Searching PubMed Programmatically

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:

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


Finding Citations to Non-indexed Resources in Web of Science

The Clarivate Analytics Web of Science database ( has a powerful Cited Reference Search that is useful for discovering records that have cited a particular publication. A typical use case that I have used many times is to start with a known article and discover references that cite that article.

Recently, while reading a few articles [1,2], I happened upon a use case I had not thought to try in a Web of Science Cited Reference Search; that is, searching for citations to non-indexed items like theses, databases, or software applications. For example, many software applications or web resources may not have a formal publication associated with it and so researchers may cite the application name or a website URL where the application can be accessed.

This was intriguing as I regularly use a cheminformatics toolkit, RDKit, that does not yet have a formal publication describing the software. Some experimentation and searching for “RDKit” in the Cited Reference Search, revealed that reference index matches to RDKit vary greatly and can appear within the Cited Author, Cited Work, or Title fields. Here are few examples to illustrate this, where the Cited Author is the first column, Cited Work the second column, and Cited Title the third column:

‘RDKit’ | ‘OP SOURC CHEM’ | ‘ ’

‘RDKit’ | ‘OP SOURC CHEM’ | ‘ URL:

‘Landrum, G.’ | ‘RDKIT’ | ‘ URL:

‘[Anonymous]’ | ‘ OP SOURC CHEM’ | ‘RDKit:…URL:

We can search each of these fields separately [3], select the candidates of interest, and then remove any duplicates to find all citations to RDKit. Here is a summary of what I found for ‘RDKit’:

Cited Author Search: 51 relevant variations, with 160 citing articles.

Cited Work Search: 7 relevant variations, with 13 citing articles

Cited Title Search: 15 relevant variations, with 33 citing articles

A quick sort of the combined titles revealed 6 duplicates, so in total, we found 200 RDKit citations via the Web of Science Cited Reference Search. That’s pretty cool. There are certainly many limitations with this method which I have not explored yet, but overall, I think it will be useful when trying to find non-indexed resources through citation searching.



[3] Note I did not limit to a particular index, so this includes the Science Citation Index Expanded as well as others.

Machine-readable Data and The International Year of the Periodic Table 2019

2019 marks the 150th anniversary of the Periodic Table. The United Nations General Assembly and UNESCO have proclaimed 2019 as the International Year of the Periodic Table of Chemical Elements (#IYPT2019). There are many activities, projects, and celebrations planned this year promoting the Periodic Table of Elements listed on the IYPT2019 website:

You may also be interested in reading some of our print and electronic books related to the Periodic Table: Scout Search for TI(periodic table).

At Rodgers Library, we have been interested in interacting with machine-readable periodic table data. As such, we were excited to learn that the U.S. National Library of Medicine recently released an interactive PubChem Periodic Table of Elements that allows both human and machine access to the underlying data. For example, here is a variety of associated element property data in machine-readable JSON format from the PubChem Periodic Table of Elements:

JSON data can be processed using scientific software and/or programming languages. We have created an example tutorial using MATLAB code. In the tutorial, we download the PubChem machine-readable periodic table JSON data and assemble a table of element names and corresponding International Chemical Identifiers (InChIs). We then create plots of Melting Point/Boiling Point vs. Atomic Number. Check out the MATLAB Live Notebook below, you are free to use and adapt the code as desired:

Plot of Temperature (Celsius) of Melting/Boiling Point versus Atomic Number.
Plot of Temperature (Celsius) of Melting/Boiling Point versus Atomic Number.

Enjoy, and have fun with the Periodic Table of the Elements!

Chemical & Engineering Data and Mathematical Functions available from NIST

The National Institute of Standards and Technology (NIST) provides public access to a multitude of compiled chemical and engineering experimental and computational 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:

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

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:

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.

A Short History of 3D Services at Rodgers Library

Our 3D services started back in November 2012 where we made 3D printing available to the entire UA community. We had one Bits from Bytes 3D Touch Printer. I think we got more use out of that 3D Touch Printer than it was ever designed for! Students and faculty quickly started to fabricate 3D parts for scholarly work and classroom projects. We have seen so many exciting projects from art sculpture to robot parts to laboratory equipment.

Since 2012, we have gone through multiple 3D printers, have trained hundreds of users, and have successfully 3D printed thousands of parts. After the 3D Touch, we purchased a couple of MakerBots, and then two 3D Systems Cube Pros. We quickly outgrew the aforementioned hobbyist level 3D Printers and are now running two professional Stratasys uPrint SE 3D printers. About a year ago, we added a NextEngine 3D scanner and by early next year we will have two 3D stereoscopy workstations to further advance our 3D operations and services for the UA community. A huge thanks to our administration, Rodgers Staff, College of Engineering, and all of our users across campus for making our 3D Studio such a success.

Interestingly, while our 3D printers and training courses have evolved rapidly since our debut in late 2012, our core mission for 3D services has never changed. Rodgers Library 3D services are a self-service operation. We provide the tools and training, and then you do the 3D printing.

