W. John MacMullen
Assistant Professor
Graduate School of Library and Information Science
University of Illinois at Urbana-Champaign
332 LIS Bldg., MC 493, 501 East Daniel St.
Champaign IL 61820
217-265-0741
wjohn at illinois dot edu


Research | Teaching | Service | Education | Publications | Awards | Conferences

Research

My research investigates the practical problems scientists face that result from information overload and the large-scale fragmentation of information and knowledge due to the increasing specialization of disciplines. In particular, I am studying how life scientists use information resources such as structured data sets and the biomedical literature in their work processes. From a theoretical perspective, I am interested in advancing what we know about human information interactions, particularly cognitive processes involved in readers' interpretations of text, data, and images. From a development perspective, I am interested in methods and systems for de-fragmenting and integrating data and literature to facilitate the discovery process, from both the top-down and end-user perspectives.

My current projects focus on the creation and use of Gene Ontology annotations in model organism databases. This research has been funded by the National Library of Medicine (NLM) and an unrestricted research gift from Microsoft Research (Gary Marchionini and Catherine Marshall, PIs). My group is also investigating related issues in scholarly communication and data curation, such as identifying and characterizing authors' claims and evidence in experimental articles, and exploring impacts of temporal constructs in complex use cases for secondary reuse of scientific data.


Funded research projects
  • Principal Investigator, "Information Integration Using Annotation Evidence". National Library of Medicine Individual Biomedical Informatics Fellowship (1F37LM009194-01), 2006-2008, $72,344.

  • Principal Investigator, "Manual literature annotations as potential evidence for annotation behavior principles, document features, and interface design". GSLIS ICR Seed Fund grant, 2008, $7,555.

  • co-Principal Investigator (with Carole Palmer), "A Graduate Program for Scientific Communication Specialists: Getting Past the Prototype in Biological Informatics". National Science Foundation (NSF) (IIS-0534567), 2005-2009, $249,189.

  • Researcher, "The Data Conservancy : A Digital Research and Curation Virtual Organization", National Science Foundation (NSF) (OCI/ITR-DataNet 0830976), Sayeed Choudhury, Principal Investigator, 2009-2014, $20,000,000.

Student researchers for 2009: Margaret Gross (GSLIS), Sheena Beaverson (GSLIS), Dan Lou (GSLIS).
Research group alumni: Jennifer Hill (GSLIS), Bojana Skarich (GSLIS), Katie Lobner (GSLIS), Shu-wen Huang (GSLIS), Zilong Wang (Statistics), Liu Yang (Industrial Engineering)

Teaching

Spring 2010
  • LIS530BLE, Health Sciences Information Services and Resources
Fall 2009
  • LIS501D, Information Organization and Access (syllabus on Moodle)
  • LIS590BI, Introduction to Biological Informatics Problems and Resources (syllabus on Moodle)
  • Office hours: Mondays, 2:00 - 3:00 CT, Tuesdays, 4:00 - 5:00 CT, or by appointment (email is the best contact method).
Spring 2009
Fall 2008
Spring 2008
Fall 2007
at the University of North Carolina
  • Bioinformatics Research Review (INLS 279), Fall 2005. (syllabus)
  • Health Sciences Information (INLS 225) (now INLS 705), Spring 2005. (syllabus; requires username & password)
  • Management for Information Professionals (INLS 131), Summer 2003. (syllabus; requires Onyen & password)

Service

Committees
  • GSLIS Bioinformatics Coordinator
  • UIUC M.S. in Bioinformatics Steering Committee
  • UIUC GSLIS Doctoral Studies committee, AY 2008-2009, 2009-2010
  • UIUC GSLIS Curriculum committee, AY 2007-2008
  • Faculty Advisor, UIUC GSLIS Student Chapter of the American Society for Information Science & Technology (ASIS&T), AY 2007-2008, 2008-2009, 2009-2010
  • Medical Library Association, Medical Library Education Section, Chair Elect and 2010 Annual Meeting Programming Committee Chair
Ad hoc peer reviewing
Ph.D. Advising
  • Ellen Rubenstein (dissertation committee member, 2009)
  • Brant Chee (exam committee member, 2009)
  • Karen Wickett (exam committee member, 2009)
  • Thomas Dousa (exam committee member, 2008)
  • Qin Wei (exam committee member, 2008)
  • Dan Wright (exam committee member, 2007)
Master's Advising
  • Shu-wen Huang, M.S. in Bioinformatics, 2009 (thesis: "Comparative analysis of molecular networks in gastrointestinal stromal tumor and leiomyosarcoma")
  • Margaret Gross, M.S. in LIS (thesis advisor)

