genular

const gene = {
    // Unique identifier for the gene, corresponding to the NCBI Gene ID.
    geneID: { type: Number, index: { unique: true } },

    // Taxonomy-related information, detailing the classification and biological context of the gene.
    tax: {
        id: { type: Number, index: true }, // Numeric identifier for the taxonomic classification from gene2accession.tax_id.
        name: {
            name: { type: String }, // Descriptive name of the taxonomy category from taxdump.names.dmp.name_txt.
            unique: { type: String }, // A unique descriptor for taxonomy to facilitate fast lookups.
            type: { type: Number }, // Numerical code representing the taxonomy type for categorization purposes.
        },
    },
    updated: { type: Date, default: Date.now }, // Timestamp of the last update to this gene record.

    // Current status of the gene (e.g., "Predicted", "Validated") reflecting the validation level in research.
    geneStatus: { type: String },

    // Accession numbers associated with this gene, providing links to various sequence databases.
    accession: {
        rna: { type: String }, // Accession number for RNA sequences from gene2accession.
        protein: [{ type: String }], // List of protein accession numbers associated with this gene.
        gene: [{ type: String }], // List of genomic nucleotide accession numbers.
        peptide: { type: String }, // Accession number for peptide sequences.
    },

    // Data representing gene expression profiles across various cell types.
    singleCellExpressions: {
        effectSizes: [
            {
                i: { type: String }, // Identifier for the cell type, possibly following a standard nomenclature.
                c: { type: String }, // Contextual information including biological or medical categorizations.
                s: { type: Number } // Marker score quantifying gene expression uniqueness across cell types.
            }
        ]
    },

    // Aggregated cross-referencing data with other genomic databases for extended metadata and linkages.
    crossReference: {
        bulk: [
            {
                dbName: { type: String }, // Name of the external database for cross-referencing.
                value: { type: String }, // Corresponding identifier or value in the external database.
            }
        ],
        enseGeneID: { type: String }, // ENSEMBL gene identifier providing a direct link to ENSEMBL database.
        enseProtID: [{ type: String }], // List of ENSEMBL protein identifiers associated with this gene.
        enseRnaID: [{ type: String }], // List of ENSEMBL RNA identifiers.
        pubMed: [{ type: Number }], // Array of PubMed IDs for referencing literature.
    },

    // Information specifying the gene's location and orientation on the genome.
    genePos: {
        start: { type: Number }, // Starting position of the gene on its respective chromosome.
        end: { type: Number }, // Ending position of the gene.
    },
    orientation: { type: String }, // Orientation of the gene on the chromosome (e.g., '+', '-', '?').
    symbol: { type: String, index: true }, // Commonly used symbol or abbreviation for the gene.
    locTag: { type: String }, // Locus tag providing an alternative gene identifier.

    // Details of the chromosome where the gene is located, providing contextual genomic information.
    chrom: {
        pos: { type: Number }, // Positional index of the chromosome.
        type: { type: String }, // Type of the chromosome (e.g., "MT" for mitochondrial).
        loc: { type: String }, // Specific location descriptor on the chromosome.
    },
    desc: { type: String }, // Verbose description or annotation of the gene.

    // Categorical gene type providing insights into the gene's function and characteristics.
    geneType: { type: Number }, // Numeric code representing the gene's functional category.

    // Data relating to Mendelian Inheritance in Man (MIM), linking genes to clinical features. (requires omim license)
    // mim: [
    //     {
    //         id: { type: String, index: true }, // Unique MIM identifier.
    //         relation: { type: String }, // Relationship type between the gene and its MIM entry (e.g., gene, phenotype).
    //         cui: { type: Number }, // Concept Unique Identifier in medical databases.
    //     }
    // ],

    // Gene Ontology (GO) annotations providing insights into biological processes, cellular components, and molecular functions.
    ontology: [
        {
            id: { type: Number }, // GO identifier for referencing specific GO terms.
            term: { type: String }, // Descriptive term from the Gene Ontology.
            cat: { type: String }, // Category of the GO term (e.g., biological process, molecular function).
            pubMed: [{ type: Number }], // PubMed references supporting the association.
        },
    ],

    // Defines relationships with other genes, including orthologs and functional similarities.
    geneRelations: [
        {
            relationType: { type: String }, // Nature of the relationship (e.g., ortholog, readthrough sibling).
            similarGenes: [{ type: String }], // Array of gene identifiers denoting related genes.
        },
    ],

