Skip to content

Latest commit

 

History

History
204 lines (173 loc) · 58.2 KB

publications_selected.md

File metadata and controls

204 lines (173 loc) · 58.2 KB
title
Selected BBOP publications

**Please note: this page is hand-curated and may be out of date. See our Paperpile folder of BBOP publications for a more complete list. Last updated 2025-02-27

  1. Hegde H, Vendetti J, Goutte-Gattat D, Caufield JH, Graybeal JB, Harris NL, Karam N, Kindermann C, Matentzoglu N, Overton JA, Musen MA, Mungall CJ. A change language for ontologies and knowledge graphs. Database (Oxford). Oxford University Press (OUP); 2025 Jan 22;2025. https://doi.org/10.1093/database/baae133 PMCID: PMC11753292
  2. Balhoff JP, Mungall CJ. Whelk: An OWL EL+RL reasoner enabling new use cases. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. http://dx.doi.org/10.4230/TGDK.2.2.7
  3. Vestito L, Jacobsen JOB, Walker S, Cipriani V, Harris NL, Haendel MA, Mungall CJ, Robinson P, Smedley D. Efficient reinterpretation of rare disease cases using Exomiser. NPJ Genom Med. Springer Science and Business Media LLC; 2024 Dec 18;9(1):65. http://dx.doi.org/10.1038/s41525-024-00456-2 PMCID: PMC11655964
  4. Kelliher JM, Xu Y, Flynn MC, Babinski M, Canon S, Cavanna E, Clum A, Corilo YE, Fujimoto G, Giberson C, Johnson LYD, Li KJ, Li P-E, Li V, Lo C-C, Lynch W, Piehowski P, Prime K, Purvine S, Rodriguez F, Roux S, Shakya M, Smith M, Sarrafan S, Cholia S, McCue LA, Mungall C, Hu B, Eloe-Fadrosh EA, Chain PSG. Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource. Comput Struct Biotechnol J. Elsevier BV; 2024 Dec;23:3575–3583. http://dx.doi.org/10.1016/j.csbj.2024.09.018
  5. Reese JT, Chimirri L, Bridges Y, Danis D, Caufield JH, Wissink K, McMurry JA, Graefe AS, Casiraghi E, Valentini G, Jacobsen JO, Haendel M, Smedley D, Mungall CJ, Robinson PN. Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools. medRxiv. 2024 Nov 7; http://dx.doi.org/10.1101/2024.07.22.24310816 PMCID: PMC11302616
  6. Clark T, Caufield H, Parker JA, Manir SA, Amorim E, Eddy J, Gim N, Gow B, Goar W, Haendel M, Hansen JN, Harris N, Hermjakob H, Joachimiak M, Jordan G, Lee I-H, McWeeney S, Nebeker C, Nikolov M, Shaffer J, Sheffield N, Sheynkman G, Stevenson J, Chen JY, Mungall C, Wagner A, Kong SW, Ghosh SS, Patel B, Williams A, Munoz-Torres MC. AI-readiness for biomedical data: Bridge2AI recommendations. bioRxivorg. Cold Spring Harbor Laboratory; 2024 Nov 7;2024.10. 23.619844. https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=NCdltcYAAAAJ:PELIpwtuRlgC PMCID: PMC11526931
  7. Caufield H, Kroll C, O’Neil ST, Reese JT, Joachimiak MP, Hegde H, Harris NL, Krishnamurthy M, McLaughlin JA, Smedley D, Haendel MA, Robinson PN, Mungall CJ. CurateGPT: A flexible language-model assisted biocuration tool. arXiv [cs.CL]. 2024. http://arxiv.org/abs/2411.00046
  8. Toro S, Anagnostopoulos AV, Bello SM, Blumberg K, Cameron R, Carmody L, Diehl AD, Dooley DM, Duncan WD, Fey P, Gaudet P, Harris NL, Joachimiak MP, Kiani L, Lubiana T, Munoz-Torres MC, O’Neil S, Osumi-Sutherland D, Puig-Barbe A, Reese JT, Reiser L, Robb SM, Ruemping T, Seager J, Sid E, Stefancsik R, Weber M, Wood V, Haendel MA, Mungall CJ. Dynamic Retrieval Augmented Generation of ontologies using artificial intelligence (DRAGON-AI). J Biomed Semantics. 2024 Oct 17;15(1):19. https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-024-00320-3 PMCID: PMC11484368
