The LOTUS initiative for open knowledge management in natural products research (Q112143478)

3.9.7

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R

4.1.2

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Wikidata

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Java

17

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Kotlin

1.6.0

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OPSIN

2.6.0

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Molconvert

20.19

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Manubot

0.5.3

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Chemistry Development Kit

2021.09.2

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Global Names Architecture

2.5

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Tidyverse

1.3.1

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Matplotlib

3.5.0

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pandas

1.3.4

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SciPy

1.7.3

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OpenJDK

15

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Log4j

2.14.1

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RDF4J

3.7.4

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JUnit

5.8.1

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rotl

3.0.11

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ChemmineR

3.42.1

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ggalluvial

0.12.3

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ggtree

3.2.0

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ggtreeExtra

1.4.0

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Plotly

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rentrez

1.2.3

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treeio

1.18.0

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UpSetR

1.4.0

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webchem

1.1.1

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faerun

on focus list of Wikimedia project

0.3.20

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GitHub

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Zenodo

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WikiProject Chemistry/Natural products

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1 reference

19 March 2024

https://api.unpaywall.org/v2/10.7554/elife.70780?email=unpaywall_01@example.com

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access restriction status

open access

1 reference

based on heuristic

inferred from online access status

cites work

KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research

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Taxonomists need better access to published data

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All natural

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Pharmacognosy in the digital era: shifting to contextualized metabolomics.

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On disciplinary fragmentation and scientific progress

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Dissemination of original NMR data enhances reproducibility and integrity in chemical research

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Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery?

0 references

The Semantic Web: ESWC 2017 Satellite Events

0 references

Alkamid database: Chemistry, occurrence and functionality of plant N-alkylamides.

0 references

ggalluvial: Layered Grammar for Alluvial Plots

0 references

Save those molecules! Molecular biodiversity and life*

0 references

ChemmineR: a compound mining framework for R.

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One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome

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NPCARE: database of natural products and fractional extracts for cancer regulation

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Cognate and cognitive ecopharmacognosy — in an anthropogenic era

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Sixty Challenges – A 2030 Perspective on Natural Products and Medicines Security

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A data citation roadmap for scientific publishers

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Bringing Citations and Usage Metrics Together to Make Data Count

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The misuse of colour in science communication

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Seaweed metabolite database (SWMD): A database of natural compounds from marine algae

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Spatial and evolutionary predictability of phytochemical diversity

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ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

0 references

What does ‘nature’ mean?

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Making your database available through Wikipedia: the pros and cons

0 references

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

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Use of natural products as chemical library for drug discovery and network pharmacology

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Comprehensive Toxic Plants-Phytotoxins Database and Its Application in Assessing Aquatic Micropollution Potential

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SANCDB: a South African natural compound database

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MetaboLights: a resource evolving in response to the needs of its scientific community

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InChI - the worldwide chemical structure identifier standard

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Ten Simple Rules for Developing Public Biological Databases

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Open collaborative writing with Manubot

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MassBank: a public repository for sharing mass spectral data for life sciences

0 references

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

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Matplotlib: A 2D Graphics Environment

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Binding of anti-Trypanosoma natural products from African flora against selected drug targets: a docking study

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ReDU: a framework to find and reanalyze public mass spectrometry data

0 references

CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria

0 references

Actinobacteria in natural products research: Progress and prospects

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MIBiG 2.0: a repository for biosynthetic gene clusters of known function

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Plant Secondary Metabolite Diversity and Species Interactions

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TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine

0 references

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

0 references

An update on PUG-REST: RESTful interface for programmatic access to PubChem.

0 references

PubChem 2019 update: improved access to chemical data

0 references

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

0 references

StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes

0 references

Sachem: a chemical cartridge for high-performance substructure search.

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Interoperable chemical structure search service

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Bias in peer review

0 references

The TRUST Principles for digital repositories

0 references

The stringdist Package for Approximate String Matching

0 references

Chemical Name to Structure: OPSIN, an Open Source Solution

0 references

DiaNat-DB: a molecular database of antidiabetic compounds from medicinal plants

0 references

WikiPathways: connecting communities

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The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

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Repository scale classification and decomposition of tandem mass spectral data

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Open Data in Science

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Chemical fingerprinting for the evaluation of unintended secondary metabolic changes in transgenic food crops

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NANPDB: A Resource for Natural Products from Northern African Sources

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ProCarDB: a database of bacterial carotenoids

0 references

Credit data generators for data reuse

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NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity

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BIOFACQUIM: A Mexican Compound Database of Natural Products

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FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web.

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SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript

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Visualization of very large high-dimensional data sets as minimum spanning trees

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Robustifying Scholia: paving the way for knowledge discovery and research assessment through Wikidata

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Automated assembly of a reference taxonomy for phylogenetic data synthesis

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Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

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Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation

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Evolution of endophyte-plant symbioses.

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DataWarrior: an open-source program for chemistry aware data visualization and analysis

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RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

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Recent breakthroughs in metabolomics promise to reveal the cryptic chemical traits that mediate plant community composition, character evolution and lineage diversification.

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BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts

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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

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Review on natural products databases: where to find data in 2020

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COCONUT online: Collection of Open Natural Products database

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webchem: An R Package to Retrieve Chemical Information from the Web

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Predatory impacts of alien decapod Crustacea are predicted by functional responses and explained by differences in metabolic rate

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Advances in computational metabolomics and databases deepen the understanding of metabolisms

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The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

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The Natural Products Atlas 2.0: a database of microbially-derived natural products

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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Wikidata as a knowledge graph for the life sciences

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Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

0 references

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

0 references

Welcome to the Tidyverse

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The FAIR Guiding Principles for scientific data management and stewardship

0 references

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

0 references

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

0 references

ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data

0 references

Carotenoids Database: structures, chemical fingerprints and distribution among organisms

0 references

TMDB: a literature-curated database for small molecular compounds found from tea.

0 references

NPASS: natural product activity and species source database for natural product research, discovery and tool development

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Chemical Space and Biological Target Network of Anti-Inflammatory Natural Products

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Recent studies on terpenoids in Aspergillus fungi: Chemical diversity, biosynthesis, and bioactivity

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ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

The NAPRALERT Database as an Aid for Discovery of Novel Bioactive Compounds

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

Chemotaxonomie der Pflanzen

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

Phytochemistry and plant taxonomy — an essay on the chemotaxonomy of higher plants

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

rentrez: An R package for the NCBI eUtils API

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

Micromolecular Evolution, Systematics and Ecology

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

rotl : an R package to interact with the Open Tree of Life data

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

KNApSAcK: A Comprehensive Species-Metabolite Relationship Database

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

Automated assembly of a reference taxonomy for phylogenetic data synthesis.

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

Interactive Web-Based Data Visualization with R, plotly, and shiny

31 August 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

SciPy 1.0—Fundamental Algorithms for Scientific Computing in Python

23 October 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.70780

High-confidence structural annotation of metabolites absent from spectral libraries

19 November 2023

2 references

https://opencitations.net/index/api/v1/references/10.7554/ELIFE.70780

1 December 2023

https://opencitations.net/index/api/v1/citations/10.1038/S41587-021-01045-9

Essai sur les propriétés médicales des plantes, comparées avec leurs formes extérieures et leur classification naturelle

1 December 2023

1 reference

https://opencitations.net/index/api/v1/references/10.7554/ELIFE.70780