    // Information on gene-associated disorders, aiding in clinical and research contexts. (requires omim license)
    geneDisorder: [
        {
            name: { type: String }, // Name of the associated disorder.
            loc: { type: String }, // Cytogenetic location related to the disorder.
        },
    ],
    // Comprehensive protein data linked to the gene, including identifiers and functional information.
    protein: [
        {
            // GENULAR proteinID = geneID + protein mass + protein length + crc32(sequence)
            proteinID: { type: Number, index: { unique: true } }, // , dropDups: true
            accession: [{ type: String, index: true }], // Array of accession numbers from various protein databases.
            symbol: { type: String }, // Standard symbol or abbreviation for the protein.
            name: { type: String }, // Full name providing detailed protein identification.
            // Database cross-references providing a network of protein-related information.
            databaseIDs: {
                pdbID: [{ type: String }], // Array of Protein Data Bank IDs linking to 3D structural data.
                goID: [{ type: String }], // Array of Gene Ontology IDs indicating associated biological processes, cellular components, and molecular functions.
                unigeneID: { type: String }, // UniGene cluster ID, providing a unique identifier for a set of related sequences.
                interProID: [{ type: String }], // Array of InterPro IDs, denoting the protein families, domains, and functional sites.
                Pfam: [{ type: String }], // Array of Protein family IDs from the Pfam database, categorizing proteins based on shared functional domains.
                PROSITE: [{ type: String }], // Array of PROSITE IDs, identifying protein domains, families, and functional sites through patterns and profiles.
                UniGene: { type: String }, // Redundant with unigeneID, possibly consider clarifying or ensuring distinct usage.
                PDBsum: [{ type: String }], // Array of PDBsum IDs for detailed protein structural and functional summaries.
                ProteinModelPortal: { type: String }, // IDs linking to the Protein Model Portal for comparative protein structure models.
                DIP: { type: String }, // Database of Interacting Proteins ID, denoting specific protein-protein interactions.
                MINT: { type: String }, // Molecular INTeraction database ID, referencing documented protein interaction data.
                STRING: { type: String }, // STRING database IDs, providing comprehensive protein-protein interaction networks.
                BindingDB: { type: String }, // Binding Database ID, related to the interaction of proteins with small, chemically defined molecules.
                ChEMBL: { type: String }, // ChEMBL ID, indicating bioactive molecule information with drug-like properties.
                DEPOD: { type: String }, // Dephosphorylation database ID, offering data on protein dephosphorylation.
                iPTMnet: { type: String }, // Integrated Post-Translational Modification Network ID, detailing protein post-translational modifications.
                PhosphoSite: { type: String }, // PhosphoSite ID, providing information on phosphorylation sites within proteins.
                SwissPalm: { type: String }, // SwissPalm ID, related to protein S-palmitoylation data.
                UniCarbKB: { type: String }, // Unified carbohydrate knowledgebase ID, cataloging information on protein glycosylation.
                BioMuta: { type: String }, // BioMuta ID, referencing a compendium of cancer-associated genetic variations.
                DMDM: { type: String }, // Domain Mapping of Disease Mutations ID, linking protein domains to disease mutations.
                EPD: { type: String }, // Eukaryotic Promoter Database ID, related to transcription start sites of eukaryotic genes.
                MaxQB: { type: String }, // MaxQuant database ID for quantitative proteomics data.
                PaxDb: { type: String }, // Protein abundance database ID, offering information on protein concentration levels.
                PRIDE: { type: String }, // Proteomics Identifications Database ID, for datasets and protein identifications.
                GeneID: { type: String }, // NCBI Gene ID, providing a unique identifier for a gene.
                KEGG: { type: String }, // KEGG ID, denoting entries in the Kyoto Encyclopedia of Genes and Genomes database.
                CTD: { type: String }, // Comparative Toxicogenomics Database ID, linking genes to environmental chemicals.
                GeneCards: { type: String }, // GeneCards ID, offering comprehensive information on human genes.
                HPA: [{ type: String }], // Human Protein Atlas ID, linking to protein expression profiles across human tissues.
                MalaCards: { type: String }, // MalaCards ID, providing an integrated database of human maladies and their annotations.
                neXtProt: { type: String }, // NeXtProt ID, offering a protein-centric view of human proteins in health and disease.
                PharmGKB: { type: String }, // Pharmacogenomics Knowledgebase ID, linking genes, drugs, and diseases.
                HOGENOM: { type: String }, // Database of homologous genes from fully sequenced organisms.
                HOVERGEN: { type: String }, // Database of homologous vertebrate genes, providing comparative genomics data.
                InParanoid: { type: String }, // Database ID for eukaryotic ortholog groups, aiding in comparative genomics analysis.
                KO: { type: String }, // KEGG Orthology ID, relating genes to their functions.
                PhylomeDB: { type: String }, // Database ID for complete collections of phylogenetic data.
                TreeFam: { type: String }, // TreeFam database ID, offering phylogenetic tree data of gene families.
                SignaLink: { type: String }, // Signaling pathway database ID, for biological signaling networks.
                SIGNOR: { type: String }, // SIGNOR ID, detailing signaling and regulatory events.
                EvolutionaryTrace: { type: String }, // ID linking to the Evolutionary Trace database for protein function prediction.
                GeneWiki: { type: String }, // Gene Wiki ID, providing collaborative gene summaries.
                GenomeRNAi: { type: String }, // GenomeRNAi ID, referencing RNA interference data for genomes.
                PRO: { type: String }, // Protein Ontology ID, offering structured information on protein entities.
                Proteomes: { type: String }, // UniProt Proteomes ID, denoting a complete set of proteins thought to be expressed by an organism.
                Bgee: { type: String }, // Database for gene expression evolution, providing expression data in different organisms.
                CleanEx: { type: String }, // Database ID for accessing expression data and gene expression atlases.
            },
            citations: [
                {
                    title: { type: String }, // Descriptive title of the referenced publication or citation.
                    pubmedID: { type: String }, // Unique identifier in the PubMed database, linking to the publication's abstract and details.
                    doi: { type: String }, // Standardized Digital Object Identifier providing a persistent link to the publication's online location.
                    scope: [{ type: String }], // The context or specific aspects of the publication that are relevant to the gene entry.
                },
            ],