  9. Danis D, Bamshad MJ, Bridges Y, Caballero-Oteyza A, Cacheiro P, Carmody LC, Chimirri L, Chong JX, Coleman B, Dalgleish R, Freeman PJ, Graefe ASL, Groza T, Hansen P, Jacobsen JOB, Klocperk A, Kusters M, Ladewig MS, Marcello AJ, Mattina T, Mungall CJ, Munoz-Torres MC, Reese JT, Rehburg F, Reis BCS, Schuetz C, Smedley D, Strauss T, Sundaramurthi JC, Thun S, Wissink K, Wagstaff JF, Zocche D, Haendel MA, Robinson PN. A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery. HGG Adv. Elsevier BV; 2024 Oct 10;6(1):100371. http://dx.doi.org/10.1016/j.xhgg.2024.100371 PMCID: PMC11564936
  10. Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, Harris NL, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SMC, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, Mungall CJ, McLaughlin JA, Osumi-Sutherland D. The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics. bioRxiv. 2024. http://dx.doi.org/10.1101/2024.09.18.613276
  11. Niyonkuru E, Caufield JH, Carmody LC, Gargano MA, Toro S, Whetzel PL, Blau H, Gomez MS, Casiraghi E, Chimirri L, Reese JT, Valentini G, Haendel MA, Mungall CJ, Robinson PN. Leveraging generative AI to accelerate biocuration of medical actions for rare disease. medRxiv. 2024 Aug 22; http://dx.doi.org/10.1101/2024.08.22.24310814 PMCID: PMC11370550
  12. Chan LE, Casiraghi E, Reese J, Harmon QE, Schaper K, Hegde H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, Mungall CJ, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int J Med Inform. 2024 Jul;187:105461. http://dx.doi.org/10.1016/j.ijmedinf.2024.105461 PMCID: PMC11188727
  13. Bridges YS, de Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Osumi-Sutherland DJ, Robinson PN, Smedley D, Jacobsen JOB. Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. bioRxiv. 2024. p. 2024.06.13.598672. https://www.biorxiv.org/content/10.1101/2024.06.13.598672v1
  14. Mullen KR, Tammen I, Matentzoglu NA, Mather M, Mungall CJ, Haendel MA, Nicholas FW, Toro S, Vertebrate Breed Ontology Consortium, the. The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. arXiv e-prints. 2024 Jun 1;arXiv:2406.02623. https://ui.adsabs.harvard.edu/abs/2024arXiv240602623M
  15. Avaylon M, Ly R, Tritt A, Dichter B, Bouchard KE, Mungall CJ, Ruebel O. Methods for linking data to online resources and ontologies with applications to neurophysiology. ArXiv. 2024 May 30;abs/2406.00063. http://dx.doi.org/10.48550/arXiv.2406.00063
  16. Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA Jr, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11;11(1):363. http://dx.doi.org/10.1038/s41597-024-03171-w PMCID: PMC11009265
  17. Joachimiak MP, Miller MA, Harry Caufield J, Ly R, Harris NL, Tritt A, Mungall CJ, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. arXiv [cs.LG]. 2024. http://arxiv.org/abs/2404.03044
  18. Cappelletti L, Rekerle L, Fontana T, Hansen P, Casiraghi E, Ravanmehr V, Mungall CJ, Yang J, Spranger L, Karlebach G, Caufield JH, Carmody L, Coleman B, Oprea T, Reese Jb>, Valentini G, Robinson PN. Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning. Bioinform Adv. 2024 Mar 4; https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae036/7619101
  19. Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, Kim H, Moxon S, Reese JT, Haendel MA, Robinson PN, Mungall CJ. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinformatics. 2024 Mar 4;40(3). http://dx.doi.org/10.1093/bioinformatics/btae104 PMCID: PMC10924283
  20. Reese JT, Danis D, Caufield JH, Groza T, Casiraghi E, Valentini G, Mungall CJ, Robinson PN. On the limitations of large language models in clinical diagnosis. medRxiv. 2024 Feb 26; http://dx.doi.org/10.1101/2023.07.13.23292613 PMCID: PMC10370243
