Department Blog

Health Sciences Libraries

Comparing Veterinary Databases: Beyond PubMed

October 28th, 2009 by Mary Wood

Working on a website for a presentation to VMD400B acted as a reminder of how too few of us in veterinary medicine and animal science make use of valuable and effective databases beyond PubMed. The following chart compares six potentially useful databases on just a few points, but emphasizes the wealth of information to be found in CAB and BIOSIS. There are more than just these six databases to consider: list of Health Sciences databases; lists of databases by subject.

vet med database comparisonMany databases are proprietary, made available to UC Davis affiliates by UC Davis Library subscription. Free resources that will remain available even after graduation include Agricola and GoogleScholar. (Clicking on the graph will link to a larger image).

About the image:
The original graph was edited using the Picnik editor that is embedded into the free Flickr photo hosting site.

Resources for music and video online: legal downloading and streaming alternatives

October 21st, 2009 by

In a recent post on the DMCA-info listserve, Jan Carmikle, the UC Davis Designated Agent for Digital Millennium Copyright Act notices, sent out a welcomed listing of both legal download sites and alternatives to legal downloading, namely streaming.
The compilation of resources provided by Educause is in response to the The Higher Education Opportunity Act which requires all colleges and universities to offer legal alternatives to unauthorized downloading.

The collection of resources is available on the Educause website:

Note: the site is continuously updated.

Legal downloading & streaming alternatives for music, games & video

Legal downloading & streaming alternatives for music, games & video

The Educause site includes a diverse assortment of legal alternatives to downloading, including streaming music, streaming video, online games, along with some legal P2P file sharing sites.
The streaming video sites include classic and contemporary award winning films such as those found at The Criterion Collection: online cinematheque, along with a lengthy listing of sites providing streaming access to popular TV and movie titles from commercial producers/vendors from Disney to Zune…
Many of these sites do have online stores for purchase of related products.

Looking for Educational Videos or Podcasts?

It takes a little wading around to find educational resources but they are there, though definitely buried. After keyword searching and scrolling through the channels, collections and ‘recently added’  lists, I came up with the following educational shows on Hulu:

Milestones in Science & Engineering:

The Nobel Prize (short clips):
Wired Science:

Hulu links out to some of the commercial sites, providing short clips as is the case with the TLC Discovery Health show (short clips): Big Medicine

Downloading Video and Audio Podcasts for Players or to view on your computer:

Higher Education Video and Audio Podcasts are available through iTunes (UC Davis on iTunesU) and Zune (higher education section) both requiring software downloads…but well worth it.

A favorite among the many streaming video sites is Hulu which offers an assortment of TV and video content through its channels and collections and some may be of interest to educators.
For example, in the Hulu Collections you’ll find President Obama’s speeches: and related TV and video collections.

Other Hulu services include the Publishing and design tools from their Hulu Labs:

Keep up on issues of copyright and the Digital Millennium Copyright Act in action:

Subscribe to one of the UC Davis listserves: Copyright-info and DMCA-info.
Find out more about the Digital Millennium Copyright Act (DMCA) at the UC Davis Innovation Access: connecting research to the market.

About the image:

The original family snapshot was cropped and edited using the built-in image editor on the free Flickr site. We used the pro features in the embedded Picnik editor (additional fonts, icons, images to overlay your photos). Subscription to the pro version provides access to the stand-alone Picnik editing site and allows the users to pull images from a variety of photo sites across the web at a cost of $24.00 for the annual subscription. Even the free Flickr accounts can be linked to the free Picnik editor via the ‘edit’ button; pro Picnik subscriptions can be linked through a login when in Flickr or Picnik. Both options allow for an arsenal of online quick editing features. To access the editor, log into your free or pro Flickr account, then click the edit button directly above any of the pictures you have uploaded.
View a larger version of the Picnik embellished image using the Halloween ghosts, copyright symbol, arrows, black and white view, item focus in blue and, my favorite, the editable lightening rod.

