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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; 187:105461. [PMID: 38643701 DOI: 10.1016/j.ijmedinf.2024.105461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
OBJECTIVE Female reproductive disorders (FRDs) are common health conditions that may present with significant symptoms. Diet and environment are potential areas for FRD interventions. We utilized a knowledge graph (KG) method to predict factors associated with common FRDs (for example, endometriosis, ovarian cyst, and uterine fibroids). MATERIALS AND METHODS We harmonized survey data from the Personalized Environment and Genes Study (PEGS) on internal and external environmental exposures and health conditions with biomedical ontology content. We merged the harmonized data and ontologies with supplemental nutrient and agricultural chemical data to create a KG. We analyzed the KG by embedding edges and applying a random forest for edge prediction to identify variables potentially associated with FRDs. We also conducted logistic regression analysis for comparison. RESULTS Across 9765 PEGS respondents, the KG analysis resulted in 8535 significant or suggestive predicted links between FRDs and chemicals, phenotypes, and diseases. Amongst these links, 32 were exact matches when compared with the logistic regression results, including comorbidities, medications, foods, and occupational exposures. DISCUSSION Mechanistic underpinnings of predicted links documented in the literature may support some of our findings. Our KG methods are useful for predicting possible associations in large, survey-based datasets with added information on directionality and magnitude of effect from logistic regression. These results should not be construed as causal but can support hypothesis generation. CONCLUSION This investigation enabled the generation of hypotheses on a variety of potential links between FRDs and exposures. Future investigations should prospectively evaluate the variables hypothesized to impact FRDs.
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Affiliation(s)
- Lauren E Chan
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA.
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; European Laboratory for Learning and Intelligent Systems, ELLIS
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Quaker E Harmon
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Kevin Schaper
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy; European Laboratory for Learning and Intelligent Systems, ELLIS
| | - Charles Schmitt
- National Institute of Environmental Health Sciences, Office of Data Science, Durham, NC, USA
| | - Alison Motsinger-Reif
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, Durham, NC, USA
| | - Janet E Hall
- National Institute of Environmental Health Sciences, Clinical Research Branch, Durham, NC, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter N Robinson
- European Laboratory for Learning and Intelligent Systems, ELLIS; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Melissa A Haendel
- University of North Carolina, Dept. of Genetics, Chapel Hill, NC, USA
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2
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Huang Y, Bu L, Zhu S, Zhou S. Integration of nontarget analysis with machine learning modeling for prioritization of odorous volatile organic compounds in surface water. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134367. [PMID: 38653135 DOI: 10.1016/j.jhazmat.2024.134367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/29/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Assessing the odor risk caused by volatile organic compounds (VOCs) in water has been a big challenge for water quality evaluation due to the abundance of odorants in water and the inherent difficulty in obtaining the corresponding odor sensory attributes. Here, a novel odor risk assessment approach has been established, incorporating nontarget screening for odorous VOC identification and machine learning (ML) modeling for odor threshold prediction. Twenty-nine odorous VOCs were identified using two-dimensional gas chromatography-time of flight mass spectrometry from four surface water sampling sites. These identified odorants primarily fell into the categories of ketones and ethers, and originated mainly from biological production. To obtain the odor threshold of these odorants, we trained an ML model for odor threshold prediction, which displayed good performance with accuracy of 79%. Further, an odor threshold-based prioritization approach was developed to rank the identified odorants. 2-Methylisoborneol and nonanal were identified as the main odorants contributing to water odor issues at the four sampling sites. This study provides an accessible method for accurate and quick determination of key odorants in source water, aiding in odor control and improved water quality management. ENVIRONMENTAL IMPLICATION: Water odor episodes have been persistent and significant issues worldwide, posing severe challenges to water treatment plants. Unpleasant odors in aquatic environments are predominantly caused by the occurrence of a wide range of volatile organic chemicals (VOCs). Given the vast number of newly-detected VOCs, experimental identification of the key odorants becomes difficult, making water odor issues complex to control. Herein, we propose a novel approach integrating nontarget analysis with machine learning models to accurate and quick determine the key odorants in waterbodies. We use the approach to analyze four samples with odor issues in Changsha, and prioritized the potential odorants.
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Affiliation(s)
- Yuanxi Huang
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha 410082, China
| | - Lingjun Bu
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha 410082, China.
| | - Shumin Zhu
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha 410082, China
| | - Shiqing Zhou
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha 410082, China
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Yamagata Y, Kushida T, Onami S, Masuya H. Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. BMC Med Inform Decis Mak 2024; 23:301. [PMID: 38778394 PMCID: PMC11110177 DOI: 10.1186/s12911-024-02516-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND One significant challenge in addressing the coronavirus disease 2019 (COVID-19) pandemic is to grasp a comprehensive picture of its infectious mechanisms. We urgently need a consistent framework to capture the intricacies of its complicated viral infectious processes and diverse symptoms. RESULTS We systematized COVID-19 infectious processes through an ontological approach and provided a unified description framework of causal relationships from the early infectious stage to severe clinical manifestations based on the homeostasis imbalance process ontology (HoIP). HoIP covers a broad range of processes in the body, ranging from normal to abnormal. Moreover, our imbalance model enabled us to distinguish viral functional demands from immune defense processes, thereby supporting the development of new drugs, and our research demonstrates how ontological reasoning contributes to the identification of patients at severe risk. CONCLUSIONS The HoIP organises knowledge of COVID-19 infectious processes and related entities, such as molecules, drugs, and symptoms, with a consistent descriptive framework. HoIP is expected to harmonise the description of various heterogeneous processes and improve the interoperability of COVID-19 knowledge through the COVID-19 ontology harmonisation working group.
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Affiliation(s)
- Yuki Yamagata
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Tatsuya Kushida
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki, 305-0074, Japan
| | - Shuichi Onami
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hiroshi Masuya
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki, 305-0074, Japan
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4
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Kim DH, Lee S, Ahn J, Kim JH, Lee E, Lee I, Byun S. Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways. ENVIRONMENTAL RESEARCH 2024; 249:118437. [PMID: 38346486 DOI: 10.1016/j.envres.2024.118437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
The widespread prevalence of micro and nanoplastics in the environment raises concerns about their potential impact on human health. Recent evidence demonstrates the presence of nanoplastics in human blood and tissues following ingestion and inhalation, yet the specific risks and mechanisms of nanoplastic toxicity remain inadequately understood. In this study, we aimed to explore the molecular mechanisms underlying the toxicity of nanoplastics at both systemic and molecular levels by analyzing the transcriptomic/metabolomic responses and signaling pathways in the intestines of mice after oral administration of nanoplastics. Transcriptome analysis in nanoplastic-administered mice revealed a notable upregulation of genes involved in pro-inflammatory immune responses. In addition, nanoplastics substantially reduced the expression of tight junction proteins, including occludin, zonula occluden-1, and tricellulin, which are crucial for maintaining gut barrier integrity and function. Importantly, nanoplastic administration increased gut permeability and exacerbated dextran sulfate sodium-induced colitis. Further investigation into the underlying molecular mechanisms highlighted significant activation of signaling transsducer and activator of transcription (STAT)1 and STAT6 by nanoplastic administration, which was in line with the elevation of interferon and JAK-STAT pathway signatures identified through transcriptome enrichment analysis. Additionally, the consumption of nanoplastics specifically induced nuclear factor kappa-B (NF-κB) and extracellular signal-regulated kinase (ERK)1/2 signaling pathways in the intestines. Collectively, this study identifies molecular mechanisms contributing to adverse effects mediated by nanoplastics in the intestine, providing novel insights into the pathophysiological consequences of nanoplastic exposure.
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Affiliation(s)
- Da Hyun Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sungho Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jisong Ahn
- Research Group of Traditional Food, Korea Food Research Institute, Wanju, 55365, Republic of Korea; Department of Food Science and Technology, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Jae Hwan Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Eunjung Lee
- Research Group of Traditional Food, Korea Food Research Institute, Wanju, 55365, Republic of Korea; Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Sanguine Byun
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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5
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Glauer M, Neuhaus F, Flügel S, Wosny M, Mossakowski T, Memariani A, Schwerdt J, Hastings J. Chebifier: automating semantic classification in ChEBI to accelerate data-driven discovery. DIGITAL DISCOVERY 2024; 3:896-907. [PMID: 38756223 PMCID: PMC11094693 DOI: 10.1039/d3dd00238a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/26/2024] [Indexed: 05/18/2024]
Abstract
Connecting chemical structural representations with meaningful categories and semantic annotations representing existing knowledge enables data-driven digital discovery from chemistry data. Ontologies are semantic annotation resources that provide definitions and a classification hierarchy for a domain. They are widely used throughout the life sciences. ChEBI is a large-scale ontology for the domain of biologically interesting chemistry that connects representations of chemical structures with meaningful chemical and biological categories. Classifying novel molecular structures into ontologies such as ChEBI has been a longstanding objective for data scientific methods, but the approaches that have been developed to date are limited in several ways: they are not able to expand as the ontology expands without manual intervention, and they are not able to learn from continuously expanding data. We have developed an approach for automated classification of chemicals in the ChEBI ontology based on a neuro-symbolic AI technique that harnesses the ontology itself to create the learning system. We provide this system as a publicly available tool, Chebifier, and as an API, ChEB-AI. We here evaluate our approach and show how it constitutes an advance towards a continuously learning semantic system for chemical knowledge discovery.
