FAQ

Chemical Information Retrieval FAQ

instructions
Bill Hooker suggested the OAD site for ideas on questions you may wish to answer

1. What are primary, secondary and tertiary sources?

A primary source is the source of information. In other words, the primary source will give you more information than anything else one would be able to find. Primary sources can a journal article, lab notebook, or patent. For instance, the lab notebook used to record the data of the experiment performed or the published results of that experiment would be primary sources for that experiment. A secondary source, on the other hand, is not the source of information but rather analyzes and talks about information from other sources, usually primary sources. A common example of a secondary source is a review article. Lastly, a tertiary source is similar to a secondary source in that it analyzes and talks about information from other sources. In addition, tertiary sources generalize and summarize information from primary and/or sources. Examples of tertiary sources include encyclopedias and Wikipedia.

References:
"Primary, Secondary and Tertiary Sources." PORT: Penn Online Research Tutorial. 15 October 2009.
<http://gethelp.library.upenn.edu/PORT/sources/primary_secondary_tertiary.html>
"Primary, Secondary and Tertiary Sources." University of Maryland University Libraries. 15 October 2009. <http://www.lib.umd.edu/guides/primary-sources.html>
[SWS] [Full Marks JCB]

2. List 10 primary sources for chemical information

  1. Journal Articles [1]
  2. Lab Notebook [5]
  3. Dissertations [1]
  4. Conference Proceedings [2]
  5. Patents [3]
  6. Technical Reports [4]
  7. Scientific Experiments [4]
  8. Correspondence [5]
  9. Speeches [3]
  10. Interviews [5]

References:
1. http://www-sul.stanford.edu/depts/swain/hosted/cinf/workshop98aug/ways/184lec2.html#confpapers
2. http://www.indiana.edu/~cheminfo/acs800/soced_wash.html
3. http://www.lib.umd.edu/guides/primary-sources.html
4. http://guides.lib.msu.edu/page.phtml?page_id=2469
5. http://library.albany.edu/usered/dr/prisci.html
[VN] [Full Marks JCB]

3. List 10 secondary or tertiary sources of chemical information

  1. Encyclopedia and Dictionary (Such as Wikipedia) [1]
  2. Chemical information handbooks and databases (Such as the CRC Handbook or SciFinder) [3]
  3. Text books [3]
  4. Internet blogs (Such as friendfeed) [1]
  5. Lecture notes [1]
  6. Journal Article (Review article) [1]
  7. Monograph (Such as the United State Pharmacopoeia) [1]
  8. Guide books or lab manual [2]
  9. Criticism and Commentary [2]
  10. Websites (Which can also be considered primary depending on the source) [1]

References:
1. "Primary, Secondary and Tertiary Sources" http://www.lib.umd.edu/guides/primary-sources.html
2. "Primary, Secondary and Tertiary Sources" http://library.uwsp.edu/guides/webtutorials/primary.htm
3. "Primary, Secondary and Tertiary Sources in Health Science" http://www.biomed.lib.umn.edu/inst/sourcesinhs.pdf
[WYM] [Full Marks JCB]

4. Describe the typical sections of a journal article and their purpose

There are six major sections in a scientific journal article, abstract, introduction, experimental, results/discussion, references, and supplemental info. The abstract section is a short concise paragraph on the entire article. It includes some basic information, significant results, and what those results mean. This section is usually around 300 words. The next section is the introduction. In this section, the general and background info is given about your research topic. This section is for people who don't know all the specifics of your particular field to get a better understanding of your research topic. After the intro is the experimental section. Here, all your information about the experiments you did is listed in this section. All the specifics, quantities, temps, and other variables should be listed. Next is the results section. Here are all the charts and graphs made from your data, and any raw results from any experiments. After that comes the discussion. Here is where the interpretations of the results are listed. Any new discoveries are listed and what your final conclusions are. All assumptions made from results are discussed here. Next is the conclusions, where you close the article with a few statements, and discuss future projects and other work. After that is the references section. Here is a list of all the articles you used for your paper in the format listed by the specific journal. The last section of the journal article is the supplemental section. Here is where all your NMRs, IRs, MSs, etc are added. If anyone wants to see your information about a certain compound you synthesized, they would look here for that information.

References
http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWsections.html
[Nick Paparoidamis] [Full Marks JCB]

5. Provide a brief history of peer review in chemistry and its function

The peer-review process is an essential attribute of the publication process of most scientific journals. This process involves subjecting of scientific research papers submitted to the journal to independent scrutiny by other experts in the same scientific area (by peers). During the peer-review process the following is carefully examined: the relevance of the manuscript to the journal; whether the manuscript contains enough scientific or technological merit; whether the manuscript is useful in broadening knowledge and science; whether the ideas described are novel and make a sufficient contribution; whether the study design, execution and conclusions are valid. [1] It is very interesting to observe how peer-review functions evolved over centuries to take on this modern aspect.

