The schema below is auto-generatated via the SocialGene Python Package.

# pip install socialgene
sg_schema --nodes  --markdown
sg_schema --rels  --markdown

Nodes

Label	Description	NF results subdirectory	Neo4j header file	Unique on	properties
assembly	Represents a single genome/assembly/BGC. If the input was a FASTA file or if assembly wasn’t in the genbank metadata then this will represent the file the data came from.	genomic_info	assembly.header	uid	[‘uid’, ‘altitude’, ‘bio_material’, ‘bioproject’, ‘biosample’, ‘cell_line’, ‘cell_type’, ‘chromosome’, ‘clone’, ‘clone_lib’, ‘collected_by’, ‘collection_date’, ‘country’, ‘cultivar’, ‘culture_collection’, ‘db_xref’, ‘dev_stage’, ‘ecotype’, ‘environmental_sample’, ‘focus’, ‘germline’, ‘haplogroup’, ‘haplotype’, ‘host’, ‘identified_by’, ‘isolate’, ‘isolation_source’, ‘lab_host’, ‘lat_lon’, ‘macronuclear’, ‘map’, ‘mating_type’, ‘metagenome_source’, ‘mol_type’, ‘note’, ‘organelle’, ‘organism’, ‘pcr_primers’, ‘plasmid’, ‘pop_variant’, ‘proviral’, ‘rearranged’, ‘segment’, ‘serotype’, ‘serovar’, ‘sex’, ‘specimen_voucher’, ‘strain’, ‘sub_clone’, ‘submitter_seqid’, ‘sub_species’, ‘sub_strain’, ‘tissue_lib’, ‘tissue_type’, ‘transgenic’, ‘type_material’, ‘variety’]
assembly	Represents a single Mibig entry	genomic_info	assembly.header	uid	[‘uid’]
chebi	Represents a ChEBI term	None	None	uid	[‘uid’]
chembl	Represents a CHEMBL term	None	None	uid	[‘uid’]
chemical_compound:substructure	Represents a chemical substructure	None	None	inchi, CanonicalSmiles	[‘uid’, ‘MolWt’, ‘HeavyAtomMolWt’, ‘ExactMolWt’, ‘NumValenceElectrons’, ‘NumRadicalElectrons’, ‘HeavyAtomCount’, ‘NumAliphaticCarbocycles’, ‘NumAliphaticHeterocycles’, ‘NumAliphaticRings’, ‘NumAromaticCarbocycles’, ‘NumAromaticHeterocycles’, ‘NumAromaticRings’, ‘NumHAcceptors’, ‘NumHDonors’, ‘NumHeteroatoms’, ‘NumRotatableBonds’, ‘NumSaturatedCarbocycles’, ‘NumSaturatedHeterocycles’, ‘NumSaturatedRings’, ‘RingCount’, ‘MolLogP’, ‘MolMR’, ‘AnonymousGraph’, ‘ElementGraph’, ‘CanonicalSmiles’, ‘MurckoScaffold’, ‘ExtendedMurcko’, ‘MolFormula’, ‘AtomBondCounts’, ‘DegreeVector’, ‘Mesomer’, ‘HetAtomTautomer’, ‘HetAtomProtomer’, ‘RedoxPair’, ‘Regioisomer’, ‘NetCharge’, ‘SmallWorldIndexBR’, ‘SmallWorldIndexBRL’, ‘ArthorSubstructureOrder’, ‘HetAtomTautomerv2’, ‘inchi’]
chemical_compound	Represents a chemical compound	None	None	inchi, CanonicalSmiles	[‘uid’, ‘MolWt’, ‘HeavyAtomMolWt’, ‘ExactMolWt’, ‘NumValenceElectrons’, ‘NumRadicalElectrons’, ‘HeavyAtomCount’, ‘NumAliphaticCarbocycles’, ‘NumAliphaticHeterocycles’, ‘NumAliphaticRings’, ‘NumAromaticCarbocycles’, ‘NumAromaticHeterocycles’, ‘NumAromaticRings’, ‘NumHAcceptors’, ‘NumHDonors’, ‘NumHeteroatoms’, ‘NumRotatableBonds’, ‘NumSaturatedCarbocycles’, ‘NumSaturatedHeterocycles’, ‘NumSaturatedRings’, ‘RingCount’, ‘MolLogP’, ‘MolMR’, ‘AnonymousGraph’, ‘ElementGraph’, ‘CanonicalSmiles’, ‘MurckoScaffold’, ‘ExtendedMurcko’, ‘MolFormula’, ‘AtomBondCounts’, ‘DegreeVector’, ‘Mesomer’, ‘HetAtomTautomer’, ‘HetAtomProtomer’, ‘RedoxPair’, ‘Regioisomer’, ‘NetCharge’, ‘SmallWorldIndexBR’, ‘SmallWorldIndexBRL’, ‘ArthorSubstructureOrder’, ‘HetAtomTautomerv2’, ‘inchi’]
