Undergraduate Genetics Digital Library



Academic Genetics Research Digital Library

Design Proposal

Suzanne Kosempel

Rutgers University

Digital Libraries (17:610:553:90)

Spring 2015

Term Project - Final

Submitted to Professor Tefko Saracevic

April 27, 2015

Table of Contents

I. Abstract

II. Purpose

III. Objectives

IV. Design

V. Content/Organization

a. Home Page

b. Genetics Sub-fields

c. Online Journals

d. Open Access Journals/Databases

e. eBooks

f. Conference Proceedings/Symposiums

g. Dissertations/Theses

h. Video Tutorials and Websites

VI. Access

VII. Content Management & Preservation

VIII. Services

IX. Metatdata – Dublin Core

X. Evaluation

XI. Legal Issues

XII. Conclusion

I. Abstract

This proposal for an Academic Genetics Digital Library will outline the content to be included and the preliminary design hierarchy as well as discuss how I see the digital library included within Rutgers University for use by undergraduate students. Further, I would seek to provide coded access to this digital library to all Advanced Placement (AP) Biology or Human Genetics high school programs within the state of New Jersey. This connection to the AP high school courses will hopefully inspire and encourage high school students to pursue future genetics studies within Rutgers University. With the addition of this digital library to Rutgers University Libraries, undergraduate students will be able to quickly connect to genetics information and genetics resources available through Rutgers Library and on the web.

II. Purpose

The purpose of the Academic Genetics Research Digital Library (Genetics DL) is to provide a central digital location within the Rutgers University Libraries (RUL) for an overview of genetics and to further connect users to information on sub-fields within genetics. It is also the goal to centralize (in one convenient online location) resources on the field of genetics and its sub-fields including highly ranked online journals, databases, proceedings from national and international conferences and symposiums, dissertations and theses from fellow Rutgers’ students, open access journals and articles, a bibliography of ebooks and links to video tutorials from the World Wide Web.

This Genetics DL would complement other digital collections at Rutgers in RUcore (Rutgers University Community Repository). It is in line with the RUL mission statement, “The Rutgers University Libraries support and enrich the instructional, research, and public service missions of the University through the stewardship of scholarly information and the delivery of information services.” (Rutgers University Libraries [RUL], 2014) In addition it furthers the RUL 2014-2015 Strategic Plan’s specific initiative to “Leverage the considerable expertise of library faculty and staff in digital library development, metadata creation, bibliometrics, repository development, research data management services, and consultation on all aspects of open access and scholarly publishing.” (RUL, 2014)

There are currently no specific research guides within the Rutgers University Libraries for genetics except for a stem cell research guide under the subject of biology and a video tutorial that provides some assistance with many sub-fields of biology including genetics. The Genetics DL can help fill this gap by providing a starting place for genetics academic research within RUL.

III. Objectives

The Genetics DL will be a resource for undergraduate students and NJ high school AP students to use for course work and academic research on papers, projects and lab work. It will aim to connect these users to digital resources but it will also aim to expose AP high school students to undergraduate level resources and to expose undergraduate Rutgers’ students to graduate student research through the use of Rutgers Core depository. The Genetics DL will strive to support the Rutgers Department of Genetics Undergraduate Learning Goals which are to know terms, concepts and theories in genetics and be able to analyze published research articles in genetics (School of Arts and Sciences, Rutgers, 2015). Having this digital library will help undergraduate students and AP high school students to connect to the appropriate journals, databases and open access sources that contain information on genetics. Plus, if they are in need of an overview of a genetics sub-field or key terms with which to start searches for pertinent articles within that sub-field, this digital library will point them in the initial direction.

IV. Design

Initially, I was inspired by the design of the Rutgers Nursing Tutorial which since has been retired and turned into a research guide within the RUL. I liked the idea of straightforward tabs with a hierarchy of information organized within each tab. I envision the Genetics DL having a tab for the sub-fields of genetics with a dropdown menu for several fields. It will also have tabs for Online Journals, Open Access Journals, eBooks, Conference Proceedings/Symposiums, Dissertations/Theses and Video Tutorials & Websites. The program that I used to create the website for viewing won’t allow for a screen capture of the dropdown menus as they are set up as a rollover dropdown. This resulted in me utilizing the table in figure 4.1 to illustrate the dropdown menu structure.

