Monarch Tool, Standard and Data Registry
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.
Standards developed or significantly supported by the Monarch Initiative
Phenopackets
| Phenopackets | |
|---|---|
| PURL | http://phenopackets.org/ |
| Cite | |
| Resource category | Data Exchange |
| Documentation | https://phenopacket-schema.readthedocs.io/en/latest/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Foundational |
| Main repository | https://github.com/phenopackets/phenopacket-schema |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
Simple Standard for Ontology Mappings (SSSOM)
| Simple Standard for Ontology Mappings (SSSOM) | |
|---|---|
| PURL | https://standards.monarchinitiative.org/sssom |
| Cite | https://doi.org/10.1093/database/baac035 |
| Resource category | Data Exchange |
| Documentation | https://mapping-commons.github.io/sssom/spec/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/mapping-commons/sssom/ |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards | SSSOM Toolkit,SSSOM Model |
Human Phenotype Ontology
| Human Phenotype Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/hp.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://obophenotype.github.io/human-phenotype-ontology/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | HPO, Phenomics First |
| Role in Monarchs strategic vision | Foundational |
| Main repository | https://github.com/obophenotype/human-phenotype-ontology |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
obographs
| obographs | |
|---|---|
| PURL | https://github.com/geneontology/obographs |
| Cite | |
| Resource category | Data Exchange |
| Documentation | https://incatools.github.io/ontology-access-kit/datamodels/obograph/index.html |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/geneontology/obographs |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Mondo Disease Ontology
| Mondo Disease Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/mondo.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://mondo.readthedocs.io/en/latest/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Foundational |
| Main repository | https://github.com/monarch-initiative/mondo |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Genotype Ontology
| Genotype Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/geno.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://github.com/monarch-initiative/GENO-ontology |
| Monarch role in the development | Lead |
| Grants involved in this standard | Monarch R24 |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/GENO-ontology |
| Responsible contact in Monarch | Matt Brush, https://orcid.org/0000-0002-1048-5019, @mbrush |
| Project boards |
Scientific Evidence and Provenance Information Ontology
| Scientific Evidence and Provenance Information Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/sepio.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://github.com/monarch-initiative/SEPIO-ontology |
| Monarch role in the development | Lead |
| Grants involved in this standard | Monarch R24 |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/SEPIO-ontology |
| Responsible contact in Monarch | Matt Brush, https://orcid.org/0000-0002-1048-5019, @mbrush |
| Project boards |
Vertebrate Breed Ontology
| Vertebrate Breed Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/vbo.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://github.com/monarch-initiative/vertebrate-breed-ontology |
| Monarch role in the development | Lead |
| Grants involved in this standard | Monarch R24 |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/vertebrate-breed-ontology |
| Responsible contact in Monarch | Sabrina Toro, https://orcid.org/0000-0002-4142-7153, @sabrinatoro |
| Project boards |
The Unified Phenotype Ontology (uPheno)
| The Unified Phenotype Ontology (uPheno) | |
|---|---|
| PURL | https://github.com/obophenotype/upheno |
| Cite | |
| Resource category | Ontology |
| Documentation | https://obophenotype.github.io/upheno/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Core |
| Main repository | https://obophenotype.github.io/upheno/ |
| Responsible contact in Monarch | James McLaughlin, https://orcid.org/0000-0002-8361-2795, @udp |
| Project boards | uPheno 2 Ontology Development |
Medical Action Ontology
| Medical Action Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/maxo.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://github.com/monarch-initiative/MAxO |
| Monarch role in the development | Lead |
| Grants involved in this standard | HPO |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
Ontology of Biological Attributes
| Ontology of Biological Attributes | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/oba.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://obophenotype.github.io/upheno/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards | OBA Ontology Development (uPheno board) |
Uberon Anatomy Ontology
| Uberon Anatomy Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/uberon.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://obophenotype.github.io/uberon/ |
| Monarch role in the development | Co-Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Foundational |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Phenomics Integrated Ontology (PHENIO)
| Phenomics Integrated Ontology (PHENIO) | |
|---|---|
| PURL | https://github.com/monarch-initiative/phenio |
| Cite | |
