scholarly journals On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - A Review on Natural Products Databases

2019 ◽  
Author(s):  
Maria Sorokina ◽  
Christoph Steinbeck
Keyword(s):  
Natural Products ◽  
Open Access ◽  
Scientific Community ◽  
Natural Compounds ◽  
Data Sources ◽  
Scientific Publications ◽  
Rapid Multiplication ◽  
Zinc Database ◽  
Single Dataset ◽  
Supplementary Material

Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

Scientific Authorship and E-commons

2010 ◽  
pp. 193-205
Author(s):  
Luc Schneider
Keyword(s):  
Open Access ◽  
Open Source ◽  
Scientific Knowledge ◽  
Scientific Community ◽  
Scientific Literature ◽  
Source Model ◽  
Public Domain ◽  
Scientific Publications ◽  
Scientific Authorship ◽  
The Web

This contribution tries to assess how the Web is changing the ways in which scientific knowledge is produced, distributed and evaluated, in particular how it is transforming the conventional conception of scientific authorship. After having properly introduced the notions of copyright, public domain and (e-)commons, I will critically assess James Boyle's (2003, 2008) thesis that copyright and scientific (e-) commons are antagonistic, but I will mostly agree with the related claim by Stevan Harnad (2001a,b, 2008) that copyright has become an obstacle to the accessibility of scientific works. I will even go further and argue that Open Access schemes not only solve the problem of the availability of scientific literature, but may also help to tackle the uncontrolled multiplication of scientific publications, since these publishing schemes are based on free public licenses allowing for (acknowledged) re-use of texts. However, the scientific community does not seem to be prepared yet to move towards an Open Source model of authorship, probably due to concerns related to attributing credit and responsability for the expressed hypotheses and results. Some strategies and tools that may encourage a change of academic mentality in favour of a conception of scientific authorship modelled on the Open Source paradigm are discussed.

Memorandum “Open Metadata”

2015 ◽  
Vol 54 (04) ◽  
pp. 376-378 ◽  
Author(s):  
M. Dugas ◽  
K. -H. Jöckel ◽  
T. Friede ◽  
O. Gefeller ◽  
M. Kieser ◽  
...  
Keyword(s):  
Health Care ◽  
Case Report ◽  
Open Access ◽  
Scientific Community ◽  
Epidemiological Studies ◽  
International Standards ◽  
Medical Documentation ◽  
Scientific Publications ◽  
The Public ◽  
Routine Patient Care

SummaryAt present, most documentation forms and item catalogs in healthcare are not accessible to the public. This applies to assessment forms of routine patient care as well as case report forms (CRFs) of clinical and epidemiological studies. On behalf of the German chairs for Medical Informatics, Biometry and Epidemiology six recommendations to developers and users of documentation forms in healthcare were developed. Open access to medical documentation forms could substantially improve information systems in health-care and medical research networks. Therefore these forms should be made available to the scientific community, their use should not be unduly restricted, they should be published in a sustainable way using international standards and sources of documentation forms should be referenced in scientific publications.

scholarly journals A new model for scientific publications: A Managing Editor’s view

2020 ◽  
Vol 10 (1) ◽  
pp. 220-245
Author(s):  
Leire Kortabarria
Keyword(s):  
Open Access ◽  
Scientific Community ◽  
Open Access Journal ◽  
Scientific Publications ◽  
Economic Implications ◽  
New Model ◽  
Journal Publishing ◽  
Acceso Abierto ◽  
Mainstream Journal

In this essay, we will first set out the context in which Oñati Socio-Legal Series was created. We will then aim to offer a non-exhaustive view of what an open access journal is and what it implies for scholars and for publishers, and the, sometimes, stark differences in each one’s view. From here, we will move on to draw a succinct description of the implications of the mainstream journal publishing scheme, with a stress on the commercial and economic implications. We will then narrow the focus and zero in on the case of Oñati Socio-Legal Series. Drawing on the case of this journal, we will argue why it is possible to expand a 100% free Open Access journal model, with no charges whatsoever on the authors, and why it is necessary for the scientific community. En este artículo, primeramente dibujaremos el contexto en el que se creó Oñati Socio-Legal Series. A continuación, nos proponemos ofrecer una visión general de lo que constituye el acceso abierto y de sus implicaciones para académicos y editoriales, y las diferencias, a veces enormes, entre ambas perspectivas. Después, describiremos brevemente las implicaciones del escenario dominante en la publicación de revistas científicas, poniendo el acento en las implicaciones comerciales y económicas. Estrecharemos luego el ámbito y nos centraremos en el caso de Oñati Socio-Legal Series. Sirviéndonos del ejemplo de esa revista, argumentaremos por qué es posible expandir un modelo 100% de acceso abierto, sin imposición de cobros a los autores, y por qué un modelo así es necesario para la comunidad científica.