            // Section for detailing protein sequence similarity indices as per RefSeq data.
            refSeq: {
                // Collection of UniRef similarity indices corresponding to different levels of sequence similarity.
                uniref: {
                    s50: { type: String }, // UniRef50 ID indicating a cluster with 50% sequence similarity.
                    s90: { type: String }, // UniRef90 ID indicating a cluster with 90% sequence similarity.
                    s100: { type: String }, // UniRef100 ID indicating a cluster with 100% sequence similarity.
                },
            },

            // Information on protein families derived from Pfam database classifications.
            proteinFamily: {
                accession: { type: String }, // Unique Pfam accession number identifying the protein family.
                name: { type: String }, // The name assigned to the protein family for easier reference.
                description: { type: String }, // Detailed description of the protein family, outlining defining characteristics.
                value: { type: String }, // Quantitative value or metric (e.g., e-value) associated with the protein family classification.
            },

            // Details on protein motifs as identified and described in the PROSITE database.
            proteinMotifs: [
                {
                    id: { type: String }, // Unique identifier for the protein motif within PROSITE.
                    description: { type: String }, // Detailed explanation of the motif, including its biological significance.
                    sequence: { type: String }, // The specific amino acid sequence pattern of the motif.
                }
            ],

            // Array capturing information about protein-protein interactions.
            interactionPartners: [
                {
                    partnerID: { type: String }, // UniProt ID of the interacting protein partner.
                    score: { type: Number }, // A score quantifying the strength or confidence of the interaction.
                },
            ],

            // Comprehensive details regarding the protein sequence.
            sequence: {
                length: { type: Number }, // The total number of amino acids in the protein sequence.
                mass: { type: Number }, // The molecular mass of the protein, typically in Daltons.
                checksum: { type: String }, // Checksum value for verifying the integrity of the protein sequence.
                modified: { type: Date }, // The date when the protein sequence was last modified.
                version: { type: Number }, // Version number indicating updates or revisions to the protein sequence.
                sequence: { type: String }, // The complete amino acid sequence of the protein.
            },

            // Metadata related to the existence and source of the protein information.
            existence: { type: Number }, // Numerical code indicating the evidence level for the protein's existence.
            relevance: { type: Number }, // Indicates the source database's confidence level: higher for Swiss-Prot (sprot) and lower for TrEMBL (trembl).
            uniParcID: { type: String }, // Identifier in the UniParc database, providing a cross-reference to the protein sequence.
            uniParcVersion: { type: Number }, // Version number of the protein sequence in the UniParc database.
        }
    ]
};