CDLINFO

Change to PubMed’s Automatic Term Mapping will affect phrase searching.  NLM plans to improve the ability of PubMed to find appropriate Medical Subject Headings (MeSH terms) by removing the phrase list table from the Automatic Term Mapping.

What is MeSH and why does this matter?
Indexers use the MeSH terms to describe the subject content of articles as they are added to MEDLINE in PubMed.  We can then retrieve citations relevant to our topic no matter what terminology the author used to describe the subject.  So, usually when PubMed interprets our query into MeSH, our results are more complete.

How will removing the phrase list help?
Currently PubMed searches the words input against a MeSH translation table, then against the journals translation table, then against the phrase list table, and finally against the author index.  If the complete phrase as entered in the query is not found in the MeSH table, but is found in the phrase list, the system stops the Automatic Term Mapping process.  An example of a search query that currently retrieves a phrase but not a MeSH is chronic urinary tract infections.  Currently the query retrieves 141 citations covering all years (1965 to present) containing the exact phrase.  When the Automatic Term Mapping no longer includes the phrase list, the query will retrieve 2475 citations covering all years containing the word chronic, the MeSH urinary tract infections, and the phrase urinary tract infections.

What are the adverse effects of this change?
You may find that PubMed interprets terms in your query inappropriately to MeSH.  For example, if you are interested in mongolian spots, currently PubMed interprets your query as a phrase and retrieves 44 citations covering all years.  When the Automatic Term Mapping no longer includes the phrase list, the query will retrieve 92 citations covering all years containing the MeSH down syndrome or the word mongolian as well as the MeSH exanthema or the word spots.  To retrieve ONLY the concept mongolian spots (the 44 citations containing that exact phrase,) you will need to use quotation marks: “mongolian spots”.

What action should you take?
If you use either the PubMed Cubby or BioMail to regularly update your results on a topic, you may wish to check your strategies now and once again following the change to Automatic Term Mapping.

For the PubMed Cubby, to find out if your stored strategies include phrases or terms that will be affected by this change,
1. Log into the Cubby
2. On the list of your stored searches, click on the name of a search.  This takes you to the Stored Search Information screen for that search.
3. Click on the Search button to retrieve citations for that query (without updating it)
4. On the screen with the search results, click on Details; look for multi-word terms in the PubMed Query box that are tagged with [All Fields].

After the change is implemented, you should check again to make sure that terms have not retrieved inappropriate MeSH for your topic.

For BioMail,
1. Log into BioMail
2. Highlight your strategy and copy it
3. Go to PubMed and paste it into the search box
4. Click on Go; follow the instructions above for checking Details

We recommend checking to see how PubMed interpreted your query by clicking Details anytime you are searching PubMed. For further information and assistance in searching PubMed, contact your campus reference librarians; campus contact info and guides available here: http://www.cdlib.org/guides/pubmed/

In some browsers (e.g., Netscape 4.x versions, Opera, and Mozilla) when the font size is much larger than the default settings, the entire Web page is not visible on the screen.  In the case of Melvyl-T, this means that horizontal scrolling is required to view the right hand portion of the Melvyl-T Advanced search screen, where the Results box is found.  This is problematic, since catalog users, not seeing the Results box, may believe their searches retrieved zero results.  Please be sure your default font size settings allow for viewing of the entire screen for the Melvyl-T catalog, as well as for many of the new databases.

Vendors are removing support for older browser versions, e.g., Netscape 4.x. The removal of support for older browser versions may cause problems for UC library users in locales that have not yet moved to the most recent browser versions in their public areas and training rooms.  These changes will have a negative impact on the work of library staff and researchers alike.

Here are some examples of recent changes in browser requirements:

Ovid:
Ovid has just announced a change in their browser support:
Effective June 30, 2003, Ovid’s minimum browser requirements will be upgraded to Internet Explorer 5.x and above, and Netscape 6.x and above. Some of Ovid’s new features also require JavaScript and cookies to be enabled.

CSA:
For the Internet Database Service Version 6.0 (IDS 6.0), released last fall, CSA recommends using Netscape 5.0 or newer, or Internet Explorer 6.0 or newer.  CSA’s IDS 6.0 contains advanced features that are not compatible with the old browsers, and users may get random errors depending on which browser is used.

Melvyl-T
Melvyl-T requires recent versions of browsers to view special characters:
To view special characters, e.g., accented Western characters and Chinese, Japanese, and Korean, in Melvyl-T we recommend the most recent versions of Internet Explorer or Netscape be installed on your computer (IE 5.0 and above and Netscape 6.0 and above).  In addition, you must have a font that can display the characters.  A free font that displays most of the characters in Melvyl-T records is Ariel Unicode MS, which is supplied with Office 2000, or can be obtained from the Microsoft site.  This font can be used on Windows or Macintosh computers.  Some older browsers and older computers can make use of the character displays described here but it may be necessary to download fonts for individual languages one at a time.

