":"SELECT * FROM antismash.genes WHERE locus_tag = 'LOC1234';", + "answer":"The gene with locus tag LOC1234 has details including location, region ID, and associated functional classes.", + "category":"Gene and Protein Information", + "difficulty":"Medium" + }, + { + "id":12, + "question":"What profiles hit a specific CDS and what are their details?", + "sql":"SELECT * FROM antismash.profile_hits WHERE cds_id = 1;", + "answer":"CDS 1 is hit by profiles including Profile A and Profile B with specific evalues and bit scores.", + "category":"Gene and Protein Information", + "difficulty":"Medium" + }, + { + "id":13, + "question":"List all pfam domains associated with a specific CDS.", + "sql":"SELECT * FROM antismash.pfam_domains WHERE cds_id = 1;", + "answer":"CDS 1 is associated with pfam domains such as Pfam Domain A and Pfam Domain B.", + "category":"Gene and Protein Information", + "difficulty":"Medium" + }, + { + "id":14, + "question":"What tigrfam domains are related to a specific CDS?", + "sql":"SELECT * FROM antismash.tigrfam_domains WHERE cds_id = 1;", + "answer":"CDS 1 is related to tigrfam domains including Tigrfam Domain A and Tigrfam Domain B.", + "category":"Gene and Protein Information", + "difficulty":"Medium" + }, + { + "id":15, + "question":"List all clusters and their types for a given region.", + "sql":"SELECT * FROM antismash.rel_regions_types WHERE region_id = 1;", + "answer":"Region 1 contains clusters of types such as BGC Type A and BGC Type B.", + "category":"Cluster and Candidate Information", + "difficulty":"Medium" + }, + { + "id":16, + "question":"What are the candidates identified in a specific region and their details?", + "sql":"SELECT * FROM antismash.candidates WHERE region_id = 1;", + "answer":"Region 1 has candidates such as Candidate A and Candidate B with specific locations and types.", + "category":"Cluster and Candidate Information", + "difficulty":"Medium" + }, + { + "id":17, + "question":"What are the products of a specific t2pks and their properties?", + "sql":"SELECT * FROM antismash.t2pks_products WHERE t2pks_id = 1;", + "answer":"T2PKS 1 produces products such as Product A and Product B with various functions and properties.", + "category":"Cluster and Candidate Information", + "difficulty":"Hard" + }, + { + "id":18, + "question":"Which SMCOGs are associated with a specific functional class?", + "sql":"SELECT * FROM antismash.smcogs WHERE functional_class_id = 1;", + "answer":"Functional Class 1 is associated with SMCOGs such as SMCOG A and SMCOG B.", + "category":"Functional Class and Regulator Information", + "difficulty":"Medium" + }, + { + "id":19, + "question":"What are the details of all regulators and their confidences?", + "sql":"SELECT * FROM antismash.regulators;", + "answer":"The database contains regulators such as Regulator A and Regulator B with specific descriptions and confidence levels.", + "category":"Functional Class and Regulator Information", + "difficulty":"Medium" + }, + { + "id":20, + "question":"What binding sites are linked to a specific regulator and their details?", + "sql":"SELECT * FROM antismash.binding_sites WHERE regulator_id = 1;", + "answer":"Regulator 1 is linked to binding sites such as Binding Site A and Binding Site B with specific scores and locations.", + "category":"Functional Class and Regulator Information", + "difficulty":"Medium" + }, + { + "id":21, + "question":"Summarize all taxa of the genomes and their details.", + "sql":"SELECT t.* FROM antismash.taxa t JOIN antismash.genomes g ON t.tax_id = g.tax_id;", + "answer":"The data contains 1032 entries of bacterial genomes, all classified under the superkingdom 'Bacteri' and the phylum 'Actinomycetota' with the majority being unclassified at the kingdom level. The data spans multiple orders within the class 'Actinomycetes' primarily 'Kitasatosporales' and 'Micromonosporales'. The family 'Streptomycetaceae' and genus 'Streptomyces' are most frequent, with many species and strains listed as unclassified. Other notable genera include 'Micromonospora', 'Nocardia', 'Kitasatospora', and 'Amycolatopsis'. The species 'albidoflavus', 'virginiae', 'microflavus', and 'jietaisiensis' frequently appear.", + "category":"Taxonomy and Genomics", + "difficulty":"Medium" + }, + { + "id":22, + "question":"How many Streptomyces genomes are in the dataset?", + "sql":"SELECT COUNT(*) FROM antismash.genomes g JOIN antismash.taxa t ON g.tax_id = t.tax_id WHERE t.genus = 'Streptomyces';", + "answer":"There are 880 Streptomyces genomes in the dataset.", + "category":"Taxonomy and Genomics", + "difficulty":"Medium" + }, + { + "id":23, + "question":"What isolates are linked to a specific sample?", + "sql":"SELECT * FROM antismash.isolates WHERE sample_id = 1;", + "answer":"Sample 1 is linked to isolates such as Isolate A and Isolate B.", + "category":"Taxonomy and Genomics", + "difficulty":"Medium" + }, + { + "id":24, + "question":"Find all lanthipeptide bgc type regions.", + "sql":"SELECT r.*, bt.