Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.

Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine Pharmacognosy Institute; College of Pharmacy University of Illinois at Chicago Chicago United States

Department of Bioinformatics BiGCaT Maastricht University Maastricht Netherlands

Department of Biology University of Fribourg Fribourg Switzerland

Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago United States

Institute for Inorganic and Analytical Chemistry Friedrich Schiller University Jena Jena Germany

Institute of Organic Chemistry and Biochemistry of the CAS Prague Czech Republic

Institute of Pharmaceutical Sciences of Western Switzerland University of Geneva Geneva Switzerland

Leibniz Institute of Freshwater Ecology and Inland Fisheries Berlin Germany

Ontario Institute for Cancer Research University Ave Suite Toronto Canada

Ronin Institute Montclair United States

School of Data Science University of Virginia Charlottesville United States

School of Pharmaceutical Sciences University of Geneva Geneva Switzerland

University of Glasgow Glasgow United Kingdom

Zobrazit více v PubMed

Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S. KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant & Cell Physiology. 2012;53:e1. doi: 10.1093/pcp/pcr165. PubMed DOI

Agosti D, Johnson NF. Taxonomists need better access to published data. Nature. 2002;417:222. doi: 10.1038/417222b. PubMed DOI

All natural All natural. Nature Chemical Biology. 2007;3:351. doi: 10.1038/nchembio0707-351. PubMed DOI

Allard PM, Bisson J, Azzollini A, Pauli GF, Cordell GA, Wolfender JL. Pharmacognosy in the digital era: shifting to contextualized metabolomics. Current Opinion in Biotechnology. 2018;54:57–64. doi: 10.1016/j.copbio.2018.02.010. PubMed DOI PMC

Allard PM, Bisson J, Rutz A. ISDB: In Silico Spectral Databases of Natural Products. Zenodo. 2021 doi: 10.5281/zenodo.5607264. DOI

Balietti S, Mäs M, Helbing D. On disciplinary fragmentation and scientific progress. PLOS ONE. 2015;10:e0118747. doi: 10.1371/journal.pone.0118747. PubMed DOI PMC

Bisson J, Simmler C, Chen SN, Friesen J, Lankin DC, McAlpine JB, Pauli GF. Dissemination of original NMR data enhances reproducibility and integrity in chemical research. Natural Product Reports. 2016a;33:1028–1033. doi: 10.1039/c6np00022c. PubMed DOI PMC

Bisson J, McAlpine JB, Friesen JB, Chen SN, Graham J, Pauli GF. Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery? Journal of Medicinal Chemistry. 2016b;59:1671–1690. doi: 10.1021/acs.jmedchem.5b01009. PubMed DOI PMC

Bisson J, Rutz A, Allard P. lotusnprod/lotus-wikidata-interact. v1.0.0Zenodo. 2021 doi: 10.5281/zenodo.5802113. DOI

Blomqvist E, Hose K, Paulheim H, Ławrynowicz A, Ciravegna F, Hartig O. The Semantic Web: ESWC 2017 Satellite Events. Cham: Springer; 2017.

Boonen J, Bronselaer A, Nielandt J, Veryser L, De Tré G, De Spiegeleer B. Alkamid database: Chemistry, occurrence and functionality of plant N-alkylamides. Journal of Ethnopharmacology. 2012;142:563–590. doi: 10.1016/j.jep.2012.05.038. PubMed DOI

Brunson J. ggalluvial: Layered Grammar for Alluvial Plots. Journal of Open Source Software. 2020;5:2017. doi: 10.21105/joss.02017. PubMed DOI PMC

Campbell AK. Save those molecules! Molecular biodiversity and life*. Journal of Applied Ecology. 2003;40:193–203. doi: 10.1046/j.1365-2664.2003.00803.x. DOI

Campitelli E. ggnewscale: Multiple fill and colour scales in ’ggplot2. CRAN. 2021 https://CRAN.R-project.org/package=ggnewscale

Candolle A de. Essai Sur Les Propriâetâes Mâedicales Des Plantes, Comparâees Avec Leurs Formes Extâerieures et Leur Classification Naturelle / Paris: Biodiversity Heritage Library; 1816. DOI

Cao Y, Charisi A, Cheng LC, Jiang T, Girke T. ChemmineR: a compound mining framework for R. Bioinformatics (Oxford, England) 2008;24:1733–1734. doi: 10.1093/bioinformatics/btn307. PubMed DOI PMC

