science – the Undergraduate Science Librarian

Headline: Traditional librarians and information scientists start to talk to one another!

One of the great things about the Geological Society of America Annual Meeting is that the organization for geoscience librarians, the Geoscience Information Society (GSIS) meets right along with them as an official part of the conference. This brings librarians and scientists together in a wonderfully engaging setting. Now, I’m betting that most of the geoscientists present don’t realize that there are librarians in their midst, but it’s great start to be in the same building for a little while.

speech_bubbles — Librarians tend to care a bit more about metadata than scientists - they just want to do the science.

I’ve attended sessions related to data preservation and more traditional library related stuff. Permeating the talks at these sessions is the idea that librarians and the scientists dealing with data and information seem to be at the beginning of discussions about how they should work together. This is encouraging.

The most visible folks on the scientists side are a group of folks from the USGS and state geological surveys. These organizations have federal or state mandates to make their data available, so some scientists at these organizations have been tasked to develop the complex systems needed to share this information (The Geoscience Information Network, for example). While in some cases, the scientists are unfamiliar with the systems and metadata standards developed for libraries that could assist them, others are building on the work of librarians, and others are encountering brand new issues that need new standards and practices.

I like seeing this, and I think we need to see more of it. And for the most part, I think that the librarians have the responsibility of reaching out to the scientists (online, in person, at conferences, etc.) to start discussions about how we can help.

What I’m not entirely clear about, is how I can directly impact these efforts. My tentative thoughts on this include working with faculty at my (small) institution to make their data accessible via appropriate external repositories (but do they want to share?), and working with the Geoscience Information Society to reach out to scientists to continue the conversation. I’m not a cataloger (and I don’t want to be one), but their metadata experience could be highly valuable to scientists trying to manage their large quantities of information, and we need to try to let them know that.

culture

I believe I would be a “Data-Driven Nerd”

Virginia Hughs just posted her classification of scientists, and I believe this classification helps me understand why I ended up in librarianship. According to her classifications (in which I see almost all of my scientist friends), I would be a “Data-Driven Nerd”:

These are guys and gals who seem to spend every waking hour in the lab. They’re precise and thorough. They like new technologies that get them better — and more, always more — data. They hate writing up their papers because there’s never enough good data to say something definitive. They generally see no need for (and have no patience for) journalists, unless lapsing into an effusive geek-out moment over some surprising new data.

I think it was my love of data and data analysis (although I didn’t love collecting the data in the field so much) that pushed me over into librarianship, where I get to look at other peoples data and publications all day.

I was a geologist by training, but I always felt like a bit of an outsider because while I love being outside, I didn’t love fieldwork particularly.

Check out her excellent post: where do you fit in?

Uncategorized

A review of the Scopus iPhone App

A little while ago I downloaded the new iPhone app from Scopus, called Scopus Alert Lite. I have finally had a chance to explore it.

Scopus Alerts Lite iPhone App Screen Shot — A screen shot of the search screen from the Scopus Alerts Lite iPhone App

The app is free, although your institution will need a subscription to Scopus in order for you to use it. Theoretically, you should be able to register using your Scopus user id and password, plus the email address from the institution that provides your subscription. This may encourage some users to sign up for an account. Most of the users I know (faculty and students) don’t realize the benefits of creating a user account with the databases they use. This simple authentication didn’t work for me, and it took several emails to Scopus support to resolve the issue. The app does provide a button to contact support if you fail to authenticate, which was how I got in contact with the folks that resolved the problem.

Despite the challenges of registering, I believe that when it works, this is one of the better ways of authenticating subscription content for the iPhone. You can use it anywhere, you don’t have to be on your campus WiFi network or use VPN (like the ACS app) or go through a proxy server (like some database mobile websites).

The app is rather slow to load, and several times I received an error message asking me to log in again. Restarting the app seemed to solve the problem.

Because the app is focused on setting up citation and search alerts, not general searching, there are some limitations.

The biggest limitation is that, for any search, you can’t see more than 50 results, although it will tell you how many total results are available. I think this is a badly needed feature. I kept feeling like I was being short-changed. You can change the sorting order of the results list. The default is by date, but you can also sort by relevancy and citation count.

The second limitation seems to be with author searches. Scopus.com has a very nice author ID feature, which helps you identify all works by the same individual no matter what permutation of their name each article uses. The Scopus Alerts iPhone app doesn’t seem to take advantage of this feature.

Affiliation searches are very easy, allowing you to find publications from a particular institution.

