Chemical Literature (Chem 184/284)

Lecture 7: Types of Primary Literature, Part I:
Journals, Conference Papers, Preprints and Copyright

Primary Literature: Publication of Information

• Publication is, as the name implies, the making public of information, by whatever means -- oral, printed or electronic.
• Publication has become a means not only for disseminating information, but also a tool for evaluating a scholar's performance: "Publish or perish."

Types of Publication

• Journals
• Technical Reports
• Patents
• Conference Papers
• Dissertations
  • All of the above are making the transition from print to electronic media.
• Electronic Preprints

Scientific Journals

Types of Journals - Scope

• Nature; Science
  Very broad, covering all of science (more or less...)
• Journal of the American Chemical Society; Physical Review Letters
  Covering all of a major section of science, such as chemistry, biology or geology.
• Journal of Organic Chemistry; Journal of Biological Chemistry
  Covering a major subsection of science, such as organic chemistry or solid state physics
• Biogeochemistry; Nano Letters
  Covering a highly specialized area of research.

Types of Journals - Type of Article

• News and reviews: Science News; Chemical & Engineering News
  These magazines specialize in short summaries of "hot" current research, usually in language aimed at the non-specialist, often written by professional journalists (with some scientific background) rather than by professional scientists.
• Major reviews: Accounts of Chemical Research; Chemical Society Reviews
  These journals specialize in longer articles summarizing the research in a particular field, usually over a specified chronological range. These are generally written by scientists who are expert in the field.
• Major original papers: Dalton Transactions; Tetrahedron
  These journals (the majority of scholarly journals) carry full-length articles on original research.
• Brief communications: Organic Letters, Rapid Communications in Mass Spectrometry
  Some journals specialize in rapid publication of short announcements of research results.
• Mixtures of the above: Science; Nature
  
• Note that some electronic journals are now adding social software for their relevant scientific communities. See, for example, ACS Nano, with its ACS Nanotation site, or the Wiki and "Ask the Expert" features of ACS Chemical Biology,

Structure of a Journal Article

• The structure will vary with the type of article (see above), but a typical full research article will include:
  • Bibliographic information (article title, authors, author addreses (may include e-mail)
  • Abstract (may include keywords)
  • Introduction
  • Experimental section; depending on the topic, these may be reagents and reactions, or computational methods.
  • Results and Discussion
  • Conclusions
  • Acknowledgements
  • References
  • The article may have supplementary or supporting information. For print journals, this usually comes on microfiche; electronic journals may have links to the material online.
• See, for example:
  Jiangang Chen, Qiaolin Deng, Renxiao Wang, Kendall N. Houk, Donald Hilvert, Shape Complementarity, Binding-Site Dynamics, and Transition State Stabilization: A Theoretical Study of Diels-Alder Catalysis by Antibody 1E9
  ChemBioChem, 1 (4), 255-261.

  Compare it with:
  Shin-ichi Yoshida, Tsuyoshi Ogiku, Hiroshi Ohmizu, and Tameo Iwasaki, First Stereocontrolled Syntheses of Unsymmetrically Substituted Bislactone Lignans: Stereocontrolled Syntheses of Four Possible Isomers of Methyl 4,8-Dioxoxanthoxylol
  J. Org. Chem., 62 (5), 1310-1316

• Letters, rapid communications and the like are usually shorter, and may omit some of the sections in the list above. See for example:
  John M. Keith and Eric N. Jacobsen, Asymmetric Hydrocyanation of Hydrazones Catalyzed by Lanthanide-PYBOX Complexes , Organic Letters, 6 (2), 153-155

  Or:
  Brian P. Buffin, Philip J. Squattrito1 and Abiola O. OjewoleThe pH dependent phase transfer of an organometallic complex: synthesis, characterization, and crystal structure of a W(0) tetracarbonyl with an acidic pyridine–imine ligand , Inorganic Chemistry Communications, 7 (1), 14-17.

