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 | phenopackets |
| Cite | Ladewig, M. S., Jacobsen, J. O. B., Wagner, A. H., Danis, D., El Kassaby, B., Gargano, M., Groza, T., Baudis, M., Steinhaus, R., Seelow, D., Bechrakis, N. E., Mungall, C. J., Schofield, P. N., Elemento, O., Smith, L., McMurry, J. A., Munoz-Torres, M., Haendel, M. A., & Robinson, P. N. (2023). GA4GH Phenopackets: A practical introduction. Advanced Genetics, 4(1), 2200016. https://doi.org/10.1002/ggn2.202200016 |
| Resource category | Data Exchange |
| Documentation | https://phenopacket-schema.readthedocs.io/en/latest/introduction.html |
| 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 | Jules Jacobsen, https://orcid.org/0000-0002-3265-1591, @julesjacobsen |
| Project boards |
Simple Standard for Ontology Mappings
| Simple Standard for Ontology Mappings | |
|---|---|
| PURL | sssom |
| Cite | Matentzoglu, N., Balhoff, J. P., Bello, S. M., Bizon, C., Brush, M., Callahan, T. J., Chute, C. G., Duncan, W. D., Evelo, C. T., Gabriel, D., Graybeal, J., Gray, A., Gyori, B. M., Haendel, M., Harmse, H., Harris, N. L., Harrow, I., Hegde, H. B., Hoyt, A. L., Hoyt, C. T., Jiao, D., Jiménez-Ruiz, E., Jupp, S., Kim, H., Köhler, S., Liener, T., Long, Q., Malone, J., McLaughlin, J. A., McMurry, J. A., Moxon, S., Munoz-Torres, M. C., Osumi-Sutherland, D., Overton, J. A., Peters, B., Putman, T., Queralt-Rosinach, N., Shefchek, K., Solbrig, H., Thessen, A., Tudorache, T., Vasilevsky, N., Wagner, A. H., & Mungall, C. J. (2022). A simple standard for sharing ontological mappings (SSSOM). Database, 2022, baac035. https://doi.org/10.1093/database/baac035 |
| Resource category | Data Exchange |
| Documentation | https://mapping-commons.github.io/sssom |
| 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 | hp |
| Cite | Gargano, M. A., Matentzoglu, N., Coleman, B., Addo-Lartey, E. B., Anagnostopoulos, A. V., Anderton, J., Avillach, P., Bagley, A. M., Bakštein, E., Balhoff, J. P., Baynam, G., Bello, S. M., Berk, M., Bertram, H., Bishop, S., Blau, H., Bodenstein, D. F., Botas, P., Boztug, K., Čady, J., Callahan, T. J., Cameron, R., Carbon, S. J., Castellanos, F., Caufield, J. H., Chan, L. E., Chute, C. G., Cruz-Rojo, J., Dahan-Oliel, N., Davids, J. R., de Dieuleveult, M., de Souza, V., de Vries, B. B. A., de Vries, E., DePaulo, J. R., Derfalvi, B., Dhombres, F., Diaz-Byrd, C., Dingemans, A. J. M., Donadille, B., Duyzend, M., Elfeky, R., Essaid, S., Fabrizzi, C., Fico, G., Firth, H. V., Freudenberg-Hua, Y., Fullerton, J. M., Gabriel, D. L., Gilmour, K., Giordano, J., Goes, F. S., Moses, R. G., Green, I., Griese, M., Groza, T., Gu, W., Guthrie, J., Gyori, B., Hamosh, A., Hanauer, M., Hanušová, K., He, Y. O., Hegde, H., Helbig, I., Holasová, K., Hoyt, C. T., Huang, S., Hurwitz, E., Jacobsen, J. O. B., Jiang, X., Joseph, L., Keramatian, K., King, B., Knoflach, K., Koolen, D. A., Kraus, M. L., Kroll, C., Kusters, M., Ladewig, M. S., Lagorce, D., Lai, M. C., Lapunzina, P., Laraway, B., Lewis-Smith, D., Li, X., Lucano, C., Majd, M., Marazita, M. L., Martinez-Glez, V., McHenry, T. H., McInnis, M. G., McMurry, J. A., Mihulová, M., Millett, C. E., Mitchell, P. B., Moslerová, V., Narutomi, K., Nematollahi, S., Nevado, J., Nierenberg, A. A., Čajbiková, N. N., Nurnberger, J. I., Ogishima, S., Olson, D., Ortiz, A., Pachajoa, H., Perez