For each of the articles found, you can get their citations and references (number of each and item information). However, the app doesn’t provide links to publisher websites or institutional link resolvers to help you locate the full text (some publishers are providing their own apps for that.)

Unfortunately, alerts don’t transfer between web and iPhone – there is no way to access alerts you have already set up at Scopus.com, and it doesn’t appear that you can get your iPhone alerts on your computer at this time.

I am happy to see this first attempt at an app from Scopus. Despite some challenges, I think their method of authentication is actually one of the easiest I’ve seen (once you set it up once, you are all set, and you don’t need to re-authenticate each time). I hope to see some increased functionality in the future, especially access to additional search results.

You can read the complete official description of the iPhone app from Scopus (including an FAQ) on the Scopus website.

Uncategorized

iPhone Apps for the Scientific Literature

There is no shortage of useful apps for scientists. From compasses to calculators, the iPhone/iTouch has become a very useful tool for many scientists.

An increasing number of scientific literature producers are now offering Apps to let you search and read the scientific literature. Here are a few:

iPhone sunset in the Andes, courtesy of Flickr user Gonzalo Baeza Hernández

Nature.com – Free – From Nature Publishing Group, the folks who bring you the journal Nature. You can search and browse journals, and read articles for free (until April 30, 2010).
ACS Mobile – $2.99 – From the American Chemical Society. Browse and search across all ACS publications, get the latest news items from C&E News, and read full text articles for institutional subscribers via institutional WiFi or VPN.
PubMed On Tap – $2.99 – One of several applications available for searching PubMed, this app allows you to easily view PDF documents from PubMed Central and email them to yourself for future use. Advanced searching techniques are also supported.
arXiview, ArXiv, ArXivReader – $0.99, Free, $0.99 – Multiple apps allow you to search papers deposited in the arXiv.org e-print repository for physics, math, computer science and quantitative biology
iResearch – Free – Browse and search journal articles from American Institute of Physics publications. Access articles via institutional subscriptions. Download articles for offline reading.
IOPscience Express – Free – Browse and search articles from the last two years from Institute of Physics publications

While there are a lot of useful apps for geologists, including a host of statewide geologic map applications, I can’t find any apps to search the geoscience literature. In addition, there are notable gaps from some of the big science publishers including Springer and Elsevier.

Update (5/5/2010): Scopus (the citation database from Elsevier) now has an iPhone app. They launched a “lite” app a couple of weeks ago, and so far I can’t find a paid app, but I’m guessing one might be coming.

web2.0

Data, Data, Data – ScienceOnline2010

The other major theme to emerge from the sessions I attended at ScienceOnline2010 was data. All kinds of data.

Data storage - old and new. Courtesy of Flickr user lan-S

Data about articles and journals. Data about oceans and fish and climate. Data about scientists, their DNA, their babies (and their babies DNA too, I suppose).

20 years ago, getting your hands on a data set meant knowing someone who knew someone who might be able to send you a disc.

These days, more and more data sets are being shared on the open web. Sometimes they are easy to find and use, and sometimes not so much. Sometimes the data require a bit of skill with Excel, and sometimes the data require multiple servers and extensive programming skills.

But it’s out there.

I attended a very interesting session led by John Hogenesch about cloud computing. Some of this was way over my head – I’m not as familiar with bioinformatics as I’d like to be one day, and I only have minimal knowledge of how geneticists are actually using this information. None-the-less, it was informative to learn about the various trends in cloud computing. Some of them I am already very familiar with – like wiki’s, Gmail, Google Docs. I learned more about some services that I only know a bit about. For example, Google Knol is being used by PLoS to write and publish their “Currents Influenza” online. Since the authoring, editing and publishing is done online, the journal can quickly get items published and available. I learned about some services that allow for remote storage and query of information, and how these services can be less expensive (and easier to run) than hosting your own servers.

Jacqueline Floyd and Chris Rowan presented a session on “Earth Science, Web 2.0+, and Geospatial Applications”. Since my background is in geology, I was particularly intrigued by some of the resources discussed here. The discussion at the end of the talk centered around some of the difficulties of finding spatial information (some of which I have discussed before). For example, the USGS provides a wide range of spatial data – geophysical data, hydrological data, geologic data. Some of this is easier to find (and use) than others. For example, recent earthquake data is available is an easy to use Google Earth format, but data older than one month requires more complicated searching (including detailed latitude and longitude coordinates) and the search output requires manipulation to create a visualization. It could be easier.