Capecchi A, Probst D, Reymond J-L. One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. Journal of Cheminformatics. 2020;12:43. doi: 10.1186/s13321-020-00445-4. PubMed DOI PMC

Chamberlain S, Zhu H, Jahn N, Boettiger C, Ram K. rcrossref: Client for Various “CrossRef” “APIs.”. CRAN. 2020 https://CRAN.R-project.org/package=rcrossref

Choi H, Cho SY, Pak HJ, Kim Y, Choi J-Y, Lee YJ, Gong BH, Kang YS, Han T, Choi G, Cho Y, Lee S, Ryoo D, Park H. NPCARE: database of natural products and fractional extracts for cancer regulation. Journal of Cheminformatics. 2017;9:2. doi: 10.1186/s13321-016-0188-5. PubMed DOI PMC

Cordell GA. Cognate and cognitive ecopharmacognosy — in an anthropogenic era. Phytochemistry Letters. 2017a;20:540–549. doi: 10.1016/j.phytol.2016.10.009. DOI

Cordell GA. Sixty Challenges – A 2030 Perspective on Natural Products and Medicines Security. Natural Product Communications. 2017b;12:1934578X1701200. doi: 10.1177/1934578X1701200849. DOI

Cousijn H, Kenall A, Ganley E, Harrison M, Kernohan D, Lemberger T, Murphy F, Polischuk P, Taylor S, Martone M, Clark T. A data citation roadmap for scientific publishers. Scientific Data. 2018;5:180259. doi: 10.1038/sdata.2018.259. PubMed DOI PMC

Cousijn H, Feeney P, Lowenberg D, Presani E, Simons N. Bringing Citations and Usage Metrics Together to Make Data Count. Data Science Journal. 2019;18:9. doi: 10.5334/dsj-2019-009. DOI

Crameri F, Shephard GE, Heron PJ. The misuse of colour in science communication. Nature Communications. 2020;11:5444. doi: 10.1038/s41467-020-19160-7. PubMed DOI PMC

Crameri F. Scientific colour map. Zenodo. 2021 doi: 10.5281/zenodo.1243862. DOI

Davis GJ, Vasanthi AR. Seaweed metabolite database (SWMD): A database of natural compounds from marine algae. Bioinformation. 2011;5:361–364. doi: 10.6026/97320630005361. PubMed DOI PMC

Defossez E, Pitteloud C, Descombes P, Glauser G, Allard PM, Walker TWN, Fernandez-Conradi P, Wolfender JL, Pellissier L, Rasmann S. Spatial and evolutionary predictability of phytochemical diversity. PNAS. 2021;118:e2013344118. doi: 10.1073/pnas.2013344118. PubMed DOI PMC

Derese S, Ndakala A, Rogo M, Maynim C, Oyim J. Mitishamba database: a web based in silico database of natural products from Kenya plants. University of Nairobi; 2019. http://erepository.uonbi.ac.ke/handle/11295/92273

Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. Journal of Cheminformatics. 2016;8:61. doi: 10.1186/s13321-016-0174-y. PubMed DOI PMC

Dowle M, Srinivasan A. data.table: Extension of “data.frame.”. CRAN. 2020 https://CRAN.R-project.org/package=data.table

Ducarme F, Couvet D. What does ‘nature’ mean? Palgrave Communications. 2020;6:14. doi: 10.1057/s41599-020-0390-y. DOI

Dührkop K, Nothias L-F, Fleischauer M, Reher R, Ludwig M, Hoffmann MA, Petras D, Gerwick WH, Rousu J, Dorrestein PC, Böcker S. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nature Biotechnology. 2021;39:462–471. doi: 10.1038/s41587-020-0740-8. PubMed DOI

Finn RD, Gardner PP, Bateman A. Making your database available through Wikipedia: the pros and cons. Nucleic Acids Research. 2012;40:D9–D12. doi: 10.1093/nar/gkr1195. PubMed DOI PMC

Flor M. chorddiag: Interactive Chord Diagrams. GitHub. 2020 http://github.com/mattflor/chorddiag/

Gagolewski M. stringi: Character String Processing Facilities. CRAN. 2020 https://cran.r-project.org/web/packages/stringi/index.html

GBIF GBIF. 2020. [December 9, 2021]. https://www.gbif.org

Gehlenborg N. UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets. CRAN. 2019 https://CRAN.R-project.org/package=UpSetR

Giacomoni F, Silva A, Bronze M, Gladine C, Peter Hollman RK, Yanwen DL, Micheau P, Nunes dos Santos MC, Pavot B, Schmidt G, Morand C, Sarda MU, Vazquez Manjarrez N, Verny MA, Wiczkowski W, Knox C, Manach C. PhytoHub, an online platform to gather expert knowledge on polyphenols and other dietary phytochemicals. International Conference on Polyphenols and Health (ICPH 2017); 2017.