Posted by: Bernadette Daly Swanson

Sciences Libraries Restructuring: Background and Comments

October 19th, 2009 by

We invite the UC Davis community of faculty, staff, and students to send comments regarding the sciences libraries restructuring efforts. A web site: Sciences Libraries Restructuring (, presents background information regarding what has occurred thus far, including answers to Recently Received Questions, and areas for which we welcome comments and suggestions to be used as part of the decision-making process for library collections and services.

These are challenging times for all of us. The UC Davis General Library employees rely heavily on input from the faculty, staff, and students to acquire/license collections and to design services that will meet the research, teaching, patient care, and community service goals of the campus.

Vet Med Information via PubMed

October 19th, 2009 by Mary Wood

PubMed provides references to journal articles in the life sciences, with a concentration on biomedicine. While human clinical medicine remains the primary focus, PubMed does index a limited number of veterinary medicine and animal science journals.

One of several PubMed “Special Queries” is Veterinary Medicine / Animal Health.   It retrieves citations to journal literature, combining subject search terms, title words, and veterinary and animal health journal titles.  Essentially, it applies a search filter over any search terms you use, limiting the results to veterinary related resources.

PubMed Search and Veterinary Information Resources

PubMed Search and Veterinary Information Resources

The PubMed Search and Veterinary Information Resources page provides links to additional resources and organizations.

Enter PubMed from the Health Sciences Libraries page to ensure access to all of the full-text journals subscribed to by the library.  To apply the Veterinary Medicine / Animal Health filter to a search, enter PubMed from the HSL site and type “veterinary[sb]” into the search query; that set can then be combined with any other search term.

On the rugged digital shores of Davis Island: in Second Life® with the MH214 Class

October 5th, 2009 by

Over the past couple of months my work as a librarian has extended from the Health Sciences Libraries to the rugged digital shores of Davis Island in the virtual world of Second Life®. Our journey into the popular 3D virtual environment was part of the new online course, MH214, The Internet and the Future of Patient Care which is a collaboration between the UC Davis Extension and the UC Davis Health Informatics Certificate Program. Participants in the course led by Peter Yellowlees MD, were invited to:

“Explore the profound impact of the Internet on the delivery of health care from the patient and provider perspectives, including the Internet’s role as an information source, a communication tool and a conduit for clinical consultations and chronic disease management. Consider the changing nature of the doctor-patient relationship and the potential of the Internet to enhance access to and quality of care. Explore the future of health care in an information age where care will become increasingly personalized and distributed.” Peter Yellowlees MD

Conference Area with Student Blogs on Med. Projects, Davis Island

On the digital shores of Davis Island

UC Davis Online Learning Campus & Second Life®: a Look at the Software

The MH214 course found its home online at the UC Davis Online Learning Campus (which uses the popular Moodle open-source course management system). The students and instructors also used a suite of familiar social networking sites including Facebook, Twitter and Blogspot (e.g.: Peter Yellowlees’ blog), where students followed, commented and shared insights on weekly readings and topics for discussion, then submitting assignments and discussion posts to the MH214 home at the UC Davis Extension’s site.

UC Davis Extension Online Campus Site

UC Davis Extension Online Campus Site

In the Second Life® sessions, students learned some of the basics of building in 3D environments, importing media and touring some of the well known health care, non-profit and government projects such as Cisco’s Virtual Palomar West, Imperial College London’s Medical School and the Second Health Polyclinic, Virtual Ability Island, Virtual Hallucinations (named one of ScienceRoll’s Top 10 Virtual Medical Sites in Second Life®), NOAA and and a variety of other organizations using the environment for learning and health related purposes.

Just How Big is Second Life®?

The total land area of Second Life® is now equivalent to approximately two billion square meters – roughly the size of the state of Rhode Island. There are well over 20,000 CPUs conncected together simulating the virtual environment. This popular virtual world is the brain child of Philip Rosedale, a UC San Diego Engineering Graduate. Prepare to be inspired: TED: Talks with Second Life creator, Philip Rosedale.

Let’s take a look at some of the numbers in the Sept. 22, 2009 Linden Lab press release.

Virtual goods & user created content: residents create more than 250,000 new virtual goods every day. User created content now amounts to more than 270 terabytes and growing 100% every year.

