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_config.yml
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name: KG-Registry
title: The Knowledge Graph Registry
markdown: kramdown
highlighter: rouge
url: https://kghub.org
baseurl: /kg-registry
imgurl: /images
repo: https://github.com/Knowledge-Graph-Hub/kg-registry
repo_src: https://github.com/Knowledge-Graph-Hub/kg-registry/blob/main/
author:
name: KG-Hub, a team based at the Lawrence Berkeley National Laboratory
plugins:
- jekyll-sitemap
- jekyll-feed
feed:
disable_in_development: true
## --Anything above this line can be edited in _config_header.yml --
## --Everything below this line automatically generated in _config.yml --
resources:
- activity_status: active
category: Aggregator
contacts:
- category: Individual
email: [email protected]
github: YaphetKG
label: Yaphet Kebede
orcid: 0000-0002-5046-0246
description: A Translator Knowledge Provider offering multiple sub-graphs in KGX
format.
domain: health
id: automat
layout: resource_detail
name: Automat
products:
- category: GraphProduct
description: Robokop KG (Automat)
id: robokopkg
is_kgx: true
name: robokopkg
url: https://stars.renci.org/var/plater/bl-3.1.2/RobokopKG/latest/kgx_files
- category: GraphProduct
description: Robokop Plus
id: robokopplus
is_kgx: true
name: robokopplus
url: https://stars.renci.org/var/plater/bl-3.1.2/RobokopPlus/latest/kgx_files
- category: GraphProduct
description: Biolink Automat
id: biolink_automat
is_kgx: true
name: biolink_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/Biolink_Automat/latest/kgx_files
- category: GraphProduct
description: CTD Automat
id: ctd_automat
infores_id: automat-ctd
is_kgx: true
name: ctd_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/CTD_Automat/latest/kgx_files
- category: GraphProduct
description: DrugCentral Automat
id: drugcentral_automat
infores_id: automat-drug-central
is_kgx: true
name: drugcentral_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/DrugCentral_Automat/latest/kgx_files
- category: GraphProduct
description: GTEx Automat
id: gtex_automat
infores_id: automat-gtex
is_kgx: true
name: gtex_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/GTEx_Automat/latest/kgx_files
- category: GraphProduct
description: GtoPdb Automat
id: gtopdb_automat
infores_id: automat-gtopdb
is_kgx: true
name: gtopdb_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/GtoPdb_Automat/latest/kgx_files
- category: GraphProduct
description: GWASCatalog Automat
id: gwascatalog_automat
infores_id: automat-gwas-catalog
is_kgx: true
name: gwascatalog_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/GWASCatalog_Automat/latest/kgx_files
- category: GraphProduct
description: Hetio Automat
id: hetio_automat
is_kgx: true
name: hetio_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/Hetio_Automat/latest/kgx_files
- category: GraphProduct
description: HGNC Automat
id: hgnc_automat
infores_id: automat-hgnc
is_kgx: true
name: hgnc_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/HGNC_Automat/latest/kgx_files
- category: GraphProduct
description: HMDB Automat
id: hmdb_automat
infores_id: automat-hmdb
is_kgx: true
name: hmdb_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/HMDB_Automat/latest/kgx_files
- category: GraphProduct
description: HumanGOA Automat
id: humangoa_automat
infores_id: automat-human-goa
is_kgx: true
name: humangoa_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/HumanGOA_Automat/latest/kgx_files
- category: GraphProduct
description: IntAct Automat
id: intact_automat
infores_id: automat-intact
is_kgx: true
name: intact_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/IntAct_Automat/latest/kgx_files
- category: GraphProduct
description: OntologicalHierarchy Automat
id: ontologicalhierarchy_automat
is_kgx: true
name: ontologicalhierarchy_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/OntologicalHierarchy_Automat/latest/kgx_files
- category: GraphProduct
description: PANTHER Automat
id: panther_automat
infores_id: automat-panther
is_kgx: true
name: panther_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/PANTHER_Automat/latest/kgx_files
- category: GraphProduct
description: PHAROS Automat
id: pharos_automat
infores_id: automat-pharos
is_kgx: true
name: pharos_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/PHAROS_Automat/latest/kgx_files
- category: GraphProduct
description: STRING-DB Automat
id: stringdb_automat
is_kgx: true
name: stringdb_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/STRING-DB_Automat/latest/kgx_files
- category: GraphProduct
description: UberGraph Automat
id: ubergraph_automat
is_kgx: true
name: ubergraph_automat
url: https://stars.renci.org/var/plater/bl-3.1.2/UberGraph_Automat/latest/kgx_files
repository: ''
url: https://robokop.renci.org/api-docs/docs/category/automat
- activity_status: active
category: DataModel
contacts:
- category: Individual
email: [email protected]
github: sierra-moxon
label: Sierra Taylor Moxon
orcid: 0000-0002-8719-7760
description: Entity and association taxonomy and datamodel for life-sciences data
domain: upper
id: biolink
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: Biolink-Model
products:
- category: DataModelProduct
description: OWL release of Biolink-Model
id: biolink-model.owl.ttl
name: Biolink-Model OWL release
repository: https://github.com/biolink/biolink-model/
url: https://w3id.org/biolink/biolink-model.owl.ttl
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
label: Jim Balhoff
description: The “cam-kp” Exposures Knowledge Graph (in development).
