Table 1.
Resources for microbial and human metabolic pathway reconstructions.
| Databases or Repositories | Description | References |
|---|---|---|
| BiGG database | A publicly accessible repository for benchmark GEMs with open access. | [59] |
| Virtual Metabolic Human (VMH) |
A freely accessible database for human and gut microbial metabolic reconstructions (GEMs) with open access. | [60] |
| ModelSEED | A web-based platform for metabolic modeling and analysis. | [61] |
| Human Metabolic Atlas (HMA) |
An open access web-based platform for studying human metabolism. | [33,62] |
| HumanCyc | A curated database of experimentally validated metabolic pathways for studying human metabolism. | [63] |
| KEGG | A comprehensive resource comprising databases of large-scale molecular datasets and detailed pathway information. | [64,65] |
| LIPID MAPS | A database providing information on lipid structures, pathways, and lipid-related genes; enzymes; and metabolites. | [66] |
| Human Metabolome Database (HMDB) | A comprehensive resource that provides information on the chemical composition, biological roles, and disease associations of metabolites found in the human body. | [67] |
| BRENDA | An enzyme- and ligand-focused information retrieval system. | [68] |
| REACTOME | An open access database for biological pathways. | [69] |
| UniProt | An open access database for curated protein information. | [70] |
| Human Protein Atlas (HPA) | A comprehensive resource providing information on the expression and localization of proteins in human tissues and cells. | [71] |
| ProteomicsDB | A comprehensive resource for exploring and analyzing protein expression data from a variety of organisms and tissues. | [72] |
| Entrez gene | Gene-centered information, including gene sequences, annotations, functional data, and genetic variations. | [73] |
| Gene Expression Omnibus (GEO) | A public repository that provides access to a vast collection of gene expression data from various experiments and studies. | [74] |
| Array Express (AE) | A public database of functional genomics experiments and gene expression profiles. | [75] |
| European Genome-phenome Archive (EGA) | A secure and controlled-access database for hosting and sharing human genetic and phenotypic data. | [76] |
| Genotype-Tissue Expression (GTEx) | A catalog of genetic variants and their influence on gene expression across multiple human tissues. | [77] |
| Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task (STARNET) | A computational method for reconstructing cell lineage trees from single-cell transcriptomic data. | [78] |
| BioModels | A collection of biological models that encompasses various organisms and biological processes. | [79] |