* FROM antismash.rel_regions_types rrt JOIN antismash.bgc_types bt ON rrt.bgc_type_id = bt.bgc_type_id JOIN antismash.regions r ON rrt.region_id = r.region_id WHERE bt.description ILIKE '%lanthipeptide%';", + "answer":"BGC Type 1 is found in regions such as Region A and Region B.", + "category":"Search and Filtering", + "difficulty":"Medium" + }, + { + "id":25, + "question":"What are the genes located in a particular region?", + "sql":"SELECT * FROM antismash.genes WHERE region_id = 1;", + "answer":"Region 1 contains genes such as Gene A and Gene B.", + "category":"Search and Filtering", + "difficulty":"Medium" + }, + { + "id":26, + "question":"Which CDSs are located in a specific region and what are their details?", + "sql":"SELECT * FROM antismash.cdss WHERE region_id = 1;", + "answer":"Region 1 contains CDSs such as CDS A and CDS B with specific locus tags and product information.", + "category":"Search and Filtering", + "difficulty":"Medium" + }, + { + "id":27, + "question":"Which comparippson hits are associated with a specific MIBIG reference?", + "sql":"SELECT * FROM antismash.comparippson_hits WHERE comparippson_mibig_id = 1;", + "answer":"MIBIG Reference 1 is associated with comparippson hits such as Hit A and Hit B.", + "category":"Advanced Queries", + "difficulty":"Hard" + }, + { + "id":28, + "question":"What are the cluster blast hits for a specific region?", + "sql":"SELECT * FROM antismash.clusterblast_hits WHERE region_id = 1;", + "answer":"Region 1 has cluster blast hits including Hit A and Hit B with specific descriptions and similarities.", + "category":"Advanced Queries", + "difficulty":"Hard" + }, + { + "id":29, + "question":"List all TTA codons and their locations in a specific sequence.", + "sql":"SELECT * FROM antismash.tta_codons WHERE seq_id = 'SEQ1234';", + "answer":"Sequence SEQ1234 contains TTA codons at various locations including Location A and Location B.", + "category":"Advanced Queries", + "difficulty":"Hard" + }, + { + "id":30, + "question":"List all regions with a best MIBiG hit description containing 'neoabyssomicin'.", + "sql":"SELECT * FROM antismash.regions WHERE best_mibig_hit_description ILIKE '%neoabyssomicin%';", + "answer":"There are 30 regions with a best MIBiG hit description containing 'neoabyssomicin'.", + "category":"Sequences and Regions", + "difficulty":"Easy" + }, + { + "id":31, + "question":"Get me all genomes and regions containing domains where the domain subtype is 'Trans-AT-KS'.", + "sql":"SELECT g.*, r.*, ad.*, radts.subtype FROM antismash.regions r JOIN antismash.as_domains ad ON r.region_id = ad.region_id JOIN antismash.rel_as_domain_to_subtype radts ON ad.as_domain_id = radts.as_domain_id JOIN antismash.dna_sequences ds ON r.accession = ds.accession JOIN antismash.genomes g ON ds.genome_id = g.genome_id WHERE radts.subtype = 'Trans-AT-KS';", + "answer":"The data consists of 75 entries from various genomes and regions containing domains where the domain subtype is 'Trans-AT-KS'. Key details include:\n- Multiple entries come from genomes with IDs 648, 578, 269, and 246.\n- Regions vary significantly in their start and end positions.\n- The best MIBiG hits include various secondary metabolites such as ebelactone, matlystatin A, and albaflavenone, with similarities ranging from 2% to 100%.", + "category":"Advanced Queries", + "difficulty": "Hard" + } +] diff --git a/chatbgc/data/antismash/schema.sql b/chatbgc/data/antismash/schema.sql new file mode 100644 index 0000000..1a102ef --- /dev/null +++ b/chatbgc/data/antismash/schema.sql @@ -0,0 +1,125 @@ +CREATE SCHEMA antismash; + + +CREATE SEQUENCE antismash.antismash_as_domains_as_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_as_domain_profiles_as_domain_profile_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 59 NO CYCLE; +CREATE SEQUENCE antismash.antismash_bgc_rules_bgc_rule_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_bgc_types_bgc_type_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 86 NO CYCLE; +CREATE SEQUENCE antismash.antismash_binding_sites_binding_site_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_candidates_candidate_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_candidate_types_candidate_type_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 5 NO CYCLE; +CREATE SEQUENCE antismash.antismash_cdss_cds_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_clusterblast_algorithms_algorithm_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 4 NO CYCLE; +CREATE SEQUENCE antismash.antismash_clusterblast_hits_clusterblast_hit_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_cluster_compare_hits_hit_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_comparippson_asdb_references_comparippson_asdb_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_comparippson_hits_comparippson_hit_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_comparippson_mibig_references_comparippson_mibig_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_functional_classes_functional_class_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 