Figure 4.1

|Home |Genetics Sub-fields |Online Journals/Databases |More… |

| |Classical Genetics | |Open Access Journals |

| |Behavioral Genetics | |eBooks |

| |Clinical Genetics | |Conference Proceedings/Symposiums |

| |Molecular Genetics | |Dissertations/Theses |

| |Population, Quantitative and | |Video Tutorials and |

| |Ecological Genetics | |Websites |

| |Genomics | | |

| |Cytogenetics | | |

| |Biochemical Genetics | | |

Figure 4.2 shows a screen capture of the home page but you can access the digital library prototype at .

Figure 4.2

[pic]

Currently, the Genetics DL is designed in a very simple grey, black and white. If this digital library is accepted by Rutgers to be included in RUL, I would include the Rutgers Logo and change the colors to red and white with black font and use blue font for linked text.

V. Content/Organization

Home Page

This page will serve as the “about” page to introduce the library and its purpose. The navigational menu will be on every page as will a search box to search the entire site. I would have had to pay extra to include a search box for my prototype so it does not include one. Please see section VI on Access (p. 12) for further discussion of the search feature that I propose. Please see figure 4.2 above for the home page or follow this link to the home page . The navigation bar has 4 top-level elements as seen in figure 4.1 above: Home, Genetics Sub-fields, Online Journals/Databases, More… Under Genetics Sub-fields there is a dropdown menu with 8 additional levels and under More… there are 4 additional levels. This navigation menu will be present in all pages and a “you are here” indicator will inform you which page you are on. If this digital library prototype is accepted, I would have all 8 elements visible at the top of each page instead of hiding 4 under the More… tab as shown in the page template I used for the prototype.

Genetics Sub-fields

As previously shown above, the library will have general information about different sub-fields within genetics and each sub-field will have its own page. Access to these pages will be through a dropdown menu under Genetics Sub-fields, (see figure 5.3). Currently, I have the following sub-fields: classical genetics, behavioral genetics, clinical genetics, molecular genetics, population/quantitative/ecological genetics, genomics, cytogenetics and biochemical genetics. Each page will provide an overview of the genetics sub-field as well as key terms to use for online searches. For example, the page for the sub-field Genomics will contain a list of search terms: genotyping, gene mapping, epigenetics, genomic imprinting, genomic instability, recombinant DNA, DNA sequencing, bioinformatics, microarrays, polymorphisms, DNA methylation, transcriptomics, epistasis, heterosis, and pleiotropy.

See figure 5.4 or visit

to see the example.

Figure 5.3

[pic]

Figure 5.4

[pic]

Online Journals/Databases

The library will also have access to top ranked journals specifically dealing with the fields of genetics as well as links to the databases which contain articles on the different paradigms of genetics, genetics research and structural information about nucleic acids contained in the Nucleic Acid Database at Rutgers (NDB). The journals were chosen based on their SJR ranking on the SCImago website (). Please see section VI on Access (p. 12) and section XI on Legal Issues (p. 15) for further discussion on access to these journals and databases. Preferrably, if access is granted through RUL under their licensing agreement, the Genetics DL would provide links directly to these journals. Please see the prototype page which lists 18 journals and 6 databases at this time.

Open Access Journals

This will be a separate access page for Open Access Journals which will each be linked to their site. Please see the prototype page which lists 38 linked journals at this time. Also, I have included a link to SOAR, Rutgers Scholarly Open Access Repository.

eBooks

This section will be a bibliography with links to various online books available through RUL. One important piece of information I obtained from a 2004 Rutgers Library Advisory Committee meeting which discussed a Validation Process Focus Group report, was that students in the Rutgers department of Genetics preferred all library materials to be available electronically (RUL, 2004). Therefore, I did not focus on any print material bibliographies. For this section, there may be an added benefit if I group the ebooks by genetics sub-fields allowing for browsing. Please see section XI on Legal Issues (p. 15) for further discussion of how access to these resources will be handled.

I placed a few ebook titles on various topics of genetics within the prototype library which can be viewed at . Going forward, I would hope to link each item to the actual electronic source assuming the digital library is accepted under the RUL licensing agreement.

Conference Proceedings/Symposiums

Currently, I have listed several conferences, some with links, which include or focus on genetic topics. These include:

- International Conference on Human Genetics

- International Mouse Genome Conference

- International Bioethics Conference

- International Symposium on Mutation in the Genome: Detection, Genome Sequencing & Interpretation

- The European Human Genetics Conference

- Symposium in Clinical Genetics

- EMBO Conference Series: Chromatin and Epigenetics

- MDA Scientific Conference

- International Symposium on ALS/MND

- Autism Speaks National Autism Conference.

