Table 1.
The connectivity of the VMH: list of external resources connected to the database's entities and the corresponding coverages
| Database | Description | URL | Coverage |
|---|---|---|---|
| Metabolites | |||
| BIGG | ‘BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. It integrates more than 70 published genome scale networks.’ | http://bigg.ucsd.edu/ | 4670/5180 = 90.2% |
| Biocyc | ‘BioCyc integrates sequenced genomes with predicted metabolic pathways for thousands of organisms and provides extensive bioinformatics tools.’ | https://biocyc.org/ | 863/5180 = 16.7% |
| ChEBI | ‘Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities. The database is focused on ‘small’ chemical compounds, such as atoms, molecules, ions, etc.’ | https://www.ebi.ac.uk/chebi/ | 4770/5180 = 92.1% |
| Chemspider | ‘ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry. It provides fast access to over 60 million structures, properties, and associated information.’ | http://www.chemspider.com/ | 1357/5180 = 26.2% |
| Drugbank | ‘The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.’ | https://www.drugbank.ca/ | 271/5180 = 5.2% |
| EPA | ‘United States Envrionmental Protection Agency – Chemistry Dashboard.’ | https://comptox.epa.gov/dashboard/ | 793/5180 = 15.3% |
| Foodb | ‘FooDB is a comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients.’ | http://foodb.ca/ | 1354/5180 = 26.1% |
| HMDB | ‘The Human Metabolome Database (HMDB) is a freely available database containing detailed information about 114 100 small molecule metabolites found in the human body.’ | http://www.hmdb.ca/ | 5008/5180 = 96.7% |
| KEGG | ‘The Kyoto Encyclopedia of Genes and Genomes integrates genomic, chemical and systemic functional information. KEGG is an integrated database resource consisting of eighteen databases.’ | http://www.genome.jp/kegg/ | 4773/5180 = 92.1% |
| MetanetX | ‘MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks and biochemical pathways.’ | https://www.metanetx.org/ | 4989/5180 = 96.3% |
| METLIN | ‘METLIN is a comprehensive MS/MS metabolite database. METLIN includes 961 829 molecules ranging from lipids, steroids, plant & bacteria metabolites, small peptides, carbohydrates, exogenous drugs/metabolites, central carbon metabolites and toxicants.’ | https://metlin.scripps.edu/ | 1372/5180 = 26.5% |
| ModelSEED | ‘ModelSEED is a resource for the reconstruction, exploration, comparison, and analysis of metabolic models.’ | http://modelseed.org/ | 1606/5180 = 31.0% |
| PDMAP | ‘The PD map is a manually curated knowledge repository established to describe molecular mechanisms of PD. It compiles literature-based information on PD into an easy to explore and freely accessible interactive molecular interaction map.’ | https://pdmap.uni.lu/MapViewer/ | 282/5180 = 5.4% |
| PubChem | ‘Pubchem is an open chemistry database that collects information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and others.’ | https://pubchem.ncbi.nlm.nih.gov/ | 4979/5180 = 96.1% |
| KNApSAcK | ‘KNApSAcK is a comprehensive species-metabolite relationship database.’ | http://kanaya.naist.jp/KNApSAcK/ | 446/5180 = 8.6% |
| Wikipedia | ‘Wikipedia is a free online encyclopedia, created and edited by volunteers around the world and hosted by the Wikimedia Foundation.’ | https://www.wikipedia.org/ | 757/5180 = 14.6% |
| Reactions | |||
| BRENDA | ‘BRENDA is the main collection of enzyme functional data available to the scientific community.’ | http://www.brenda-enzymes.org/ | 14864/17730 = 83.8% |
| COG | ‘Phylogenetic classification of proteins encoded in complete genomes.’ | https://www.ncbi.nlm.nih.gov/COG/ | 11238/17730 = 63.4% |
| MetanetX | ‘MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks and biochemical pathways.’ | https://www.metanetx.org/ | 6302/17730 = 35.5% |
| ModelSEED | ‘ModelSEED is a resource for the reconstruction, exploration, comparison, and analysis of metabolic models.’ | http://modelseed.org/ | 2542/17730 = 14.3% |
| KEGG Reaction | ‘The Kyoto Encyclopedia of Genes and Genomes integrates genomic, chemical and systemic functional information. KEGG is an integrated database resource consisting of eighteen databases.’ | http://www.genome.jp/kegg/ | 14095/17730 = 79.5% |
| KEGG Orthology | ‘The KO (KEGG Orthology) database is a database of molecular functions represented in terms of functional orthologs.’ | http://www.genome.jp/kegg/ | 11238/17730 = 63.4% |
