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3. ChatGPT usage in the Reactome curation process

Author

Tiwari, Krishna Kumar, primary, Matthews, Lisa, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Orlic-Milacic, Marija, additional, Rothfels, Karen, additional, Ragueneau, Eliot, additional, Gong, Chuqiao, additional, Stephan, Ralf, additional, Li, Nancy, additional, Wu, Guanming, additional, Stein, Lincoln D, additional, D'eustachio, Peter, additional, and Hermjakob, Henning, additional

Published
2023
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4. The Reactome Pathway Knowledgebase 2024

Author

Milacic, Marija, primary, Beavers, Deidre, additional, Conley, Patrick, additional, Gong, Chuqiao, additional, Gillespie, Marc, additional, Griss, Johannes, additional, Haw, Robin, additional, Jassal, Bijay, additional, Matthews, Lisa, additional, May, Bruce, additional, Petryszak, Robert, additional, Ragueneau, Eliot, additional, Rothfels, Karen, additional, Sevilla, Cristoffer, additional, Shamovsky, Veronica, additional, Stephan, Ralf, additional, Tiwari, Krishna, additional, Varusai, Thawfeek, additional, Weiser, Joel, additional, Wright, Adam, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2023
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5. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

Author

Orlic-Milacic, Marija, primary, Rothfels, Karen, additional, Matthews, Lisa, additional, Wright, Adam, additional, Jassal, Bijay, additional, Shamovsky, Veronica, additional, Trinh, Quang, additional, Gillespie, Marc, additional, Sevilla, Cristoffer, additional, Tiwari, Krishna, additional, Ragueneau, Eliot, additional, Gong, Chuqiao, additional, Stephan, Ralf, additional, May, Bruce, additional, Haw, Robin, additional, Weiser, Joel, additional, Beavers, Deidre, additional, Conley, Patrick, additional, Hermjakob, Henning, additional, Stein, Lincoln D., additional, D’Eustachio, Peter, additional, and Wu, Guanming, additional

Published
2023
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6. The Reactome Pathway Knowledgebase 2024.

Author

Milacic, Marija, Beavers, Deidre, Conley, Patrick, Gong, Chuqiao, Gillespie, Marc, Griss, Johannes, Haw, Robin, Jassal, Bijay, Matthews, Lisa, May, Bruce, Petryszak, Robert, Ragueneau, Eliot, Rothfels, Karen, Sevilla, Cristoffer, Shamovsky, Veronica, Stephan, Ralf, Tiwari, Krishna, Varusai, Thawfeek, Weiser, Joel, and Wright, Adam

Published
2024
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7. Using the Reactome Database

Author

Rothfels, Karen, primary, Milacic, Marija, additional, Matthews, Lisa, additional, Haw, Robin, additional, Sevilla, Cristoffer, additional, Gillespie, Marc, additional, Stephan, Ralf, additional, Gong, Chuqiao, additional, Ragueneau, Eliot, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Wright, Adam, additional, Weiser, Joel, additional, Beavers, Deidre, additional, Conley, Patrick, additional, Tiwari, Krishna, additional, Jassal, Bijay, additional, Griss, Johannes, additional, Senff‐Ribeiro, Andrea, additional, Brunson, Timothy, additional, Petryszak, Robert, additional, Hermjakob, Henning, additional, D'Eustachio, Peter, additional, Wu, Guanming, additional, and Stein, Lincoln, additional

Published
2023
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8. Functional Annotation of Disease Variants in Reactome

Author

Orlic-Milacic, Marija, Rothfels, Karen, Matthews, Lisa, Wright, Adam, Jassal, Bijay, Shamovsky, Veronica, Trinh, Quang, Gillespie, Marc, Sevilla, Cristoffer, Tiwari, Krishna, Ragueneau, Eliot, Gong, Chuqiao, Stephan, Ralf, May, Bruce, Haw, Robin, Weiser, Joel, Beavers, Deidre, Conley, Patrick, Hermjakob, Henning, Stein, Lincoln D., D'Eustachio, Peter, and Wu, Guanming

Abstract

Supplementary Tables and Supplementary Methods for the research article "Functional Annotation of Disease Variants in Reactome".