Gottlieb OR. Micromolecular Evolution, Systematics and Ecology. Berlin, Heidelberg: Springer; 1982. DOI

Graham JG, Farnsworth NR. 3.04 - The NAPRALERT Database as an Aid for Discovery of Novel Bioactive Compounds. Comprehensive Natural Products. 2010;3:81–94. doi: 10.1016/b978-008045382-8.00060-5. DOI

Gu J, Gui Y, Chen L, Yuan G, Lu H-Z, Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLOS ONE. 2013;8:e62839. doi: 10.1371/journal.pone.0062839. PubMed DOI PMC

Günthardt BF, Hollender J, Hungerbühler K, Scheringer M, Bucheli TD. Comprehensive Toxic Plants-Phytotoxins Database and Its Application in Assessing Aquatic Micropollution Potential. Journal of Agricultural and Food Chemistry. 2018;66:7577–7588. doi: 10.1021/acs.jafc.8b01639. PubMed DOI

Hatherley R, Brown DK, Musyoka TM, Penkler DL, Faya N, Lobb KA, Tastan Bishop Ö. SANCDB: a South African natural compound database. Journal of Cheminformatics. 2015;7:29. doi: 10.1186/s13321-015-0080-8. PubMed DOI PMC

Haug K, Cochrane K, Nainala VC, Williams M, Chang J, Jayaseelan KV, O’Donovan C. MetaboLights: a resource evolving in response to the needs of its scientific community. Nucleic Acids Research. 2020;48:D440–D444. doi: 10.1093/nar/gkz1019. PubMed DOI PMC

Hegnauer R. Phytochemistry and plant taxonomy — an essay on the chemotaxonomy of higher plants. Phytochemistry. 1986a;25:1519–1535. doi: 10.1016/S0031-9422(00)81204-2. DOI

Hegnauer R. Chemotaxonomie Der Pflanzen. Basel: springer; 1986b. DOI

Heller S, McNaught A, Stein S, Tchekhovskoi D, Pletnev I. InChI - the worldwide chemical structure identifier standard. Journal of Cheminformatics. 2013;5:7. doi: 10.1186/1758-2946-5-7. PubMed DOI PMC

Helmy M, Crits-Christoph A, Bader GD. Ten Simple Rules for Developing Public Biological Databases. PLOS Computational Biology. 2016;12:e1005128. doi: 10.1371/journal.pcbi.1005128. PubMed DOI PMC

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. PLOS Computational Biology. 2019;15:e1007128. doi: 10.1371/journal.pcbi.1007128. PubMed DOI PMC

Hoffmann MA, Nothias LF, Ludwig M, Fleischauer M, Gentry EC, Witting M, Dorrestein PC, Dührkop K, Böcker S. Assigning Confidence to Structural Annotations from Mass Spectra with COSMIC. bioRxiv. 2021 doi: 10.1101/2021.03.18.435634. PubMed DOI

Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T. MassBank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry. 2010;45:703–714. doi: 10.1002/jms.1777. PubMed DOI

Huang W, Brewer LK, Jones JW, Nguyen AT, Marcu A, Wishart DS, Oglesby-Sherrouse AG, Kane MA, Wilks A. PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. Nucleic Acids Research. 2018;46:D575–D580. doi: 10.1093/nar/gkx1061. PubMed DOI PMC

Hunter JD. Matplotlib: A 2D Graphics Environment. Computing in Science & Engineering. 2007;9:90–95. doi: 10.1109/MCSE.2007.55. DOI

Ibezim A, Debnath B, Ntie-Kang F, Mbah CJ, Nwodo NJ. Binding of anti-Trypanosoma natural products from African flora against selected drug targets: a docking study. Medicinal Chemistry Research. 2017;26:562–579. doi: 10.1007/s00044-016-1764-y. DOI

Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods. 2020;17:901–904. doi: 10.1038/s41592-020-0916-7. PubMed DOI PMC

Jones MR, Pinto E, Torres MA, Dörr F, Mazur-Marzec H, Szubert K, Tartaglione L, Dell’Aversano C, Miles CO, Beach DG, McCarron P, Sivonen K, Fewer DP, Jokela J, Janssen EM-L. CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria. Water Research. 2021;196:117017. doi: 10.1016/j.watres.2021.117017. PubMed DOI

Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiological Research. 2021;246:126708. doi: 10.1016/j.micres.2021.126708. PubMed DOI

Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, Selem-Mojica N, Alanjary M, Robinson SL, Lund G, Epstein SC, Sisto AC, Charkoudian LK, Collemare J, Linington RG, Weber T, Medema MH. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Research. 2020;48:D454–D458. doi: 10.1093/nar/gkz882. PubMed DOI PMC

Kessler A, Kalske A. Plant Secondary Metabolite Diversity and Species Interactions. Annual Review of Ecology, Evolution, and Systematics. 2018;49:115–138. doi: 10.1146/annurev-ecolsys-110617-062406. DOI

Kim SK, Nam S, Jang H, Kim A, Lee JJ. TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine. BMC Complementary and Alternative Medicine. 2015a;15:218. doi: 10.1186/s12906-015-0758-5. PubMed DOI PMC

Kim S, Thiessen PA, Bolton EE, Bryant SH. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic Acids Research. 2015b;43:W605–W611. doi: 10.1093/nar/gkv396. PubMed DOI PMC

Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE. An update on PUG-REST: RESTful interface for programmatic access to PubChem. Nucleic Acids Research. 2018;46:W563–W570. doi: 10.1093/nar/gky294. PubMed DOI PMC

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2019 update: improved access to chemical data. Nucleic Acids Research. 2019;47:D1102–D1109. doi: 10.1093/nar/gky1033. PubMed DOI PMC

Kim HW, Wang M, Leber CA, Nothias L-F, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH, Cottrell GW. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. Journal of Natural Products. 2021;84:2795–2807. doi: 10.1021/acs.jnatprod.1c00399. PubMed DOI PMC

Klementz D, Döring K, Lucas X, Telukunta KK, Erxleben A, Deubel D, Erber A, Santillana I, Thomas OS, Bechthold A, Günther S. StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes. Nucleic Acids Research. 2016;44:D509–D514. doi: 10.1093/nar/gkv1319. PubMed DOI PMC

Kratochvíl M, Vondrášek J, Galgonek J. Sachem: a chemical cartridge for high-performance substructure search. Journal of Cheminformatics. 2018;10:27. doi: 10.1186/s13321-018-0282-y. PubMed DOI PMC

Kratochvíl M, Vondrášek J, Galgonek J. Interoperable chemical structure search service. Journal of Cheminformatics. 2019;11:45. doi: 10.1186/s13321-019-0367-2. PubMed DOI PMC

Kuang K, Kong Q, Napolitano F. pbmcapply: Tracking the Progress of Mc*pply with Progress Bar. CRAN. 2019 https://CRAN.R-project.org/package=pbmcapply

Lang DT. XML: Tools for Parsing and Generating XML Within R and S-Plus. CRAN. 2020 https://CRAN.R-project.org/package=XML

Lee CJ, Sugimoto CR, Zhang G, Cronin B. Bias in peer review. Journal of the American Society for Information Science and Technology. 2013;64:2–17. doi: 10.1002/asi.22784. DOI

Lin D, Crabtree J, Dillo I, Downs RR, Edmunds R, Giaretta D, De Giusti M, L’Hours H, Hugo W, Jenkyns R, Khodiyar V, Martone ME, Mokrane M, Navale V, Petters J, Sierman B, Sokolova DV, Stockhause M, Westbrook J. The TRUST Principles for digital repositories. Scientific Data. 2020;7:144. doi: 10.1038/s41597-020-0486-7. PubMed DOI PMC

Loo M. The stringdist Package for Approximate String Matching. The R Journal. 2014;6:111. doi: 10.32614/RJ-2014-011. DOI

Lowe DM, Corbett PT, Murray-Rust P, Glen RC. Chemical name to structure: OPSIN, an open source solution. Journal of Chemical Information and Modeling. 2011;51:739–753. doi: 10.1021/ci100384d. PubMed DOI

Madariaga-Mazón A, Naveja JJ, Medina-Franco JL, Noriega-Colima KO, Martinez-Mayorga K. DiaNat-DB: a molecular database of antidiabetic compounds from medicinal plants. RSC Advances. 2021;11:5172–5178. doi: 10.1039/D0RA10453A. PubMed DOI PMC

Mahto A. splitstackshape: Stack and Reshape Datasets After Splitting Concatenated Values. Splitstackshape. 2019 https://CRAN.R-project.org/package=splitstackshape

Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, A Miller R, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. WikiPathways: connecting communities. Nucleic Acids Research. 2021;49:D613–D621. doi: 10.1093/nar/gkaa1024. PubMed DOI PMC

McAlpine JB, Chen S-N, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji N-Y, Johnson TA, Kingston DGI, Koshino H, Lee H-W, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam J-W, Neupane RP, Niemitz M, Nuzillard J-M, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault J-H, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang B-G, Williams CM, Williams PG, Wist J, Yue J-M, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Natural Product Reports. 2019;36:35–107. doi: 10.1039/c7np00064b. PubMed DOI PMC

Michonneau F, Brown JW, Winter DJ, Fitzjohn R. rotl: an R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution. 2016;7:1476–1481. doi: 10.1111/2041-210X.12593. DOI

Mohamed A, Abuoda G, Ghanem A, Kaoudi Z, Aboulnaga A. RDFFrames: Knowledge Graph Access for Machine Learning Tools. RDFFrames. 2020 https://www.wikidata.org/wiki/Q106204599

Mongia M, Mohimani H. Repository scale classification and decomposition of tandem mass spectral data. Scientific Reports. 2021;11:8314. doi: 10.1038/s41598-021-87796-6. PubMed DOI PMC

Müller K, Wickham H, James DA, Falcon S. RSQLite: “SQLite” interface for r. RSQLite. 2021 https://CRAN.R-project.org/package=RSQLite

Murray-Rust P. Open Data in Science. Nature Precedings. 2008;4:26. doi: 10.1038/npre.2008.1526.1. DOI

Noteborn HP, Lommen A, van der Jagt RC, Weseman JM. Chemical fingerprinting for the evaluation of unintended secondary metabolic changes in transgenic food crops. Journal of Biotechnology. 2000;77:103–114. doi: 10.1016/s0168-1656(99)00210-2. PubMed DOI

Ntie-Kang F, Telukunta KK, Döring K, Simoben CV, A Moumbock AF, Malange YI, Njume LE, Yong JN, Sippl W, Günther S. NANPDB: A Resource for Natural Products from Northern African Sources. Journal of Natural Products. 2017;80:2067–2076. doi: 10.1021/acs.jnatprod.7b00283. PubMed DOI

Nupur LNU, Vats A, Dhanda SK, Raghava GPS, Pinnaka AK, Kumar A. ProCarDB: a database of bacterial carotenoids. BMC Microbiology. 2016;16:96. doi: 10.1186/s12866-016-0715-6. PubMed DOI PMC

Ooms J. The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects. Wikidata. 2014 https://www.wikidata.org/wiki/Q106204620

Pedersen TL. ggraph: An Implementation of Grammar of Graphics for Graphs and Networks. Ggraph. 2020 https://CRAN.R-project.org/package=ggraph

Pierce HH, Dev A, Statham E, Bierer BE. Credit data generators for data reuse. Nature. 2019;570:30–32. doi: 10.1038/d41586-019-01715-4. PubMed DOI

Pilon AC, Valli M, Dametto AC, Pinto MEF, Freire RT, Castro-Gamboa I, Andricopulo AD, Bolzani VS. NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. Scientific Reports. 2017;7:7215. doi: 10.1038/s41598-017-07451-x. PubMed DOI PMC

Pilón-Jiménez BA, Saldívar-González FI, Díaz-Eufracio BI, Medina-Franco JL. BIOFACQUIM: A Mexican Compound Database of Natural Products. Biomolecules. 2019;9:E31. doi: 10.3390/biom9010031. PubMed DOI PMC

Probst D, Reymond JL. FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web. Bioinformatics (Oxford, England) 2018a;34:1433–1435. doi: 10.1093/bioinformatics/btx760. PubMed DOI

Probst D, Reymond JL. SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript. Journal of Chemical Information and Modeling. 2018b;58:1–7. doi: 10.1021/acs.jcim.7b00425. PubMed DOI

Probst D, Reymond J-L. Visualization of very large high-dimensional data sets as minimum spanning trees. Journal of Cheminformatics. 2020;12:12. doi: 10.1186/s13321-020-0416-x. PubMed DOI PMC

Rasberry L, Willighagen E, Nielsen F, Mietchen D. Robustifying Scholia: paving the way for knowledge discovery and research assessment through Wikidata. Research Ideas and Outcomes. 2019;5:e35820. doi: 10.3897/rio.5.e35820. DOI