The origins of the peer-review are thought to be ancient Greece when manuscripts of Hippocrates (460-370 BCE) and works of Aristotle (380-322 BCE) were written. Aristotle reported his and his colleagues’ findings and observations in his biological writings. These writings were altered by others before they reached modern days, but it was more an attempt to ‘improve’ rather than ‘review’. [2]

The first practice of a similar to peer review process was discovered in Syria and described by Ishaq bin Ali al-Rahwi (854-931 CE) in his book Ethics of the Physician. It was a requirement of a visiting physician to make duplicate notes of the conditions of the patient receiving medical care. After the patient’s recovery or death, the notes were carefully examined by a local council of physicians in determination whether the medical care provided met established standards or not. If the maltreatment was identified, the physician was held accountable and could be sued by the patient.[2]

After invention of the printing press in 1436 (completed in 1440) by Johannes Gutenberg, the easy distribution of information allowed authors to reach out to a wide range of a hungry for information herd, enabling them to debate and discuss the matters that concerned them. From the other side, the Holy Inquisition of the Catholic Church saw this as a threat of new heretic ideas and inventions. Therefore, it was important to screen and investigate all "suspected" novelties going into and coming out of the press. As the negative consequence of such regulations, many authors had to pay with their lives for published ideas.[2]

In 1620, Fransis Bacon (1561-1626) introduced his way of generation and evaluation of new scientific ideas in his Novum Organum. Many English scholars were inspired by his work. They formed groups and held meetings where they discussed and debated over origins and validity of different theories and new discoveries.[2]

Eventually, the Royal Society of London was formed, and by 1665 they had their own journal, Philosophical Transactions. [3] This journal, edited by Henry Oldenburg is considered to be the first journal to formalize the peer review process. Everything what was published in the journal at that time depended on the editor. [2]
Philosophical_Transactions.JPG
In 1731, all scientific manuscripts sent to the Royal Society of Edinburg for publication in Medical Essays and Observations were inspected by a selected group of experts who provided their recommendations on the future advance of these manuscripts. The present-day peer-review process evolved from this 18th century practice. [2].

As science was becoming more diverse, complex and specialized, in the 1900s, the necessity for outside assistance and the recruitment of outside reviewers was increasing. But, there was no any systematic movement in the peer-review process, it was developing desultory. The type of peer review implemented depended on the editor. The pre-1976 Lancet considered peer review unimportant and didn’t use it at all. Other journals, like Journal of the American Medical Association, used internal review, and consulted outside experts only on rare occasions. But journals like British Medical Journal, utilized a very modern-sounding approach of the outside expert peer-review by at least 1893. [4] The reason behind the differences in the scientific review approaches by various journals lied in the need for some journals to fill their pages with articles. That is why some editors tried to avoid strict, expensive and time consuming review process. In addition to that, editors were under tremendous pressure to publish material provided by the owners of the journals. But in the case of well-respected and known journals, which didn’t have the excess of space for articles, they had to be more discriminating as to what they published, so the authors had to compete to publish their manuscripts. Such journals were setting the standards of quality to published material. [5]

Since then the peer-review process continued to develop, and in modern days, the practice of a double-blind review has been adapted, where the authors are unaware of the identity of the reviews and the reviewers are unaware of the identity of the authors and institutions. [2] The thorough examination of the peer-review process was started by the Coles with their evaluation of the peer review of grants at the National Science Foundation. But, the publication of Stephen Lock’s book, A Difficult Balance, in 1985 and the conference held by Journal of the American Medical Association in 1989 in Chicago have changed the field. Other peer review conferences held afterwards (up to 2005) had a tremendous impact on the research into editorial processes which not only broadened the knowledge about the peer-review process, but also improved quality of the journal publications. [5]

Even though the current system of peer review is not perfect, it’s still comforting to know that publications we use to base our thinking and work upon have been carefully examined by the experts in that field.

References:
1. Nayak Barum Kumar, Maniar Ranjit, Moreker Sunil (2005), The agony and the ecstasy of the peer-review process, Indian journal of ophthalmology, 50(3), p. 153-155.
2. Ray Spier (2002), The history of the peer-review process, Trends in Biotechnology, 20 (8), p. 357-358 [357].
(DOI: doi:10.1016/S0167-7799(02)01985-6 )
3. http://www.visionlearning.com/library/module_viewer.php?mid=159
4. Dale J Benos, Edlira Bashari, Jose M Chaves, Amit Gaggar, Niren Kapoor, Martin LaFrance, Ronert Mans, David Mayhew, Sara McGowan, Abigail Polter, Yawar Qadri, Shanta Sarfare, Kevin Schultz, Ryan Splittgerber, Jason Stephenson, Cristy Tower, R. Grace Walton, and Alexander Zotov (2007), The ups and downs of peer review, Advances in physiology education, 31(2), p. 145-152
5. Drummond Rennie (2008), 1: Editorial peer review: its development and rationale, Peer review in health sciences.

