Chemical Information Sources/Science Writing Aids
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 word processing 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, though some older journals have been digitized and made available to libraries to purchase or subscribe annually to maintain access. For reasons including budget pressures, space limitations and user preferences, many libraries have dropped their print subscriptions in favor of online-only access to current journals. Many libraries are also acquiring electronic books (e-books), and in some cases changing their acquisitions model to favor e-books over the print when both are available. Regardless of format, scientists must write about and publish the results of their experiments.
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 can serve as chemistry writing guide, such as The Short Guide to Writing About Chemistry and The Art of Scientific Writing: From Student Reports to Professional Publications in Chemistry and Related Fields, and you can find more titles by searching "scientific writing" and related topics in an online book seller or a library catalog. Most notable is The ACS Style Guide, the 3rd edition of which appeared in 2006. Chapter 1 (Writing a Scientific Paper) and Chapter 14 (References) are available online. along with other online writing guides.
Word Processing Tools
Images can easily be inserted into modern word processing programs such as Microsoft Word or Open Office. These programs come with spellchecker dictionaries, but unfortunately, the scientific vocabulary is quite limited in them. Chemistry Dictionary V3.0 is a zipped dictionary of 104,000 chemical terms that you can add to your MS Word or Open Office dictionaries. There's also Chemistry Add-In for Word, which will allow you to add chemical information to a Word document as Chemical Markup Language (CML): names, concise formulas, and 2-D structures. 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.
Some chemists, especially those oriented toward the physical/theoretical side and/or UNIX operating system users, prefer the LaTeX document processing system in combination with the corresponding citation manager, BibTeX.
Chemical Drawing and Nomenclature Programs; Chemical Information Management
Ideally, a chemical drawing program would integrate easily with word processing software and would also give some assistance with the complex formal nomenclature system of chemistry. The software program CLiDE operates like Optical Character Recognition (OCR) software for chemistry. Clide can convert 2D representations of structures into MDL's mol file or CambridgeSoft's ChemBioDraw 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 ChemBioDraw (now part of PerkinElmer). ChemBioDraw is available on its own or as part of the ChemBioOffice suite which also includes ChemBio3D, ChemBioFinder and E-Notebook, The opening screen of ChemBioDraw is typical of such programs, with selections of pre-drawn chemical objects to choose from. CambridgeSoft does offer academic pricing, including ChemDraw Std for less than $200. Some chemical software producers provide free software, though some may specify academic use only. Popular products include ACD/Labs' ACD/ChemSketch Freeware, ChemAxon's Marvin Suite (which includes MarvinSketch), and Accelrys' No-fee Accelrys Draw.
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. ACD/Name will properly name over 90 percent of the organic substances that are drawn with the program. ACD/Labs includes IUPAC naming for molecules of up to 50 atoms and three rings in ACD/ChemSketch, and they also provide an extension for to generate systematic names in ChemBioDraw.
Several chemical structure drawing programs discussed above are part of suites that includes additional functionality to serve as chemical information managers. CambridgeSoft's ChemBioOffice package includes E-Notebook and other programs that integrate with MS Excel. Others have developed products that work with existing relational database software, such as Accelerys' Accord.
Reference Management Software
Most reference (or bibliographic) management software programs, 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 Web of Science or SciFinder and import the records directly into a personal database, without the need to key in any information. Once loaded, the data can be re-used in the writing process, embedding references (numbered or author-date) throughout the paper while dynamically creating the associated list of references. Such programs typically have a large number of output styles that automatically format each reference to meet the requirements of various publishers and official style guides. Along with the citation data, the programs can also capture the article URLs, and in some cases you can attach the full-text to the record in your database.
Citation managers may be either freeware or require purchase, reside in and/or store references locally or in the cloud (or both, based on user preferences).
A comparison of reference management software programs can be found here. EndNote (desktop-based) and RefWorks (web-based) are commonly used programs, while more recent options, especially open source options have gained in popularity. Papers is an iOS program that also works as an iPhone/iPad app, while Mendeley combines reference management with social networking by allowing users to share the research papers they find. Zotero, which does an especially good job of capturing references from web pages, is another up and coming program.
Each program naturally has distinctive features, strong points, and drawbacks. The programs are rapidly evolving, responding to the advances made by their competition. Hence, one should be sure to consult recent reviews and product literature to make an informed decision.
CASSI (Chemical Abstracts Service Source Index) and The ACS Style Guide
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 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 freely available CASSI, the Chemical Abstracts Service (CAS) Source Index. CASSI can confirm publication titles and abbreviations, as well as CODEN, ISBN, or ISSN codes. CASSI contains a listing of publications indexed by CAS since 1907. Some libraries may still have the now discontinued CASSI database in print or on CD which contained additional data fields not available on the free version including library holdings, though they had not been updated for many years. The web version returns a maximum of 50 results, so searches should be as specific as possible. Ber will not retrieve Berichte der Deutschen Chemischen Gesellschaft, but Ber. Dtsch. Chem. Ges. will.
Finally, societies and other journal publishers provide significant guidance on their web sites to assist authors in preparing manuscripts for submission to their journals, often under a link entitled "Instructions for Authors". Obviously, these instructions need to be carefully followed if one wishes their manuscript to receive serious attention from the editors. For example, to assist both authors of papers and books and editors of American Chemical Society (ACS) publications, the ACS has produced The ACS Style Guide. There you will find instructions and examples on the format required to cite all sorts of documents in a bibliography. In addition, the guide includes 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.
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 discussed in this chapter may be out of the price range of students, many of them are free or have very low prices for academic users.