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resources.yaml
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id: https://monarchinitiative.org/registry
name: Monarch Tool, Standard and Data Registry
description: |
The Monarch Tool, Standard and Data Registry aims to provide a centralised view of
the diverse ecosystem of tools, data and standards that Monarch supports.
data:
- id: http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
download:
- url: http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
release_status: public
file_format: tsv
category: Biomedical Data
documentation: https://hpo-annotation-qc.readthedocs.io/en/latest/annotationFormat.html#phenotype-hpoa-format
name: HPOA - Disease Annotations
monarch_contribution: Lead
monarch_role: Core
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt
download:
- url: http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt
release_status: public
file_format: tsv
category: Biomedical Data
documentation: https://hpo.jax.org/app/download/annotation
name: HPOA - Phenotype to Gene Associations
monarch_contribution: Lead
monarch_role: Core
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt
download:
- url: http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt
release_status: public
file_format: tsv
category: Biomedical Data
documentation: https://hpo.jax.org/app/download/annotation
name: HPOA - Gene to Phenotype Associations
monarch_contribution: Lead
monarch_role: Core
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://data.monarchinitiative.org/monarch-kg/hpoa
download:
- url: https://data.monarchinitiative.org/monarch-kg-dev/latest/rdf/hpoa_disease_phenotype.nt.gz
release_status: development snapshot
file_format: nt.gz
category: Knowledge Graph Ingestibles
documentation: https://monarch-initiative.github.io/monarch-ingest/Sources/HPOA/
name: HPOA Knowledge Graph Ingestible
monarch_role: Core
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://data.monarchinitiative.org/monarch-kg/alliance
download:
- url: https://data.monarchinitiative.org/monarch-kg-dev/latest/rdf/alliance.nt.gz
release_status: development snapshot
file_format: nt.gz
category: Knowledge Graph Ingestibles
documentation: https://monarch-initiative.github.io/monarch-ingest/Sources/Alliance/
name: Alliance Knowledge Graph Ingestible
monarch_contribution: Lead
monarch_role: Core
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/Knowledge-Graph-Hub/kg-covid-19
name: KG Covid-19
monarch_contribution: Lead
category: Knowledge Graph
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/eco-kg
name: ECO KG
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/kg-idg
name: KG IDG
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/kg-phenio
name: KG Phenio
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Core
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/kg-obo
name: KG OBO
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/kg-microbe
name: KG Microbe
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/Knowledge-Graph-Hub/sri-reference-kg
name: SRI Reference KG
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://monarch-initiative.github.io/monarch-ingest
name: Monarch KG
category: Knowledge Graph
monarch_contribution: Lead
monarch_role: Core
icon: resource-monarch
url: https://monarch-initiative.github.io/monarch-ingest
description: Monarch's Knowledge Graph integrates resources from a wide
variety of sources to provide a comprehensive view of the relationships between genes,
diseases, phenotypes, and other biomedical entities.
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
standards:
- id: http://phenopackets.org/
name: Phenopackets
monarch_contribution: Lead
category: Data Exchange
documentation: https://phenopacket-schema.readthedocs.io/en/latest/
url: http://phenopackets.org/
icon: resource-phenopackets
grants:
- Phenomics First
monarch_role: Foundational
description: An ISO-endorsed open standard for sharing disease and phenotype information.
repository: https://github.com/phenopackets/phenopacket-schema
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://standards.monarchinitiative.org/sssom
name: Simple Standard for Ontology Mappings (SSSOM)
short_name: SSSOM
monarch_contribution: Lead
documentation: https://mapping-commons.github.io/sssom/spec/
url: https://mapping-commons.github.io/sssom/spec/
description: A simple metadata standard for describing semantic mappings.
