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PubChem Periodic Table and Element Pages
PubChem (https://pubchem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with 3.5 million unique users per month at peak. About half of them are between ages 18 and 24, suggesting that PubChem is heavily used by undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These new services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional information, such as bioactivities and health and safety data, available in PubChem Compound pages for specific elements and their isotopes.
Introduction
The periodic table of chemical elements is one of the most recognized tools in science. Its simplicity and grace may make it easy to overlook the wealth of information contained therein. The periodic table organizes all known elements in a tabular format in order of increasing atomic number. The tabular organization (left to right and top to bottom) is very important, reflecting key trends and commonalities. There is much students in the classrom can learn about chemistry from the periodic table and they should get familar with it.
The periodic table in its present form is considered to be first introduced in 1869 by a Russian chemist, Dimitry Mendeleev, although there had been earlier attempts to classify elements by their similarities. As we mark the 150th anniversary of the periodic table, the scientific community has declared 2019 to be “The International Year of the Periodic Table”.1 PubChem (Figure 1) (https://pubchem.ncbi.nlm.nih.gov) 2-4 joins this celebration by launching the PubChem Periodic Table and corresponding Element pages.
Figure 1. Snapshot of PubChem Homepage (https://pubchem.ncbi.nlm.nih.gov). The PubChem Periodic Table can be accessed by clicking the Periodic Table icon (indicated with the green box).
PubChem is a public chemical information resource, developed and maintained by the U.S. National Institutes of Health. With 3.5 million unique users per month at peak, it is considered as one of the top five chemistry web sites in the world in terms of web traffic. About 40% of PubChem users are aged between 18 and 24, many of which are likely to be students enrolled in academic institutions. This suggests PubChem’s great potential as a chemical education resource.
PubChem provides for a given chemical a Compound Summary page, a comprehensive overview of all information available within PubChem for that chemical. While the Compound Summary page is appropriate to present data for most chemicals, it is not designed for displaying information specific to elements (such as electronegativity and electron configuration). The PubChem Periodic Table and Element pages help you navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional information, such as bioactivities, health and safety data, available in PubChem Compound pages for specific elements and their isotopes. The present paper provides an overview of the PubChem Periodic Table and Element pages.
Periodic Table
PubChem Periodic Table (Figures 2-4) can be accessed by clicking the Periodic Table icon on the PubChem homepage (https://pubchem.ncbi.nlm.nih.gov) (Figure 1). Alternatively, it can also be directly accessed via the following URL: https://pubchem.ncbi.nlm.nih.gov/ptable/
The PubChem Periodic Table provides three distinct views: Table View, List View, and Game View.
Figure 2. Snapshot of the Table View of PubChem Periodic Table (https://pubchem.ncbi.nlm.nih.gov/ptable/). The elements can be colored according to their properties, by using the drop-down menu available at the upper-right corner of the table.
• The Table View (https://pubchem.ncbi.nlm.nih.gov/ptable/#view=table) is the traditional periodic table any scientist would instantly recognize. The elements can be colored according to various elemental properties (atomic mass, standard state, group block, electron configuration, etc.) with the selected property value displayed for each element, by using the drop-down menu available at the top-right corner.
Figure 3. Snapshot of the List View of PubChem Periodic Table (https://pubchem.ncbi.nlm.nih.gov/ptable/).
• The List View (https://pubchem.ncbi.nlm.nih.gov/ptable/#view=list) allows one to see a set of properties available for each element all at once. Using the search box at the top-left corner, one can quickly find an element of interest. The “Download” button at the top-right corner allows one to download all data presented on the Periodic Table.
Figure 4. Snapshot of the Game View of PubChem Periodic Table (https://pubchem.ncbi.nlm.nih.gov/ptable/).
• The Game View (https://pubchem.ncbi.nlm.nih.gov/ptable/#view=game), added as an educational feature, helps test one’s knowledge of element names and symbols. The game has three levels of difficulty (easy, medium, and hard).
