name: BioGPS
description: BioGPS is an extensible and customizable gene annotation portal that aggregates gene-centric data (expression profiles, functional annotations, pathways, interactions, ontologies) from numerous external resources using a community-driven plugin system. It enables interactive expression visualization across tissues/cell types and provides programmatic and bulk access to underlying annotation tables.
contacts: [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "http://biogps.org/about/"}], "label": "BioGPS / The Scripps Research Institute"}]
products: [{"category": "GraphicalInterface", "description": "Main BioGPS web portal with searchable gene pages, expression charts, and plugin system aggregating external annotations", "format": "http", "id": "biogps.portal", "name": "BioGPS Portal", "product_url": "http://biogps.org/"}, {"category": "ProgrammingInterface", "description": "REST-style API for retrieving gene annotations and expression data (JSON/TSV responses)", "format": "http", "id": "biogps.api", "name": "BioGPS API", "product_url": "http://biogps.org/api/"}, {"category": "Product", "description": "Bulk annotation and expression data downloads (gene expression compendia, annotation tables)", "format": "http", "id": "biogps.downloads", "name": "BioGPS Downloads", "product_url": "http://biogps.org/downloads/"}, {"category": "DocumentationProduct", "description": "FAQ and usage guidance including plugin system overview and data interpretation notes", "format": "http", "id": "biogps.faq", "name": "BioGPS FAQ / Help", "product_url": "http://biogps.org/faq/"}, {"category": "GraphProduct", "description": "Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases", "edge_count": 500958, "id": "pharmkg.graph", "name": "PharmKG graph", "node_count": 7603, "original_source": ["omim", "drugbank", "pharmgkb", "ttd", "sider", "humannet", "ncbigene", "mesh", "pubchem", "gnbr", "biogps", "connectivitymap"], "product_url": "https://zenodo.org/record/4077338", "secondary_source": ["pharmkg"]}, {"category": "Product", "description": "Gene expression data aggregated from GTEx, BioGPS, Bgee and other expression databases", "format": "http", "id": "genecards.expression.data", "name": "GeneCards Expression Data", "original_source": ["gtex", "biogps", "bgee"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 403 error when accessing file"]}]
raw_data: {"activity_status": "active", "category": "Aggregator", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "http://biogps.org/about/"}], "label": "BioGPS / The Scripps Research Institute"}], "creation_date": "2025-08-12T00:00:00Z", "description": "BioGPS is an extensible and customizable gene annotation portal that aggregates gene-centric data (expression profiles, functional annotations, pathways, interactions, ontologies) from numerous external resources using a community-driven plugin system. It enables interactive expression visualization across tissues/cell types and provides programmatic and bulk access to underlying annotation tables.", "domains": ["genomics", "biomedical", "biological systems"], "homepage_url": "http://biogps.org/", "id": "biogps", "last_modified_date": "2025-09-10T00:00:00Z", "layout": "resource_detail", "name": "BioGPS", "products": [{"category": "GraphicalInterface", "description": "Main BioGPS web portal with searchable gene pages, expression charts, and plugin system aggregating external annotations", "format": "http", "id": "biogps.portal", "name": "BioGPS Portal", "product_url": "http://biogps.org/"}, {"category": "ProgrammingInterface", "description": "REST-style API for retrieving gene annotations and expression data (JSON/TSV responses)", "format": "http", "id": "biogps.api", "name": "BioGPS API", "product_url": "http://biogps.org/api/"}, {"category": "Product", "description": "Bulk annotation and expression data downloads (gene expression compendia, annotation tables)", "format": "http", "id": "biogps.downloads", "name": "BioGPS Downloads", "product_url": "http://biogps.org/downloads/"}, {"category": "DocumentationProduct", "description": "FAQ and usage guidance including plugin system overview and data interpretation notes", "format": "http", "id": "biogps.faq", "name": "BioGPS FAQ / Help", "product_url": "http://biogps.org/faq/"}, {"category": "GraphProduct", "description": "Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases", "edge_count": 500958, "id": "pharmkg.graph", "name": "PharmKG graph", "node_count": 7603, "original_source": ["omim", "drugbank", "pharmgkb", "ttd", "sider", "humannet", "ncbigene", "mesh", "pubchem", "gnbr", "biogps", "connectivitymap"], "product_url": "https://zenodo.org/record/4077338", "secondary_source": ["pharmkg"]}, {"category": "Product", "description": "Gene expression data aggregated from GTEx, BioGPS, Bgee and other expression databases", "format": "http", "id": "genecards.expression.data", "name": "GeneCards Expression Data", "original_source": ["gtex", "biogps", "bgee"], "product_url": "https://www.genecards.org/", "warnings": ["File was not able to be retrieved when checked on 2025-10-21_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-15_ HTTP 403 error when accessing file", "File was not able to be retrieved when checked on 2025-10-21: HTTP 403 error when accessing file"]}], "publications": [{"authors": ["Wu C", "Orozco C", "Boyer J", "Leglise M", "Goodale J", "Batalov S", "Hodge CL", "Haase J", "Janes J", "Huss JW 3rd", "Su AI"], "doi": "10.1186/gb-2009-10-11-r130", "id": "doi:10.1186/gb-2009-10-11-r130", "journal": "Genome Biology", "title": "BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources", "year": "2009"}]}