Merge pull request #84 from berkeleybop/nlharris-patch-17

Update links and publications
berkeleybop · Dec 10, 2024 · 5e6b8a7 · 5e6b8a7
2 parents ddebe92 + de438ec
commit 5e6b8a7
Showing 1 changed file with 16 additions and 14 deletions.
diff --git a/project/monarch/index.md b/project/monarch/index.md
@@ -12,37 +12,39 @@ twitter: monarchinit
 ---
 
 The [Monarch Initiative](http://monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.
-Monarch encompasses multiple components: interface, data, ontologies, software and algorithms. These are listed, with links, on [this page](https://beta.monarchinitiative.org/about/licensing).
+Monarch encompasses multiple components: interface, data, ontologies and other standards, software and algorithms. These are listed, with links, on [this page](https://monarchinitiative.org/about).
 
 ## Ontologies created or maintained by Monarch
 
- * [Human Phenotype Ontology (HPO)](http://www.human-phenotype-ontology.org/)
+ * [Human Phenotype Ontology (HPO)](https://hpo.jax.org/)
  * [Mondo Disease Ontology](https://mondo.monarchinitiative.org/)
  * [Genotype Ontology (GENO)](http://obofoundry.org/ontology/geno.html)
  * [Environmental conditions, treatments and exposures ontology (ECTO)](https://github.com/EnvironmentOntology/environmental-exposure-ontology)
- * [Scientific Evidence and Provenance Information Ontology](https://github.com/monarch-initiative/SEPIO-ontology)
+ * [Scientific Evidence and Provenance Information Ontology (SEPIO)](https://github.com/monarch-initiative/SEPIO-ontology)
  * [Unified phenotype ontology (uPheno)](https://github.com/obophenotype/upheno)
  * [Medical Action Ontology (MAxO)](https://github.com/monarch-initiative/MAxO)
+ * [Phenomics Integrated Ontology (PHENIO)](https://github.com/monarch-initiative/phenio/)
 
 ## Architecture
 
-![img](https://beta.monarchinitiative.org/img/Monarch-Architecture2.7b58322f.png)
+![img](https://monarchinitiative.org/assets/architecture-BmDHYnsa.png)
 
-## Communication and internal docs for team members
+## Selected References
 
- * [GitHub](https://github.com/monarch-initiative/)
- * Mailing lists
-    * monarch-internal (ask Julie to be added)
- * [Google Drive](https://drive.google.com/drive/u/1/folders/0B1ggMLKFepMxOWlJWVpPSXFHWGM)
+* Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O’Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res. 2023 Nov 24; [http://dx.doi.org/10.1093/nar/gkad1082](http://dx.doi.org/10.1093/nar/gkad1082) PMID: 38000386
+
+* Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai M-C, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI Jr, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2023 Nov 11; [http://dx.doi.org/10.1093/nar/gkad1005](http://dx.doi.org/10.1093/nar/gkad1005) PMID: 37953324
 
-## References
+* Chan LE, Thessen AE, Duncan WD, Matentzoglu N, Schmitt C, Grondin CJ, Vasilevsky N, McMurry JA, Robinson PN, Mungall CJ, Haendel MA. The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J Biomed Semantics. 2023 Feb 24;14(1):3. [http://dx.doi.org/10.1186/s13326-023-00283-x](http://dx.doi.org/10.1186/s13326-023-00283-x) PMCID: PMC9951428
 
-* Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, ..., Yüksel Z, Helbig I, <b>Mungall CJ</b>, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207–D1217. http://dx.doi.org/10.1093/nar/gkaa1043 PMCID: PMC7778952
-* Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, <b>Mungall CJ</b>, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol. 2020 Nov;16(11):e1008376. http://dx.doi.org/10.1371/journal.pcbi.1008376 PMID: 33232313
+* Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. Nature Publishing Group; 2022 Jun 15;40(6):817–820. [https://www.nature.com/articles/s41587-022-01357-4](https://www.nature.com/articles/s41587-022-01357-4)
 
-* Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, <b>Harris NL</b>, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. Jamia Open. Oxford University Press; 2020 Sep 11; https://academic.oup.com/jamiaopen/advance-article-abstract/doi/10.1093/jamiaopen/ooaa030/5904414
+* Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, ..., Yüksel Z, Helbig I, <b>Mungall CJ</b>, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207–D1217. [http://dx.doi.org/10.1093/nar/gkaa1043](http://dx.doi.org/10.1093/nar/gkaa1043) PMCID: PMC7778952
+
+* Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, <b>Harris NL</b>, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. Jamia Open. Oxford University Press; 2020 Sep 11; [https://academic.oup.com/jamiaopen/advance-article-abstract/doi/10.1093/jamiaopen/ooaa030/5904414](https://academic.oup.com/jamiaopen/advance-article-abstract/doi/10.1093/jamiaopen/ooaa030/5904414)
 
- * Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, Essaid S, Fey P, Grove C, Gourdine J-P, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: An integrative data and analytic platform connecting phenotypes to genotypes across species. _Nucleic Acids Res._ 2019 Nov 8; [http://dx.doi.org/10.1093/nar/gkz997](http://dx.doi.org/10.1093/nar/gkz997) PMID: 31701156 
+ * Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, Essaid S, Fey P, Grove C, Gourdine J-P, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: An integrative data and analytic platform connecting phenotypes to genotypes across species. _Nucleic Acids Res._ 2019 Nov 8; [http://dx.doi.org/10.1093/nar/gkz997](http://dx.doi.org/10.1093/nar/gkz997) PMID: 31701156
+
  * Haendel MA, McMurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. A Census of Disease Ontologies. Annu Rev Biomed Data Sci [Internet]. Annual Reviews; 2018 Jul 20;1(1):305–331. Available from: https://doi.org/10.1146/annurev-biodatasci-080917-013459
  * Vasilevsky NA, Foster ED, Engelstad ME, ... Mungall C, Holm IA, Rageth K, Brownstein CA, Shefchek K, McMurry JA, Robinson PN, Köhler S, Haendel MA. Plain-language medical vocabulary for precision diagnosis. Nat Genet. 2018 Apr;50(4):474–476. http://dx.doi.org/10.1038/s41588-018-0096-x PMCID: PMC6258202
  * Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Others (2018). Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D1018–D1027.