Databases

Searching PubMed Programmatically

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Earlier this semester, we taught a workshop on how to use the NCBI Entrez Direct (EDirect) [1] tool to search and compile PubMed and related data from a Unix Shell. EDirect is a great tool and has an approachable learning curve. You may consider using EDirect if, for example, you would like to compile custom bibliographic datasets, perform many searches, or discover related linked data.

All of our workshop materials including code and slides are openly available on GitHub:

https://github.com/vfscalfani/EDirectChemInfo

Check it out and let us know if you have any questions. We would be happy to help you.

[1] https://www.ncbi.nlm.nih.gov/books/NBK179288/

Chemical & Engineering Data and Mathematical Functions available from NIST

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The National Institute of Standards and Technology (NIST) provides public access to a multitude of compiled chemical and engineering experimental and computational data (https://www.nist.gov/data). Much of the data available from NIST is critically evaluated and extracted from the primary literature; however, there is also unique data available, collected at NIST facilities. For example, NIST obtained the Radionuclide Half-Life Measurements.

To browse a full list of these specialized NIST data resources, we recommend using the NIST Data Gateway: https://srdata.nist.gov/gateway/gateway?dblist=0.

Within the NIST Data Gateway, you will see a full list of data available from NIST, such as the Atomic Spectra Database, Chemistry WebBook, Ionic Liquids Database, and Property Data Summaries for Advanced Materials. There are also useful Mathematics resources like the NIST Digital Library of Mathematical Functions and Guide to Available Mathematical Software. These mathematics resources contain an index of mathematical functions along with an index of software than can compute mathematical functions.

So, check out the NIST Data Gateway, and let us know if you need help navigating any of the NIST resources!

Clarivate Analytics Web of Science and Publons

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If you are a Web of Science user, you may have noticed the addition of a Publons tab near the top of the Web of Science interface. Publons is a platform to track, share, and receive recognition for your peer reviews. The Publons platform integrates into ORCID, which allows you then to populate your ORCID scholarly profile with peer review data. Registration for a Publons account is free and if you have an ORCID, you can register with your ORCID credentials. After creating your Publons profile, peer reviews are added and verified various ways depending on the relationship of the publisher to Publons.  For example, some publishers will send peer-review data directly to Publons in an automated workflow, while other publishers require a manual process such as sending Publons the confirmation e-mail you receive after completing a peer-review.

Here are a couple of Publon profiles from faculty members at The University of Alabama:

https://publons.com/author/195591/ian-m-mcdonough#profile

https://publons.com/author/1231001/laura-morett#profile

The review information displayed on the Publon profile varies by publisher. Some publishers allow the actual text of the review to be publicly displayed such as PLOS One, while others like RSC Advances only allow the Journal title to be displayed. You can browse the individual Publon Journal policies here.

Publons is an interesting platform and one certainly worth exploring more as peer review is an activity generally not visible to the public. As more scholars create Publon profiles, we may even start to see integration into information databases.

AHS Download Technique

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The AHS International (The Vertical Flight Technical Society) database is sort of quirky.  When doing a search and seeking to download a paper, a screen pops up and appears to be asking you to BUY the paper.  But there is no cost.  Note the price is $0.00 since UA has a subscription.  Just click on “ADD TO CART” and “START CHECKOUT” next “CONTINUE” and then “COMPLETE ORDER.” A link will appear to the PDF of the paper.

AHS International

Discover a Database- BIOSIS Previews

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BIOSIS Previews contains life science data not indexed by MEDLINE or Scopus and has in-depth coverage of many areas relevant to medical research such as proteomics, gene therapy, psychiatry, biotechnology, biochemistry, experimental medicine etc. BIOSIS Previews combines the content of Biological Abstracts and Biological Abstracts/RRM (Reports, Reviews, Meetings), therefore providing widespread coverage of approximately 5,500 life science journals as well as 1,500 items from review articles, books, proceedings, meeting abstracts, notes, technical letters international meetings, book chapters, software reviews and life science patents. BIOSIS previews is restricted to the University of Alabama faculty, students and staff, and it covers  publications from 1926 to the present with weekly updates It is not included in Scout. A tutorial for BIOSIS Previews is available here.  BIOSIS previews may be worth a look as an addition to your usual sources.