chemical_compound:substrate	Mibig substrate (e.g. NRPS monomer)	None	None	inchi, CanonicalSmiles	[‘uid’, ‘MolWt’, ‘HeavyAtomMolWt’, ‘ExactMolWt’, ‘NumValenceElectrons’, ‘NumRadicalElectrons’, ‘HeavyAtomCount’, ‘NumAliphaticCarbocycles’, ‘NumAliphaticHeterocycles’, ‘NumAliphaticRings’, ‘NumAromaticCarbocycles’, ‘NumAromaticHeterocycles’, ‘NumAromaticRings’, ‘NumHAcceptors’, ‘NumHDonors’, ‘NumHeteroatoms’, ‘NumRotatableBonds’, ‘NumSaturatedCarbocycles’, ‘NumSaturatedHeterocycles’, ‘NumSaturatedRings’, ‘RingCount’, ‘MolLogP’, ‘MolMR’, ‘AnonymousGraph’, ‘ElementGraph’, ‘CanonicalSmiles’, ‘MurckoScaffold’, ‘ExtendedMurcko’, ‘MolFormula’, ‘AtomBondCounts’, ‘DegreeVector’, ‘Mesomer’, ‘HetAtomTautomer’, ‘HetAtomProtomer’, ‘RedoxPair’, ‘Regioisomer’, ‘NetCharge’, ‘SmallWorldIndexBR’, ‘SmallWorldIndexBRL’, ‘ArthorSubstructureOrder’, ‘HetAtomTautomerv2’, ‘inchi’]
chemical_fragment	Represents a chemical fragment as defined by rdkit.Chem.Descriptors	None	None	uid	[]
classyfire	Represents a classyfire chemical ontology term	None	None	uid	[‘uid’, ‘name’, ‘definition’]
gnps_cluster	Represents a GNPS molecular networking cluster	None	None	cluster_index, workflow_uuid	[‘workflow_uuid’, ‘defaultgroups’, ‘g1’, ‘g2’, ‘g3’, ‘g4’, ‘g5’, ‘g6’, ‘gnpslinkout_cluster’, ‘gnpslinkout_network’, ‘mqscore’, ‘mzerrorppm’, ‘massdiff’, ‘rtmean’, ‘rtmean_min’, ‘rtstderr’, ‘uniquefilesources’, ‘uniquefilesourcescount’, ‘cluster_index’, ‘componentindex’, ‘number_of_spectra’, ‘parent_mass’, ‘precursor_charge’, ‘precursor_mass’, ‘sumprecursor_intensity’]
gnps_library_spectrum	Represents a GNPS library spectrum	None	None	uid	[‘uid’, ‘compound_name’, ‘compound_source’, ‘pi’, ‘data_collector’, ‘adduct’, ‘precursor_mz’, ‘exactmass’, ‘charge’, ‘cas_number’, ‘pubmed_id’, ‘smiles’, ‘inchi’, ‘inchi_aux’, ‘library_class’, ‘ionmode’, ‘libraryqualitystring’, ‘mqscore’, ‘tic_query’, ‘rt_query’, ‘mzerrorppm’, ‘sharedpeaks’, ‘massdiff’, ‘libmz’, ‘specmz’, ‘speccharge’, ‘moleculeexplorerdatasets’, ‘moleculeexplorerfiles’, ‘molecular_formula’, ‘inchikey’, ‘inchikey_planar’]
gnps_organism	Represents an organism (as defined by GNPS)	None	None	uid	[‘uid’]
goterm	Represent a GO term	goterms	goterms.header	uid	[‘uid’, ‘name’, ‘namespace’]
hmm	Represents a single non-redundant HMM model	hmm_info	sg_hmm_nodes.header	uid	[‘uid’]
hmm_source	Represents the source of an HMM model (e.g. PFAM)	hmm_info	hmm_source.header	uid	[‘uid’, ‘:LABEL’, ‘rel_path’, ‘name’, ‘acc’, ‘notes’, ‘description’, ‘date’, ‘hash’, ‘hash_used’, ‘model_length’, ‘super_category’, ‘category’, ‘subcategory’, ‘ga’, ‘tc’, ‘nc’]
instrument	Represents an instrument	None	None	uid	[‘uid’]
ion_source	Represents an ion source	None	None	uid	[‘uid’]
