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Periodicity, visualization, and design

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Abstract

This paper explores the development of the chemical table as a tool designed for chemical information visualization. It uses a historical context to investigate the purpose of chemical tables and charts, analyzing them from the perspective of theory of tables, cartography, and design. It suggests reasons why the two-dimensional periodic table remains the de facto standard for chemical information display.

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Notes

  1. The perspective taken here is that of object oriented analysis and design (OOAD), a software engineering paradigm (Larman 2005; Odell 1998). In OOAD a system is modeled as a group of interacting objects, each representing an entity of interest. The goal of OOAD is to produce a conceptual model of information that exists within a problem domain under investigation.

  2. The word "affordance" was originally coined by the perceptual psychologist Gibson (1977) as part of his ecological model of perception. Gibson introduced the term to describe opportunities for a human to interact with objects populating a cognized representation of the real world. Humans make sense of the environment by exploring and interacting with it, and thereby form a representation of the surrounding world.

  3. Visual analytics tools and techniques are used “to synthesize information and derive insight from massive, dynamic, ambiguous, and often conflicing data; detect the expected and discover the unexpected; provide timely, defensible, and understandable assessments; and communicate assessment effectively for action” (Thomas and Cook 2006).

  4. In 1864, five years before Mendeleev, Lothar Meyer published a periodic table in the first edition of his chemistry textbook, Die modernen Theorien der Chemie, that employed atomic weights to organize 28 elements into 6 families exhibiting similar chemical and physical attributes. Many of Lothar Meyer’s innovations both anticipate Mendeleev’s table and surpass it, including: creation of gaps for future elemental discoveries, horizontal relationships, and trends in valance across the table. See Scerri (2007, 92–98) for more details.

  5. A scatter plot is “a plot of two variables, x and y, measured independently to produce bivariate pairs (x i, y i), and displayed as individual points on a coordinate grid typically defined by horizontal and vertical axes, where there is no necessary functional relation between x and y” (Friendly and Denis 2005).

  6. Today, a scatter plot is the de facto charting method. In 1983 Tufte (1983) had estimated that 70–80% of all published scientific charts were scatter plots.

  7. See Kauffman (1999) and Scerri (1998) for images and details.

  8. Jacques Bertin published his rules in 1967 as Sémiologie Graphique. Les diagrammes, les réseaux, les cartes with Marc Barbut et al. It is a seminal work in the field of information visualization that has influenced contemporary exponents such as Edward Tufte (1983, 1990). Bertin built upon Ferdinand de Saussure's (1916) theory of semiology, the study of signs used for communication, to interpret graphics as a collection of visual signs that may be assembled within the constraints of well-defined grammar so as to support both qualitative and quantitative reasoning about data. For Bertin, a graphical representation should sustain both information memory and information discovery.

  9. A cartogram is a map in which some attribute of an object such as population is used to scale the region to which it belongs. Population cartograms scale a region’s area proportional to population density, thus increasing regional areas of high population density, and decreasing areas for regions of low population density.

  10. Mercator and Mollweide are two well-known projections. See Snyder (1987) for a comprehensive list of examples.

  11. This problem has been recognized for some time in the cartographic community where examples of the non-Euclidean nature of nearness include disease propagation (Cliff and Haggett 1998) and movement and interaction at the urban, regional, and national scales (Worboys et al. 1998; Puu and Beckmann 1999).

  12. Railsback has observed that the concept of ionic potential and periodicity may be traced back to Cartledge (1928) who created a periodic table based on ionic potential that considered ions, and showed some elements at two locations as well.

  13. Here for example, red and brown symbols communicate each ion's solubility.

  14. The term cognitive load is used in cognitive psychology to refer to the amount of effort associated with thinking and reasoning (including perception, memory, language, etc.). Information visualization and user interface design communities (of which there is much overlap) focus on developing interfaces to information that minimize the amount of thinking necessary to understand how the interface gives access to the data. They often invoke a basic theory put forth by cognitive psychologist Miller (1956) that short term memory puts restrictions on the amount of information an individual can recall as part of work practice, saying that it is limited to 7 ± 2 chunks of information. For example, say a chemist is viewing a computer generated three-dimensional ball-and-stick model of a large molecule in which elemental type is specified only by the color of its respective ball. For an organic molecule, this amounts to seven colors—one each for C (grey), H (white), O (red), N (blue), F (green), S (yellow), and P (orange). Visualization becomes a straightforward task with each color easily mapped onto a member of the short list of elements. Now the chemist studies a protein with each of its twenty possible amino acids uniquely colored. It becomes a far more difficult, if not impossible, task to remember all twenty colors and match them to their respective amino acids.

  15. The term separation of concerns was originally used by the computer scientist Dijkstra (1982) in an essay that considered design issues related to problem decomposition and the trade-offs between conflicting requirements.

  16. MVC originated with the computer scientist Reenskaug (1979) as a method for transforming a data model that resided in a computer into a representation that could invoke a meaningful mental image of that data, hence a visualization.

  17. For a review of Joseph Cornell’s work see Joseph Cornell (McShine 1980).

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Marchese, F.T. Periodicity, visualization, and design. Found Chem 15, 31–55 (2013). https://doi.org/10.1007/s10698-012-9154-0

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