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      The Immune Epitope Database (IEDB): 2018 update

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          Abstract

          The Immune Epitope Database (IEDB, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available and easily searchable to the public. The scope of the IEDB extends across immune epitope data related to all species studied and includes antibody, T cell, and MHC binding contexts associated with infectious, allergic, autoimmune, and transplant related diseases. 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 to grow in quantity and complexity. Here we present an update on our current efforts and future goals.

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          The FAIR Guiding Principles for scientific data management and stewardship

          Mark D Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg … (2016)
          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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            PubChem Substance and Compound databases

            Sunghwan Kim, Paul Thiessen, Evan Bolton … (2015)
            PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.
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              Database resources of the National Center for Biotechnology Information

              Richa Agarwala, Tanya Barrett, Jeff Beck … (2017)
              Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
              Article 0 comments Cited 635 times – based on 0 reviews     Review now
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                Author and article information

                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 (Print): 08 January 2019
                Publication date (Electronic): 24 October 2018
                Publication date PMC-release: 24 October 2018
                Volume: 47
                Issue: Database issue , Database issue
                Pages: D339-D343
                Affiliations
                [1 ]La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA
                [2 ]Knocean Inc., Toronto, Ontario M2P 2T3, Canada
                [3 ]Leidos Health, LLC, San Diego, CA 92121, USA
                [4 ]University of California San Diego, Department of Medicine, La Jolla, CA 92093, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 858 752 6914; Fax: +1 858 752 6987; Email: bpeters@ 123456liai.org

                Present address: Bjoern Peters, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

                Author information
                http://orcid.org/0000-0003-2136-1801
                http://orcid.org/0000-0003-1381-7434
                Article
                Publisher ID: gky1006
                DOI: 10.1093/nar/gky1006
                PMC ID: 6324067
                PubMed ID: 30357391
                SO-VID: 0e36bd6a-6437-49b7-929c-47015c605729
                Copyright © © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 11 October 2018
                Date revision received : 09 October 2018
                Date received : 14 September 2018
                Page count
                Pages: 5
                Funding
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: HHSN272201200010C
                Categories
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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