One can select one of the three views by clicking the “TABLE”, “LIST W/ PROPERTIES” and “GAME” tabs, available above the upper-right corner of the Periodic Table. By default, the Table View is presented. The Periodic Table is optimized for printing and/or saving as the Portable Document Format (PDF), hiding unnecessary user interface (UI) components (e.g., the icons and dropdown menu).
Element Pages
Clicking an element in the Table or List Views of PubChem Periodic Table directs you to the corresponding Element page (Figure 5). This page presents a wide variety of element information, including atomic properties (electron affinity, electronegativity, ionization potential, oxidation states, electron configuration, etc.) as well as isotopes, history, uses, and, most importantly, information source. PubChem Element page content comes from scientific articles5-12 and various authoritative data sources, such as the International Union of Pure and Applied Chemistry (IUPAC) Commission on Isotopic Abundances and Atomic Weights (CIAAW)13, National Institute of Standard and Technology (NIST)14, International Atomic Energy Agency (IAEA)15, Thomas Jefferson National Accelerator Facility (Jefferson Lab)16, and Los Alamos National Laboratory17.
Figure 5. Snapshot of the Element page for carbon, accessible via the URL: https://pubchem.ncbi.nlm.nih.gov/element/Carbon.
At the top of each Element page is a periodic table, which allows one to quickly move to other elements’ pages. The Table of Contents on the right column helps the user to readily locate desired information. The data presented on the Element page can be downloaded using the “Download” button at the top-right corner.
The element page can also be reached directly via URLs that includes atomic number, symbol, or name (all case-insensitive). For example, the following URLs are for the Element page for carbon:
https://pubchem.ncbi.nlm.nih.gov/element/Carbon
https://pubchem.ncbi.nlm.nih.gov/element/C
https://pubchem.ncbi.nlm.nih.gov/element/6
Machine-Readable Elemental Data
The data presented in the Periodic Table and Element pages can be downloaded by clicking the “Download” button available at the top-right corner of the List View of the Periodic Table and the respective element pages. The data are available in various formats, including XML, JSON, ASNT, and CSV (for the Periodic Table data only). Programmatic access to these data are supported through PUG-REST and PUG-View, which are Representational State Transfer (REST)-like interface to PubChem information. For example, the following PUG-REST request URL allows one to retrieve key elemental data presented in the Periodic Table in CSV format:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/periodictable/CSV
It is also possible to download the annotations presented on the Element page using the following PUG-View request (with hydrogen as an example):
https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/element/1/JSON
Conclusions
The PubChem Periodic Table and Element pages help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional information, such as bioactivities and health and safety data, available in PubChem Compound pages for specific elements and their isotopes. The data presented on the Periodic Table and Element pages are integrated from scientific articles and authoritative data sources. These data can be downloaded in machine-readable formats through the web browser or programmatically, giving the user access to the data in his or her own program.
Acknowledgments
We are grateful to Dr. Jason Telford, who organized Spring 2019 ConfChem Newsletter. We also thank the members of the Committees on Computers in Chemical Education (CCCE) for providing valuable feedback about PubChem resources. We are thankful for the overall efforts of the entire PubChem team and other teams throughout NCBI, without of which this work would not be possible. This research was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health, U.S. Department of Health and Human Services.
Contributions
AG generated the user interface. JZ compiled and integrated element information. PT created the PUG REST interface. EB contributed to the design. SK wrote the initial draft and SK, AG, JZ, PT, and EB revised it. All authors read and approved the final manuscript.
References
- IUPAC International Year of Periodic Table 2019. https://www.iypt2019.org/ (accessed 5/2/2019)
2. Kim, S.; Chen, J.; Cheng, T.; Gindulyte, A.; He, J.; He, S.; Li, Q.; Shoemaker, B. A.; Thiessen, P. A.; Yu, B.; Zaslavsky, L.; Zhang, J.; Bolton, E. E., PubChem 2019 update: improved access to chemical data. Nucleic Acids Research 2018, gky1033-gky1033.