| Wikipedia | ‘Wikipedia is a free online encyclopedia, created and edited by volunteers around the world and hosted by the Wikimedia Foundation.’ | https://www.wikipedia.org/ | 4/17730 = 0.02% |
| Human genes | |||
| ChEMBL | ‘ChEMBL is a database of bioactive drug-like small molecules, it contains 2D structures, calculated properties and abstracted bioactivities.’ | https://www.ebi.ac.uk/chembl/ | 3689/3695 = 99.8% |
| ClinGene | ‘ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.’ | https://www.clinicalgenome.org/ | 3695/3695 = 100.0% |
| DECIPHER | ‘DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants.’ | https://decipher.sanger.ac.uk/ | 3695/3695 = 100.0% |
| DiseaseMeth | ‘The human disease methylation database, DiseaseMeth version 2.0 is a web based resource focused on the aberrant methylomes of human diseases.’ | http://bio-bigdata.hrbmu.edu.cn/diseasemeth/index.html | 3695/3695 = 100.0% |
| Ensembl | ‘Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.’ | http://www.ensembl.org/ | 3695/3695 = 100.0% |
| Entrez gene | ‘The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website.’ | https://www.ncbi.nlm.nih.gov/gene | 3695/3695 = 100.0% |
| Geno2MP | ‘The Geno2MP browser displays the aggregate variants found by exome sequencing data from a wide variety of Mendelian gene discovery projects and enables users to go from Genotypes to Mendelian Phenotypes found in individuals with that genotype.’ | http://geno2mp.gs.washington.edu/Geno2MP/#/ | 3682/3695 = 99.7% |
| GHR | ‘Genetics Home Reference (GHR) is a service of the National Library of Medicine (NLM), which is part of the National Institutes of Health, an agency of the U.S. Department of Health and Human Services.’ | https://ghr.nlm.nih.gov/ | 3688/3695 = 99.8% |
| GWAS Catalog | ‘GWAS Catalog is the NHGRI-EBI Catalog of published genome-wide association studies.’ | https://www.ebi.ac.uk/gwas/home | 3692/3695 = 99.9% |
| GWAS Central | ‘GWAS Central is a database of summary level findings from genetic association studies, both large and small.’ | https://www.gwascentral.org/ | 3695/3695 = 100.0% |
| HGNC | ‘The Hugo Gene Nomenclature Committee is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.’ | https://www.genenames.org/ | 3695/3695 = 100.0% |
| Human protein Atlas | ‘The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.’ | https://www.proteinatlas.org/ | 3695/3695 = 100.0% |
| LOVD | ‘The Leiden Open (source) Variation Database (LOVD) provides a flexible, freely available tool for Gene-centered collection and display of DNA variations.’ | http://www.lovd.nl/3.0/home | 3695/3695 = 100.0% |
| OMIM | ‘Online Mendelian Inheritance in Man is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship.’ | https://www.omim.org/ | 3695/3695 = 100.0% |
| Uniprot | ‘UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.’ | http://www.uniprot.org/ | 3695/3695 = 100.0% |
| WikiGene | ‘WikiGenes is a non-profit initiative to provide a global collaborative knowledge base for the life sciences.’ | https://www.wikigenes.org/ | 3695/3695 = 100.0% |
| Wikipedia | ‘Wikipedia is a free online encyclopedia, created and edited by volunteers around the world and hosted by the Wikimedia Foundation.’ | https://www.wikipedia.org/ | 2088/3695 = 56.5% |
| Disease | |||
| 1000 genomes | ‘A deep catalog of human genetic variation.’ | http://phase3browser.1000genomes.org/Homo_sapiens/ | 255/255 = 100.0% |
| CellLines | https://www.coriell.org/ | 241/255 = 94.5% | |
| ClinGene Dosage | ‘The Clinical Genome Resource (ClinGen) consortium is curating genes and regions of the genome to assess whether there is evidence to support that these genes/regions are dosage sensitive and should be targeted on a cytogenomic array.’ | https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ | 255/255 = 100.0% |
| ClinicalTrials.gov | ‘ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world.’ | https://clinicaltrials.gov/ct2/home | 130/255 = 50.9% |
| ClinVar | ‘ClinVar aggregates information about genomic variation and its relationship to human health.’ | https://www.ncbi.nlm.nih.gov/clinvar/ | 255/255 = 100.0% |
| EuroGenTest | ‘EuroGenTest is part of the OrphaNet portal for rare diseases and orphan drugs. EuroGenTest provides information on diagnostic tests able to establish a diagnosis of a rare disease and that need a rare technical competence, or that is the best standard in a given country.’ | https://www.orpha.net/consor/cgi-bin/ClinicalLabs_Search.php?lng=EN | 228/255 = 89.4% |
