What is the NP-MRD - The NP-MRD is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD supports NMR data deposition and associated metadata from NP studies characterizing new and known compounds. Why should I deposit my data? - Journal mandate will require raw data upload with manuscript - Permanent storage of your NMR data in an open, searchable platform - Complies with mandates from funding agencies for data deposition - Openly accessible spectra - Increased citations for your work - Opportunity for new collaborations with external research groups - Offers tools for compound dereplication - Provides test data for researchers creating new informatics tools for natural products discovery - Data cannot be lost when a lab member leaves, or a hard drive fails Who runs the NP-MRD? - The NP-MRD is run by a research consortium led by Dr. John Cort from the Pacific Northwest National Laboratory (PNNL). The consortium includes Professors Roger Linington (Simon Fraser University), David Wishart (University of Alberta) and Lloyd Sumner (University of Missouri). It is funded by the National Institutes of Health through the CARBON program supported by the Center for Complementary and Integrative Health and the Office of Dietary Supplements. Is this a commercial database? - No. This database is maintained under FAIR principles, meaning that the data are openly and freely available for all users. The website does not have a paywall, and all data in the database are accessible users anywhere in the world. Why are you developing this database? - Over the last 50 years, researchers have obtained NMR data on hundreds of thousands of natural products. Unfortunately, most of these data are now irretrievably lost. A high-quality database of NMR data will create new opportunities for compound dereplication, de novo structure elucidation, and data integration strategies for bioactive natural products discovery. By contributing your NMR data you are gaining recognition for the discoveries you have made, and contributing to the body of knowledge required to advance the field of natural products discovery. Why is depositing data different than reporting the NMR data in a paper? - Publications typically report NMR data for natural products as NMR data tables, or as images of spectra in the Supporting Information. In both cases, significant information is lost compared to the information contained in the original raw free-induction decay (FID). Depositing the original data ensures that these data are maintained and permanently accessible to the research community. Are scientific journals mandating raw data upload with publication? - Some scientific journals are beginning to ask for raw data deposition and data availability statements with publication. As the natural products community adapts to this change, NP-MRD is equipped to meet all the requirements set by journals and support your research.
Depositing Data
How to use NP-MRD deposition platform - The NP-MRD deposition platform is a quick and easy way to upload your data to a public repository. For an in-depth tutorial on how to use our platform, visit the instructions page on the deposition home page, and see the documentation for 'Starting Your Deposition'. What compounds can I upload? - We accept data for new and known compounds isolated from natural products. This includes small molecules derived from plants, fungi, bacteria, marine organisms, or animals. Can I upload compounds that are already in the NP-MRD? - Yes, you can upload data for compounds that already exist in our database. We hope to acquire a good range of experimental data for each compound, including different NMR experiments, solvents, and frequency. All data will be displayed on the NP card for each compound. Can I upload synthetic compounds included in my study? - If you synthesize a true natural product and acquire NMR data, you may upload the data for this structure. Synthetic derivatives or non-natural products, however, are not currently accepted in the NP-MRD. We kindly ask that you deposit compounds of this type on another platform. Can I upload compounds that are isolated from a natural product co-culture experiment? - Yes, you can deposit compounds from a natural product combined culture experiment. We ask that you input the information for all, or both of the genera and species used for isolation, respectively. Can I include known natural products that I characterized via chemical synthesis? - Yes, if you synthesize a true natural product and acquire NMR data, you may upload the data for this structure. Synthetic natural product data are useful to confirm or reassign compound structures.
Compound Data
What are SMILES? - SMILES, (Simplified Molecular Input Line Entry System) is the chemical notation used to describe a compound's structure. This code allows users to represent a chemical structure in a computer-readable way. You can get the SMILES of a structure using ChemDraw, ChemSketch or any other molecule drawing software. Then simply draw your structure on the draw pad and copy this as 'SMILES'. What experimental spectra can I include in my upload? - You may upload all NMR experiments used in the characterization of the natural product compounds in your study. We accept all experiment types including 1D and 2D. These can be zipped into one folder for each compound. Can I upload data a mixture? - Though mixtures are not currently supported in the drag-and-drop deposition platform, you may upload your mixture using ‘Option 4’ of the NP-MRD deposition service. See https://np-mrd.org/submissions What taxonomic identifier can I use I do not know the genus/species of the source from which I isolated the compound? - If you do not know the genus of your natural product, you may input the nearest known taxonomic identifier e.g., family, class, etc.
Unpublished Data (Presubmissions)
Can I deposit data related to a paper has been submitted to a journal for review, but is not yet published? - Yes, you can deposit this data under the 'Deposit Data from an ‘UNPUBLISHED article’ option. You are required to add details of the publication and set an embargo period for when you would like this data to be displayed on NP-MRD. What can I set as the embargo period if I don’t know when my paper will be published? - If you do not want your data online prior to publication, you may select to ‘Display Data Online Only After Article is Published’. You may attach the DOI once the paper is published, using the link provided in the confirmation email. The system will also track the literature for your publication based on the details provided in the presubmission.
Data Privacy
Is the data I deposit publicly visible? - If you deposit data for a new or known compound from a published article, the data you deposit will be publicly visible within 24 hours on the NP-MRD website. - If you deposit data for an article that is not yet published, you may choose when you wish to make this data publicly available. If you deposit any data and wish to retract the same, you may contact us immediately so we can intervene and retrieve the data. I've completed my submission, where is my data? - Publishing data from drag & drop submissions in our database is not an immediate process. For more information check out our [Data Publishing and Sharing](/article-pipeline-docs/data_publishing_and_sharing.html) instructions. Will NP-MRD provide a Data Availability Statement? - Yes, you will receive a Data Availability Statement via confirmation email within 24 hours of deposition. This will include a report of the data uploaded, summarizing compound information and spectra, and the accession number for your deposition. Where can I find the NP-MRD accession number of my deposition? - The Deposition ID is found in the completed submission confirmation email you receive within 24 hours of successful deposition. This can be used as the data availability accession number, if required. Where can I find the NP-MRD ID of my compound? - The NP-MRD ID can be found on the NP card for your compound. This accession number is displayed in brackets next to the compound name and under the Record Information section of the NP card. Other accession numbers are displayed as appropriate. What can I do if I made a mistake in my deposition? - If you made a mistake or deposited data in error, please contact the NP-MRD team as soon as possible so our team can intercept the data and reset the submission link, allowing you to deposit again and correct any errors.