| Resource category | Ontology |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | Monarch R24 |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Environmental Exposure Ontology
| Environmental Exposure Ontology | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/ecto.owl |
| Cite | |
| Resource category | Ontology |
| Documentation | https://github.com/EnvironmentOntology/environmental-exposure-ontology |
| Monarch role in the development | Lead |
| Grants involved in this standard | TBD |
| Role in Monarchs strategic vision | Support |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Dead simple owl design pattern (DOS-DP) exchange format
| Dead simple owl design pattern (DOS-DP) exchange format | |
|---|---|
| PURL | https://github.com/INCATools/dead_simple_owl_design_patterns |
| Cite | |
| Resource category | Data Exchange |
| Documentation | https://incatools.github.io/dead_simple_owl_design_patterns/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Support |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Knowledge Graph Change Language
| Knowledge Graph Change Language | |
|---|---|
| PURL | https://github.com/INCATools/kgcl |
| Cite | |
| Resource category | Ontology Curation |
| Documentation | https://incatools.github.io/kgcl/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | Bosch Gift |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Babelon - A simple standard for managing ontology translations and language profiles
| Babelon - A simple standard for managing ontology translations and language profiles | |
|---|---|
| PURL | https://github.com/monarch-initiative/babelon |
| Cite | |
| Resource category | Data Exchange |
| Documentation | https://monarch-initiative.github.io/babelon/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | HPO |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/babelon |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
Tools and Services developed or significantly supported by the Monarch Initiative
Exomiser
| Exomiser | |
|---|---|
| PURL | https://tools.monarchinitiative.org/exomiser |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://exomiser.readthedocs.io/en/latest/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Foundational |
| Main repository | https://github.com/exomiser/Exomiser |
| Responsible contact in Monarch | Jules Jacobsen, https://orcid.org/0000-0002-3265-1591, @julesjacobsen |
| Project boards |
Monarch Knowledge Graph & Services
| Monarch Knowledge Graph & Services | |
|---|---|
| PURL | https://monarchinitiative.org/ |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://monarch-initiative.github.io/monarch-ingest/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Foundational |
| Main repository | https://github.com/monarch-initiative/monarch-app |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Monarch App
| Monarch App | |
|---|---|
| PURL | https://monarch-app.monarchinitiative.org/ |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://monarch-app.monarchinitiative.org/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarch-app |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Monarch API
| Monarch API | |
|---|---|
| PURL | http://api-v3.monarchinitiative.org |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://monarch-app.monarchinitiative.org/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarch-app |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Ontology Development Kit (ODK)
| Ontology Development Kit (ODK) | |
|---|---|
| PURL | https://tools.monarchinitiative.org/odk |
| Cite | |
| Resource category | Ontology Maintenance |
| Documentation | https://github.com/INCATools/ontology-development-kit |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards | ODK Milestones |
Ontology Access Kit (OAK)
| Ontology Access Kit (OAK) | |
|---|---|
| PURL | https://tools.monarchinitiative.org/oak |
| Cite | |
| Resource category | Ontology Use |
| Documentation | https://incatools.github.io/ontology-access-kit/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/INCATools/ontology-access-kit |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
SSSOM Toolkit
| SSSOM Toolkit | |
|---|---|
| PURL | https://tools.monarchinitiative.org/sssom-toolkit |
| Cite | |
| Resource category | Mapping |
| Documentation | https://mapping-commons.github.io/sssom-py |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
Monarch Ontology Lookup Service
| Monarch Ontology Lookup Service | |
|---|---|
| PURL | https://tools.monarchinitiative.org/ols |
| Cite | |
| Resource category | Ontology Use |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/ontotools-docker |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
POET
| POET | |
|---|---|
| PURL | https://tools.monarchinitiative.org/poet |
| Cite | |
| Resource category | Data Curation |
| Documentation | TBD |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/TheJacksonLaboratory/POET |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL)
| LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) | |
|---|---|
| PURL | https://tools.monarchinitiative.org/lirical |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://lirical.readthedocs.io/en/latest/ |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/TheJacksonLaboratory/LIRICAL |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
PhEval
| PhEval | |
|---|---|
| PURL | https://github.com/monarch-initiative/pheval |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://monarch-initiative.github.io/pheval/ |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval |
| Responsible contact in Monarch | Jules Jacobsen, https://orcid.org/0000-0002-3265-1591, @julesjacobsen |
| Project boards |
obographviz
| obographviz | |
|---|---|
| PURL | https://github.com/INCATools/obographviz |
| Cite | |
| Resource category | Ontology Use |
| Documentation | https://github.com/INCATools/obographviz#readme |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/INCATools/obographviz |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
ubergraph
| ubergraph | |
|---|---|
| PURL | https://github.com/INCATools/ubergraph |
| Cite | |
| Resource category | Ontology Use |
| Documentation | TBD |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/INCATools/ubergraph |
| Responsible contact in Monarch | Jim Balhoff, https://orcid.org/0000-0002-8688-6599, @balhoff |
| Project boards |
whelk
| whelk | |
|---|---|
| PURL | https://github.com/balhoff/whelk |
| Cite | |
| Resource category | Ontology Use |
| Documentation | TBD |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/balhoff/whelk |
| Responsible contact in Monarch | Jim Balhoff, https://orcid.org/0000-0002-8688-6599, @balhoff |
| Project boards |
robot
| robot | |
|---|---|
| PURL | https://github.com/ontodev/robot |
| Cite | |
| Resource category | Ontology Use |
| Documentation | https://robot.obolibrary.org |
| Monarch role in the development | Contributor |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | https://github.com/ontodev/robot |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
Data Harmonizer
| Data Harmonizer | |
|---|---|
| PURL | https://github.com/cidgoh/DataHarmonizer |
| Cite | |
| Resource category | Data Curation |
| Documentation | TBD |
| Monarch role in the development | Contributor |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | https://github.com/cidgoh/DataHarmonizer |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
OntoGPT
| OntoGPT | |
|---|---|
| PURL | https://github.com/monarch-initiative/ontogpt |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/ontogpt/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/ontogpt |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
TALISMAN
| TALISMAN | |
|---|---|
| PURL | https://github.com/monarch-initiative/talisman |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/talisman/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/talisman/ |
| Responsible contact in Monarch | Marcin Joachimiak, https://orcid.org/0000-0001-8175-045X, @realmarcin |
| Project boards |
CurateGPT
| CurateGPT | |
|---|---|
| PURL | https://github.com/monarch-initiative/curate-gpt |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://github.com/monarch-initiative/curate-gpt |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/curate-gpt |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
semsimian
| semsimian | |
|---|---|
| PURL | https://github.com/monarch-initiative/semsimian |
| Cite | |
| Resource category | Mapping |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/semsimian |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Monarch Python Toolkit
| Monarch Python Toolkit | |
|---|---|
| PURL | https://github.com/monarch-initiative/monarch-app |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/monarch-py/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/monarch-app/backend |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Babelon Toolkit
| Babelon Toolkit | |
|---|---|
| PURL | https://github.com/monarch-initiative/babelon |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/babelon/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/babelon |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
Fenominal
| Fenominal | |
|---|---|
| PURL | https://github.com/monarch-initiative/fenominal |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/fenominal/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/fenominal |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
Koza
| Koza | |
|---|---|
| PURL | https://github.com/monarch-initiative/koza |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://koza.monarchinitiative.org/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/fenominal |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
LinkML
| LinkML | |
|---|---|
| PURL | https://linkml.io/ |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://linkml.io/linkml-model/docs/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/linkml/linkml |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Monarch Ingest
| Monarch Ingest | |
|---|---|
| PURL | https://monarch-initiative.github.io/monarch-ingest |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/monarch-ingest |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarch-ingest |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Monarch Mapping Commons
| Monarch Mapping Commons | |
|---|---|
| PURL | https://github.com/monarch-initiative/monarch-mapping-commons |
| Cite | |
| Resource category | Mapping |
| Documentation | https://github.com/monarch-initiative/monarch-mapping-commons |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarch-mapping-commons |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
HPO Language Translations
| HPO Language Translations | |
|---|---|
| PURL | https://github.com/obophenotype/hpo-translations |
| Cite | |
| Resource category | Ontology Maintenance |
| Documentation | https://obophenotype.github.io/hpo-translations/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/obophenotype/hpo-translations |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