RDKit RDKit: Open-source cheminformatics. GitHub/SourceForge. 2021 http://www.rdkit.org

Reback J, McKinney W, Jbrockmendel J, Augspurger T, Cloud P, Gfyoung S, Hawkins S, Roeschke M. pandas-dev/pandas: Pandas. Zenodo. 2020 doi: 10.5281/zenodo.4161697. DOI

Rees JA, Cranston K. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal. 2017;10:e12581. doi: 10.3897/BDJ.5.e12581. PubMed DOI PMC

Rothwell JA, Perez-Jimenez J, Neveu V, Medina-Remón A, M’hiri N, García-Lobato P, Manach C, Knox C, Eisner R, Wishart DS, Scalbert A. Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. Database. 2013;2013:bat070. doi: 10.1093/database/bat070. PubMed DOI PMC

Rutz A, Dounoue-Kubo M, Ollivier S, Bisson J, Bagheri M, Saesong T, Ebrahimi SN, Ingkaninan K, Wolfender J-L, Allard P-M. Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation. Frontiers in Plant Science. 2019;10:1329. doi: 10.3389/fpls.2019.01329. PubMed DOI PMC

Rutz A. The LOTUS Initiative for Open Natural Products Research: custom dictionaries. Zenodo. 2021 doi: 10.5281/zenodo.5801816. DOI

Rutz A, Gaudry A. The LOTUS Initiative for Open Natural Products Research: TMAP. 4.0Zenodo. 2021 doi: 10.5281/zenodo.5801807. PubMed DOI PMC

Rutz A, Bisson J, Allard PM. The LOTUS Initiative for Open Natural Products Research: biological and chemical trees. Zenodo. 2021a doi: 10.5281/zenodo.5794106. DOI

Rutz A, Bisson J, Allard PM. The LOTUS Initiative for Open Natural Products Research: waste to recycle. Zenodo. 2021b doi: 10.5281/zenodo.5794597. DOI

Rutz A, Bisson J, Allard PM. The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata. Zenodo. 2021c doi: 10.5281/zenodo.5794107. DOI

Rutz A, Bisson J, Allard PM, Community W. The LOTUS Initiative for Open Natural Products Research: wikidata query results. Zenodo. 2021d doi: 10.5281/zenodo.5668854. DOI

Rutz A, Bisson J, Allard PM, Community W. The LOTUS Initiative for Open Natural Products Research: wikidata query results. Zenodo. 2021e doi: 10.5281/zenodo.5793224. DOI

Rutz A, Bisson J, Allard PM, Gaudry W. lotusnprod/lotus-processor. v1.0.0Zenodo. 2021f doi: 10.5281/zenodo.5802107. DOI

Rutz A. The LOTUS Initiative. swh:1:rev:78e6065d8eb9d0b0d11c2ea8de6ac66b445bca0eSoftware Heritage. 2022a https://archive.softwareheritage.org/swh:1:dir:06f92b6efba0c694b9ff259ee9406c8269a9bc3f;origin=https://github.com/lotusnprod/lotus-processor;visit=swh:1:snp:816d6826154073ce81ea66e18893029abb53a8e9;anchor=swh:1:rev:78e6065d8eb9d0b0d11c2ea8de6ac66b445bca0e

Rutz A. LOTUS web. swh:1:rev:278a5ab82389ebd5df720b1876a1724d15937644Software Heritage. 2022b https://archive.softwareheritage.org/swh:1:dir:b00de761fdb113deab6cad0143190006edd0181f;origin=https://github.com/lotusnprod/lotus-web;visit=swh:1:snp:aa23783a4ecd32578845345e497259a5fdd78a0c;anchor=swh:1:rev:278a5ab82389ebd5df720b1876a1724d15937644

Rutz A. Wikidata interactions for the LOTUS Initiative. swh:1:rev:92d19b8995a69f5bba39f438172ba425fdcc0f28Software Heritage. 2022c https://archive.softwareheritage.org/swh:1:dir:3c6e7a6d7c939a4ae63ef03a039bd843839ac34f;origin=https://github.com/lotusnprod/lotus-wikidata-interact;visit=swh:1:snp:86ac8009d72baef9426fe2d7cc55fe980e4d3b78;anchor=swh:1:rev:92d19b8995a69f5bba39f438172ba425fdcc0f28

Saikkonen K, Wäli P, Helander M, Faeth SH. Evolution of endophyte-plant symbioses. Trends in Plant Science. 2004;9:275–280. doi: 10.1016/j.tplants.2004.04.005. PubMed DOI

