Project Title: Cytoscape visualization of chem2bio2rdf data

1. Spring 2010: S637 Final Project Possibilitieshttp://ella.slis.indiana.edu/~katy/S637-S10/project5.htmlPresentation schedule on Tue March 2Wells Library 030:*10:50a Ying Ding, dingying@indiana.edu*11:00a Colin Allen, colallen@indiana.edu*11:10a John Walsh, john.a.walsh@gmail.com(5 min warning)*11:20a Margaret M. Clements, mclements6@yahoo.com*11:30a Jennifer Robinson, jenmetar@indiana.edu*11:40a Micki McGee, mickimcgee@gmail.com(Rich presents?)*11:50a Jon Duke, jduke@regenstrief.org(Katy presents)

2. Project Title: Cytoscape visualization of chem2bio2rdf data Name of Client: Ying Ding (dingying@indiana.edu) Brief description of project goal and value: Cytoscape is a popularly visualization tool used in biomedical area. It is user-friendly to visualize various networked data, especially data in biomedical domain. In this project, we want to figure out on how to use cytoscape to visualize Linked Open Data (LOD) datasets. Chem2bio2rdf is a LOD RDF dataset in chemical biology area. How to visualize these RDF data with associations on gene, compound, disease, drug and side effects by using Cytoscape. Reference: http://www.cytoscape.org http://chem2bio2rdf.org

3. Project Title: Visualization of IVL RDF data Name of Client: Ying Ding (dingying@indiana.edu) Brief description of project goal and value: Information Visualization Lab (IVL) data has been converted to RDF data based on ontology. We would like to explore the potential of using Google visualization API and Flex on how to visualize such data (people, presentation, papers, projects, grants). If desired, how to integrate your visualization algorithms to the Semantic Web Portal we developed recently. Reference: http://vivo.slis.indiana.edu http://code.google.com/apis/visualization http://www.adobe.com/products/flex

4. InPhO: The Indiana Philosophy Ontology http://inpho.cogs.indiana.edu/ Client: Colin Allen, colallen@indiana.edu Brief description of project goal and value: Visualizing relationships among philosophers & philosophical ideas: timelines, concept maps, influence networks, etc. Practical goals of building user interfaces for exploring and navigating philosophical resources, and identifying the foundational role of philosophy in the history and current development of science. Reference The project goal is InPhO visualization, see http://inpho.cogs.indiana.edu/ Colin’s slides are at http://inpho.cogs.indiana.edu:16080/Slides/S637/

5. Project Title: Symbolic Visualization of the Chymistry of Isaac Newton Name of Client: John Walsh, 812-856-0707, jawalsh@indiana.edu Brief description of project goal and value:Isaac Newton wrote and transcribed about a million words on the subject of alchemy, or chymistry, of which only a tiny fraction has today been published. Newton's alchemical manuscripts are graphically and visually rich, full of alchemical symbols; Newton's own illustrations; difficult scribal, editorial, and representational challenges; and complex graphic organizational schemes. The Chymistry of Isaac Newton <http://www.chymistry.org> is a project, funded by the NSF and NEH, to digitize and edit Newton's alchemical manuscripts. See details at http://ella.slis.indiana.edu/~jawalsh/tmp/newton_vis_proposal Pointers to relevant publications, online sites, etc. The Chymistry of Isaac Newtonhttp://www.chymistry.org/ “Symbol Guide.”The Chymistry of Isaac Newton.http://webapp1.dlib.indiana.edu/newton/reference/symbols.do

6. Project Title: Visualizing the Essential Patent Space of Telecommunications Standards by Family, Company, and Country Name and Contact Information: Margaret M. Clements, Ph.D., mclements6@yahoo.com Description of the Project Goal: Standards, in the innovation and intellectual property community, are developed by industry leaders as a way to advance technologies. By setting and defining essential technological standards, it it is hoped that the innovation can be stimulated and advanced by making products that are interconnective and interoperable. Common examples of products that are governed by patent standards include the video cassette recorder, blu-ray technology, the USB, Global System for Mobile Communications (GSM), etc. This project relates to standards developed by and for the telecommunications industry. The European Telecommunications Standards Institute (ETSI) seeks to eliminate barriers to innovation by establishing global standards for Information and Communications Technologies (ICT). As a non-profit organization, ETSI is comprised of 766 organizations from 63 countries. The standards it develops, reviews and evaluates apply to telephones (both fixed and mobile), radio, internet, and broadcast technologies. By developing technology standards that result from industry cooperation and collaboration, it is believed that barriers to innovation can be reduced. However, it is possible and likely that distortions can also arise in the system.