• Review articles aren't truly primary literature -- they summarize previously published research. So, experimental information is generally absent, but the references section can be huge. For example:
  Michael A. van der Horst and Klaas J. Hellingwerf, Photoreceptor Proteins, "Star Actors of Modern Times": A Review of the Functional Dynamics in the Structure of Representative Members of Six Different Photoreceptor Families , Accounts of Chemical Research, 37 (1), 13-20

  Or:
  Jérôme Lacour and Virginie Hebbe-Viton, Recent developments in chiral anion mediated asymmetric chemistry, Chemical Society Reviews 2003 32 (6), 373-382.

• The precise structure required will vary somewhat from journal to journal; nearly all use an "Instructions to Authors" section to inform prospective authors of their requirements, including methods of submission, article format, citation styles for references, etc.. Print journals normally publish instructions to authors in the first issue of each volume, while electronic journal sites will link to the instructions from the journal home page.

Electronic Journals vs. Print Journals

• Electronic journals had their origins as publicly accessible versions of the computer files used in publishing the print versions of the journals. Gradually, they have taken on a life of their own. Some electronic journals have no print counterpart at all. Many traditional journals now treat the electronic form as the "definitive" version, and the print as a subsidiary publication. As more electronic journals incorporate information in forms impossible in print (audio, video, manipulable data files, etc.), this trend is bound to continue.
• Most electronic journals began in the mid-1990's or later, so it is still the case that some journals have little or no content from earlier years. However, this is rapidly changing as more and more journal backfiles are being made available in electronic form, such as Physical Review and Journal of the American Chemical Society. An organization called JSTOR provides backfiles from wide range of journals including Proceedings of the National Academy of Sciences of the United States of America and Science.

  Note that some publishers (e.g. Elsevier and the American Chemical Society) integrate the back files with the current issues, while others (e.g. American Physical Society, AAAS, Springer) have separate backfile operations. In nearly all cases, if backfiles have been digitized "after the fact", access must be purchased separately from current subscriptions.

• Note that there is not a lot of standardization of features or interfaces for electronic journals. Each publisher has their own approach and there is considerable competition to provide new bells and whistles. One that is provoking cooperation among journal publishers is cross-reference linking. Many e-journals let you jump from a cited article reference in one paper to the full text of the cited article. There may also be links to databases.
• Some electronic versions of traditional journals publish on the Web before the print issue apppears. See for example, the Articles ASAP section of Inorganic Chemistry online. This early publication has had a significant impact on publication priority for patent searching. Note that articles will now list not only the date of print publication, but the date the article first appeared on the Web, for purposes of establshing publishing priority.
• An increasing number of online journals have some form of alerting service, which allows the user to receive e-mail notice when articles fitting a user-defined set of criteria appear online. Some alert to new articles or new issues of particular journals, see ACS Journals Alerts. Others allow the user to search a journal or journals for a particular topic, such as Elsevier ScienceDirect. One of the most recent developments are journals with RSS feeds to disseminate selected information to interested scientists.
• Every peer-reviewed journal will have some instructions to prospective authors on how to submit manuscripts, what format(s) to use, how to cite references, etc. In the print arena, these instructions were usually published in the first issue of each volume. In the electronic arena, there is usually a link on the journal homepage permanently available with the latest version of the "instructions to authors". Unsurprisingly, there is no standardizaiton of how this section is named, or where on the page it will appear, from one publisher to the next.
• While maintaining a large, sophisticated e-journal site is not cheap, it is possible to publish relatively inexpensively on the Web. This has lead to such phenomena as Web-only journals (see: Internet Journal of Chemistry at http://www.ijc.com/), and to free Web distribution of some journals on the Web, where the publisher wishes to obtain higher visibility for the science presented therein. See, for example, SciELO at http://www.scielo.org for Latin American journals or J-STAGE at http://www.jstage.jst.go.jp/browse/-char/en for Japanese journals. However, Web-only journals in chemistry have met with limited success. For example, the Internet Journal of Chemistry recently ended its acceptance of new papers and now exists only as an archive. Over the course of its existence, the number of articles published per year declined steadily from 38 in 1998 to 4 in 2004. But see the discussion of Open Access below.