Voice Chat (VoIP): 18 billion minutes of voice chat have been used in Second Life® since voice was introduced in 2007, making Linden Lab a major VoIP provider.

Text Chat: Approximately 1,250 text-based messages are sent every second in Second Life®, and more than 600 million words are typed on an average day.

Where are these people from? Roughly 60% of active Second Life® Residents based outside of the US, representing more than 200 countries, and the Second Life® Viewer available in 10 languages.

Some of the UC Davis Virtual Locations:

The following video gives a glimpse of two of the UC Davis locations visited during the September 10th session, take a look at the following video capture from the class (available via YouTube) which includes quick visits to the 3D UC Davis Virtual Hallucinations facility (scale replica of the Sacramento County Mental Health Treatment Center on Stockton Blvd.) and the Bioterrorism Defense Training facility based on another Sacramento building to mimic an actual setting that might be used as a Strategic National Stockpile distribution site for Northern California in the event of a bioterrorist attack.

Gathered for the Sept. 10th class discussion & tour of health facilities

Gathered for the Sept. 10th class discussion & tour of health facilities

The instructors for the class were seasoned virtual reality proponents, Peter Yellowlees MD, Martin Leamon MD, Bernadette Daly Swanson MLIS and James (Linden) Cook MD, who is also one of the early developers of the Second Life® and employed by the creator, Linden Lab. The feedback from the students has been positive and will be shared by Peter Yellowlees MD in an upcoming publication.

Broadband, updated Graphics Cards, Headsets with Microphones:

So what does it take to log into virtual worlds? System requirements for Second Life® require broadband Internet access and a compatible graphics card. Options for courses using both Moodle® and the synchronous Second Life®, include the integration of both systems using the open-source SLoodle®, which provides a tested suite of tools whereby content such as course slides can be uploaded into the online course management system and then accessed by the instructors and students in Second Life®.

What are other institutions doing in Second Life®?

New Media Consortium (NMC) provides access to case studies via their online portfolio.

Last month, the University of Texas, entire 16 campus system, announced its participation in a year-long project to explore the use of virtual worlds for learning.

The MH214 Class:

Students logged into the UC Davis Extension’s online learning campus and the virtual world from different parts of the country and across time zones, and brought a rich variety of expertise to the class. The group included professionals already in the fields of health care, IT and education, including a nurse, physician, online records specialists and students from the Certificate Health Informatics Program. At the times when the class logged in, between 6:00 PM PDT and 9:00 PDT, there were between 65,000 – 75,000 people logged in from around the world. We used a combination of text chat, IM and voice (VOIP) and communicated through our microphone/headsets and the more traditional fingertips.

Discussing readings and student blog posts (typing action indicates text chat)

Discussing readings and student blog posts (typing action indicates text chat)

Joining the Virtual World:

Joining the Second Life® community requires creating a user account at the web site, choosing an avatar and name (not your actual name), then downloading the software which is similar to a web browser (shown below). Through the Second Life® viewer the user logs into the 3D world using the avatar name and password.

Check the system requirements for using SL (broadband & updated graphics cards)

Check the system requirements for using SL (broadband & updated graphics cards)

Online Orientation via YouTube Videos, Tutorials at First Login & the Help Islands:

Before registering and downloading the software, the students were encouraged to view one or more of the introductory videos from the MH214 YouTube Playlist.

Introductory videos to Second Life uploaded to YouTube for the class

Explore the website: then join, download software, login

A brief orientation to Second Life®:

As part of the first login, new users can select from a variety of orientation areas. The MH214 class were asked to spend an hour in one of these areas to become familiar with the navigation keys and the Second Life® viewer interface. That week once we were all logged in and feeling a little more oriented, we met at the private class location, UC Davis Island.