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Affiliation(s)
| | | | | | - Marie Wosny
- Institute for Implementation Science in Health Care, University of Zurich Switzerland
- School of Medicine, University of St. Gallen Switzerland
| | | | | | - Johannes Schwerdt
- Otto von Guericke University Magdeburg Germany
- University of Applied Sciences Merseburg Germany
| | - Janna Hastings
- Institute for Implementation Science in Health Care, University of Zurich Switzerland
- School of Medicine, University of St. Gallen Switzerland
- Swiss Institute of Bioinformatics Switzerland
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6
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Dhar R, Chakraborty S. Effect of continuous microwave processing on enzymes and quality attributes of bael beverage. Food Chem 2024; 453:139621. [PMID: 38761728 DOI: 10.1016/j.foodchem.2024.139621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
Bael (Aegle marmelos) beverage was pasteurized using continuous-microwave (MW) and traditional thermal processing and the activity of native enzymes, pulp-hydrolyzing enzymes, bioactive, physicochemical, and sensory properties were analyzed. First-order and linear biphasic models fitted well (R2 ≥ 0.90) for enzyme inactivation and bioactive alteration kinetics, respectively. For the most resistant enzyme, polyphenoloxidase (PPO), the inactivation target of ≥ 90 % was achieved at 90 °C TMW (final temperature under MW) and 95 °C for 5 min (conventional thermal). MW treatment displayed faster enzyme inactivation and better retention of TPC and AOC. MW treatment at 90 °C TMW showed 5.3 min D-value, 90% total carotenoid content, 3.42 crisp sensory score (out of 5), and no or minor change in physicochemical attributes. Thermal and MW treatment caused the loss of 14 and 10 bioactive compounds, respectively. The secondary and tertiary structural modifications of PPO enzyme-protein revealed MW's lethality primarily due to its thermal effects.
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Affiliation(s)
- Rishab Dhar
- Department of Food Engineering and Technology, Institute of Chemical Technology (ICT), Matunga, Mumbai, Maharashtra 400019, India
| | - Snehasis Chakraborty
- Department of Food Engineering and Technology, Institute of Chemical Technology (ICT), Matunga, Mumbai, Maharashtra 400019, India.
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7
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Yamagata Y, Fukuyama T, Onami S, Masuya H. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Sci Data 2024; 11:485. [PMID: 38729991 PMCID: PMC11087592 DOI: 10.1038/s41597-024-03331-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Although cellular senescence is a key factor in organismal aging, with both positive and negative effects on individuals, its mechanisms remain largely unknown. Thus, integrating knowledge is essential to explain how cellular senescence manifests in tissue damage and age-related diseases. Here, we propose an ontological model that organizes knowledge of cellular senescence in a computer-readable form. We manually annotated and defined cellular senescence processes, molecules, anatomical structures, phenotypes, and other entities based on the Homeostasis Imbalance Process ontology (HOIP). We described the mechanisms as causal relationships of processes and modelled a homeostatic imbalance between stress and stress response in cellular senescence for a unified framework. HOIP was assessed formally, and the relationships between cellular senescence and diseases were inferred for higher-order knowledge processing. We visualized cellular senescence processes to support knowledge utilization. Our study provides a knowledge base to help elucidate mechanisms linking cellular and organismal aging.
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Affiliation(s)
- Yuki Yamagata
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Tsubasa Fukuyama
- AXIOHELIX CO. LTD., 8F Kubota Bldg., 1-12-17 Kandaizumicho, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hiroshi Masuya
- Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, Kouyadai 3-1-1 Tsukuba, Ibaraki, 305-0074, Japan.
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8
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Boas Lichty KE, Loughran RM, Ushijima B, Richards GP, Boyd EF. Osmotic stress response of the coral and oyster pathogen Vibrio coralliilyticus : acquisition of catabolism gene clusters for the compatible solute and signaling molecule myo -inositol. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575920. [PMID: 38766061 PMCID: PMC11100586 DOI: 10.1101/2024.01.16.575920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known as osmolytes. The osmotic stress response and compatible solutes used by the coral and oyster pathogen Vibrio coralliilyticus were unknown. In this study, we showed that to alleviate osmotic stress V. coralliilyticus biosynthesized glycine betaine (GB) and transported into the cell choline, GB, ectoine, dimethylglycine, and dimethylsulfoniopropionate, but not myo -inositol. Myo -inositol is a stress protectant and a signaling molecule that is biosynthesized and used by algae. Bioinformatics identified myo -inositol ( iol ) catabolism clusters in V. coralliilyticus and other Vibrio, Photobacterium, Grimontia, and Enterovibrio species. Growth pattern analysis demonstrated that V. coralliilyticus utilized myo -inositol as a sole carbon source, with a short lag time of 3 h. An iolG deletion mutant, which encodes an inositol dehydrogenase, was unable to grow on myo -inositol. Within the iol clusters were an MFS-type ( iolT1) and an ABC-type ( iolXYZ) transporter and analyses showed that both transported myo -inositol. IolG and IolA phylogeny among Vibrionaceae species showed different evolutionary histories indicating multiple acquisition events. Outside of Vibrionaceae , IolG was most closely related to IolG from a small group of Aeromonas fish and human pathogens and Providencia species. However, IolG from hypervirulent A. hydrophila strains clustered with IolG from Enterobacter, and divergently from Pectobacterium, Brenneria, and Dickeya plant pathogens. The iol cluster was also present within Aliiroseovarius, Burkholderia, Endozoicomonas, Halomonas, Labrenzia, Marinomonas, Marinobacterium, Cobetia, Pantoea, and Pseudomonas, of which many species were associated with marine flora and fauna. IMPORTANCE Host associated bacteria such as V. coralliilyticus encounter competition for nutrients and have evolved metabolic strategies to better compete for food. Emerging studies show that myo -inositol is exchanged in the coral-algae symbiosis, is likely involved in signaling, but is also an osmolyte in algae. The bacterial consumption of myo -inositol could contribute to a breakdown of the coral-algae symbiosis during thermal stress or disrupt the coral microbiome. Phylogenetic analyses showed that the evolutionary history of myo -inositol metabolism is complex, acquired multiple times in Vibrio, but acquired once in many bacterial plant pathogens. Further analysis also showed that a conserved iol cluster is prevalent among many marine species (commensals, mutualists, and pathogens) associated with marine flora and fauna, algae, sponges, corals, molluscs, crustaceans, and fish.
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Arora C, Matic M, Bisceglia L, Di Chiaro P, De Oliveira Rosa N, Carli F, Clubb L, Nemati Fard LA, Kargas G, Diaferia GR, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F. The landscape of cancer-rewired GPCR signaling axes. CELL GENOMICS 2024; 4:100557. [PMID: 38723607 PMCID: PMC11099383 DOI: 10.1016/j.xgen.2024.100557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/17/2024] [Accepted: 04/10/2024] [Indexed: 05/15/2024]
Abstract
We explored the dysregulation of G-protein-coupled receptor (GPCR) ligand systems in cancer transcriptomics datasets to uncover new therapeutics opportunities in oncology. We derived an interaction network of receptors with ligands and their biosynthetic enzymes. Multiple GPCRs are differentially regulated together with their upstream partners across cancer subtypes and are associated to specific transcriptional programs and to patient survival patterns. The expression of both receptor-ligand (or enzymes) partners improved patient stratification, suggesting a synergistic role for the activation of GPCR networks in modulating cancer phenotypes. Remarkably, we identified many such axes across several cancer molecular subtypes, including many involving receptor-biosynthetic enzymes for neurotransmitters. We found that GPCRs from these actionable axes, including, e.g., muscarinic, adenosine, 5-hydroxytryptamine, and chemokine receptors, are the targets of multiple drugs displaying anti-growth effects in large-scale, cancer cell drug screens, which we further validated. We have made the results generated in this study freely available through a webapp (gpcrcanceraxes.bioinfolab.sns.it).