repository: https://github.com/mapping-commons/sssom/
icon: resource-sssom
project_boards:
- name: SSSOM Toolkit
id: "https://github.com/orgs/mapping-commons/projects/4/views/1?groupedBy%5BcolumnId%5D=3008850&visibleFields=%5B%22Title%22%2C%22Assignees%22%2C%22Status%22%2C3008850%2C%22Linked+Pull+Requests%22%2C%22Milestone%22%2C%22Labels%22%5D"
- name: SSSOM Model
id: "https://github.com/orgs/mapping-commons/projects/3/views/1?visibleFields=%5B%22Title%22%2C%22Assignees%22%2C%22Status%22%2C%22Milestone%22%2C3005838%5D&groupedBy%5BcolumnId%5D=3005838"
category: Data Exchange
grants:
- Phenomics First
monarch_role: Core
citation: https://doi.org/10.1093/database/baac035
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: http://purl.obolibrary.org/obo/hp.owl
name: Human Phenotype Ontology
short_name: HPO
icon: resource-hpo
monarch_contribution: Lead
category: Ontology
monarch_role: Foundational
documentation: https://obophenotype.github.io/human-phenotype-ontology/
description: Provides a standardized vocabulary of phenotypic abnormalities in human disease.
repository: https://github.com/obophenotype/human-phenotype-ontology
url: https://hpo.jax.org/app/
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
grants:
- HPO
- Phenomics First
- id: https://github.com/geneontology/obographs
documentation: https://incatools.github.io/ontology-access-kit/datamodels/obograph/index.html
url: https://github.com/geneontology/obographs
name: obographs
monarch_contribution: Lead
category: Data Exchange
monarch_role: Support
description: The obographs ontology format aims and providing a simple graph-oriented JSON format for ontologies.
repository: https://github.com/geneontology/obographs
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Phenomics First
- id: http://purl.obolibrary.org/obo/mondo.owl
documentation: https://mondo.readthedocs.io/en/latest/
url: https://mondo.monarchinitiative.org/
name: Mondo Disease Ontology
short_name: Mondo
icon: resource-mondo
monarch_contribution: Lead
category: Ontology
monarch_role: Foundational
description: Aims to harmonize disease definitions across the world.
repository: https://github.com/monarch-initiative/mondo
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Phenomics First
- id: http://purl.obolibrary.org/obo/geno.owl
documentation: https://github.com/monarch-initiative/GENO-ontology
url: https://github.com/monarch-initiative/GENO-ontology
name: Genotype Ontology
short_name: GENO
monarch_contribution: Lead
category: Ontology
monarch_role: Core
description: An ontology that represents the levels of genetic variation specified in genotypes.
repository: https://github.com/monarch-initiative/GENO-ontology
contact:
name: Matt Brush
email: [email protected]
orcid: https://orcid.org/0000-0002-1048-5019
github: "@mbrush"
grants:
- Monarch R24
- id: http://purl.obolibrary.org/obo/sepio.owl
documentation: https://github.com/monarch-initiative/SEPIO-ontology
url: https://github.com/monarch-initiative/SEPIO-ontology
name: Scientific Evidence and Provenance Information Ontology
short_name: SEPIO
monarch_contribution: Lead
category: Ontology
monarch_role: Core
description: An ontology that supports the description of evidence and provenance information for scientific claims.
repository: https://github.com/monarch-initiative/SEPIO-ontology
contact:
name: Matt Brush
email: [email protected]
orcid: https://orcid.org/0000-0002-1048-5019
github: "@mbrush"
grants:
- Monarch R24
- id: http://purl.obolibrary.org/obo/vbo.owl
documentation: https://github.com/monarch-initiative/vertebrate-breed-ontology
url: https://github.com/monarch-initiative/vertebrate-breed-ontology
name: Vertebrate Breed Ontology
short_name: VBO
monarch_contribution: Lead
category: Ontology
monarch_role: Core
description: An ontology created to serve as a single computable resource for vertebrate breed names.
repository: https://github.com/monarch-initiative/vertebrate-breed-ontology
contact:
name: Sabrina Toro
email: [email protected]
orcid: https://orcid.org/0000-0002-4142-7153
github: "@sabrinatoro"
grants:
- Monarch R24
- id: https://github.com/obophenotype/upheno
name: The Unified Phenotype Ontology (uPheno)
short_name: uPheno
monarch_contribution: Lead
category: Ontology
monarch_role: Core
icon: resource-upheno
url: https://obophenotype.github.io/upheno/
documentation: https://obophenotype.github.io/upheno/
description: Aims to unify the annotation of phenotypes across species.