[A. Caltabiano] [Full Marks JCB]

6. What are article-level metrics?

Article-level metrics are like an impact factor for journal articles. This will indicate a value to the reader on the quality of the article.
As more journals are created as well as information from other sources, blogs etc, you do not have time to read everything, this would help you to streamline the acquisition or measure of the worth of the article.

PLoS provide additional and regularly updated context, or metrics, to the article, which currently includes data on:

citations: provided by Scopus , PubMed Central and CrossRef are used to represent the number of citations

online usage: This denotes the amount of times the article has been "accessed". Articles are provided in three different formats - PDF, HTML, and XML

social bookmarks: Uses CiteULike and Connotea to denote how many times users bookmark a site. This can be used to denote how popular an article is.

comments/notes: Users can provide comments or notes (not anonymously), this interaction is counted as well, or a rating can be provided.

blog posts about the article: Many blogs are written about articles, there are blog agrigators that look into this, such asPostgenomic , Nature Blogs , and Bloglines .

ratings of the article: PLoS allows for "star" ratings of articles where readers can rate the information as they read it.

There is a variety of known issues with article level metrics. The first issue would arise from robots (and meta crawlers) skewing the metric. PLoS has removed a list of robots from its online usage data, but the removal of this is exhaustive and would most likely reamin in some of these metrics. Scopus indercounts the number of citations due to duplicates in the database.

Metrics Example: Grigoryan G, Zhou F, Lustig SR, Ceder G, Morgan D, et al. 2006 Ultra-Fast Evaluation of Protein Energies Directly from Sequence. PLoS Comput Biol 2(6): e63. doi:10.1371/journal.pcbi.0020063

The Public Library of Science (PLoS) has a nice website dedicated to this, as they are the initial provider of article level metrics.
[JBS] [Full Marks JCB]

7. List 10 Science2.0 applications in chemistry and what features they exhibit

XML/RSS web feeds - Gives constant updates when information on a website is updated.
Blogs - Updates on science topics, bros discussing research, etc.
Wikipedia and the like - Encyclopedia updated by users and containing information on various science topics
Second life - Can make molecules, interact with other chemists.


References:
http://oreilly.com/web2/archive/what-is-web-20.html
[Branden Farlow] [Partial Marks JCB]

8. List 5 Open Access journals where chemists can publish their work and how much they cost

Bentham open (source)

Information is under the heading 'Individual Membership'
  • Cost: $800.00 per manuscript

BMC chemical Biology (source)

Information is under the heading 'Article Processing Charges'.
  • Cost: $1700.00

Beilstein Journal of Organic Chemistry (source)

Information is under the heading 'No Publication Fee'.
  • Cost: No publication fee. The journal is fully financed by Beilstein Institution.

Atmospheric Chemistry and Physics (source)

Information is under the heading 'Service Charges' in a table.
  • Cost: Depending on what the formatting of the entry is. Ranges from 23 to 38 euros per page

Chemistry Central Journal (source)

Information is under the heading 'Article-processing charges'.
  • Cost: $665.00 per manuscript with $50.00 surcharge is the payment was not via credit card.
[Jose Quejada] [Full Marks JCB]

9. List the Creative Commons Options and describe each one

Attribution

  • Credit is required, but the material is free to use.

Attribution Share Alike

  • Commercially, others can use your work, but they have to give credit and be under the same license that the original work is.

Attribution No Derivatives

  • The material cannot be altered, but can be distributed with credit to the original author.

Attribution Non-Commercial

  • Others can use your work as long as they give credit, and their work does not have to be under the same liscense.

Attribution Non-Commercial Share Alike

  • Like Attribution Share Alike, others can use your work, but must be under the same license. However, your work can be translated, altered, and redistributed non-commercially.

Attribution Non-Commercial No Derivative

  • The work cannot be altered. It can be distributed with proper credit, and must cite the original source.
(source)
[S.Shore] [Full Marks JCB]

10. Describe the different impact factors and how they are calculated
The Impact Factor, not impact factor, is published in the Journal of Citation Reports by Thompson ISI. IF is branded by Thompson ISI. Although other journals publish impact factors, they are considered if, for example aggregated if. There is a huge debate on IF and their importance. What if an article is published in a high impact journal that is minimally cited compared to one journal in a lower impact journal that’s heavily cited.