Not sure what browser version to choose for upgrading?
The following browsers support most of the web standards created by the World Wide Web Consortium including CSS, XHTML, and the DOM (a means of controlling the behavior of web pages):

Mozilla
http://www.mozilla.org/

IE6 or higher for Windows
http://www.microsoft.com/windows/ie/default.asp

IE5 or higher for Macintosh
http://www.microsoft.com/mac/products/ie/ie_default.asp?navindex=s7a

Netscape 6 or higher for all platforms
http://channels.netscape.com/ns/browsers/download.jsp

a. The CDL Welcomes Peter Brantley; Thanks John Ober (Dan Greenstein)

I am very pleased to announce the appointment of Peter Brantley to the position of Director of Technologies for the CDL.  The Director of Technologies has lead responsibility for the development and management of the technical infrastructure and the technical staff supporting CDL operations.  In partnership with co-library staff from the campuses and the wider digital library community, the position also oversees development of new technologies and provides leadership in establishing a technical research agenda.

Peter is clearly one of the luminaries in the community of research libraries with significant digital development programs.  He is currently Director, Information Technology Services, Division of Libraries and NYU Press at New York University.  In that role he has led the deployment of many campus-wide applications including e-reserves, electronic gateways, and web services and has managed digital library development projects of national scope and partnerships.  Peter is a participant in the Internet2/Mace Shibboleth project for user authentication and authorization, which has direct implications for digital library services.  The Digital Library Federation and the Coalition of Networked Information are partners in the Shibboleth project and Peter has represented NYU in both of those organizations.

Many UC staff will remember and appreciate Peter’s earlier ties to UC.  He served as Director of Academic Information Systems at the Library and Center for Knowledge Management at UC San Francisco, and more recently as Director of Computing Services for the College of Letters and Science at Berkeley.  The CDL is thrilled to welcome Peter back to the UC community and the west coast.  He expects to take up his position on March 24, 2003.

This will mark the conclusion of John Ober’s interim responsibility as Director of CDL Technologies, which he has carried since May 2002 (along with his position as Director of Education and Strategic Innovation).  John’s tenure has had the challenges of major technical transitions and expansion.  These include the Melvyl-T project, the addition of SFX/UC-eLinks, establishment or redesign of Counting California, the Online Archive of California, and a Consortial Borrowing System, and a renegotiation of data center machine room services.  We are extremely thankful for John’s willingness to step into the breach and for the successful and quietly confident nature of his leadership during the recruitment for a permanent director.  John will resume full-time attention to education, outreach, evaluation and strategic planning for the CDL and also lend his expertise in those areas to systemwide library planning.

As you have the opportunity, I urge you to welcome Peter to the family of UC libraries and to thank John for a job well done.

b. Ravikumar Gudipati Joins Access Programming Group

Ravikumar Gudipati will be joining the Access Programming Group in the new Programmer/Analyst position on April 7th. Ravi has more than eleven years of experience with software development in the internet environment, working for a diverse group of organizations that include PG&E, Telephia Market Track, Barclays, Hollywood Deluxe Color Lab, Walt Disney, and Minnesota Schools.  He has worked extensively with such technologies as Java, Perl, JSP, servlets, RDBMS, and XML to develop a range of web-based applications ranging from such functions as data warehousing to college student and staff administration to circuit management and database conversion.

As promised earlier this year, the CDL now has an updated information page, “Using Citation Management Software with Vendor Databases” (previously titled, “The A&I Transition and Citation Management Software”).  We have revised it with input from UC library staff and discussions with vendors.

This Web page is available on the CDL public site so that it can be accessed by all users of citation management software: http://www.cdlib.org/news/citman.html

It is also linked to from the Adaptable Outreach and Instructional Materials page <http://www.cdlib.org/libstaff/comm/outreach/> from Other Resources, EndNote, ProCite and Reference Manager.  Library staff can modify it for their own use at their campuses, if desired.

The document contains the following information:
–Background: steps taken prior to the transition to address this issue
–What is currently working: databases, direct searching, filters, and direct export, including exceptions, caveats, and cautions
–Known problems, including alternatives if they exist
–How to get help
–How to report problems

The CDL will continue to update this page as the landscape changes in the area of citation management software.

The eScholarship Repository <http://repositories.cdlib.org/escholarship/> has reached several major milestones since its launch in April 2002.  The Repository offers University of California faculty a central online location for depositing working papers, technical reports, research results, datasets with commentary, and peer-reviewed series.  It is free for scholars to upload papers and free for users to download them.  The CDL guarantees persistent access to the content.

