Chemical Information Sources/The Publication Process 1

Chemical Information Sources/The PublicationProcess

Primary, Secondary, and Tertiary Sources

Introduction

Traditionally, scientific research work is first published in journal articles (known as the primary literature). It is thenpicked up in various secondary tools whose purpose is to better organize the primary literature and make the retrievalof items of interest much easier. Most important of these are the abstracting and indexing (A&I) services such asChemical Abstracts Service, the Science Citation Index and Scopus. There are differences among secondary A&Iservices both with respect to the depth and breadth of coverage of chemistry and with respect to the swiftness withwhich the average reference to a new primary work makes its way into the A&I databases. A very significant changein scientific publishing is now underway. Innovations such as the American Chemical Society's "As soon aspublishable" process for new journal articles make possible the appearance of Web editions of original researcharticles several weeks before the corresponding print versions. The shift to electronic journals as the archival recordof science is nearly complete. Many chemistry libraries have decided to stop subscribing to printed journals. With somuch new information available, there are other sources that help to sift through, condense, and re-package the mostimportant discoveries. For example, some people write reviews of what has been happening in a given scientific areaover a period of time. Of course, once the new discoveries have been validated and deemed important enough, theywill find their way into various books, encyclopedias, and other secondary sources.

Types of Primary Literature

PRIMARY LITERATURE refers to the first place a researcher will reveal to the scientific community in a publiclyaccessible document the results of scientific investigations. In many cases, the document that describes these resultshas undergone rigorous review by one or more peers who help insure the integrity of scientific knowledge.Increasingly, however, we are seeing appear on the Web PREPRINTS, unreviewed literature that is posted by theoriginal author. More traditional primary publications include scientific journal articles, published conferenceproceedings, technical reports, dissertations or theses, and patents. All of these are collectively calledDOCUMENTS.Different types of information and different levels of detail are found in each of the DOCUMENT TYPES ofprimary literature (journal article, patent, dissertation, etc.). Since that is the case, it is sometimes important todistinguish the document type when a search is being conducted. Therefore, the type of primary document may becoded in a database or printed abstracting or indexing journal that covers more than one type of document in order toaid in retrieval.Let's look at a few journal titles that one might expect to find in any respectable chemistry library. The AmericanChemical Society Committee on Professional Training publishes a Recommended Journal List [1] for UndergraduatePrograms. On the list are commercial news journals such as Science and Nature, primary research journals such asInorganic Chemistry, and primary journals designed to rapidly communicate new research results such as ChemicalCommunications and Tetrahedron Letters. Also on the list are some secondary sources, such as Chemical Reviews.On the other hand, a new movement in scientific publishing is OPEN ACCESS, defined by the Budapest Opean Access Initiative [2] as the free availability of literature on the open internet permitting users to read, download, copy, distribute, and print the full-text. Publication fees are levied to the authors instead of libraries paying a subscription for the journal. All manuscripts submitted to open access journal still undergo the rigorous peer review process. The potential audience for an open access article is much greater than that in a subscription based journal. However, most of the prestigious journals in chemistry are subscription based making them more attractive to authors. The Directory

Chemical Information Sources/The Publication Process 2

of Open Access Journals [3] contains a few thousand open access journal titles, some of them in chemistry. There arealso hybrid open access journals, such as the Royal Society of Chemistry's Chemistry World [4] which draws relevantarticles from all RSC journals and provides free access to those articles highlighted in the tool. Another example isthe AuthorChoice option of the American Chemical Society.SPARC (Scholarly Publishing and Academic Resources Coalition) [5] was developed by ARL (Association ofResearch Libraries) to advocate changes in scholarly communication. There is an Open Access Working Groupinitiated by SPARC that is building a framework for the collective advocacy of open access to research.Writing and Publishing a Journal Article in Chemistry

Before a chemist writes a paper he/she must determine its intended audience and what journals reach it. If the authorpicks the wrong journal it may be returned with the comment that the “work is not appropriate for this journal.” Anauthor should do a literature search on the topic to determine which journals have published papers in that area.When selecting a journal its prestige, access, and impact should be considered. One way of determining those factorsis to consult a database called Journal Citation Reports [6] published by Thomson Reuters. It offers a systematic,objective means to critically evaluate the world's leading journals, with quantifiable, statistical information. Oneimportant criterion is the Impact Factor, a measure of the frequency with which the "average article" in a journal hasbeen cited in a particular year or period. Thus, authors should consult Journal Citation Reports to find journals intheir specialty with high impact factors. Once a journal is chosen the chemist must consult the “Instructions forAuthors” page which is on the journal’s web site. An author may submit a manuscript to one journal. If it is rejectedhe/she may offer it to another periodical for consideration.Two recommended sources: Robinson, M. S. (2008). Write like a chemist: A guide and resource. Oxford: OxfordUniversity Press.Day, R. A., & Gastel, B. (2011). How to write and publish a scientific paper. Santa Barbara, Calif: Greenwood.