domain: health
id: cam-kp
layout: resource_detail
name: Exposures KP (cam kp)
url: https://github.com/ExposuresProvider/cam-kp-api
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: jeevangelista
label: John Erol Evangelista
description: The Common Fund Data Ecosystem (CFDE) aims to facilitate better integration,
and reuse of Common Fund data to accelerate discoveries in biomedical research.
domain: health
id: cfde
layout: resource_detail
name: Data Distillery Knowledge Graph
url: https://dd-kg-ui.cfde.cloud/about
- activity_status: active
category: DataModel
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: Automatic translation of UCSC chromosome bands to OWL classes
domain: chemistry and biochemistry
id: chr
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: Monochrom Ontology
products:
- category: DataModelProduct
description: OWL release of Monochrom Ontology
id: chr.owl
name: Monochrom Ontology OWL release
repository: http://purl.obolibrary.org/obo/chr.owl
url: http://purl.obolibrary.org/obo/chr.owl
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Casey Ta
- category: Individual
label: Vincent Emonet
- category: Individual
label: Michel Dumontier
description: A Translator Knowledge Provider integrating clinical data.
domain: health
id: clinical-data-kp
layout: resource_detail
name: Clinical Data KP
url: https://ncats.nih.gov/research/research-activities/translator/projects
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Gregory Hyde
description: A Translator Knowledge Provider exploring connections hypotheses.
domain: health
id: connections-hypothesis-kp
layout: resource_detail
name: Connections Hypothesis KP
url: https://github.com/di2ag/chp_api
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: https://github.com/bioannidis
orcid: 0000-0002-8367-0733
description: Drug Repurposing Knowledge Graph (DRKG) is a comprehensive biological
knowledge graph relating genes, compounds, diseases, biological processes, side
effects and symptoms.
domain: health
id: drkg
layout: resource_detail
name: DRKG
repository: https://github.com/gnn4dr/DRKG
url: https://github.com/gnn4dr/DRKG
- activity_status: active
category: DataSource
contacts:
- category: Individual
email: [email protected]
github: cthoyt
label: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DrugBank
domain: health
id: drugbank
layout: resource_detail
name: drugbank
products:
- category: Product
description: OWL release of drugbank
id: drugbank.owl
name: drugbank OWL release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/drugbank/drugbank.owl
- category: Product
description: OBO release of drugbank
id: drugbank.obo
name: drugbank OBO release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/drugbank/drugbank.obo
- category: MappingProduct
description: SSSOM release of drugbank
id: drugbank.sssom
name: drugbank SSSOM release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/drugbank/drugbank.sssom
repository: https://github.com/biopragmatics/obo-db-ingest
url: https://biopragmatics.github.io/obo-db-ingest/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: diatomsRcool
label: Anne Thessen
description: A knowledge graph of plant traits starting with Planteome and EOL TraitBank.
