The Natural Products Atlas : an open access knowledge base for microbial natural products discovery

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries

Applying PDP Lessons Learned About Inclusive Teaching and Assessment

Much of the ISEE Professional Development Program (PDP)’s long-term value arises from participants transferring teaching approaches they develop in the course of designing and facilitating a PDP inquiry activity to other contexts throughout their careers. PDP participants encounter frameworks such as the inquiry framework and the equity and inclusion focus areas, and are encouraged explicitly to become informed consumers of further scholarship on teaching and learning. Many participants resonate especially with the PDP’s emphasis on equity and inclusion in STEM teaching, and meld lessons from the PDP with their lived experiences as well as other scholarship on equity-minded or culturally responsive educational practices. Our panel shares four perspectives on extending lessons from the PDP to new contexts: mentoring students and developing interactive lessons in molecular biology, designing astronomy activities from a culturally relevant and culturally responsive standpoint, incorporating inquiry activities into a large astronomy lecture course, and helping academic programs across a university adopt equity-minded practices for assessing learning outcomes

Utilizing Equitable and Inclusive Design Principles to Promote STEM Identity of Community College Transfer Students

Research suggests that developing an identity as a person in STEM is necessary for learners from marginalized groups to persist in STEM education and careers. These learners may perceive that their race, gender, or other characteristics make it difficult for their peers and supervisors to recognize them as scientists or engineers, thus disrupting their ability to maintain successful degree progress and to pursue their STEM career aspirations. Here we discuss the specific ways we designed inquiry workshops to not only clarify difficult core STEM content, but to also promote learners’ competence, performance, and targeted recognition as scientists. Our workshops were designed for students interested in chemistry, climate science, physics, and toxicology at the University of California, Santa Cruz (UCSC), Workshops for Engineering & Science Transfers (WEST) 2019 program. In designing our workshops, we focused on promoting the scientific identities of our learners by incorporating authentic ways for students to receive recognition from both peers and instructional facilitators, as well as allowing students to tap into their own personal interests and values. Insights from our designed assessments for learners’ understanding of our content demonstrate the success of our initiatives and provide further areas of improvement. Our goals are to create inclusive workshops to support students from all backgrounds, with emphasis on underrepresented backgrounds (community college, first generation, students of color, women, and LGBTQ+ students, etc.) as well as support them in other contexts, such as when mentoring STEM students in academic laboratory settings

The Natural Products Atlas - data download

Download files from the Natural Products Atlas (npatlas.org). van Santen, J. A.; Jacob, G.; Leen Singh, A.; Aniebok, V.; Balunas, M. J.; Bunsko, D.; Carnevale Neto, F.; Castaño-Espriu, L.; Chang, C.; Clark, T. N.; Cleary Little, J. L.; Delgadillo, D. A.; Dorrestein, P. C.; Duncan, K. R.; Egan, J. M.; Galey, M. M.; Haeckl, F. P. J.; Hua, A.; Hughes, A. H.; Iskakova, D.; Khadilkar, A.; Lee, J.-H.; Lee, S.; LeGrow, N.; Liu, D. Y.; Macho, J. M.; McCaughey, C. S.; Medema, M. H.; Neupane, R. P.; O’Donnell, T. J.; Paula, J. S.; Sanchez, L. M.; Shaikh, A. F.; Soldatou, S.; Terlouw, B. R.; Tran, T. A.; Valentine, M.; van der Hooft, J. J. J.; Vo, D. A.; Wang, M.; Wilson, D.; Zink, K. E.; Linington, R. G.* "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”, ACS Central Science, 2019, 5, 11, 1824-1833. 10.1021/acscentsci.9b00806 Now includes ontological data from: NP Classifier - https://npclassifier.ucsd.edu/ ClassyFire - http://classyfire.wishartlab.com/ Including archived versions, extra data download types, and new MIBiG and GNPS IDs Includes dump of compounds deemed out of scope and removed from DB on May 19, 2021. The latest versions (v2021_08 onward) include the ontological data in the full JSON download

The Natural Products Atlas - data download

Download files from the Natural Products Atlas (npatlas.org). van Santen, J. A.; Jacob, G.; Leen Singh, A.; Aniebok, V.; Balunas, M. J.; Bunsko, D.; Carnevale Neto, F.; Castaño-Espriu, L.; Chang, C.; Clark, T. N.; Cleary Little, J. L.; Delgadillo, D. A.; Dorrestein, P. C.; Duncan, K. R.; Egan, J. M.; Galey, M. M.; Haeckl, F. P. J.; Hua, A.; Hughes, A. H.; Iskakova, D.; Khadilkar, A.; Lee, J.-H.; Lee, S.; LeGrow, N.; Liu, D. Y.; Macho, J. M.; McCaughey, C. S.; Medema, M. H.; Neupane, R. P.; O’Donnell, T. J.; Paula, J. S.; Sanchez, L. M.; Shaikh, A. F.; Soldatou, S.; Terlouw, B. R.; Tran, T. A.; Valentine, M.; van der Hooft, J. J. J.; Vo, D. A.; Wang, M.; Wilson, D.; Zink, K. E.; Linington, R. G.* "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”, ACS Central Science, 2019, 5, 11, 1824-1833. 10.1021/acscentsci.9b00806 Now includes ontological data from: NP Classifier - https://npclassifier.ucsd.edu/ ClassyFire - http://classyfire.wishartlab.com/ Including archived versions, extra data download types, and new MIBiG and GNPS IDs Includes dump of compounds deemed out of scope and removed from DB on May 19, 2021. The latest versions (v2021_08 onward) include the ontological data in the full JSON download