Workflow Tools for the Academic Publishing Ecosystem

As digital content accelerates, the pace of literature consumption, discovery tools and work flow technologies play a growing role in the publishing industry and scientific reading. The spectrum of players include authors, publishers, librarians, and the reader. The work flow of reading is changing constantly. In the old days, scientists had to walk two miles in the snow to the medical library to photocopy an article. Then, after reading, they stored the paper copy in large filing cabinets.

Today, literature consumers search PubMed or Ovid and then downloads a PDF of any article that interests them. Or they can read it on the screen. They no longer have to walk through that snow to the library but the library staff works long hours setting up the OpenURL systems that make this work flow happen with a click-and-download system.

The literature consumer can download articles one at a time, can attach them to their EndNote library, or can store them on their hard drive. Now this work flow is changing. There are new technologies in Beta test. And we are bringing you three in this library newsblog. In two of them you can download multiple selected articles with one click and in another you can rent articles for 24 hours for 99 cents.

These new technologies only work with the latest browser versions and require plugins or add-ons.

Finding Full Text using EndNote 13

Using EndNote 13, you can set up the utility called Find Full Text in the EndNote preferences as explained in the above linked blog post. You highlight from 1 to a 1000 references, hit Find Full Text, and after several passes, the PDFs all come in and are linked to your EndNote record. If the journal is not owned by NJH Tucker Library, Endnote downloads a PubMed URL where affilitated users can see if UCDenver owns it.

PubGet

Using PubGet, you can search directly on the PubGet page. If NJH Tucker Library owns the title, you can read the PDF copy of multiple articles, right there on the webpage WITHOUT downloading it. It’s like a preview. Then you can download it if you want. You can sign in and save some keepers. From your keeper list of 15, you click on download PDFs and you can download with one click all those we own or that are open access. There is an interface with PubMed called PaperPlane to download multiple articles from search results.

DeepDyve

Using DeepDyve, you can rent an article and read its full-text for up to 24 hours for as little as $0.99! These articles can only be viewed at DeepDyve and cannot be downloaded, printed or shared. You can preview the first page before you rent. There a link to download from the publisher which you can try before you rent if you think it’s owned by NJH Tucker Library or open access.

Both PubGet and DeepDyve use search engine type searching returning thousands of results. Both are in Beta and don’t always work. PubGet is quirky on the Mac and will not work with Windows IE v.6.

See other blog posts for details on these three work flow technologies.

EndNote X3 – Finding Full Text

This works best with EndNote libraries where the citations have been downloaded from PubMed or Ovid. If manually entered or edited, the appropriate system connections often cannot be made.

Set up your Endnote Preferences

(found under the EndNote X3 menu)

[To use this system, you must enable Web browser cookies. If you have not consciously disabled them, they are probably enabled.]

Set your Display Fields choices:

From the EndNote X3 menu –> Preferences –> Display Fields

Rearrange your display fields so you can see that you have a filed attachment.

Suggested arrangement:

Add Access to Your Institution’s Library

Tucker Medical Library has a system to make journal articles accessible with an OpenURL Path. This is the OpenURL web address to the Tucker online library. It is where EndNote will be directed to search for matching references.

You need the appropriate OpenURL path for EndNote 13. It is:

http://bl7ur7bu2p.search.serialssolutions.com/

From the Endnote X3 menu –> Preferences –> Find Full Text

• Enter  this URL in the OpenURL path box
• Check:
  • DOI
  • PubMed
  • OpenURL
• Uncheck ISI web of Knowledge
• Save

To find and retrieve full text:

1. Select the reference(s) to which you want to add full text.
2. In the library window, you can highlight up to 1000 references. For example, you can select a single reference, or hold down the Command or control key to highlight individual references, or use Edit –> Select All to select an entire Group of displayed references. Or, open an individual reference for editing.
3. From the References menu, select Find Full Text –> Find Full Text. (Using a Windows machine, if you have a reference open, you can use the right-click contextual menu to select Find Full Text.)
4. EndNote begins searching for and downloading full text for the selected references. Full text downloading happens in the background, which may affect the performance of other operations.
5. To the lower left, you will see the Find Full Text reporting area where it will tell you that it is searching, has found or not found the PDF or has found a URL. Click on any of these menus and you will retrieve the number of articles indicated. Tucker Library may own the article even though Endnote did not find it.
6. This system will not work for accessing remotely the holding of the University of Colorado Denver Health Sciences Library because they do not use a true proxy system.
7. EndNote does find the URL of journals that are online but not owned by NJH Tucker Library. Using the PubMed URL, you can go to PubMed and find the articles. To see the FindIt! icon, you need to follow these steps:
   1. Open a new browser window or tab
   2. Go to the Tucker Library Website and click on PubMed to activate the specialized URL in this browser.
   3. Go back to you citation and reload the page. The NJH FindIt! Icon will appear.
   4. Use it to get the article from UCDenver if affiliated, or from interlibrary loan.