domain: organisms
id: eco-kg
layout: resource_detail
name: eco-KG
repository: https://github.com/Knowledge-Graph-Hub/eco-kg
url: https://kghub.org/eco-kg/index.html
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: Ontology rendering of the EcoSIM Land System Model
domain: environment
id: ecosim
layout: resource_detail
name: ecosim
products:
- category: Product
description: OWL release of ecosim
id: ecosim.owl
name: ecosim OWL release
repository: http://purl.obolibrary.org/obo/ecosim.owl
url: http://purl.obolibrary.org/obo/ecosim.owl
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Jason Flannick
description: A Translator Knowledge Provider focusing on genetic data.
domain: health
id: genetics-kp
layout: resource_detail
name: Genetics KP
url: ''
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Chris Mungall
orcid: 0000-0002-6601-2165
description: Translation of JGI GOLD path terms to OWL
domain: environment
id: goldterms
layout: resource_detail
name: GOLD Environmental Paths
products:
- category: Product
id: goldterms.owl
name: main GOLDTERMS OWL release
url: https://w3id.org/goldterms/goldterms.owl
repository: https://github.com/cmungall/gold-ontology
url: https://gold.jgi.doe.gov/
- activity_status: active
category: DataSource
contacts:
- category: Individual
email: [email protected]
github: cthoyt
label: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: HUGO Gene Nomenclature Committee
domain: biological systems
fairsharing_id: FAIRsharing.amcv1e
id: hgnc
infores_id: hgnc
layout: resource_detail
name: hgnc
products:
- category: Product
description: OWL release of hgnc
id: hgnc.owl
name: hgnc OWL release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.owl
- category: Product
description: OBO release of hgnc
id: hgnc.obo
name: hgnc OBO release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.obo
- category: MappingProduct
description: SSSOM release of hgnc
id: hgnc.sssom
name: hgnc SSSOM release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.sssom
repository: https://github.com/biopragmatics/obo-db-ingest
url: https://biopragmatics.github.io/obo-db-ingest/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Katy Börner
description: The HRA Knowledge Graph (HRA KG) is a linked open data resource that
integrates anatomical structures, cell types, and biomarkers to support cross-scale
biological queries.
domain: health
id: hra-kg
layout: resource_detail
license:
id: http://creativecommons.org/licenses/by/4.0/
label: CC BY 4.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
name: Human Reference Atlas Knowledge Graph (HRA KG)
repository: https://github.com/hubmapconsortium/hra-kg
url: https://apps.humanatlas.io/dashboard/data
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
github: karafecho
label: Kara Fecho
orcid: 0000-0002-6704-9306
description: The ICEES-based Exposures Knowledge Graph.
domain: health
id: icees-kg
layout: resource_detail
name: Exposures KP (icees-kg)
products:
- category: GraphProduct
description: KGX distribution of the ICEES Exposures KP
id: icees_kgx_files
is_kgx: true
name: KGX distribution of the ICEES Exposures KP
url: https://stars.renci.org/var/plater/bl-2.1/icees_kgx_files/
repository: ''
url: ''
- activity_status: active
category: DataSource
contacts:
- category: Individual
email: [email protected]
github: cthoyt
label: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: InterPro is a database of protein families, domains and functional
sites in which identifiable features found in known proteins can be applied to
unknown protein sequences
domain: biological systems
id: interpro
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: InterPro
products:
- category: Product
description: OWL release of InterPro
id: interpro.owl
name: InterPro OWL release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/interpro/interpro.owl
- category: Product
description: OBO release of InterPro
id: interpro.obo
name: InterPro OBO release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/interpro/interpro.obo
- category: MappingProduct
description: SSSOM release of InterPro
id: interpro.sssom
name: InterPro SSSOM release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/interpro/interpro.sssom
repository: https://github.com/biopragmatics/obo-db-ingest
url: https://biopragmatics.github.io/obo-db-ingest/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: justaddcoffee
label: Justin Reese
description: A knowledge graph for COVID-19 and SARS-COV-2.
domain: organisms
id: kg-covid-19
layout: resource_detail
name: KG-COVID-19
products:
- category: GraphProduct
description: KGX nodes and edges for KG-COVID-19
id: kg-covid-19.kgx
is_kgx: true
name: KG-COVID-19 graph
url: https://kghub.io/kg-covid-19/
repository: https://github.com/Knowledge-Graph-Hub/kg-covid-19
url: https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: oolonek
label: Pierre-Marie Allard
description: Experimental natural products knowledge graph.