The goal would be to include links to the proceedings or reports from the current and past years. The prototype page can be viewed at

Dissertations/Theses

I would like the Genetics DL to include access to Rutgers graduate students’ dissertations and theses that pertain to the fields of genetics or to the discussion of bioethics. At this point, RUcore is the Rutgers University repository for both open access and private dissertations. I would like the Genetics DL and Rutgers Electronic Theses and Dissertations (RUetd) search feature to be linked.

Video Tutorials and Websites

This section includes videos that provide information on terms used within genetics as well as information on the different paradigms within Genetics. I have included 5 videos in the Genetics DL. This section also provides links to educational websites that are excellent references for learning and further research. Please see to view them.

VI. Access

I would like the Genetics DL to be a digital library offered through RUL to be able to offer access to the many journals and databases listed. As it contains licensed material, it will need to be accessed with a student’s Net ID. A separate ID will need to be created for every high school participating in the Advanced Placement access. This ID will be used for every AP student within that particular high school, similar to one ID being shared for access to services and databases required for individual graduate courses outside of RUL. At the end of the school year, the ID will be terminated and a new ID will be supplied should the high school wish to continue to participate. It is possible that an annual fee payable to Rutgers may have to be assessed for a high school’s participation in access to the licensed materials.

Originally, I thought the Genetics DL could be included as a special collection in RUcore however to fit there, it could not contain licensed materials that are copyrighted. This digital library is intended to work within RUL and should appear to be seamless, however if it is determined that it should sustain itself as a stand alone site, it will only be able to offer open access resources and indexed information only to copyrighted resources. It will require a search engine and a server. For the search engine, I would recommend the Google Custom Search Engine mainly because I could not find anything close to its reasonable pricing structure and because of Google’s reputation. I would hope it could be transferred to the Rutgers Eden server but it could be supported by an outside server.

VII. Content Management and Preservation

If this digital library proposal to RUL is accepted, it will require a staff member to continuously update ebook resources and add new journals and databases as well as monitor key search terms and any new information that may be pertinent to add to the sub-field pages. Linked websites should be monitored and updated as well. Should the feedback survey in the section on Evaluation be utilized, someone must process the evaluation feedback.

It is most important that the staff member in charge of this digital library stay in communication with the Rutgers Genetics department to learn of any information needs that could be incorporated into the digital library and to stay informed on the development of any new paradigms that may need to be included.

VIII. Services

One of the best possible services that the Genetics DL could be a part of is the Research Guides under RUL Services and Tools. The Research Guides help narrow the resources available to the specific topic of interest. The content of the Genetics DL, the journals and databases, could be picked out and included as a subject guide for Genetics. In addition, either a link to the Genetics DL home page or to each individual page on the different sub-fields could be provided. I would also like to see the “Ask a librarian” research assistance be included on all of the pages of the Genetics DL.

Looking to the future, it would be very interesting to include video of any special lectures held at Rutgers with the appropriate permissions. I have also noticed that some professors have websites with lecture notes which could be linked to the Genetics DL as well.

IX. Metadata – Dublin Core

As most of the material from the Genetic DL will be taken from RUL, metadata will be needed for any dissertations, theses or added materials that may be deposited. RUcore, already assigns metadata to these materials and uses an OAIS model for preservation. If this digital library was to stand on its own, I would choose to use the Dublin Core metadata system for its simplicity and completeness. The 15 elements can succinctly cover most of the information needed concerning any added genetics information, including any URL’s to any information that comes from other websites.

X. Evaluation

I believe it is important to evaluate the specific services libraries provide. Asking for evaluation of these services helps them to evolve. A digital library can be evaluated based on its design and interface, usability, content, and context as well as how it served its purpose or provided a service. As part of Rutgers Libraries, there is a survey which is available online however, it asks for a specific physical library to evaluate. I would like to incorporate a short survey that addresses the content and design and successful outcome of using the Genetics DL. This survey could be a pop-up design that gives the library user the option to deny participating in the survey. These questions were taken from the article Evaluating Hierarchical Organisation Structures for Exploring Digital Libraries (2014) by Hall, Fernando, Stevenson, Clough, Soroa and Agirre.

