is a General purpose Resource.
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
Email: helpdesk@pombase.org
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pombase.genes ⚠ | PomBase gene names | gene_IDs_names.tsv | Product | tsv | Tab-delimited file of systematic ID, ... |
| pombase.genes-products ⚠ | PomBase gene names and products | gene_IDs_names_products.tsv | Product | tsv | Tab-delimited file of systematic ID, ... |
| pombase.to-uniprot | PomBase to UniProt map | PomBase2UniProt.tsv (27.0 KB) | Mapping | tsv | Tab-delimited file with the PomBase s... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| kg-monarch.graph | KGX Distribution of KG-Monarch | monarch-kg.tar.gz (220.2 MB) | Graph | kgx | had primary source | KGX Distribution of KG-Monarch |
| kg-monarch.graph.jsonl | KGX JSON-L Distribution of KG-Monarch | monarch-kg.jsonl.tar.gz (301.0 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.rdf | RDF Distribution of KG-Monarch | monarch-kg.nt.gz (838.5 MB) | Graph | rdfxml | had primary source | RDF Distribution of KG-Monarch |
| kg-monarch.graph.neo4j | Neo4j Dump of KG-Monarch | monarch-kg.neo4j.dump (1.3 GB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch |
| kg-monarch.graph.duckdb | DuckDB database of KG-Monarch | monarch-kg.duckdb (6.4 GB) | Graph | mixed | had primary source | DuckDB database of KG-Monarch |
| kg-monarch.graph.jsonl.edges | KGX JSON-L Distribution of KG-Monarch Edges | monarch-kg.jsonl.tar.gz (465.3 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.jsonl.nodes | KGX JSON-L Distribution of KG-Monarch Nodes | monarch-kg.jsonl.tar.gz (465.3 MB) | Graph | kgx-jsonl | had primary source | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.neo4j.edges | Neo4j Dump of KG-Monarch Edges | monarch-kg_edges.neo4j.csv (4.1 GB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch Edges |
| kg-monarch.graph.neo4j.nodes | Neo4j Dump of KG-Monarch Nodes | monarch-kg_nodes.neo4j.csv (333.4 MB) | Graph | neo4j | had primary source | Neo4j Dump of KG-Monarch Nodes |
| rnacentral.portal | RNAcentral Portal | rnacentral.org | Graphical Interface | http | had primary source | Web portal for searching and browsing... |
| rnacentral.api | RNAcentral REST API | api | Programming Interface | http | had primary source | REST API for programmatic access to R... |
| rnacentral.ftp | RNAcentral FTP Archive | RNAcentral | Product | http | had primary source | FTP archive with current and archived... |
| rnacentral.public-db | RNAcentral Public Postgres Database | public-database | Data Model | postgres | had primary source | Public PostgreSQL database for direct... |
| obo-db-ingest.pombase.tsv | pombase Nodes TSV | pombase.tsv (140.4 KB) | Product | tsv | had primary source | pombase Nodes TSV |
| iptmnet.ptm | iPTMnet PTM Table | ptm.txt (42.1 MB) | Graph | tsv | was derived from | Current iPTMnet PTM record table with... |
| kg-alzheimers.graph ⚠ | KGX Distribution of KG-Alzheimers | kg-alzheimers.tar.gz (201.1 MB) | Graph | kgx | had primary source | KGX Distribution of KG-Alzheimers |
| sri-reference-kg.graph | SRI-Reference KG (KGX distribution) | monarch-kg.tar.gz (219.4 MB) | Graph | kgx | had primary source | KGX distribution of the SRI-Reference KG |
| neo.model | neo OWL release | neo.owl (2.0 GB) | Ontology | owl | had primary source | OWL release of neo |
| neo.obo | NEO (OBO format) | neo.obo (650.1 MB) | Ontology | obo | had primary source | OBO format release of NEO, built from... |
| obo-db-ingest.pombase.obo | pombase OBO | pombase.obo (226.8 KB) | Product | obo | had primary source | pombase OBO |
| obo-db-ingest.pombase.owl | pombase OWL | pombase.owl (412.9 KB) | Product | owl | had primary source | pombase OWL |
| obo-db-ingest.pombase.json | pombase OBO Graph JSON | pombase.json (359.4 KB) | Product | json | had primary source | pombase OBO Graph JSON |
| hcop.web | HCOP Search | hcop | Graphical Interface | http | was derived from | HCOP web search for orthologs of one ... |
| hcop.all-seven-column | HCOP All Species Orthologs (7 column) | human_all_hcop_seven_column.txt.gz (25.2 MB) | Mapping | tsv | was derived from | All human ortholog assertions from HC... |
| hcop.all-sixteen-column | HCOP All Species Orthologs (16 column) | human_all_hcop_sixteen_column.txt.gz (39.9 MB) | Mapping | tsv | was derived from | All human ortholog assertions from HC... |
| hcop.species-downloads | HCOP Per-species Bulk Downloads | tsv | Product | http | was derived from | HCOP bulk downloads page with pre-com... |
| yeastract.community | CommunityYeastract | community | Graphical Interface | http | was informed by | CommunityYeastract, a set of automati... |
PomBase
Created: March 25, 2025 | Last modified: September 23, 2026