domain: organisms
id: kg-enp
layout: resource_detail
name: kg-enp
repository: https://github.com/enpkg/enpkg_full
url: https://enpkg.commons-lab.org/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
github: caufieldjh
label: J. Harry Caufield
orcid: 0000-0001-5705-7831
description: a Knowledge Graph for Illuminating the Druggable Genome
domain: health
id: kg-idg
layout: resource_detail
name: KG-IDG
products:
- category: GraphProduct
description: KGX Distribution of KG-IDG
id: kg-idg.tar.gz
is_kgx: true
name: KGX Distribution of KG-IDG
url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-microbe.tar.gz
repository: https://github.com/Knowledge-Graph-Hub/kg-idg
url: https://kghub.org/kg-idg/index.html
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: A Knowledge Graph about microbes
domain: organisms
id: kg-microbe
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: KG Microbe
products:
- category: GraphProduct
description: KGX Distribution of KGM
id: kg-microbe.tar.gz
is_kgx: true
name: KGX Distribution of KGM
url: https://kg-hub.berkeleybop.io/kg-microbe/current/kg-microbe.tar.gz
repository: https://github.com/Knowledge-Graph-Hub/kg-microbe
url: https://kghub.org/kg-microbe/index.html
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: Monarch Initiative Knowledge Graph
domain: health
id: kg-monarch
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: KG Monarch
products:
- category: GraphProduct
description: KGX Distribution of KGM
id: kg-monarch.tar.gz
is_kgx: true
name: KGX Distribution of KGM
url: https://kg-hub.berkeleybop.io/kg-monarch/current/kg-monarch.tar.gz
repository: https://github.com/monarch-initiative/monarch-ingest
url: https://kghub.org/kg-monarch/index.html
- activity_status: active
category: DataModel
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: A data model for describing change operations at a high level on an
ontology or ontology-like artefact, such as a Knowledge Graph
domain: other
id: kgcl
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: Knowledge Graph Change Language
products:
- category: DataModelProduct
description: OWL release of Knowledge Graph Change Language
id: kgcl.owl
name: Knowledge Graph Change Language OWL release
- category: DataModelProduct
description: OBO release of Knowledge Graph Change Language
id: kgcl.obo
name: Knowledge Graph Change Language OBO release
repository: https://github.com/INCATools/kgcl/
url: https://w3id.org/kgcl
- activity_status: active
category: DataModel
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: mixs
domain: environment
id: mixs
layout: resource_detail
name: mixs
products:
- category: DataModelProduct
description: OWL release of mixs
id: mixs.owl
name: mixs OWL release
- category: DataModelProduct
description: OBO release of mixs
id: mixs.obo
name: mixs OBO release
repository: https://w3id.org/mixs
url: https://w3id.org/mixs
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Sandrine Muller
orcid: 0000-0001-5998-3003
description: A Translator Knowledge Provider for molecular data.
domain: health
id: molecular-data-kp
layout: resource_detail
name: Molecular Data KP
products:
- category: GraphProduct
description: KGX nodes for Molecular Data KP
id: nodes.tsv
is_kgx: true
name: Nodes for Molecular Data KP
url: https://molepro.s3.amazonaws.com/nodes.tsv
- category: GraphProduct
description: KGX edges for Molecular Data KP
id: edges.tsv
is_kgx: true
name: Edges for Molecular Data KP
url: https://molepro.s3.amazonaws.com/edges.tsv
repository: ''
url: ''
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Gustavo Glusman
- category: Individual
label: Guangrong Qin
description: A Translator Knowledge Provider incorporating multiomics data.
domain: health
id: multiomics-kp
layout: resource_detail
name: Multiomics KP
repository: ''
url: ''
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: Noctua Entity Ontology
domain: biological systems
id: neo
layout: resource_detail
name: neo
products:
- category: Product
description: OWL release of neo
id: neo.owl
name: neo OWL release
repository: https://github.com/geneontology/neo/
url: http://purl.obolibrary.org/obo/go/noctua/neo.owl
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Jim Balhoff
description: A Translator Knowledge Provider dedicated to ontology-based services.