npatlas	Represents a single NPAtlas entry	None	None	uid	[‘uid’, ‘original_name’, ‘mol_formula’, ‘mol_weight’, ‘exact_mass’, ‘inchikey’, ‘smiles’, ‘cluster_id’, ‘node_id’, ‘synonyms’, ‘inchi’, ‘m_plus_h’, ‘m_plus_na’, ‘genus’, ‘species’]
npclassifier_class	Represents a NPClassifier class	None	None	uid	[‘uid’]
npclassifier_pathway	Represents a NPClassifier pathway	None	None	uid	[‘uid’]
npclassifier_superclass	Represents a NPClassifier superclass	None	None	uid	[‘uid’]
npmrd	Represents a single NP-MRD entry	None	None	uid	[‘uid’]
nucleotide	Represents a single nucleotide sequence (e.g. a contig/scaffold/chromosome)	genomic_info	locus.header	uid	[‘uid’, ‘external_id’, ‘altitude’, ‘bio_material’, ‘bioproject’, ‘biosample’, ‘cell_line’, ‘cell_type’, ‘chromosome’, ‘clone’, ‘clone_lib’, ‘collected_by’, ‘collection_date’, ‘country’, ‘cultivar’, ‘culture_collection’, ‘db_xref’, ‘dev_stage’, ‘ecotype’, ‘environmental_sample’, ‘focus’, ‘germline’, ‘haplogroup’, ‘haplotype’, ‘host’, ‘identified_by’, ‘isolate’, ‘isolation_source’, ‘lab_host’, ‘lat_lon’, ‘macronuclear’, ‘map’, ‘mating_type’, ‘metagenome_source’, ‘mol_type’, ‘note’, ‘organelle’, ‘organism’, ‘pcr_primers’, ‘plasmid’, ‘pop_variant’, ‘proviral’, ‘rearranged’, ‘segment’, ‘serotype’, ‘serovar’, ‘sex’, ‘specimen_voucher’, ‘strain’, ‘sub_clone’, ‘submitter_seqid’, ‘sub_species’, ‘sub_strain’, ‘tissue_lib’, ‘tissue_type’, ‘transgenic’, ‘type_material’, ‘variety’]
parameters	Parameters and environmental variables used during database creation	parameters	parameters.header	uid	[‘uid’, ‘SG_LOC_NEO4J’, ‘SG_LOC_HMMS’, ‘NEO4J_dbms_memory_pagecache_size’, ’NEO4J_dbms_memory_heap_initial__size’, ’NEO4J_dbms_memory_heap_max__size’, ‘HMMSEARCH_IEVALUE’, ‘HMMSEARCH_BACKGROUND’, ‘HMMSEARCH_BIASFILTER’, ‘HMMSEARCH_NULL2’, ‘HMMSEARCH_SEED’, ‘HMMSEARCH_Z’, ‘HMMSEARCH_DOMZ’, ‘HMMSEARCH_F1’, ‘HMMSEARCH_F2’, ‘HMMSEARCH_F3’, ‘HMMSEARCH_E’, ‘HMMSEARCH_DOME’, ‘HMMSEARCH_INCE’, ‘HMMSEARCH_INCDOME’, ‘HMMSEARCH_BITCUTOFFS’, ‘platform’, ‘architecture’, ‘py_executable’, ‘py_version’, ‘genome_download_command’]
protein	Represents a non-redundant protein	protein_info	protein_ids.header	uid	[‘uid’, ‘crc64’, ‘sequence’]
publication	Represents a publication	None	None	doi	[‘doi’, ‘pmid’, ‘authors’, ‘title’, ‘journal’, ‘year’]
publication	Represents a publication	None	None	doi	[‘doi’, ‘pmid’, ‘authors’, ‘title’, ‘journal’, ‘year’]
spectrum	Represents a GNPS molecular networking spectrum	None	None	uid	[‘uid’, ‘original_filename’, ‘parentmass’, ‘charge’, ‘rettime’, ‘assembly’]
taxid	Represents a single taxon within NCBI taxonomy	taxdump_process	taxid.header	uid	[‘uid’, ‘name’, ‘rank’]
tigrfam_mainrole	Represents a TIGRFAM main role	tigrfam_info	tigrfam_mainrole.header	uid	[‘uid’]
tigrfam_role	Represents a TIGRFAM role	tigrfam_info	tigrfam_role.header	uid	[‘uid’]
tigrfam_subrole	Represents a TIGRFAM sub role	tigrfam_info	tigrfam_subrole.header	uid	[‘uid’]

