Open Access and Databases Revisited

Utilizing the Directory of Open Access Journals, the list of journals Dr. Medina contributes to, posted previously, was once again employed to find out which, if any, of the journals are open access. Perhaps there are more comprehensive tools than this directory available, however the site claims to cover some biology and life sciences scholarly journals. Using this directory it was found that she has contributed to two open access journals: BMC Genomics and Emerging Infectious Diseases.

I then explored the UC Merced Libraries website to see if any of the databases utilized in a previous posting are available to the faculty there. All but ProQuest Direct were present in their A-Z database list. This however does not prove she has not used it for research because during the time period she has been publishing, she has been associated with different universities and organizations that may have a different variety of databases available.

While I was at the UC Merced University Library I happened to check the Biological Sciences pathfinder I found there. Below is the list of suggested databases:

-BioOne
-BioSIS (via Web of Science)
-Current Protocols Collection
-Karger Online Journals
-MEDLINE (via PubMed)
-National Center for BiotechnologyInformation Bookshelf
-Public Library of Science (PLOS)- Biology
-PubMed
-Web of Science
-Zoological Record

Clusty.com

In a previous class lecture, it was suggested that we may wish to utilize the search engine Clusty.com to find further information on our scientists. For exploration of this tool I simply inserted "Monica Medina" in the search box. This retrieved approximately 194 results. Using the "cluster" option in the side bar, I quickly narrowed it down to 19 results by clicking the link of "Merced, Sciences" which appeared to be the most relevant. This led me to many resources I had previously discovered on my own, however, I discovered that Dr. Medina is associated with the UC Merced Computational BiologyJournal Club . Their mission is to:

• "Raise awareness of current content in Computational Biology, Bioinformatics, Comparative and Functional Genetics and Genomics, Systems Biology, and Molecular Evolution.

• Sharpen critical assessment of the scientific literature and the scientific it mediates.

• Familiarize with the people, groups and societies having an impact in Computational Biology and allied fields.

• Broaden and deepen biological knowledge.

• Provide a community of support for the scientific aims of its participants. "

Interestingly the club's site offers a list of journal titles that they subscribe to, many of which Dr. Medina utilizes for her own publications and research. I feel that this is strong evidence that this is an important source of information and resources for Dr. Medina. Further results within Clusty.com offered some support for a hunch I had that organizations financing her research may also provide her with places for networking with other individuals, another personal and interactive source of information for her. According to her lab's website, her funding sources include: The National Science Foundation (with which it was found, with assistance from Clusty.com, that she is involved in an Geoscience Outreach Workshop), The Department of Energy, UC MexUS-CONACYT, and the International Census of Marine Microbes. Also within the Clusty.com results, a full slide show of a presentation she gave at a conference in Dec. 2004 entitled "Systematics and the Origin of Species. On Ernst Mayr's 100th Anniversary". Her presentation was entitled "Genomes and Phylogeny". Also the search results led me to discover that she is involved with a research project tied to the Smithsonian Tropical Research Institute. Lastly, the Clusty search offered me an article in a UC Merced newsletter that reports "Medina has maintained ties with her former employer, the nearby Joint Genome Institute at Lawrence Berkeley National Laboratory, and is participating in developing the UC Merced Genome Center, a donor-funded core lab featuring the microarray and sequencing equipment she will need" ("Professor pursues marine invertebrate evolution studies." (2006). Panorama UC Merced 2(5). Retrieved February 20, 2009, from http://panorama.ucmerced.edu/panorama_03012006/pages/medina.htm).

This search offered insight into where Dr. Medina may exchange information and ideas with her colluegues in a face-to-face environment.

Databases

In response to a comment made on a January 30th post, I explored four different databases to see which databases covered the journals Dr. Medina contributes to. (If you remember, I felt that the publications she writes in may also be the publications she scans and actively searches for information.) The databases I chose to explore were Biological Abstracts (BIOSIS), Academic Search Complete, ProQuest Direct, and Science Direct. I especially chose BIOSIS for its reputation in the field of biological sciences. Similarly Science Direct was chosen for it proximately in subject. Academic Search Complete and ProQuest Direct were selected because of their broadness and popularity. Below, the list of publications has again been posted with the addition of notation for the database(s) that include each journal within the margin.