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Affiliation(s)
- Chakit Arora
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marin Matic
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Luisa Bisceglia
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Natalia De Oliveira Rosa
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Francesco Carli
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lauren Clubb
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lorenzo Amir Nemati Fard
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giorgos Kargas
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Ranka Vukotic
- Azienda Ospedaliero-Universitaria Pisana, Via Roma, 67, 56126 Pisa, Italy
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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Rutherford KM, Lera-Ramírez M, Wood V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics 2024; 227:iyae007. [PMID: 38376816 PMCID: PMC11075564 DOI: 10.1093/genetics/iyae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/13/2024] [Indexed: 02/21/2024] Open
Abstract
PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community.
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Affiliation(s)
- Kim M Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Manuel Lera-Ramírez
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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11
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Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, Dos Santos G, Tabone CJ. FlyBase: updates to the Drosophila genes and genomes database. Genetics 2024; 227:iyad211. [PMID: 38301657 DOI: 10.1093/genetics/iyad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 02/03/2024] Open
Abstract
FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.
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Affiliation(s)
- Arzu Öztürk-Çolak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Damien Goutte-Gattat
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Victoria K Jenkins
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Beverley B Matthews
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Gilberto Dos Santos
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Tabone
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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12
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Duke R, McCoy R, Risko C, Bursten JRS. Promises and Perils of Big Data: Philosophical Constraints on Chemical Ontologies. J Am Chem Soc 2024; 146:11579-11591. [PMID: 38640489 DOI: 10.1021/jacs.3c11399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Chemistry is experiencing a paradigm shift in the way it interacts with data. So-called "big data" are collected and used at unprecedented scales with the idea that algorithms can be designed to aid in chemical discovery. As data-enabled practices become ever more ubiquitous, chemists must consider the organization and curation of their data, especially as it is presented to both humans and increasingly intelligent algorithms. One of the most promising organizational schemes for big data is a construct termed an ontology. In data science, ontologies are systems that represent relations among objects and properties in a domain of discourse. As chemistry encounters larger and larger data sets, the ontologies that support chemical research will likewise increase in complexity, and the future of chemistry will be shaped by the choices made in developing big data chemical ontologies. How such ontologies will work should therefore be a subject of significant attention in the chemical community. Now is the time for chemists to ask questions about ontology design and use: How should chemical data be organized? What can be reasonably expected from an organizational structure? Is a universal ontology tenable? As some of these questions may be new to chemists, we recommend an interdisciplinary approach that draws on the long history of philosophers of science asking questions about the organization of scientific concepts, constructs, models, and theories. This Perspective presents insights from these long-standing studies and initiates new conversations between chemists and philosophers.
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Affiliation(s)
- Rebekah Duke
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Ryan McCoy
- Department of Philosophy, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Chad Risko
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Julia R S Bursten
- Department of Philosophy, University of Kentucky, Lexington, Kentucky 40508, United States
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13
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Vidović D, Waller A, Holmes J, Sklar LA, Schürer SC. Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. Drug Discov Today 2024; 29:103953. [PMID: 38508231 DOI: 10.1016/j.drudis.2024.103953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
The Illuminating the Druggable Genome (IDG) consortium generated reagents, biological model systems, data, informatic databases, and computational tools. The Resource Dissemination and Outreach Center (RDOC) played a central administrative role, organized internal meetings, fostered collaboration, and coordinated consortium-wide efforts. The RDOC developed and deployed a Resource Management System (RMS) to enable efficient workflows for collecting, accessing, validating, registering, and publishing resource metadata. IDG policies for repositories and standardized representations of resources were established, adopting the FAIR (findable, accessible, interoperable, reusable) principles. The RDOC also developed metrics of IDG impact. Outreach initiatives included digital content, the Protein Illumination Timeline (representing milestones in generating data and reagents), the Target Watch publication series, the e-IDG Symposium series, and leveraging social media platforms.
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Affiliation(s)
- Dušica Vidović
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anna Waller
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Larry A Sklar
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Autophagy, Inflammation, & Metabolism (AIM) Center, University of New Mexico, Albuquerque, NM, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA; Frost Institute for Data Science & Computing, University of Miami, Miami, FL, USA.
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14
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Bhattacharjee S, Saha B, Saha S. Symptom-based drug prediction of lifestyle-related chronic diseases using unsupervised machine learning techniques. Comput Biol Med 2024; 174:108413. [PMID: 38608323 DOI: 10.1016/j.compbiomed.2024.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/13/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND AND OBJECTIVES Lifestyle-related diseases (LSDs) impose a substantial economic burden on patients and health care services. LSDs are chronic in nature and can directly affect the heart and lungs. Therapeutic interventions only based on symptoms can be crucial for prompt treatment initiation in LSDs, as symptoms are the first information available to clinicians. So, this work aims to apply unsupervised machine learning (ML) techniques for developing models to predict drugs from symptoms for LSDs, with a specific focus on pulmonary and heart diseases. METHODS The drug-disease and disease-symptom associations of 143 LSDs, 1271 drugs, and 305 symptoms were used to compute direct associations between drugs and symptoms. ML models with four different algorithms - K-Means, Bisecting K-Means, Mean Shift, and Balanced Iterative Reducing and Clustering using Hierarchies (BIRCH) - were developed to cluster the drugs using symptoms as features. The optimal model was saved in a server for the development of a web application. A web application was developed to perform the prediction based on the optimal model. RESULTS The Bisecting K-means model showed the best performance with a silhouette coefficient of 0.647 and generated 138 drug clusters. The drugs within the optimal clusters showed good similarity based on i) gene ontology annotations of the gene targets, ii) chemical ontology annotations, and iii) maximum common substructure of the drugs. In the web application, the model also provides a confidence score for each predicted drug while predicting from a new set of input symptoms. CONCLUSION In summary, direct associations between drugs and symptoms were computed, and those were used to develop a symptom-based drug prediction tool for LSDs with unsupervised ML models. The ML-based prediction can provide a second opinion to clinicians to aid their decision-making for early treatment of LSD patients. The web application (URL - http://bicresources.jcbose.ac.in/ssaha4/sdldpred) can provide a simple interface for all end-users to perform the ML-based prediction.
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Affiliation(s)
- Sudipto Bhattacharjee
- Department of Computer Science and Engineering, University of Calcutta, JD-2, Sector-III, Salt Lake, Kolkata, 700098, India.
| | - Banani Saha
- Department of Computer Science and Engineering, University of Calcutta, JD-2, Sector-III, Salt Lake, Kolkata, 700098, India.
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, 700091, India.
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15
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Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024:gkae300. [PMID: 38686803 DOI: 10.1093/nar/gkae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.
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Affiliation(s)
- Marine Bugnon
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mathilde Goullieux
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology, Geneva University Hospital (HUG), CH-1205 Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, CH-1015 Lausanne, Switzerland
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16
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Bleker C, Ramšak Ž, Bittner A, Podpečan V, Zagorščak M, Wurzinger B, Baebler Š, Petek M, Križnik M, van Dieren A, Gruber J, Afjehi-Sadat L, Weckwerth W, Županič A, Teige M, Vothknecht UC, Gruden K. Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. PLANT COMMUNICATIONS 2024:100920. [PMID: 38616489 DOI: 10.1016/j.xplc.2024.100920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
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Affiliation(s)
- Carissa Bleker
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Andras Bittner
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Vid Podpečan
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Bernhard Wurzinger
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Annelotte van Dieren
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Juliane Gruber
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Leila Afjehi-Sadat
- Mass Spectrometry Unit, Core Facility Shared Services, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Anže Županič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Markus Teige
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ute C Vothknecht
- Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia.
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17
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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, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data 2024; 11:363. [PMID: 38605048 PMCID: PMC11009265 DOI: 10.1038/s41597-024-03171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.