de Nanclares, G., Peters, A., Putman, T., Rapp, C. K., Rath, A., Reese, J., Rekerle, L., Roberts, A. M., Roy, S., Sanders, S. J., Schuetz, C., Schulte, E. C., Schulze, T. G., Schwarz, M., Scott, K., Seelow, D., Seitz, B., Shen, Y., Similuk, M. N., Simon, E. S., Singh, B., Smedley, D., Smith, C. L., Smolinsky, J. T., Sperry, S., Stafford, E., Stefancsik, R., Steinhaus, R., Strawbridge, R., Sundaramurthi, J. C., Talapova, P., Tenorio Castano, J. A., Tesner, P., Thomas, R. H., Thurm, A., Turnovec, M., van Gijn, M. E., Vasilevsky, N. A., Vlčková, M., Walden, A., Wang, K., Wapner, R., Ware, J. S., Wiafe, A. A., Wiafe, S. A., Wiggins, L. D., Williams, A. E., Wu, C., Wyrwoll, M. J., Xiong, H., Yalin, N., Yamamoto, Y., Yatham, L. N., Yocum, A. K., Young, A. H., Yüksel, Z., Zandi, P. P., Zankl, A., Zarante, I., Zvolský, M., Toro, S., Carmody, L. C., Harris, N. L., Munoz-Torres, M. C., Danis, D., Mungall, C. J., Köhler, S., Haendel, M. A., & Robinson, P. N. (2024). The Human Phenotype Ontology in 2024: Phenotypes around the world. Nucleic Acids Research, 52(D1), D1333–D1346. https://doi.org/10.1093/nar/gkad1005 |
| 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 | 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 | mondo |
| Cite | Vasilevsky, N. A., Matentzoglu, N. A., Toro, S., Flack, J. E., Hegde, H., Unni, D. R., Alyea, G., Amberger, J. S., Babb, L., Balhoff, J. P., Bingaman, T. I., Burns, G. A., Callahan, T. J., Carmody, L. C., Chan, L. E., Chang, G. S., Dumontier, M., Failla, L. E., Flowers, M. J., Garrett, H. A., Gration, D., Groza, T., Hanauer, M., Harris, N. L., Helbig, I., Hilton, J. A., Himmelstein, D. S., Hoyt, C. T., Kane, M. S., Köhler, S., Lagorce, D., Larralde, M., Lock, A., López Santiago, I., Maglott, D. R., Malheiro, A. J., Meldal, B. H. M., McMurry, J. A., Munoz-Torres, M., Nelson, T. H., Ochoa, D., Oprea, T. I., Osumi-Sutherland, D., Parkinson, H., Pendlington, Z. M., Rath, A., Rehm, H. L., Remennik, L., Riggs, E. R., Roncaglia, P., Ross, J. E., Shadbolt, M. F., Shefchek, K. A., Similuk, M. N., Sioutos, N., Sparks, R., Stefancsik, R., Stephan, R., Stupp, D., Sundaramurthi, J. C., Tammen, I., Thaxton, C. L., Valasek, E., Wagner, A. H., Welter, D., Whetzel, P. L., Whiteman, L. L., Wood, V., Xu, C. H., Zankl, A., Zhang, X. A., Chute, C. G., Robinson, P. N., Mungall, C. J., Hamosh, A., & Haendel, M. A. (2022). Mondo: Unifying diseases for the world, by the world [Preprint]. medRxiv. https://doi.org/10.1101/2022.04.13.22273750 |
| 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 | Sabrina Toro, https://orcid.org/0000-0002-4142-7153, @sabrinatoro |
| Project boards |
Genotype Ontology
| Genotype Ontology | |
|---|---|
| PURL | geno |
| Cite | Monarch Initiative. (n.d.). GENO-ontology [Source code]. GitHub. https://github.com/monarch-initiative/GENO-ontology |
| 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 | sepio |