A journal can make an impact in different ways. Generally people know of Impact Factor; however there different variations the impact factor that describes the journal specifically. For example, an article can have an immediacy index, which describes how many times the journal is referenced in that year divided by the total articles of that year. There is also half life, a type of impact factor that describes that article's impact within a certain number of years. Aggregate impact factor specifically describes how often the journal is referenced to in a given time period and topic. Thus, the aggregate impact factor is subject based.

Journals are given an index that is usually given by a ratio of cited over total. (Note that the IF can not be determined until the entire year is over. eg, 2009 must be over. Thus the 2009 impact factor will be published in 2010.

The numerator is given by counting the number of times the article is published two year preceding.
The denominator is given by the total number of primary sources referencing the article and published in those two years - Primary sources and some secondary sources; secondary sources specifically are only reviews for journals.

For example:

The 2009 impact factor journal is determined by sum of the number of times the article is cited by in 2008 and 2007 (numerator). As for the denominator, total number of articles the journal published in 2007 and 2008. This ratio, will become the impact factor for the following year.

References
http://thomsonreuters.com/products_services/science/free/essays/impact_factor/
http://en.wikipedia.org/wiki/Impact_factor
http://www.sph.uth.tmc.edu/library/handouts/impact_factors.pdf
http://www.sciencegateway.org/impact/

[BPL] [Full Marks JCB]

11. Describe the ILL process at Drexel and the typical associated costs

When a book, journal article, or other form of media is unavailable at Drexel Libraries, students and faculty may use an Interlibrary Loan (ILL) program to obtain the desired materials from other participating colleges and universities. Drexel offers two different ILL services: EZ borrow and ILLiad. The programs require University ID number (EZ borrow) or a Drexel domain username (ILLiad) to enroll, which ensures that that only members associated with Drexel may use the service, as a substantial cost is associated with ILL programs. An interview with Peggy Dominy revealed that the cost associated with each transaction is around $29 as of "a couple years ago" - it has likely increased slightly up to this point. Also as a result of this cost, only 10 requests may be made by undergraduates, and 20 for graduate students.

The following information is required to obtain an article by ILL: full journal title, year, volume, and pages. Requests are greatly expedited when a DOI or ISBN is included. Requests are usually filled within a week, but some rare materials can take longer. If hard copy materials are ordered, they can be picked up at the library through which the ILL was requested. Most articles, however, are directly emailed to the user for convenience.

EZ Borrow: http://palci.library.pitt.edu/~ursa/DREXEL_login.html.
ILLiad: http://illiad.library.drexel.edu/illiad/logon.html.

References:
http://www.library.drexel.edu/services/illfaq.
http://www.library.drexel.edu/services/borrowfromotherlibraries.

[Kyle R. Hess] [Full Marks JCB]

12. Describe the doctrine of fair use in US copyright law and abroad

The doctrine of fair use in US copyright law refers to the right to reproduce copyrighted material if such use is considered "fair". Section 107 of the copyright law lists the circumstances under which one may fairly reproduce part of a copyrighted material without the copyright owner's authorization. Some instances considered to be fair use include research, scholarship, parody, education, and news reporting. The concept of fair use varies widely between countries.
There are four main criteria used to determine if the use of a copyrighted work is considered fair. The first criterion is the purpose of the use. If the work is being used in an educational context, for example, the use is likely fair. Using the work in a non-profit way helps, but does not guarantee fair use. The second criterion is the nature of the work borrowed. Factual works are considered more fair to use than artistic works. A work that is educational or not-for-profit is easier to classify as fair to use. The third criterion is amount. Using only a small part of the copyrighted work is considered more fair than borrowing a relatively huge chunk of the original. Note that there is no specific amount of material considered fair. The fourth criterion used to determine fair use is the effect. The effect refers to the effect that the new work will have on the market. Borrowing from the copyrighted material is fair as long as doing so does not interfere with the profit of the author of the original work. It may seem clear to decide fair use based upon these four criteria, but often times these criteria can prove exceedingly ambiguous.
References:
http://www.copyright.gov/fls/fl102.html About the doctrine of fair use
http://www.copyright.gov/title17/92chap1.html#107 Section 107 of the US copyright law
http://en.wikipedia.org/wiki/Fair_use In-depth look at fair use

[Tyler Butler] [Full Marks JCB]

13. How are chemistry data shared and how does US and foreign law apply to databases?

Chemistry data is now shared mostly in internet databases. These data bases can be free or charge a subscription fee. Some free websites are the Pubchem, zinc, NIST chemistry web book, NMR shifts data base, plus many more. The Depth first website at, http://depth-first.com/articles/2007/01/24/thirty-two-free-chemistry-databases, has a list of of thirty-two free databases. There are many data basis that are not free of charge but may have the subscriptions purchased for you by your university or company. As Drexel students we have access to Sci Finder, Beilstein Crossfire, Web of Science, plus others. A complete list of these data basis for Drexel Students can be found at http://library.drexel.edu/resources/databases/chemistry. These data basis, escpcially the free ones, typically contain more general data, such as solubility, MW, B.P, M.P, and spectrum signals. To find more detailed data typically a literature search is required on a database such as SciFinder and the appropriate article must be located. Although today much of the chemistry data can be found in online databasis, hard copies sources still are used.