One of the last sessions I attended at the conference was a presentation by PLoS managing editor Peter Binfield about article level metrics. Peter discussed some of the things that the PLoS journals are doing to attempt to measure the impact of individual articles, not the entire journal. The new metrics were announced in a blog post last summer, and you can see the metrics at work on any article in any of the PLoS journals. They are using open data and API’s from lots of sources: social bookmarking (like CiteULike and Connotea), citation information (from Google Scholar and Scopus), page views and PDF downloads and lots more. I think that this is an exciting new way to shed more light on what is going on with individual articles, but there are some challenges ahead. How will tenure committees analyze this stuff? (Will they bother?) What does it mean if your article was only downloaded 300 times but your colleague (in a larger discipline like genetics) had an article downloaded 3000 times? And all of this data they are collecting can lead to lots of analysis. Librarians have traditionally used citation analysis as a way of understanding the literature of a community, and hopefully these new metrics will give them more tools to use.

communication, information literacy

ScienceOnline 2010

This weekend I am in the Raleigh-Durham area for the Science Online 2010 conference.

The ScienceOnline 2010 conference is a collection of science writers, bloggers and researchers gathered to discuss the dissemination of scientific information in all its forms online. Of course, I think one could make the argument that almost all scientific communication is now online. How many scientific publications aren’t available online? None come to mind.

More specifically, topics at the conference relate to some of the new forms of communicating science (to the public and among scientists) – blogs, twitter, new forms of scientific journals, software applications and more.

I spend a large part of my time at work teaching undergraduate students about how scientists communicate with each other – teaching them to tell the difference between news stories aimed at the general public and scientific articles, teaching them how a review article is different than a primary research article.

One of the things I struggle with is how we teach students to deal with the new and exciting changes that are developing in science communication. How can students evaluate a comment on a journal article over at PLoS ONE? How can they locate a journal article that is available free in an institutional repository but not on the publishers web site? Where does a blog post about a primary research article (like those at ResearchBlogging.org) fit in with news articles, primary research articles or review articles?

So far I have only attended one workshop and the opening keynote address, both of which have been excellent. This conference is a great opportunity to discuss some of these issues with other folks who are thinking about the same things – I’m really looking forward to the sessions over the weekend.

information literacy, undergraduate

Adding value to a basic journal article PDF

Publishing journal articles online opens up a wide variety of options: hyperlinking references, including video and audio, archiving data along with the article, etc. (You can see some ideas about future scientific articles from Elsevier and Cell here). Most of these options are not normally exercised, and most users still view journal articles as online PDF’s, which they then either save or print.

Sometimes these PDF’s including an often annoying page at the front or back re-stating copyright information or indicating that the material was downloaded through a particular institutions subscription.

Just today, I downloaded an article from an August issue of Science and was pleasantly surprised that this ‘cover page’ actually included some useful information. In addition to providing the normal article metadata, the links provided may actually be useful, at least to those with a subscription.

SciencePDFinfo — Information included on the "cover page" of a recently downloaded article from Science.

I especially noted the first item in the list of links informing readers that there had been a correction (in this case a relatively minor correction to a figure), and links to articles cited by this paper, including those articles available for free.

I wondered if a similar method was used when a paper was retracted. A brief search turned up the PDF of a retracted paper published in 2006 and retracted in 2007. Across the first page of the article in red letters was printed:

Retracted

At the end of the PDF of the 2006 article was the text of the “Editorial Expression of Concern” published 7 months later, and the official retraction of the paper published 9 months after that.

So here, in one PDF document, we have the history of this paper.

This is vital for the undergraduate students I serve. Without this, a student would have no idea that an article had been retracted for any reason. This is just one more tool to help novice scientists get into the world of their scientific disciplines.

chemistry, information literacy, undergraduate

My own personal “Chemistry Week”

The image "Chemoluminescence" is courtesy of Flickr user "everyone's idle"

The official, American Chemical Society “Chemistry Week” was last week, October 18-24th. Lots of exciting events took place in lots of wonderful locations.

But this week, October 26-30, is my own personal Chemistry Week. This week, I will teach 4 two hour information literacy sessions to organic chemistry students, provide the lesson plan and all in-class content for three additional sections of organic chemistry, and teach a session on evaluating resources and expanding your literature search to senior seminar students.

I recently gave a presentation about what types of things we talk about at the various levels. I enjoy teaching theses sessions, and I believe they are useful to the students.

This year I’m trying to focus on assessment – are the students actually learning what we want them to learn? Do they already know it before our session? Do they think the sessions are useful?