Nearly 100 UC institutes, departments, research units, and centers from 9 UC campuses have joined the repository.  The eScholarship Repository contains 1,200 papers. Users have logged 60,000 full-text downloads of repository scholarship.  Usage statistics show that over 95 percent of repository users are coming from outside UC, including 38 countries.  This demonstrates the increased visibility the repository offers UC faculty.

A wide range of subjects can be found in the repository, including social science, business, education, humanities, and the sciences.  The Anderson School of Management at UCLA, Center for Studies in Higher Education at Berkeley, University of California Energy Institute (a Multi-Campus Research Unit), Economics Department at Santa Barbara, Center for Conservation Biology at Riverside, and Scripps Institution of Oceanography at San Diego are just a few of the UC academic departments and research units with repository sites.

The eScholarship Repository also supports peer-reviewed series, which offer scholars an alternative to for-profit journals.  The University of California International and Area Studies (UCIAS) Digital Collection <http://repositories.cdlib.org/uciaspubs/> has been available since summer 2002.  Further information on starting a repository peer-reviewed series can be found at <http://repositories.cdlib.org/escholarship/peer_review.html>.

The complete March 12, 2003 press release on the eScholarship Repository can be found at <http://repositories.cdlib.org/escholarship/milestones.pdf>.  Additional information on the repository is available at <http://repositories.cdlib.org/escholarship/about.html> or through your campus eScholarship liaison <http://escholarship.cdlib.org/liaisons.html>.

The CDL Joint Steering Committee on Shared Collections (JSC) recommended, and SOPAG concurred, that selected freely available ejournal content be linked (via UC-eLinks), cataloged by Shared Cataloging, entered into the CDL Directory, and monitored as other resources are (see the JSC notes of May 20, 2002 at http://www.cdlib.org/libstaff/sharedcoll/jsc/ ).  Although the resources may be open access, these actions represent considerable investments but are designed to reduce similar kinds of investments each campus might have to make in these resources.  Even though a license will not be signed for these resources and there is no formal negotiation process with a vendor, as much as possible, these open access resources will follow existing procedures for licensed packages.  There are two categories of such ejournals:

1. Open access ejournals that are indexed by shared abstracting & indexing databases e.g., J. of Clinical Investigation and the BioMed Central journals–all indexed in PubMed.  These will be added as described above as they are recommended or discovered.  The Joint Steering Committee has asked bibliographer groups to alert them to such titles and the abstracting/indexing sources that cover them.  The recent JSC surveys specifically asked about such titles.

2. “Unsubscribed” (i.e., there is no historic print base in UC) titles to which all campuses have access as part of a CDL publisher package contract.

Once resources have been selected, the Shared Catalog Program (SCP) at UCSD will catalog them.  UC-eLinks will be implemented, where possible.  The resources will be added to the CDL Directory and announced via CDL Directory weekly updates and in CDLINFO.  For each resource or package, either a resource liaison will be assigned or the SCP department will be responsible for monitoring long-term access to that resource.

Remember, in the CDL Directory, you can limit your search to items available to the general public (under the “available to:” pull down) and in the search results all openly available resource titles are in green and include a note stating that they are available to the general public.

NOTE: New resources listed below are not yet in the CDL Directory of Collections and Services; they will be added within the next 2 weeks.  You can access them directly from the URL provided.

A list of recently added content is always available at: http://www.cdlib.org/news/whatsnew.html

a. Berkeley Electronic Press Journals (bepress)

Endorsed by the CDL Joint Steering Committee on Shared Collections, four additional journals from the Berkeley Electronic Press (bepress) have been licensed for all campuses by the CDL.  In addition to the valuable content these journals represent, the decision to license them was influenced by a desire to support bepress’s innovative models of scholarly communication.  A number of UC faculty serve as editors for these new reasonably priced journals.

The CDL’s three-year agreement (2002-2004) for bepress titles included twelve economics titles in three series.  Two additional economics journals are now available and have been added to the agreement:

Journal of Agricultural & Food Industrial Organization: http://www.bepress.com/jafio

Studies in Nonlinear Dynamics & Econometrics: http://www.bepress.com/snde (Note that this was previously published by MIT Press)

In addition to the economics titles, the CDL’s agreement with bepress now also includes a political science and an engineering title:

The Forum: A Journal of Applied Research in Contemporary Politics: http://www.bepress.com/forum

International Journal of Chemical Reactor Engineering: http://www.bepress.com/ijcre

Additional information on bepress can be found at: http://www.bepress.com