The Natural Products Atlas - data download
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Download files from the Natural Products Atlas (npatlas.org). 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 Villalobos, J.; Soldatou, S.; Rudolf, J. D.; Janssen, E. M.-L.; Duncan, K. R.; Linington, R. G.* "The Natural Products Atlas 2.0: A Database of Microbially-Derived Natural Products", Nucleic Acids Research, 2022, 50, D1, 11, D1317-D1323. 10.1093/nar/gkab941 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. Starting in v2024_09 - compounds with exclusions are included as a separate file but kept in the database for reference.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.006 | 0.007 |
| Research integrity | 0.001 | 0.005 |
| Insufficient payload (model declined to judge) | 0.000 | 0.020 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it