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Affiliation(s)
- Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Ignacio J Tripodi
- Computer Science Department, Interdisciplinary Quantitative Biology, University of Colorado Boulder, Boulder, CO, 80301, USA
| | - Adrianne L Stefanski
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Luca Cappelletti
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
| | - Sanya B Taneja
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jordan M Wyrwa
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15206, USA
| | - Charles Tapley Hoyt
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard D Boyce
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15206, USA
| | - Scott A Malec
- Division of Translational Informatics, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA
| | - Deepak R Unni
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Marcin P Joachimiak
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter N Robinson
- Berlin Institute of Health at Charité-Universitatsmedizin, 10117, Berlin, Germany
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Emanuele Cavalleri
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
| | - Tommaso Fontana
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
- ELLIS, European Laboratory for Learning and Intelligent Systems, Milan Unit, Italy
| | - Marco Mesiti
- AnacletoLab, Dipartimento di Informatica, Universit`a degli Studi di Milano, Via Celoria 18, 20133, Milan, Italy
| | - Lucas A Gillenwater
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Brook Santangelo
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Nicole A Vasilevsky
- Data Collaboration Center, Critical Path Institute, 1840 E River Rd. Suite 100, Tucson, AZ, 85718, USA
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tellen D Bennett
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Patrick B Ryan
- Janssen Research and Development, Raritan, NJ, 08869, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Michael G Kahn
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Bada
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - William A Baumgartner
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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18
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Talbott EO, Malek AM, Arena VC, Wu F, Steffes K, Sharma RK, Buchanich J, Rager JR, Bear T, Hoffman CA, Lacomis D, Donnelly C, Mauna J, Vena JE. Case-control study of environmental toxins and risk of amyotrophic lateral sclerosis involving the national ALS registry. Amyotroph Lateral Scler Frontotemporal Degener 2024:1-10. [PMID: 38591179 DOI: 10.1080/21678421.2024.2336108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024]
Abstract
Objective: Neurotoxic chemicals are suggested in the etiology of amyotrophic lateral sclerosis (ALS). We examined the association of environmental and occupational risk factors including persistent organochlorine pesticides (OCPs) and ALS risk among cases from the Centers for Disease Control and Prevention National ALS Registry and age, sex, and county-matched controls. Methods: Participants completed a risk factor survey and provided a blood sample for OCP measurement. ALS cases were confirmed through the Registry. Conditional logistic regression assessed associations between ALS and risk factors including OCP levels. Results: 243 matched case-control pairs (61.7% male, mean [SD] age = 62.9 [10.1]) were included. Fifteen of the 29 OCPs examined had sufficient detectable levels for analysis. Modest correlations of self-reported years of exposure to residential pesticide mixtures and OCP serum levels were found (p<.001). Moreover, occupational exposure to lead including soldering and welding with lead/metal dust and use of lead paint/gasoline were significantly related to ALS risk (OR = 1.77, 95% CI: 1.11-2.83). Avocational gardening was a significant risk factor for ALS (OR = 1.57, 95% CI: 1.04-2.37). ALS risk increased for each 10 ng/g of α-Endosulfan (OR = 1.42, 95% CI: 1.14-1.77) and oxychlordane (OR = 1.24, 95% CI: 1.01-1.53). Heptachlor (detectable vs. nondetectable) was also associated with ALS risk (OR = 3.57, 95% CI: 1.50-8.52). Conclusion: This national case-control study revealed both survey and serum levels of OCPs as risk factors for ALS. Despite the United States banning many OCPs in the 1970s and 1980s, their use abroad and long half-lives continue to exert possible neurotoxic health effects.
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Affiliation(s)
- Evelyn O Talbott
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Angela M Malek
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Vincent C Arena
- Department of Biostatistics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Fan Wu
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Kristen Steffes
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Ravi K Sharma
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Jeanine Buchanich
- Department of Behavioral and Community Health Sciences, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Judith R Rager
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Todd Bear
- Department of Behavioral and Community Health Sciences, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Caroline A Hoffman
- Department of Epidemiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - David Lacomis
- Departments of Neurology and Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA, and
| | - Chris Donnelly
- Department of Neurobiology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Jocelyn Mauna
- Department of Neurobiology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - John E Vena
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
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19
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Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol 2024; 15:1351678. [PMID: 38638909 PMCID: PMC11024261 DOI: 10.3389/fmicb.2024.1351678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/20/2024] Open
Abstract
Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.
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Affiliation(s)
- Brook E. Santangelo
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Madison Apgar
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Casey G. Martin
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - John Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, CO, United States
| | - Elena Wall
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcin P. Joachimiak
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Biosystems Data Science Department, Berkeley, CA, United States
| | - Lawrence E. Hunter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
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20
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Galgonek J, Vondrášek J. The IDSM mass spectrometry extension: searching mass spectra using SPARQL. Bioinformatics 2024; 40:btae174. [PMID: 38561173 PMCID: PMC11034985 DOI: 10.1093/bioinformatics/btae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
SUMMARY The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its unique feature is the ability to search for compounds through SPARQL based on their molecular structure. We extended IDSM to enable mass spectra databases to be integrated and searched for based on mass spectrum similarity. As sources of mass spectra, we employed the MassBank of North America database and the In Silico Spectral Database of natural products. AVAILABILITY AND IMPLEMENTATION The extension is an integral part of IDSM, which is available at https://idsm.elixir-czech.cz. The manual and usage examples are available at https://idsm.elixir-czech.cz/docs/ms. The source codes of all IDSM parts are available under open-source licences at https://github.com/idsm-src.
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Affiliation(s)
- Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 160 00, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 160 00, Czech Republic
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21
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Hong Y, Xu H, Liu Y, Zhu S, Tian C, Chen G, Zhu F, Tao L. DDID: a comprehensive resource for visualization and analysis of diet-drug interactions. Brief Bioinform 2024; 25:bbae212. [PMID: 38711369 DOI: 10.1093/bib/bbae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/01/2024] [Accepted: 04/21/2024] [Indexed: 05/08/2024] Open
Abstract
Diet-drug interactions (DDIs) are pivotal in drug discovery and pharmacovigilance. DDIs can modify the systemic bioavailability/pharmacokinetics of drugs, posing a threat to public health and patient safety. Therefore, it is crucial to establish a platform to reveal the correlation between diets and drugs. Accordingly, we have established a publicly accessible online platform, known as Diet-Drug Interactions Database (DDID, https://bddg.hznu.edu.cn/ddid/), to systematically detail the correlation and corresponding mechanisms of DDIs. The platform comprises 1338 foods/herbs, encompassing flora and fauna, alongside 1516 widely used drugs and 23 950 interaction records. All interactions are meticulously scrutinized and segmented into five categories, thereby resulting in evaluations (positive, negative, no effect, harmful and possible). Besides, cross-linkages between foods/herbs, drugs and other databases are furnished. In conclusion, DDID is a useful resource for comprehending the correlation between foods, herbs and drugs and holds a promise to enhance drug utilization and research on drug combinations.
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Affiliation(s)
- Yanfeng Hong
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Hongquan Xu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Sisi Zhu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Chao Tian
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Gongxing Chen
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
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22
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Liu L, Yang L, Cao S, Gao Z, Yang B, Zhang G, Zhu R, Wu D. CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides. Brief Bioinform 2024; 25:bbae190. [PMID: 38678388 PMCID: PMC11056021 DOI: 10.1093/bib/bbae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 04/30/2024] Open
Abstract
Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia (https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This repository, structured as a composite knowledge network, offers a wealth of information encompassing various aspects of cyclic peptides, such as cyclic peptides' sources, categorizations, structural characteristics, pharmacokinetic profiles, physicochemical properties, patented drug applications, and a collection of crucial publications. Supported by a user-friendly knowledge retrieval system and calculation tools specifically designed for cyclic peptides, CyclicPepedia will be able to facilitate advancements in cyclic peptide drug development.
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Affiliation(s)
- Lei Liu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P. R. China
| | - Liu Yang
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Suqi Cao
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Zhigang Gao
- Department of General Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
| | - Bin Yang
- Shanghai Southgene Technology Co., Ltd., Shanghai 201203, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Ruixin Zhu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P. R. China
| | - Dingfeng Wu
- National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, P. R. China
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23
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Quaglia F, Chasapi A, Nugnes MV, Aspromonte MC, Leonardi E, Piovesan D, Tosatto SCE. Best practices for the manual curation of intrinsically disordered proteins in DisProt. Database (Oxford) 2024; 2024:baae009. [PMID: 38507044 PMCID: PMC10953794 DOI: 10.1093/database/baae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 02/03/2024] [Indexed: 03/22/2024]
Abstract
The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure. Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses or their involvement in diseases (such as cancer and neurodevelopmental disorders). DisProt offers detailed information on the structural states of IDPs/IDRs, including state transitions, interactions and their functions, all provided as curated annotations. One of the central activities of DisProt is the meticulous curation of experimental data from the literature. For this reason, to ensure that every expert and volunteer curator possesses the requisite knowledge for data evaluation, collection and integration, training courses and curation materials are available. However, biocuration guidelines concur on the importance of developing robust guidelines that not only provide critical information about data consistency but also ensure data acquisition.This guideline aims to provide both biocurators and external users with best practices for manually curating IDPs and IDRs in DisProt. It describes every step of the literature curation process and provides use cases of IDP curation within DisProt. Database URL: https://disprot.org/.