repository: https://obophenotype.github.io/upheno/
project_boards:
- name: uPheno 2 Ontology Development
id: "https://github.com/orgs/obophenotype/projects/15/views/1?visibleFields=%5B%22Title%22%2C%22Assignees%22%2C13049768%5D&groupedBy%5BcolumnId%5D=13049768"
contact:
name: James McLaughlin
email: [email protected]
orcid: https://orcid.org/0000-0002-8361-2795
github: "@udp"
grants:
- Phenomics First
- id: http://purl.obolibrary.org/obo/maxo.owl
name: Medical Action Ontology
monarch_contribution: Lead
category: Ontology
documentation: https://github.com/monarch-initiative/MAxO
monarch_role: Core
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
grants:
- HPO
- id: http://purl.obolibrary.org/obo/oba.owl
name: Ontology of Biological Attributes
monarch_contribution: Lead
category: Ontology
documentation: https://obophenotype.github.io/upheno/
project_boards:
- name: OBA Ontology Development (uPheno board)
id: "https://github.com/orgs/obophenotype/projects/15/views/1?visibleFields=%5B%22Title%22%2C%22Assignees%22%2C13049768%5D&groupedBy%5BcolumnId%5D=13049768"
monarch_role: Core
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Phenomics First
- id: http://purl.obolibrary.org/obo/uberon.owl
name: Uberon Anatomy Ontology
description: An integrated cross-species anatomy ontology.
monarch_contribution: Co-Lead
category: Ontology
monarch_role: Foundational
icon: resource-uberon
url: https://obophenotype.github.io/uberon/
documentation: https://obophenotype.github.io/uberon/
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Phenomics First
- id: https://github.com/monarch-initiative/phenio
name: Phenomics Integrated Ontology (PHENIO)
monarch_contribution: Lead
category: Ontology
monarch_role: Core
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Monarch R24
- id: http://purl.obolibrary.org/obo/ecto.owl
documentation: https://github.com/EnvironmentOntology/environmental-exposure-ontology
name: Environmental Exposure Ontology
monarch_contribution: Lead
category: Ontology
monarch_role: Support
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- TBD
- id: https://github.com/INCATools/dead_simple_owl_design_patterns
name: Dead simple owl design pattern (DOS-DP) exchange format
monarch_contribution: Lead
category: Data Exchange
documentation: https://incatools.github.io/dead_simple_owl_design_patterns/
monarch_role: Support
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
grants:
- Phenomics First
- id: https://github.com/INCATools/kgcl
name: Knowledge Graph Change Language
monarch_contribution: Lead
category: Ontology Curation
documentation: https://incatools.github.io/kgcl/
grants:
- Bosch Gift
monarch_role: Community
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/monarch-initiative/babelon
name: Babelon - A simple standard for managing ontology translations and language profiles
category: Data Exchange
documentation: https://monarch-initiative.github.io/babelon/
monarch_contribution: Lead
monarch_role: Support
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
repository: https://github.com/monarch-initiative/babelon
grants:
- HPO
tools:
- id: https://tools.monarchinitiative.org/exomiser
name: Exomiser
monarch_contribution: Lead
category: Clinical Diagnosis
monarch_role: Foundational
icon: resource-exomiser
url: https://exomiser.monarchinitiative.org/exomiser/
documentation: https://exomiser.readthedocs.io/en/latest/
description: A tool for finding potential disease-causing variants in whole-exome or whole-genome sequencing data.
repository: https://github.com/exomiser/Exomiser
contact:
name: Jules Jacobsen
email: [email protected]
orcid: https://orcid.org/0000-0002-3265-1591
github: "@julesjacobsen"
- id: https://monarchinitiative.org/
name: Monarch Knowledge Graph & Services
category: Clinical Diagnosis
icon: resource-monarch
url: https://monarchinitiative.org/
description: Integrates gene, disease, and phenotype data across species.
repository: https://github.com/monarch-initiative/monarch-app
monarch_contribution: Lead
monarch_role: Foundational
documentation: https://monarch-initiative.github.io/monarch-ingest/
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://monarch-app.monarchinitiative.org/
name: Monarch App
category: Clinical Diagnosis
icon: resource-monarch
url: https://monarch-app.monarchinitiative.org/
description: A web application for exploring the Monarch Knowledge Graph.