  21. Eloe-Fadrosh EA, Mungall CJ, Miller MA, Smith M, Patil SS, Kelliher JM, Johnson LYD, Rodriguez FE, Chain PSG, Hu B, Thornton MB, McCue LA, McHardy AC, Harris NL, Reddy TBK, Mukherjee S, Hunter CI, Walls R, Schriml LM. A practical approach to using the Genomic Standards Consortium MIxS reporting standard for comparative genomics and metagenomics. Methods Mol Biol. 2024;2802:587–609. https://link.springer.com/protocol/10.1007/978-1-0716-3838-5_20 PMID: 38819573
  22. O’Neil ST, Schaper K, Elsarboukh G, Reese JT, Moxon SAT, Harris NL, Munoz-Torres MC, Robinson PN, Haendel MA, Mungall CJ. Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration. bioRxiv. 2024. p. 2024.01.31.578275. https://www.biorxiv.org/content/biorxiv/early/2024/02/02/2024.01.31.578275
  23. Groza T, Caufield H, Gration D, Baynam G, Haendel MA, Robinson PN, Mungall CJ, Reese JT. An evaluation of GPT models for phenotype concept recognition. BMC Med Inform Decis Mak. BioMed Central; 2024 Jan 31;24(1):1–12. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-024-02439-w
  24. Harris NL, Fields CJ, Hokamp K, Just J, Khetani R, Maia J, Ménager H, Munoz-Torres MC, Unni D, Williams J. BOSC 2023, the 24th annual Bioinformatics Open Source Conference. F1000Res. F1000 Research Ltd; 2023 Dec 7;12:1568. https://f1000research.com/articles/12-1568/pdf
  25. 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 PMID: 38000386
  26. 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 PMID: 37953324
  27. Matentzoglu N, Caufield JH, Hegde HB, Reese JT, Moxon S, Kim H, Harris NL, Haendel MA, Mungall CJ. MapperGPT: Large Language Models for Linking and Mapping Entities. arXiv [cs.CL]. 2023. http://arxiv.org/abs/2310.03666
  28. Antony B, Blau H, Casiraghi E, Loomba JJ, Callahan TJ, Laraway BJ, Wilkins KJ, Antonescu CC, Valentini G, Williams AE, Robinson PN, Reese JT, Murali TM, N3C consortium. Predictive models of long COVID. EBioMedicine. 2023 Sep 4;96:104777. http://dx.doi.org/10.1016/j.ebiom.2023.104777 PMID: 37672869
  29. Reese J, Danis D, Caufield JH, Casiraghi E, Valentini G, Mungall CJ, Robinson PN. On the limitations of large language models in clinical diagnosis. medRxiv. 2023. p. 2023.07.13.23292613. https://www.medrxiv.org/content/10.1101/2023.07.13.23292613v1
  30. Carmody LC, Gargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Ladewig MS, Lewis-Smith D, Lochmueller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Kraus ML, Seitz B, Similuk MN, Sparks T, Strauss T, Swietlik EM, Thompson R, Zhang XA, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. medRxiv. 2023. https://www.medrxiv.org/content/10.1101/2023.07.13.23292612v1
  31. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics. 2023 Jul 1;39(7). http://dx.doi.org/10.1093/bioinformatics/btad418 PMCID: PMC10336030
  32. Joachimiak MP, Harry Caufield J, Harris N, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv [q-bio.GN]. 2023. http://arxiv.org/abs/2305.13338
  33. Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome. 2023 Apr 19; https://link.springer.com/10.1007/s00335-023-09992-1 PMID: 37076585

  34. Karlebach G, Carmody L, Sundaramurthi JC, Casiraghi E, Hansen P, Reese J, Mungall CJ, Valentini G, Robinson PN. An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinformatics. 2023 Apr 3;39(4). https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798 PMCID: PMC10079350

  35. 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 PMCID: PMC9951428
  36. Cappelletti L, Taverni S, Fontana T, Joachimiak MP, Reese J, Robinson P, Casiraghi E, Valentini G. Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs. Bioinformatics and Biomedical Engineering. Springer Nature Switzerland; 2023. p. 372–383. http://dx.doi.org/10.1007/978-3-031-34960-7_26