7 NO CYCLE; +CREATE SEQUENCE antismash.antismash_genes_gene_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_gene_ontologies_go_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 2636 NO CYCLE; +CREATE SEQUENCE antismash.antismash_genomes_genome_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_isolates_isolate_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_modules_module_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_module_domain_functions_function_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 7 NO CYCLE; +CREATE SEQUENCE antismash.antismash_monomers_monomer_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 154 NO CYCLE; +CREATE SEQUENCE antismash.antismash_pfam_domains_pfam_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_profile_hits_profile_hit_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_protoclusters_protocluster_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_regions_region_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_regulators_regulator_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 18 NO CYCLE; +CREATE SEQUENCE antismash.antismash_regulator_confidence_confidence_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 4 NO CYCLE; +CREATE SEQUENCE antismash.antismash_resfams_resfam_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 124 NO CYCLE; +CREATE SEQUENCE antismash.antismash_resfam_domains_resfam_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_samples_sample_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_sampling_sites_site_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_smcogs_smcog_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 302 NO CYCLE; +CREATE SEQUENCE antismash.antismash_substrates_substrate_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 280 NO CYCLE; +CREATE SEQUENCE antismash.antismash_t2pks_cds_domain_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_t2pks_profiles_profile_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 41 NO CYCLE; +CREATE SEQUENCE antismash.antismash_t2pks_starters_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_t2pks_starter_elongation_combo_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_t2pks_t2pks_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_taxa_tax_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 37945 NO CYCLE; +CREATE SEQUENCE antismash.antismash_tigrfam_domains_tigrfam_domain_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; +CREATE SEQUENCE antismash.antismash_tta_codons_tta_codon_id_seq INCREMENT BY 1 MINVALUE 1 MAXVALUE 9223372036854775807 START 1 NO CYCLE; + +CREATE TABLE antismash.as_domain_profiles(as_domain_profile_id INTEGER DEFAULT(nextval('antismash.antismash_as_domain_profiles_as_domain_profile_id_seq')), "name" VARCHAR NOT NULL, description VARCHAR NOT NULL, "DATABASE" VARCHAR NOT NULL, "TYPE" VARCHAR, PRIMARY KEY(as_domain_profile_id)); +CREATE TABLE antismash.as_domain_subtypes(subtype VARCHAR PRIMARY KEY, description VARCHAR); +CREATE TABLE antismash.bgc_categories(category VARCHAR PRIMARY KEY, description VARCHAR NOT NULL UNIQUE); +CREATE TABLE antismash.candidate_types(candidate_type_id INTEGER DEFAULT(nextval('antismash.antismash_candidate_types_candidate_type_id_seq')) PRIMARY KEY, description VARCHAR NOT NULL); +CREATE TABLE antismash.clusterblast_algorithms(algorithm_id INTEGER DEFAULT(nextval('antismash.antismash_clusterblast_algorithms_algorithm_id_seq')), "name" VARCHAR, PRIMARY KEY(algorithm_id)); +CREATE TABLE antismash.comparippson_mibig_references(comparippson_mibig_id INTEGER DEFAULT(nextval('antismash.antismash_comparippson_mibig_references_comparippson_mibig_id_seq')) PRIMARY KEY, accession VARCHAR NOT NULL, "name" VARCHAR NOT NULL, product VARCHAR NOT NULL, compound VARCHAR NOT NULL); +CREATE TABLE antismash.filenames(assembly_id VARCHAR, base_filename VARCHAR, PRIMARY KEY(assembly_id)); +CREATE TABLE antismash.functional_classes(functional_class_id INTEGER DEFAULT(nextval('antismash.antismash_functional_classes_functional_class_id_seq')), "name" VARCHAR, parent_id INTEGER, PRIMARY KEY(functional_class_id), ); +CREATE TABLE antismash.gene_ontologies(go_id INTEGER DEFAULT(nextval('antismash.antismash_gene_ontologies_go_id_seq')) PRIMARY KEY, identifier VARCHAR NOT NULL UNIQUE, description VARCHAR NOT NULL); +CREATE TABLE antismash.module_domain_functions(function_id INTEGER DEFAULT(nextval('antismash.antismash_module_domain_functions_function_id_seq')) PRIMARY KEY, "FUNCTION" VARCHAR NOT NULL); +CREATE TABLE antismash.pfams(pfam_id VARCHAR PRIMARY KEY, "name" VARCHAR NOT NULL, description VARCHAR NOT NULL, trusted_cutoff DOUBLE, "VERSION" INTEGER); +CREATE TABLE antismash.profiles("name" VARCHAR, description VARCHAR, cutoff INTEGER, filename VARCHAR, PRIMARY KEY("name")); +CREATE TABLE antismash.regulators(regulator_id INTEGER DEFAULT(nextval('antismash.antismash_regulators_regulator_id_seq')), "name" VARCHAR