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Bioinformatics Workshop: Information Integration
 

Literature and Data

Libraries
Bibliographic Software
 
 
 
Indexing Literature

Keeping Order for the Literature

Think about catalog systems in traditional libraries and bookstores

Libraries and bookstores have historically relied on an "inventory" system to locate and retrieve books. They can be searched by author, title, subect, ISBN, or other selected indexing terms and retrieved by whichever index is used to put them on the shelf. In the case of libraries, this has been the "call number" assigned to each book.

Articles are indexed similarly, by author, title, subject, and additional fields, including the journal citation (volume, issue, date, pages). Once the citation is located in an index, the article can be found on a library shelf in the appropriate journal volume.

The challange for electronic resources

As more and more journal articles become available electronically, each one must have a unique URL. Since the journal is no longer on the shelf, the URL becomes the article's "call number" or virtual shelf location. Keeping track of the URL can be a challenge.

  • It may change if a different publisher takes over the journal.
  • It can be in several formats if the article is available from more than one source.
  • It change if the publisher redesigns the web site.

Libraries and publishers are trying to ease the problem by providing persistent links or static URLs, but the system is by no means standardized yet.

The UMDNJ Libraries have been using a cgi program to translate the URLs you used to see on our alphabetic journal lists to the the journal's URL at the publisher's or vendor's web site. Because the library maintains a master table of cgi numbers with matching journal URLs, the link on the journal list remained static, even if the destination URL changed.

Another solution is the OpenURL standard. Journal publishers and database vendors have been cooperating with the National Information Standards Organization (NISO) to develop a syntax for the transmission of metatata that describes the article in a standard format and allows retrieval of the full text through an enabled database.

A link resolver, such as Serials Solutions (Serials Solutions) or Findit @ UMDNJ (Ex Libris), uses the OpenURL standard. The libraries maintain a knowledge base of the libraries' subscriptions, as well as additional free journal sources. When you search in a database (source), such as Ovid Medline or PubMed, references are checked against the knowledge base. If the system finds that the journal issue is available, an OpenURL is built and sent to the target (publisher or aggregator) and the article is retrieved on your desktop.

A sample OpenURL would look something like:

http://ssfaaa.edu/sfxlcl?rft.genre=article@rft.issn=000=0012&ref.volume=12&rft.issue=3
&rft.spage=1&rft.epage=8rft.date=2004&rft.aulast=Smith&rft.aufirst=Paul

Notice that this OpenURL uses:

  • the journal's issn number, volume, issue, and date
  • the article's start and end page
  • the author's last and first name

Another development is the use of the Digital Object Identifier (DOI). This unique number is assigned to an article and is supposed to travel with it no matter where it is located. CrossRef.org maintains a database of DOIs that member libraries can access and use with an OpenURL link resolver such as Serials Solutions or Findit @ UMDNJ. The simplified URL might look something like

http://server.univ.edu/id=doi:123/4567

For more information about Findit @ UMDNJ see:

For more information on the OpenURL standard, see The OpenURL Framework for Context-Sensitive Services on the NISO web site.

For more information about the DOI and OpenURL, see

 

Page last updated October 8, 2007

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