3. Kim, S.; Thiessen, P. A.; Bolton, E. E.; Chen, J.; Fu, G.; Gindulyte, A.; Han, L. Y.; He, J. E.; He, S. Q.; Shoemaker, B. A.; Wang, J. Y.; Yu, B.; Zhang, J.; Bryant, S. H., PubChem Substance and Compound databases. Nucleic Acids Research 2016, 44, D1202-D1213.
4. Kim, S., Getting the most out of PubChem for virtual screening. Expert. Opin. Drug Discov. 2016, 11, 843-855.
5. Slater, J. C., ATOMIC RADII IN CRYSTALS. J. Chem. Phys. 1964, 41, 3199-3204.
6. Allred, A. L., ELECTRONEGATIVITY VALUES FROM THERMOCHEMICAL DATA. Journal of Inorganic & Nuclear Chemistry 1961, 17, 215-221.
7. Allen, L. C., ELECTRONEGATIVITY IS THE AVERAGE ONE-ELECTRON ENERGY OF THE VALENCE-SHELL ELECTRONS IN GROUND-STATE FREE ATOMS. J. Am. Chem. Soc. 1989, 111, 9003-9014.
8. Mann, J. B.; Meek, T. L.; Allen, L. C., Configuration energies of the main group elements. J. Am. Chem. Soc. 2000, 122, 2780-2783.
9. Mann, J. B.; Meek, T. L.; Knight, E. T.; Capitani, J. F.; Allen, L. C., Configuration energies of the d-block elements. J. Am. Chem. Soc. 2000, 122, 5132-5137.
10. Myers, R. T., THE PERIODICITY OF ELECTRON-AFFINITY. J. Chem. Educ. 1990, 67, 307-308.
11. Meija, J.; Coplen, T. B.; Berglund, M.; Brand, W. A.; De Bievre, P.; Groning, M.; Holden, N. E.; Irrgeher, J.; Loss, R. D.; Walczyk, T.; Prohaska, T., Atomic weights of the elements 2013 (IUPAC Technical Report). Pure Appl. Chem. 2016, 88, 265-291.
12. Meija, J.; Coplen, T. B.; Berglund, M.; Brand, W. A.; De Bievre, P.; Groning, M.; Holden, N. E.; Irrgeher, J.; Loss, R. D.; Walczyk, T.; Prohaska, T., Isotopic compositions of the elements 2013 (IUPAC Technical Report). Pure Appl. Chem. 2016, 88, 293-306.
13. Commission on Isotopic Abundances and Atomic Weights. http://ciaaw.org/ (accessed 5/2/2019).
14. National Institute of Standards and Technology Physical Measurement Laboratory. https://www.nist.gov/pml (accessed 5/2/2019).
15. International Atomic Energy Agency - Nuclear Data Section Atomic Mass Data Center (AMDC). https://www-nds.iaea.org/amdc/ (accessed 5/2/2019).
16. Thomas Jefferson National Accelerator Facility - Office of Science Education It's Elemental - The Periodic Table of Elements. https://education.jlab.org/itselemental/ (accessed 5/2/2019).
17. Los Alamos National Laboratory Periodic Table of Elements. https://periodic.lanl.gov/index.shtml (accessed 5/2/2019).
Comments
Dynamic Default View
Since this newsletter was posted, there has been some change in how the default view of the PubChem Periodic Table is determined.
Now it's determined dynamically based on the width of the web browser. Because the traditional, Table View (https://pubchem.ncbi.nlm.nih.gov/ptable/#view=table) is somewhat wide to fit within the browser window (for example, when you are accessing the page from a mobile device), so the default view for a narrow window is set to the List View (https://pubchem.ncbi.nlm.nih.gov/ptable/#view=list). For a wider window, the Table view is the default.
