Blog
About

  • Record: found
  • Abstract: found
  • Article: not found

PubChem 2019 update: improved access to chemical data

Read this article at

ScienceOpenPublisherPMC
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      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. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. 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.

      Related collections

      Most cited references 28

      • Record: found
      • Abstract: not found
      • Article: not found

      Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

        Bookmark
        • Record: found
        • Abstract: found
        • Article: found
        Is Open Access

        The Pfam protein families database: towards a more sustainable future

        In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          KEGG: new perspectives on genomes, pathways, diseases and drugs

          KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was developed for the purpose of defining nodes of molecular networks, but now the content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases. The newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined. Furthermore, the DISEASE and DRUG databases have been improved by systematic analysis of drug labels for better integration of diseases and drugs with the KEGG molecular networks. KEGG is moving towards becoming a comprehensive knowledge base for both functional interpretation and practical application of genomic information.
            Bookmark

            Author and article information

            Affiliations
            National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
            Author notes
            To whom correspondence should be addressed. Tel: +1 301 451 1811; Fax: +1 301 480 4559; Email: bolton@ 123456ncbi.nlm.nih.gov
            Journal
            Nucleic Acids Res
            Nucleic Acids Res
            nar
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            08 January 2019
            29 October 2018
            29 October 2018
            : 47
            : Database issue , Database issue
            : D1102-D1109
            30371825 6324075 10.1093/nar/gky1033 gky1033
            Published by Oxford University Press on behalf of Nucleic Acids Research 2018.

            This work is written by (a) US Government employee(s) and is in the public domain in the US.

            Counts
            Pages: 8
            Product
            Funding
            Funded by: National Institutes of Health 10.13039/100000002
            Categories
            Database Issue

            Genetics

            Comments

            Comment on this article