The Secondary Literature

The terms "primary," "secondary," and "tertiary" literature are interpreted differently by different authors. We willcall SECONDARY LITERATURE such things as textbooks, treatises, monographs and "edited texts" (books withchapters written by different authors), encyclopedias and dictionaries, handbooks and data compilations, reviewarticles and review serials, bibliographies, and indexing and abstracting services.All of these secondary works have in common the goal of repackaging and better organizing the new informationreported by researchers in the primary literature. Since there is additional work involved in creating the secondaryworks (that is, they gather their information and facts from the primary works), they are always less current than theprimary literature.

The Temporal Relationship Between New Primary Literature and the Secondary Literature

Depending on the type of effort expended in their compilation, the secondary works require varying periods of timeto repackage or explicate new knowledge. Thus, there is a definite flow of scientific information [7] from theinception of a research idea through the various types of secondary sources. One can typically expect to find therepackaged new knowledge or pointers to/summaries of new primary works in:•• Indexing tools: a few days to several weeks after the new primary work appears.•• Abstracting tools: one to nine months or more after the new primary work appears.•• Review articles: one to three years or more after the new primary work appears.•• Various collected works: repackaged in the form of handbooks, dictionaries, encyclopedias, etc., the most

important facts and data appear two to five years or more after new primary works are published.It is important to understand that the lag time is only partially linked to the frequency of updating of the secondarypublication or database. Taking examples from several decades ago, the time lag for two journal articles entered inthe Chemical Abstracts Service database, which at the time was only updated weekly, can be seen in the following

Chemical Information Sources/The Publication Process 3

abstracts:1. CA abstract 93:25540j appeared in the volume 93 no. 3 (July 21, 1980) issue of Chemical Abstracts, but the

original journal article was in the v. 102 no. 7 (March 26, 1980) issue of the Journal of the American ChemicalSociety. Time lag: apparently 117 days.

2. CA abstract 106:205033s appeared in CA issue v. 106 no. 24 (June 15, 1987), but in the v. 37 no. 1 (April 1987)issue of the Journal of Photochemistry. Time lag: perhaps 60-75 days.

Thus, the fact that an abstracting or indexing journal is updated every week or even daily does not necessarily meanthat the primary literature covered in that A&I update is the new primary literature that appeared that week. Quite thecontrary, there is almost always some lag time between the appearance of the new primary literature and its coveragein the secondary sources. However, with some abstracting or indexing sources, notably ingenta [8] (formerly,UnCover), the time lag is quite small, on the order of a few days.A development that is reducing the time lag between the publication of new primary literature and its inclusion inA&I services is the electronic publishing of new journal articles long before the appearance of the print versions. The"As Soon As Publishable" (ASAP) policy of the American Chemical Society and similar early publication policies ofother primary publishers (e.g., Springer) have tended to drastically reduce the lag time. Under ASAP, the articlespublished in ACS journals appear in the electronic versions of the primary journals some two to six weeks prior tothe corresponding print title. The references to the articles are also fed into the Chemical Abstracts database (whichis a part of the ACS) much earlier than those for the primary journals of other publishers.Other categories of secondary works are directories, buyers' guides, biographical works, etc. These cannot be relatedeasily to the primary literature in a temporal sense.

Types of Electronic Sources

There are databases that correspond to the different primary and secondary printed sources. They can be categorizedas:• BIBLIOGRAPHIC - provide a bibliography of documents, perhaps with abstracts (summaries), and increasingly

with links to the full texts of the primary documents. Each record includes the elements needed to identify thedocument including journal title, author(s), article title, volume number, issue number, pages, and year ofpublication.

• NON-BIBLIOGRAPHIC - numeric, text, dictionary, and directory databases.Non-bibliographic databases are sometimes called FACTUAL or SOURCE databases, as opposed to bibliographicdatabases that traditionally give only pointers to primary publications that have facts in them.The Internet, especially applications based on the World-Wide Web, is accelerating the creation of true full-text databases and blurring the distinction between abstracting/indexing databases and primary journals. Scientific full-text databases on the Web include graphics, for example, the Web versions of the American Chemical Society journals. Both HTML versions and pdf versions of the articles are found in some databases. The HTML versions may have enhanced features such as links in the references of the bibliography of an article to ABSTRACTS (summaries) of the cited articles in an A&I database, with further links to the full-text Web version of the cited older articles. For example, it is now possible to link directly from the various options for searching the Chemical Abstracts database to over 1,000 primary journals through the ChemPort [9] option. A project (CrossRef [10]) provides direct links from the citations in an article to the cited article without having to visit an A&I service as an intermediate step. CrossRef is also the official DOI (Digital Object Identifier) registration agency for scholarly and professional publications. Thus, if we find a DOI identifier, such as 10.1021/ci050354f, you can link to the full text of the article by entering in your browser the DOI preceded by http:/ / dx. doi. org/ , as in: http:/ / dx. doi. org/ 10.