Published
2023
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9. The reactome pathway knowledgebase 2022

Author

Gillespie, Marc, primary, Jassal, Bijay, additional, Stephan, Ralf, additional, Milacic, Marija, additional, Rothfels, Karen, additional, Senff-Ribeiro, Andrea, additional, Griss, Johannes, additional, Sevilla, Cristoffer, additional, Matthews, Lisa, additional, Gong, Chuqiao, additional, Deng, Chuan, additional, Varusai, Thawfeek, additional, Ragueneau, Eliot, additional, Haider, Yusra, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Weiser, Joel, additional, Brunson, Timothy, additional, Sanati, Nasim, additional, Beckman, Liam, additional, Shao, Xiang, additional, Fabregat, Antonio, additional, Sidiropoulos, Konstantinos, additional, Murillo, Julieth, additional, Viteri, Guilherme, additional, Cook, Justin, additional, Shorser, Solomon, additional, Bader, Gary, additional, Demir, Emek, additional, Sander, Chris, additional, Haw, Robin, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2021
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10. reactome pathway knowledgebase 2022.

Author

Gillespie, Marc, Jassal, Bijay, Stephan, Ralf, Milacic, Marija, Rothfels, Karen, Senff-Ribeiro, Andrea, Griss, Johannes, Sevilla, Cristoffer, Matthews, Lisa, Gong, Chuqiao, Deng, Chuan, Varusai, Thawfeek, Ragueneau, Eliot, Haider, Yusra, May, Bruce, Shamovsky, Veronica, Weiser, Joel, Brunson, Timothy, Sanati, Nasim, and Beckman, Liam

Published
2022
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11. The reactome pathway knowledgebase

Author

Jassal, Bijay, primary, Matthews, Lisa, additional, Viteri, Guilherme, additional, Gong, Chuqiao, additional, Lorente, Pascual, additional, Fabregat, Antonio, additional, Sidiropoulos, Konstantinos, additional, Cook, Justin, additional, Gillespie, Marc, additional, Haw, Robin, additional, Loney, Fred, additional, May, Bruce, additional, Milacic, Marija, additional, Rothfels, Karen, additional, Sevilla, Cristoffer, additional, Shamovsky, Veronica, additional, Shorser, Solomon, additional, Varusai, Thawfeek, additional, Weiser, Joel, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2019
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12. The reactome pathway knowledgebase.

Author

Jassal, Bijay, Matthews, Lisa, Viteri, Guilherme, Gong, Chuqiao, Lorente, Pascual, Fabregat, Antonio, Sidiropoulos, Konstantinos, Cook, Justin, Gillespie, Marc, Haw, Robin, Loney, Fred, May, Bruce, Milacic, Marija, Rothfels, Karen, Sevilla, Cristoffer, Shamovsky, Veronica, Shorser, Solomon, Varusai, Thawfeek, Weiser, Joel, and Wu, Guanming

Published
2020
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13. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.

Author

Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, and Wu G

Subjects
Humans, Databases, Genetic, Disease genetics, Phenotype, Molecular Sequence Annotation
Abstract

Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for >11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for >4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome's data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity. Database URL: https://reactome.org/., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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14. ChatGPT usage in the Reactome curation process.

Author

Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, and Hermjakob H

Abstract

Appreciating the rapid advancement and ubiquity of generative AI, particularly ChatGPT, a chatbot using large language models like GPT, we endeavour to explore the potential application of ChatGPT in the data collection and annotation stages within the Reactome curation process. This exploration aimed to create an automated or semi-automated framework to mitigate the extensive manual effort traditionally required for gathering and annotating information pertaining to biological pathways, adopting a Reactome "reaction-centric" approach. In this pilot study, we used ChatGPT/GPT4 to address gaps in the pathway annotation and enrichment in parallel with the conventional manual curation process. This approach facilitated a comparative analysis, where we assessed the outputs generated by ChatGPT against manually extracted information. The primary objective of this comparison was to ascertain the efficiency of integrating ChatGPT or other large language models into the Reactome curation workflow and helping plan our annotation pipeline, ultimately improving our protein-to-pathway association in a reliable and automated or semi-automated way. In the process, we identified some promising capabilities and inherent challenges associated with the utilisation of ChatGPT/GPT4 in general and also specifically in the context of Reactome curation processes. We describe approaches and tools for refining the output given by ChatGPT/GPT4 that aid in generating more accurate and detailed output.

Published
2023
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15. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.

Author

Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, and Wu G

Abstract

Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open source, manually curated, peer-reviewed database of human biological pathways, provides annotations for over 4000 disease variants of close to 400 genes in the context of ∼800 disease reactions constituting ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics (ACMG). Reactome's pathway-based, reaction-specific disease variant dataset and data model provide a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.

Published
2023
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16. The reactome pathway knowledgebase 2022.

Author

Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, and D'Eustachio P

Subjects
COVID-19 metabolism, Data Curation, Genome, Human, Host-Pathogen Interactions, Humans, Proteins genetics, Signal Transduction, Software, Antiviral Agents pharmacology, Knowledge Bases, Proteins metabolism
Abstract

The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied ('dark') proteins from analyzed datasets in the context of Reactome's manually curated pathways., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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