U.S copyright law does apply to chemical databases. First of all, if the material is copyrightable, then none of the data can be used or distributed in any way shape or form. The factual data on un-copyrighted material can be used and distibuted unless the data was arranged or manipulated in an original way, then direct copy of the arranged data is against copyright law. This is because the data is now considered an original work of authorship, but the actual data itself is considered a fact and can be used. The information above is from the Journal of Technology Law and Policy, Vol. 3, issue 1, Fall 1997 which i found on the following website, http://grove.ufl.edu/~techlaw/vol3/issue1/austin.html.

[JD] [Full Marks JCB]

14. How do Gold and Green Open Access strategies work?

Open access is defined by the free availability of academic, electronic journal articles. There are two types in which open accessed is used, green and gold, which is defined by this site http://www.ercim.org/publication/Ercim_News/enw64/jeffery.html as the following:
[NAD] [Full Marks JCB]

15. Is it better to use your Real Name or a Pseudonym when using science 2.0?

When it comes to the online world, being anonymous is starting to become part of a bygone error of distrust amongst internet users. It was safer to be anonymous when no one knew what could be done with your personal information online. Now with internet no longer in its infancy it has become a topic of debate on whether or not to remain a mysterious pseudonym. More specifically the question is, for the scientific world and science 2.0 is being anonymous the way to go. The answer to this question is still a matter of opinion as is with the rest of the internet, however there is a level of trust that can be put behind a scientific opinion of someone online who is willing to back their comment with their name and possibly a picture, depending on the site in use.

References:
my sources of a few opinions were provided on the Harvard blog site, Digital Natives. Three blog writers, kurquoise ,dianakimball, nikkileon, spoke on the topic of their digital name. The author names attached to their article alone show that not everyone has the same opinion. The common opinion on the subject is that if your going to use your name watch what you say and how you act online. Your comments, pictures, papers, everything can be found with a little time and effort if your going to use your name. Also it is wise to make sure you stand behind what you post, if your name is linked to it people can and most likely will hold you accountable for your opinions and literature.Science 2.0 may be in its infancy but a reputation is still a reputation and it anything with your name attached to it can affect it. Now If you use a pseudonym, it doesn't mean you can post anything that pops into your head, but it allows for a little bit of anominity and a buffer between people knowing exactly who you are and knowing your online name. If you use a pseudonym people will learn to recognize that name over time and it becomes your name and with it the source of possible reputation.
[JShamberg] [Full Marks JCB]


16. What is an Eigenfactor score & how is it received in the scientific community?


An Eigenfactor score is a natural science and social science journal importance rating, generated by an algorithm based on the number of incoming citations within the last 5 years. The Eigenfactor score was created by biologist Carl T. Bergstrom. Unlike the impact factor, the Eigenfactor score takes into consideration the importance of each incoming citation, not just the volume. For example, a citation from a reputable journal such as Nature (Eigenfactor score= 1.992) would contribute much more than a citation from a poorly ranked journal like Chemistry World (Eigenfactor score= 0.00033406). Eigenfactor scores can be obtained free of charge from the website (see link in references below).

While most are fond of the Eigenfactor score, others argue that it discriminates to journals that publish a small volume of articles. Because of this, a "journal usage factor" is being created. However, one of the biggest issues is how a journal Eigenfactor score influences people's perception of the value of the individual articles within that journal. It would obviously be unfair to say that all of the articles published in Chemistry World are inferior to those in Nature. Another pain point concerning Eigenfactor scores is how the journal scores are reflected onto the authors themselves. In general, the Eigenfactor score seems to be more favorably accepted over the impact factor, yet it is no way a perfect system.