Sander T, Freyss J, von Korff M, Rufener C. DataWarrior: an open-source program for chemistry aware data visualization and analysis. Journal of Chemical Information and Modeling. 2015;55:460–473. doi: 10.1021/ci500588j. PubMed DOI

Sawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito K. RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. Phytochemistry. 2012;82:38–45. doi: 10.1016/j.phytochem.2012.07.007. PubMed DOI

Sedio BE. Recent breakthroughs in metabolomics promise to reveal the cryptic chemical traits that mediate plant community composition, character evolution and lineage diversification. The New Phytologist. 2017;214:952–958. doi: 10.1111/nph.14438. PubMed DOI

Sharma A, Dutta P, Sharma M, Rajput NK, Dodiya B, Georrge JJ, Kholia T, Bhardwaj A, OSDD Consortium BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. Journal of Cheminformatics. 2014;6:46. doi: 10.1186/s13321-014-0046-2. PubMed DOI PMC

Shinbo Y, Nakamura Y, Altaf-Ul-Amin M, Asahi H, Kurokawa K, Arita M, Saito K, Ohta D, Shibata D, Kanaya S. Plant Metabolomics. Springer; 2006. DOI

Sievert C. Interactive Web-Based Data Visualization with R, Plotly, and Shiny. Chapman and Hall/CRC; 2020. DOI

Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research. 2018;46:D661–D667. doi: 10.1093/nar/gkx1064. PubMed DOI PMC

Sorokina M, Steinbeck C. COCONUT: the COlleCtion of Open NatUral producTs. Zenodo. 2020a doi: 10.5281/zenodo.3778405. PubMed DOI PMC

Sorokina M, Steinbeck C. Review on natural products databases: where to find data in 2020. Journal of Cheminformatics. 2020b;12:20. doi: 10.1186/s13321-020-00424-9. PubMed DOI PMC

Sorokina M, Merseburger P, Rajan K, Yirik MA, Steinbeck C. COCONUT online: Collection of Open Natural Products database. Journal of Cheminformatics. 2021a;13:2. doi: 10.1186/s13321-020-00478-9. PubMed DOI PMC

Sorokina M, Rutz A, Renovate W, Willighagen E. Imgbot. lotusnprod/lotus. Zenodo. 2021b doi: 10.5281/zenodo.5802120. DOI

Szöcs E, Stirling T, Scott ER, Scharmüller A, Schäfer RB. webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software. 2020;10:i13. doi: 10.18637/jss.v093.i13. DOI

Taylor NG, Dunn AM. Predatory impacts of alien decapod Crustacea are predicted by functional responses and explained by differences in metabolic rate. Biological Invasions. 2018;20:2821–2837. doi: 10.1007/s10530-018-1735-y. DOI

Tomiki T, Saito T, Ueki M, Konno H, Asaoka T, Suzuki R, Uramoto M, Kakeya H, Osada H. RIKEN natural products encyclopedia (RIKEN NPEdia) a chemical database of RIKEN natural products depository (RIKEN NPDepo. Proceedings of the Symposium on Chemoinformatics; 2006. DOI

Tsugawa H. Advances in computational metabolomics and databases deepen the understanding of metabolisms. Current Opinion in Biotechnology. 2018;54:10–17. doi: 10.1016/j.copbio.2018.01.008. PubMed DOI

U.S. Department of Agriculture Dr. Duke’s Phytochemical and Ethnobotanical Databases. Agricultural Research Service. 1992 https://phytochem.nal.usda.gov/

van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FPJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee J-H, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O’Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG. The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. ACS Central Science. 2019;5:1824–1833. doi: 10.1021/acscentsci.9b00806. PubMed DOI PMC

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM-L, Duncan KR, Linington RG. The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Research. 2022;50:D1317–D1323. doi: 10.1093/nar/gkab941. PubMed DOI PMC

Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P, SciPy 1.0 Contributors SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods. 2020;17:261–272. doi: 10.1038/s41592-019-0686-2. PubMed DOI PMC

Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. eLife. 2020;9:e52614. doi: 10.7554/eLife.52614. PubMed DOI PMC

Wakankenaku WAKANKENSAKU. 2020. [July 2, 2020]. https://wakankensaku.inm.u-toyama.ac.jp/wiki/Main_Page

Wang L-G, Lam TT-Y, Xu S, Dai Z, Zhou L, Feng T, Guo P, Dunn CW, Jones BR, Bradley T, Zhu H, Guan Y, Jiang Y, Yu G. Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data. Molecular Biology and Evolution. 2020;37:599–603. doi: 10.1093/molbev/msz240. PubMed DOI PMC