  37. Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN, N3C Consortium, RECOVER Consortium. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. http://dx.doi.org/10.1016/j.ebiom.2022.104413 PMCID: PMC9769411
  38. Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 Mar 3; https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad031/7068118 PMID: 36866529
  39. Thessen A, Cooper L, Swetnam T, Hegde H, Reese J, Elser J, Jaiswal P. Using knowledge graphs to infer gene expression in plants. Frontiers Artificial Intelligence Appl. 2023;6. https://www.frontiersin.org/articles/10.3389/frai.2023.1201002
  40. Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023 May 17;18(5):e0285433. http://dx.doi.org/10.1371/journal.pone.0285433 PMCID: PMC10191354
  41. Karlebach G, Carmody L, Sundaramurthi JC, Casiraghi E, Hansen P, Reese J, Mungall CJ, Valentini G, Robinson PN. An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinformatics. 2023 Apr 3;39(4). https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798 PMCID: PMC10079350
  42. Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G. GRAPE for fast and scalable graph processing and random-walk-based embedding. Nature Computational Science. Nature Publishing Group; 2023 Jun 26;3(6):552–568. https://www.nature.com/articles/s43588-023-00465-8
  43. Cappelletti L, Taverni S, Fontana T, Joachimiak MP, Reese J, Robinson P, Casiraghi E, Valentini G. Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs. Bioinformatics and Biomedical Engineering. Springer Nature Switzerland; 2023. p. 372–383. http://dx.doi.org/10.1007/978-3-031-34960-7_26
  44. Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D. Brain Data Standards - A method for building data-driven cell-type ontologies. Sci Data. 2023 Jan 24;10(1):50. http://dx.doi.org/10.1038/s41597-022-01886-2 PMCID: PMC9873614
  45. Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN, N3C Consortium, RECOVER Consortium. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. http://dx.doi.org/10.1016/j.ebiom.2022.104413 PMCID: PMC9769411
  46. Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris NL, Wilkins K, Antony B, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J, N3C consortium. Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res Clin Pract. 2022 Nov 15;194:110157. http://dx.doi.org/10.1016/j.diabres.2022.110157 PMCID: PMC9663381
  47. Vasilevsky N, Matentzoglu N, Toro S, Flack J, Hamosh A, Robinson P, Haendel M, Mungall C. 129. Standardization of cancer terminology in the Mondo Disease Ontology. Cancer Genet. Elsevier; 2022 Nov 1;268:41. https://doi.org/10.1016/j.cancergen.2022.10.132
  48. Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database. 2022 Oct 8;2022. http://dx.doi.org/10.1093/database/baac087 PMID: 36208225
  49. 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
  50. Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ, The Biomedical Data Translator Consortium. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. Wiley; 2022 Jun 6; https://onlinelibrary.wiley.com/doi/10.1111/cts.13302
  51. Fecho K, Thessen AT, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dančík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su A, Qin G, Zhu Q, Biomedical Data Translator Consortium. Progress Toward a Universal Biomedical Data Translator. Clin Transl Sci. Wiley Online Library; 2022 May 25; http://dx.doi.org/10.1111/cts.13301 PMID: 35611543
  52. Danis D, Jacobsen JOB, Balachandran P, Zhu Q, Yilmaz F, Reese J, Haimel M, Lyon GJ, Helbig I, Mungall CJ, Beck CR, Lee C, Smedley D, Robinson PN. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. Genome Med. 2022 Apr 28;14(1):44. http://dx.doi.org/10.1186/s13073-022-01046-6 PMID: 35484572