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Affiliation(s)
- Federica Quaglia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Via Giovanni Amendola, 122/O, Bari 70126, Italy
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, Padova 35131, Italy
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, 6th km Harilaou - Thermis 57001 Thermi, Thessalonica 57001, Greece
| | - Maria Victoria Nugnes
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, Padova 35131, Italy
| | | | - Emanuela Leonardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, Padova 35131, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, Padova 35131, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, Padova 35131, Italy
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24
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Azzi R, Bordea G, Griffier R, Nikiema JN, Mougin F. Enriching the FIDEO ontology with food-drug interactions from online knowledge sources. J Biomed Semantics 2024; 15:1. [PMID: 38438913 PMCID: PMC10913206 DOI: 10.1186/s13326-024-00302-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
The increasing number of articles on adverse interactions that may occur when specific foods are consumed with certain drugs makes it difficult to keep up with the latest findings. Conflicting information is available in the scientific literature and specialized knowledge bases because interactions are described in an unstructured or semi-structured format. The FIDEO ontology aims to integrate and represent information about food-drug interactions in a structured way. This article reports on the new version of this ontology in which more than 1700 interactions are integrated from two online resources: DrugBank and Hedrine. These food-drug interactions have been represented in FIDEO in the form of precompiled concepts, each of which specifies both the food and the drug involved. Additionally, competency questions that can be answered are reviewed, and avenues for further enrichment are discussed.
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Affiliation(s)
- Rabia Azzi
- Univ. Bordeaux, Inserm, BPH, U1219, F-33000, Bordeaux, France
- CHU de Bordeaux, Service d'information médicale, F-33000, Bordeaux, France
| | - Georgeta Bordea
- Univ. Bordeaux, Inserm, BPH, U1219, F-33000, Bordeaux, France
- Univ. La Rochelle, L3i, F-17000, La Rochelle, France
| | - Romain Griffier
- Univ. Bordeaux, Inserm, BPH, U1219, F-33000, Bordeaux, France
- CHU de Bordeaux, Service d'information médicale, F-33000, Bordeaux, France
| | - Jean Noël Nikiema
- Department of Management, Evaluation and Health Policy, School of Public Health, Université de Montréal, Québec, Canada
| | - Fleur Mougin
- Univ. Bordeaux, Inserm, BPH, U1219, F-33000, Bordeaux, France.
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25
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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; 40:btae104. [PMID: 38383067 PMCID: PMC10924283 DOI: 10.1093/bioinformatics/btae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/16/2023] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
MOTIVATION Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. RESULTS Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM's native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. AVAILABILITY AND IMPLEMENTATION SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.
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Affiliation(s)
- J Harry Caufield
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Harshad Hegde
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Vincent Emonet
- Institute of Data Science, Faculty of Science and Engineering, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Nomi L Harris
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcin P Joachimiak
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | | | - HyeongSik Kim
- Robert Bosch LLC, Sunnyvale, CA 94085, United States
| | - Sierra Moxon
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Justin T Reese
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Melissa A Haendel
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO 80217, United States
| | | | - Christopher J Mungall
- Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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26
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Oprea TI, Bologa C, Holmes J, Mathias S, Metzger VT, Waller A, Yang JJ, Leach AR, Jensen LJ, Kelleher KJ, Sheils TK, Mathé E, Avram S, Edwards JS. Overview of the Knowledge Management Center for Illuminating the Druggable Genome. Drug Discov Today 2024; 29:103882. [PMID: 38218214 PMCID: PMC10939799 DOI: 10.1016/j.drudis.2024.103882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) project aims to aggregate, update, and articulate protein-centric data knowledge for the entire human proteome, with emphasis on the understudied proteins from the three IDG protein families. KMC collates and analyzes data from over 70 resources to compile the Target Central Resource Database (TCRD), which is the web-based informatics platform (Pharos). These data include experimental, computational, and text-mined information on protein structures, compound interactions, and disease and phenotype associations. Based on this knowledge, proteins are classified into different Target Development Levels (TDLs) for identification of understudied targets. Additional work by the KMC focuses on enriching target knowledge and producing DrugCentral and other data visualization tools for expanding investigation of understudied targets.
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Affiliation(s)
- Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Cristian Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Stephen Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Vincent T Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Anna Waller
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Keith J Kelleher
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Timothy K Sheils
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Ewy Mathé
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Sorin Avram
- Coriolan Dragulescu Institute of Chemistry, Timisoara, Romania
| | - Jeremy S Edwards
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA.
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27
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Liu P, Ren Y, Tao J, Ren Z. GIT-Mol: A multi-modal large language model for molecular science with graph, image, and text. Comput Biol Med 2024; 171:108073. [PMID: 38359660 DOI: 10.1016/j.compbiomed.2024.108073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/25/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Large language models have made significant strides in natural language processing, enabling innovative applications in molecular science by processing textual representations of molecules. However, most existing language models cannot capture the rich information with complex molecular structures or images. In this paper, we introduce GIT-Mol, a multi-modal large language model that integrates the Graph, Image, and Text information. To facilitate the integration of multi-modal molecular data, we propose GIT-Former, a novel architecture that is capable of aligning all modalities into a unified latent space. We achieve a 5%-10% accuracy increase in properties prediction and a 20.2% boost in molecule generation validity compared to the baselines. With the any-to-language molecular translation strategy, our model has the potential to perform more downstream tasks, such as compound name recognition and chemical reaction prediction.
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Affiliation(s)
- Pengfei Liu
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China; School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, Guangdong Province, China
| | - Yiming Ren
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China
| | - Jun Tao
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, Guangdong Province, China
| | - Zhixiang Ren
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China.
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28
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Hari A, Zarrabi A, Lobo D. mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers. NAR Genom Bioinform 2024; 6:lqae010. [PMID: 38312936 PMCID: PMC10836943 DOI: 10.1093/nargab/lqae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/06/2024] Open
Abstract
Numerous methods exist to produce and refine genome-scale metabolic models. However, due to the use of incompatible identifier systems for metabolites and reactions, computing and visualizing the metabolic differences and similarities of such models is a current challenge. Furthermore, there is a lack of automated tools that can combine the strengths of multiple reconstruction pipelines into a curated single comprehensive model by merging different drafts, which possibly use incompatible namespaces. Here we present mergem, a novel method to compare, merge, and translate two or more metabolic models. Using a universal metabolic identifier mapping system constructed from multiple metabolic databases, mergem robustly can compare models from different pipelines, merge their common elements, and translate their identifiers to other database systems. mergem is implemented as a command line tool, a Python package, and on the web-application Fluxer, which allows simulating and visually comparing multiple models with different interactive flux graphs. The ability to merge, compare, and translate diverse genome scale metabolic models can facilitate the curation of comprehensive reconstructions and the discovery of unique and common metabolic features among different organisms.
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Affiliation(s)
- Archana Hari
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle Baltimore, MD 21250, USA
| | - Arveen Zarrabi
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle Baltimore, MD 21250, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle Baltimore, MD 21250, USA
- Greenebaum Comprehensive Cancer Center and Center for Stem Cell Biology & Regenerative Medicine, University of Maryland, School of Medicine, 22 S. Greene Street, Baltimore, MD 21201, USA
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29
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Moresis A, Restivo L, Bromilow S, Flik G, Rosati G, Scorrano F, Tsoory M, O'Connor EC, Gaburro S, Bannach-Brown A. A minimal metadata set (MNMS) to repurpose nonclinical in vivo data for biomedical research. Lab Anim (NY) 2024; 53:67-79. [PMID: 38438748 PMCID: PMC10912024 DOI: 10.1038/s41684-024-01335-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
Although biomedical research is experiencing a data explosion, the accumulation of vast quantities of data alone does not guarantee a primary objective for science: building upon existing knowledge. Data collected that lack appropriate metadata cannot be fully interrogated or integrated into new research projects, leading to wasted resources and missed opportunities for data repurposing. This issue is particularly acute for research using animals, where concerns regarding data reproducibility and ensuring animal welfare are paramount. Here, to address this problem, we propose a minimal metadata set (MNMS) designed to enable the repurposing of in vivo data. MNMS aligns with an existing validated guideline for reporting in vivo data (ARRIVE 2.0) and contributes to making in vivo data FAIR-compliant. Scenarios where MNMS should be implemented in diverse research environments are presented, highlighting opportunities and challenges for data repurposing at different scales. We conclude with a 'call for action' to key stakeholders in biomedical research to adopt and apply MNMS to accelerate both the advancement of knowledge and the betterment of animal welfare.