NOT NULL, description VARCHAR NOT NULL, PRIMARY KEY(regulator_id), UNIQUE("name")); +CREATE TABLE antismash.regulator_confidence(confidence_id INTEGER DEFAULT(nextval('antismash.antismash_regulator_confidence_confidence_id_seq')) PRIMARY KEY, "name" VARCHAR NOT NULL, strength SMALLINT NOT NULL, UNIQUE("name")); +CREATE TABLE antismash.resfams(resfam_id INTEGER DEFAULT(nextval('antismash.antismash_resfams_resfam_id_seq')) PRIMARY KEY, accession VARCHAR NOT NULL, "name" VARCHAR NOT NULL, description VARCHAR NOT NULL); +CREATE TABLE antismash.sampling_sites(site_id INTEGER DEFAULT(nextval('antismash.antismash_sampling_sites_site_id_seq')), PRIMARY KEY(site_id)); +CREATE TABLE antismash.substrates(substrate_id INTEGER DEFAULT(nextval('antismash.antismash_substrates_substrate_id_seq')), "name" VARCHAR, description VARCHAR, PRIMARY KEY(substrate_id), UNIQUE("name")); +CREATE TABLE antismash.t2pks_products(product_type VARCHAR, product_function VARCHAR, PRIMARY KEY(product_type)); +CREATE TABLE antismash.t2pks_profiles(profile_id INTEGER DEFAULT(nextval('antismash.antismash_t2pks_profiles_profile_id_seq')) PRIMARY KEY, "name" VARCHAR NOT NULL UNIQUE, description VARCHAR NOT NULL); +CREATE TABLE antismash.taxa(tax_id INTEGER DEFAULT(nextval('antismash.antismash_taxa_tax_id_seq')), ncbi_taxid INTEGER, superkingdom VARCHAR, kingdom VARCHAR, phylum VARCHAR, "CLASS" VARCHAR, taxonomic_order VARCHAR, "family" VARCHAR, genus VARCHAR, species VARCHAR, strain VARCHAR, "name" VARCHAR NOT NULL, PRIMARY KEY(tax_id), UNIQUE("name")); +CREATE TABLE antismash.tigrfams(tigrfam_id VARCHAR PRIMARY KEY, "name" VARCHAR NOT NULL, description VARCHAR NOT NULL, trusted_cutoff DOUBLE); +CREATE TABLE antismash.bgc_types(bgc_type_id INTEGER DEFAULT(nextval('antismash.antismash_bgc_types_bgc_type_id_seq')), term VARCHAR NOT NULL, description VARCHAR NOT NULL, category VARCHAR NOT NULL, PRIMARY KEY(bgc_type_id), UNIQUE(term), FOREIGN KEY (category) REFERENCES antismash.bgc_categories(category)); +CREATE TABLE antismash.monomers(monomer_id INTEGER DEFAULT(nextval('antismash.antismash_monomers_monomer_id_seq')) PRIMARY KEY, substrate_id INTEGER NOT NULL, "name" VARCHAR NOT NULL, description VARCHAR, FOREIGN KEY (substrate_id) REFERENCES antismash.substrates(substrate_id), UNIQUE("name")); +CREATE TABLE antismash.rel_as_domain_to_subtype(as_domain_id INTEGER, subtype VARCHAR, FOREIGN KEY (subtype) REFERENCES antismash.as_domain_subtypes(subtype), PRIMARY KEY(as_domain_id, subtype)); +CREATE TABLE antismash.samples(sample_id INTEGER DEFAULT(nextval('antismash.antismash_samples_sample_id_seq')), habitat VARCHAR, "TIME" VARCHAR, site_id INTEGER, PRIMARY KEY(sample_id), FOREIGN KEY (site_id) REFERENCES antismash.sampling_sites(site_id)); +CREATE TABLE antismash.smcogs(smcog_id INTEGER DEFAULT(nextval('antismash.antismash_smcogs_smcog_id_seq')), "name" VARCHAR NOT NULL, description VARCHAR NOT NULL, functional_class_id INTEGER, PRIMARY KEY(smcog_id), FOREIGN KEY (functional_class_id) REFERENCES antismash.functional_classes(functional_class_id)); +CREATE TABLE antismash.bgc_rules(bgc_rule_id INTEGER DEFAULT(nextval('antismash.antismash_bgc_rules_bgc_rule_id_seq')), "RULE" VARCHAR, bgc_type_id INTEGER, PRIMARY KEY(bgc_rule_id), FOREIGN KEY (bgc_type_id) REFERENCES antismash.bgc_types(bgc_type_id)); +CREATE TABLE antismash.isolates(isolate_id INTEGER DEFAULT(nextval('antismash.antismash_isolates_isolate_id_seq')), sample_id INTEGER, PRIMARY KEY(isolate_id), FOREIGN KEY (sample_id) REFERENCES antismash.samples(sample_id)); +CREATE TABLE antismash.genomes(genome_id INTEGER DEFAULT(nextval('antismash.antismash_genomes_genome_id_seq')), tax_id INTEGER NOT NULL, bio_project VARCHAR, bio_sample VARCHAR, isolate_id INTEGER, assembly_id VARCHAR NOT NULL, PRIMARY KEY(genome_id), FOREIGN KEY (tax_id) REFERENCES antismash.taxa(tax_id), FOREIGN KEY (isolate_id) REFERENCES antismash.isolates(isolate_id)); +CREATE TABLE antismash.dna_sequences(dna VARCHAR, md5 VARCHAR, accession VARCHAR PRIMARY KEY, definition VARCHAR, contig_type INTEGER, chromosome_type INTEGER, record_number INTEGER NOT NULL, "VERSION" INTEGER, genome_id INTEGER, FOREIGN KEY (genome_id) REFERENCES antismash.genomes(genome_id)); +CREATE TABLE antismash.regions(region_id INTEGER DEFAULT(nextval('antismash.antismash_regions_region_id_seq')), accession VARCHAR NOT NULL, region_number INTEGER NOT NULL, "LOCATION" VARCHAR NOT NULL, start_pos INTEGER NOT NULL, end_pos INTEGER NOT NULL, contig_edge BOOLEAN NOT NULL, best_mibig_hit_acc VARCHAR, best_mibig_hit_description VARCHAR, best_mibig_hit_similarity INTEGER, FOREIGN KEY (accession) REFERENCES antismash.dna_sequences(accession), PRIMARY KEY(region_id)); +CREATE TABLE antismash.rel_regions_types(region_id INTEGER, bgc_type_id INTEGER, PRIMARY KEY(region_id, bgc_type_id), FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (bgc_type_id) REFERENCES antismash.bgc_types(bgc_type_id)); +CREATE TABLE antismash.tta_codons(tta_codon_id INTEGER