The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery | ACS Central Science

Abstract:  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.

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery | ACS Central Science

Abstract:  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.

OPEN SCHOLARSHIP position statement from the Biochemical Society and Portland Press

“Currently: ? We publish two fully-OA journals, and one of these is currently sustained by article publishing charges (APC) at an article-by-article level; in addition, we publish five hybrid journals where authors may opt to pay an APC to have their article published OA. ? For titles on the hybrid model we avoid ‘double dipping’ (charging twice for the same articles) through two routes: APCs are discounted for corresponding authors based at subscribing institutions; in addition, subscription prices are set, each year, based on the number of paywalled articles in the preceding years to account for OA content published in hybrid titles. ? There are a variety of mechanisms employed by different publishers to avoid double-dipping. We are supportive of efforts to standardize and agree common principles around transparent pricing of hybrid journals that demonstrate, objectively, the avoidance of double dipping….

Looking ahead: ? We are seeking to transition our hybrid journals to full-OA in a way that supports researchers and keeps the Society financially viable. ? We strongly believe that the ability to publish research should not be linked to individual researchers’ ability to pay; we are enthusiastic about all opportunities to remove author-facing invoices from OA publishing. To enable a transition away from paywalls, we seek to offer as much APC-free OA as possible that will be supported though continuing and new partnerships with institutions, consortia and funders….

Guide to PHARMACOLOGY

This website, originally created in a collaboration between The British Pharmacological Society (BPS) and the International Union of Basic and Clinical Pharmacology (IUPHAR) and now developed jointly with funding from the Wellcome Trust, is intended to become a “one-stop shop” portal to pharmacological information. One of the main aims is to provide a searchable database with quantitative information on drug targets and the prescription medicines and experimental drugs that act on them….The Guide to PHARMACOLOGY database is licensed under the Open Data Commons Open Database License (ODbL). Its contents are licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported license….”

Which domains do open-access journals do best in? A 5-year longitudinal study – Yan – 2018 – Journal of the Association for Information Science and Technology – Wiley Online Library

Abstract:  Although researchers have begun to investigate the difference in scientific impact between closed-access and open-access journals, studies that focus specifically on dynamic and disciplinary differences remain scarce. This study serves to fill this gap by using a large longitudinal dataset to examine these differences. Using CiteScore as a proxy for journal scientific impact, we employ a series of statistical tests to identify the quartile categories and disciplinary areas in which impact trends differ notably between closed- and open-access journals. We find that closed-access journals have a noticeable advantage in social sciences (for example, business and economics), whereas open-access journals perform well in medical and healthcare domains (for example, health profession and nursing). Moreover, we find that after controlling for a journal’s rank and disciplinary differences, there are statistically more closed-access journals in the top 10%, Quartile 1, and Quartile 2 categories as measured by CiteScore; in contrast, more open-access journals in Quartile 4 gained scientific impact from 2011 to 2015. Considering dynamic and disciplinary trends in tandem, we find that more closed-access journals in Social Sciences gained in impact, whereas in biochemistry and medicine, more open-access journals experienced such gains.

Preprints made Outlaws

“The Commission of Biochemical Editors of the International Union of Biochemistry is proposing to take firm and, it hopes, lethal steps against the Information Exchange Groups which have been organized, over the past four years, from the National Institutes of Health in the United States. At a meeting in Vienna a week ago, the editors of six principal journals agreed to propose to their editorial boards that in the future they would not accept articles or other communications previously circulated through the Information Exchange Groups….”

Preprints made Outlaws

“The Commission of Biochemical Editors of the International Union of Biochemistry is proposing to take firm and, it hopes, lethal steps against the Information Exchange Groups which have been organized, over the past four years, from the National Institutes of Health in the United States. At a meeting in Vienna a week ago, the editors of six principal journals agreed to propose to their editorial boards that in the future they would not accept articles or other communications previously circulated through the Information Exchange Groups….”

Universal Language: The Pistoia Alliance Takes on Indescribable Biology | Open Health News

“Over the past year, another Pistoia project, HELM, has entered the public domain after gradual development by an assortment of Alliance members. An open source language and set of editing tools for working with large biomolecules, HELM has already become a foundational part of research in at least three large pharmaceutical companies….”