Relationships

Label	Relationship	NF results subdirectory	Neo4j header file
ALTERNATIVE_PARENTS	(npatlas)-[:ALTERNATIVE_PARENTS]->(classyfire)	None	None
ASSEMBLES_TO	(nucleotide)-[:ASSEMBLES_TO]->(assembly)	genomic_info	assembly_to_locus.header
ANNOTATES	(hmm)-[:ANNOTATES]->(protein)	parsed_domtblout	protein_to_hmm_header.header
BLASTP	(protein)-[:BLASTP]->(protein)	diamond_blastp	blastp.header
CONTAINS	(chemical_compound)-[:CONTAINS]->(chemical_fragment)	None	None
DIRECT_PARENT	(npatlas)-[:DIRECT_PARENT]->(classyfire)	None	None
ENCODES	(nucleotide)-[:ENCODES]->(protein)	genomic_info	locus_to_protein.header
FROM	(gnps_library_spectrum)-[:FROM]->(instrument)	None	None
FROM	(gnps_cluster)-[:FROM]->(assembly)	None	None
FROM	(gnps_library_spectrum)-[:FROM]->(ion_source)	None	None
FROM	(gnps_library_spectrum)-[:FROM]->(gnps_organism)	None	None
GO_ANN	(hmm_source)-[:GO_ANN]->(goterm)	tigrfam_info	tigrfam_to_go.header
GOTERM_RELS	(goterm)-[:GOTERM_RELS]->(goterm)	goterms	go_to_go.header
HAS	(npatlas)-[:HAS]->(publication)	None	None
HAS	(npatlas)-[:HAS]->(gnps_library_spectrum)	None	None
HAS	(npatlas)-[:HAS]->(npmrd)	None	None
IS_A	(npatlas)-[:IS_A]->(npclassifier_pathway)	None	None
IS_A	(classyfire)-[:IS_A]->(classyfire)	None	None
IS_A	(npatlas)-[:IS_A]->(npclassifier_class)	None	None
IS_A	(gnps_library_spectrum)-[:IS_A]->(npclassifier_pathway)	None	None
IS_TAXON	(assembly)-[:IS_TAXON]->(taxid)	genomic_info	assembly_to_taxid.header
IS_A	(gnps_library_spectrum)-[:IS_A]->(npclassifier_superclass)	None	None
IS_A	(gnps_library_spectrum)-[:IS_A]->(npclassifier_class)	None	None
IS_A	(gnps_library_spectrum)-[:IS_A]->(chemical_compound)	None	None
IS_A	(npatlas)-[:IS_A]->(chemical_compound)	None	None
INTERMEDIATE_NODES	(npatlas)-[:INTERMEDIATE_NODES]->(classyfire)	None	None
IS_A	(npatlas)-[:IS_A]->(npclassifier_superclass)	None	None
LIBRARY_HIT	(gnps_cluster)-[:LIBRARY_HIT]->(gnps_library_spectrum)	None	None
LOWEST_CLASS	(npatlas)-[:LOWEST_CLASS]->(classyfire)	None	None
MMSEQS2	(protein)-[:MMSEQS2]->(protein)	mmseqs2_cluster	mmseqs2.header
MOLECULAR_NETWORK	(gnps_cluster)-[:MOLECULAR_NETWORK]->(gnps_cluster)	None	None
MAINROLE_ANN	(tigrfam_role)-[:MAINROLE_ANN]->(tigrfam_mainrole)	tigrfam_info	tigrfamrole_to_mainrole.header
PRODUCES	(taxid)-[:PRODUCES]->(npatlas)	None	None
PRODUCES	(assembly)-[:PRODUCES]->(npatlas)	None	None
PROTEIN_TO_GO	(protein)-[:PROTEIN_TO_GO]->(goterm)	protein_info	protein_to_go.header
ROLE_ANN	(hmm_source)-[:ROLE_ANN]->(tigrfam_role)	tigrfam_info	tigrfam_to_role.header
SYNONYM	(classyfire)-[:SYNONYM]->(chebi)	None	None
SOURCE_DB	(hmm)-[:SOURCE_DB]->(hmm_source)	hmm_info	hmm_source_relationships.header
SIMILAR	(chemical_compound)-[:SIMILAR]->(chemical_compound)	None	None
SUBROLE_ANN	(tigrfam_role)-[:SUBROLE_ANN]->(tigrfam_subrole)	tigrfam_info	tigrfamrole_to_subrole.header
TAXON_PARENT	(taxid)-[:TAXON_PARENT]->(taxid)	taxdump_process	taxid_to_taxid.header