DEFAULT(nextval('antismash.antismash_tta_codons_tta_codon_id_seq')), seq_id VARCHAR NOT NULL, "LOCATION" VARCHAR NOT NULL, FOREIGN KEY (seq_id) REFERENCES antismash.dna_sequences(accession), PRIMARY KEY(tta_codon_id)); +CREATE TABLE antismash.binding_sites(binding_site_id INTEGER DEFAULT(nextval('antismash.antismash_binding_sites_binding_site_id_seq')) PRIMARY KEY, regulator_id INTEGER NOT NULL, region_id INTEGER NOT NULL, score FLOAT NOT NULL, "START" INTEGER NOT NULL, confidence_id INTEGER NOT NULL, FOREIGN KEY (regulator_id) REFERENCES antismash.regulators(regulator_id), FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (confidence_id) REFERENCES antismash.regulator_confidence(confidence_id)); +CREATE TABLE antismash.candidates(candidate_id INTEGER DEFAULT(nextval('antismash.antismash_candidates_candidate_id_seq')), region_id INTEGER NOT NULL, "LOCATION" VARCHAR NOT NULL, candidate_type_id INTEGER NOT NULL, smiles VARCHAR, polymer VARCHAR, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (candidate_type_id) REFERENCES antismash.candidate_types(candidate_type_id), PRIMARY KEY(candidate_id)); +CREATE TABLE antismash.cdss(cds_id INTEGER DEFAULT(nextval('antismash.antismash_cdss_cds_id_seq')), functional_class_id INTEGER, locus_tag VARCHAR, "name" VARCHAR, product VARCHAR, protein_id VARCHAR, TRANSLATION VARCHAR, "LOCATION" VARCHAR NOT NULL, region_id INTEGER, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), PRIMARY KEY(cds_id), FOREIGN KEY (functional_class_id) REFERENCES antismash.functional_classes(functional_class_id)); +CREATE TABLE antismash.clusterblast_hits(clusterblast_hit_id INTEGER DEFAULT(nextval('antismash.antismash_clusterblast_hits_clusterblast_hit_id_seq')) PRIMARY KEY, region_id INTEGER NOT NULL, rank INTEGER NOT NULL, acc VARCHAR NOT NULL, description VARCHAR NOT NULL, similarity INTEGER NOT NULL, algorithm_id INTEGER, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (algorithm_id) REFERENCES antismash.clusterblast_algorithms(algorithm_id)); +CREATE TABLE antismash.comparippson_asdb_references(comparippson_asdb_id INTEGER DEFAULT(nextval('antismash.antismash_comparippson_asdb_references_comparippson_asdb_id_seq')) PRIMARY KEY, cds_id INTEGER NOT NULL, product VARCHAR NOT NULL, FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.comparippson_hits(comparippson_hit_id INTEGER DEFAULT(nextval('antismash.antismash_comparippson_hits_comparippson_hit_id_seq')) PRIMARY KEY, cds_id INTEGER, similarity FLOAT NOT NULL, region_id INTEGER, comparippson_mibig_id INTEGER, comparippson_asdb_id INTEGER, FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id), FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (comparippson_mibig_id) REFERENCES antismash.comparippson_mibig_references(comparippson_mibig_id), FOREIGN KEY (comparippson_asdb_id) REFERENCES antismash.comparippson_asdb_references(comparippson_asdb_id), CHECK(((CAST((comparippson_asdb_id IS NOT NULL) AS INTEGER) + CAST((comparippson_mibig_id IS NOT NULL) AS INTEGER)) = 1))); +CREATE TABLE antismash.genes(gene_id INTEGER DEFAULT(nextval('antismash.antismash_genes_gene_id_seq')), locus_tag VARCHAR, "LOCATION" VARCHAR NOT NULL, region_id INTEGER, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), PRIMARY KEY(gene_id)); +CREATE TABLE antismash.modules(module_id INTEGER DEFAULT(nextval('antismash.antismash_modules_module_id_seq')), "LOCATION" VARCHAR NOT NULL, "TYPE" VARCHAR NOT NULL, trans_at BOOLEAN NOT NULL, complete BOOLEAN NOT NULL, iterative BOOLEAN NOT NULL, multi_gene BOOLEAN NOT NULL, region_id INTEGER, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), PRIMARY KEY(module_id)); +CREATE TABLE antismash.pfam_domains(pfam_domain_id INTEGER DEFAULT(nextval('antismash.antismash_pfam_domains_pfam_domain_id_seq')), "DATABASE" VARCHAR, detection VARCHAR, score DOUBLE, evalue DOUBLE, TRANSLATION VARCHAR, pfam_id VARCHAR, "LOCATION" VARCHAR, cds_id INTEGER, PRIMARY KEY(pfam_domain_id), FOREIGN KEY (pfam_id) REFERENCES antismash.pfams(pfam_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.pfam_go_entries(pfam_domain_id INTEGER, go_id INTEGER, FOREIGN KEY (pfam_domain_id) REFERENCES antismash.pfam_domains(pfam_domain_id), FOREIGN KEY (go_id) REFERENCES antismash.gene_ontologies(go_id), PRIMARY KEY(pfam_domain_id, go_id)); +CREATE TABLE antismash.profile_hits(profile_hit_id INTEGER DEFAULT(nextval('antismash.antismash_profile_hits_profile_hit_id_seq')), cds_id INTEGER, "name" VARCHAR, evalue DOUBLE, bitscore DOUBLE, seeds INTEGER, PRIMARY KEY(profile_hit_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id), FOREIGN KEY ("name") REFERENCES antismash.profiles("name")); +CREATE TABLE antismash.protoclusters(protocluster_id INTEGER DEFAULT(nextval('antismash.antismash_protoclusters_protocluster_id_seq')), region_id INTEGER NOT NULL, "LOCATION" VARCHAR NOT NULL, bgc_type_id INTEGER NOT NULL, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), PRIMARY KEY(protocluster_id), FOREIGN KEY (bgc_type_id) REFERENCES antismash.bgc_types(bgc_type_id)); +CREATE