| Cite | Monarch Initiative. (n.d.). SEPIO-ontology [Source code]. GitHub. https://github.com/monarch-initiative/SEPIO-ontology |
| 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 | vbo |
| Cite | Mullen, K. R., Tammen, I., Matentzoglu, N. A., Mather, M., Balhoff, J. P., Esdaile, E., Leroy, G., Park, C. A., Rando, H. M., Saklou, N. T., Webb, T. L., Vasilevsky, N. A., Mungall, C. J., Haendel, M. A., Nicholas, F. W., & Toro, S. (2025). The Vertebrate Breed Ontology: Toward effective breed data standardization. Journal of Veterinary Internal Medicine, 39(4), e70133. https://doi.org/10.1111/jvim.70133 |
| Resource category | Ontology |
| Documentation | https://monarch-initiative.github.io/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
| The Unified Phenotype Ontology | |
|---|---|
| PURL | upheno |
| Cite | Matentzoglu, N., Bello, S. M., Stefancsik, R., Alghamdi, S. M., Anagnostopoulos, A. V., Balhoff, J. P., Balk, M. A., Bradford, Y. M., Bridges, Y., Callahan, T. J., Caufield, H., Cuzick, A., Carmody, L. C., Caron, A. R., de Souza, V., Engel, S. R., Fey, P., Fisher, M., Gehrke, S., Grove, C., Hansen, P., Harris, N. L., Harris, M. A., Harris, L., Ibrahim, A., Jacobsen, J. O. B., Köhler, S., McMurry, J. A., Munoz-Fuentes, V., Munoz-Torres, M. C., Parkinson, H., Pendlington, Z. M., Pilgrim, C., Robb, S. M., Robinson, P. N., Seager, J., Segerdell, E., Smedley, D., Sollis, E., Toro, S., Vasilevsky, N., Wood, V., Haendel, M. A., Mungall, C. J., McLaughlin, J. A., & Osumi-Sutherland, D. (2025). The Unified Phenotype Ontology: A framework for cross-species integrative phenomics. Genetics, 229(3), iyaf027. https://doi.org/10.1093/genetics/iyaf027 |
| 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://github.com/obophenotype/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 | maxo |
| 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 | oba |
| Cite | Stefancsik, R., Balhoff, J. P., Balk, M. A., et al. (2023). The Ontology of Biological Attributes (OBA)—Computational traits for the life sciences. Mammalian Genome, 34, 364–378. https://doi.org/10.1007/s00335-023-09992-1 |
| Resource category | Ontology |
| Documentation | https://obophenotype.github.io/bio-attribute-ontology |
| Monarch role in the development | Lead |
| Grants involved in this standard | Phenomics First |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/obophenotype/bio-attribute-ontology |
| 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 | uberon |
| Cite | Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012). Uberon, an integrative multi-species anatomy ontology. Genome Biology, 13(1), R5. |
| DOI: https://doi.org/10.1186/gb-2012-13-1-r5 | |
| PubMed: https://pubmed.ncbi.nlm.nih.gov/22293552 |
Haendel, M. A., Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. A., Bradford, Y., Comte, A., Dahdul, W. M., Dececchi, T. A., Druzinsky, R. E., Hayamizu, T. F., Ibrahim, N., Lewis, S. E., Mabee, P. M., Niknejad, A., Robinson-Rechavi, M., Sereno, P. C., & Mungall, C. J. (2014). Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics, 5(1), 21.