The International Action “Open Access Week — 2009”

2009 ◽  
pp. 97-98
Author(s):  
Yulia V. Samodova
Keyword(s):  
Open Access ◽  
Scientific Community ◽  
International Scientific Community ◽  
International Action ◽  
The World

Information on the coming Open Access Week which will be held from 19 to 23 October 2009. Interest in the results of scientific researches all over the world has led to consolidation of forces of the international scientific community and to expand the now-annual event from a single day to seven days.

Recent Progress Towards Synthesis of the Indolizidine Alkaloid 195B

2020 ◽  
Vol 17 (2) ◽  
pp. 82-90 ◽  
Author(s):  
Ghodsi Mohammadi Ziarani ◽  
Fatemeh Mohajer ◽  
Zohreh kheilkordi
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Recent Progress ◽  
Human Life ◽  
Natural Compounds ◽  
Biologically Active ◽  
Pharmaceutical Chemistry ◽  
Biological Perspective ◽  
Highly Active

Background: Natural products have been received attention due to their importance in human life as those are biologically active. In this review, there are some reports through different methods related to the synthesis of the indolizidine 195B which was extracted from poisonous frog; however, due to respect nature, the synthesis of natural compounds such as indolizidine has been attracted much attention among scientists and researchers. Objective: This review discloses the procedures and methods to provide indolizidine 195B from 1989 to 2018 due to their importance as a natural product. Conclusion: There are several methods to give rise to the indolizidine 195B as a natural product that is highly active from the biological perspective in pharmaceutical chemistry. In summary, many protocols for the preparations of indolizidine 195B from various substrates, several reagents, and conditions have been reported from different aromatic and aliphatic.

scholarly journals Partitioning Pattern of Natural Products Based on Molecular Properties Descriptors Representing Drug-Likeness

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 546
Author(s):  
Miroslava Nedyalkova ◽  
Vasil Simeonov
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
De Novo ◽  
Target Prediction ◽  
Natural Compounds ◽  
Discovery Process ◽  
Drug Discovery Process ◽  
Unique Source ◽  
The Times ◽  
Partitioning Pattern

A cheminformatics procedure for a partitioning model based on 135 natural compounds including Flavonoids, Saponins, Alkaloids, Terpenes and Triterpenes with drug-like features based on a descriptors pool was developed. The knowledge about the applicability of natural products as a unique source for the development of new candidates towards deadly infectious disease is a contemporary challenge for drug discovery. We propose a partitioning scheme for unveiling drug-likeness candidates with properties that are important for a prompt and efficient drug discovery process. In the present study, the vantage point is about the matching of descriptors to build the partitioning model applied to natural compounds with diversity in structures and complexity of action towards the severe diseases, as the actual SARS-CoV-2 virus. In the times of the de novo design techniques, such tools based on a chemometric and symmetrical effect by the implied descriptors represent another noticeable sign for the power and level of the descriptors applicability in drug discovery in establishing activity and target prediction pipeline for unknown drugs properties.

scholarly journals Natural Products Targeting the Mitochondria in Cancers

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 92
Author(s):  
Yue Yang ◽  
Ping-Ya He ◽  
Yi Zhang ◽  
Ning Li
Keyword(s):  
Natural Products ◽  
Anticancer Drugs ◽  
Web Of Science ◽  
Keyword Search ◽  
Biological Activities ◽  
Natural Compounds ◽  
New Drugs ◽  
Antitumor Effects ◽  
Regulate Cell Growth ◽  
Anticancer Drug Discovery

There are abundant sources of anticancer drugs in nature that have a broad prospect in anticancer drug discovery. Natural compounds, with biological activities extracted from plants and marine and microbial metabolites, have significant antitumor effects, but their mechanisms are various. In addition to providing energy to cells, mitochondria are involved in processes, such as cell differentiation, cell signaling, and cell apoptosis, and they have the ability to regulate cell growth and cell cycle. Summing up recent data on how natural products regulate mitochondria is valuable for the development of anticancer drugs. This review focuses on natural products that have shown antitumor effects via regulating mitochondria. The search was done in PubMed, Web of Science, and Google Scholar databases, over a 5-year period, between 2015 and 2020, with a keyword search that focused on natural products, natural compounds, phytomedicine, Chinese medicine, antitumor, and mitochondria. Many natural products have been studied to have antitumor effects on different cells and can be further processed into useful drugs to treat cancer. In the process of searching for valuable new drugs, natural products such as terpenoids, flavonoids, saponins, alkaloids, coumarins, and quinones cover the broad space.

