Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 32 (Web Server issue), W16-9

PubCrawler: Keeping Up Comfortably With PubMed and GenBank

Affiliations

PubCrawler: Keeping Up Comfortably With PubMed and GenBank

Karsten Hokamp et al. Nucleic Acids Res.

Abstract

The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. A new output format and more flexibility for the email formatting help PubCrawler cope with increasing challenges arising from browser incompatibilities and mail filters, therefore making it suitable for a wide range of users.

Figures

Figure 1
Figure 1
A sample output from a PubCrawler results page. An index at the top provides a quick overview of how many new results were retrieved for each query. Aliases can be used to provide descriptive handles for them. Numbers are reported for the total amount of hits and for the previously unseen items that are filtered out for presentation. Older hits are accessible through links up to an adjustable age limit. Multiple queries can be combined under the same alias. Hyperlinks help navigating through the page to get easily from one section to the next. For each article or sequence a checkbox is provided. Using these allows narrowing down the list of interesting items, which can then be retrieved with the click of a button in a format of choice from the NCBI site.
Figure 2
Figure 2
Overview of PubCrawler accounts. The graph presents the total number of new registrations (sum of grey and black bars) as well as the total number of active accounts (black bars), which are those with one or more queries configured and a working email address. For each year's end a horizontal line indicates the number of active accounts and the differences per year are expressed in numbers.

Similar articles

  • GenBank
    DA Benson et al. Nucleic Acids Res 34 (Database issue), D16-20. PMID 16381837.
    GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from …
  • [Keeping Up to Date With the Relevant Literature: 'Really Simple syndication'-(RSS)-feeds Within PubMed]
    E Leclercq et al. Ned Tijdschr Geneeskd 152 (4), 221-4. PMID 18320950.
    For clinicians, researchers and policy makers in healthcare, it is important to keep up to date with the newest medical-scientific information. The large amount of new in …
  • GenBank
    DA Benson et al. Nucleic Acids Res 33 (Database issue), D34-8. PMID 15608212.
    GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from indi …
  • Database Resources of the National Center for Biotechnology Information
    DL Wheeler et al. Nucleic Acids Res 34 (Database issue), D173-80. PMID 16381840.
    In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources …
  • FeatureExtract--extraction of Sequence Annotation Made Easy
    R Wernersson. Nucleic Acids Res 33 (Web Server issue), W567-9. PMID 15980537.
    Work on a large number of biological problems benefits tremendously from having an easy way to access the annotation of DNA sequence features, such as intron/exon structu …
See all similar articles

Cited by 13 PubMed Central articles

See all "Cited by" articles
Feedback