1021/ ci050354f [11]. A revolutionary step in the publishing of electronic journal articles was taken in 2007 by the Royal Society of Chemistry when they introduced their RSC Prospect [12] project. This provides hyperlinks from words in the article to their definitions in such works as the IUPAC Compendium of Chemical Terminology [13] (the

Chemical Information Sources/The Publication Process 4

Gold Book) and various bioscience ONTOLOGIES (schemes that show the relationship of all of the concepts andterms in a subject field). In addition, compounds are linked to structural depictions and other data about them.Most primary chemistry journals are now available on the Web. See the list of WWW versions of ChemistryElectronic Journals [14] list accessible through the Indiana University Chemistry Library.

Options for Database Searching

The options for database searching include:• ONLINE SEARCHING of remote databases outside the boundaries of the organization where the search is

performed.VENDORS of online search services (for example, STN International) lease or acquire databases from the databasePRODUCERS (such as Chemical Abstracts Service or Thomson Reuters) and make them available on remotecomputers. For a given vendor, which may have dozens or hundreds of databases on its computers, the databases areall searched by a common COMMAND LANGUAGE or graphical user interface (GUI). In the vast majority ofthese cases, there is a fee for searching the databases. Another option is to search free chemistry databases on theWeb. Usually, the quality and range of search features of the free Web databases are not as great as those of thecommercial databases. In addition, there are many differences in the search interfaces that the user encounters amongfree Internet databases. Nevertheless, they should not be ignored for certain types of searches.• IN-HOUSE SEARCHING of databases within the organization.Large organizations now routinely load databases on their own computers. Several new models of providingdatabase searching are now being explored with the advent of client/server computer systems and WEB SERVICES[15].

Tertiary Sources: Guides to the Literature

We will consider works that are designed to teach you how to use primary and secondary works to be TERTIARYworks. Many of these are GUIDES [16] of one sort or another, and indeed, this Wikibook is an example of a guide.Guides are covered more thoroughly in another chapter.

Summary

There are many different types of publications and databases in which the vast literature of chemistry is published.From the primary literature (places where original research is first published) through the secondary literature (whichrepackages the important findings first reported in the primary literature), the searcher has many options from whichto choose. It is the goal of Chemical Information Sources to acquaint you with those tools so that you can makeintelligent choices about how to efficiently satisfy your chemical information needs. While you may not consideryourself a master of all of them, you will at least have an awareness of the existence of the best tools to answer yourquestions once you have worked through all of the chapters of this guide.SIRCh Links for The Publication ProcessProblem Set on this topic [17]

Chemical Information Sources/The Publication Process 5

References[1] http:/ / portal. acs. org/ portal/ PublicWebSite/ about/ governance/ committees/ training/ acsapproved/ CTP_006024[2] http:/ / www. soros. org/ openaccess/ read[3] http:/ / www. doaj. org/[4] http:/ / www. rsc. org/ chemistryworld/ index. asp[5] http:/ / www. arl. org/ sparc/ about/ index. shtml[6] http:/ / thomsonreuters. com/ products_services/ science/ science_products/ a-z/ journal_citation_reports/[7] http:/ / www. lib. uwaterloo. ca/ usered/ grad/ researchskills/ flow_of_info. html[8] http:/ / www. ingentaconnect. com/ ;jsessionid=50h8kc626du0k. alice[9] http:/ / www. chemport. org/[10] http:/ / www. crossref. org/[11] http:/ / dx. doi. org/ 10. 1021/ ci050354f[12] http:/ / www. rsc. org/ Publishing/ Journals/ ProjectProspect/[13] http:/ / goldbook. iupac. org/[14] http:/ / www. libraries. iub. edu/ index. php?pageId=5226[15] http:/ / en. wikipedia. org/ wiki/ Web_services[16] http:/ / www. indiana. edu/ ~cheminfo/ 00-02. html[17] http:/ / www. indiana. edu/ ~cheminfo/ C471/ 471ex4. html

Article Sources and Contributors 6

Article Sources and ContributorsChemical Information Sources/The Publication Process  Source: http://en.wikibooks.org/w/index.php?oldid=2266453  Contributors: Adrignola, BruceS8852, BruceSNJIT, Gary DormanWiggins, 1 anonymous edits

LicenseCreative Commons Attribution-Share Alike 3.0 Unported//creativecommons.org/licenses/by-sa/3.0/