Phenomizer
| Phenomizer | |
|---|---|
| PURL | https://github.com/TheJacksonLaboratory/Phenomiser |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://github.com/TheJacksonLaboratory/Phenomiser |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/TheJacksonLaboratory/Phenomiser |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
Phenogrid
| Phenogrid | |
|---|---|
| PURL | https://github.com/monarch-initiative/phenogrid |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://github.com/monarch-initiative/phenogrid |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/phenogrid |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Monarch Assistant
| Monarch Assistant | |
|---|---|
| PURL | https://github.com/monarch-initiative/monarch-assistant |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://github.com/monarch-initiative/monarch-assistant |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarch-assistant |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
pheval.llm
| pheval.llm | |
|---|---|
| PURL | https://github.com/monarch-initiative/pheval.llm |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://monarch-initiative.github.io/pheval.llm |
| Monarch role in the development | Co-Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/pheval.llm |
| Responsible contact in Monarch | Leonardo Chimirri, https://orcid.org/0000-0002-6912-8518, @leokim-l |
| Project boards |
phenopacket2prompt
| phenopacket2prompt | |
|---|---|
| PURL | https://github.com/monarch-initiative/phenopacket2prompt |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://monarch-initiative.github.io/phenopacket2prompt/ |
| Monarch role in the development | Co-Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/monarch-initiative/phenopacket2prompt |
| Responsible contact in Monarch | Leonardo Chimirri, https://orcid.org/0000-0002-6912-8518, @leokim-l |
| Project boards |
AutoMAxO
| AutoMAxO | |
|---|---|
| PURL | https://github.com/monarch-initiative/automaxo/ |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/automaxo |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/automaxo/ |
| Responsible contact in Monarch | Enock Niyonkuru, https://orcid.org/0000-0002-7981-8133, @enockniyonkuru |
| Project boards |
Datasets developed by the Monarch Initiative
HPOA - Disease Annotations
| HPOA - Disease Annotations | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa |
| Cite | |
| Resource category | Biomedical Data |
| Documentation | https://hpo-annotation-qc.readthedocs.io/en/latest/annotationFormat.html#phenotype-hpoa-format |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
HPOA - Phenotype to Gene Associations
| HPOA - Phenotype to Gene Associations | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt |
| Cite | |
| Resource category | Biomedical Data |
| Documentation | https://hpo.jax.org/app/download/annotation |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
HPOA - Gene to Phenotype Associations
| HPOA - Gene to Phenotype Associations | |
|---|---|
| PURL | http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt |
| Cite | |
| Resource category | Biomedical Data |
| Documentation | https://hpo.jax.org/app/download/annotation |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Peter Robinson, https://orcid.org/0000-0002-0736-9199, @pnrobinson |
| Project boards |
HPOA Knowledge Graph Ingestible
| HPOA Knowledge Graph Ingestible | |
|---|---|
| PURL | https://data.monarchinitiative.org/monarch-kg/hpoa |
| Cite | |
| Resource category | Knowledge Graph Ingestibles |
| Documentation | https://monarch-initiative.github.io/monarch-ingest/Sources/HPOA/ |
| Monarch role in the development | |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
Alliance Knowledge Graph Ingestible
| Alliance Knowledge Graph Ingestible | |
|---|---|
| PURL | https://data.monarchinitiative.org/monarch-kg/alliance |
| Cite | |
| Resource category | Knowledge Graph Ingestibles |
| Documentation | https://monarch-initiative.github.io/monarch-ingest/Sources/Alliance/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
KG Covid-19
| KG Covid-19 | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/kg-covid-19 |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
ECO KG
| ECO KG | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/eco-kg |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
KG IDG
| KG IDG | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/kg-idg |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
KG Phenio
| KG Phenio | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/kg-phenio |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
KG OBO
| KG OBO | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/kg-obo |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
KG Microbe
| KG Microbe | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/kg-microbe |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
SRI Reference KG
| SRI Reference KG | |
|---|---|
| PURL | https://github.com/Knowledge-Graph-Hub/sri-reference-kg |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Community |
| Main repository | |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Monarch KG
| Monarch KG | |
|---|---|
| PURL | https://monarch-initiative.github.io/monarch-ingest |
| Cite | |
| Resource category | Knowledge Graph |
| Documentation | TBD |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |