PubChem in 2021: new data content and improved web interfaces

Kim, Sunghwan; Chen, Jie; Cheng, Tiejun; Gindulyte, Asta; He, Jia; He, Siqian; Li, Qingliang; Shoemaker, Benjamin A.; Thiessen, Paul A.; Yu, Bo; Zaslavsky, Leonid; Zhang, Jian Jian; Bolton, Evan E

doi:10.1093/nar/gkaa971

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PubChem in 2021: new data content and improved web interfaces

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Author(s): 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 , Evan E Bolton

Publication date (Electronic): 05 November 2020

Journal: Nucleic Acids Research

Publisher: Oxford University Press

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Abstract

PubChem ( https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. 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 from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. 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 syndrome coronavirus 2 (SARS-CoV-2).

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Clinical Characteristics of Coronavirus Disease 2019 in China

Wei-jie Guan, Zheng-yi Ni, Yu Hu … (2020)

Abstract Background Since December 2019, when coronavirus disease 2019 (Covid-19) emerged in Wuhan city and rapidly spread throughout China, data have been needed on the clinical characteristics of the affected patients. Methods We extracted data regarding 1099 patients with laboratory-confirmed Covid-19 from 552 hospitals in 30 provinces, autonomous regions, and municipalities in mainland China through January 29, 2020. The primary composite end point was admission to an intensive care unit (ICU), the use of mechanical ventilation, or death. Results The median age of the patients was 47 years; 41.9% of the patients were female. The primary composite end point occurred in 67 patients (6.1%), including 5.0% who were admitted to the ICU, 2.3% who underwent invasive mechanical ventilation, and 1.4% who died. Only 1.9% of the patients had a history of direct contact with wildlife. Among nonresidents of Wuhan, 72.3% had contact with residents of Wuhan, including 31.3% who had visited the city. The most common symptoms were fever (43.8% on admission and 88.7% during hospitalization) and cough (67.8%). Diarrhea was uncommon (3.8%). The median incubation period was 4 days (interquartile range, 2 to 7). On admission, ground-glass opacity was the most common radiologic finding on chest computed tomography (CT) (56.4%). No radiographic or CT abnormality was found in 157 of 877 patients (17.9%) with nonsevere disease and in 5 of 173 patients (2.9%) with severe disease. Lymphocytopenia was present in 83.2% of the patients on admission. Conclusions During the first 2 months of the current outbreak, Covid-19 spread rapidly throughout China and caused varying degrees of illness. Patients often presented without fever, and many did not have abnormal radiologic findings. (Funded by the National Health Commission of China and others.)

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Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area

Safiya Richardson, Jamie Hirsch, Mangala Narasimhan … (2020)

There is limited information describing the presenting characteristics and outcomes of US patients requiring hospitalization for coronavirus disease 2019 (COVID-19).

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Is Open Access

UniProt: a worldwide hub of protein knowledge

(2018)

Abstract The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

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Author and article information

Contributors

Sunghwan Kim:

ORCID: http://orcid.org/0000-0001-9828-2074

Jie Chen:

ORCID: http://orcid.org/0000-0001-7680-4978

Tiejun Cheng:

ORCID: http://orcid.org/0000-0002-4486-3356

Asta Gindulyte:

ORCID: http://orcid.org/0000-0001-9600-5305

Jia He:

ORCID: http://orcid.org/0000-0002-6513-8938

Siqian He:

ORCID: http://orcid.org/0000-0002-1707-4167

Qingliang Li:

ORCID: http://orcid.org/0000-0002-6453-236X

Benjamin A Shoemaker:

ORCID: http://orcid.org/0000-0002-1356-285X

Paul A Thiessen:

ORCID: http://orcid.org/0000-0002-1992-2086

Bo Yu:

ORCID: http://orcid.org/0000-0003-3952-8921

Leonid Zaslavsky:

ORCID: http://orcid.org/0000-0001-5873-4873

Jian Zhang:

ORCID: http://orcid.org/0000-0002-6192-4632

Evan E Bolton:

ORCID: http://orcid.org/0000-0002-5959-6190

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 08 January 2021

Publication date (Electronic): 05 November 2020

Publication date PMC-release: 05 November 2020

Volume: 49

Issue: D1

Pages: D1388-D1395

Affiliations

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services , Bethesda, MD, 20894, USA