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Affiliation(s)
- Anastasios Moresis
- Roche Pharma Research and Early Development, Data & Analytics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Leonardo Restivo
- Neuro-Behavioral Analysis Unit, Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sophie Bromilow
- Group Legal Department, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Gunnar Flik
- Discovery, Charles River Laboratories, Groningen, the Netherlands
| | | | - Fabrizio Scorrano
- Emerging Technologies, Comparative Medicine, Novartis International AG, Basel, Switzerland
| | - Michael Tsoory
- Behavioral and Physiological Phenotyping Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eoin C O'Connor
- Roche Pharma Research and Early Development, Neuroscience & Rare Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| | | | - Alexandra Bannach-Brown
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
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30
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Fischer M, Brauer J. Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations. ChemistryOpen 2024:e202300273. [PMID: 38385822 DOI: 10.1002/open.202300273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.
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Affiliation(s)
- Michael Fischer
- Crystallography and Geomaterials, Faculty of Geosciences, University of Bremen, Klagenfurter Straße 2-4, 28359, Bremen, Germany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359, Bremen, Germany
| | - Jakob Brauer
- Crystallography and Geomaterials, Faculty of Geosciences, University of Bremen, Klagenfurter Straße 2-4, 28359, Bremen, Germany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359, Bremen, Germany
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Sullivan MJ, Terán I, Goh KG, Ulett GC. Resisting death by metal: metabolism and Cu/Zn homeostasis in bacteria. Emerg Top Life Sci 2024; 8:45-56. [PMID: 38362914 PMCID: PMC10903455 DOI: 10.1042/etls20230115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
Metal ions such as zinc and copper play important roles in host-microbe interactions and their availability can drastically affect the survival of pathogenic bacteria in a host niche. Mechanisms of metal homeostasis protect bacteria from starvation, or intoxication, defined as when metals are limiting, or in excess, respectively. In this mini-review, we summarise current knowledge on the mechanisms of resistance to metal stress in bacteria, focussing specifically on the homeostasis of cellular copper and zinc. This includes a summary of the factors that subvert metal stress in bacteria, which are independent of metal efflux systems, and commentary on the role of small molecules and metabolic systems as important mediators of metal resistance.
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Affiliation(s)
- Matthew J. Sullivan
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia
| | - Ignacio Terán
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Kelvin G.K. Goh
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia
| | - Glen C. Ulett
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia
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Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol 2024; 14:1282859. [PMID: 38414974 PMCID: PMC10897000 DOI: 10.3389/fimmu.2023.1282859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 02/29/2024] Open
Abstract
Introduction The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
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Affiliation(s)
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Inna Kuperstein
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Marc E. Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- St. John’s University, Queens, NY, United States
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Felicia Burtscher
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Yusuke Hiki
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan
| | - Noriko F. Hiroi
- Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan
- Keio University School of Medicine, Tokyo, Japan
| | - Finterly Hu
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Nhung Pham
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Francesco Messina
- Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases’ Lazzaro Spallanzani’ - IRCCS, Rome, Italy
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Maria Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
| | - Kinza Rian
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Aurélien Naldi
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
| | | | - Viviam Bermudez
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnau Montagud
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
| | - Vincent Noël
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | | | | | - Benjamin M. Gyori
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - John A. Bachman
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - Augustin Luna
- Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Janet Piñero
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura I. Furlong
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Adrien Rougny
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
- Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
| | - Yohan Jarosz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rupert W. Overall
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Robert Phair
- Integrative Bioinformatics, Inc., Mountain View, CA, United States
| | - Livia Perfetto
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Lisa Matthews
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | | | | | - Luis Cristobal Monraz Gomez
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Jean Marie Ravel
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Guanming Wu
- Oregon Health Sciences University, Portland, OR, United States
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laurence Calzone
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Peter D’Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany
| | | | - Emmanuel Barillot
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Rudi Balling
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Behr AS, Borgelt H, Kockmann N. Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management. J Cheminform 2024; 16:16. [PMID: 38326906 PMCID: PMC10851519 DOI: 10.1186/s13321-024-00807-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
As scientific digitization advances it is imperative ensuring data is Findable, Accessible, Interoperable, and Reusable (FAIR) for machine-processable data. Ontologies play a vital role in enhancing data FAIRness by explicitly representing knowledge in a machine-understandable format. Research data in catalysis research often exhibits complexity and diversity, necessitating a respectively broad collection of ontologies. While ontology portals such as EBI OLS and BioPortal aid in ontology discovery, they lack deep classification, while quality metrics for ontology reusability and domains are absent for the domain of catalysis research. Thus, this work provides an approach for systematic collection of ontology metadata with focus on the catalysis research data value chain. By classifying ontologies by subdomains of catalysis research, the approach is offering efficient comparison across ontologies. Furthermore, a workflow and codebase is presented, facilitating representation of the metadata on GitHub. Finally, a method is presented to automatically map the classes contained in the ontologies of the metadata collection against each other, providing further insights on relatedness of the ontologies listed. The presented methodology is designed for its reusability, enabling its adaptation to other ontology collections or domains of knowledge. The ontology metadata taken up for this work and the code developed and described in this work are available in a GitHub repository at: https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat .
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Affiliation(s)
- Alexander S Behr
- Laboratory of Equipment Design, Faculty of Biochemical and Chemical Engineering, TU-Dortmund University, Emil-Figge-Strasse 68, 44139, Dortmund, NRW, Germany.
| | - Hendrik Borgelt
- Laboratory of Equipment Design, Faculty of Biochemical and Chemical Engineering, TU-Dortmund University, Emil-Figge-Strasse 68, 44139, Dortmund, NRW, Germany
| | - Norbert Kockmann
- Laboratory of Equipment Design, Faculty of Biochemical and Chemical Engineering, TU-Dortmund University, Emil-Figge-Strasse 68, 44139, Dortmund, NRW, Germany
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34
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Koole L, Martinez-Martinez P, Amelsvoort TV, Evelo CT, Ehrhart F. Interactive neuroinflammation pathways and transcriptomics-based identification of drugs and chemical compounds for schizophrenia. World J Biol Psychiatry 2024; 25:116-129. [PMID: 37961844 DOI: 10.1080/15622975.2023.2281514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVES Schizophrenia is a psychiatric disorder affecting 1% of the population. Accumulating evidence indicates that neuroinflammation is involved in the pathology of these disorders by altering neurodevelopmental processes and specifically affecting glutamatergic signalling and astrocytic functioning. The aim of this study was to curate interactive biological pathways involved in schizophrenia for the identification of novel pharmacological targets implementing pathway, gene ontology, and network analysis. METHODS Neuroinflammatory pathways were created using PathVisio and published in WikiPathways. A transcriptomics dataset, originally created by Narla et al. was selected for data visualisation and analysis. Transcriptomics data was visualised within pathways and networks, extended with transcription factors, pathways, and drugs. Network hubs were determined based on degrees of connectivity. RESULTS Glutamatergic, immune, and astrocytic signalling as well as extracellular matrix reorganisation were altered in schizophrenia while we did not find an effect on the complement system. Pharmacological agents that target the glutamate receptor subunits, inflammatory mediators, and metabolic enzymes were identified. CONCLUSIONS New neuroinflammatory pathways incorporating the extracellular matrix, glutamatergic neurons, and astrocytes in the aetiology of schizophrenia were established. Transcriptomics based network analysis provided novel targets, including extra-synaptic glutamate receptors, glutamate transporters and extracellular matrix molecules that can be evaluated for therapeutic strategies.
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Affiliation(s)
- Lisa Koole
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Pilar Martinez-Martinez
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
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Amaya-Rodriguez CA, Carvajal-Zamorano K, Bustos D, Alegría-Arcos M, Castillo K. A journey from molecule to physiology and in silico tools for drug discovery targeting the transient receptor potential vanilloid type 1 (TRPV1) channel. Front Pharmacol 2024; 14:1251061. [PMID: 38328578 PMCID: PMC10847257 DOI: 10.3389/fphar.2023.1251061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024] Open
Abstract
The heat and capsaicin receptor TRPV1 channel is widely expressed in nerve terminals of dorsal root ganglia (DRGs) and trigeminal ganglia innervating the body and face, respectively, as well as in other tissues and organs including central nervous system. The TRPV1 channel is a versatile receptor that detects harmful heat, pain, and various internal and external ligands. Hence, it operates as a polymodal sensory channel. Many pathological conditions including neuroinflammation, cancer, psychiatric disorders, and pathological pain, are linked to the abnormal functioning of the TRPV1 in peripheral tissues. Intense biomedical research is underway to discover compounds that can modulate the channel and provide pain relief. The molecular mechanisms underlying temperature sensing remain largely unknown, although they are closely linked to pain transduction. Prolonged exposure to capsaicin generates analgesia, hence numerous capsaicin analogs have been developed to discover efficient analgesics for pain relief. The emergence of in silico tools offered significant techniques for molecular modeling and machine learning algorithms to indentify druggable sites in the channel and for repositioning of current drugs aimed at TRPV1. Here we recapitulate the physiological and pathophysiological functions of the TRPV1 channel, including structural models obtained through cryo-EM, pharmacological compounds tested on TRPV1, and the in silico tools for drug discovery and repositioning.
