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PubChem 2019 update: improved access to chemical data
<span title="2018-10-29">2018</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
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PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem. ...
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. ...
ACKNOWLEDGEMENTS We appreciate the hundreds of data contributors for making their data openly accessible within PubChem. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1033">doi:10.1093/nar/gky1033</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30371825">pmid:30371825</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6324075/">pmcid:PMC6324075</a>
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Automated evaluation of consistency within the PubChem Compound database
<span title="2019-02-19">2019</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a>
</i>
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We have applied the ALATIS approach, which is based on the international chemical shift identifier (InChI) model, to the full PubChem Compound database to generate unique and reproducible compound and ...
This exercise also served to identify entries with discrepancies between structures and chemical formulas or InChI strings. ...
Acknowledgements We thank the PubChem support team for answering our inquiries and facilitating easy download of the data entries. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sdata.2019.23">doi:10.1038/sdata.2019.23</a>
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<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6380220/">pmcid:PMC6380220</a>
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Norine: update of the nonribosomal peptide resource
<span title="2020-01-08">2019</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
</i>
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To maintain a high data quality, successive filters are applied to automatically validate the NRP annotations and only validated data is inserted in the database. ...
Norine, the unique resource dedicated to nonribosomal peptides (NRPs), is now updated with a new pipeline to automate massive sourcing and enhance annotation. ...
E.R. has developed rBAN, the Kendrick Formula Predictor, and parts of the pipeline in relation to peptide structures and also participates in data correction. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1000">doi:10.1093/nar/gkz1000</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31691799">pmid:31691799</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145658/">pmcid:PMC7145658</a>
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SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update
<span title="2020-01-08">2019</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
</i>
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We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant ...
The data are freely accessible and downloadable at https://signor.uniroma2.it/. ...
Following the MI2CAST recommendations, chemicals and small ligands are now linked to the ChEBI database (14) and, whenever the chemical is not annotated in this database, the reference database is PUBCHEM ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz949">doi:10.1093/nar/gkz949</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31665520">pmid:31665520</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145695/">pmcid:PMC7145695</a>
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The human DEPhOsphorylation Database DEPOD: 2019 update
<span title="2019-01-01">2019</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a>
</i>
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In addition, we have improved the data access as all the data in DEPOD can now be easily downloaded in a user-friendly format. ...
We report here an update to DEPOD by integrating and/or linking to annotations from 69 other open access databases including disease associations, phosphorylating kinases, protein interactions, and also ...
The authors would like to thank the users of DEPOD and colleagues for their feedback (see also the acknowledgments section online). ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baz133">doi:10.1093/database/baz133</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31836896">pmid:31836896</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6911163/">pmcid:PMC6911163</a>
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502102034/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6911163&blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext">
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The Immune Epitope Database (IEDB): 2018 update
<span title="2018-10-24">2018</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
</i>
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Having been publicly accessible for >10 years, the recent focus of the IEDB has been improved query and reporting functionality to meet the needs of our users to access and summarize data that continues ...
Here we present an update on our current efforts and future goals. ...
ACKNOWLEDGEMENTS We wish to acknowledge the work of the entire IEDB curation and development teams. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1006">doi:10.1093/nar/gky1006</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30357391">pmid:30357391</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6324067/">pmcid:PMC6324067</a>
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SANCDB: an update on South African natural compounds and their readily available analogs
<span title="2021-05-05">2021</span>
<i title="Springer (Biomed Central Ltd.)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a>
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With the emergence of newer chemoinformatic technologies, existing chemical databases require constant updates to facilitate information accessibility and integration by users. ...
To our knowledge, this feature is not available in other NP databases. Additionally, for easier access to information by users, the database and website interface were updated. ...
These steps have been incorporated into an automated update pipeline in the backend which fetches updated analog data from the respective Mcule and MolPort database APIs monthly. ...
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-021-00514-2">doi:10.1186/s13321-021-00514-2</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33952332">pmid:33952332</a>
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PubChem in 2021: new data content and improved web interfaces
<span title="2020-11-05">2020</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
</i>
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Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory ...
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. ...
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa971">doi:10.1093/nar/gkaa971</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33151290">pmid:33151290</a>
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The Role of Vitamins in Neurodegenerative Disease: An Update
<span title="2021-09-22">2021</span>
<i title="MDPI AG">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jgmgd4z6dzhzziggcczoforhve" style="color: black;">Biomedicines</a>
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Hormesis is also an essential factor that is very helpful to determine the effective dose of vitamins. ...
A deficiency in or dysregulation of vitamins adversely affects the neuronal metabolism, which may lead to neurodegenerative diseases. ...
The authors also would like to acknowledge Biorender (https://app.biorender.com/biorender-templates (accessed on 20 April 2020)) for providing an efficient platform to create all the figures. ...
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PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources
<span title="2020-07-13">2020</span>
<i title="Walter de Gruyter GmbH">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/e3tvwb7firdzllv7m6od4chvoi" style="color: black;">Chemistry Teacher International</a>
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Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources. ...
These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities ...
Acknowledgments: We are grateful to Dr. Jason Telford, who organized Spring 2019 ConfChem Newsletter. ...
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Maintenance, update and further development of EFSA's Chemical Hazards: OpenFoodTox 2.0
<span title="">2021</span>
<i title="Wiley">
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The data collection for new data types has been continued with further expansion of the data model to incorporate new data types including physicochemical properties (OHT 1 to 23-5), degradation and bioaccumulation ...
Case studies on OHT 201 to report mechanistic data are illustrated. ...
The authors are grateful to JRC colleagues (Clemens Wittwehr and Alicia Paini) for the valuable discussions on OECD Harmonised Templates (OHTs). ...
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Database resources of the National Center for Biotechnology Information
<span title="2020-10-23">2020</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
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Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. ...
All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov. ...
ACKNOWLEDGEMENTS The authors would like to thank all of the NCBI staff who through their dedicated efforts continue to allow NCBI to provide our full collection of services to the community.
FUNDING ...
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Application of Permeation Enhancers in Oral Delivery of Macromolecules: An Update
<span title="2019-01-19">2019</span>
<i title="MDPI AG">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyicatbz75hkld675oqybzylzu" style="color: black;">Pharmaceutics</a>
</i>
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The application of permeation enhancers (PEs) to improve transport of poorly absorbed active pharmaceutical ingredients across the intestinal epithelium is a widely tested approach. ...
of conventional oral formulations that have progressed to clinical testing. ...
© 2019 by the authors. ...
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pharmaceutics11010041">doi:10.3390/pharmaceutics11010041</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30669434">pmid:30669434</a>
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Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag
<span title="2021-03-08">2021</span>
<i title="Springer Science and Business Media LLC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a>
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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. ...
Benchmarking datasets from earlier publications are used to show how experimental knowledge and existing datasets can be used to detect and fill gaps in compound databases to progressively improve large ...
Regular updates/deposition of relevant third-party data resources in PubChem such as HMDB, CompTox and the Blood Exposome database will help ensure that this content can be included and updated in PubChemLite ...
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Enhancing the Discovery of Chemistry Theses by Registering Substances and Depositing in PubChem
<span title="2021-05-07">2021</span>
<i title="University of Alberta Libraries">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zb2ivzoufjgurks4atgdfnzfh4" style="color: black;">Issues in Science and Technology Librarianship</a>
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Chemical substances from theses are not widely accessible as searchable machine-readable formats. ...
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 ...
Finally, we thank NIH/NLM/NCBI PubChem staff for their helpful responses related to chemical file formats and data submission questions. ...
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