Science Writing Aids
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Introduction
The objective of this chapter is to introduce you to some tools that will assist in the task of writing. Included are such things as chemical structure drawing programs that integrate with wordprocessing programs or structure-searching databases, bibliography reference manager software (products/reference tools that facilitate putting bibliographic references in the proper format) as well as tools to help you formally name chemical substances, etc. One of the most important things to grasp in this session is the conventions used in formal science writing, such as the use of abbreviations for journal titles and the frequent omission of article titles from the citations. The terms CITATION and REFERENCE are used interchangeably in this context to refer to items of a bibliography.
That science has advanced so rapidly in the last few centuries is largely due to the major developments in communications and publishing technology, starting with the invention of the printing press and movable type. Much of the archival record of science still exists only in the format of the printed word, and paper-based forms of communication will remain a very important part of science for some time to come. Scientists must write about and publish the results of their experiments, but increasingly there is the option to read their works in electronic format.
As a scientist, you will be called upon to write many different types of compositions, ranging from laboratory notebooks to grant proposals, technical reports, and journal articles. There are books that attempt to teach you how to write better, such as The ACS Style Guide, the 3rd edition of which appeared in 2006. This chapter does not duplicate the material in such books. However, there are science writing courses on the Internet that you can take advantage of, if you are so inclined. In this chapter, we will become acquainted with other tools that can help make the process of writing scientific documents much easier.
Images can easily be inserted into modern wordprocessing programs such as Microsoft Word or WordPerfect. These programs come with spellchecker dictionaries, but unfortunately, the scientific vocabulary is quite limited in them. Scientific dictionary programs to supplement wordprocessing dictionaries can be found at ChemSW, Chemistry Software for Windows. Graphing and data analysis programs make the task of visualizing data much simpler nowadays. These are designed to provide a combination of the common, frequently used features found in spreadsheet, visualization, and statistical software. One such package is KaleidaGraph. There are even scientific writing packages that handle mathematical expressions, such as MacKichan Software's Scientific Notebook.
A bewildering array of products could be considered tools to aid in writing, and many of those can be found among the products at ChemSW (formerly, WindowChem Software). In this lesson, we will cover the major tools that can help you write better scientific documents.
Chemical Drawing and Nomenclature Programs
Ideally, a chemical drawing program would integrate easily with wordprocessing software and would also give some assistance with the complex formal nomenclature system of chemistry. The software program CLiDE that operates like Optical Character Recognition (OCR) software for chemistry. Clide can convert 2D representations of structures into MDL's mol file or CambridgeSoft's ChemDraw formats. A free source for converting drawn structures into computer-readable form is OSRA, Optical Structure Recognition. The program is designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES.
One of the most popular chemistry structure drawing programs is CambridgeSoft's ChemDraw.
The opening screen of ChemDraw is typical of such programs, with selections of pre-drawn chemical objects to choose from. A version of ChemDraw that serves as a WWW structure client is available free to educational users at the present time. Other producers of chemical drawing software also give academics free copies of their drawing products--either the full versions, as with MDL's ISIS/Draw, or freeware versions such as ACD's ChemSketch or Chemaxon's Marvin.
Several programs have been developed to take the image of the chemical structure one step further--to give it an acceptable IUPAC (International Union of Pure and Applied Chemistry) name. Thus, a program, such as AUTONOM will properly name close to 90 percent of the organic substances that are drawn with the program. ACD's Name program claims even higher accuracy.
Personal Database Software Packages (Citation Managers)
Several of the chemical structure drawing packages discussed above are part of a package of programs that can manage bibliographic data and even physical and chemical data in a single database. Thus, ISIS/Draw and ISIS/Base complement one another. Likewise, CambridgeSoft has the ChemOffice suite for drawing, modeling, and information handling that includes ChemFinder. Others have developed products that work with existing relational database software, such as Accelrys's Accord for MS Excel or Access.
The more general personal bibliography manager software packages, such as ProCite, Reference Manager, and EndNote, while lacking in chemical capabilities, have other important features that make them very useful. For example, one can download records from a bibliographic database such as Science Citation Index and import the records directly into a personal database, without manipulating the data. Once loaded, the data can be re-used in the writing process. Such programs typically have a number of style sheets that allow the data in the records to be changed to suit the requirements of various publishers or authoritative style guides. You can also mark a point in a manuscript and tie it to a reference in the bibliography that is automatically generated from the database. A nice feature of the personal database software is the capability to capture certain data from the Web, such as the TITLE and URL of a Web document and automatically load them into the database. Once a record has been formed for a Web page, the record can be recalled and automatically loaded through a Web browser. For additional information on the features of these three popular bibliography managers, see: Bibliographic Reference Managers.
CASSI (Chemical Abstracts Service Source Index) and The ACS Style Guide
Apparently in order to save printing space in the days when there were few scientific journals, scientists began to use abbreviations to refer to journal titles. With only a handful of scientific journals in existence in the early years of of the 19th century, it was easy to know from the abbreviation what journal was being referred to. However, there are now literally tens of thousands of journals. Yet many scientists, chemists included, still use abbreviated forms of the titles of the journals they cite. A tool to help figure out the correct abbreviation to use or to decipher puzzling journal title abbreviations when they are encountered is CASSI, Chemical Abstracts Service Source Index. Below is the answer screen from a search of the CASSI CD-ROM for the German journal with abbreviated title: Ber. Dtsch. Chem. Ges..
(Reproduced with permission of CAS, a division of the American Chemical Society.)
The journals published by the American Chemical Society are among the most important and highly cited scientific journals in the world. Likewise, books published by the ACS are also very respected. To assist both authors of papers and books and editors of ACS publications, the ACS has produced The ACS Style Guide. There you will find instuctions and examples on the format required to cite all sorts of documents in a bibliography. In addition, the guide has a list of abbreviations for the most frequently cited journal titles. Other topics include grammar, style, usage, illustrations, tables, lists, and units of measure, as well as the conventions used in chemistry. It also covers numerous related topics, from peer review and copyrights to oral presentations and the ACS ethical guidelines for publication.
Conclusion
There are many software products and printed works that can make scientific writing considerably easier than it was a few years ago. Although some of the products discussed above may be out of the price range of students, many of them are free or have very low prices for academic users.
Link to Internet Sources for Science Writing Aids
This wiki page was originally created by Gary Wiggins. If you have a legitimate desire to contribute to its contents, please request an account from the sysop, Dr. David J. Wild, by e-mailing him at djwild @ indiana.edu