repository: https://github.com/monarch-initiative/monarch-app
monarch_contribution: Lead
monarch_role: Core
documentation: https://monarch-app.monarchinitiative.org/
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: http://api-v3.monarchinitiative.org
name: Monarch API
category: Clinical Diagnosis
url: https://monarch-app.monarchinitiative.org/
description: The Monarch API is used to access information from the Monarch Knowledge Graph programmatically.
repository: https://github.com/monarch-initiative/monarch-app
monarch_contribution: Lead
monarch_role: Core
documentation: https://monarch-app.monarchinitiative.org/
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://tools.monarchinitiative.org/odk
name: Ontology Development Kit (ODK)
category: Ontology Maintenance
description: A toolkit and workflow system for managing the ontology life-cycle.
monarch_contribution: Lead
monarch_role: Support
documentation: https://github.com/INCATools/ontology-development-kit
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
project_boards:
- name: ODK Milestones
id: "https://github.com/orgs/INCATools/projects/2/views/1?groupedBy%5BcolumnId%5D=Milestone"
- id: https://tools.monarchinitiative.org/oak
name: Ontology Access Kit (OAK)
short_name: OAK
category: Ontology Use
description: A python toolkit for accessing and visualising ontologies.
icon: resource-oak
url: https://github.com/INCATools/ontology-access-kit
monarch_contribution: Lead
monarch_role: Support
documentation: https://incatools.github.io/ontology-access-kit/
repository: https://github.com/INCATools/ontology-access-kit
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://tools.monarchinitiative.org/sssom-toolkit
name: SSSOM Toolkit
category: Mapping
description: A python toolkit for processing SSSOM mapping files.
monarch_contribution: Lead
documentation: https://mapping-commons.github.io/sssom-py
monarch_role: Support
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: https://tools.monarchinitiative.org/ols
url: https://ols.monarchinitiative.org/
name: Monarch Ontology Lookup Service
category: Ontology Use
description: An instance of EBI's OLS for hosting Monarch-specific development snapshots of ontologies.
monarch_contribution: Lead
monarch_role: Support
repository: https://github.com/monarch-initiative/ontotools-docker
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: https://tools.monarchinitiative.org/poet
url: https://poet.jax.org/
name: POET
category: Data Curation
monarch_role: Support
repository: https://github.com/TheJacksonLaboratory/POET
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://tools.monarchinitiative.org/lirical
name: LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL)
short_name: LIRICAL
category: Clinical Diagnosis
icon: lirical
url: https://thejacksonlaboratory.github.io/LIRICAL/stable/
description: LIkelihood Ratio Interpretation of Clinical AbnormaLities performs
phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics.
monarch_role: Core
documentation: https://lirical.readthedocs.io/en/latest/
repository: https://github.com/TheJacksonLaboratory/LIRICAL
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://github.com/monarch-initiative/pheval
name: PhEval
category: Benchmarking
documentation: https://monarch-initiative.github.io/pheval/
repository: https://github.com/monarch-initiative/pheval
monarch_role: Core
description: PhEval is a Python package for evaluating phenotype-powered variant prioritisation systems such as Exomiser.
contact:
name: Jules Jacobsen
email: [email protected]
orcid: https://orcid.org/0000-0002-3265-1591
github: "@julesjacobsen"
- id: https://github.com/INCATools/obographviz
name: obographviz
category: Ontology Use
documentation: https://github.com/INCATools/obographviz#readme
repository: https://github.com/INCATools/obographviz
monarch_role: Support
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/INCATools/ubergraph
name: ubergraph
category: Ontology Use
repository: https://github.com/INCATools/ubergraph
monarch_role: Support
contact:
name: Jim Balhoff
email: [email protected]
orcid: https://orcid.org/0000-0002-8688-6599
github: "@balhoff"
- id: https://github.com/balhoff/whelk
name: whelk
category: Ontology Use
repository: https://github.com/balhoff/whelk
monarch_role: Support
contact:
name: Jim Balhoff
email: [email protected]
orcid: https://orcid.org/0000-0002-8688-6599
github: "@balhoff"
- id: https://github.com/ontodev/robot
name: robot
category: Ontology Use
documentation: https://robot.obolibrary.org
monarch_contribution: Contributor
repository: https://github.com/ontodev/robot
monarch_role: Community
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: https://github.com/cidgoh/DataHarmonizer
name: Data Harmonizer
category: Data Curation
monarch_contribution: Contributor
monarch_role: Community
repository: https://github.com/cidgoh/DataHarmonizer
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/monarch-initiative/ontogpt
name: OntoGPT
category: Data Curation
documentation: https://monarch-initiative.github.io/ontogpt/
monarch_contribution: Lead
monarch_role: Core
icon: onto-gpt
url: https://github.com/monarch-initiative/ontogpt
repository: https://github.com/monarch-initiative/ontogpt
description: OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding.