Millions of books for Learning, Instruction and Research

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What is WorldCat? It is a huge database that lists over 179 million records held in over 10,000 libraries worldwide. It includes records that represent 400 languages. The dates of the records covered go as early as 1000 BC to present. WorldCat is updated daily. WorldCat is a powerful tool, and a great time saver for the researchers. One search can look at over 10,000 libraries at once.

 

What things are listed on WorldCat? Some of the things that are listed are books, film, newspapers, manuscripts, maps, video and audio recordings, microfilm, websites and internet resources.

 

How do I search WorldCat?  One can search by keyword, title, author or subject. You can further filter results by publication year, language, author or type of publication. The advanced search allows you to search with three different search fields by combining subject, title, author, keyword or ISBN. You can also limit your search to your specific institution’s library. After searching, WorldCat provides a list of resources that match your search query.

 

From The University of Alabama Libraries’ website: 

  • Under Research Tools, Click on Databases
  • Click on “W”
  • Select WorldCat. Remote access requires authentication. MyBama Id and Password is required.
  • From there you can perform a basic search or an Advanced Search. The advanced search allows you to limit your search by language, type of item, (book, Internet, article, etc), date of publication etc. If you do not select any item the default search will look at all the items.

Search Results: After all the results for books are shown one can click on the title for a more detailed information about the item.  The results will also indicate if the UA Libraries has an item. If you click on holding library, you will be taken to the catalog of that particular library where you will find more information about the book.

  • Lastly don’t forget about Interlibrary loan. You can Interlibrary Loan items that UA Libraries do not own
  • Click on link Interlibrary Loan from UA libraries website
  • Log in at ILLiad with your Bama ID and password
  • Fill out ILLiad form and click on “submit”

For more questions: Email a Librarian at Rodgers or Reference by Appointment Or call Arian Abdulla 205-348-2108

ORCID – Get your own Unique Author Identifier

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Have you ever tried to find a specific researcher’s scholarship through a database search? Chances are you have run into some challenges such as discovering multiple Researchers with the same name. One potential way to refine your search would be to limit the results to the Researcher’s Institution. But, what if the Researcher has held positions at multiple Institutions? Multiple search queries and further refinement would be necessary.

One solution to this difficulty of locating a specific Researcher is the use of an ORCID unique author identifier. By using a unique identifier for authors, searching for a specific researcher is straightforward and only requires knowing the author’s identifier. However, this will only work if the researcher has registered for an identifier such as ORCID (www.orcid.org).

Registering for an ORCID identifier is easy and free. Simply register, add your scholarship works, and then use your ORCID identifier. Your ORCID identifier can be used when submitting publications, applying for grants, and on your personal webpages.

The University of Alabama recently became ORCID Institutional members, and so we will have more information about ORCID soon.

However, a few points you may be interested in:

  • Scientific and Engineering databases have already started to add Author Identifiers as a search option (e.g. Web of Science).
  • Several publishers and grant agencies are now requiring an Author Identifier with submission.
  • Importing your scholarship citations and other works into ORCID can be somewhat automated and painless. For example, I was able to export my citations from Google Scholar and then bulk import them into my ORCID Identifier profile.

Here is my ORCID identifier webpage for an example of how your ORCID identifier will appear to the public:

http://orcid.org/0000-0002-7363-531X

We encourage you to check out ORCID at www.orcid.org and get your own unique Author Identifier today!

WorldCat Presentation on Feb. 3

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Rodgers Library will offer a short presentation on access to books for research, instruction, learning, and personal interest – primarily books found in libraries of other universities nationwide.

Where:  Scholars’ Station, Rodgers Library for Science and Engineering

When:  2:00- 2:30 P.M., Wednesday, February 3, 2016

Audience:  For all UA faculty and graduate students

The focus is on Worldcat.  During our presentation, we will share with you important information about the WorldCat database and how to use it in your work.  WorldCat is a master list of books found in most college and university libraries in the United States, plus books in many other libraries such as the Seattle Public Library.