Education

Publications

Peer-reviewed journal articles and conference papers
  • Hill, Jennifer I.; MacMullen, W. John; Palmer, Carole. Characteristics of bioinformatics employment advertisements. To appear in the Proceedings of the 2009 Annual Meeting of the American Society for Information Science & Technology (ASIS&T). [abstract]
  • MacMullen, W. John (2006). Quantifying literature citations, index terms, and Gene Ontology annotations in the Saccharomyces Genome Database to assess results-set clustering utility. In Proceedings of the 69th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), Vol. 43. [abstract]   [supplementary data]
  • MacMullen, W. John and Denn, Sheila O. (2005). Information problems in molecular biology and bioinformatics. Journal of the American Society for Information Science & Technology 56(5), 447-456 (special issue on bioinformatics). [abstract]
  • MacMullen, W. John, Vaughan, K.T.L., & Moore, Margaret E. (2004). Planning bioinformatics education and information services in an academic health sciences library. College & Research Libraries 65(4), 320-333.
Peer-reviewed short conference papers and posters
  • Bartlett, Joan C.; Hemminger, Bradley M.; Kampov-Polevoi, Julia; MacMullen, W. John; & Benoit, Gerald. Evolving Curricula in LIS-focused Bioinformatics Programs. Short paper for panel discussion at the 2009 Annual Meeting of the American Society for Information Science & Technology (ASIS&T). [abstract]
  • MacMullen, W. John (2008). Searching for Uses and Users in Gene Ontology Research. Short paper & poster for the Annual Meeting of the American Society for Information Science & Technology (ASIS&T), October 2008. [abstract]   [full text & poster]
  • MacMullen, W. John (2008). Understanding biocurators: Attributes and roles of model organism database curators. Poster for the Medical Library Association (MLA) Annual Meeting, May 2008. [abstract]   [poster]
  • MacMullen, W. John (2007). A Research Design for Measuring Variation in Database Curators' Annotations Through Prospective Randomized Controlled Studies. Poster for the 3rd International Digital Curation Conference, Washington DC, December 2007. [abstract]   [poster]
  • MacMullen, W. John (2007). Measuring variation in curators' GO annotations through a controlled multi-MOD study. Poster for the Second International Biocurator Meeting, San Jose CA, October 2007. [abstract] [poster]
  • MacMullen, W. John (2007). Contextual Analysis of Variation and Quality in Human-Curated Gene Ontology Annotations. Poster at the 2007 Association for Library and Information Science Education (ALISE) annual conference doctoral poster competition. Awarded Honorable Mention. [abstract]   [poster]
  • MacMullen, W. John (2006). Facets and measures of Gene Ontology annotation quality in model organism databases. In Proceedings of the 69th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), Vol. 43. [abstract]   [full text & poster]
  • MacMullen, W. John (2005). Inter-database annotation linkages in model organism databases. In Proceedings of the 68th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), Vol. 42. [abstract] Also presented at the First International Biocurator Meeting, December 2005.
  • MacMullen, W. John (2004). Effects of geographic factors on the education and training of health sciences librarians in the mid-Atlantic states. Medical Library Association (MLA) 2004 Annual Conference, p. 59.
  • MacMullen, W. John (2003). Discovery support systems for the integration of biomedical knowledge. Canadian Journal of Information and Library Science, 27(4), 78. Abstract from Connections 8 conference, Long Island NY, June 2003.
  • MacMullen, W. John (2003). PROMIS: An XML-based metadata framework for proteomics. In Proceedings of the 66th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), Vol. 40, pp. 526-527. [full poster]
