Engineering & Mathematics Notebook

Monday, 12 July 2010

Fun with Journal Table of Contents (TOCs)

With print serials, a classic way to keep up with new journal content is to skim the Table of Contents (TOC) of a journal issue. This form of serendipitous browsing not only provides an overview of current content but can lead to unexpected discoveries. It is limited, however, since you can only scan one TOC at a time and you need access to the print publication to do so. As journals have migrated to digital formats, however, the static TOC has become dynamic and STM publishers provide various ways to present them. These modes of distribution not only facilitate access bu offer new ways to present the information embedded in TOCs.

A classic way to get digital TOCs is by signing up for email alerts. You then receive periodic listings of TOCs for one or more serials with hyperlinks which typically go to the journals’ home pages. Nearly all the major publishers – Nature Publishing Group (NPG), American Chemical Society (ACS), and IEEE are just a few examples – provide email alerts, sometimes with the ability to customize them to fit particular search queries.

Email alerts for TOCs are handy but if you don’t want this sort of content filling up your mailbox, you can sign up for RSS feeds of TOCs and then browse them at your leisure in a feed readers such as Google Reader or Bloglines. These generally free tools enable you to organize your RSS feeds into folders by topics, publications, and other facets and provide an efficient means of scanning multiple TOCs at all once. You can also pick up feeds in some email programs and via mobile devices. In addition, you can embed RSS widgets into web pages, blogs, and other Web 2.0 media. Tools like Yahoo Pipes lets you to combine feeds from multiple publications (the sample linked from here combines feeds from three journals focusing on nanotechnolog).

A useful tool for identifying TOC alerts in your target subjects is provided by the Joint Information Systems Committee (JISC) of the U.K. Its complimentary Journal Table of Contents Service has compiled TOC feeds for thousands of scholarly journals. You can screen for these TOCs by title, subject, and publisher, then select the journals that interest you, and view the feeds for their TOCs; clicking on an entry will take you to the journal’s site, and if they are in the Tufts collection or are open access, you can view the full text. You also export your selections as an OPML (Outline Processor Markup Language) file, which is an XML-based format for exporting and importing RSS feeds to and from feed readers. A recent subject search on engineering retrieved feeds for 765 titles divided into 10 major categories as defined by Ulrich’s Periodicals Directory; many of these titles are the top journals in their respective fields and are available in the Tufts collection. JISC also provides an option to set up an account so that you can save your TOCs and view them from within the JISC portal rather than through a feed reader.

Another notable aspect of the migration of TOCs to the digital world concerns the use of multimedia. Print journals in the biology and chemistry realm in particular are noteworthy for including images and pictograms in their TOCs – for scientists focusing on a particular structure, this provides for faster and more meaninful scanning than text might provide. The online variants of TOCs can take this further by providing TOC images as slide shows or 3D animations, as evidenced by, for example, the TOC of ACS Chemical Biology.

The examples listed above are just a sampling of how TOCs can become a useful research tool and as publishers of STM journals work with new web-based technologies, more applications will doubtless emerge.

Posted in Research Tools

Friday, 04 June 2010

Keeping up with the News: Google Scholar Alerts

Last month, Google Scholar introduced a new feature to help researchers keep up with new additions to the vast realm of sources which Scholar indexes: Google Alerts. The Alerts feature enables you to specify search criteria and then receive emails each time an item is added to Google Scholar which meets your search criteria. This feature is analogous to email alerts offered by other literature citation databases and helps compensate for the fact that Google Scholar doesn’t (yet) offer RSS feeds.

The process for creating an alert is simple: execute a search in either the default Google Scholar basic search box or in the Advanced Search screen. In the results list, click the envelope icon in the Scholar selection bar. In the Alerts screen which appears, modify the alert query as required, enter an email address, specify whether you want 10 or 20 results, and then click the Create Alert button. You will receive an email containing links to new Scholar entries matching your search criteria as they are received. You can specify as many alerts as you like and you don’t need to set up an account or submit personal information to do so.

As with all literature databases, the trick for developing effective searches alerts is to apply words or phrases which are neither too broad (resulting in an overwhelming, possibly meaningless set of alerts) or too narrow (causing key items to be overlooked). Google Scholar does not offer the extensive "under the hood control" that some other databases do, but you can use the Advanced Search options to refine your criteria. At present, not all Advanced Search criteria seems applicable for alerts but you can try, for example, restricting search results only to sources coded for specific disciplines or authors. Note that date ranges are not meaningful for search alerts, in part because many sources which Google Scholar tracks do not contain meaningful metadata about publication dates, but also the intent of the alerts is to highlight new content in Google Scholar, not screen for particular publication dates.

