name: LncBook
description: LncBook is a comprehensive database of human long non-coding RNAs (lncRNAs) with multi-omics annotations. It accommodates 95,243 lncRNA genes and 323,950 transcripts, integrated from multiple resources including GENCODE, RefLnc, CHESS, FANTOM-CAT, and BIGTranscriptome, with strict quality control and curation. The database provides abundant annotations including conservation features across 40 vertebrates, disease/trait-associated variants, DNA methylation profiles, expression profiles across 9 biological contexts, lncRNA-encoded small proteins, lncRNA-protein interactions, and lncRNA-miRNA interactions.
contacts: []
products: [{"category": "GraphicalInterface", "description": "Main web portal for searching and browsing human long non-coding RNAs with multi-omics annotations", "format": "http", "id": "lncbook.portal", "name": "LncBook Portal", "product_url": "https://ngdc.cncb.ac.cn/lncbook/home"}, {"category": "GraphicalInterface", "description": "Browse conservation features of lncRNA genes across 40 vertebrates", "format": "http", "id": "lncbook.conservation", "name": "Conservation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/conservation"}, {"category": "GraphicalInterface", "description": "Browse 959,138 disease/trait-associated variants across lncRNA genes", "format": "http", "id": "lncbook.variation", "name": "Variation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/variation"}, {"category": "GraphicalInterface", "description": "Browse DNA methylation profiles in 16 diseases (14 cancers and 2 neurodevelopmental disorders)", "format": "http", "id": "lncbook.methylation", "name": "Methylation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/methylation"}, {"category": "GraphicalInterface", "description": "Browse expression profiles across 9 biological contexts (normal tissue, organ development, cell differentiation, etc.)", "format": "http", "id": "lncbook.expression", "name": "Expression Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/expression"}, {"category": "GraphicalInterface", "description": "Browse 34,012 small proteins encoded by lncRNAs", "format": "http", "id": "lncbook.sprotein", "name": "Small Protein Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/sprotein"}, {"category": "GraphicalInterface", "description": "Browse lncRNA-miRNA and lncRNA-protein interactions (146,092,274 lncRNA-miRNA and 772,745 lncRNA-protein interactions)", "format": "http", "id": "lncbook.interaction", "name": "Interaction Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/interaction"}, {"category": "GraphicalInterface", "description": "ID conversion tool across 14 resources", "format": "http", "id": "lncbook.conversion", "name": "ID Conversion Tool", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/conversion"}, {"category": "GraphicalInterface", "description": "BLAST search tool for sequence similarity", "format": "http", "id": "lncbook.blast", "name": "BLAST Search", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/blast"}, {"category": "GraphicalInterface", "description": "Genomic location annotation and classification tool", "format": "http", "id": "lncbook.classification", "name": "Classification Tool", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/classification"}, {"category": "GraphicalInterface", "description": "LGC coding potential prediction tool", "format": "http", "id": "lncbook.lgc", "name": "LGC Coding Potential Predictor", "product_url": "https://ngdc.cncb.ac.cn/lgc"}, {"category": "DocumentationProduct", "description": "Comprehensive database statistics and analysis results", "format": "http", "id": "lncbook.statistics", "name": "Statistics Page", "product_url": "https://ngdc.cncb.ac.cn/lncbook/statistics"}, {"category": "Product", "description": "Downloadable data files including gene annotations, expression profiles, and multi-omics annotations", "format": "http", "id": "lncbook.downloads", "name": "Downloads", "product_url": "https://ngdc.cncb.ac.cn/lncbook/download", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}]
raw_data: {"activity_status": "active", "category": "DataSource", "creation_date": "2019-01-05T00:00:00Z", "description": "LncBook is a comprehensive database of human long non-coding RNAs (lncRNAs) with multi-omics annotations. It accommodates 95,243 lncRNA genes and 323,950 transcripts, integrated from multiple resources including GENCODE, RefLnc, CHESS, FANTOM-CAT, and BIGTranscriptome, with strict quality control and curation. The database provides abundant annotations including conservation features across 40 vertebrates, disease/trait-associated variants, DNA methylation profiles, expression profiles across 9 biological contexts, lncRNA-encoded small proteins, lncRNA-protein interactions, and lncRNA-miRNA interactions.", "domains": ["genomics", "biological systems"], "homepage_url": "https://ngdc.cncb.ac.cn/lncbook/home", "id": "lncbook", "last_modified_date": "2025-10-21T00:00:00Z", "layout": "resource_detail", "name": "LncBook", "products": [{"category": "GraphicalInterface", "description": "Main web portal for searching and browsing human long non-coding RNAs with multi-omics annotations", "format": "http", "id": "lncbook.portal", "name": "LncBook Portal", "product_url": "https://ngdc.cncb.ac.cn/lncbook/home"}, {"category": "GraphicalInterface", "description": "Browse