Chemical Information Sources/Science Writing Aids

1
Chemical Information Sources/Science Writing
Aids
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 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
[1]
and The Art of Scientific Writing: From Student
Reports to Professional Publications in Chemistry and Related Fields
[2]
, and you can find more titles by searching
"scientific writing" and related topics in Amazon. Most notable is The ACS Style Guide
[3]
, the 3rd edition of which
appeared in 2006. Chapter 1 (Writing a Scientific Paper)
[4]
and Chapter 14 (References)
[5]
are available online.
along with other online writing guides
[6]
.
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
[7]
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
[8]
, 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
[9]
. There are even scientific writing packages that handle
mathematical expressions, such as MacKichan Software's Scientific Notebook
[10]
.
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
[11]
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
[12]
formats. A free source for converting drawn
structures into computer-readable form is OSRA
[13]
, Optical Structure Recognition. The program is designed to
convert graphical representations of chemical structures, such as they appear in journal articles, patent documents,
Chemical Information Sources/Science Writing Aids
2
textbooks, trade magazines etc., into SMILES.
One of the most popular chemistry structure drawing programs is CambridgeSoft's ChemBioDraw
[14]
(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
[15]
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
[16]
, ChemAxon's
Marvin Suite
[17]
(which includes MarvinSketch), and Accelrys' No-fee Accelrys Draw
[18]
.
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
[19]
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
[14]
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
[20]
.
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
manipulating the data. 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 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. Along with the citation data, the programs can also capture the
article URLs, and in some cases you can attach the PDFs to the record in your database.
A comparison of reference management software programs can be found here
[21]
. EndNote
[22]
(desktop-based) and
RefWorks
[23]
(web-based) are commonly used programs, while more recent options have gained in popularity.
Papers
[24]
is an iOS program that also works as an iPhone/iPad app, while Mendeley
[25]
combines reference
management with social networking by allowing users to share the research papers they find.
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 CASSI, the CAS Source Index. CASSI can confirm publication titles and abbreviations, as well as
CODEN, ISBN, or ISSN codes. The CASSI database contains a listing of publications indexed by Chemical
Abstracts Service (CAS) since 1907. CASSI on CD-ROM
[26]
, also includes holdings information for 350 libraries
(up to 1998), to help you identify libraries who own the journal you need. Many libraries also received CASSI in
print, and CAS also provides a free web version of CASSI
[27]
that does not include library holdings. Also with the
free version, search results are limited to the first 50, so searches should be as specific as possible. Ber will not
retrieve Berichte der Deutschen Chemischen Gesellschaft, but Ber. Dtsch. Chem. Ges. will.
Chemical Information Sources/Science Writing Aids
3
To assist both authors of papers and books and editors of ACS publications, the ACS has produced The ACS Style
Guide
[3]
. 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.
Summary
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.
CIIM Link for further study
SIRCh Link for Science Writing Aids
Problem Set for this topic
[28]
References
[1] http:/ / www. amazon. com/ Short-Guide-Writing-About-Chemistry/ dp/ 0205550606
[2] http:/ / www. amazon. com/ Art-Scientific-Writing-Professional-Publications/ dp/ 3527298290
[3] http:/ / www. oup. com/ us/ catalog/ general/ subject/ Chemistry/ ?view=usa& ci=9780841239999
[4] http:/ / www. oup. com/ us/ samplechapters/ 0841234620/
[5] http:/ / pubs. acs. org/ userimages/ ContentEditor/ 1246030496632/ chapter14. pdf
[6] http:/ / en. wikibooks. org/ wiki/ Chemical_Information_Sources/ SIRCh/ Science_Writing_Aids
[7] http:/ / www. chemistry-blog. com/ dictionary/
[8] http:/ / chem4word.codeplex.com/
[9] http:/ / www. synergy. com/
[10] http:/ / www.tcisoft.com/
[11] http:/ / www.simbiosys.ca/ clide/ index.html
[12] http:/ / www.cambridgesoft.com/
[13] http:/ / cactus. nci. nih.gov/ cgi-bin/ osra/ index. cgi
[14] http:/ / www.cambridgesoft.com/ software/ ChemBioOffice/
[15] http:/ / scistore.cambridgesoft.com/
[16] http:/ / www.acdlabs.com/ resources/ freeware/ chemsketch/
[17] http:/ / www.chemaxon.com/ marvin/
[18] http:/ / accelrys. com/ products/ informatics/ cheminformatics/ draw/ index. html
[19] http:/ / www.acdlabs.com/ products/ draw_nom/ nom/ name/
[20] http:/ / accelrys. com/ products/ informatics/ accord-overview. html
[21] http:/ / en. wikipedia. org/ wiki/ Comparison_of_reference_management_software
[22] http:/ / www.endnote.com/
[23] http:/ / www.refworks. com/
[24] http:/ / mekentosj. com/ papers/
[25] http:/ / www.mendeley. com/
[26] http:/ / www.cas. org/ products/ cd/ cassi/ index.html
[27] http:/ / cassi. cas. org/ search. jsp
[28] http:/ / www.indiana. edu/ ~cheminfo/ C471/ 471ex3.html
Article Sources and Contributors
4
Article Sources and Contributors
Chemical Information Sources/Science Writing Aids Source: http://en.wikibooks.org/w/index.php?oldid=2195341 Contributors: Adrignola, Avicennasis, Gary Dorman Wiggins, Tmvogel, 6
anonymous edits
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