| GARD | ‘The Genetic and Rare Diseases Information Center (GARD) provides the public with access to current, reliable, and easy-to-understand information about rare or genetic diseases.’ | https://rarediseases.info.nih.gov/ | 184/255 = 72.2% |
| Genetic Alliance | ‘Disease InfoSearch provides information about diseases and their related support and advocacy networks.’ | http://diseaseinfosearch.org | 191/255 = 74.9% |
| Gene Reviews | ‘GeneReviews, an international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Each chapter in GeneReviews is written by one or more experts on the specific condition or disease and goes through a rigorous editing and peer review process before being published online.’ | https://www.ncbi.nlm.nih.gov/books/NBK1116/ | 88/255 = 34.1% |
| Geno2MP | ‘The Geno2MP browser displays the aggregate variants found by exome sequencing data from a wide variety of Mendelian gene discovery projects and enables users to go from Genotypes to Mendelian Phenotypes found in individuals with that genotype.’ | http://geno2mp.gs.washington.edu/Geno2MP/#/ | 248/255 = 97.2% |
| GHR | ‘Genetics Home Reference (GHR) is a service of the National Library of Medicine (NLM), which is part of the National Institutes of Health, an agency of the U.S. Department of Health and Human Services.’ | https://ghr.nlm.nih.gov/ | 183/255 = 71.8% |
| GTR | ‘The Genetic Testing Registry (GTR) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials.’ | https://www.ncbi.nlm.nih.gov/gtr/ | 241/255 = 94.5% |
| GWAS Catalog | ‘GWAS Catalog is the NHGRI-EBI Catalog of published genome-wide association studies.’ | https://www.ebi.ac.uk/gwas/home | 187/255 = 73.3% |
| GWAS Central | ‘GWAS Central is a database of summary level findings from genetic association studies, both large and small.’ | https://www.gwascentral.org/ | 253/255 = 99.2% |
| LOVD | ‘The Leiden Open (source) Variation Database (LOVD) provides a flexible, freely available tool for Gene-centered collection and display of DNA variations.’ | http://www.lovd.nl/3.0/home | 254/255 = 99.6% |
| MalaCards | ‘MalaCards is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes.’ | https://www.malacards.org/ | 206/255 = 80.8% |
| MGI | ‘MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.’ | http://www.informatics.jax.org/ | 241/255 = 94.5% |
| OMIM | ‘Online Mendelian Inheritance in Man is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship.’ | https://www.omim.org/ | 247/255 = 96.9% |
| OMIM Clinical Symptoms | Synopsis of clinical symptoms. | https://omim.org/clinicalSynopsis/ | 230/255 = 90.2% |
| OrphaNet | ‘OrphaNet is the portal for rare diseases and orphan drugs.’ | https://www.orpha.net/consor/cgi-bin/index.php?lng=EN | 223/255 = 87.5% |
| Wikipedia | ‘Wikipedia is a free online encyclopedia, created and edited by volunteers around the world and hosted by the Wikimedia Foundation.’ | https://www.wikipedia.org/ | 201/255 = 78.8% |
| Microbe | |||
| ENA | ‘The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.’ | https://www.ebi.ac.uk/ena | 806/818 = 98.5% |
| Ensembl Bacteria | ‘Ensembl Bacteria is a browser for bacterial and archaeal genomes.’ | http://bacteria.ensembl.org/index.html | 808/818 = 98.8% |
| GOLD | ‘Genomes Online Database (GOLD) is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.’ | https://gold.jgi.doe.gov/ | 798/818 = 97.6% |
| IMG | ‘The mission of the Integrated Microbial Genomes & Microbiomes(IMG/M) system is to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE’s Joint Genome Institute (JGI).’ | https://img.jgi.doe.gov/ | 772/818 = 94.4% |
| KBASE | ‘A collaborative, open environment for systems biology of plants, microbes and their communities.’ | https://kbase.us/ | 804/818 = 98.3% |
| MicrobeWiki | ‘MicrobeWiki is a free wiki resource on microbes and microbiology, authored by students at many colleges and universities.’ | https://microbewiki.kenyon.edu/index.php/MicrobeWiki | 799/818 = 97.7% |
| NCBI Taxonomy | ‘The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.’ | https://www.ncbi.nlm.nih.gov/taxonomy | 817/818 = 99.9% |
| Uniprot | ‘UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.’ | http://www.uniprot.org/ | 815/818 = 99.6% |