References:
http://en.wikipedia.org/wiki/Eigenfactor
http://www.eigenfactor.org/index.php
http://pubs.acs.org/cen/science/86/8621sci1.html
http://www.pnas.org/content/106/17/6883.full
[LC] [Full Marks JCB]

17. What pros and cons of modern peer review are currently being discussed?

hint - use the discussion on Shirley Wu's post Is Peer Review Necessary? as a starting point
Peer review is an important part of determining whether a piece of scientific writing is accurate, but this system is also flawed. In many cases when papers are submitted to a peer reviewed journal the topic may not be closely related to the reviewers' field of expertise. In this case many of the mistakes or incorrect conclusions will be missed; and people are mislead to think that the papers are correct since they have been "peer reviewed". Peer reviews are supposed to be scholarly peers who are just as or more knowledgeable then the author of the piece. There was also a study done where there were mistakes purposely put into papers and were mostly missed by peer reviewers (2)-Raloff. This shows that peer review is not as reliable as a source as some believe it to be. Some journals also have to many papers to possibly give a good amount of attention to so more mistakes are overlooked.
Peer reviews are considered to validate a piece of writing. Its existence is beneficial in the sense that if someone is writing false results another person can point this out before other readers are mislead. Due to peer reviews science has moved forward in the sense that it allows people to challenge one another and also poses a threat for people who are not thorough or dishonest. This also is motivation for a writer who will have their work criticized. Knowing that someone can call out your mistakes will only make you work harder to make all of your points valid. On the other hand, people are aware that not every invalid point made or mistake will be caught, so the benefits to science do not always apply.
Peer reviews should be used as a tool to point out mistakes, but one cannot rely on them alone for accreditation.

References:
1) Discussion on Shirley Wu's post.
2) Raloff,Janet. "‘CRAP’ paper accepted for publication". Science News. Web. June 2009.
http://www.sciencenews.org/view/generic/id/44706/title/%E2%80%98CRAP%E2%80%99_paper_accepted_for_publication
3)Mann, Micheal, and Gavin Schmidt. "Peer Review: A Necessary But Not Sufficient Condition." RealClimate. Web. 27 Oct. 2009. http://www.realclimate.org/index.php/archives/2005/01/peer-review-a-necessary-but-not-sufficient-condition/.
[ C. Petrongolo] [Full Marks JCB]


18. What proportion of OA chemistry journals actually charge any author-side fees?

Open Access journals vary in whether they require publication fees from the author. By submitting to an open access journal, the author may have to pay to have the article open to the public, without need of a subscription. Bill Hooker carried out a survey of the chemistry journals in the Directory of Open Access Journals and found the following:
49% of open access journals do not charge publication fees,
42% of open access journals do charge publication fees
9% of the open access journals did not display information on publication fees.

Reference
http://www.sennoma.net/main/archives/2009/03/authorpays_in_oa_chemistry_jou.php
[EFrankel] [Full Marks JCB]

19. What are the typical sections of a patent and their purpose?

1. Cover Page – The cover page of a patent contains mainly the bibliographic information pertaining to the patent. No legal information is found on the cover page, but information such as historical facts, filing dates, serial number, title, inventors’ names, and patent number. At the bottom of the cover page, the number of claims and drawings pertaining to the patent are found.

2. Specification (Disclosure) – The specification, or disclosure, contains the description of the invention and has certain writing requirements which vary depending upon the country or region it is submitted in. It also contains the title of the invention, cross-reference to related applications, statement regarding federally sponsored research, if applicable, background of the invention, summary of the invention, description of the drawings, detailed description of the invention, sequence listing, and claims. The detailed description of the invention has two sections, which are the general explanation of the invention and how to practice it and specific examples of how to practice the invention. Also, a sequence listing for every nucleic acid that is longer than 10 amino acids must be found in this section of the patent.

3. Claims – The claims section must tell exactly what the author considers as his or her invention so that people who may be infringing upon the patent can know what is covered under the patent by law. A patent must contain at least one claim, which is composed of two sections: the preamble and the body. Also, claims can be independent or dependent. An independent claim contains all the necessary information and does not depend upon another claim. A dependent claim contains all the information for that particular claim but refers to and is limited by another claim.
References:
http://www.patentlens.net/daisy/patentlens/202.html
[LReuther] [Full Marks JCB]

20. What is self-archiving? What are the reasons behind the push for self-archiving of journal articles?

- Self-archiving is a technique used to store a digital document (research) on a publicly accessible website. The title, author, date of work, etc. are pasted onto the website, and the full text of the document is attached for open access. An example would be for a researcher of an institution to self-archive a copy of his work before he submits this to a journal for publishing. This would allow access by all in the institution as well as in other institutions.
- There are a vast amount of journals worldwide available for purchase by various institutions and individuals alike. Typically an institution will only be able to afford a small percentage of these journals. This creates a direct problem for researchers and publishers. In order for research to gain momentum and funding it must have a certain amount of impact. Impact is the amount of times the article is cited in other research articles. This impact directly relates to the ability of the research to be applied and added to by other researchers. Self-archiving is a simple and relatively quick way to increase impact. By allowing more people to view the articles, impact will go up substantially.
- Not all publishers accept self-archiving. Only about 68% of journals are okay with self-archiving. (http://www.eprints.org/openaccess/self-faq/)
- ACS does not accept self-archiving.
References:
http://www.ercim.org/publication/Ercim_News/enw64/harnad.html
http://www.eprints.org/openaccess/self-faq/