domain: other
id: ontology-kp
layout: resource_detail
name: Ontology KP
repository: ''
url: ''
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: cthoyt
label: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ORCID in OWL
domain: other
id: orcid
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: ORCID
products:
- category: Product
description: OWL release of ORCID in OWL
id: orcidio.owl
name: ORCID in OWL OWL release
- category: Product
description: OBO release of ORCID in OWL
id: orcidio.obo
name: ORCID in OWL OBO release
repository: https://github.com/cthoyt/orcidio
url: https://github.com/cthoyt/orcidio
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
label: Deanne M. Taylor
description: Petagraph is a large-scale biomedical knowledge graph integrating multi-omics
and clinical data, built on the Unified Biomedical Knowledge Graph (UBKG).
domain: health
id: petagraph
layout: resource_detail
license:
id: https://www.nlm.nih.gov/databases/umls.html
label: UMLS
name: Petagraph
products:
- category: GraphProduct
description: A multi-omics biomedical knowledge graph
id: petagraph
name: Petagraph Knowledge Graph (Neo4J)
url: https://ubkg-downloads.xconsortia.org/
repository: https://github.com/TaylorResearchLab/Petagraph
url: https://github.com/TaylorResearchLab/Petagraph
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: https://github.com/callahantiff/
label: Tiffany Callahan
description: PheKnowLator (Phenotype Knowledge Translator) or pkt_kg is the first
fully customizable knowledge graph (KG) construction framework enabling users
to build complex KGs that are Semantic Web compliant and amenable to automatic
Web Ontology Language (OWL) reasoning, generate contemporary property graphs,
and are importable by today’s popular graph toolkits.
domain: organisms
id: pheknowlator
layout: resource_detail
name: PheKnowLator
repository: https://github.com/callahantiff/PheKnowLator
url: https://github.com/callahantiff/PheKnowLator
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: caufieldjh
label: J. Harry Caufield
description: An ontology for accessing and comparing knowledge concerning phenotypes
across species and genetic backgrounds.
domain: phenotype
id: phenio
layout: resource_detail
license:
id: https://creativecommons.org/publicdomain/zero/1.0/
label: CC0 1.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
name: An integrated ontology for Phenomics
products:
- category: Product
description: OWL version of phenio
id: phenio.owl
name: phenio
url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl
- biolink_compatibility:
is_compatible: true
produced_by:
category: ProcessProduct
id: phenio.kgx.repo
name: Process for producing KG-Phenio
url: https://github.com/Knowledge-Graph-Hub/kg-phenio
version: 4.2.5
category: GraphProduct
description: KGX version of phenio
id: phenio.kgx
is_kgx: true
name: phenio KG
url: https://kg-hub.berkeleybop.io/kg-phenio/20241203/kg-phenio.tar.gz
repository: https://github.com/monarch-initiative/phenio
url: https://github.com/obophenotype/phenio
usages:
- description: PHENIO is used by the Monarch Initiative for cross-species inference.
As an example, the disease of Parkinsonism may compared on the basis of its
phenotype in humans vs. mouse genes and genotypes known to impact these phenotypes.
id: cross-species-inference
label: PHENIO is used by the Monarch Initiative for cross-species inference
publications:
- doi: doi:10.1093/nar/gkw1128
id: doi:10.1093/nar/gkw1128
preferred: true
title: 'The Monarch Initiative: an integrative data and analytic platform connecting
phenotypes to genotypes across species'
type: actual
url: https://monarchinitiative.org/HP:0001300#disease
users:
- category: Organization
label: The Monarch Initiative
url: https://monarchinitiative.org/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
github: marinkaz
label: Marinka Zitnik
description: PrimeKG (Precision Medicine Knowledge Graph) integrates 20 high-quality
biomedical resources to describe 17,080 diseases with over 4 million relationships
across ten major biological scales.
domain: health
id: primekg
layout: resource_detail
license:
id: https://opensource.org/licenses/MIT
label: MIT License
name: PrimeKG
products:
- category: GraphProduct
description: The full PrimeKG dataset containing disease relationships.