  53. Jacobsen JO, Kelly C, Cipriani V, Consortium GER, Mungall CJ, Reese J, Danis D, Robinson PN, Smedley D. Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease. Hum Mutat. Wiley; 2022 Apr 7; https://onlinelibrary.wiley.com/doi/10.1002/humu.2438 PMID: 35391505
  54. Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde H, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. A Simple Standard for Sharing Ontological Mappings (SSSOM). Database. 2022 May 25;2022. http://dx.doi.org/10.1093/database/baac035 PMID: 35616100.
  55. Sternberg PW, Agapite J, …, Mungall CJ, …, Zhou P, Zytkovicz M, The Alliance of Genome Resources Consortium. Harmonizing model organism data in the Alliance of Genome Resources. Genetics. Oxford University Press (OUP); 2022 Feb 25; https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac022/6537086
  56. Hu, B., Canon, S., Eloe-Fadrosh, E. A., Anubhav, Babinski, M., Corilo, Y., Davenport, K., Duncan, W. D., Fagnan, K., Flynn, M., Foster, B., Hays, D., …, Mouncey, N., Mungall, C.J., … Chain, P. S. G. (2022). Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. Frontiers in Bioinformatics, 1. https://doi.org/10.3389/fbinf.2021.826370
  57. Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG. ECO: the Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Res. Oxford University Press; 2021 Nov 19; https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkab1025/6431816
  58. Eloe-Fadrosh, E.A., Ahmed, F., Anubhav, Babinski, M., Baumes, J., Borkum, M., Bramer, L., Canon, S., Christianson, D.S., Corilo, Y.E. Davenport, K.W., Davis, B., Drake, M., Duncan, W.D., … Chain, P.S.G., McCue, L.A., Mans, D., Mungall, C.J., Mouncey, N.J., Fagnan, K.T. (2022). The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D828–D836, https://doi.org/10.1093/nar/gkab990
  59. Coleman B, Casiraghi E, Blau H, Chan L, Haendel MA, Laraway B, Callahan TJ, Deer RR, Wilkins KJ, Reese J, Robinson PN. Risk of new-onset psychiatric sequelae of COVID-19 in the early and late post-acute phase. World Psychiatry. Wiley; 2022 Jun;21(2):319–320. https://onlinelibrary.wiley.com/doi/10.1002/wps.20992 PMID: 35524622
  60. Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, Mungall C, Oprea TI, Robinson PN. Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. NAR Genom Bioinform. 2021 Dec;3(4):lqab113. http://dx.doi.org/10.1093/nargab/lqab113 PMCID: PMC8652379
  61. Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou L-P, Thomas PD, Mungall CJ, Blake JA, D’Eustachio P. Reactome and the Gene Ontology: Digital convergence of data resources. Bioinformatics. 2021 May 8; http://dx.doi.org/10.1093/bioinformatics/btab325 PMID: 33964129
  62. Reese J, Coleman B, Chan L, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh J, Mungall CJ, Williams AE, Robinson PN. Cyclooxygenase inhibitor use is associated with increased COVID-19 severity. medRxiv, 2021. http://dx.doi.org/10.1101/2021.04.13.21255438
  63. Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia J-M, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities. mSystems. American Society for Microbiology Journals; 2021 Feb 23;6(1). https://msystems.asm.org/content/6/1/e01194-20
  64. Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, ..., Yüksel Z, Helbig I, Mungall CJ, 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
  65. Joachimiak MP. Zinc against COVID-19? Symptom surveillance and deficiency risk groups. PLoS Negl Trop Dis. 2021 Jan;15(1):e0008895. http://dx.doi.org/10.1371/journal.pntd.0008895 PMCID: PMC7781367
  66. Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2020 Dec 8; http://dx.doi.org/10.1093/nar/gkaa1113 PMID: 33290552