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/monarch-initiative/talisman
name: TALISMAN
category: Data Curation
documentation: https://monarch-initiative.github.io/talisman/
monarch_contribution: Lead
monarch_role: Core
url: https://github.com/monarch-initiative/talisman/
repository: https://github.com/monarch-initiative/talisman/
description: TALISMAN is a Python package for summarizing gene set functions using large language models (LLMs).
contact:
name: Marcin Joachimiak
email: [email protected]
orcid: https://orcid.org/0000-0001-8175-045X
github: "@realmarcin"
- id: https://github.com/monarch-initiative/curate-gpt
name: CurateGPT
category: Data Curation
documentation: https://github.com/monarch-initiative/curate-gpt
monarch_contribution: Lead
monarch_role: Core
icon: curate-gpt
url: https://curategpt.io/
repository: https://github.com/monarch-initiative/curate-gpt
description: AI Assisted Ontology Curation.
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/monarch-initiative/semsimian
name: semsimian
category: Mapping
monarch_contribution: Lead
icon: semsimian
url: https://github.com/monarch-initiative/semsimian
description: Semantic Similarity in Rust.
monarch_role: Support
repository: https://github.com/monarch-initiative/semsimian
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://github.com/monarch-initiative/monarch-app
name: Monarch Python Toolkit
category: Data Curation
monarch_role: Support
documentation: https://monarch-initiative.github.io/monarch-py/
monarch_contribution: Lead
repository: https://github.com/monarch-initiative/monarch-app/backend
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/monarch-initiative/babelon
name: Babelon Toolkit
category: Data Curation
documentation: https://monarch-initiative.github.io/babelon/
monarch_contribution: Lead
monarch_role: Support
repository: https://github.com/monarch-initiative/babelon
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: https://github.com/monarch-initiative/fenominal
name: Fenominal
category: Data Curation
monarch_role: Support
documentation: https://monarch-initiative.github.io/fenominal/
monarch_contribution: Lead
repository: https://github.com/monarch-initiative/fenominal
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://github.com/monarch-initiative/koza
name: Koza
category: Data Curation
monarch_role: Core
documentation: https://koza.monarchinitiative.org/
monarch_contribution: Lead
repository: https://github.com/monarch-initiative/fenominal
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://linkml.io/
name: LinkML
description: The Linked Data Modeling Language (LinkML) is a flexible
modeling language that allows you to author schemas (models) in YAML that
describe the structure of your data.
repository: https://github.com/linkml/linkml
documentation: https://linkml.io/linkml-model/docs/
icon: resource-linkml
url: https://linkml.io/
monarch_role: Core
category: Data Curation
monarch_contribution: Lead
contact:
name: Chris Mungall
email: [email protected]
orcid: https://orcid.org/0000-0002-6601-2165
github: "@cmungall"
- id: https://monarch-initiative.github.io/monarch-ingest
name: Monarch Ingest
documentation: https://monarch-initiative.github.io/monarch-ingest
description: The Monarch Ingest pulls in data from a wide variety of biomedical data sources and generates Biolink-compliant KGX files that are used to build the Monarch KG.
repository: https://github.com/monarch-initiative/monarch-ingest
monarch_role: Core
category: Data Curation
monarch_contribution: Lead
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/monarch-initiative/monarch-mapping-commons
name: Monarch Mapping Commons
icon: resource-monarch
monarch_role: Core
category: Mapping
description: SSSOM Mappings collected and curated by the Monarch Initiative.