[ABilinski] [Full Marks JCB]

21. How do I access Drexel's electronic resources & databases off campus?

  1. You will need to download the Cisco VPN client to access Drexel's restricted network. The following set by step guide will walk you through the steps to gain access to Drexel's Virtual Private Network.
  2. First proceed to the Drexel's Software download page at https://software.drexel.edu
  3. When attempting to access this page you will be prompted for a user name and password
  4. Use your supplied drexel credentials (aka username) inculding the ""@drexel.edu i.e XYZ89@drexel.edu
  5. Use the same password you set to access drexel one and blackboard (password is case sensitive)
  6. Proceed to click students
    1. If you have a Macintosh Computer
      1. Click Macintosh Software
      2. Click on Cisco VPN
      3. Note: there are different versions of the client depending on the version of the operating system
      4. to check the version of your operating system click the apple in the far upper left-hand corner of your screen and select "about this mac"
      5. a box will come up with the version of your software (i.e this apple is version 10.6.1 thus i will want to download the client that will be compatible, in this case i will want to download OSX 10.4 and above from the Drexel Software site.
      6. when the client is downloaded proceed to install the client as if it were any other simple mac installation
      7. I will address connection credentials later on
    2. If you have a Windows Computer
      1. Click on PCsoftware
      2. click on Cisco VPN
      3. There currently is only one version available for download, proceed to download "CiscoVPN.exe"
      4. Note: this version is known to work with Windows XP and Vista @ 32-bit, it is unknown when a compatible version for windows 7 will be released
      5. Proceed to open the MS-DOS executable file labeled CiscoVPN.exe
      6. One the client has been installed it is advisable that you restart your computer
  7. Once the client has been installed on either a Macintosh or a PC, open the Cisco VPN client
  8. You want to make sure you have a good internet connection before proceeding wth the following steps
  9. Click connect within the client and you will be prompted for a username and password
  10. the credentials you enter within the client are similar as those used to access Drexel's Software download website
  11. Example: "XYZ89" for the username (do not include the @drexel.edu at this point) and use your case sensitive password used to also access drexel one and blackboard
  12. Once fully connected you can access all of Drexel's resources as if you were using and on-campus computer
  13. If there are any questions or problems the IRT help desk can be contacted at consult@drexel.edu or via telephone at 215-895-2020

References:
http://www.drexel.edu/irt/networks/offCampus/
[Joshua J. Derrer] [Full Marks JCB]

22. Find five repositories in which chemistry papers could be deposited.

1.Drexel's Repository
2.Harvard's Repository
3.UPenn's Repository
4.Scribd
5.PubMed

References:
D Space- List of Repositories
[MS] [Full Marks JCB]

23. How do journals convert from Toll Access to Open Access?

Many of the open access journals that are available now, once began as toll access journals and publications. Toll access is close to what it sounds like, in order to use the journal the user must pay a fee. This fee would reduce the cost to the author/publisher of the paper. Open access journals are almost the complete opposite, the information is free to users to access, however there is an extra cost for the publisher to get his/her work out there to more people.[1]

Journals can convert from a TA (toll access) to a OA(open access) in two different ways. The gradual method is a way for journals that have toll access to slowly transition into an open access. This is done by giving the authors an option to pay an article-processing fee (APC). If the author chooses to pay this extra fee, then their article will be placed in an OA (open access) section of the website. This is more of a 50/50 toll access journal then a full open access journal. The second method is a sudden conversion to open access. This process again is what it sounds like, a company that has attempted to be a Toll access and is not getting enough subscribers, and may change to an open access quite rapidly. This happens by the journals charging a relatively low APC, which is attractive to authors to publish their articles with them, due to the low cost and the free access for customers to access their work[1].

The Open Society Institute has made a guide for how to convert a Toll Access sites into an open access journal. This guide is complete with business strategies, product services, and information about the electronic marketplace[2].

An example a gradual change is Royal Society of Chemistry's Open Science[1]. A sudden conversion would be much like Hindawi Publishing Corporation, which is a smaller company that attempted to start in a toll market and was struggling, then the company decided to change over to the open access directory methods [1].

The list of companies that converted from Toll Access to Open access is here

The Open Access Directory is a list compiled of most of the journals that are open access, and free for viewers. [note from Bill Hooker: see DOAJ also JCB]

The opposite scenario of when an Open access journal changes to a Toll Access. When this happens all of the existing free documents remain free, however anything added after that day the public will have to pay to access. An example of this would be what happened with the Journal of Visualized Experiments[3].