We are very proud of the scholarship that has been created across campus using the Rodgers Library 3D Studio. One of the areas that we have been focused on in Rodgers Library is 3D printing molecular structures. Over the past several years, we have had the pleasure of collaborating with numerous researchers on and off campus to help advance molecular visualization with 3D printed molecules, extended solids, and polymeric structures. Check out some of our work below (all open access too!):

Scalfani, V. F.; Williams, A. J.; Tkachenko, V.; Karapetyan, K.; Pshenichnov, A.; Hanson, R. M.; Liddie, J. M.; Bara, J. E. Programmatic conversion of crystal structures into 3D printable files using Jmol. Journal of Cheminformatics 2016, 8, 66. DOI: 10.1186/s13321-016-0181-z

Scalfani, V. F.; Turner, C. H.; Rupar, P. A.; Jenkins, A. H.; Bara, J. E. 3D Printed Block Copolymer Nanostructures. Journal of Chemical Education 2015, 92, 1866-1870. DOI: 10.1021/acs.jchemed.5b00375

Scalfani, V. F.; Vaid, T. P. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups. Journal of Chemical Education 2014, 91, 1174-1180. DOI: 10.1021/ed400887t

If you have not visited our 3D Studio in Rodgers Library, I highly encourage you to do so!  You can take a short training course with one of our staff members and then immediately get started fabricating 3D parts independently. Check out our Standard Operating Procedures here for more information:

On Scientific Facts, Copyright, and Fair Use

Scientific and other facts are excluded from copyright protection [1]. As such, for scientific facts, we do not generally need to worry about whether Fair Use applies. While facts are not copyrighted, they are often buried within copyrighted documents such as published journal articles. Content within journal articles that are not clearly facts may then be copyrighted and/or open to debate about reuse of this content via Fair Use.

Some examples of facts in scientific journal articles are the melting point of gold, the chemical structure of Vincristine, or the bond dissociation energy of a carbon-hydrogen bond. Reuse of these facts does not require any permission, even if they were originally published in a copyrighted document. You can reuse this type of data in your own work. You will, however, want to give proper attribution and cite the original resource, so that other researchers know the origin of the data. Some exceptions exist as it is often acceptable to not cite well-known facts (e.g. at sea-level, water boils at 100 °C).

In contrast, any descriptions, explanations, figures, and illustrations are generally protected by copyright in journal articles. To reuse this material, you will need to ask permission from the copyright holder or determine if Fair Use applies [1, 2].

A few years ago, I asked two scientists, who are experts in data reuse, if scientific photographic images count as facts. So for example, a microscope image of a cell, or a nanometer length scale image of a material’s microstructure. One scientist replied “no, these images are not facts because they are a photograph, and photographs can be copyrighted.”  The other scientist replied “it depends on how good your lawyer is!”

Happy Fair Use Week!


[1] Copyright Basics from the US Copyright Office,

[2] Code of Best Practices in Fair Use,

ORCID – Get your own Unique Author Identifier

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 (

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:

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

Searching for Publications from UA Researchers

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

Makerspaces on UA Campus

Over the past year, UA has brought in a tremendous amount of new fabrication resources to help complete your research project. We recently created this Makerspace subject guide to help you learn about topics such as 3D printing, laser cutting, Arduinos, and much more. Check it out here:

If there are any books or other resources we do not have for your project, send a recommendation to Vincent F. Scalfani.

Bio-Rad KnowitAll U Spectra Database

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:

And let us know what you think here:

Emerging Scholars Posters

Congratulations to all of the UA Emerging Scholars (over 500!) that presented at the Sixth Annual University of Alabama Undergraduate Research and Creative Activity Conference. We were very proud to be able to participate in this event and also display a number of the posters after the conference in Rodgers Library.

If you have not heard of the Emerging Scholars program, check it out here:

We are looking forward to working with the new and seasoned emerging scholars next year. Feel free to contact us anytime during the course of your research. Check out our Libguides for an overview of our services:

Access to Library resources

Access to UA Libraries electronic resources on campus is straightforward; computers on the network are recognized as UA affiliated and are permitted access. Off-campus access is easy too.  After you enter the UA Libraries Web site, you may be asked to authenticate.   This is done simply by executing a login with your myBama ID and password.  Once this is completed you are ready to search, read, and download electronic resources.

Use of UA VPN for off-campus access to library resources isn’t necessary, so this approach is not recommended. 

Enjoy Rodgers Library for Science and Engineering.

Don’t forget about Dissertations!

Published Dissertations/theses are extremely useful when researching a field. They often provide a very nice basic introduction to the subject, a great collection of references, and excellent insights for future work. I have found that many dissertations also provide a level of detail which you will not find in peer-reviewed journals, for example, a worked calculation or sample data analysis. You may also glean information about how you would like to organize your own dissertation/thesis. So don’t forget about searching for your research topic in our ProQuest Dissertations & Theses Database!

Rodgers Library Fall 2012 Workshops

We are excited to announce the first five scheduled workshops for the Fall 2012 Semester.  All scheduled for 5-6 pm on Thursdays, Rodgers Library first floor Scholars Station. RSVP to if you plan on attending or would like more information. We should be able to accommodate about 20 people in the Scholars Station.

  1. September 27th – Searching Literature, Chemicals and Reactions with SciFinder Database
  2. October 11th – Introduction to ChemBioDraw Software
  3. October 25th – Strategies  For Efficiently Searching and Reading  Scientific Literature
  4. November 8th – Strategies for Creating Awesome Scientific Posters and Presentations
  5. December 6th – Citation Management For Scientists

Makeover at Rodgers Library 99% Complete

Welcome new and returning students to this UA Fall 2012 semester. The renovations at Rodgers Library are nearly complete, save for a few accessories that need to be mounted and/or configured. We are very excited and pleased with the renovated 1st floor of Rodgers Library. New furnishings, new group study rooms, new computers, new technology, we’ve got it all.  The redesigned south end of the Rodgers Library first floor houses multiple work tables and computers loaded with scientific software. The area is completely surrounded by windows, likely one of the best views on campus. If you have not already seen the new Rodgers library, come check us out – you won’t be disappointed. Incidentally, we have a new Science and Engineering Librarian (yours truly). I just finished a graduate Ph.D. chemistry program myself and know how challenging it can be to navigate library resources. We are all very much looking forward to helping you succeed with your classes and research. Roll Tide.