Effective Literature Searching

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Before you can make a successful search, analyze your topic.  Decide:

What are the main concepts?

What are the primary keywords related to each concept?

What alternative keywords or synonyms represent each of these concepts?

Normally, this will involve doing some reading about the topic in a source such as a review article or a textbook. If a review article or textbook is not helpful, a quick online search, may help you develop an initial understanding of the topic. The steps outlined below take you through these initial points and the subsequent steps of a literature search:

Literature Searching Tips:

  1. Select and identify your topic. What is the topic of your research?

Example: Grassland management and butterflies. What aspect of this topic are you particularly interested in? Example: Grassland management and butterfly diversity.

State your topic as a question: Does the way in which grassland are managed have an impact on butterfly diversity?

  1. Find Background Information: Once you have identified the key terms or subjects for your topic, look for them in a textbook, general or subject encyclopedia, or subject glossary.
  2. Deciding which databases to use. The most effective way to search journal articles on a topic is to use a database such as PubMed/Medline, Web of Science, Google Scholar or Scopus.
  3. Develop a search strategy. Develop an initial list of keywords that can be used to research your topic. Search the Scout Catalog and other databases using those keywords. Revise your keywords as needed to broaden or narrow the search. Use Boolean operators (AND, OR and NOT). Boolean operators allow you to combine your search terms in many different combinations. Databases often contain buttons or drop-down menus that allow you to select for Boolean operators.
  4. Refine your search: If your initial search brought up few results try these tips: Try alternative less specific keywords; check spelling, Use OR to include synonyms, and include more database coverage. If you have too many results try: more specific keywords. Use AND to include additional keywords, and use NOT to exclude certain words.
  5. Saving your Search: The databases may have the option to create a personal account that allows you to save a copy of your search. This is strongly recommended. Always save or print the useful articles that you find. In many databases you can export your articles to reference management software such as EndNote.
  6. Managing your information: EndNote helps you to store and manage your references. EndNote is also built into the Microsoft Word. One can automatically insert citations and create a bibliography using this feature. The University of Alabama maintains a site license agreement for EndNote, which provides unlimited licensing for faculty, staff, and students. http://oit.ua.edu/oit/services/software-licensing/endnote/

In summary here are the 5 key tips for effective literature searches:

  1. Make a start with Scout from UA libraries. http://www.lib.ua.edu/#/home  At Scout you can search the library’s collection in print and online, from manuscripts to books to individual and journal articles.
  2. Follow the Literature searching tips as described above.
  3. See resources for your subject areas. These resources are tailored library guides for each discipline to help you find the key databases and information sources that are relevant to your research area.  http://guides.lib.ua.edu/
  4. Get the full text of an article through many of our databases. http://www.lib.ua.edu/#/databases?page=1
  5. Use the Inter-library Loan services if the University of Alabama Libraries do not have any item you need.  https://ua.illiad.oclc.org/illiad/

Created by Arian Abdulla

Latest on Standards

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Standards are a basic tool of scientists and engineers. At Rodgers Library we use SAI Global to find and order individual standards. SAI Global covers standards from many standards organizations, such as ASME and SAE.  Our approach is to order most standards on demand.  However, since ASTM standards are in high demand, we recently subscribed to ASTM Compass.  In the case of SAI Global users can easily search the database, but the library takes care of the download piece.  ASTM Compass is handled differently.  It is delivered to desktops and users can search and download independently.

Tip 9: Research Guides

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Tip 9:   Research Guides.  We have developed a series of simple and convenient guides to get faculty and students started when first using the library.  They’re called LibGuides.   Each guide is built to acquaint you with library resources which are available to support your work.  We have a guide for every major subject area:  geology, nursing, civil engineering, etc.   The guides cover ways to find books, list important databases, identify research tools, and point to key Internet resources.

Go to LibGuides.

Tip 3: Databases

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Tip 3:  Databases.    Databases offer a great way to find information on specific subjects.  It’s often good advice to start a search using a database that matches with a particular discipline, such as the IEEE Digital Library (electrical engineering) or BIOSIS Previews (biology), for example.  General purpose science databases such as the Web of Science or Scopus are great too.  Each database has its own special interface.  While searching a database, you can “click through” to full-text content when available.

