October 29, 2004

PubChem Databases searchable through NCBI Entrez

From NCBIannounce (http://www.ncbi.nlm.nih.gov/mailman/listinfo/ncbi-announce):
The PubChem Substance, Compound, and BioAssay databases are now available through the Entrez system. PubChem is a catalog of small organic molecules that contains chemical structures and information on biological activity. PubChem is intended to support the Molecular Libraries and Imaging component of the NIH Roadmap Initiative. PubChem's chemical structure database may be searched on the basis of descriptive terms, chemical properties, and structural similarity. When possible, PubChem's chemical structure records are linked to other NCBI databases, which include PubMed and NCBI's protein 3D structure database, for example. PubChem also contains the results of high-throughput biological screening experiments.

Posted by Kevin Messner at 12:39 PM

October 19, 2004

Health Informatics Seminar on Medical Language Processing Research October 21

On Thursday, October 21, The University Libraries will co-sponsor a presentation in the Health Informatics Seminar Series. Dr. Alexa McCray, Director of the National Center for Biomedical Communication, a division of the National Library of Medicine, will be speaking on "Mapping the Gene Ontology into the Unified Medical Language System." The seminar will be held in room 2-101 Basic Sciences and Biomedical Engineering at 3:15.

Dr. McCray's research interests include medical language interpretation and processing, digital libraries, and consumer health informatics. The Unified Medical Language System is an automated language processing system for health sciences topics. Its applications include forming part of the query processing system for the PubMed bibliographic information search service. The Gene Ontology is another controlled vocabulary system being developed for the biomolecular sciences, an attempt to bring order to wide variations in terminology which may be applied by scientists to very similar genes, gene products, and functions.

Some of Dr. McCray's work on the topic was recently reported in: Lomax, J. and McCray, A. Mapping the Gene Ontology into the Unified Medical Language System. Comparative and Functional Genomics 5(4): 354-361 (2004). Dr. McCray's presentation is a part of the University Libraries' celebration of National Medical Libraries Month.

Posted by Kevin Messner at 12:42 AM

NIH Asserts that Open Access be Provided to Research Manuscripts it Funds

nihlogo.gifFollowing a summer of pressure from Congress on the subject, and a series of meetings of NIH officials, publishers, advocacy groups, researchers, and librarians, the National Institutes of Health have issued a Notice on Enhanced Public Access to NIH Research Information, marking out an important new position in providing access to research literature funded by the government agency.

The notice states, "NIH intends to request that its grantees and supported Principal Investigators provide the NIH with electronic copies of all final version manuscripts upon acceptance for publication if the research was supported in whole or in part by NIH funding." The manuscripts will be housed in the National Library of Medicine's PubMed Central journal archive service. Open access journals such as those published by BioMedCentral, Public Library of Science, and many other titles already comply with the proposed NIH policy.

NIH currently funds over a quarter of the medical research performed worldwide. The agency's move is a response to the growing unavailability of the research literature to the scientific community, due in large part to rapid inflation over the past decade in the sci-tech publishing sector. The "Open Access" movement has emerged in response to the crisis, seeking publishing models that will provide more consistent access to the research literature to both researchers who produce and read the literature, and to the general public which funds much of the research through NIH, NSF, and other government agencies.

NIH has prepared a web site explaining its stance on public access to the literature: http://www.nih.gov/about/publicaccess/index.htm. The agency seeks comments on its policy proposal. Comments should be submitted by November 16, 2004.

Posted by Kevin Messner at 12:41 AM

PLoS Medicine Inaugural Issue to Release October 19

pmed_cover_200.gifThe Public Library of Science (PLoS), a non-profit publisher dedicated to an open access model of scientific journal publication, will unveil its new journal, PLoS Medicine, on October 19.

PLoS launched its first journal, PLoS Biology, in October 2003. PLoS Medicine PLoS seeks to publish high-profile research articles in these two flagship journals, to compete in the top tier of publications in their respective fields. PLoS Medicine "aims to publish outstanding human studies that substantially enhance the understanding of human health and disease." After less than one year of publication, PLoS Biology recently increased its online publication schedule to a weekly release, one indication of a welcome reception with the biology research community.