DOI: https://doi.org/10.1186/2041-1480-5-21
PubMed: https://pubmed.ncbi.nlm.nih.gov/24742169
|
| 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 | https://github.com/obophenotype/uberon |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards | |
Phenomics Integrated Ontology
| Phenomics Integrated Ontology | |
|---|---|
| PURL | phenio |
| Cite | Monarch Initiative. (n.d.). phenio [Source code]. GitHub. https://github.com/monarch-initiative/phenio |
| Resource category | Ontology |
| Documentation | https://monarch-initiative.github.io/phenio |
| 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/phenio |
| Responsible contact in Monarch | Harry Caufield, https://orcid.org/0000-0001-5705-7831, @caufieldjh |
| Project boards |
Environmental Conditions, Treatments and Exposures Ontology
| Environmental Conditions, Treatments and Exposures Ontology | |
|---|---|
| PURL | ecto |
| Cite | Matentzoglu, N. A., Vasilevsky, N. A., Balhoff, J. P., Bello, S. M., Brush, M. H., Carbon, S., Carmody, L. C., Cooper, L., Courtot, M., Diehl, A. D., Duncan, W. D., Harris, N. L., Haendel, M. A., Mungall, C. J., Osumi-Sutherland, D., Relevo, R., Segerdell, E., Smith, C. L., & Robinson, P. N. (2023). The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond https://doi.org/10.1186/s13326-023-00283-x |
| 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 | https://github.com/EnvironmentOntology/environmental-exposure-ontology |
| Responsible contact in Monarch | Anne Thessen, https://orcid.org/0000-0002-2908-3327, @diatomsRcool |
| Project boards |
Dead simple owl design pattern (DOS-DP) exchange format
| Dead simple owl design pattern (DOS-DP) exchange format | |
|---|---|
| PURL | 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 | 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 | 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 | exomiser |
| Cite | Smedley, D., Schubach, M., Jacobsen, J. O. B., Köhler, S., Zemojtel, T., Spielmann, M., Jäger, M., Hochheiser, H., Washington, N. L., McMurry, J. A., Haendel, M. A., Mungall, C. J., Lewis, S. E., Groza, T., Valentini, G., & Robinson, P. N. (2016). A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease. The American Journal of Human Genetics, 99(3), 595–606. https://doi.org/10.1016/j.ajhg.2016.07.005 |
| Resource category | Clinical Diagnosis |
| Documentation | https://exomiser.readthedocs.io |
| 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 | monarch_kg_services |
| 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 | monarch_app |
| 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 | monarch_api |
| 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
| Ontology Development Kit | |
|---|---|
| PURL | odk |
| Cite | Matentzoglu, N., Goutte-Gattat, D., Tan, S. Z. K., Balhoff, J. P., Carbon, S., Caron, A. R., Duncan, W. D., Flack, J. E., Haendel, M., Harris, N. L., Hogan, W. R., Hoyt, C. T., Jackson, R. C., Kim, H., Kir, H., Larralde, M., McMurry, J. A., Overton, J. A., Peters, B., Pilgrim, C., Stefancsik, R., Robb, S. M. C., Toro, S., Vasilevsky, N. A., Walls, R., Mungall, C. J., & Osumi-Sutherland, D. (2022). Ontology Development Kit: A toolkit for building, maintaining and standardizing biomedical ontologies. Database, 2022, baac087. https://doi.org/10.1093/database/baac087 |
| Resource category | Ontology Maintenance |
| Documentation | https://incatools.github.io/ontology-development-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-development-kit |
| Responsible contact in Monarch | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards | ODK Milestones |
Monarch OLS
| Monarch OLS | |
|---|---|
| PURL | monarch_ols |
| Cite | EBISPOT. (n.d.). OLS4 [Source code]. GitHub. https://github.com/EBISPOT/ols4 |
| Resource category | Registry |
| Documentation | https://github.com/monarch-initiative/ontotools-docker |
| 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 |
Ontology Access Kit
| Ontology Access Kit | |
|---|---|
| PURL | oak |
| Cite | INCATools. (n.d.). ontology-access-kit [Source code]. GitHub. https://github.com/INCATools/ontology-access-kit |
| 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 | OAK Project Board |
SSSOM Toolkit
| SSSOM Toolkit | |
|---|---|
| PURL | sssom_py |
| 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 |
POET
| POET | |
|---|---|
| PURL | 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 | 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 | pheval |