Anti-aging natural compounds and their role in the regulation of metabolic pathways leading to longevity

2021 ◽  
Vol 21 ◽  
Author(s):  
Aqsa Muzammil ◽  
Muhammad Waqas ◽  
Ahitsham Umar ◽  
Muhammad Sufyan ◽  
Abdur Rehman ◽  
...  
Keyword(s):  
Natural Products ◽  
Metabolic Pathways ◽  
Natural Compounds ◽  
Chronic Obstructive ◽  
Telomere Shortening ◽  
Age Related ◽  
Chronic Obstructive Pulmonary Diseases ◽  
Extended Lifespan ◽  
Ancient Times

: Aging is an unavoidable process, leads to cell senescence due to physiochemical changes in an organism. Anti-aging remedies have always been of great interest since ancient times. The purpose of anti-aging activities is to increase the life span and the quality of life. Anti-aging activities are primarily involved in the therapies of age-related disorders such as Parkinson's disease (PD), Alzheimer's disease (AD), cardiovascular diseases, cancer and chronic obstructive pulmonary diseases. These diseases are triggered by multiple factors that are involved in numerous molecular pathways including telomere shortening, NF-κB pathway, adiponectin receptor pathway, insulin and IGF signaling pathway, AMPK, mTOR and mitochondria dysfunction. Natural products are known as effective molecules to delay the aging process through influencing metabolic pathways and thus ensure an extended lifespan. These natural compounds are being utilized in drug design and development through computational and high throughput techniques for effective pro-longevity drugs. A comprehensive study of natural compounds demonstrated with their anti-aging activities along with databases of natural products for drug designing was executed and summarized in this review article.

scholarly journals Zugang für alle? Rhetorik und Realität der Open Access‑Initiativen

2018 ◽  
Vol 69 (4) ◽  
pp. 161-170 ◽  
Author(s):  
Herbert Hrachovec
Keyword(s):  
Open Access ◽  
Scientific Community ◽  
Wissenschaftliche Publikationen

ZusammenfassungDie Initiative, wissenschaftliche Publikationen, deren Entstehung in Universitäten und Forschungsinstituten zumeist von der öffentlichen Hand finanziert wird, der Öffentlichkeit auch entgeltfrei zugänglich zu machen, hat ein breites Echo gefunden. Angestoßen von der Budapester und der Berliner Erklärung (2002 und 2003) hat sie zum Aufbau einer leistungsfähigen Infrastruktur zwecks Erfassung, Distribution und Archivierung dieser Arbeiten geführt. Die damit verbundene Institutionalisierung wurde im Lauf der Zeit allerdings erfolgreicher als der Aufruf zur Mitbeteiligung an die „scientific community“, die Verwaltung ihrer Ergebnisse selbst in die Hand zu nehmen. Die Hauptakteure sind nun Bibliotheken, Hochschulleitungen und Fördereinrichtungen. Ein Grund für diesen, die anfänglichen Betreiber der Initiative enttäuschenden, Umstand liegt in ihrem Ansatz selbst. Er übergeht, wie erst hinterher auffällt, die bestehende sozio-ökonomische Infrastruktur des Verlagswesens und die mit ihm gekoppelten Interessen der Wissenschaftlerinnen. In der Folge hat der Impuls zwar neue Verhältnisse geschaffen, aber paradoxer Weise zugunsten der wissenschaftlichen Großverlage, gegen die er ursprünglich gerichtet war.

Exploring Possibilities for Transforming Established Subscription-based Scientific Journals into Open Access Journals

2016 ◽  
Vol 55 (06) ◽  
pp. 481-487 ◽  
Author(s):  
Stefanie Kuballa ◽  
Mareike Schulze ◽  
Claudia Böhm ◽  
Olaf Gefeller ◽  
Jan Haaf ◽  
...  
Keyword(s):  
Open Access ◽  
Information And Communication Technologies ◽  
Communication Technologies ◽  
Open Access Publishing ◽  
Scientific Publications ◽  
Open Access Journals ◽  
Important Approach ◽  
Information And Communication ◽  
International Research Project

SummaryBackground: Based on today‘s information and communication technologies the open access paradigm has become an important approach for adequately communicating new scientific knowledge.Objectives: Summarizing the present situa -tion for journal transformation. Presenting criteria for adequate transformation as well as a specific approach for it. Describing our exemplary implementation of such a journal transformation.Methods: Studying the respective literature as well as discussing this topic in various discussion groups and meetings (primarily of editors and publishers, but also of authors and readers), with long term experience as editors and /or publishers of scientific publications as prerequisite.Results: There is a clear will, particularly of political and funding organizations, towards open access publishing. In spite of this, there is still a large amount of scientific knowl edge, being communicated through subscription-based journals. For successfully transforming such journals into open access, sixteen criteria for a goal-oriented, stepwise, sustainable, and fair transformation are suggested. The Tandem Model as transformation approach is introduced. Our exemplary implementation is done in the Trans-O-MIM project. It is exploring strategies, models and evaluation metrics for journal transforma tion. As instance the journal Methods of Information in Medicine will apply the Tandem Model from 2017 onwards.Conclusions: Within Trans-O-MIM we will reach at least nine of the sixteen criteria for adequate transformation. It was positive to implement Trans-O-MIM as international research project. After first steps for transforming Methods have successfully been made, challenges will remain, among others, in identifying appropriate incentives for open access publishing in order to support its transformation.

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