References:
[1]“Converting to Open Access
[2] Guide to Business Planning for Converting a Subscription-Based Journal to Open Access
[3]"JoVE Leaves Open Access Behind"

[JP]

[Full Marks JCB]

24. What is a DOI and why are they used?

DOI stands for Digital Object Identifier. They are used to name entities located within a digital system. A DOI is exactly what its name implies; an identifier of objects somewhere in a digital environment. The main benefit of using a DOI is that they allow for interoperabiliy, which simply means that even if an identifier is used in a specific context, another person can use the identifier in a completely different system without having to know all of the assumptions made by the original assigner.

The DOI system has profoundly impacted scholarly publishing. In the past, the sharing of digital information was riddled with problems. The most critical of these issues were protecting intellectual property rights and information retrieval. Although the popular opinion was that internet information should be free, it was the perogative of commercial publishers to make a profit. It was also very difficult to find specific information, and then at a later time and place, retrieve the same information. Often the URL would simply disappear or provide a link to an irrelavent page. With a DOI, a specific document is connected with a unique numerical code. This code can be used to locate the document wherever it may be located, regardless of whether the original location has changed or not. It also helps to protect copywritten material by ensuring the data source is legitimate.

References:
DOI System Overview
Digital Object Identifiers: Promise and Problems for Scholarly Publishing

[Adam Myers] [Full Marks JCB]

25. What are the significant events that lead to the open access movement in scientific publishing?

Using scientific journals to distribute key research findings begins with the first print of The Philosophical Transactions of the Royal Society in 1665. Since then, the subscription-based journal has been the traditional vehicle for sharing scientific knowledge. However, subscription-based knowledge sharing has its own limitations, which include low speed and narrow accessibility to the general public. This issue is further exasperated by a sharp increase in the subscription rate to scholarly journals, which is estimated at annual growth rate of 8–10%. Many universities paid hefty fee to attain access to scientific journals, and some schools were forced to cancel their subscription. This potential issue was one of the key drivers for initiating OA movement.
The first open access website (arXiv) was created by Paul Ginsparg from Los Alamos. His intention was to provide scientists a free domain to share research prior to journal publication. His efforts mark the beginning of the OA initiate. Three years later, Steven Harnad further drove the OA initiative forward by asking the researchers to self-archive their papers in public websites. Late 90s witnessed several significant events that have major impact on OA movement. It begins with the installment of the Scholarly Publishing and Academic Resources Coalition (SPARC) for publishing low cost journal and the implementation of PubMed by Harold Varmus to promote free on-line access to pre- and post-prints of journal articles. In 2000, Harold Varmus and other scientists founded the Public Library of Science (PloS). The goal was to encourage scientists to publish their work only in journals that are free in PubMed. The establishment of BioMed Central (BMC) is another major event as part of OA movement. BMC operates with an “author-pays” model which enables their journals free to the public. The last few years further witnessed the significant progress made in the OA movement. To highlight a few, for example, some major journals (e.g. PNAS) are gradually implementing OA. Furthermore, Library associations, government institutions and nonprofit organizations are joining forces in OA movement. Lastly, more countries around the world are embracing OA. France, Germany, Spain, and the Netherlands began to kick off OA and self-archiving initiatives.


Reference:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525322/

[Li Li] [Full Marks JCB]

26. What are the responsibilities of the library requesting an interlibrary loan and the library supplying the interlibrary loan?

According to the American Library Association’s Interlibrary Loan Code for the United States, the responsibilities of a requesting library are as follows:
The requesting library's ILL system must be up to date. The user has a right to privacy. The library needs to provide adequate information on the requested material that meets the suppliers demands. It is preferred that the loan be transmitted electronically. The library is subject to laws pertaining to the sharing or copying of the material. If a requested loan is borrowed and damaged in any way, then the material must be compensated in a way that the supplier library sees fit. The library will take full responsibility of the user if the user mishandles the item in respect. If the requesting library makes a renewal request and the supplying library does not respond, then the requesting library can assume that the renewal has been granted. The supplying library has the right to have their materials shipped in a manner that they prefer and the packaging must prevent damage. All dates should be kept. If the requesting library does not comply with this code the supplying library may suspend the requesting library from any loans.
The supplying library should consider all requests regardless of format. It should update its interlibrary lending service. As stated above the library should maintain the confidentiality of the user. The supplying library should be able to fulfill requests in a timely manner and if it is unable to do so, then it should state why. When a request is being filled it should send enough information so the request. The due date of the item should be upheld. The material should be sent electronically. The supplying library has the right to recollect the material at any moment. The library should respond to request for renewals. If this code is not adhered to then the requesting library has the right to hinder this service.
references:
http://www.ala.org/ala/mgrps/divs/rusa/resources/guidelines/interlibrary.cfm
http://www.upf.edu/sgen/normativa/propia/apar10/angles/loan.htm
[Keith DeNivo] [Full Marks JCB]