Videos showing some of the activities and discussions can be seen on the YouTube video playlist of the MH214 Class

View the YouTube Playlist of videos from the class

View the YouTube Playlist of videos from the class

Looking for Peer-Reviewed Journal Articles on Health care & Second Life®:

Students made use of free peer reviewed journals on the web, as well as journal articles from UC Davis licensed journal subscriptions. Some of the free peer reviewed journals include Journal of Virtual Worlds Research (JVWR) and the Journal of Medical Internet Research. A special issue dedicated to virtual worlds and health care was published by JVWR in August 2009:
Journal of Virtual Worlds Research, Vol 2, No 2: 3D Virtual Worlds for Health and Healthcare and
A Survey of Health-Related Activities on Second Life® in the Journal of Medical Internet Research.

The best way to find relevant articles in PubMed on research being conducted in the environment or review articles about Second Life®, is to search using the Medical Subject Headings (MeSH) that are the backbone of this massive database.
In order to retrieve relevant articles, this is the query I used:
“User-Computer Interface”[MAJR] AND (virtual environment OR second life)
This query currently retrieves 860 articles… of course, way too many for most purposes, so we encourage adding extra keywords or MeSH terms to the search such as the following query with a focus on consumer health information and education which currently retrieves 212 results:
“User-Computer Interface”[MAJR] AND (virtual environment OR second life) AND (“Education”[MeSH] OR “Consumer Health Information”[Mesh])

Articles related to some of the locations visited included the following two by UC Davis faculty:

Peter Yellowlees, James N. Cook, Shayna L. Marks, Daniel Wolfe, Elanor Mangin. Can virtual reality be used to conduct mass prophylaxis clinic training? A pilot program. Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science. March 2008, 6(1): 36-44.

PM Yellowlees, JN Cook. Education about hallucinations using an internet virtual reality system: a qualitative survey. Academic Psychiatry. 2006 Nov-Dec 2006, 30(6):534-9

View the recent issue of freely available peer reviewed journals

View the recent issue of freely available peer reviewed journals

If You Plan to Visit:

If you’re logging into Second Life®, be sure to contact us. During the registration process you will select a name (not your actual name). Here are our names if you would like to contact us once you log in. Peter is known as Nash Baldwin; Martin is Grommet Wallace; Bernadette is HVX Silverstar and James is James Linden.

Firefox toolbars to the virtual world: MH214 Health Informatics Class toolbar

For anyone using the Firefox browser… or for anyone who wants a quick way to reach the MH214 class locations in Second Life®… read on!
Download and install the toolbar with quick links to the Second Life locations visited during the last sessions, as well as additional links.
Toolbar links include:
Davis Island (private – MH214 students & faculty only.. sorry)
Cisco’s Virtual Palomar West Hospital with RFID tracking for visitors
Imperial College London: Second Health Polyclinic (NHS funding)
Virtual Hallucinations public location (UC Davis)
Library Studios (my island in process)
UC Davis Extension Class Online Campus site

Note: The Second Life® viewer must be installed on your computer to use the toolbar. When you click on the buttons on the toolbar, they will launch the SLurl (SL URL) map site with coordinates for Second Life® and allow you to click through to the location which launches your SL viewer which allows you to login to the chosen location.

Customized Firefox Toolbar for download

Click to view larger image

More about the Mozilla Firefox browser

Take a tour of some of the Medical Builds in Second Life®:

Cisco’s Virtual Palomar West
Second Health London Polyclinic
Virtual Hallucinations (updated version)
on the private Davis Island
Mass Prophylaxis Clinic Training facility on Prophylaxis Island (also private).

YouTube Video:

Tour the locations shown during the 3rd Annual Conference at UCDMC: Innovations in Informatics Conference:
Virtual Tour of the very cool Health & Medical Builds in Second Life® 720p HD version.
Note: an updated Flash video player is required to view HD on YouTube.

Create an account and login to Second Life® to visit the locations

Create an account and login to Second Life® to visit the locations


Health Informatics, UC Davis Extension. 2009. Online Certificate Program in Health Informatics. Retrieved October 5, 2009, from

YouTube video playlist for the MH214 Class in Second Life ®
Swanson, B. (2009, Sept. 16). UC Davis Health Informatics Class in Second Life® [Video files]. Retrieved from

Bernadette Daly Swanson, MLIS
HVX Silverstar in Second Life®