Go to full list of databases.

WorldCat and Books

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Books are an important resource in science, engineering, and nursing. Both students and faculty can benefit from content in books.  Books are a great source to learn about a topic or find information for a classroom activity. Books often have content suitable for research activities as well. Whatever the purpose, books are an essential tool for scholarship.

Annually, thousands of sci-tech and nursing books are published by professional associations and commercial publishers.  Many of these books are acquired as print or e-books by Rodgers Library for Science and Engineering. We do not, however, acquire every title that’s published even if there’s a match with UA’s curriculum and research agendas. Still it’s important to remember that nearly all books are acquired by one or more academic libraries in North America.

The good news: Academic libraries in North America share collections and all of us are beneficiaries of this resource sharing. In essence you have access to most of the books owned by other academic libraries. WorldCat is the primary database used to make this happen. WorldCat contains both current and archival books on every subject.  Go to WorldCat database.

Evidence Based Databases – Nursing & Allied Health

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Nursing and Health Sciences Resources available from UA Libraries that addresses ………..

What is Evidence Based?
Which databases cover Evidence based articles?
Who can use the evidence based resources?
What is a systematic review?

The Joanna Briggs Institute’s Evidence Based Practice database of systematic reviews and Cochrane Library are available and they complement each other to investigate the evidenced based literature in the field. UA Libraries now subscribes to both resources.

Joanna Briggs Institute (JBI) on OVID
JBI’s evidence-based practice model is considered a benchmark in the healthcare industry—encouraging healthcare professionals to implement an effective evidence-based practice program to provide the best possible patient care. It provides a detailed searching demonstration of this resource and includes information on the subject based nodes along with a review of the seven different publication types (including Best Practice Information Sheets, Evidence–Based Recommended Practices and Consumer Information Sheets) that can be used immediately to inform treatment and guide practice.

Cochrane Library
Cochrane Collection Plus is the most comprehensive collection of databases from the Cochrane Library. This is an essential source of high quality health care data for providers, patients and those responsible for researching, teaching, funding and administrating at all levels of the medical profession. Cochrane Collection Plus combines the NHS Economic Evaluation Database (NHS EED) and Health Technology Assessments (HTA) with the Cochrane Database of Systematic Reviews (CDSR), Database of Abstracts of Reviews of Effects (DARE) and Cochrane Central Register of Controlled Trials. Systematic reviews are found in two of these databases: the Cochrane Database of Systematic Reviews (CDSR) and the Database of Abstracts of Reviews of Effectiveness (DARE).

Searching for Publications from UA Researchers

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Interested in finding publications from researchers at The University of Alabama?  Try the “Organization-Enhanced” search feature from the Web of Science database. Here are a few recent publications from our very own science and engineering faculty:

Jordon, J. B.; Horstemeyer, M. F., Microstructure-Sensitive Fatigue Modeling of AISI 4140 Steel. Journal of Engineering Materials and Technology-Transactions of the Asme 2014, 136 (2). Read it HERE.

Hirschmann, T. C.; Araujo, P. T.; Muramatsu, H.; Rodriguez-Nieva, J. F.; Seifert, M.; Nielsch, K.; Kim, Y. A.; Dresselhaus, M. S., Role of Intertube Interactions in Double- and Triple-Walled Carbon Nanotubes. Acs Nano 2014, 8 (2), 1330-1341. Read it HERE

Keel, W. C.; Manning, A. M.; Holwerda, B. W.; Lintott, C. J.; Schawinski, K., The Ultraviolet Attenuation Law in Backlit Spiral Galaxies. Astronomical Journal 2014, 147 (2). Read it HERE

Sayler, F. M.; Grano, A. J.; Smatt, J. H.; Linden, M.; Bakker, M. G., Nanocasting of hierarchically porous Co3O4, Co, NiO, Ni, and Ag, monoliths: Impact of processing conditions on fidelity of replication. Microporous Mesoporous Mat. 2014, 184, 141-150. Read it HERE

Google Scholar – The Basics

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Google Scholar is a subset of Google Web Search that supports search for scholarly literature. By searching Google Scholar from the Library’s home page, you will automatically have direct access, both on and off campus, to subscription articles already paid for through UA Libraries.