Each student in the organic lab is completing a brief follow up survey, so we can get a sense of how useful the session is and whether the students actually learned what we wanted to teach them. For this follow up survey we are asking a few questions about learning outcomes, plus a couple of attitudinal questions.

In the upper level seminar, students are filling out a brief survey about their previous research experiences, to give me a sense of their comfort level with certain resources (Scopus or SciFinder) and to allow them the opportunity to ask any research questions prior to our session (I’m not anticipating that they will have many). While students are normally not very good at assessing their own weaknesses, this will give us some information about student attitudes toward research.

I’m excited about seeing the result – hopefully they will allow the chemistry faculty and I to continue to improve the way we teach about the chemical literature and literature searching.

projects

I really like my job

smiley face stickers courtesy of Flickr user South Carolinas Northern Kingdom — smiley face stickers courtesy of Flickr user "South Carolina's Northern Kingdom"

I enjoy searching for information – tracking down obscure citations and rejoicing over finding a related article in a different field. I love a search that goes from online resources to older print materials and back again.

I was asked recently to work with a faculty member to do a literature review for a journal manuscript in science education, and I have been having a lot of fun tracking things down.

I had a starting place – a list of preliminary sources and a rough draft of the paper – to guide my work, but it took off in many directions.

So, what techniques have I pursued?

Starting from the preliminary bibliography, I can examine the works cited sections of those papers to find additional relevant material.
In addition, I can use Scopus to track citations forward in time.
Exploring keywords in multiple databases. Like any search, there isn’t just one way to describe the topic we are searching.
Using Google and other specialized search engines to explore the web. There is a lot of science education material on the web that has been posted by various educators.

I was working with a topic I found interesting, in a field I am familiar with, with a faculty member who is nice to work with. It all adds up to job satisfaction.

information literacy, undergraduate

Information Literacy in Upper Level Undergraduate Biology

Over the next couple of weeks, I will be teaching information literacy sessions in three different senior-level undergraduate Biology seminar classes. Although the topics differ, the content that I discuss is fairly similar.

Finding (and understanding) a topic

I don’t discuss this in every class, but in a class where students have (mostly) free range to select a topic, I try to give them some resources that will help them narrow the field.

I point them to relevant science news sites and blogs. ResearchBlogging.org is one of my favorites because it leads the students directly back to the primary literature. I discuss the merits of browsing a journal’s table of contents, and provide them with links to appropriate journals for their field. This is all normally done with an in class exercise that gets them to look at some of these resources. Hopefully they may come away with a topic idea.

Do students appreciate this guidance? I’m not sure.

Review of primary vs. review articles

Most of the faculty I speak with say that their Senior-level students already know the difference between a review article and a primary research article. I find that some students can tell them apart, but the majority can’t identify a review article when they see it. Some students have had information literacy sessions in sophomore and junior level classes where I discuss this in detail (throwing in science news and blogs too) but I don’t see all of our Biology majors, so it is kind of hit-or-miss.

As a result, I normally spend the first 10 minutes of a 50 minute session reviewing the difference between these article types.

I ask students to examine two different articles and for each I ask them:

How is the article organized?
Whose research and experiments are the authors writing about? Their own? Or the research of others?

This isn’t rocket science, and at the senior level, these questions are fairly easy to answer for these students. They just may not have been asked to look at these before.

After we identify the review and primary research articles, we talk about how each of them can be useful.

Can you use either for this particular assignment?
If you can’t use a review article for this assignment, how can it still be useful to you?

Finding appropriate articles

This section is normally the main reason why the faculty member contacted me in the first place. I normally focus on a few basic principles:

Choosing an appropriate resource for the topic you are searching
Selecting appropriate language and terms to use for your search
Understanding the nature of citations and how tracking them forward or backward in time can help you find additional information.

Students sometimes have topics already chosen, sometimes they don’t. The session will involve some hands on time searching an appropriate resource (often Scopus).

And of course, we talk about how to get their hands on the actual full text of an article.

What I don’t spend time on

It may be controversial, but I don’t spend time teaching Boolean logic, unless I have more than one session with the students (and even then I don’t call it by name).

I don’t get into specifics about citing sources unless we have more than one session, although I will recommend the use of Zotero or another citation manager.

I haven’t really talked much about open access, open science or other emerging forces in scientific communication. I do want to find time to work open access into the conversation in the future – perhaps in the bit about how to get the full text.

Is any of this similar or different than what other librarians talk about in upper level biology classes?