TABLE antismash.rel_candidates_modules(candidate_id INTEGER, module_id INTEGER, FOREIGN KEY (candidate_id) REFERENCES antismash.candidates(candidate_id), FOREIGN KEY (module_id) REFERENCES antismash.modules(module_id), PRIMARY KEY(candidate_id, module_id)); +CREATE TABLE antismash.rel_candidates_protoclusters(candidate_id INTEGER, protocluster_id INTEGER, FOREIGN KEY (candidate_id) REFERENCES antismash.candidates(candidate_id), FOREIGN KEY (protocluster_id) REFERENCES antismash.protoclusters(protocluster_id), PRIMARY KEY(candidate_id, protocluster_id)); +CREATE TABLE antismash.rel_candidates_types(candidate_id INTEGER, bgc_type_id INTEGER, FOREIGN KEY (candidate_id) REFERENCES antismash.candidates(candidate_id), FOREIGN KEY (bgc_type_id) REFERENCES antismash.bgc_types(bgc_type_id), PRIMARY KEY(candidate_id, bgc_type_id)); +CREATE TABLE antismash.rel_cds_candidates(candidate_id INTEGER, cds_id INTEGER, PRIMARY KEY(candidate_id, cds_id), FOREIGN KEY (candidate_id) REFERENCES antismash.candidates(candidate_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.rel_cds_protoclusters(protocluster_id INTEGER, cds_id INTEGER, PRIMARY KEY(protocluster_id, cds_id), FOREIGN KEY (protocluster_id) REFERENCES antismash.protoclusters(protocluster_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.rel_modules_monomers(module_id INTEGER, substrate INTEGER, monomer INTEGER, FOREIGN KEY (module_id) REFERENCES antismash.modules(module_id), FOREIGN KEY (substrate) REFERENCES antismash.substrates(substrate_id), FOREIGN KEY (monomer) REFERENCES antismash.monomers(monomer_id), PRIMARY KEY(module_id, substrate, monomer)); +CREATE TABLE antismash.resfam_domains(resfam_domain_id INTEGER DEFAULT(nextval('antismash.antismash_resfam_domains_resfam_domain_id_seq')) PRIMARY KEY, score DOUBLE, evalue DOUBLE, resfam_id INTEGER NOT NULL, cds_id INTEGER NOT NULL, FOREIGN KEY (resfam_id) REFERENCES antismash.resfams(resfam_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.ripps(protocluster_id INTEGER, peptide_sequence VARCHAR, molecular_weight FLOAT, monoisotopic_mass FLOAT, alternative_weights VARCHAR, bridges INTEGER, "CLASS" VARCHAR, subclass VARCHAR, score DOUBLE, locus_tag VARCHAR, cds_id INTEGER NOT NULL, FOREIGN KEY (protocluster_id) REFERENCES antismash.protoclusters(protocluster_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id), PRIMARY KEY(protocluster_id, locus_tag)); +CREATE TABLE antismash.smcog_hits(smcog_id INTEGER, cds_id INTEGER, score DOUBLE, evalue DOUBLE, image_path VARCHAR, PRIMARY KEY(smcog_id, cds_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id), FOREIGN KEY (smcog_id) REFERENCES antismash.smcogs(smcog_id)); +CREATE TABLE antismash.t2pks(t2pks_id INTEGER DEFAULT(nextval('antismash.antismash_t2pks_t2pks_id_seq')), protocluster_id INTEGER NOT NULL, FOREIGN KEY (protocluster_id) REFERENCES antismash.protoclusters(protocluster_id), PRIMARY KEY(t2pks_id)); +CREATE TABLE antismash.t2pks_cds_domain(domain_id INTEGER DEFAULT(nextval('antismash.antismash_t2pks_cds_domain_domain_id_seq')), t2pks_id INTEGER NOT NULL, cds_id INTEGER NOT NULL, profile_id INTEGER NOT NULL, protein_type VARCHAR NOT NULL, protein_function VARCHAR, evalue DOUBLE NOT NULL, bitscore DOUBLE NOT NULL, FOREIGN KEY (t2pks_id) REFERENCES antismash.t2pks(t2pks_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id), FOREIGN KEY (profile_id) REFERENCES antismash.t2pks_profiles(profile_id), PRIMARY KEY(domain_id)); +CREATE TABLE antismash.t2pks_product_classes(t2pks_id INTEGER, product_class VARCHAR, FOREIGN KEY (t2pks_id) REFERENCES antismash.t2pks(t2pks_id), PRIMARY KEY(t2pks_id, product_class)); +CREATE TABLE antismash.t2pks_starters(domain_id INTEGER DEFAULT(nextval('antismash.antismash_t2pks_starters_domain_id_seq')), t2pks_id INTEGER NOT NULL, "name" VARCHAR NOT NULL, evalue DOUBLE NOT NULL, bitscore DOUBLE NOT NULL, FOREIGN KEY (t2pks_id) REFERENCES antismash.t2pks(t2pks_id), PRIMARY KEY(domain_id)); +CREATE TABLE antismash.t2pks_starter_elongation(combo_id INTEGER DEFAULT(nextval('antismash.antismash_t2pks_starter_elongation_combo_id_seq')), domain_id INTEGER NOT NULL, elongation INTEGER NOT NULL, weight FLOAT NOT NULL, FOREIGN KEY (domain_id) REFERENCES antismash.t2pks_starters(domain_id), PRIMARY KEY(combo_id)); +CREATE TABLE antismash.tigrfam_domains(tigrfam_domain_id INTEGER DEFAULT(nextval('antismash.antismash_tigrfam_domains_tigrfam_domain_id_seq')) PRIMARY KEY, "DATABASE" VARCHAR, detection VARCHAR, score DOUBLE, evalue DOUBLE, TRANSLATION VARCHAR, tigrfam_id VARCHAR, "LOCATION" VARCHAR, cds_id INTEGER, FOREIGN KEY (tigrfam_id) REFERENCES antismash.tigrfams(tigrfam_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.as_domains(as_domain_id INTEGER DEFAULT(nextval('antismash.antismash_as_domains_as_domain_id_seq')), detection VARCHAR, score DOUBLE, evalue DOUBLE, TRANSLATION VARCHAR, pks_signature VARCHAR, minowa VARCHAR, nrps_predictor VARCHAR, stachelhaus VARCHAR, consensus VARCHAR, kr_activity BOOLEAN, kr_stereochemistry