  67. Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Patterns (N Y). 2020 Nov 9;100155. http://dx.doi.org/10.1016/j.patter.2020.100155 PMCID: PMC7649624
  68. Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, 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
  69. Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, 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
  70. Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL, UNC Biocuration Core, Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry JA, Haendel MA, Smedley D. Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. Am J Hum Genet. 2020 Sep 3;107(3):403–417. http://dx.doi.org/10.1016/j.ajhg.2020.06.021 PMCID: PMC7477017
  71. Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM, Mungall CJ. Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. Open Biol. 2020 Sep;10(9):200149. http://dx.doi.org/10.1098/rsob.200149 PMCID: PMC7536087
  72. Wood-Charlson EM, Anubhav, Auberry D, Blanco H, Borkum MI, Corilo YE, Davenport KW, Deshpande S, Devarakonda R, Drake M, Duncan WD, Flynn MC, Hays D, Hu B, Huntemann M, Li P-E, Lipton M, Lo C-C, Millard D, Miller K, Piehowski PD, Purvine S, Reddy TBK, Shakya M, Sundaramurthi JC, Vangay P, Wei Y, Wilson BE, Canon S, Chain PSG, Fagnan K, Martin S, McCue LA, Mungall CJ, Mouncey NJ, Maxon ME, Eloe-Fadrosh EA. The National Microbiome Data Collaborative: enabling microbiome science. Nat Rev Microbiol. nature.com; 2020 Jun;18(6):313–314. http://dx.doi.org/10.1038/s41579-020-0377-0 PMID: 32350400
  73. Alliance of Genome Resources Consortium. Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 2020 Jan 8;48(D1):D650–D658. http://dx.doi.org/10.1093/nar/gkz813 PMCID: PMC6943066
  74. Hoyt C, Mungall C, Vasilevsky N, Domingo-Fernández D, Healy M, Colluru V. Extension of Roles in the ChEBI Ontology. ChemRxiv; 2020;
  75. 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 PMID: 31701156
  76. Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP Köhler S, Robinson PN, Mungall C Oprea TI. How many rare diseases are there? Nat Rev Drug Discov, 2019 Nov 5. https://www.nature.com/articles/d41573-019-00180-y
  77. Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ Vision TJ. A Logical Model of Homology for Comparative Biology. Syst. Biol. 2019, p. 588822. http://dx.doi.org/10.1093/sysbio/syz067
  78. Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S Balhoff JP, Albou L-P, Good B, Gaudet P, Lewis SE, Mungall CJ. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet, nature.com; 2019 Oct;51(10):1429–1433. http://dx.doi.org/10.1038/s41588-019-0500-1 PMID: 31548717
  79. The Alliance of Genome Resources Consortium. The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. Genetics. 2019. p. 1189–1196. http://dx.doi.org/10.1534/genetics.119.302523
  80. Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA. ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics , 2019 Jul 29;20(1):407. http://dx.doi.org/10.1186/s12859-019-3002-3 PMID: 31357927
  81. Carbon S Champieux R, McMurry JA, Winfree L, Wyatt LR, Haendel MA. An analysis and metric of reusable data licensing practices for biomedical resources. PLoS One. 2019 Mar 27;14(3):e0213090. http://dx.doi.org/10.1371/journal.pone.0213090 PMID: 30917137
  82. Dunn NA, Unni D, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE. Apollo: Democratizing genome annotation. PLoS Comput Biol. 2019 Feb;15(2):e1006790. http://dx.doi.org/10.1371/journal.pcbi.1006790 PMCID: PMC6380598
  83. Mungall CJ, Koehler S, Robinson P, Holmes I, Haendel M. k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction. bioRxiv. 2019. https://www.biorxiv.org/content/10.1101/048843v3