conservation features of lncRNA genes across 40 vertebrates", "format": "http", "id": "lncbook.conservation", "name": "Conservation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/conservation"}, {"category": "GraphicalInterface", "description": "Browse 959,138 disease/trait-associated variants across lncRNA genes", "format": "http", "id": "lncbook.variation", "name": "Variation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/variation"}, {"category": "GraphicalInterface", "description": "Browse DNA methylation profiles in 16 diseases (14 cancers and 2 neurodevelopmental disorders)", "format": "http", "id": "lncbook.methylation", "name": "Methylation Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/methylation"}, {"category": "GraphicalInterface", "description": "Browse expression profiles across 9 biological contexts (normal tissue, organ development, cell differentiation, etc.)", "format": "http", "id": "lncbook.expression", "name": "Expression Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/expression"}, {"category": "GraphicalInterface", "description": "Browse 34,012 small proteins encoded by lncRNAs", "format": "http", "id": "lncbook.sprotein", "name": "Small Protein Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/sprotein"}, {"category": "GraphicalInterface", "description": "Browse lncRNA-miRNA and lncRNA-protein interactions (146,092,274 lncRNA-miRNA and 772,745 lncRNA-protein interactions)", "format": "http", "id": "lncbook.interaction", "name": "Interaction Browser", "product_url": "https://ngdc.cncb.ac.cn/lncbook/omics/interaction"}, {"category": "GraphicalInterface", "description": "ID conversion tool across 14 resources", "format": "http", "id": "lncbook.conversion", "name": "ID Conversion Tool", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/conversion"}, {"category": "GraphicalInterface", "description": "BLAST search tool for sequence similarity", "format": "http", "id": "lncbook.blast", "name": "BLAST Search", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/blast"}, {"category": "GraphicalInterface", "description": "Genomic location annotation and classification tool", "format": "http", "id": "lncbook.classification", "name": "Classification Tool", "product_url": "https://ngdc.cncb.ac.cn/lncbook/tools/classification"}, {"category": "GraphicalInterface", "description": "LGC coding potential prediction tool", "format": "http", "id": "lncbook.lgc", "name": "LGC Coding Potential Predictor", "product_url": "https://ngdc.cncb.ac.cn/lgc"}, {"category": "DocumentationProduct", "description": "Comprehensive database statistics and analysis results", "format": "http", "id": "lncbook.statistics", "name": "Statistics Page", "product_url": "https://ngdc.cncb.ac.cn/lncbook/statistics"}, {"category": "Product", "description": "Downloadable data files including gene annotations, expression profiles, and multi-omics annotations", "format": "http", "id": "lncbook.downloads", "name": "Downloads", "product_url": "https://ngdc.cncb.ac.cn/lncbook/download", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 404 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 404 error when accessing file"]}, {"category": "GraphicalInterface", "description": "Web portal for searching and browsing ncRNA sequences, structures, and annotations", "format": "http", "id": "rnacentral.portal", "name": "RNAcentral Portal", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/"}, {"category": "ProgrammingInterface", "description": "REST API for programmatic access to RNAcentral data", "format": "http", "id": "rnacentral.api", "name": "RNAcentral REST API", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/api"}, {"category": "Product", "description": "FTP archive with current and archived release files (sequences and annotations)", "format": "http", "id": "rnacentral.ftp", "name": "RNAcentral FTP Archive", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral"}, {"category": "DataModelProduct", "description": "Public PostgreSQL database for direct SQL access to RNAcentral data", "format": "postgres", "id": "rnacentral.public-db", "name": "RNAcentral Public Postgres Database", "original_source": ["5srrnadb", "crd", "dictybase", "ena", "ensembl", "evlncrnas", "expressionatlas", "flybase", "genecards", "greengenes", "gtrnadb", "hgnc", "intact", "lncbase", "lncbook", "lncipedia", "lncrnadb", "malacards", "mgnify", "mirbase", "mirgenedb", "modomics", "noncode", "pdbe", "pirbase", "plncdb", "pombase", "rdp", "rediportal", "rfam", "rgd", "ribocentre", "ribovision", "sgd", "silva", "snodb", "snopy", "snornadatabase", "srpdb", "tair", "tarbase", "tmrnawebsite", "zfin", "zwd", "rnacentral"], "product_url": "https://rnacentral.org/help/public-database"}], "publications": [{"authors": ["Zhao Li", "Lin Liu", "Changrui Feng", "Yuxin Qin", "Jingfa Xiao", "Zhang Zhang", "Lina Ma"], "id": "https://doi.org/10.1093/nar/gkac999", "journal": "Nucleic Acids Research", "preferred": true, "title": "LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations", "year": "2023"}, {"authors": ["Lina Ma", "Jingfa Cao", "Lin Liu", "Qiuye Du", "Zhilei Li", "Dahai Zou", "Vladimir B. Bajic", "Zhang Zhang"], "id": "https://doi.org/10.1093/nar/gky960", "journal": "Nucleic Acids Research", "title": "LncBook: a curated knowledgebase of human long non-coding RNAs", "year": "2019"}]}