Peer Review

• The majority of scientific journals publish peer-reviewed articles, also called refereed articles.
• In these journals, the editor sends submitted articles out to persons expert in the field of the article.
• The referee comments on the article and the research it presents.
• The editor then decides whether to accept the article as is, send it back to the author for revision, or reject it outright.
• Reviewing helps uphold scientific standards, but it adds to the delay between research and publication -- often a year between submission and publication.
• Traditionally, reviewing is anonymous, but there has been some movement, especially in new, electronic-only journals, toward naming the referees, and even posting the referee commments with the article. This is not yet widespread, however.
• Note that electronic processing methods, such as e-mail of manuscripts between authors, editors and referees is speeding up the process.

Conference Papers

• Papers presented at a conference are often the fastest way of publishing hot new information.
• But conference papers are often hard to locate in print; indexing can be slow, and they are not refereed in most cases.

Accessing Conference Papers

• Conference papers in chemistry are infrequently available in electronic form. Searching general web databases like Google may yield conference papers which have been mounted on the Web by their authors. Some scientific societies maintain subscription-only collections of their conference proceedings online. See, for example, the Association for Computing Machinery (ACM) at http://portal.acm.org/ or the Institute for Electrical and Electronics Engineers (IEEE) at http://ieeexplore.ieee.org/xpl/conferences.jsp. The American Chemical Society publishes selected conference proceedings in book form as part of the ACS Symposium Series. None of this series is yet available in electronic form.
• Chemical Abstracts indexes conference papers in chemistry. Other indexes are specially devoted to conferences, such as Conference Papers Index and PapersFirst.
• Papers may be published as part of a journal, as a special monograph, or as part of a monographic series -- and may require several tries on MELVYL or PEGASUS to locate some references. See guide to Finding Conference Proceedings at http://www.library.ucsb.edu/subjects/conferences.html.

Electronic Preprints

Preprints vs. Journal Articles

• Most preprints follow the same general format as journal articles -- introduction, experimental, conclusions, references, etc.
• However, preprints are not refereed. An article may be submitted to a preprint server without any peer review. Users have to depend on the reputation of the authors to assure quality, rather than the reputation of the editors or publishers. Some of the major preprint servers do have articles posted by crackpots as well as by highly reputable scientists.
• Note that there is division among journal publishers as to whether an article previously appearing as a preprint can be accepted for publication in a journal. The rule of thumb at the moment in chemistry journals is: No. Physics journals, on the other hand, are much more receptive of articles which have been previously preprinted online.
• In part due to the issues above, and in part due to the "culture" of chemistry as opposed to physics, electronic preprints have not caught on as widely in chemistry...yet. However, Chemical Abstracts Service does selectively index preprints from the major servers (see below).

Finding Preprints in Chemistry

• The arXiv.org e-Print Archive at http://arxiv.org/ is the original preprint server in the sciences, starting in August, 1991, at Los Alsmos National Laboratory. It is a fully automated electronic archive and distribution server for research papers. Archives maintained at arXiv include many areas of physics and related disciplines (including chemical physics), mathematics, nonlinear sciences, computational linguistics, and quantitative biology. Also available at a number of mirror sites around the world.
• The Preprint Archive at http://www.sciencedirect.com/preprintarchive is a permanent web archive and distribution medium for research articles in the field of chemistry. Launched in August, 2000 as the Chemistry Preprint Server, it ceased to accept new articles in May, 2004 due to a lack of interest from the chemical community. However, registered users can still access the articles which were submitted in 2000-2004.