The open access academic publishing movement has emerged as a response to rapidly increasing journal subscription prices, and inconsistent support of online journal access, by many commercial and society publishers. In an open access model, published literature is made freely available to the public, not only to institutions or individuals who can pay the costs of subscription, licensing, and account maintenance. Instead, costs of publication are paid for by authors (typically from research or institutional grants).

Under PLoS’ open access model, “A complete version of the work and all supplemental materials…is deposited immediately upon initial publication in at least one online repository…that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving (for the biomedical sciences, PubMed Central is such a repository).” PLoS articles are published with the understanding that all users are free to copy, use, and distribute the article to others (so long as authorship is attributed).

The journal has prepared an FAQ with further details on their publishing model and the publication process. The University Libraries are an institutional member of Public Library of Science. As a membership benefit, authors from the U of M who publish in either PLoS journal will receive a 10% discount on publication charges.

Consistent with its open access policy, PLoS Medicine will be available online for free to the academic community and to the general public. The print form of the journal will also be available at the Bio-Medical and Veterinary Medical libraries.

Posted by Kevin Messner at 12:40 AM

Journal Cancellations for 2005

Journal cuts, particularly in the sciences, have seemingly become an annual ritual in many academic libraries, and the U of M Libraries are no exception. High annual price inflation rates for research journals in science and technology (inflation of circa 10%, per year -- meaning prices of journals double about every seven years), increased costs associated with providing online journal access, and essentially flat library budgets, mean that the Libraries are able to provide fewer journals each year.

A list of journals which are being cut for 2005 is available at http://www.lib.umn.edu/articles/jcancel2005.phtml. In a few cases where noted, a duplicate print copy of a journal is being cut, but another copy is still available at the University. In other cases, only the print form of the journal is being cut and the online version retained.

While this latter move preserves current access to the journal, it is important to note that it is a perilous management strategy, because we do not typically own access to the online journals. Rather, our annual access licenses are essentially lease agreements. Hence, if we have to cancel the online subscription -- or even if we do continue to subscribe, but the publisher changes the terms of their license agreement at some point in the future -- we can easily lose access to years we have already paid for.

In the molecular biosciences, cuts in the past several years have primarily focused on duplicate subscriptions to journals held in print at libraries on both the Minneapolis and Saint Paul parts of campus (e.g., one subscription at Bio-Med, and another at Magrath Library). Because of this strategy and the purchase of online access for most key journals, the cuts have not had a deep impact. However, there are very few duplicates and other "easy cuts" (e.g., foreign titles) left in the collections. Assuming current inflation trends continue, subscription cuts will quickly become evident and difficult for many bioscience researchers on campus.

To avoid serious deficits in access to the core bioscience literature, it is vital that faculty take initiative and insist University administration move to provide significant, lasting funding increases to the University Libraries. However the Libraries provide access to the subscription-based literature in the coming years, it is absolutely clear that access will be increasingly expensive.

Taking a long-term view, faculty should also consider journal costs when they are choosing where to publish and what journals to serve as editors. Journals from commercial publishers (e.g., Elsevier, Wiley, Springer, Blackwell, etc.) are typically most prone to high inflation, though journals from society publishers (e.g., ACS, ASM, EMBO) are by no means immune to substantial price increases -- especially when societies sell or outsource their journal operations to commercial puslishers. For example, EMBO outsourced its journals to the commercial Nature Publishing Group at the end of 2003, and NPG immediately doubled the U of M's subscription price for EMBO Journal and EMBO Reports.

Posted by Kevin Messner at 12:27 AM

ILLiad for ILL is coming soon!

What is ILLiad? It's the new interlibrary loan (ILL) management software that will be implemented in Fall Semester 2004. Interlibrary loan is the process by which the U of M Libraries, in coopoeration with other libraries across the country, can get a copy of an article or a book not owned by the University Libraries to fill particular library user needs. With ILLiad, you'll be able to:

- submit ILL requests more conveniently. With ILLiad, you enter your address and other personal information only once, when you register.
- view the status and history of all your ILL requests
- order online, any time, any place!
- view your articles electronically

Please note: your ILLiad account will be separate from your MNCAT account.

Watch for further information in the coming weeks about how you can register for and start using ILLiad to improve your ILL experience!