repository: https://github.com/monarch-initiative/monarch-mapping-commons
documentation: https://github.com/monarch-initiative/monarch-mapping-commons
url: https://github.com/monarch-initiative/monarch-mapping-commons
monarch_contribution: Lead
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/obophenotype/hpo-translations
name: HPO Language Translations
monarch_role: Support
category: Ontology Maintenance
description: Infrastructure to collect and coordinate HPO language translations.
repository: https://github.com/obophenotype/hpo-translations
documentation: https://obophenotype.github.io/hpo-translations/
url: https://obophenotype.github.io/hpo-translations/
monarch_contribution: Lead
contact:
name: Nicolas Matentzoglu
email: [email protected]
orcid: https://orcid.org/0000-0002-7356-1779
github: "@matentzn"
- id: https://github.com/TheJacksonLaboratory/Phenomiser
name: Phenomizer
monarch_role: Core
category: Clinical Diagnosis
description: A web application for clinical diagnostics in human genetics using semantic similarity searches in ontologies.
repository: https://github.com/TheJacksonLaboratory/Phenomiser
documentation: https://github.com/TheJacksonLaboratory/Phenomiser
url: https://hpo.jax.org/app/tools/phenomizer
monarch_contribution: Lead
contact:
name: Peter Robinson
email: [email protected]
orcid: https://orcid.org/0000-0002-0736-9199
github: "@pnrobinson"
- id: https://github.com/monarch-initiative/phenogrid
name: Phenogrid
monarch_role: Core
category: Clinical Diagnosis
description: Phenogrid is a web component that visualizes semantic similarity calculations provided by OWLSim, as provided through APIs from the Monarch Initiative.
repository: https://github.com/monarch-initiative/phenogrid
documentation: https://github.com/monarch-initiative/phenogrid
url: https://github.com/monarch-initiative/phenogrid
monarch_contribution: Lead
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/monarch-initiative/monarchr
name: monarchr
monarch_role: Core
category: Ontology Use
description: R package for easy access, manipulation, and analysis of the Monarch Initiative or other KGX-formatted knowledge graphs.
repository: https://github.com/monarch-initiative/monarchr
documentation: https://github.com/monarch-initiative/monarchr
url: https://github.com/monarch-initiative/monarchr
monarch_contribution: Lead
contact:
name: Shawn O'Neil
email: [email protected]
orcid: https://orcid.org/0000-0001-6220-7080
github: "@oneilsh"
- id: https://github.com/monarch-initiative/phenomics-assistant
name: Phenomics Assistant
monarch_role: Core
category: Clinical Diagnosis
description: An LLM retrieval augmented generation (RAG) agent for Monarch Initiative.
repository: https://github.com/monarch-initiative/phenomics-assistant
documentation: https://github.com/monarch-initiative/phenomics-assistant
url: https://github.com/monarch-initiative/phenomics-assistant
monarch_contribution: Lead
contact:
name: Kevin Schaper
email: [email protected]
orcid: https://orcid.org/0000-0003-3311-7320
github: "@kevinschaper"
- id: https://github.com/monarch-initiative/pheval.llm
name: pheval.llm
category: Benchmarking
description: LLM Benchmarking in differential diagnostics.
repository: https://github.com/monarch-initiative/pheval.llm
documentation: https://monarch-initiative.github.io/pheval.llm
monarch_role: Support
monarch_contribution: Co-Lead
contact:
name: Leonardo Chimirri
email: [email protected]
orcid: https://orcid.org/0000-0002-6912-8518
github: "@leokim-l"
- id: https://github.com/monarch-initiative/phenopacket2prompt
name: phenopacket2prompt
category: Clinical Diagnosis
description: Creation of prompts from phenopackets, in multiple languages, intended for prompting LLMs.
repository: https://github.com/monarch-initiative/phenopacket2prompt
documentation: https://monarch-initiative.github.io/phenopacket2prompt/
monarch_role: Support
monarch_contribution: Co-Lead
contact:
name: Leonardo Chimirri
email: [email protected]
orcid: https://orcid.org/0000-0002-6912-8518
github: "@leokim-l"
- id: https://github.com/monarch-initiative/automaxo/
name: AutoMAxO
category: Data Curation
description: Streamline the creation of ontology annotations of MAxO via LLMs.