To attach a file manually

If you have a full text copy of any remaining articles that did not get the Full Text this way, you can link this copy to its record manually.

1. Place your cursor in the File Attachments field
2. Use Menu: References –> File Attachments –> Attach File
3. Browse and locate your file
4. You can attach more than one file

PubGet – Read before you download.

National Jewish Health Tucker Medical Library has recently teamed up with Pubget to give you another access point to the millions of biomedical articles. Instead of search results linking to papers, such as you find in PubMed or Ovid, with Pubget, the search results are the papers, if the NJH Tucker Library owns them. You can preview them without downloading them, or save, manage, and share them—all online. You can also download and save multiple PDFs with one click.

Pubget was created in 2007 by a research scientist at Harvard, who was frustrated with how long it took to get to journal PDFs. Now this free tool serves over 100,000 scientists at over 150 schools around the world –and now National Jewish has joined the group.

Features to try:

• Perform advanced searches in PubGet using any PubMed or Google Scholar field tag. This page explains the search commands: http://pubget.com/site/help/use.
• Turn any search into an RSS feed and keep updated via your favorite reader. Just click on the RSS icon.
• Customize your “Latest Issues” and keep up on the contents of the latest journal issues every time you log in.
• Keep your lab’s published works up to date. Search with your name add the Pubget Widget to your lab page or blog (with a little HTML knowledge!): http://pubget.com/widgetizer/create
• Download the Firefox Plugin so you can download papers in bulk: http://pubget.com/site/help/firefox_extension
• Use the tool, PaperPlane, to get access to multiple PDFs in PubGet when you are searching in PubMed.
• Get a list of PMIDs, separate them with commas and paste them in the search bar.

Pubget is free of charge to users at National Jewish Health. Learn more about getting started here (link to video) or just start searching now at:

http://njhealth.pubget.com.

This is a beta test version and already bugs have been found when using with the Mac. It is supposed to be compatible with Macs and Windows. It is also not compatible with versions of I.E. (6 and back).

Help screens can be found at:
http://pubget.com/site/help/

DeepDyve. Research. Rent. Read.

DeepDyve is an online rental service for scientific, technical and medical research with over 30 million articles from thousands of authoritative journals. The DeepDyve user can rent an article and read its full-text for up to 24 hours for as little as $0.99. These articles can only be viewed at DeepDyve and cannot be downloaded, printed or shared. The user also has the option of choosing the Silver or Gold monthly plans. These plans provide even greater flexibility by allowing you to easily rent more articles per month, for longer periods of time.

DeepDyve has aggregated millions of articles from leading, peer-reviewed journals that are often hard to find using other search engines. Their KeyPhrase search technology could be considered a new technology. No need to find the right two or three words to express what you want. You can copy a sentence, paragraph or even an entire document to find all the related articles without a lot of extraneous results. You’ll be able to read the first page of any article to get an overview of what’s inside.

Some of the articles in DeepDyve are “open-access” and marked as “Free” for any user to read. “Premium” articles, that often have an annual subscription or pay-per-view fee, can conveniently be rented from DeepDyve. When you find a Premium article, simply click on the rental button. “Rent” a Premium article for $0.99.

Every article in the results list indicates whether the article is Free, Preview Only, or for Rent for $0.99. By clicking on the title you are taken to a page where you can download the free articles, see the preview, or rent the article. All of these choices also have a link to see the “Original Article on Publisher’s Site.” If NJH Tucker Library owns the article, you will be able to get the article downloaded. It is recommended to always try this link before renting. If a publisher charge window comes up at the publisher’s site, affiliated users can still take that information to UCDenver HSLibrary Find Journals page and see if they own it. NJ Staff can get the article on interlibrary loan for $5.

