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PubChem in 2021: new data content and improved web interfaces
2020
Nucleic Acids Research
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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
2021
Issues in Science and Technology Librarianship
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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
2020
Nucleic Acids Research
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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
2021
Bioinformatics
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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
2020
Nucleic Acids Research
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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
2021
Journal of Cheminformatics
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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
2021
Frontiers in Pharmacology
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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
2021
Journal of Cheminformatics
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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
2021
Journal of Cheminformatics
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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
2021
F1000Research
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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
2021
Nucleic Acids Research
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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)
2022
Journal of Clinical and Diagnostic Research
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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
2021
Nucleic Acids Research
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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
2021
Nucleic Acids Research
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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
2021
Bioinformatics
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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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