| Cite | Bridges, Y., Souza, V., Cortes, K. G., Haendel, M., Harris, N. L., Korn, D. R., Marinakis, N. M., Matentzoglu, N., McLaughlin, J. A., Mungall, C. J., Odell, A., Osumi-Sutherland, D., Robinson, P. N., Smedley, D., & Jacobsen, J. O. B. (2025). Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval – Phenotypic inference evaluation framework. BMC Bioinformatics, 26(1), 87. https://doi.org/10.1186/s12859-025-06105-4. |
| Resource category | Benchmarking |
| Documentation | https://monarch-initiative.github.io/pheval |
| Monarch role in the development | Lead |
| 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 | 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 | 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 | 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 | 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 | data_harmonizer |
| 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 | ontogpt |
| Cite | Caufield, J. H., Hegde, H., Emonet, V., Harris, N. L., Joachimiak, M. P., Matentzoglu, N., Kim, H., Moxon, S., Reese, J. T., Haendel, M. A., Robinson, P. N., & Mungall, C. J. (2024). Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. Bioinformatics, 40(3). https://doi.org/10.1093/bioinformatics/btae104 |
| 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 |
Aurelian
| Aurelian | |
|---|---|
| PURL | aurelian |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://github.com/monarch-initiative/aurelian |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/aurelian |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Knowledge Graph Registry
| Knowledge Graph Registry | |
|---|---|
| PURL | kg_registry |
| Cite | Knowledge Graph Hub. (n.d.). kg-registry [Source code]. GitHub. https://github.com/Knowledge-Graph-Hub/kg-registry |
| Resource category | Registry |
| Documentation | https://github.com/Knowledge-Graph-Hub/kg-registry |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/Knowledge-Graph-Hub/kg-registry |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Knowledge Graph Hub
| Knowledge Graph Hub | |
|---|---|
| PURL | kg_hub |
| Cite | Caufield, J. H., Putman, T., Schaper, K., Unni, D. R., Hegde, H., Callahan, T. J., Cappelletti, L., Moxon, S. A. T., Ravanmehr, V., Carbon, S., Chan, L. E., Cortes, K., Shefchek, K. A., Elsarboukh, G., Balhoff, J. P., Fontana, T., Matentzoglu, N., Bruskiewich, R. M., Thessen, A. E., Harris, N. L., Munoz-Torres, M. C., Haendel, M. A., Robinson, P. N., Joachimiak, M. P., Mungall, C. J., & Reese, J. T. (2023). KG-Hub — Building and exchanging biological knowledge graphs (arXiv:2302.10800). arXiv. https://arxiv.org/abs/2302.10800 |
| Resource category | Registry |
| Documentation | https://github.com/Knowledge-Graph-Hub/knowledge-graph-hub.github.io |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/Knowledge-Graph-Hub/knowledge-graph-hub.github.io |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
LinkML Registry
| LinkML Registry | |
|---|---|
| PURL | linkml_registry |
| Cite | LinkML. (n.d.). linkml-registry [Source code]. GitHub. https://github.com/linkml/linkml-registry |
| Resource category | Registry |
| Documentation | https://linkml.io/linkml-registry/registry |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Support |
| Main repository | https://github.com/linkml/linkml-registry |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
TALISMAN
| TALISMAN | |
|---|---|
| PURL | 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 | curate_gpt |
| Cite | Caufield, H., Kroll, C., O’Neil, S. T., Reese, J. T., Joachimiak, M. P., Hegde, H., Harris, N. L., Krishnamurthy, M., McLaughlin, J. A., Smedley, D., Haendel, M. A., Robinson, P. N., & Mungall, C. J. (2024). CurateGPT: A flexible language-model assisted biocuration tool. arXiv [cs.CL]. http://arxiv.org/abs/2411.00046 |
| Resource category | Data Curation |
| Documentation | https://monarch-initiative.github.io/curategpt |
| 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 | 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 | monarch_py |
| 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 | 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 | 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 | 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 |
Linked Data Modeling Language
| Linked Data Modeling Language | |
|---|---|
| PURL | linkml |
| Cite | Moxon, S., Solbrig, H., Unni, D., Jiao, D., Bruskiewich, R., Balhoff, J., Vaidya, G., Duncan, W., Hegde, H., Miller, M., Brush, M., Harris, N., Haendel, M., & Mungall, C. (2021). The Linked Data Modeling Language (LinkML): A general-purpose data modeling framework grounded in machine-readable semantics. CEUR Workshop Proceedings, 3073, 148–151 |
