Tag: PubChem

Biosystems retiring March 2022 — use PubChem Pathways

The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content.

NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the PubChem blog for more details on PubChem Pathways.

Table 1 presents a snapshot of the richer and more extensive data coverage in PubChem Pathways.

Source database BioSystems PubChem Pathways
(as of 8/10/21)
BioCyc 15,259 records 15,037 records
PlantCyc 64,851 records
Reactome 20,478 records 26,407 records
Plant Reactome 18,910 records
NCI Pathway Interaction DB 188 records 745 records
Wiki Pathways 1,478 records 1,823 records
Lipid Maps 14 records 15 records
PharmGKB 147 records
PathBank 110,315 records
COVID-19 Disease Map 20 records
INOH 511 records
GO 44,525 records
KEGG 902,026 records

Table 1: Coverage for BioSystems records in PubChem Pathways. In anticipation of retiring BioSystems, we will begin directing relevant queries to PubChem Pathways to provide users with a richer dataset and enhanced user experience.

Continue reading “Biosystems retiring March 2022 — use PubChem Pathways”

Webinar on current access to TOXNET resources

NLM staff will participate in the next American Chemical Society webinar for the chemical information and cheminformatics community: An Overview of NLM’s Post-TOXNET Resources. TOXNET (the TOXicology Data NETwork) was retired in December 2019 as part of the reorganization associated with the NLM Strategic Plan. Most of TOXNET’s databases have been incorporated into other NLM resources such as PubChem and Bookshelf, or continue to be available elsewhere. This webinar will show you where to go now for TOXNET information.

  • Date and Time: Tuesday, March 17 at 1:00pm EDT.
  • Register 

A live Q&A session will follow the webinar.

The periodic table turns 150!

The periodic table turns 150!

NCBI and PubChem are celebrating the 150th anniversary of the periodic table of chemical elements, one of the most recognized tools in science. The scientific community has declared 2019 to be “The International Year of the Periodic Table”. We’re celebrating by launching the PubChem Periodic Table and Element pages, where you can find chemical element data and data sources. There’s always more to learn, so check out the PubChem blog for more about this incredible old resource.

5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more

Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

NCBI Minute: Getting the Most out of Web BLAST Tabular Format

The NCBI web BLAST service has several useful download formats, including tabular formats. All formats allow you to easily save your BLAST results for processing, editing, and annotating.

This video will show you how to use basic Unix tools and EDirect to expand and enhance your tabular saved BLAST results. You will also see learn how to add useful information like taxonomy and sequence titles.

Continue reading “5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more”

May 9 NCBI Minute: Integrating PubChem into Your Chemistry Teaching

May 9 NCBI Minute: Integrating PubChem into Your Chemistry Teaching

Next Wednesday, May 9, 2018, NCBI staff will show you how to use PubChem as a cheminformatics education resource. In addition to learning about tools and services for chemical information search, analysis, and download, you will also see examples of how instructors incorporate PubChem in Cheminformatics OLCC (On-Line Chemistry Courses), an intercollegiate hybrid course.

Date and time: Wednesday, May 9, 2018 12:00 – 12:30 PM EDT

Register here: https://bit.ly/2q5wtsF

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

5 NCBI articles in 2018 Nucleic Acids Research database issue

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

Continue reading “5 NCBI articles in 2018 Nucleic Acids Research database issue”

Essentials of Glycobiology, Third Edition & New Glycan Website Now Available at NCBI

Essentials of Glycobiology, Third Edition & New Glycan Website Now Available at NCBI

Glycobiology—the study of the structure, biosynthesis, biology, and evolution of glycans (the sugar chains synthesized by all living cells)—is a rapidly growing field in the natural sciences, with broad relevance to many areas of basic research, biomedicine, and biotechnology.

NCBI has two new glycobiology resources: the third edition of a definitive work in the field, Essentials of Glycobiology, and a new NCBI Glycans website that includes links to some useful external resources as well as the Symbol Nomenclature for Glycans (SNFG).

essentials of glycobiology

Continue reading “Essentials of Glycobiology, Third Edition & New Glycan Website Now Available at NCBI”

June 7th NCBI Minute: PubChem: A source of laboratory chemical safety information

June 7th NCBI Minute: PubChem: A source of laboratory chemical safety information

On June 7, 2017, NCBI staff will show you how to use PubChem’s Laboratory Chemical Safety Summary (LCSS) to find the most relevant chemical safety information including flammability, toxicity, exposure limits and symptoms, first aid, handling and clean up.

Date and time: Wednesday, June 7, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; you can also learn about future webinars on this page.

Identifying and Correlating Chemical Names & Synonyms

This blog post is intended for people who refer to chemical names/symbols and synonyms in databases like PubMed and PubChem, or in their own scientific papers. There is a similar post for gene symbols and names.

During the research and publishing process, scientists need to refer to their chemicals-of-interest. While there are standardized nomenclatures (IUPAC, SMILESInChITM, etc.), different labs sometimes use different names for the same chemical.

The NCBI PubChem project has set up a system to identify and correlate these various names as well as ‘alias’, ‘synonym’, or ‘also known as’ terms that have been used in the literature.

Continue reading “Identifying and Correlating Chemical Names & Synonyms”

NCBI’s Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database

On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information’s PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting & Exposition in Philadelphia.

Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.
Figure 1. Drs. Bryant and Bolton receive the American Chemical Society 2016 Herman Skolnik Award.

Continue reading “NCBI’s Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database”