is a Data Source.
ReconX refers to the Recon series of genome-scale reconstructions of human metabolism, beginning with Recon 1 - the global reconstruction of the human metabolic network based on genomic and bibliomic data. These reconstructions account for thousands of metabolic reactions, metabolites, and gene-protein-reaction associations, providing a computable, constraint-based model of human metabolism. The reconstructions are reused by pathway aggregators and are maintained through the Virtual Metabolic Human (VMH) and BiGG Models resources.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| reconx.vmh | Virtual Metabolic Human Portal | www.vmh.life | GraphicalInterface | http | Virtual Metabolic Human web portal fo... |
| reconx.model ⚠ | Recon Human Metabolic Reconstruction | #downloadview | DataModelProduct | sbml | Genome-scale human metabolic reconstr... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| pathwaycommons.downloads | Pathway Commons Data Downloads | v14 | Product | mixed | was derived from | Download directory for Pathway Common... |
| pathwaycommons.sif | SIF Network Format | pc-hgnc.sif.gz (9.4 MB) | Product | sif | was derived from | PC v14 Simple Interaction Format netw... |
| pathwaycommons.gmt | GMT Gene Set Format | pc-hgnc.gmt.gz (256.4 KB) | Product | ❔ | was derived from | PC v14 Gene Matrix Transposed gene se... |
| pathwaycommons.txt | Extended SIF TXT Format | pc-hgnc.txt.gz (110.3 MB) | Product | txt | was derived from | PC v14 tab-delimited extended SIF nod... |
ReconX denotes the Recon series of community genome-scale reconstructions of human metabolism. The foundational Recon 1 model provided a global reconstruction of the human metabolic network built from genomic annotation and an extensive literature (bibliomic) review, and later versions (Recon 2, Recon 3D) substantially expanded coverage. These reconstructions form a computable, constraint-based representation of human metabolism used for systems biology and metabolic modeling.
The Recon reconstructions account for thousands of biochemical reactions, metabolites, and gene-protein-reaction associations spanning human metabolic pathways. They support constraint-based modeling approaches such as flux balance analysis.
Recon models are distributed in SBML and related systems biology model formats and are accessible through the Virtual Metabolic Human (VMH) portal and the BiGG Models database. The reconstruction is also reused by pathway aggregators such as Pathway Commons.
The Recon reconstructions were developed by the Palsson group at UC San Diego and the Thiele group, and are maintained through the Virtual Metabolic Human (VMH) resource.
Duarte NC, Becker SA, Jamshidi N, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS (2007) 104(6):1777-1782. doi:10.1073/pnas.0610772104
Created: June 03, 2026 | Last modified: June 05, 2026