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Affiliation(s)
- Cesar A. Amaya-Rodriguez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Departamento de Fisiología y Comportamiento Animal, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panamá
| | - Karina Carvajal-Zamorano
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Daniel Bustos
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Melissa Alegría-Arcos
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago, Chile
| | - Karen Castillo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile
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Witting M, Malik A, Leach A, Bridge A, Aimo L, Conroy MJ, O'Donnell VB, Hoffmann N, Kopczynski D, Giacomoni F, Paulhe N, Gassiot AC, Poupin N, Jourdan F, Bertrand-Michel J. Challenges and perspectives for naming lipids in the context of lipidomics. Metabolomics 2024; 20:15. [PMID: 38267595 PMCID: PMC10808356 DOI: 10.1007/s11306-023-02075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. OBJECTIVES In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. METHODS & RESULTS In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. CONCLUSION Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks.
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Affiliation(s)
- Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354, Freising-Weihenstephan, Germany
| | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Lucila Aimo
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Matthew J Conroy
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Valerie B O'Donnell
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nils Hoffmann
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Dominik Kopczynski
- Institute for Analytical Chemistry, Universität Wien, Währingerstrasse 38, 1090, Vienna, Austria
| | - Franck Giacomoni
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Nils Paulhe
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Amaury Cazenave Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute, and Precision Medicine TRP, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France.
- I2MC, Inserm U1297, Université de Toulouse, Toulouse, France.
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Hager MS, Hofland ML, Varella AC, Bothner B, Budak H, Weaver DK. Untargeted metabolomics profiling of oat ( Avena sativa L.) and wheat ( Triticum aestivum L.) infested with wheat stem sawfly ( Cephus cinctus Norton) reveals differences associated with plant defense and insect nutrition. FRONTIERS IN PLANT SCIENCE 2024; 15:1327390. [PMID: 38328705 PMCID: PMC10848266 DOI: 10.3389/fpls.2024.1327390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Introduction Wheat stem sawfly (WSS), Cephus cinctus Norton, is a major pest of common bread wheat (Triticum aestivum L.) and other cultivated cereals in North America. Planting of cultivars with solid stems has been the primary management strategy to prevent yield loss due to WSS infestation, however expression of this phenotype can vary depending on environmental conditions and solid stems hinder biological control of WSS via braconid parasitoids Bracon cephi (Gahan) and Bracon lissogaster Muesebeck. In the hollow stems of oat (Avena sativa L.), WSS larvae experience 100% mortality before they reach late instars, but the mechanisms for this observed resistance have not been characterized. Objective The objective of this study was to explore additional sources of resistance outside of the historic solid stem phenotype. Methods Here, we use an untargeted metabolomics approach to examine the response of the metabolome of two cultivars of oat and four cultivars of spring wheat to infestation by WSS. Using liquid chromatography-mass spectrometry (LC-MS), differentially expressed metabolites were identified between oat and wheat which were associated with the phenylpropanoid pathway, phospholipid biosynthesis and signaling, the salicylic acid signaling pathway, indole-3-acetic acid (IAA) degradation, and biosynthesis of 1,4-benzoxazin-3-ones (Bxs). Several phospho- and galacto- lipids were found in higher abundance in oat, and with the exception of early stem solidness cultivar Conan, both species experienced a decrease in abundance once infested. In all wheat cultivars except Conan, an increase in abundance was observed for Bxs HMDBOA-glc and DIBOA-β-D-glucoside after infestation, indicating that this pathway is involved in wheat response to infestation in both solid and hollow stemmed cultivars. Differences between species in compounds involved in IAA biosynthesis, degradation and inactivation suggest that wheat may respond to infestation by inactivating IAA or altering the IAA pool in stem tissue. Conclusion We propose that the species differences found here likely affect the survival of WSS larvae and may also be associated with differences in stem architecture at the molecular level. Our findings suggest pathways to focus on for future studies in elucidating plant response to WSS infestation.
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Affiliation(s)
- Megan S. Hager
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States
- Wheat Stem Sawfly Laboratory, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Megan L. Hofland
- Wheat Stem Sawfly Laboratory, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Andrea C. Varella
- Corteva Agriscience™, Woodstock Research and Development Centre, Tavistock, ON, Canada
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Hikmet Budak
- Department of Agriculture, Arizona Western College, Yuma, AZ, United States
| | - David K. Weaver
- Wheat Stem Sawfly Laboratory, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
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Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B. Coordinating virus research: The Virus Infectious Disease Ontology. PLoS One 2024; 19:e0285093. [PMID: 38236918 PMCID: PMC10796065 DOI: 10.1371/journal.pone.0285093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/12/2023] [Indexed: 01/22/2024] Open
Abstract
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
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Affiliation(s)
- John Beverley
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Shane Babcock
- National Center for Ontological Research, Buffalo, NY, United States of America
- Air Force Research Laboratory, Wright Patterson Air Force Base, Riverside, OH, United States of America
| | - Gustavo Carvalho
- Department of Cognitive Science, Northwestern University, Evanston, IL, United States of America
| | - Lindsay G. Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Sebastian Duesing
- Department of Philosophy, Loyola University, Chicago, IL, United States of America
| | - Yongqun He
- Computational Medicine and Bioinformatics, University of Michigan Medical School, He Group, Ann Arbor, MI, United States of America
| | - Regina Hurley
- National Center for Ontological Research, Buffalo, NY, United States of America
- Department of Philosophy, Northwestern University, Evanston, IL, United States of America
| | - Eric Merrell
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Pathology, University of California, San Diego, CA, United States of America
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
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McDonald AG, Lisacek F. Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens. Sci Rep 2024; 14:1649. [PMID: 38238389 PMCID: PMC10796942 DOI: 10.1038/s41598-023-51012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
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Affiliation(s)
- Andrew G McDonald
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
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40
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Chang X, Yan S, Zhang Y, Zhang Y, Li L, Gao Z, Lin X, Chi X. GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases. NPJ Syst Biol Appl 2024; 10:4. [PMID: 38218959 PMCID: PMC10787761 DOI: 10.1038/s41540-024-00330-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Knowledge bases have been instrumental in advancing biological research, facilitating pathway analysis and data visualization, which are now widely employed in the scientific community. Despite the establishment of several prominent knowledge bases focusing on signaling, metabolic networks, or both, integrating these networks into a unified topological network has proven to be challenging. The intricacy of molecular interactions and the diverse formats employed to store and display them contribute to the complexity of this task. In a prior study, we addressed this challenge by introducing a "meta-pathway" structure that integrated the advantages of the Simple Interaction Format (SIF) while accommodating reaction information. Nevertheless, the earlier Global Integrative Network (GIN) was limited to reliance on KEGG alone. Here, we present GIN version 2.0, which incorporates human molecular interaction data from ten distinct knowledge bases, including KEGG, Reactome, and HumanCyc, among others. We standardized the data structure, gene IDs, and chemical IDs, and conducted a comprehensive analysis of the consistency among the ten knowledge bases before combining all unified interactions into GINv2.0. Utilizing GINv2.0, we investigated the glycolysis process and its regulatory proteins, revealing coordinated regulations on glycolysis and autophagy, particularly under glucose starvation. The expanded scope and enhanced capabilities of GINv2.0 provide a valuable resource for comprehensive systems-level analyses in the field of biological research. GINv2.0 can be accessed at: https://github.com/BIGchix/GINv2.0 .