Q1: How much of the collection do you believe you explored? (0–100 % in 10 %

steps)

Q2: Please rate how good an overview over the collection you got (7-point semantic

differential; good–bad)

Q3: Please rate how organised you felt the collection was (7-point semantic

differential; organised–random)

Q4: Please rate how understandable the collection was (7-point semantic differential;

understandable–not understandable)

Q5: Please rate how familiar you are with the topics covered in the collection (7-point

semantic differential; familiar–unfamiliar)

Q6: Please rate how confident you are about what you would expect to see in the

various parts of the collection (7-point semantic differential; confident–not confident)

Q7: How easy was it to navigate the hierarchy? (5-point semantic differential; very difficult –very easy)

Q8: How easy was it to find the items you selected? (5-point semantic differential; very

difficult–very easy)

Q9: How satisfied are you with the items you found? (5-point semantic differential; very

unsatisfied–very satisfied)

Q10: How successful do you feel you were in completing the task? (5-point semantic

differential; very unsuccessful–very successful)

XI. Legal Issues

Many issues govern the content of the Genetics DL including copyright protection of the authors and licensing rights protection. In my prototype, I have only linked the open access journals, websites and the videos publically located on YouTube. The journals, databases and ebooks listed would all be available under the RUL licensing agreements and hopefully under those agreements, could be linked for access within the Genetics DL. Therefore, this digital library would be restricted to the use of Rutgers students and can only be accessed with an appropriate student Net ID. For demonstration purposes, I did quote some information from other websites for general information under the genomics tab however, should this digital library be formally accepted and developed, original content must be created to populate the sections describing each genetics sub-field.

It would be very difficult to establish this digital library as a stand alone special collection as content must be accessible under some form of license. Belonging to an academic institution which already has acquired access and restricting access to that institution’s students is the best possible solution. However, this library could stand on its own with open access resources, public websites and indexed information on copyrighted resources as stated in section VI on Access.

XII. Conclusion

My goal for this proposal was to create a digital library resource for Rutgers University that centralized materials on genetics, acting as an online resource guide for undergraduate students. At a minimum, it could exist as a Rutgers University Library resource guide for genetics as none exists at this time. The Academic Genetics Research Digital Library could reduce the search time for students and provide them with background information on sub-fields, guidance on where to begin searching for specific research, terms to use for searching specific genetic paradigms and websites and videos for additional descriptive and investigative information.

In order to include top journals and databases which are not open access, the digital library must be included in a licensing agreement for access to articles. This digital library is designed to be included within an academic environment focused on research and knowledge sharing. Therefore, access will have to be restricted to Rutgers University students. However, it would be helpful to expose future advanced placement high school students to this resource as well, hoping to encourage further studies in genetics within Rutgers University.

Looking to the future, perhaps this digital library could link to genetics department faculty resources and websites, perhaps even providing access to key note lectures or current hot topics with the genetics fields. This digital library could be an online conduit for the genetics department to Rutgers University Libraries in addition to being a resource to students.

References

Google. (2015). Google Custom Search Engine. Retrieved April 20, 2015 from

Groden, J., & Lieberman, M. A. (2001). Overview of genetics for the clinician. Epilepsia, 42 Suppl 52-10.

Hall, M., Fernando, S., Stevenson, M., Clough, P., Soroa, A., & Agirre, E. (2014). Evaluating hierarchical organisation structures for exploring digital libraries. Information Retrieval, 17(4), 351-379. doi:10.1007/s10791-014-9242-y

National Information Standards Organization (NISO). (2013). The Dublin Core Metadata Element Set. Retrieved 3-5-2015 from 

OMICS Group. (2014). OMICS International Genetics and Molecular Biology Journals. Retrieved April 20, 2015 from

Rutgers University Community Repository. (2015). Preservation. Retrieved April 22, 2015 from

Rutgers University Libraries. (2004) Validation Process Focus Group Reports. Retrieved March 27, 2015 from

Rutgers University Libraries. (2014). Rutgers University Libraries strategic plan. Retrieved April 6, 2015 from

Scimago Lab. (2007-2015). SCImago Journal & Country Rank. Retrieved on April 6, 2015

from

School of Arts and Sciences, Rutgers. 2015. Department of Genetics Undergraduate Learning Goals. Retrieved on April 6, 2015 from

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