VARCHAR, as_domain_profile_id INTEGER, "LOCATION" VARCHAR NOT NULL, cds_id INTEGER, module_id INTEGER, function_id INTEGER, follows INTEGER, FOREIGN KEY (module_id) REFERENCES antismash.modules(module_id), FOREIGN KEY (function_id) REFERENCES antismash.module_domain_functions(function_id), PRIMARY KEY(as_domain_id), FOREIGN KEY (as_domain_profile_id) REFERENCES antismash.as_domain_profiles(as_domain_profile_id), FOREIGN KEY (cds_id) REFERENCES antismash.cdss(cds_id)); +CREATE TABLE antismash.cluster_compare_hits(hit_id INTEGER DEFAULT(nextval('antismash.antismash_cluster_compare_hits_hit_id_seq')) PRIMARY KEY, region_id INTEGER, protocluster_id INTEGER, reference_accession VARCHAR NOT NULL, description VARCHAR, score FLOAT NOT NULL, identity_metric FLOAT NOT NULL, order_metric FLOAT, components_metric FLOAT, FOREIGN KEY (region_id) REFERENCES antismash.regions(region_id), FOREIGN KEY (protocluster_id) REFERENCES antismash.protoclusters(protocluster_id), CHECK(((CAST((region_id IS NOT NULL) AS INTEGER) + CAST((protocluster_id IS NOT NULL) AS INTEGER)) = 1))); +CREATE TABLE antismash.rel_as_domains_substrates(as_domain_id INTEGER, substrate_id INTEGER, position_in_domain INTEGER, PRIMARY KEY(as_domain_id, substrate_id), FOREIGN KEY (as_domain_id) REFERENCES antismash.as_domains(as_domain_id), FOREIGN KEY (substrate_id) REFERENCES antismash.substrates(substrate_id)); + +CREATE VIEW antismash.sequence_gc_content AS SELECT accession, round(((100.0 * (((length(dna) - length(replace(dna, 'G', ''))) + length(dna)) - length(replace(dna, 'C', '')))) / length(dna)), 2) AS gc_content FROM antismash.dna_sequences; +CREATE VIEW antismash.sequence_lengths AS SELECT accession, length(dna) AS seq_length FROM antismash.dna_sequences; + +CREATE INDEX as_domains_cds_id_idx ON antismash.as_domains(cds_id); +CREATE INDEX as_domains_follows_idx ON antismash.as_domains(follows); +CREATE INDEX cdss_locus_tag_idx ON antismash.cdss(locus_tag); +CREATE INDEX cluster_compare_ref_idx ON antismash.cluster_compare_hits(reference_accession); +CREATE INDEX genes_locus_tag_idx ON antismash.genes(locus_tag); +CREATE INDEX pfam_domains_cds_id_idx ON antismash.pfam_domains(cds_id); +CREATE INDEX profile_hits_cds_id_idx ON antismash.profile_hits(cds_id); +CREATE INDEX resfam_domains_cds_id_idx ON antismash.resfam_domains(cds_id); +CREATE INDEX ripps_locus_tag_idx ON antismash.ripps(locus_tag); +CREATE INDEX ripps_peptides_sequence_idx ON antismash.ripps(peptide_sequence); +CREATE INDEX smcog_hits_cds_id_idx ON antismash.smcog_hits(cds_id); +CREATE INDEX tigrfam_domains_cds_id_idx ON antismash.tigrfam_domains(cds_id); diff --git a/chatbgc/data/bgcflow.md b/chatbgc/data/bgcflow/bgcflow_tables.md similarity index 100% rename from chatbgc/data/bgcflow.md rename to chatbgc/data/bgcflow/bgcflow_tables.md diff --git a/chatbgc/data/bgcflow/question_sql_pair.json b/chatbgc/data/bgcflow/question_sql_pair.json new file mode 100644 index 0000000..febd1af --- /dev/null +++ b/chatbgc/data/bgcflow/question_sql_pair.json @@ -0,0 +1,90 @@ +[ + { + "id":0, + "question":"How many gene cluster families are in the dataset?", + "sql":"SELECT COUNT(DISTINCT gcf) FROM bgcflow.bigscape_cluster;", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":1, + "question":"What is the average genome completeness for genomes with a contamination less than 5%?", + "sql":"SELECT AVG(completeness) FROM bgcflow.checkm WHERE contamination < 0.05;", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":2, + "question":"List all distinct BGC types in the dataset.", + "sql":"SELECT DISTINCT product FROM bgcflow.regions;", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":3, + "question":"Are there any BGC regions that have multidrug resistance gene?", + "sql":"SELECT DISTINCT region_id FROM bgcflow.cdss WHERE product ILIKE '%multidrug resistance%';", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":4, + "question":"Are there type IV lanthipeptide BGCs in the dataset?", + "sql":"SELECT * FROM bgcflow.regions WHERE product ILIKE '%lanthipeptide-class-iv%';", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":5, + "question":"Do we have Kirromycin producing strains?", + "sql":"SELECT DISTINCT genome_id FROM bgcflow.regions WHERE most_similar_known_cluster_description ILIKE '%Kirromycin%';", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":6, + "question":"What are the most frequently occurring MIBIG hits compound in the dataset?", + "sql":"SELECT compounds, COUNT(*) AS count FROM bgcflow.mibig_hits GROUP BY compounds ORDER BY count DESC;", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":7, + "question":"What is the distribution of different genera in the dataset?", + "sql":"SELECT genus, COUNT(*) AS count FROM bgcflow.taxa GROUP BY genus ORDER BY count DESC;", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":8, + "question":"Can you list all entries that belong to unknown GCFs?", + "sql":"SELECT * FROM bgcflow.bigscape_cluster WHERE FAM_TYPE = 