| Resource category | Data Curation |
| Documentation | https://linkml.io/linkml/ |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/linkml |
| Responsible contact in Monarch | Chris Mungall, https://orcid.org/0000-0002-6601-2165, @cmungall |
| Project boards |
Monarch Ingest
| Monarch Ingest | |
|---|---|
| PURL | 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 Registry
| Monarch Mapping Registry | |
|---|---|
| PURL | monarch_mapping_registry |
| Cite | Monarch Initiative. (n.d.). monarch-mapping-commons [Source code]. GitHub. https://github.com/monarch-initiative/monarch-mapping-commons |
| Resource category | Registry |
| 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 | Nicolas Matentzoglu, https://orcid.org/0000-0002-7356-1779, @matentzn |
| Project boards |
HPO Language Translations
| HPO Language Translations | |
|---|---|
| PURL | 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 | 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 | 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 |
monarchr
| monarchr | |
|---|---|
| PURL | monarchr |
| Cite | |
| Resource category | Ontology Use |
| Documentation | https://github.com/monarch-initiative/monarchr |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/monarchr |
| Responsible contact in Monarch | Shawn O'Neil, https://orcid.org/0000-0001-6220-7080, @oneilsh |
| Project boards |
Phenomics Assistant
| Phenomics Assistant | |
|---|---|
| PURL | phenomics_assistant |
| Cite | |
| Resource category | Clinical Diagnosis |
| Documentation | https://github.com/monarch-initiative/phenomics-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/phenomics-assistant |
| Responsible contact in Monarch | Kevin Schaper, https://orcid.org/0000-0003-3311-7320, @kevinschaper |
| Project boards |
pheval.llm
| pheval.llm | |
|---|---|
| PURL | 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 | 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 | 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 |
pheval.exomiser
| pheval.exomiser | |
|---|---|
| PURL | pheval.exomiser |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.exomiser |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.exomiser |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.ai_marrvel
| pheval.ai_marrvel | |
|---|---|
| PURL | pheval.ai_marrvel |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.ai_marrvel |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.ai_marrvel |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.phen2gene
| pheval.phen2gene | |
|---|---|
| PURL | pheval.phen2gene |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.phen2gene |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.phen2gene |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.gado
| pheval.gado | |
|---|---|
| PURL | pheval.gado |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.gado |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.gado |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.svanna
| pheval.svanna | |
|---|---|
| PURL | pheval.svanna |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.svanna |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.svanna |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.lirical
| pheval.lirical | |
|---|---|
| PURL | pheval.lirical |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.lirical |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.lirical |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
pheval.phenogenius
| pheval.phenogenius | |
|---|---|
| PURL | pheval.phenogenius |
| Cite | |
| Resource category | Benchmarking |
| Documentation | https://github.com/monarch-initiative/pheval.phenogenius |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/pheval.phenogenius |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
phenotype2phenopacket
| phenotype2phenopacket | |
|---|---|
| PURL | phenotype2phenopacket |
| Cite | |
| Resource category | Data Curation |
| Documentation | https://github.com/monarch-initiative/phenotype2phenopacket |
| Monarch role in the development | Lead |
| Grants involved in this standard | |
| Role in Monarchs strategic vision | Core |
| Main repository | https://github.com/monarch-initiative/phenotype2phenopacket |
| Responsible contact in Monarch | Yasemin Bridges, https://orcid.org/0009-0002-1371-3782, @yaseminbridges |
| Project boards |
Datasets developed by the Monarch Initiative
HPOA - Disease Annotations
| HPOA - Disease Annotations | |
|---|---|
| PURL | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |