Blog Close

As a closing gesture for this project, the class has been asked to make a final blog posting that includes our recommendations regarding where new scientists/engineers should be looking for information, including a variety of literature we've learned about in this course.

Below is my list of recommendations:

-Science and Nature and other broad coverage materials: that will help you keep up to date with what is occurring in disciplines outside of your own. This will allow you to think outside of the box when creating and implementing research projects but also make your projects more comprehensive.

-Discipline and sub-discipline scholarly journals: a good source for discovering what journals this encompasses is conducting a “subject group” search within ISI Web of Science or discipline searches within tools such as Ulrich’s Directory of Periodicals. Remember older materials and open access materials are just as important as the most current commercial journals.

-E-prints: searching http://arxiv.org and similar resources will allow you to further explore research projects while they are occurring.

-Your instructors: are always good sources of information! Whether you ask them directly or explore their publications, you can learn a lot from what they have already done and how they accomplished it.

-Your textbooks. The authors often include citations or well researched suggestions for supplementary reading.

-Encyclopedias: such as the Encyclopedia Britannica, offer a good starting point for exploring unfamiliar topics and offer supplementary sources that are often well established and accepted.

-Specific/pertinent laboratory websites: created to offer the public information on current projects conducted there, take advantage! Good source for learning about current trends and top researchers themselves.

-The electronic databases available for your specialization: I found the Encyclopedia of Library and Information Science to be a really interesting source that opened my eyes to the large amounts of resources available out there and can help to narrow down what databases are appropriate for specific disciplines.

-Pathfinders provided by your institution’s library. These resources make it easier to quickly find pertinent resources.

-ISI Web of Knowledge/Science

-Institutional repositories: these are archives of published works often available to the public or members of the institution and are often searchable and organized by discipline. An example of this would be the Ohio State University’s “Knowledge Bank” .

-Interdisciplinary databases and search engines: Google, Google Scholar, Academic Search Complete, Yahoo.com, Clusty.com, WorldCat are good places to start when exploring topics. Clusty.com offers features such as the clustering of search results which creates a quicker access to the needed materials because they are categorized for you.

-Professional/informal organizations and associations: these will often times provide members with bulletins or journals and offer conferences that facilitate discussion of issues within academic disciplines. These are hot beds of information that nurture burgeoning research projects and provide you with colleagues with common interests that are also great sources of information!

The Questions

In the beginning of this project, the class was given a list of questions to answer throughout the process of researching a scientist. Though many have been included in previous posts, I'd like to take the opportunity now to review these questions and the answers that I have discovered through researching Dr. Monica Medina.

Where might you find a more complete description of their research?
I think the best resource for this is Dr. Medina’s Lab website. It is maintained by her or people close to her, such as her students, so it is the most up to date and most comprehensive. It offers the public information that is unlikely to be found anywhere else.

Can you see any patterns in their literature use?
Yes. Often the same resources that she publishes in are also the resources she cites. She favors many that are listed by the UC Merced Computational Biology Journal Club on their website, an organization of which she is a member.

Would they serendipitously scan for ideas? Where?
She may serendipitously scan for ideas. If so it would be in interdisciplinary resources such as Science and Nature, or the proceedings of conferences and colloquia.

Where might they systematically look for information?
Dr. Medina would systematically search scholarly journals whose coverage is closely related to her research. Examples of these would be Molecular Ecology and Marine Biotechnology

Are there interdisciplinary aspects to their work?
Yes.

If so, how would this complicate their information seeking behavior?
Because of the interdisciplinary aspects of her work, Dr. Medina must explore more basic resources of information to get a strong grasp of the field and the more specific information that is important to her research. This makes it more difficult because she must acquire or refresh her memory on some information before she can begin to understand the more pertinent information. This slows the research process slightly and requires well established and accepted resources to fill in the “background information” needs.

Is there a possibility that their work pulls information from sub-disciplines or disciplines that have historically been working somewhat in isolation from one another?
Yes. She incorporates many sub-disciplines of biology into her work, such as phycology, malacology, and oceanography.

Is there any evidence that they participate in some form of social (computerized or otherwise) networking – especially ones where they are exchanging information with colleagues?
Yes. She has given at least on presentation at a conference but cites other conference proceedings which indicates that she is involved in some sort of formal networking group outside of her institution, the UC Merced Computational Biology Journal Club, and the “invisible college.” Though at this time there has been no evidence to support such conclusions, it may be possible that she participates in listservs or other activities that allow for the sharing of information.

Are the journals, or other information that they are citing, open access?
Very few of the resources she cites are open access. Two open access journals that she has contributed to herself are BMC Genomics and Emerging Infectious Diseases.

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.