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Entrez

The Entrez Global Query Cross-Database Search System is a powerful federated search engine that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. NCBI is part of the National Library of Medicine (NLM), itself a department of the National Institutes of Health (NIH) of the United States. Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and protein sequences and chromosome maps.

LinkOut is a service of Entrez that allows you to link directly from PubMed and other Entrez databases to a wide range of information and services beyond the Entrez system. LinkOut aims to facilitate access to relevant online resources in order to extend, clarify, and supplement information found in the Entrez databases. Using LinkOut, the following NCBI databases have been cross-referenced with StrainInfo:

Below we give a description where you can find links to StrainInfo when using the above databases, and how you can activate StrainInfo links if they are not directly available.

GenBank

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2008, 36:D25-30). All bacterial, archaeal and fungal Genbank records that correspond with genetic sequences from micro-organisms that have been deposited in at least one of the biological resource centers associated with the World Federation of Culture Collections (WFCC) are linked with the corresponding strain passport in StrainInfo.

LinkOut links to StrainInfo (and other resources) are found in the right panel of the GenBank sequence records, as illustrated in the picture below.

Genome Project

Genome Project is a searchable database at the NCBI that provides an overview of the status of individual genome sequencing and related projects such as large-scale EST, cDNA,and mapping projects organized by organism that provides links to nucleotide, protein, and mapping data present in other Entrez databases as well as links to external sites. All finished projects that have resulted in the complete genome sequence of an micro-organism that has been deposited in at least one of the biological resource centers associated with the World Federation of Culture Collections (WFCC) are linked with the corresponding strain passport in StrainInfo.

LinkOut links to StrainInfo (and other resources) are found by selecting the “LinkOut” display in the header of the Genome Project records, as illustrated in the picture below.

PubMed

The PubMed database comprises more than 19 million citations for biomedical articles from MEDLINE and life science journals. Citations may include links to full-text articles from PubMed Central or publisher web sites. All publications that have an associated list of micro-organisms that have been deposited in at least one of the biological resource centers associated with the World Federation of Culture Collections (WFCC) are linked with the corresponding publication passport in StrainInfo.

LinkOut links to StrainInfo (and other resources) are found underneath the abstract of the publication, as illustrated in the picture below. However, LinkOut links to external resources are not activated by default when using PubMed. The procedure for activating StrainInfo links in Pubmed is described below.

To activate the StrainInfo icon in PubMed you must select StrainInfo as a filter in My NCBI. The following procedure describes the different steps for setting your LinkOut preferences in My NCBI.

  1. Sign in to My NCBI using the top right panel on PubMed pages (or any other Entrez pages). If you don't have a My NCBI account yet, you should register first.
  2. Click Search Filters on the My NCBI sidebar.
  3. Click PubMed to view your current list of filters.
  4. To activate the StrainInfo LinkOut icon setting click
    • Browse Filters to browse filters and LinkOut providers by category. You can find StrainInfo using one of the following paths:
      • LinkOut > Research Materials > Culture/Stock Collections > StrainInfo
      • LinkOut > Organism-specific Filters > Organism-specific > StrainInfo
    • Search for Filters to search the filter and LinkOut provider names and descriptions. Use “straininfo” as your search criterion.
    • My Filters to see a list of your current filter and LinkOut provider icon settings.
  5. Click the check box next to the StrainInfo filter to add an icon to your PubMed displays.

Taxonomy Browser

The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. All taxa that are shared with StrainInfo are linked with the corresponding taxon passport in StrainInfo.

LinkOut links to StrainInfo (and other resources) are found under the header “External Information Resources (NCBI LinkOut)”, as illustrated in the picture below.

entrez.txt · Last modified: 2014/10/08 16:35 (external edit)