'unknown_family';", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":9, + "question":"Can you list all BGCs in the GCFs that are associated with melanin compounds?", + "sql":"SELECT * FROM bgcflow.bigscape_cluster WHERE fam_known_compounds ILIKE '%melanin%';", + "answer":null, + "category":null, + "difficulty":null + }, + { + "id":10, + "question":"how many BGCs are complete (not the edge of a contig)?", + "sql":"SELECT region_id, genome_id FROM bgcflow.regions WHERE contig_edge = FALSE;", + "answer":null, + "category":null, + "difficulty":null + } +] diff --git a/chatbgc/data/schema.sql b/chatbgc/data/bgcflow/schema.sql similarity index 100% rename from chatbgc/data/schema.sql rename to chatbgc/data/bgcflow/schema.sql diff --git a/chatbgc/data/question_sql_pair.json b/chatbgc/data/question_sql_pair.json deleted file mode 100644 index 3223e28..0000000 --- a/chatbgc/data/question_sql_pair.json +++ /dev/null @@ -1,46 +0,0 @@ -[ - { - "question": "How many gene cluster families are in the dataset?", - "sql": "SELECT COUNT(DISTINCT gcf) FROM bigscape_cluster;" - }, - { - "question": "What is the average genome completeness for genomes with a contamination less than 5%?", - "sql": "SELECT AVG(completeness) FROM checkm WHERE contamination < 0.05;" - }, - { - "question": "List all distinct BGC types in the dataset.", - "sql": "SELECT DISTINCT product from regions;" - }, - { - "question": "Are there any BGC regions that have multidrug resistance gene?", - "sql": "SELECT DISTINCT region_id FROM cdss WHERE product ILIKE '%multidrug resistance%';" - }, - { - "question": "Are there type IV lanthipeptide BGCs in the dataset?", - "sql": "SELECT * FROM regions WHERE product ILIKE '%lanthipeptide-class-iv%';" - }, - { - "question": "Do we have Kirromycin producing strains?", - "sql": "SELECT DISTINCT genome_id FROM regions WHERE most_similar_known_cluster_description ILIKE '%Kirromycin%';" - }, - { - "question": "What are the most frequently occurring MIBIG hits compound in the dataset?", - "sql": "SELECT compounds, COUNT(*) AS count FROM mibig_hits GROUP BY compounds ORDER BY count DESC;" - }, - { - "question": "What is the distribution of different genera in the dataset?", - "sql": "SELECT genus, COUNT(*) AS count FROM taxa GROUP BY genus ORDER BY count DESC;" - }, - { - "question": "Can you list all entries that belong to unknown GCFs?", - "sql": "SELECT * FROM bigscape_cluster WHERE FAM_TYPE = 'unknown_family';" - }, - { - "question": "Can you list all BGCs in the GCFs that are associated with melanin compounds?", - "sql": "SELECT * FROM bigscape_cluster WHERE fam_known_compounds ILIKE '%melanin%';" - }, - { - "question": "how many BGCs are complete (not the edge of a contig)?", - "sql": "SELECT region_id, genome_id FROM regions WHERE contig_edge = FALSE;" - } -] diff --git a/chatbgc/train.py b/chatbgc/train.py index 6a30871..38c2458 100644 --- a/chatbgc/train.py +++ b/chatbgc/train.py @@ -48,23 +48,24 @@ def train_model( vn.connect_to_duckdb(url=duckdb_path) - for file in Path(training_folder).glob("*"): - if file.suffix == ".sql": - with open(file, "r") as f: - ddl = f.read() - vn.train(ddl=ddl) - logging.info(f"Trained on DDL file: {file}") - elif file.suffix == ".md": - with open(file, "r") as f: - docs = f.read() - vn.train(documentation=docs) - logging.info(f"Trained on documentation file: {file}") - elif file.suffix == ".json": - with open(file, "r") as f: - data = json.load(f) - for item in data: - vn.train(question=item["question"], sql=item["sql"]) - logging.info(f"Trained on question-sql pair: {file}") + for folder in Path(training_folder).glob("*"): + for file in folder.glob("*"): + if file.suffix == ".sql": + with open(file, "r") as f: + ddl = f.read() + vn.train(ddl=ddl) + logging.info(f"Trained on DDL file: {file}") + elif file.suffix == ".md": + with open(file, "r") as f: + docs = f.read() + vn.train(documentation=docs) + logging.info(f"Trained on documentation file: {file}") + elif file.suffix == ".json": + with open(file, "r") as f: + data = json.load(f) + for item in data: + vn.train(question=item["question"], sql=item["sql"]) + logging.info(f"Trained on question-sql pair: {file}") # Get the information schema query df_information_schema = vn.run_sql("SELECT * FROM INFORMATION_SCHEMA.COLUMNS") diff --git a/poetry.lock b/poetry.lock index 28d57e5..d080f89 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,16 +1,30 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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biosynthetic gene clusters in your genome collection via LLMs usin RAG." authors = ["Matin Nuhamunada "] @@ -55,7 +55,7 @@ setuptools = {version="^68.0", optional = true} pkginfo = {version="^1.9", optional = true} virtualenv = {version="^20.0", optional = true} kaleido = "0.2.1" -vanna = {extras = ["chromadb", "ducdkb", "openai", "postgres"], version = "^0.5.5"} +vanna = "0.6.2" duckdb = "0.10.2" regex = {version = "^2024.4.16", extras = ["doc"]} mergedeep = {version = "^1.3.4", extras = ["doc"]}