The Crisis in Scientific Publishing

The Librarian's Lament, or: "Why don't we own that title??"

• As research grows, both scholarly societies and commercial publishers increase the number and size of journals.
• Prices increase even faster.
  • More pages per issue, more volumes per year.
  • In the print era, costs of paper and printing increased, often dramatically. While the same forces don't apply in the electronic era, software, hardware, programmers and other support staff for electronic publications have their own inflationary impact.
  • Currency exchange rates can have a drastic effect. When the dollar declines against the euro, prices of European publications for American libraries go up. Cynics note that the prices rarely go down when the situation reverses itself.
  • The fatal spiral: prices go up, so subscribers cancel, so publishers raise prices to stay afloat. Repeat until the journal dies.
  • And, in some cases, publisher rapacity.
• Library budgets no longer keep pace. Public institutions frequently encounter budget crunches from the states that fund them. Private institutions may be hit hard by stock market declines that affect endowment income. Administrators at both kinds of institutions frequently come to view the library budget as a bottomless pit.
• Situation becomes critical...with no clear solutions in sight. Electronic journals are not a solution by themselves - they address only the cost of printing. Production costs for e-journals, especially research and development, may be higher than for print journals. Nonetheless, the convenience and utility of electronic journals is pushing libraries toward subscribing to electronic forms only if they have to make a choice.
• Some organizations are pushing for dramatic changes in the nature of publishing, such as SPARC, the Scholarly Publishing and Academic Resources Coaltion, which has worked with a variety of publishers, mainly scholarly societies, to establish lower-cost journals that compete with some of the most expensive titles. This has had some effect, but by and lange expensive journals have not died. In some cases, whole editorial boards have resigned from expensive journals to start lower-priced alternatives.

Open Access: The Hottest Buzzword in Scientific Publishing

• A hot discussion is raging at the moment among scientists, funding agencies, publishers and information professionals over who should pay for access to scientific information. Many now argue that the institutions and agencies which pay for the research which goes into scientific journals should not have to pay again for access to the published results of that research. Some now advocate the notion of open access -- the idea that scientific research should be made public without cost to its readers. Even among its strongest advocates, the best method of achieving open access is controversial.
• The two principal broad approaches proposed for open access are:
  • open access journals -- Continue the traditional journal structure, but support the journals through some means other than subscription fees.
  • self-archiving -- Make authors, or their employers (universities, corporations, etc.) provide online archives of articles, either as preprints or as reprints following journal publication.
• In the former case, it is usually proposed that the cost of publication be shifted from the subscriber to the authors of the papers, who, in turn, will pass the costs on to their institutions or funding agencies. Some publishers have adopted this approach, though there is much controversy as to what a fair price to charge authors is, or even whether this will stifle publication by authors from less-wealthy institutions. BioMed Central at http://www.biomedcentral.com/home/ is a new publishing service established in recent years which has launched over 100 new titles, mainly in biomedicine, and mainly open access. They charge authors from $620 to $1570 per article depending on the journal; however, institutions can buy "memberships" in BioMed Central that allow their researchers to publish without individual charges. Academic institutional memberships range from $1725 to $8625 per year depending on the size of the institution.
• Some journals have tried to compromise by making their backfiles available free of charge, while continuing to charge subscription fees for the most recoent issues; see, for example, PubMed Central at http://www.pubmedcentral.org, or the list of free content from HighWire Press at http://highwire.stanford.edu/lists/freeart.dtl
• Advocates of self-archiving claim that their alternative is less expensive and point to the success of arXiv (see above), which has not apparently damaged the major physics journals. However, without some central authority dictating archiving standards, there are serious questions about the stability and ease of access of such archives. Both the U.S. National Institutes of Health and the British House of Commons have recently discussed possible requirements for open archives of research funded by their respective institutions. However, both have also backed off from any mandatory archiving policy at the present time.
• Some publishers of traditional journals are very leery of the open access concept, and not just the large commercial publishers. The American Chemical Society, for example, has moved very slowly in the direction of open access, for fear that a mistake in the economic model chosen could cripple the ACS journal publication arm, whose revenues provide a large fraction of the operating budget of the society as a whole.
• The University of California is exploring various options in its eScholarship initiative at http://escholarship.cdlib.org/