  • Denn, Sheila O. and MacMullen, W. John (2002). The ambiguous bioinformatics domain: A conceptual map of information science applications to molecular biology. In Proceedings of the 65th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), Vol. 39, pp. 556-558. [full poster]  
  • MacMullen, W. John, Parmelee, Mary C., Fenstermacher, David A. and Hemminger, Bradley M. (2002). Defining an open metadata framework for proteomics: The PROMIS project. In Proceedings of the 2002 American Medical Informatics Association (AMIA) Annual Symposium, p. 1093. [full poster]  
  • MacMullen, W. John and Fenstermacher, David A. (2002) Toward the development of an open metadata framework for compositional proteomics. In Caulfield, H. John, et al. (eds.), Proceedings of the 6th Joint Conference on Information Sciences (JCIS 2002), p. 1274. [full poster]
Presentations
  • Edwards, Phillip M.; MacMullen, W. John; Paquette, Scott; & Winget, Megan (2009). Junior faculty engagement at iSchools: Personal experiences during the first several years. Panel discussion at the 2009 iConference.
  • Smith, Linda C.; Cragin, Melissa; Heidorn, P. Bryan; Palmer, Carole; MacMullen, W. John (2008). Developing an Effective Data Curation Education Program. Presentation (by L.C. Smith) at the "Education for Digital Stewardship: Librarians, Archivists or Curators?" workshop at the Joint Conference on Digital Libraries (JCDL), June 20, 2008; Pittsburgh, PA.
  • MacMullen, W. John. Introduction to Digital Scientific Data. Summer Institute on Data Curation, Graduate School of Library & Information Science, University of Illinois at Urbana-Champaign, June 2, 2008.
  • Cragin, Melissa H.; D'Avolio, Leonard; MacMullen, W. John; Smith, Catherine Arnott (2007). The Effects of Context on Data Quality in Biomedical Data Reuse. (MacMullen's presentation: 'Gene Ontology annotations as an example of the impact of curatorial variation on data reuse'.) Panel at the 2007 Annual Meeting of the American Society for Information Science & Technology (ASIS&T).
  • Cragin, Melissa H.; MacMullen, W. John; Wallis, Jillian C.; Zimmerman, Ann (2006). Managing Scientific Data for Long-term Access and Use. (Panel at the 2006 ASIS&T Annual Meeting.) Presentation: 'Achieving cross-species knowledge integration with model organism databases and the Gene Ontology'. [abstract]   [full-text PDF]
  • MacMullen, W. John, Moore, Margaret E., Vaughan, K.T.L., Jenkins, Carol G., and Hemminger, Bradley M. (2003). Planning bioinformatics education and information services in an academic health sciences center library. Medical Library Association (MLA) 2003 Annual Conference.
Other publications
  • MacMullen, W. John (2006). Contextual Analysis of Variation and Quality in Human-curated Gene Ontology Annotations. Dissertation overview and poster for the 2006 i-Conference Doctoral Colloquium. PDF
  • MacMullen, W. John (2005). Annotation as Process, Thing, and Knowledge: Multi-domain studies of structured data annotation. SILS Technical Report TR-2005-02. Chapel Hill: University of North Carolina, School of Information and Library Science, Technical Report Series. PDF
  • MacMullen, W. John (2003). Requirements Definition and Design Criteria for Test Corpora in Information Science. SILS Technical Report TR-2003-03. Chapel Hill, NC: University of North Carolina, School of Information and Library Science, Technical Report Series. PDF
  • MacMullen, W. John (1998). "Anonymity, Privacy, and Security on the Internet" and "Internet Commerce: A Global Marketspace". In Dempsey, Bert J. and Jones, Paul, (Eds.), Internet Issues and Applications, 1997-98, pp. 67-85 & 133-144. Lanham, MD: Scarecrow Press, 1998. ISBN: 0810834308.
  • MacMullen, W. John (1997). Rethinking the Enterprise: Applying Business Process Re-Engineering Principles to the Evolution of Inter-Organizational Communication. Master's Thesis, UNC-Chapel Hill, School of Information and Library Science, May 1997, 93 pages.

Awards

Conference Participation