More detailed instructions for setting up Google Alerts are available from the Google Scholar website. These include guidelines for creating alerts for articles which cite a particular work that you are interested in.

The items listed in the alerts you receive from Google Scholar may display a "Get This Item at Tufts" link. Such links indicate that Tufts subscribes to the journal listed in the citation; clicking on them will provide access to the article’s full text for any Tufts affiliate. This feature can be initiated through the Google Scholar Preferences screen, where you can set links to a maximum of three libraries (including WorldCat and the NIH Library).

Posted in Research Tools

Friday, 14 May 2010

Tufts SOE intitiates blog on engineering opportunities

The Tufts School of Engineering (SOE) has set up a new blog to track the myriad of opportunities available to SOE researchers. Titled Research News, Event, Opportunities for Tufts SoE, the blog will include notifications of research opportunities as well as seminars, thesis defenses, proposal wins, and other SoE research-related news. This is a great tool for keeping abreast of current and potential research activity at the school.
The blog’s address is http://sites.tufts.edu/soeadr/. As with most blogs, the entries are also available as RSS feeds and the feed address is http://sites.tufts.edu/soeadr/feed/

Posted in Research Tools

Monday, 11 January 2010

Collections Spotlight: Reaxys Chemistry Database

This past year, the Tufts Library collections added a new entry to its set of chemistry databases: Reaxys.

Owned by Elsevier (publishers of Engineering Village, Scopus, and ScienceDirect, among others), Reaxys provides information on compounds, going back to 1771 for articles and 1876 for patents. It is based on the combined content of CrossFire Beilstein (organic chemistry), CrossFire Gmelin (inorganic and organometallic compounds), and the Patent Chemistry Database (PCD) as well as additional pharmacological, ecological and toxicological data. Searches can be done on substances, reactions, and citations (including patents) as well as by drawing chemical structures.

Reaxys differs from other databases not merely in its content, but also its focus, which is to support the chemistry-related R&D workflow. This focus is reflected in the database’s interface, which merges all search results about a compound or a reaction into a single record which displays substances, reactions, and citations as well as direct links to the full-text of articles (where available through Tufts’ subscriptions) and patents and descriptions of experimental procedures.

Reaxys also includes a “synthesis planner” for evaluating alternative synthetic routes and the ability to identify and combine reaction steps to develop an effective synthetic strategy. Search queries can be based on either reactions or bibliographic information and custom searches based on 9 types of data fields can be built and saved for future use. Search results can be exported in various formats and links are provided to eMolecules, which provides information on commercial suppliers of substances.

Posted in Chemical & Biological Engineering, Collections News, Engineering, Research Tools

Sunday, 01 November 2009

Pubget: A handy tool for getting PDFs from PubMed

PubMed is the most prominent of the various interfaces for MedLine, the Biomedical literature database published by the National Library of Medicine.  It is an index, not a full-text database. It does provide links to selected full text of articles in PubMed Central and Tufts users can access a customized version that highlights and links to the full text of articles in journals to which we subscribe.  However, you usually have to make multiple clicks to retrieve an Acrobat PDF version of an article.

A work-around for this is a website called Pubget. Although ostensibly in beta mode, Pubget already is a pretty effective tool for grabbing PDFs right from a set of search results within the Pubget interface. By default, it only retrieves PDFs from open access journals but Tufts affiliates can use the “Activate an Institution” feature to access PDFs from journals to which the University subscribes.  The PDF appears in full Acrobat glory within the Pubget window and permits the usual Acrobat functions, such as printing, saving, and emailing the visible file.

Other handy features include a utility to download PDFs in bulk; the ability to download citations for use in bibliographic managers such as EndNote, RefWorks, and Zotero; and links to “related” papers, the original PubMed abstract, and the publisher’s website.  Setting up a personal account enables you to store favorites and get alerts.  An Advanced Search feature permits article screening by PubMed ID, MESH term, chemical, and other facets.

Posted in Research Tools

Tuesday, 13 October 2009

PubMed Rapid Research Notes (RRN)

PubMed recently introduced Rapid Research Notes (RRN), to provide “permanent access to research shared through online forums designed for immediate communication.” These notes will consist of collections focusing on key topics of current conern. At present, the collection consists of Currents Influenza, which are entries from the Public Library of Science (PLoS) on the current influenza pandemic, but more topics will be added. Potential Tufts SOE audiences for the current set include Biomedical Engineering and Public Health.