The user can subscribe to one of DeepDyve’s monthly plans. If you’re an active reader or want the convenience and peace of mind of renting many articles without having a 24 hour expiration period, then you can consider one of the following plans:

• Silver Plan:
  • $9.99 per month Rent up to 20 articles per month
  • Articles are viewable for up to 7 days
• Gold Plan:
  • $19.99 per month Rent an unlimited number of articles per month
  • Articles are viewable for an unlimited amount of time

First time users will be asked to set up a DeepDyve account when choosing to rent for the first time. After completing a few quick steps, you will have rented the article. Read the article as often as you like for the next 24 hours. Because you are renting the article, as opposed to purchasing (you or the Tucker Library) and downloading it, you can only view the article from DeepDyve’s website. Some of DeepDyve’s articles are “Preview Only.” DeepDyve does not currently have permission from the publisher to rent these articles.

Other features of the DeepDyve site include:

• Get personalized suggestions on your MyDeepDyve home page. Using the Settings feature located at the upper-right portion of the screen, you can add or update the words or phrases that describe the Topics that interest you. DeepDyve will then automatically update your MyDeepDyve page each day with suggested articles based on your topic descriptions.
• Copy entire sentences, paragraphs, and even complete articles as your query. No need to come up with the perfect 2-3 words. Simply paste an interesting article into the search bar and click search.
• Find related information for every article by clicking the “More Like This” button on the search results page or any article page.
• Bookmark and save your favorite articles. They will then be displayed on your MyDeepDyve home page for easy access.
• Receive Email or RSS Alerts. From your search results screen, you can click Email Alerts or RSS Alerts. Your search query will automatically run in the background and deliver new results to you each day at your preferred destination.

E-Books at the Tucker Library – MD Consult and Stat!Ref

All E-Books are cataloged in the Impulse Catalog.

These books are on MD Consult unless noted for Stat!Ref or Ovid.

There are over 40 books on the PubMed/NCBI Bookshelf. They are also in the Impulse Catalog.

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Allergy, Asthma & Immunology

 

• Adkinson: Middleton’s Allergy, 7th ed. – 2008

Alternative Medicine

 

• Rakel: Integrative Medicine, 2nd ed. – 2007

Anesthesiology & Pain Management

 

• Miller: Miller’s Anesthesia, 7th ed. – 2009
• Walsh: Palliative Medicine, 1st ed. – 2008

Cardiology

 

• Goldberger: Clinical Electrocardiography, 7th ed. – 2006
• Libby: Braunwald’s Heart Disease, 8th ed. – 2007
• Park: Pediatric Cardiology for Practitioners, 5th ed. – 2008

Consumer Health

• AAFP Conditions A to Z – (Updated periodically) – (Stat!Ref)

Dermatology

 

• Habif: Clinical Dermatology, 4th ed. – 2004

Dictionaries and Calculators

• Jablonski’s Dictionary of Medical Acronyms & Abbreviations – 6th Ed. – (2009) – (Stat!Ref)
• Stedman’s Dictionary- (Updated periodically) – (Stat!Ref)
• MedCalc3000- (Updated periodically) – (Stat!Ref)

Emergency Medicine

 

• Auerbach: Wilderness Medicine, 5th ed. – 2007
• Marx: Rosen’s Emergency Medicine, 7th ed. – 2009
• Roberts: Clinical Procedures in Emergency Medicine, 5th ed. – 2009
• Shannon: Haddad and Winchester’s Clinical Management of Poisoning and Drug Overdose, 4th ed. – 2007

Endocrinology & Metabolism

 

• Kronenberg: Williams Textbook of Endocrinology, 11th ed. – 2008

Family Medicine

 

• Ferri: Ferri’s Clinical Advisor 2010, 1st ed. – 2009
• Rakel: Textbook of Family Medicine, 7th ed. – 2007

Gastroenterology

 

• Feldman: Sleisenger & Fordtran’s Gastrointestinal and Liver Disease, 8th ed. – 2006

Geriatric Medicine

 

• Duthie: Practice of Geriatrics, 4th ed. – 2007

Hematology

 