Features of Google Scholar
• Search all scholarly literature from one convenient place
• Explore related works, citations, authors, and publications
• Locate the complete document through your library or on the web
• Keep up with recent developments in any area of research
• Check who’s citing your publications, create a public author profile

Google Scholar

Master Databases and Learn About Research Tools

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Librarians at Rodgers Library for Science & Engineering are offering spring classes.  Is it that time of the year to start a literature review for your papers/projects? The ability to scan the literature efficiently and identify useful resources is vital.  You can learn how to apply principles of analysis to identify unbiased and valid studies.

The following classes are offered several times during the semester for your convenience:
1. Introduction to Science & Engineering Information Resources
2. Chemical & Biological Information resources
3. Physics & Astronomy Information Resources
4. Mathematics Information Resources
5. Web of Science Database
6. PubMed (Cover Systematic Review, Integrated Literature Review)
7. RefWorks
8. Introduction to Scientific Writing
9. Scientific Presentations
10. 3D Printing Training Session

For questions regarding the classes, contact Vincent F. Scalfani, vfscalfani@ua.edu
If the above classes are not what you are looking for, suggest one or request the one you want and we will be glad to assist. Contact one of the subject specialists at Rodgers anytime:
John Sandy jsandy@ua.edu

Global Plants Details Plant Type Specimens

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Scientific information on plants is useful for a wide range of studies in the life sciences.  Global Plants, offered by JSTOR, is a very helpful tool in this regard.  Global Plants features plant type specimens that are found in about 300 herbaria located around the world.  The role of herbaria is to preserve plant type specimens.  Now, with Global Plants, it is possible to easily and conveniently learn about plants in a wonderful way.  The database contains over two million high-resolution plant type specimens, digitized with great care by various cooperating herbaria. Entries in the database point to reference books and other primary resources. Plant type specimens are very important as “original vouchers of nomenclature,” according to JSTOR.   Source:  Description by JSTOR.  Global Plants is ready for the entire UA community.  

 

MEDLINE Available for Finding Health Science Research

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Recently, UA Libraries subscribed to MEDLINE. The National Library of Medicine (NLM) produces MEDLINE, and NLM provides free access to MEDLINE through PubMed. MEDLINE is also accessed through an interface provided by Ovid, a commercial database vendor.

MEDLINE is an index that is used to find articles published in biomedical journals. MEDLINE covers the journal literature from 1948 to the present. It indexes article citations from over 4,000 medical journals and the entire database consists of over 11 million citations, many with abstracts.

Enhanced features make searching easier and more powerful. Each citation in Ovid indicates whether it can be found in a journal owned by the library. Alerting tools such as AutoAlerts and eTocs are available to keep up with new articles matching the search criteria and tables of contents for new journal issues.

To search Ovid MEDLINE, click on Databases/MEDLINE from the library’s home page. If you would like more information about this database, or if you would like a demonstration of it for a class, contact Mangala Krishnamurthy in Rodgers Library. Contact mkrishna@ua.edu.

Tags: database, Medicine, MeSH, NLM, Nursing

Bio-Rad KnowitAll U Spectra Database

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We are currently running a trial of Bio-Rad’s KnowitAll U Spectra Database until June 28, 2013.

“KnowItAll U provides users with a wide array of chemistry tools and unlimited access to 1.4 million spectra (NMR, IR, Raman, MS, UV-Vis)—the world’s largest collection of spectral data.  Users can access the entire spectral collection via the KnowItAll AnyWare™ web browser interface—a full suite of tools to search, manage, and analyze spectroscopic, chromatographic and chemical information; predict NMR spectra; draw structures; create reports; and more.”

Check it out here:

http://www.lib.ua.edu/databases/trials/dbtrial.htm

And let us know what you think here:

http://www.lib.ua.edu/databases/trials/dbtfeedback.htm