Posted in Research Tools

Monday, 07 September 2009

Trend Watch: Visualization in Scholarly Applications

Publishers in the Science/Technology/Medical (STM) disciplines aren’t content to focus on optimizing text-based content and search engines in online databases. A growing number of these companies now offer visualization tools to enhance discovery.

Among the pioneers in this area are the various web sites which enable users to draw and search on chemical structures or to view existing structures in manipulable 3D models. These features are available in tools such as ChemSpider (acquired by the Royal Society of Chemistry this past spring); the Structure and Property Search feature available in the CRC Handbook of Chemistry and Physics; SciFinder from CSA; PubChem; and Molecule of the Month; to name a few  (Many of these sites used common visual engines, such as the Java-based JMOL, for 3D display of molecular images).

Another entrant is Illustrata, from Cambridge Scientific Abstracts (CSA).  Introduced in 2007, Illustrata offers “deep indexing” databases of images – including tables, charts, figures, graphs – contained within the articles and other materials that CSA indexes.  You can search on the types of images you’re interested in, then view thumbnails of the results displayed in the context of the article’s abstract and other citation details.  According to CSA, beta-testers for Illustrata found the ability to search for and view  images resulted in more precise search results, clearer understanding of the resources they were viewing, and opportunities for comparative analysis as well as inspiration for the design and presentation of their own graphics.

Earlier this year, Nature started offering 3D interactive images in the Acrobat PDF versions of some of its articles.  These images can be rotated and zoomed in or out upon, and displayed with various layers of information and graphics toggled on or off (Versions 9 and above of Acrobat Reader are required to use these tools).

And everywhere we look, Google or Yahoo maps and other geospatial engines are being used offer insights into the geography of research.  Springer’s Authormapper shows the geographic location of its authors (at least of the time of publication) in an interactive Google map (this seems like a handy tool for planning a research trip or sabbatical!). Researcher ID (previously described here) from ISI Web of Science has a similar interface for its authors within its “testing labs.”

Visualization tools are cropping up in all academic disciplines, from geology to medicine. In Tufts’ own backyard, VUE (Visual Understanding Environment) is a interdisciplinary tool for creating concept maps. The Boston Subsurface Project, developed by the Tufts Civil and Environmental Engineering Department, uses a GIS interface to highlight the relationship between the City of Boston’s soils and its history. Such projects are exemplify the statement that pictures tell a thousand stories and, as such, offer new opportunities for discovery and analysis.

Posted in Research Tools, Trend Watch

Saturday, 22 August 2009

Keeping Track of Chemical Compounds

CAS, the American Chemical Society’s division that produces the CAS registry, just announced that on September 7 it expects to register the 50 millionth unique chemical substance. Only last November, CAS registered its 40 millionth substance (a derivative of azulenobenzofuran). Per CAS, it registered its 10 millionth compound in 1990, after 33 years, and now registers approximately 12,000 new substances daily.  That means that, at the current exponential rate of registry additions, we could be celebrating the 60 millionth substance by the start of 2010.

With such an explosion – figuratively speaking – of new substance registrations, having effective systems for identifying, tracking and them becomes critical in order to facilitate research. The CAS Registry Number System is among the most prominent such systems for chemicals substances. PubChem, from the National Institutes of Health, has its own Chemical ID number system as does International Union of Pure and Applied Chemistry (IUPAC), which helped to develop the International Chemical Identifier (InChI) system. Unlike the CAS system, the PubChem and IUPAC systems are non-proprietary. Just last month, IUPAC announced that it has established the InChi Trust to further the development of its open source algorithm so chemical engineers and other chemistry researchers and professionals may expect to see increased InChis alongside the CAS numbers and the prospect of interesting ways to link substances using these unique identifiers.

Posted in Chemical & Biological Engineering, Engineering, Research Tools

Saturday, 22 August 2009

Knovel Enhances Its Interface

Knovel, the collection of Engineering technical books that Tufts provides, has just updated its interface. Enhancements include:

• Term suggestions (“Did you mean?”) if you misspelled a search term while performing a search.
• Autocompletion of terms that you start typing into
  the Knovel search box.
• The option to add the Knovel Search Engine to your web browser toolbar.
• Search lists displayed in collapsible lists, with the relevant sections of the top most relevant titles highlighted. The pertinent PDFs or interactive tables and charts are now one click away.
• G.E.T. (Graphs Equations Tables) Search, an enhanced version of Knovel’s previous search tool for retrieving data from interactive graphs, equations and tables. A pull-down menu shows all the search fields, organized by major categories, from acid-base properties to volatility. Multiple search statements can be combined and the resulting data can be sorted, filtered, and extracted to other formats, such as Excel, ASCII, and HTML.

Posted in Engineering, Research Tools