is a Data Source.
INOH (Integrating Network Objects with Hierarchies) is a highly structured, manually curated database of signal transduction and metabolic pathways. Pathways are annotated with custom event and molecule-role ontologies and span multiple organisms including mammals, Xenopus laevis, Drosophila melanogaster, and Caenorhabditis elegans. INOH data was distributed in INOH XML and BioPAX formats and is widely reused by pathway aggregators. The project appears to be no longer actively maintained.
Unknown
Unknown
Unknown
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| inoh.pathways ⚠ | INOH Pathway Data | www.inoh.org | Product | biopax | Manually curated signal transduction ... |
| 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... |
INOH (Integrating Network Objects with Hierarchies) is a highly structured, manually curated database of signal transduction pathways, with additional metabolic pathway content. Each pathway is annotated using custom ontologies that capture event types and molecular roles, enabling consistent representation of complex signaling logic across organisms.
The database covers signal transduction and metabolic pathways for mammals, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans, and canonical pathways. A representative release included 73 signal transduction diagrams and 29 metabolic pathway diagrams encompassing hundreds of subpathways, thousands of interactions, and thousands of protein entities.
INOH data was provided in INOH XML and BioPAX formats, with BioPAX Level 3 recommended for signaling data because of its ability to represent molecular states and binding topology. INOH is a recognized upstream source for pathway aggregators such as Pathway Commons.
The INOH website (www.inoh.org) is not currently reachable, and the project appears to be no longer actively maintained. Its data remains accessible through downstream aggregators.
INOH was developed by the Institute for Bioinformatics Research and Development (BIRD) under the Japan Science and Technology Agency (JST).
Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T. INOH: ontology-based highly structured database of signal transduction pathways. Database (Oxford) (2011) 2011:bar052. doi:10.1093/database/bar052
Created: June 03, 2026 | Last modified: June 05, 2026