7. The goals of this project include: 1) Map the patents that have been declared to ETSI as "essential" to the various telecommunications standards. This could be done by standards, company and geography. 2) Analyze the technologies by company and standard over time 3) Examine the geographical coverage of patent family members. 4) For those patents declared as essential, map the patent citations by industrial classification and examine this information by corporation. This project is important because it provides an important window on processes of competition and cooperation--both of which are necessary components to technological advancements. Reference: http://www.wipo.int/patent-law/en/developments/standards.html http://www.etsi.org European Technical Standards Institute http://www.uspto.gov US Patent and Trademark Office http://www.delphion.com Patent Cooperative Treat Publications http://www.espacenet.com/index.en.htm

8. Project Title: ISSOTL09: Analyzing presentations at the 2009 conference of the International Society for the Scholarship of Teaching and Learning Project Client: Jennifer Robinson, Dept of Communication and Culture Indiana University, 812-855-4607; fax: 812-855-6014, jenmetar@indiana.edu Description of Project & Goals: The International Society for the Scholarship of Teaching and Learning is a relatively new organization. It was founded in 2004 in response to the growing field of scholarship of teaching and learning that invites professors, graduate students, administrators, and even undergraduate students to formulate theory-framed, evidence-based considerations of how teaching relates to student learning in higher education. The most recent, sixth conference of the Society was held in Bloomington, Indiana in October, 2009. This year, 650 people from 15 countries attended. Because his area of scholarly activity is so new, we are still trying to understand who is involved and what they consider to be within the scope of this field of study. I envision this project as being a kind of inductive mapping of the field of the scholarship of teaching and learning, drawing from real presentations from self-identified scholars of teaching having their work peer-reviewed at the premiere scholarship of teaching and learning conference in the world. Based on this study, the Society’s Board of Directors, on which I serve as president, will be able to make informed decisions about the future of the Society and the field. The results of the study could impact decisions about future calls for proposals, the Society’s proposal for a new scholarly journal which is currently in progress, the standards for excellence of scholarship in Society conferences and publications—and even the quality of higher education around the world. Reference: Society website: www.ISSOTL.org Data in pdf form: http://www.issotl09.indiana.edu/downloads/ISSOTL09_Program_FinalDraft.pdf I can also make it available as an Excel spreadsheet

9. Project Title: The Yaddo Archive Project: Mapping a Creative Community, 1926-1980 Project Lead: Micki McGee, and Co. Curator for Yaddo, Assistant Professor, Fordham University, Department of Sociology and Anthropology 441 East Fordham Road, Dealy 401, Bronx, NY 10458 212-343-7035 voice and fax, 917-596-1815 mobile mmcgee@fordham.edu or mickimcgee@gmail.com Bloomington/Indianapolis Liaison: Richard Edwards, Assistant Professor, Media Arts and Science, Indiana University/Purdue University, School of Informatics 535 W. Michigan St., IT 489, Indianapolis, IN 46202-3103 317-278-9638, edwards9@iupui.edu or redwards7@gmail.com Brief description of project goal and value: The Yaddo Archive Project: Mapping a Creative Community, 1926-1980 aims to combine the tools of social network mapping and visualization software to develop a web-based visualization that will allow scholars and students of mid-twentieth-century American art and culture (as well as a broader cohort of fans and aficionados of American arts and letters) to chart the relationships among the artists, writers, composers, and other intellectuals affiliated with Yaddo, one of America’s oldest and most distinguished artists’ communities, as well as to track the impact that these relationships had on their creative output. Our hypothesis is that the widely held assumption that creative clusters lead to cultural productivity, but we also anticipate that a visualization of this data will reveal important patterns regarding race, gender, and institutional affiliations. This project builds on the research I conducted for the development of the exhibition and edited volume, Yaddo: Making American Culture (NYPL/Columbia University Press, 2008).

10. The key elements of the proposed project would be an interactive online graphic platform that will: • allow users to chart networks and relationships that made Yaddo a formidable force in twentieth century American arts and letters; • map and identify in particular the relationships that were forged during Yaddo visits (Yaddo friends and intimates) that later impacted American arts and letters; • chart art works, publications, and musical compositions created before, during, and after Yaddo visits with an eye toward demonstrating the impact of a Yaddo residency or residencies and the resulting relationships on subsequent artistic productivity; and, • in the long-term launch a Web 2.0 component where registered users (scholars, archivists, and biographers familiar with Yaddo and its artists, along with members of Yaddo’s current community with institutional memory of the relationships between individual artists) can contribute new information on the relationships and artworks that were fostered during Yaddo residencies. Sidebar: What is Yaddo? Founded in 1900, Yaddo is an artists' community located on a 400-acre estate in Saratoga Springs, New York with the mission of nurturing the creative process by providing an opportunity for artists to work without interruption in a supportive environment. Since its first official season in 1926, Yaddo has hosted artists, writers, composers and other creative workers including including Milton Avery, James Baldwin, Leonard Bernstein, Truman Capote, Aaron Copland, Philip Guston, Patricia Highsmith, Langston Hughes, Ted Hughes, Alfred Kazin, Ulysses Kay, Jacob Lawrence, Carson McCullers, Sylvia Plath, Katherine Anne Porter, Mario Puzo, Clyfford Still, and Virgil Thomson. Yaddo's extensive archive, numbering more than 550 boxes of materials, is now held and preserved as The Yaddo Records, at the New York Public Library's Division of Manuscripts and Archives.