Posted by Kevin Messner at 12:25 AM

October 18, 2004

Creating stable links to online journal articles with Find It

Users of online journals often need to refer colleagues or students at the University to journal articles. Intuitively, the easiest way to do this is to copy the article file and email it to those who need it, or post it on a local server and link to the file. However, usage licenses for many publishers' online journals disallow copying article files from the publishers' web servers, and increasingly subscription-based publishers make it technically difficult to copy the files from their sites.

Some users try to copy and paste the URL for an article from the journal's web site; however, these direct URLs often do not work for the recipient because they do not pass through the content access controls put in place by publishers, which require the user to prove their University affiliation. This is especially a problem when the user is working from an off-campus location.

The University Libraries' Find It service can help journal users readily create a link to the online journal article at the publisher's web site. This URL will prompt the user for U of M Internet ID authentication and lead successfully to journal content licensed to the Libraries. Links created using Find It take advantage of the dynamic linking technology behind the Find It service. Additionally, if the Libraries access to an article changes from one provider to another, or the publisher changes the structure of their website, the link created can still remain functional, unlike a regular hard link.

The instructions below will guide you through the process of creating a URL for an article with Find It:

1) If possible, find a citation for the article in a Find It-enabled bibliographic index, such as the U Libraries access to PubMed. If a citation in an index cannot be found (for example, the journal is not indexed in PubMed), for an alternate link to the journal go to Step 2b below.


2) In the index, click the Find It button for the article. This brings up a Find It menu for the article.


3) One option on the Find It menu reads "Capture the link for this citation with the Find It Link Generator." Click that link.


4) On the following page titled "Find It Link Generator," copy the URL in the text box. Paste this into a web page, WebCT page, email, etc., to provide a link to the article.


2b) If a citation to the article cannot be found in an index with Find It buttons, a link to the journal can still be created using the Libraries e-journals list. Go to the e-journals page and find the journal title of interest.


3b) RIGHT click the title link. (Mac users: )


4b) A list of options is brought up. Select "Copy Link Location" to copy the link into memory (in Internet Explorer, use "Copy Shortcut").


5b) Paste (CTRL-V) the URL into a web page, WebCT page, email, etc., to provide a link to the journal. (From there, the user will need to navigate to the article within the journal, so you should confirm that the article is actually present on the journal web site!)

Posted by Kevin Messner at 10:41 PM

I have a citation, how do I find the article? Getting from Here to There with “Find It”

For scientific journal literature provided online through the Libraries, our E-journals site is the quickest way to get from a known citation of an article to the full text of that article. Starting at a Libraries’ web page will help clarify whether the U subscribes to the journal in question, and ensures that you are prompted for your U Network ID, if necessary to access the resource.

As an example, let’s say you’re trying to find the full text for this article:

Kenyon SJ, Bromley BC. Nature. 2004 Dec 2;432(7017):598-602.

Go to the E-journals site (accessible from the University Libraries’ home page).

You want to find the journal “Nature.” Either search for Nature (use the Exact Title check box to avoid finding other titles which include the word “Nature”), or browse the “N’s” in the alphabetical list for the title. In either case, click the “Nature” title link when you find it.

A page titled “Find It: the University Libraries Linking Service” comes up. For Nature and many other journals, the title is available from more than one provider, so there are several listings on the page. Note the “Availability” in small text below each entry – the available issues may differ between providers.

Once you’ve identified a source, click the link on that entry. This link takes you to a home page for that journal, from which you can navigate to the article you need.

(On the Find It page, a form is provided to enter the particular year, volume, issue, and start page of the article you want. Depending on the particular journal and publisher, entering this information may take you directly to the article. However, this function depends entirely on the structure of the publisher’s web site and is not always successful. If it doesn’t work, try deleting the data from the form and click the link to go to the journal home page.)

If the article you're looking for isn't available through the Libraries online, try MNCAT to look for print holdings of the journal. Trouble? Contact the Bio-Medical Library (4-3260; medref@umn.edu), Magrath Library (4-1212; magrath@umn.edu), or the Infopoint chat and email service at http://infopoint.lib.umn.edu/.

Posted by Kevin Messner at 1:17 PM