repository: https://github.com/monarch-initiative/automaxo/
documentation: https://monarch-initiative.github.io/automaxo
monarch_role: Core
monarch_contribution: Lead
contact:
name: Enock Niyonkuru
email: [email protected]
orcid: https://orcid.org/0000-0002-7981-8133
github: "@enockniyonkuru"
documentations:
- id: https://oboacademy.github.io/obook/
name: OBO Academy
category: Training Materials
description: A resource for self-paced training of Semantic Engineers.
repository: https://github.com/OBOAcademy/obook/
- id: https://berkeleybop.github.io/best_practice/
name: Best practices for collaborative open source coding
category: Training Materials
description: The best practice / house style guide maintained by Monarch's LBNL team members.
repository: https://github.com/berkeleybop/berkeleybop.github.io/tree/master/best_practice
repositories:
- id: https://github.com/INCATools/ontology-development-kit
name: ODK
- id: https://github.com/monarch-initiative/monarch-ingest
name: Monarch Ingest
- id: https://github.com/monarch-initiative/cat-merge
name: CAT Merge
- id: https://github.com/monarch-initiative/closurizer
name: Closurizer
- id: https://github.com/monarch-initiative/monarch-gene-mapping
name: Monarch Gene Mapping
- id: https://github.com/monarch-initiative/kghub-downloader
name: Ontology Development Kit (ODK)
- id: https://github.com/monarch-initiative/monarch-file-server
name: Monarch File Server
- id: https://github.com/monarch-initiative/koza
name: Koza
- id: https://github.com/monarch-initiative/monarch-plater-docker
name: Monarch Plater Docker
- id: https://github.com/monarch-initiative/jenkins
name: Jenkins
- id: https://github.com/monarch-initiative/monarch-app
name: Monarch App
- id: https://github.com/monarch-initiative/monarch-ingest-dashboard
name: Monarch Ingest Dashboard
- id: https://github.com/Knowledge-Graph-Hub/universalizer
name: Universalizer
- id: https://github.com/balhoff/arachne
name: Arachne Reasoner
- id: https://github.com/biolink/biolink-model
name: Biolink Model
- id: https://github.com/biolink/biolink-model-toolkit
name: Biolink Model Toolkit
- id: https://github.com/INCATools/boomer
name: boomer
- id: https://github.com/INCATools/dosdp-tools
name: DOSDP Tools
- id: https://github.com/INCATools/semantic-sql
name: Semantic SQL
- id: https://github.com/exomiser/Exomiser
name: exomiser
- id: https://github.com/monarch-initiative/pheval.exomiser
name: PhEval Exomiser Runner
- id: https://github.com/monarch-initiative/pheval
name: PhEval
- id: https://github.com/obophenotype/human-phenotype-ontology
name: The Human Phenotype Ontology (HPO)
- id: https://github.com/TheJacksonLaboratory/hpo-web
name: hpo.jax.org (Website)
- id: https://github.com/Knowledge-Graph-Hub/knowledge-graph-hub.github.io
name: KG Hub
- id: https://github.com/biolink/kgx
name: Knowledge Graph Exchange (KGX) Format and Toolkit
- id: https://github.com/linkml/linkml-runtime
name: LinkML Runtime Toolkit
- id: https://github.com/TheJacksonLaboratory/LIRICAL
name: LIRICAL
- id: https://github.com/monarch-initiative/monarch-ui
name: Monarch UI
- id: https://github.com/monarch-initiative/mondo
name: mondo
- id: https://github.com/Knowledge-Graph-Hub/neat-ml
name: Network Embedding All the Things (NEAT)
- id: https://github.com/INCATools/ontology-access-kit
name: Ontology Access Kit (OAK)
- id: https://github.com/INCATools/oakx-grape
name: oakx-grape
- id: https://github.com/TheJacksonLaboratory/Phenomiser
name: Phenomiser
- id: https://github.com/phenopackets/phenopacket-schema
name: Phenopackets Schema
- id: https://github.com/phenopackets/phenopacket-tools
name: Phenopackets
- id: https://github.com/TheJacksonLaboratory/POET
name: POET
- id: https://github.com/linkml/prefixmaps
name: prefixmaps
- id: https://github.com/INCATools/relation-graph