The database notation will be as follows:
BIOSIS: $
Academic Search Complete: #
ProQuest Direct: %
Science Direct:@

• Proceedings of the National Academy of Science (PNAS): $ #
• Science: # %
  
• Comparative Biochemistry and Physiology:$ # @
• Molecular Ecology:$ # %
• Systematic Biology:$ # %
• Journal of Experimental Biology:$ # %
• Marine Biotechnology:$
• International Society for Microbial Ecology:
• Emerging Infectious Diseases:$ #
• BMC Genomics:$
• Molecular Ecology Notes [now: Molecular Ecology Resources, but searched under previous title]:$ #
• Annales Zoologici Fennici:$
• 10th International Coral Reef Symposium:
  
• Bulletin of Marine Science:$ #
• Molecular Biology and Evolution:$ %
• International Journal of Astrobiology:
• Molecular Phylogenetics and Evolution:$ # @

Please note that the international publications tend to be absent from the databases selected. It can be seen that the biological database BIOSIS tends to carry a lot of the sources that Dr. Medina publishes in, followed by Academic Search Complete. It should be noted that both BIOSIS and Academic Search Complete are EBSCOhost databases. It is likely that if Dr. Medina uses these journals for inspiration and research, she also favors these two databases.

Web of Science

Using the tool Web of Science, part of ISI's Web of Knowledge, I attempted to find further information on Dr. Monica Medina's work. After a few experiments utilizing trial and error I found that putting "coral" as the topic and "Medina M" as the author gets a slightly better number of results than other methods tried. Using these access points, 5 results were return all of which were authored by the person we're studying, one being a correction of an article. I decided to further explore:

Medina, M., A. G. Collins, T. L. Takaoka, J. V. Kuehl and J. L. Boore (2006). "Naked corals: skeleton loss in Scleractinia." Proc Natl Acad Sci U S A 103(24): 9096-100.

This article was chosen because it was the only one that listed her name as the first primary author and had the most citations. It was cited 37 times. Exploring further using the "analyze results" option it was found that Dr. Medina self-cited only 3 times. Of the other authors that cited her, each cited her two or three times. It is not surprising that most of the citing articles are similar in topic to Dr. Medina's, dealing mostly with genetics, evolutionary biology, marine biology, etc. It was found that most of the citing articles were published in the United States, amounting to 24, followed by Australia with 5 publications listed. Out of the 37 citations, 30 were within articles. All citing publications were in English and were from various institutions. Most of the citations to this 2006 article occured in 2008 (20 citations) and 2007 (14 citations). It would be very interesting to see if it continues to grow in popularity in 2009 and 2010.

Inspiration and Fun with Web of Science

Before being introduced to Web of Knowledge's Web of Science I had started doing a little work for this post. After reading some of the reading this week I was inspired to look at the publication years of the resources Dr. Medina and her colleagues used in in their most recent work:

Sunagawa, S., T.Z. DeSantis, Y.M. Piceno, E.L. Brodie, M.K. DeSalvo, C.R. Voolstra, E. Weil, G.L. Andersen, M. Medina (2009). Bacterial Diversity and White Plague Disease-Associated Community Changes in the Caribbean Coral Montastraea faveolata. ISME J: doi: 10.1038/ismej.2008.131

Below are the age categories used with the corresponding number of sources from this article that fell into each category.

age/year range_______# of articles____% of resources
0-2yrs old (2007-2009) -------15-------------------------22%
3-5yrs old (2004-2006) -------24-------------------------35%
6-10yrs old (2000-2003) ------13-------------------------19%
10yrs old< (1999-____) ------16-------------------------24%

Even though the way I separated the age categories may have something to do with it, I think the results tell a lot. The newest sources weren't as numerous as the 3-5yr. old. Perhaps this illustrates that it takes some time for sources to diffuse and gain momentum before some of them are readily cited. Another possible thought would be that more pertinent research just happened to be performed during in those years compared to the following. I thought it was also interesting that the oldest group of sources accounted for nearly a quarter of the cited sources for this article. Showing the importance of archiving materials; that not all important information is in the newest material and that just because something is over ten years old doesn't make it obsolete/useless. I found that the oldest source within the reference list for this article was published in 1984 by a A. Chao. I tried to look up both this author and Dr. Medina in ISI's Highly Cited but they weren't there. I also tried to look up the article by A. Chao in Web of Science but no results were found. This is possibly because they published in what looks like a Scandinavian statistics journal as the abbreviated title is "Scand J Statist". Nonetheless the Web of Knowledge/Web of Science tools seem very useful and interesting, while needing to be explored further.

Something Besides Journals.

While going through some of the reference lists of Dr. Medina's publications, I attempted to explore the other kinds of materials that were referenced along with journals. But lets first briefly talk about what kinds of journals she's using. As was suggested in lecture, Science and Nature tend to be among the most cited journals, followed by quite few discipline and sub-discipline specific journals. I found that my hunch was correct in finding many of the same journal titles that she has published in were also in her reference lists. Now lets get back to the topic at hand. What about the monographs and other resources?

Here some of the monograph titles (The titles were double checked through yahoo.com to make sure they were actually monographs. Surprisingly a few are available at Target.com. I thought this was interesting but will definitely store that in the back of my mind, just in case.)

-Veterinary Epidemiology, Principles and Methods
-Medical Microbiology, 4th edn
-Algae
-Dinoflagellates
-Corals of the World
-Corals in Space and Time: Biogeography and Evolution of the Scleractinia
-The Cnidarians and Their Evolution
-Progress in Cell Research: Symposium on Thirty Years of Progress in Mitochondrial Bioenergetics and Molecular Biology
-Phytophthora Diseases Worldwide
-Coelenterate ecology and behavior
-Multicellular animals:Anew approach to the phylogenetic order in nature

In addition to these, there are other types of resources that Dr. Medina uses. Some are:

-PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods)
-Treatise on Invertebrate Paleontology
-maanova: a software package for the analysis of spotted cDNA microarray experiments. In: The Analysis of Gene Expression Data Methods and Software
-J/MAANOVA User Manual

This sampling shows a bit of the diversity of material formats that scientists, like any other researcher, need to conduct their projects. It shows that not everything can be found in journal articles and proves that books still have great value in the realm of research.

More Questions than Answers.

Today, after viewing another student's blog, I began to search for more popular literature on Dr. Medina to see if I could get a more informal perspective that might help to answer some questions about her, her work, and information seeking behavior. Lexis Nexis Academic database and all various EBSCOhost databases were searched but few results were brought up and none were very informal. Some were articles by other people that had permission to use photos/diagrams accredited to Dr. Medina. (This did bring up an interesting point. If these other authors knew to ask Dr. Medina for these materials they must have a connection, possibly a networking connection, somewhere. Perhaps I will research this a little for a later post.) Going back to the Medina Lab website for some inspiration, I started combing through the "News" section to see if their was any mention of her being featured in any interviews or articles. Low and behold there were about two citations of such articles that look exactly what I what I was hoping for! The problem: they are all in Spanish. I searched the newspapers' website and could not find anywhere to switch languages. Now I did take a couple of years of Spanish in high school but have retained very little beyond a few key conversational phrases. So as I sat feeling frustrated from being thwarted by a language barrier, I began to ask: what do scientists do if they know there is an article out there that is pertinent to their research but they cannot read the language it was written/printed in? I would think this might happen quite often seeing as there seems like there are so many different places where research is conducted, no one could possibly know all of the languages required. So it makes me wonder: do scientists make impromptu friends within the modern language department of their university or university libraries, employ translation services, or possibly just take their skills from a few years of a language, dust them off and try to fight their way through the article, hoping they don't mistranslate and only seek assistance if they determine it is really important?