id: primekg.csv
name: PrimeKG Full Dataset
url: https://dataverse.harvard.edu/api/access/datafile/6180620
repository: https://github.com/mims-harvard/PrimeKG
url: https://zitniklab.hms.harvard.edu/projects/PrimeKG
- activity_status: active
category: Resource
contacts:
- category: Individual
email: [email protected]
github: goodb
label: Benjamin M. Good
orcid: 0000-0002-7334-7852
description: Representation of entities in Reactome
domain: biological systems
id: reacto
layout: resource_detail
name: Reactome Entity Ontology (REACTO)
products:
- category: Product
description: OWL release of Reactome Entity Ontology (REACTO)
id: reacto.owl
name: Reactome Entity Ontology (REACTO) OWL release
- category: Product
description: OBO release of Reactome Entity Ontology (REACTO)
id: reacto.obo
name: Reactome Entity Ontology (REACTO) OBO release
repository: http://purl.obolibrary.org/obo/go/extensions/reacto.owl
url: http://purl.obolibrary.org/obo/go/extensions/reacto.owl
- activity_status: active
category: DataSource
contacts:
- category: Individual
email: [email protected]
github: cmungall
label: Christopher J. Mungall
orcid: 0000-0002-6601-2165
description: Reactome from Biopax
domain: biological systems
id: reactome
layout: resource_detail
name: Reactome
products:
- category: Product
description: Conversion from BioPAX, human subset
id: reactome-hs-biopax.db.gz
name: Reactome Human from BioPAX, sqlite
url: https://s3.amazonaws.com/bbop-sqlite/reactome-hs.db.gz
- category: Product
description: Biopragmatics provided conversion, human subset
id: reactome-hs-biopragmatics.obo
name: Reactome Human, Biopragmatics
url: https://w3id.org/biopragmatics/resources/reactome/reactome.obo
repository: https://github.com/biopragmatics/obo-db-ingest
url: https://reactome.org
- activity_status: active
category: DataSource
contacts:
- category: Individual
email: [email protected]
github: cthoyt
label: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Rhea is an expert-curated knowledgebase of chemical and transport reactions
of biological interest
domain: chemistry and biochemistry
id: rhea
layout: resource_detail
license:
id: https://creativecommons.org/licenses/by/4.0/
label: CC BY 4.0
logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
name: Rhea, the Annotated Reactions Database
products:
- category: Product
description: OWL release of Rhea, the Annotated Reactions Database
id: rhea.owl
name: Rhea, the Annotated Reactions Database OWL release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl
- category: Product
description: OBO release of Rhea, the Annotated Reactions Database
id: rhea.obo
name: Rhea, the Annotated Reactions Database OBO release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/rhea/rhea.obo
- category: Product
description: SSSOM release of Rhea, the Annotated Reactions Database
id: rhea.sssom
name: Rhea, the Annotated Reactions Database SSSOM release
tags:
- biopragmatics
url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom
repository: https://github.com/biopragmatics/obo-db-ingest
url: https://biopragmatics.github.io/obo-db-ingest/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
github: emanuelecavalleri
label: Emanuele Cavalleri
description: An ontology-based KG for representing interactions involving RNA molecules.
domain: organisms
id: rna-kg
layout: resource_detail
name: RNA-KG
repository: https://github.com/AnacletoLAB/RNA-KG
url: RNA-KG.anacleto.di.unimi.it/
- activity_status: active
category: KnowledgeGraph
contacts:
- category: Individual
email: [email protected]
label: Karamarie Fecho
description: ROBOKOP (Reasoning Over Biomedical Objects linked in Knowledge Oriented
Pathways) is an open-source biomedical knowledge graph system that enables complex
queries over a large-scale integrated knowledge graph.
domain: health
id: robokop
layout: resource_detail
license:
id: https://opensource.org/licenses/MIT
label: MIT License
name: ROBOKOP
products:
- category: Product
description: A biomedical knowledge graph containing ~10 million nodes and ~250
million edges from ~30 biological data sources and bio-ontologies.
id: robokopkg
name: ROBOKOP Knowledge Graph (KG)