11. Contribution:This project will contribute to advancing work in digital humanities scholarship and will expand relationships between social network scholarship and the sociology of culture. While there has been considerable work in sociology and interdisciplinary studies regarding how artistic communities contribute to the development of cultural products (Becker, 1984) and to urban landscapes and economies (for example Currid, 2007; Zukin 1989; Kostelanetz, 2003) there have been few collaborations among scholars engaged in network theory and those involved in cultural sociology. Sociologists of culture have argued that creative production occurs in “art worlds” (Becker, 1983) and in cultural fields (Bourdieu,1993, 2003) and others outside of sociology, for example Richard Florida (2002) have argued for the economic importance of cultural clusters. But to date very few sociologists have brought together analysis of both cultural forms and social networks. Exceptions to this rule include the work of Randall Collins (2003) and Brian Uzzi and Jarrett Spiro (2005), who have begun to explore the formation of creative clusters in artists’ communities. In addition to bringing together the tools of cultural analysis with the methods of social network analysis, this research will be of practical interest to cultural institutions that aim to develop programs to foster cultural production. Existing Project Assets:Data Assets:To date more than 11,000 relationship data points and 35,000 data points overall have been culled from the Yaddo Records and recorded in data tables. These data are formatted along the following vectors: Person to Person Relationships (coded by type, including, Friend, Yaddo Friend (met there), Spouse, Liason/Lover, Sibling, Parent, Sponsor/Letter of Recommendation Provided) Person to Entity Relationships (entities, Yaddo, but also publishing houses, agents, galleries, educational institutions, museums, and award granting agencies such as foundations) Works of Art or Publications (published, performed or exhibited within 5 years and within 10 years of a Yaddo residency) Dates of Yaddo Stays (most years are granulated down to the day, but for two years in the 1930s this level of detail does not exist in the archival record) Media Assets:The Yaddo Records includes more than 550 boxes of letters, applications, photographs, journals, manuscripts, ledgers, sound recordings and other ephemera. Hundreds of key documents and photographs have been digitized for the production of the book and exhibition. A key visual resource for this project may be a series of 60 group portraits of the artists and writers in residence at Yaddo between 1926 and 1980, which, along with the network visualizations, may form the core visual materials for this project. In addition, Richard Edwards and Shannon Clute produced as series of podcasts regarding Yaddo's history that could be accessed and highlighted as part of the project materials. 

12. Upcoming publication, distribution and exhibition venues for this project: Conferences/Institutes. In August 2010 I will participate in the NEH-Digital Humanities Summer Institute on "Networks and Network Mapping for the Humanities" at UCLA's Institute for Pure and Applied Mathematics, where progress on this project will be discussed.  Journal articles will be prepared for Theory, Culture, and Society, Cultural Sociology, and the Journal of Digital Humanities after the network analysis and interpretations are completed Exhibition opportunities (online and/or physical displays) exist at Yaddo, the New York Public Library, and Fordham University. Related Links: Yaddo: Making American Culture— edited volume, Yaddo: Making American Culture (Columbia University Press, 2008) — link to exhibition documentation and installation shots— NYPL Yaddo: Making American Culture podcast— NYPL online exhibition brochure/themes— Yaddo Records, NYPL Manuscripts and Archives Records, and Finding Aid— sample historical photographs (Yaddo group portraits) (possible project visual assets)— Indiana University/Purdue University School of Informatics lecture, Mapping A Creative Community: Notes from the Yaddo Archive Project— link to Richard Edwards and Shannon Clute's YaddocastThe website for Yaddo (www.yaddo.org).

13. Project Title: Visualization of Side-Effects Profiles of Prescription Medications Name of Client: Jon Duke, Regenstrief Institute, Inc. jduke@regenstrief.org Description of Project Goals: Regenstrief Institute analyzes medication labels to determine potential drug side-effects. This information involves thousands of side-effects and thousands of drugs. Drugs belong to a number of different therapeutic classes and side-effects can be grouped in a number of different ways. We are looking to create visualizations for analysis of patterns in the adverse event data. This will require multiple dynamic views of the data with different aspects highlighted according to use case. A complementary component of the project is the visualization of drug interaction data. Drug interactions have variable severity, frequency, and clinical effects. In this project, we will be developing visualizations which convey both 1:1 interactions and multi-drug interactions in an intuitive manner to support physician decision-making. As Regenstrief is based in Indianapolis, students will need to come up at least a few times during the semester, though much of the work can be done virtually.

14. Katy: Would you have more information on the number of drugs, side effects, adverse event, and drug interaction data? Students could generate a large scale map of drugs, side effects, adverse event or drug interactions. Jon Duke: Sure, we have 5,600 drug labels covering approximately 1,900 drugs. We might start with a smaller subset though, say 300 labels for about 80 drugs. There are 3,766 different possible side effects. Each drug has an average of 76 side-effects, but it ranges from 0 to 508. There are roughly 20 broad drug categories, but it could be more granular than that. For example, Psychiatric Drugs --> Depression Drugs --> SSRI's (i.e. Prozac). So we can break things down in different ways. It would be quite a remarkable (and challenging) feat to create a large scale map of this in a sensical way.