Once the default view is loaded, this view will be shown even if the window size is adjusted. Switching between the views can be done with the tabs available at the top-left cornor of the periodic table.
Because of this dynamic default, you will see the List View on the mobile device and the table view on a large moniter connected to a Mac/PC.
Widget?
Hi Sunghwan,
I think PubChem's periodic table is really amazing, and I can see how it could be of great value to a variety of classes, in a variety of ways.
I was able to embed it into a webpage using an iframe, and was wondering if PubChem was considering creating a couple of widget options.
<p><iframe height="1100" src="https://pubchem.ncbi.nlm.nih.gov/ptable/#view=table&property=ElectronAffinity" width="1200"></iframe></p>
I note that when the width gets small you lose the "display property/trend" option, even if it is in the url (the above one is activating Electron Affinity"), and am thinking it might be of value to have a widget that could placed in a webpage and show a default property, even it it was only the element symbol and the property. (For example, you could have a series of questions dealing with bond polarity, and have the electronegativity widgit provide that data, instead of listing it in a table).
I really appreciate your sharing this valuble resource.
Cheers,
Bob
No plan for widgets.
Hi, Bob.
The PubChem Periodic Table is a public service and, if you want, you can embed it within your web page for free, using the iframes (as you mentioned). Alternatively, you can add a direct link to the periodic table (on your web page). One caveat of using the iframes is that you should deal with the width of the iframe, which may affect the dynamic layout of the periodic table.
Currently, we don’t have a plan to provide the periodic table as a widget, but we may consider it if many people request us to do so.
Thank you.
Sunghwan,
Atomic masses in PubChem
I would like to mention how element data from different sources are dealt with within PubChem. If you go to the PubChem Periodic Table and look at the atomic mass of silicon, you will see it’s listed as 28.09. If you click the silicon on the Periodic Table, you will be directed to the element page for silicon, and from there you will be able to find the atomic mass values from four different sources (https://pubchem.ncbi.nlm.nih.gov/element/14#section=Atomic-Weight).
Now you see that two sources provided a range of values for the atomic mass of silicon ([28.084, 28.086]) and the other two sources provided single values with different precisions (28.0855 and 28.09). The atomic mass “value range” reflects the “uncertainty” due to different isotopic compositions from different samples (e.g., from different geographic locations). On the other hand, the other two sources provide the “conventional” atomic mass value that can be used to compute atomic weights for unspecified samples, with disregard to the uncertainty. To learn more details about this topic, please read this PubChem blog.
https://pubchemblog.ncbi.nlm.nih.gov/2016/11/29/atomic-mass-changes-in-pubchem/
In summary, when there are multiple values for a given property, PubChem does not pick one of them as a representative value. Instead, we show all available values and explicitly state where the values come from, keeping the provenance of the data.
Two great points
Thank you Sunghwan,
I think you have brought up two very important points that students often miss. First, that even the molar mass (average isotopic composition) can vary from sample to sample for some elements. And second, that in this world of fingertip access to data, there is no excuse not to maintain the data provenance. And that is one of the advantages of PubChem over many other resources, in that you know where the data came from. Just as students should be taught to cite their literature research, they should be taught to cite their data sources.
In fact, I would argue that students should be taught not to use PubChem (or Wikipedia) as a data source citation, but use the source that provided the data to PubChem (or Wikipedia), and to even validate that source is correct (which I think is more important with Wikipedia than PubChem).
Anyways, this periodic table is a great resource that I am sure many educators and students will use, and we thank PubChem for making it available.
Cheers,
Bob
citing sources
In my opinion, Bob and Robert are both right. Robert is right that scholars (including students) should only cite sources that they have actually consulted. If they follow Bob's advice to check on the data given in Wikipedia or PubChem by going to that source, then they ought to cite that source—and they can ethically do so because they will have consulted it to verify it.