Copyright (Intellectual Property, Part I)

• Copyrights apply to the expression of an idea -- literature, art, music...or software.
• Trademarks and Service Marks cover the recognizable symbols of a company, organization or product.
• Patents cover tangible inventions. (More about patents in the next lecture!)
• Trade secrets are undisclosed inventions; theft is illegal, but...there is nothing to prevent a competitor from "reverse engineering" the product.

• Copyright applies to the tangible expression of an idea. You cannot copyright a fundamental concept of science, but you can copyright the paper which publishes its discovery. If I make extemporaneous remarks in front of a class, they are not copyrighted, but these lecture notes are copyrighted.
• Under U.S. law, you do not need to register your book, artwork, etc. to gain copyright protection. As soon as you set down your idea in tangible form, it is copyrighted. However, copyright notices and registration can affect what legal recourse you have if someone infringes your copyright.
• Copyright is for a finite length of time. However, Congress can change the length of copyright, and, in recent years, has expanded it considerably, reflecting both the increasing lifespans of authors and their heirs, and the desire of corporations to retain copyrights for longer and longer periods. For example: Under old copyright law, the first appearances of Mickey Mouse would no longer by owned by the Disney Co....but Disney lobbied for an extension of copyright and got it (not just for themselves.) Once a work is no longer under copyright,is is said to be in public domain, and anyone can use it freely.
• Copyright means that you own the right to determine how your "work" will be reproduced, distributed or performed, as well as the creation of derivative works.. You can license or assign the copyright to others, either in part or whole, for a definite or indefinite length of time. Note that most journal publishers require authors to completely transfer the copyright to the publisher. Work performed while in the employ of another (e.g. the University of California) may have the copyright automatically assigned to the employer, depending on the person's contract.
• The doctrine of "fair use" allows limited copying of materials without prior permission, for educational purposes and criticism. Interlibrary loan of articles is governed by fair use doctrine, for example. So, you can copy a journal article for your own use, but if you make 500 copies for the reader for your giant lecture class, you are infringing copyright and in violation of the law, unless you get permission from the copyright owner (usually by paying the appropriate fee.) Fair use in the electronic arena (music, video, etc.) is under heavy attack from publishers in those areas (recording companies, movie studios.)
• Another major battle of interest to scholars and researchers is the fight over the Google Book Search project (see http://books.google.com/. Google is partnering with major libraries to digitize their holdings. They are digitizing copyrighted as well as public domain works, with their position being that the copyrighted works will not be made available in full text...only indexed for search purposes. Nonetheless, many publishers are suspicious. Also, some authors and governements in the non-English speaking world are very wary of Google becoming the dominant force in online full text, saying it will be biased in favor of English language works, and are starting their own mass digitization projects.
• Many authors and other creators now publish there works with explicit statements allowing certain types of use freely, without releasing the work into public domain. For examples of this kind of "rights" statement see Creative Commons at http://creativecommons.org/.
• Note that copyright is an important concept for you both as a user of published research and as a producer of published research. Traditionally, scientific journals have required authors to transfer copyright of their articles to the publisher as a condition of publication. However, as interest in "open access" (see above) grows, more authors are demanding that they retain their copyrights, and some publishers are acceeding to their wishes.
• See the University of California's Office of Technology Transfer's Copyright Matters website at http://www.ucop.edu/ott/faculty/crprimr.html for a good FAQ on fair use and other copyright matters as they affect the UC.

This page created by Chuck Huber (huber@library.ucsb.edu).
Updated: 01/04/08 03:02:11