  84. Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2019 Jan 8;47(D1):D1186–D1194. http://dx.doi.org/10.1093/nar/gky1036 PMCID: PMC6323956
  85. Haendel MA, McMurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. A Census of Disease Ontologies. Annu Rev Biomed Data Sci. Annual Reviews; 2018 Jul 20;1(1):305–331. https://doi.org/10.1146/annurev-biodatasci-080917-013459
  86. Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep. 2018 Jul 18;8(1):10872. http://dx.doi.org/10.1038/s41598-018-28948-z PMCID: PMC6052049
  87. Vasilevsky NA, Foster ED, Engelstad ME, Carmody L, Might M, Chambers C, Dawkins HJS, Lewis J, Della Rocca MG, Snyder M, Boerkoel CF, Rath A, Terry SF, Kent A, Searle B, Baynam G, Jones E, Gavin P, Bamshad M, Chong J, Groza T, Adams D, Resnick AC, Heath AP, 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
  88. Tang H, Mungall CJ, Mi H, Thomas PD. GOTaxon: Representing the evolution of biological functions in the Gene Ontology. arXiv [q-bio.PE]. 2018. http://arxiv.org/abs/1802.06004
  89. Matentzoglu N, Malone J, Mungall C, Stevens R. MIRO: guidelines for minimum information for the reporting of an ontology. J Biomed Semantics. 2018 Jan 18;9(1):6. http://dx.doi.org/10.1186/s13326-017-0172-7 PMCID: PMC5774126
  90. Cooper L, Meier A, Laporte M-A, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res. 2018 Jan 4;46(D1):D1168–D1180. http://dx.doi.org/10.1093/nar/gkx1152 PMCID: PMC5753347
  91. Haendel MA, Mcmurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. Annual Review of Biomedical Data Science A Census of Disease Ontologies. 2018;(April):305–331.
  92. GO Consortium. Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D330–D338.
  93. Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Others. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D1018–D1027.
  94. Balhoff JP, Good BM, Carbon S, Mungall CJ. Arachne: an OWL RL reasoner applied to Gene Ontology Causal Activity Models (and beyond). Zenodo; 2018. http://dx.doi.org/10.5281/ZENODO.2397192
  95. Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JOB, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 Jan 4;45(D1):D712–D722. http://dx.doi.org/10.1093/nar/gkw1128 PMCID: PMC5210586
  96. Holmes IH, Mungall CJ. BioMake: a GNU make-compatible utility for declarative workflow management. Bioinformatics. 2017 Nov 1;33(21):3502–3504. http://dx.doi.org/10.1093/bioinformatics/btx306 PMCID: PMC5860158
  97. Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Dead simple OWL design patterns. J Biomed Semantics. 2017 Jun 5;8(1):18. http://dx.doi.org/10.1186/s13326-017-0126-0 PMCID: PMC5460348
  98. Mungall CJ, Holmes IH. WTFgenes: What’s The Function of these genes? Static sites for model-based gene set analysis. F1000Res. 2017 Apr 4. https://f1000research.com/articles/6-423/v1/pdf
  99. Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 Jan 4;45(D1):D865–D876. http://dx.doi.org/10.1093/nar/gkw1039 PMCID: PMC5210535
  100. Munoz-Torres M, Carbon S. Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools. Methods Mol Biol. 2017;1446:149–160. http://dx.doi.org/10.1007/978-1-4939-3743-1_11 PMID: 27812941
  101. Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 4;7(1):44. http://dx.doi.org/10.1186/s13326-016-0088-7 PMCID: PMC4932724
  102. Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. 2016 Sep 23;7(1):57. http://dx.doi.org/10.1186/s13326-016-0097-6 PMCID: PMC5035502
  103. Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat. 2015 Oct;36(10):922–927. http://dx.doi.org/10.1002/humu.22850 PMCID: PMC4775166
  104. Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat. 2015 Oct;36(10):979–984. http://dx.doi.org/10.1002/humu.22857 PMCID: PMC5473253