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Affiliation(s)
- Xiao Chang
- Department of Dermatology and Venereal Disease, Xuan Wu Hospital, Beijing, 100053, China
| | - Shen Yan
- Agricultural Information Institute, Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yizheng Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingchun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Luyang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhanyu Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefei Lin
- Department of Dermatology and Venereal Disease, Xuan Wu Hospital, Beijing, 100053, China
| | - Xu Chi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
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Tummler K, Klipp E. Data integration strategies for whole-cell modeling. FEMS Yeast Res 2024; 24:foae011. [PMID: 38544322 PMCID: PMC11042497 DOI: 10.1093/femsyr/foae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Data makes the world go round-and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should-in its entirety-cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
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Affiliation(s)
- Katja Tummler
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
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42
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Yin J, Chen Z, You N, Li F, Zhang H, Xue J, Ma H, Zhao Q, Yu L, Zeng S, Zhu F. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Res 2024; 52:D1490-D1502. [PMID: 37819041 PMCID: PMC10767864 DOI: 10.1093/nar/gkad818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/01/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Nanxin You
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- The Children's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Hui Ma
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Qingwei Zhao
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Gupta P, Elser J, Hooks E, D’Eustachio P, Jaiswal P, Naithani S. Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Res 2024; 52:D1538-D1547. [PMID: 37986220 PMCID: PMC10767815 DOI: 10.1093/nar/gkad1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023] Open
Abstract
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional species, spanning single-cell photoautotrophs, non-vascular plants, and higher plants, thus encompassing a wide-ranging taxonomic diversity. Currently, Plant Reactome houses a collection of 339 reference pathways, covering metabolic and transport pathways, hormone signaling, genetic regulations of developmental processes, and intricate transcriptional networks that orchestrate a plant's response to abiotic and biotic stimuli. Beyond being a mere repository, Plant Reactome serves as a dynamic data discovery platform. Users can analyze and visualize omics data, such as gene expression, gene-gene interaction, proteome, and metabolome data, all within the rich context of plant pathways. Plant Reactome is dedicated to fostering data interoperability, upholding global data standards, and embracing the tenets of the Findable, Accessible, Interoperable and Re-usable (FAIR) data policy.
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Affiliation(s)
- Parul Gupta
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Elizabeth Hooks
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sushma Naithani
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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44
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Cooper L, Elser J, Laporte MA, Arnaud E, Jaiswal P. Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology. Nucleic Acids Res 2024; 52:D1548-D1555. [PMID: 38055832 PMCID: PMC10767901 DOI: 10.1093/nar/gkad1028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/14/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology.
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Affiliation(s)
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Elizabeth Arnaud
- Digital Inclusion, Biodiversity International, 34397 Montpellier, France
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D’Eustachio P. The Reactome Pathway Knowledgebase 2024. Nucleic Acids Res 2024; 52:D672-D678. [PMID: 37941124 PMCID: PMC10767911 DOI: 10.1093/nar/gkad1025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. 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. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network.
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Affiliation(s)
- Marija Milacic
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Deidre Beavers
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Patrick Conley
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Chuqiao Gong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Marc Gillespie
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Johannes Griss
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Robin Haw
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Lisa Matthews
- NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bruce May
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | | | - Eliot Ragueneau
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | | | - Ralf Stephan
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE)
| | - Krishna Tiwari
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Thawfeek Varusai
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Joel Weiser
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Adam Wright
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Guanming Wu
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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Gao J, Mo S, Wang J, Zhang M, Shi Y, Zhu C, Shang Y, Tang X, Zhang S, Wu X, Xu X, Wang Y, Li Z, Zheng G, Chen Z, Wang Q, Tang K, Cao Z. MACC: a visual interactive knowledgebase of metabolite-associated cell communications. Nucleic Acids Res 2024; 52:D633-D639. [PMID: 37897362 PMCID: PMC10767829 DOI: 10.1093/nar/gkad914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported, no relevant database has become available so far. To address this gap, we here developed the first knowledgebase (MACC), to comprehensively describe human metabolite-associated cell communications through curation of experimental literatures. MACC currently contains: (a) 4206 carefully curated metabolite-associated cell communications pairs involving 244 human endogenous metabolites and reported biological effects in vivo and in vitro; (b) 226 comprehensive cell subtypes and 296 disease states, such as cancers, autoimmune diseases, and pathogenic infections; (c) 4508 metabolite-related enzymes and transporters, involving 542 pathways; (d) an interactive tool with user-friendly interface to visualize networks of multiple metabolite-cell interactions. (e) overall expression landscape of metabolite-associated gene sets derived from over 1500 single-cell expression profiles to infer metabolites variations across different cells in the sample. Also, MACC enables cross-links to well-known databases, such as HMDB, DrugBank, TTD and PubMed etc. In complement to ligand-receptor databases, MACC may give new perspectives of alternative communication between cells via metabolite secretion and adsorption, together with the resulting biological functions. MACC is publicly accessible at: http://macc.badd-cao.net/.
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Affiliation(s)
- Jian Gao
- School of Life Sciences, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Saifeng Mo
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jun Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Mou Zhang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yao Shi
- School of Life Sciences, Fudan University, Shanghai, China
| | - Chuhan Zhu
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuxuan Shang
- Biological Sciences, University of California Santa Barbara, CA, USA
| | - Xinyue Tang
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiyue Zhang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Xinwen Wu
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinyan Xu
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yiheng Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zihao Li
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Genhui Zheng
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zikun Chen
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qiming Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Kailin Tang
- Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
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47
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Conroy MJ, Andrews RM, Andrews S, Cockayne L, Dennis E, Fahy E, Gaud C, Griffiths W, Jukes G, Kolchin M, Mendivelso K, Lopez-Clavijo A, Ready C, Subramaniam S, O’Donnell V. LIPID MAPS: update to databases and tools for the lipidomics community. Nucleic Acids Res 2024; 52:D1677-D1682. [PMID: 37855672 PMCID: PMC10767878 DOI: 10.1093/nar/gkad896] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
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Affiliation(s)
- Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Robert M Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Lauren Cockayne
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward A Dennis
- Department of Pharmacology, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0601, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - William J Griffiths
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Maksim Kolchin
- Boehringer Ingelheim Espana SA, Carrer de Prat de la Riba, 50, 08174 Sant Cugat del Vallès, Barcelona, Spain
| | - Karla Mendivelso
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Caroline Ready
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Valerie B O’Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
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48
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De Castro E, Hulo C, Masson P, Auchincloss A, Bridge A, Le Mercier P. ViralZone 2024 provides higher-resolution images and advanced virus-specific resources. Nucleic Acids Res 2024; 52:D817-D821. [PMID: 37897348 PMCID: PMC10767872 DOI: 10.1093/nar/gkad946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses.
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Affiliation(s)
- Edouard De Castro
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Chantal Hulo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Patrick Masson
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Andrea Auchincloss
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Philippe Le Mercier
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
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49
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Altenhoff A, Bairoch A, Bansal P, Baratin D, Bastian F, Bolleman* J, Bridge A, Burdet F, Crameri K, Dauvillier J, Dessimoz C, Gehant S, Glover N, Gnodtke K, Hayes C, Ibberson M, Kriventseva E, Kuznetsov D, Frédérique L, Mehl F, Mendes de Farias* T, Michel PA, Moretti S, Morgat A, Österle S, Pagni M, Redaschi N, Robinson-Rechavi M, Samarasinghe K, Sima AC, Szklarczyk D, Topalov O, Touré V, Unni D, von Mering C, Wollbrett J, Zahn-Zabal* M, Zdobnov E. The SIB Swiss Institute of Bioinformatics Semantic Web of data. Nucleic Acids Res 2024; 52:D44-D51. [PMID: 37878411 PMCID: PMC10767860 DOI: 10.1093/nar/gkad902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available databases provided by SIB since its inception in 1998. In this paper we present the 11 databases which currently offer semantically enriched data in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable), as well as the Swiss Personalized Health Network initiative (SPHN) which also employs this enrichment. The semantic enrichment facilitates the manipulation of large data sets from public databases and private data sets. Examples are provided to illustrate that the data from the SIB databases can not only be queried using precise criteria individually, but also across multiple databases, including a variety of non-SIB databases. Data manipulation, be it exploration, extraction, annotation, combination, and publication, is possible using the SPARQL query language. Providing documentation, tutorials and sample queries makes it easier to navigate this web of semantic data. Through this paper, the reader will discover how the existing SIB knowledge graphs can be leveraged to tackle the complex biological or clinical questions that are being addressed today.
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50
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Yurekten O, Payne T, Tejera N, Amaladoss FX, Martin C, Williams M, O’Donovan C. MetaboLights: open data repository for metabolomics. Nucleic Acids Res 2024; 52:D640-D646. [PMID: 37971328 PMCID: PMC10767962 DOI: 10.1093/nar/gkad1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
MetaboLights is a global database for metabolomics studies including the raw experimental data and the associated metadata. The database is cross-species and cross-technique and covers metabolite structures and their reference spectra as well as their biological roles and locations where available. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information. In this article, we describe the continued growth and diversity of submissions and the significant developments in recent years. In particular, we highlight MetaboLights Labs, our new Galaxy Project instance with repository-scale standardized workflows, and how data public on MetaboLights are being reused by the community. Metabolomics resources and data are available under the EMBL-EBI's Terms of Use at https://www.ebi.ac.uk/metabolights and under Apache 2.0 at https://github.com/EBI-Metabolights.
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Affiliation(s)
- Ozgur Yurekten
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Payne
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Noemi Tejera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Felix Xavier Amaladoss
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Callum Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire O’Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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