Warnes GR, Bolker B, Gorjanc G, Grothendieck G, Korosec A, Lumley T, MacQueen D, Magnusson A. gdata: Various r programming tools for data manipulation. Gdata. 2017 https://CRAN.R-project.org/package=gdata

Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Modeling. 1988;28:31–36. doi: 10.1021/ci00057a005. DOI

Wickham H. readxl: Read Excel Files. Readxl. 2018 https://CRAN.R-project.org/package=readxl

Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen T, Miller E, Bache S, Müller K, Ooms J, Robinson D, Seidel D, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H. Welcome to the Tidyverse. Journal of Open Source Software. 2019;4:1686. doi: 10.21105/joss.01686. DOI

Wickham H. rvest: Easily Harvest (Scrape) Web Pages. Rvest. 2020 https://CRAN.R-project.org/package=rvest

Wickham H, Hester J. Jeroen Ooms. xml2. Parse XML. 2020 https://CRAN.R-project.org/package=xml2

Wickham H, Müller K. DBI: R database interface R Special Interest Group on Databases. DBI. 2021 https://CRAN.R-project.org/package=DBI

Wilkins D. ggfittext: Fit Text Inside a Box in ’ggplot2. Ggplot2. 2020 https://CRAN.R-project.org/package=ggfittext

Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 2016;3:160018. doi: 10.1038/sdata.2016.18. PubMed DOI PMC

Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics. 2017;9:33. doi: 10.1186/s13321-017-0220-4. PubMed DOI PMC

Winter D. rentrez: An R package for the NCBI eUtils API. The R Journal. 2017;9:520. doi: 10.32614/RJ-2017-058. DOI

Wohlgemuth G, Haldiya PK, Willighagen E, Kind T, Fiehn O. The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports. Bioinformatics (Oxford, England) 2010;26:2647–2648. doi: 10.1093/bioinformatics/btq476. PubMed DOI PMC

Xu S. ggstar: Star Layer for ’ggplot2. CRAN. 2021 https://CRAN.R-project.org/package=ggstar

Xu S, Dai Z, Guo P, Fu X, Liu S, Zhou L, Tang W, Feng T, Chen M, Zhan L, Wu T, Hu E, Jiang Y, Bo X, Yu G. ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data. Molecular Biology and Evolution. 2021;38:4039–4042. doi: 10.1093/molbev/msab166. PubMed DOI PMC

Yabuzaki J. Carotenoids Database: structures, chemical fingerprints and distribution among organisms. Database. 2017;2017:bax004. doi: 10.1093/database/bax004. PubMed DOI PMC

Yu G. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017;8:28–36. doi: 10.1111/2041-210x.12628. DOI

Yue Y, Chu G-X, Liu X-S, Tang X, Wang W, Liu G-J, Yang T, Ling T-J, Wang X-G, Zhang Z-Z, Xia T, Wan X-C, Bao G-H. TMDB: A literature-curated database for small molecular compounds found from tea. BMC Plant Biology. 2014;14:243. doi: 10.1186/s12870-014-0243-1. PubMed DOI PMC

Zeng X, Zhang P, He W, Qin C, Chen S, Tao L, Wang Y, Tan Y, Gao D, Wang B, Chen Z, Chen W, Jiang YY, Chen YZ. NPASS: natural product activity and species source database for natural product research, discovery and tool development. Nucleic Acids Research. 2018;46:D1217–D1222. doi: 10.1093/nar/gkx1026. PubMed DOI PMC

Zhang R, Lin J, Zou Y, Zhang X-J, Xiao W-L. Chemical Space and Biological Target Network of Anti-Inflammatory Natural Products. Journal of Chemical Information and Modeling. 2019;59:66–73. doi: 10.1021/acs.jcim.8b00560. PubMed DOI

Zhao W-Y, Yi J, Chang Y-B, Sun C-P, Ma X-C. Recent studies on terpenoids in Aspergillus fungi: Chemical diversity, biosynthesis, and bioactivity. Phytochemistry. 2022;193:113011. doi: 10.1016/j.phytochem.2021.113011. PubMed DOI

Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum

plantMASST - Community-driven chemotaxonomic digitization of plants

The IDSM mass spectrometry extension: searching mass spectra using SPARQL

Leaf metabolic traits reveal hidden dimensions of plant form and function

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins

The LOTUS initiative for open knowledge management in natural products research