• Hoffman: Hematology, 5th ed. – 2008

Infectious Disease

 

• Cohen & Powderly: Infectious Diseases, 2nd ed. – 2004
• Gershon: Krugman’s Infectious Diseases of Children, 11th ed. – 2004
• Long: Principles and Practice of Pediatric Infectious Diseases, 3rd ed – 2008
• Mandell: Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 7th ed. – 2009

Internal Medicine

 

• Ferri: Ferri’s Clinical Advisor 2010, 1st ed. – 2009
• Ferri: Practical Guide to the Care of the Medical Patient, 7th ed.
• Goldman: Cecil Medicine, 23rd ed. – 2007 – Saunders, An Imprint of Elsevier
• Piccini & Nilsson: The Osler Medical Handbook, 2nd ed. – 2006
• Rakel & Bope: Conn’s Current Therapy 2009, 1st ed. – 2008

Nephrology

 

• Brenner: Brenner and Rector’s The Kidney, 8th ed. – 2007

Neurology

 

• Goetz: Textbook of Clinical Neurology, 3rd ed. – 2007

Nursing

• DeGowin’s Diagnostic Examination – 9th Ed. – (2009) – (Stat!Ref) 
• Kozier & Erb’s Fundamentals of Nursing: Concepts, Process, and Practice – 8th Ed. – (2008) – (Stat!Ref)
• Lippincott Manual of Nursing Practice – 9th Ed. – (2009) – (Ovid)

Obstetrics & Gynecology

 

• Gabbe: Obstetrics, 5th ed. – 2007 – Churchill Livingstone, An Imprint of Elsevier
• Katz: Comprehensive Gynecology, 5th ed. – 2007

Oncology

 

• Abeloff: Abeloff’s Clinical Oncology, 4th ed. – 2008

Ophthalmology

 

• Yanoff & Duker: Ophthalmology, 3rd ed. – 2008

Orthopedic Surgery

 

• Browner: Skeletal Trauma, 4th ed. – 2008
• Canale & Beaty: Campbell’s Operative Orthopaedics, 11th ed. – 2007
• DeLee: DeLee and Drez’s Orthopaedic Sports Medicine, 3rd ed. – 2009
• Green & Swiontkowski: Skeletal Trauma in Children, 4th ed. – 2008

Otolaryngology

 

• Cummings: Otolaryngology, 4th ed. – 2005

Pathology

 

• Kumar: Robbins and Cotran Pathologic Basis of Disease, Professional Edition, 8th ed. – 2009
• McPherson & Pincus: Henry’s Clinical Diagnosis and Management by Laboratory Methods, 21st ed. – 2006

Pediatrics

 

• Johns Hopkins: The Harriet Lane Handbook, 18th ed. – 2008
• Kliegman: Nelson Textbook of Pediatrics, 18th ed. – 2007

Pharmacology

• Goodman & Gilman’s The Pharmacological Basis of Therapeutics – 11th Ed. – (2006) – (Stat!Ref)

Physical Medicine & Rehabilitation

 

• Frontera: Essentials of Physical Medicine and Rehabilitation, 2nd ed. – 2008

Psychiatry

 

• Jacobson: Psychiatric Secrets, 2nd ed. – 2001
• Stern: Massachusetts General Hospital Comprehensive Clinical Psychiatry, 1st ed. – 2008

Pulmonary Medicine

 

• Mason: Murray & Nadel’s Textbook of Respiratory Medicine, 4th ed. – 2005
• Taussig: Pediatric Respiratory Medicine, 2nd ed. – 2008

Radiology

 

• Adam: Grainger & Allison’s Diagnostic Radiology, 5th ed. – 2008
• Mettler: Essentials of Radiology, 2nd ed. – 2005

Rheumatology

 

• Firestein: Kelley’s Textbook of Rheumatology, 8th ed. – 2008

Sleep Medicine

 

• Chokroverty: Sleep Disorders Medicine, 3rd ed. – 2009
• Kryger: Principles and Practice of Sleep Medicine, 4th ed.

Surgery, General

 

• Khatri: Operative Surgery Manual, 1st ed. – 2003
• Townsend: Sabiston Textbook of Surgery, 18th ed. – 2007

Urology

• Wein: Campbell-Walsh Urology, 9th ed. – 2007