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PubChem in 2021: new data content and improved web interfaces

Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang (+1 others)
2020 Nucleic Acids Research  
In the past two years, PubChem made substantial improvements.  ...  Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links  ...  ACKNOWLEDGEMENTS We appreciate the hundreds of data contributors for making their data openly accessible within PubChem.  ... 
doi:10.1093/nar/gkaa971 pmid:33151290 fatcat:ntmtvuyyabhvlmpostjrq32tq4

Enhancing the Discovery of Chemistry Theses by Registering Substances and Depositing in PubChem

Vincent F. Scalfani, Barbara J. Dahlbach, Jacob Robertson
2021 Issues in Science and Technology Librarianship  
In total, 73 theses were selected for the project, resulting in about 3,000 substances registered using the IUPAC International Chemical Identifier and deposited in PubChem as either structure-data files  ...  Excluding mixtures, we found that 40% of the shared substances were new to PubChem at the time of deposition.  ...  Finally, we thank NIH/NLM/NCBI PubChem staff for their helpful responses related to chemical file formats and data submission questions.  ... 
doi:10.29173/istl2566 fatcat:ful3zqyrmbfidhm5ywjzzad3mu

TCRD and Pharos 2021: mining the human proteome for disease biology

Timothy K Sheils, Stephen L Mathias, Keith J Kelleher, Vishal B Siramshetty, Dac-Trung Nguyen, Cristian G Bologa, Lars Juhl Jensen, Dušica Vidović, Amar Koleti, Stephan C Schürer, Anna Waller, Jeremy J Yang (+7 others)
2020 Nucleic Acids Research  
These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.  ...  data available, and presenting data in machine learning ready format.  ...  In the current paper, we describe changes implemented for the 2021 version, such as new data sources and how data from these sources have been integrated into TCRD and presented in Pharos.  ... 
doi:10.1093/nar/gkaa993 pmid:33156327 pmcid:PMC7778974 fatcat:te64g6sycnfatfntehswdxk6me

The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators

Rachel Torchet, Karen Druart, Luis Checa Ruano, Alexandra Moine-Franel, Hélène Borges, Olivia Doppelt-Azeroual, Bryan Brancotte, Fabien Mareuil, Michael Nilges, Hervé Ménager, Olivier Sperandio
2021 Bioinformatics  
Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved.  ...  In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database.  ...  Marvin JS (20.5.0, 2020, http://www.chemaxon.com) is used for drawing and displaying chemical structures in both Query mode and Contribution mode of iPPI-DB.  ... 
doi:10.1093/bioinformatics/btaa1091 pmid:33416858 pmcid:PMC8034526 fatcat:sd4mjmrgf5bnbgbgj6nq7rmtue

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
The resource is committed to open access and reproducible science based on the FAIR data principles.  ...  We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome  ...  The funders had no role in study design, data analysis or preparation of this manuscript.  ... 
doi:10.1093/nar/gkaa979 pmid:33170273 fatcat:atundz637bfalivwtye3vb3twe

IDSM ChemWebRDF: SPARQLing small-molecule datasets

Jakub Galgonek, Jiří Vondrášek
2021 Journal of Cheminformatics  
In our project, we primary focused on PubChem, ChEMBL and ChEBI small-molecule datasets. These datasets are already being exported to RDF by their creators.  ...  Owing to all of these useful features, many biological and chemical databases present their data in RDF, and support SPARQL querying.  ...  Acknowledgements This work was supported by the ELIXIR CZ research infrastructure project (MEYS Grant No: LM2018131), including access to computing and storage facilities.  ... 
doi:10.1186/s13321-021-00515-1 pmid:33980298 fatcat:zwzq7jfij5aetf4yx44ovpmeym

Comprehensive Analysis of Chemical Structures That Have Been Tested as CFTR Activating Substances in a Publicly Available Database CandActCFTR

Manuel Manfred Nietert, Liza Vinhoven, Florian Auer, Sylvia Hafkemeyer, Frauke Stanke
2021 Frontiers in Pharmacology  
The integration of the KNIME software environment in the back-end facilitates a fast and user-friendly maintenance of the provided data sets and a quick extension with new functionalities, e.g., new analysis  ...  One hundred and forty-five molecules do not have a corresponding entry in PubChem or ChemSpider, which indicates that there currently is no single comprehensive database on chemical substances in the public  ...  Acquisition, analysis, and interpretation of data: MN, LV, SH, and FS. Drafting the article or revising it critically for important intellectual content: MN, SH, and FS.  ... 
doi:10.3389/fphar.2021.689205 pmid:34955819 pmcid:PMC8692862 fatcat:vxkf4n3u2rf35i5ikv72jpywzi

COCONUT online: Collection of Open Natural Products database

Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik, Christoph Steinbeck
2021 Journal of Cheminformatics  
In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface  ...  COCONUT web is freely available at https://coconut.naturalproducts.net.  ...  The web interface allows querying and parsing the data collection in various, chemically relevant ways with adequate performance.  ... 
doi:10.1186/s13321-020-00478-9 pmid:33423696 fatcat:puh3yg3ljvhf5h65saeede72wi

Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag

Emma L. Schymanski, Todor Kondić, Steffen Neumann, Paul A. Thiessen, Jian Zhang, Evan E. Bolton
2021 Journal of Cheminformatics  
Furthermore, the improvements in analytical technologies and computational mass spectrometry workflows coupled with the rapid growth in databases and increasing demand for high throughput "big data" services  ...  PubChemLite is a living collection, updating as annotation content in PubChem is updated, and exported to allow direct integration into existing workflows such as MetFrag.  ...  For instance, querying HMDB, CompTox and PubChem with the formula C 10 H 14 N 2 via the Met-Frag [26, 27] web interface (12 August 2020) returns 4, 225 and 3704 candidates, respectively.  ... 
doi:10.1186/s13321-021-00489-0 pmid:33685519 fatcat:tdogsqldbngxtdcmovrrct4hxm

CFM: a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation

Alexey Sizykh, Khalimat Murtazalieva, Yulia Vyshkvorkina, Alexey Stupnikov, Yulia A. Medvedeva
2021 F1000Research  
There is an increasing need for a data aggregator containing a structured collection of protocols - preprocessed, verified, and represented in a standardized manner to facilitate their comparison, and  ...  providing a platform for the researchers to evaluate and improve the protocols.  ...  We are also grateful to the creators and maintainers of https://pubchem.ncbi.nlm.nih.gov. References  ... 
doi:10.12688/f1000research.28439.1 fatcat:uoh4562qpvb6nebrf6cq4tdwiy

G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands

Yu-Huan Wang, Qian-Fan Yang, Xiao Lin, Die Chen, Zhi-Yin Wang, Bin Chen, Hua-Yi Han, Hao-Di Chen, Kai-Cong Cai, Qian Li, Shu Yang, Ya-Lin Tang (+1 others)
2021 Nucleic Acids Research  
Here, we report a new version, termed G4LDB 2.2 (http://www.g4ldb.com), with upgrades in both content and function.  ...  To further enhance user experience, we have also redesigned the user interface and optimized the database structure and retrieval mechanism.  ...  Updated database content Data in G4LDB 2.2 are continuously updated. The updated information includes new ligands/complexes, actives and docking models.  ... 
doi:10.1093/nar/gkab952 pmid:34718746 pmcid:PMC8728129 fatcat:bx4eycw6szbfnhm2gfmbhzqlj4

Brief about Basic Medical Sciences e-Conference 2021 ( BMS e-CON-2021)

Praveen Kumar R
2022 Journal of Clinical and Diagnostic Research  
Basic research in molecular biology, immunology and cell biology provides an infinite amount of data and knowledge.  ...  Laboratory Medicine in MBBS curriculum Brief about Basic Medical Sciences e-Conference 2021 (BMS e-CON-2021) Introduction: Islet of Langerhans, the endocrine pancreas plays a significant role in glucose  ...  and motivate them to quit smoking.  ... 
doi:10.7860/jcdr/2022/43626.16017 fatcat:mdvrqc3obze3phjpmix5obqp7q

OlfactionBase: a repository to explore odors, odorants, olfactory receptors and odorant–receptor interactions

Anju Sharma, Bishal Kumar Saha, Rajnish Kumar, Pritish Kumar Varadwaj
2021 Nucleic Acids Research  
Finally, the data in OlfactionBase on odors, odorants, olfactory receptors, human and mouse OR-odorant pairs, and other associated proteins could aid in the inference and improved understanding of odor  ...  OlfactionBase is a free, open-access web server that aims to bring together knowledge about many aspects of the olfaction mechanism in one place.  ...  Figure 4 . 4 Overview of the OlfactionBase web interface.  ... 
doi:10.1093/nar/gkab763 pmid:34469532 pmcid:PMC8728123 fatcat:fyfbsfsyabganprmlyz74wbljm

The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials

Simon D Harding, Jane F Armstrong, Elena Faccenda, Christopher Southan, Stephen P H Alexander, Anthony P Davenport, Adam J Pawson, Michael Spedding, Jamie A Davies, NC-IUPHAR
2021 Nucleic Acids Research  
We describe expansion in content over nine database releases made during the last two years, which has focussed on three main areas of infection.  ...  GtoPdb has sought to support the wider research community to understand the pharmacology of emerging drug targets for SARS-CoV-2 as well as potential targets in the host to block viral entry and reduce  ...  Buneman for technical advice and help in producing the CGTP; Dr Alasdair Gray for his advice and guidance in incorporating BioSchemas into GtoPdb; and Prof.  ... 
doi:10.1093/nar/gkab1010 pmid:34718737 pmcid:PMC8689838 fatcat:aec6cjtsxjda3dkwnjettsva4a

FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

M Delmas, O Filangi, N Paulhe, F Vinson, C Duperier, W Garrier, P -E Saunier, Y Pitarch, F Jourdan, F Giacomoni, C Frainay, Jonathan Wren
2021 Bioinformatics  
Results The use of a Semantic Web framework on biological data allows us to apply ontological based reasoning to infer new relations between entities.  ...  Availability A web interface to browse and download the extracted relations, as well as a SPARQL endpoint to directly probe the whole FORUM knowledge graph, are available at https://forum-webapp.semantic-metabolomics.fr  ...  Acknowledgements The authors express their gratitude to the PubChem, NCBI Eutils and MetaNetX support teams for helping us in the exploitation of their datasets.  ... 
doi:10.1093/bioinformatics/btab627 pmid:34478489 pmcid:PMC8570811 fatcat:v3lnv6z4ijhnlgj46dig5upwxq
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