  105. Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. TermGenie -- a web-application for pattern-based ontology class generation. J Biomed Semantics. 2014 Dec 11;5(1):48. https://doi.org/10.1186/2041-1480-5-48
  106. Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014 May 19;5:21. http://dx.doi.org/10.1186/2041-1480-5-21 PMCID: PMC4089931
  107. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park S-M, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AOM, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BBA, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan;42(Database issue):D966–74. http://dx.doi.org/10.1093/nar/gkt1026 PMCID: PMC3965098
  108. Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis SE (2013). Web Apollo: a web-based genomic annotation editing platform. Genome Biol, 2013 Aug 30;14(8):R93. http://dx.doi.org/10.1186/gb-2013-14-8-r93 PMCID: PMC4053811
  109. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012 Jan 31;13(1):R5. http://dx.doi.org/10.1186/gb-2012-13-1-r5 PMCID: PMC3334586
  110. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010 Jan 8;11(1):R2. http://dx.doi.org/10.1186/gb-2010-11-1-r2 PMCID: PMC2847714
  111. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov;7(11):e1000247. http://dx.doi.org/10.1371/journal.pbio.1000247 PMCID: PMC2774506
  112. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. 2009 Sep;19(9):1630–1638. http://dx.doi.org/10.1101/gr.094607.109 PMCID: PMC2752129
  113. Haendel MA, Gkoutos GG, Lewis SE, Mungall C. Uberon: towards a comprehensive multi-species anatomy ontology. 2009. http://precedings.nature.com/documents/3592/version/1
  114. Lee E, Harris N, Gibson M, Chetty R, Lewis S. Apollo: a community resource for genome annotation editing. Bioinformatics. Oxford University Press; 2009;25(14):1836–1837.
  115. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15;25(2):288–289. http://dx.doi.org/10.1093/bioinformatics/btn615 PMCID: PMC2639003
  116. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov;25(11):1251–1255. http://dx.doi.org/10.1038/nbt1346 PMCID: PMC2814061
  117. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005 Apr 29;6(5):R44. http://dx.doi.org/10.1186/gb-2005-6-5-r44 PMCID: PMC1175956
  118. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258–61. http://dx.doi.org/10.1093/nar/gkh036 PMCID: PMC308770
  119. FlyBase Consortium. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 2003 Jan 1;31(1):172–175. https://www.ncbi.nlm.nih.gov/pubmed/12519974 PMCID: PMC165541
  120. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599–1610. http://dx.doi.org/10.1101/gr.403602 PMCID: PMC187535
  121. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Others. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol. BioMed Central; 2002;3(12):research0081–1.
  122. Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res. 2001 Aug;11(8):1425–1433. http://dx.doi.org/10.1101/gr.180801 PMCID: PMC311077
  123. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Others (2002). Apollo: a sequence annotation editor. Genome Biol. BioMed Central; 2002;3(12):research0082–1.
  124. Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster. Genome Res. Cold Spring Harbor Lab; 2000;10(4):483–501.
  125. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O’Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science. 2000 Mar 24;287(5461):2204–2215. https://www.ncbi.nlm.nih.gov/pubmed/10731134 PMCID: PMC2754258
  126. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185–2195. https://www.ncbi.nlm.nih.gov/pubmed/10731132 PMID: 10731132