I would make the further point, which is a bit far afield of the original discussion, that one of the most valuable aspects of Wikipedia for scholarly work is to point scholars to more detailed and vetted sources.
Checking the data provenance
The best way to view PubChem is that it “delivers” from data owners to data consumers. PubChem does not “own” data, but it collects/aggregates them from hundreds of data sources and give these data to those who need them (with some exceptions like some properties computed by PubChem, e.g., molecular weights, H-bond donor/acceptor count, …). With that said, PubChem does not fix the incorrect/misleading data that it does not own. Instead, it may contact the original data source to notify the issue and ask for fix, and if the original data source fix the issue, the fix will be reflected in the next update cycle. Alternatively, PubChem may the data invisible to the user (i.e., removed from the PubChem page).
So, when you use PubChem, you often see discrepancies between the data from different sources. In that case, it is highly recommended to visit the original data sources to check the context (or metadata) of the data. [Whenever possible, PubChem presents the data along with the link to the web page that presents the same data on the original data source.] Actually, this is a very good practice, regardless of what website you are using (PubChem, Wikipedia, or anything else).
With that said, I support the idea that you should cite the actual source of the data you are talking about. If you use PubChem to find some data and stop there, you cite PubChem, but if you see some discrepancies in the data within PubChem, you will need to check individual data sources to what the data actually mean and cite the source of the data that you believe is most appropriate.
Discrepancy in the year discovered btw PubChem & Wikipedia
I was asked about the discrepancy in the year of discovery for some elements between the PubChem Periodic Table and Wikipedia data.
https://pubchem.ncbi.nlm.nih.gov/ptable/#view=table&property=YearDiscovered (PubChem P-Table)https://en.wikipedia.org/wiki/Timeline_of_chemical_element_discoveries (Wikipedia)
If you compare the year of discovery between the two sources, you will see that some elements indeed have discrepancies (+/- 1 year for some, but often more than +/-30 years for others).
The year of discovery for each element presented in the PubChem Periodic Table was collected by the history section of the PubChem element page for each element. For example, the history of Ruthenium can be accessed at:
https://pubchem.ncbi.nlm.nih.gov/element/44#section=History
This section has some paragraphs from three different sources (IUPAC, Jefferson Lab, and Los Alamos Lab). One of the PubChem scientists have read these paragraphs to collect the year of discovery for each element. However, it is not always easy to say when a particular element was discovered. For example, here is an excerpt from the history of Ruthenium:
"From the Latin word Ruthenia, Russia. In 1827, Berzelius and Osann examined the residues left after dissolving crude platinum from the Ural mountains in aqua regia. While Berzelius found no unusual metals, Osann thought he found three new metals, one of which he named ruthenium. In 1844 Klaus, generally recognized as the discoverer, showed that Osann's ruthenium oxide was very impure and that it contained a new metal. Klaus obtained 6 g of ruthenium from the portion of crude platinum that is insoluble in aqua regia.” (Los Alamos National Lab)
We can see two different years (1827 vs 1844) are mentioned here, and PubChem picked 1828, while Wikipedia picked 1844. This kind of year gaps commonly occurs for elements discovered before 20th century. This year gap is often larger than 100 years (for example, for fluorine, fluorine compounds were reported as early as back in 1670, but fluorine was isolated in 1886 (216 years later), as explained in here.
https://pubchem.ncbi.nlm.nih.gov/element/9#section=History
The PubChem member who collected the year of discovery data told me that he picked most agreed value among the three sources in the history section for each element, and if there is no clear agreement, he picked the year provided by the Jefferson lab. He said he did not take the Wikipedia values into account for this task.
Obviously, there is a great level of subjectivity when collecting/interpreting these year data. But, if you check the history section of the element, you will get a better idea why a particular year was picked as the year of discovery. Of course, considering that the interpretation of these data is quite subjective, the year data can be changed in the future (based on the feedback we get from our users).