NIAID Data Ecosystem KG
The nde (NIAID Data Ecosystem) KG contains infectious and immune-mediated disease datasets. These include datasets from NIAID-funded repositories as well as globally-relevant infectious and immune-mediated disease (IID) repositories from NIH and beyond. The datasets include -omics data, clinical data, epidemiological data, pathogen-host interaction data, flow cytometry, and imaging.
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{"activity_status": "active", "category": "KnowledgeGraph", "collection": ["okn"], "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "asu@scripps.edu"}, {"contact_type": "github", "value": "andrewsu"}], "label": "Andrew Su"}, {"category": "Individual", "contact_details": [{"contact_type": "email", "value": "plwhetzel@gmail.com"}, {"contact_type": "github", "value": "twhetzel"}], "label": "Trish Whetzel"}], "creation_date": "2025-12-08T00:00:00Z", "description": "The nde (NIAID Data Ecosystem) KG contains infectious and immune-mediated disease datasets. These include datasets from NIAID-funded repositories as well as globally-relevant infectious and immune-mediated disease (IID) repositories from NIH and beyond. The datasets include -omics data, clinical data, epidemiological data, pathogen-host interaction data, flow cytometry, and imaging.", "domains": ["biomedical", "immunology"], "evaluation_page": "resource/nde/nde_eval_automated.html", "homepage_url": "https://data.niaid.nih.gov/", "id": "nde", "last_modified_date": "2026-07-02T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://opensource.org/licenses/Apache-2.0", "label": "Apache-2.0"}, "name": "NIAID Data Ecosystem KG", "products": [{"category": "ProgrammingInterface", "description": "SPARQL endpoint for NIAID Data Ecosystem KG", "format": "http", "id": "nde.sparql", "name": "NIAID Data Ecosystem KG SPARQL", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "nde"}], "product_url": "https://apps.okn.us/nde/sparql"}, {"category": "ProgrammingInterface", "description": "Triple Pattern Fragments endpoint for NIAID Data Ecosystem KG", "format": "http", "id": "nde.tpf", "name": "NIAID Data Ecosystem KG TPF", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "nde"}], "product_url": "https://apps.okn.us/ldf/nde"}, {"category": "GraphProduct", "description": "RDF (Turtle) knowledge graph of the NIAID Data Ecosystem, harmonizing dataset and computational-tool metadata harvested from NIAID-funded and globally-relevant infectious and immune-mediated disease repositories. Served through the Proto-OKN FRINK federated SPARQL platform.", "format": "ttl", "id": "nde.graph", "name": "NIAID Data Ecosystem KG (graph)", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "nde"}, {"relation_type": "prov:hadPrimarySource", "source": "immport"}, {"relation_type": "prov:hadPrimarySource", "source": "vdjserver"}], "product_url": "https://frink.apps.renci.org/nde", "secondary_source": [{"relation_type": "prov:wasInfluencedBy", "source": "gene-expression-omnibus"}, {"relation_type": "prov:wasInfluencedBy", "source": "sra"}, {"relation_type": "prov:wasInfluencedBy", "source": "omicsdi"}, {"relation_type": "prov:wasInfluencedBy", "source": "hubmap"}, {"relation_type": "prov:wasInfluencedBy", "source": "massive"}, {"relation_type": "prov:wasInfluencedBy", "source": "pdb"}, {"relation_type": "prov:wasInfluencedBy", "source": "lincs"}]}], "publications": [{"authors": ["Ginger Tsueng", "Emily Bullen", "Candice Czech", "Dylan Welzel", "Leandro Collares", "Jason Lin", "Everaldo Rodolpho", "Zubair Qazi", "Nichollette Acosta", "Lisa M. Mayer", "Sudha Venkatachari", "Zorana Mitrovi\u0107 Vu\u010di\u010devi\u0107", "Poromendro N. Burman", "Deepti Jain", "Jack DiGiovanna", "Maria Giovanni", "Asiyah Lin", "Wilbert Van Panhuis", "Laura D. Hughes", "Andrew I. Su", "Chunlei Wu"], "doi": "10.48550/arXiv.2509.13524", "id": "https://doi.org/10.48550/arXiv.2509.13524", "journal": "arXiv", "preferred": true, "title": "The NIAID Discovery Portal: A Unified Search Engine for Infectious and Immune-Mediated Disease Datasets", "year": "2025"}], "repository": "https://github.com/NIAID-Data-Ecosystem/nde-crawlers", "taxon": ["NCBITaxon:9606"]}