The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
The Natural Products Atlas 2.0: a database of microbially-derived natural products
Open accessAbstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.
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The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423
Self-citationPubChem in 2021: new data content and improved web interfaces
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa971 · Cited by 3,953
NCBI Taxonomy: a comprehensive update on curation, resources and tools
Schoch, C. L., Ciufo, S., Domrachev, M., Hotton, C. L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B., et al. (2020) · Database · doi:10.1093/database/baaa062 · Cited by 2,635
ChEMBL: towards direct deposition of bioassay data
Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Félix, E., Magariños, M. P., Mosquera, J. F., Mutowo, P., Nowotka, M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1075 · Cited by 2,372
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
Parte, A. C., Sardà Carbasse, J., Meier-Kolthoff, J. P., Reimer, L. C., & Göker, M. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004332 · Cited by 1,989
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
Djoumbou Feunang, Y., Eisner, R., Knox, C., Chepelev, L., Hastings, J., Owen, G., Fahy, E., Steinbeck, C., Subramanian, S., Bolton, E., et al. (2016) · Journal of Cheminformatics · doi:10.1186/s13321-016-0174-y · Cited by 1,525
ChEMBL web services: streamlining access to drug discovery data and utilities
Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L., & Overington, J. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv352 · Cited by 757
COCONUT online: Collection of Open Natural Products database
Sorokina, M., Merseburger, P., Rajan, K., Yirik, M. A., & Steinbeck, C. (2021) · Journal of Cheminformatics · doi:10.1186/s13321-020-00478-9 · Cited by 665
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
Kautsar, S. A., Blin, K., Shaw, S., Navarro-Muñoz, J. C., Terlouw, B. R., van der Hooft, J. J. J., van Santen, J. A., Tracanna, V., Suarez Duran, H. G., Pascal Andreu, V., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz882 · Cited by 560
Self-citationNPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products
Kim, H. W., Wang, M., Leber, C. A., Nothias, L.-F., Reher, R., Kang, K. B., van der Hooft, J. J. J., Dorrestein, P. C., Gerwick, W. H., & Cottrell, G. W. (2021) · Journal of Natural Products · doi:10.1021/acs.jnatprod.1c00399 · Cited by 551
Cited by
The LOTUS initiative for open knowledge management in natural products research
Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondrášek, J., et al. (2022) · eLife · doi:10.7554/elife.70780 · Cited by 429
Harnessing the potential: Advances in cyanobacterial natural product research and biotechnology
Baunach, M., Guljamow, A., Miguel-Gordo, M., & Dittmann, E. (2024) · Natural Product Reports · doi:10.1039/d3np00045a · Cited by 66
Open data and algorithms for open science in AI-driven molecular informatics
Brinkhaus, H. O., Rajan, K., Schaub, J., Zielesny, A., & Steinbeck, C. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102542 · Cited by 29
Metadata
- Authors
- van Santen, J. A., Poynton, E. F., Iskakova, D., McMann, E., Alsup, T. A., Clark, T. N., Fergusson, C. H., Fewer, D. P., Hughes, A. H., McCadden, C. A., Parra, J., Soldatou, S., Rudolf, J. D., Janssen, E. M.-L., Duncan, K. R., & Linington, R. G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-10-28
- Volume
- 50
- Issue
- D1
- Pages
- D1317-D1323
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3210489033
- Cited by
- 319
- References
- 24
- FWCI
- 23.44
- Type
- journal article
- Language
- en
- Open access
- gold
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- van Santen, J. A., Poynton, E. F., Iskakova, D., McMann, E., Alsup, T. A., Clark, T. N., Fergusson, C. H., Fewer, D. P., Hughes, A. H., McCadden, C. A., Parra, J., Soldatou, S., Rudolf, J. D., Janssen, E. M.-L., Duncan, K. R., & Linington, R. G. (2022). The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab941
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
