Additional Front Material (Thesis)

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Dedication

This thesis is dedicated to my parents, who encouraged me in all things, and is particularly dedicated to my husband and my son, without whose patience and support I could not have finished this research.

“Among those who have endeavoured to promote learning and rectify judgement, it has long been customary to complain of the abuse of words, which are often admitted to signify things so different, that, instead of assisting the understanding as vehicles of knowledge, they produce error, dissension, and perplexity….” Dr. Samuel Johnson, 1752, via Nature Structural & Molecular Biology 14, 681 (2007).

“Metadata is a love note to the future.” (NYPL Labs, http://twitpic.com/6ry6ar, via @CameronNeylon @kissane)

Acknowledgements

Many thanks go to my supervisors Dr. Anil Wipat, Dr. Phillip Lord and Dr. Matthew Pocock. A special thanks goes to those people who found extra commas and other errors: Phoebe Boatright, Dr. Dagmar Waltemath, Lucy Slattery, Mélanie Courtot and Dr. Paul Williams, Jr. Past and present colleagues at Newcastle University have provided much support and inspiration, including Dr. Frank Gibson and Dr. Katherine James.

I gratefully acknowledge the support of the BBSRC and the EPSRC for funding CISBAN at Newcastle University. I also acknowledge the support of the Newcastle University Systems Biology Resource Centre, the Newcastle University Bioinformatics Support Unit and the North East regional e-Science centre.

Declaration

I declare that the following work embodies the result of my own work, that it has been composed by myself and does not include work forming part of a thesis presented successfully for a degree in this or another University.

Allyson Lister

Contributions and Papers

During the course of this work, I have been involved both in the development of a number of standards efforts and in the publishing of a number of papers.

The list below describes the standards efforts to which I have contributed and the roles I have had within those efforts:

• a developer of UniProt/TrEMBL [1];
• a program developer and contributor to the FuGE [2, 3, 4], a standard XML syntax for describing experiments;
• a core developer and coordinator of the OBI [5, 6, 7], a standard semantics for describing experiments;
• an early developer of the ISA-TAB [8] tab-delimited syntax for describing experiments;
• a developer of the minimal information checklist MIGS/MIMS for genomics and metagenomics information [9];
• an advisor for the SBO, the KiSAO and the TEDDY;
• a co-author of the SBML Level 3 Annotation package [10];
• an advisor for the Cell Behavior Ontology¹; and
• an advisor in the nascent synthetic biology standards².

I have co-authored 20 papers, specification documents, articles and technical reports during the course of this work:

1. Mélanie Courtot, Nick Juty, Christian Knupfer, Dagmar Waltemath, Anna Zhukova, Andreas Drager, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, and Nicolas Le Novère. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7(1), October 2011.
2. Stephen G. Addinall, Eva-Maria Holstein, Conor Lawless, Min Yu, Kaye Chapman, A. Peter Banks, Hien-Ping Ngo, Laura Maringele, Morgan Taschuk, Alexander Young, Adam Ciesiolka, Allyson L. Lister, Anil Wipat, Darren J. Wilkinson, and David Lydall. Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet, 7(4):e1001362+, April 2011.
3. Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. MIREOT: The minimum information to reference an external ontology term. Applied Ontology, 6(1):23–33, January 2011.
4. Allyson L. Lister, Phillip Lord, Matthew Pocock, and Anil Wipat. Annotation of SBML models through rule-based semantic integration. Journal of biomedical semantics, 1 Suppl 1(Suppl 1):S3+, 2010.
5. Andrew R. Jones and Allyson L. Lister. Managing experimental data using FuGE. Methods in molecular biology (Clifton, N.J.), 604:333–343, 2010.
6. Allyson L. Lister. Semantic integration in the life sciences. Ontogenesis,
   http://ontogenesis.knowledgeblog.org/126. January 2010.
7. Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, and Reinhard Schneider. Live coverage of intelligent systems for molecular Biology/European conference on computational biology (ISMB/ECCB) 2009. PLoS Comput Biol, 6(1):e1000640+, January 2010.
8. Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, and Reinhard Schneider. Live coverage of scientific conferences using Web technologies. PLoS Comput Biol, 6(1):e1000563+, January 2010.
9. Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra C. Janga, and Julian Huppert. Interfacing systems biology and synthetic biology. Genome biology, 10(6):309+, 2009.
10. Allyson L. Lister, Matthew Pocock, Morgan Taschuk, and Anil Wipat. Saint: a lightweight integration environment for model annotation. Bioinformatics, 25(22):3026–3027, November 2009.
11. Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. MIREOT: the minimum information to reference an external ontology term. In Barry Smith, editor, International Conference on Biomedical Ontology, pages 87–90. University at Buffalo College of Arts and Sciences, National Center for Ontological Research, National Center for Biomedical Ontology, July 2009.
12. Allyson L. Lister, Phillip Lord, Matthew Pocock, and Anil Wipat. Annotation of SBML models through Rule-Based semantic integration. In Phillip Lord, Susanna-Assunta Sansone, Nigam Shah, Susie Stephens, and Larisa Soldatova, editors, The 12th Annual Bio-Ontologies Meeting, ISMB 2009, pages 49+, June 2009.
13. The OBI Consortium. Modeling biomedical experimental processes with OBI. In Phillip Lord, Susanna-Assunta Sansone, Nigam Shah, Susie Stephens, and Larisa Soldatova, editors, The 12th Annual Bio-Ontologies Meeting, ISMB 2009, pages 41+, June 2009.
14. Andrew R. Jones, Allyson L. Lister, Leandro Hermida, Peter Wilkinson, Martin Eisenacher, Khalid Belhajjame, Frank Gibson, Phil Lord, Matthew Pocock, Heiko Rosenfelder, Javier Santoyo-Lopez, Anil Wipat, and Norman W. W. Paton. Modeling and managing experimental data using FuGE. OMICS: A Journal of Integrative Biology, 13(3):239–251, June 2009.
15. Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. The OWL of biomedical investigations. In OWLED 2008, October 2008.
16. Susanna-Assunta Sansone, Philippe Rocca-Serra, Marco Brandizi, Alvis Brazma, Dawn Field, Jennifer Fostel, Andrew G. Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister, Michael Miller, Norman Morrison, Tim Rayner, Nataliya Sklyar, Chris Taylor, Weida Tong, Guy Warner, and Stefan Wiemann. The first RSBI (ISA-TAB) workshop: ” can a simple format work for complex studies?”. OMICS: A Journal of Integrative Biology, 12(2):143–149, June 2008.
17. Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J. Allen, Samuel V. Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude dePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank O. Glockner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E. Lewis, Kelvin Li, Allyson L. Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, and Anil Wipat. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26(5):541–547, May 2008.
18. A. L. Lister, M. Pocock, and A. Wipat. Integration of constraints documented in SBML, SBO, and the SBML manual facilitates validation of biological models. Journal of Integrative Bioinformatics, 4(3):80+, 2007.
19. Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank O. Glöckner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan. eGenomics: Cataloguing our complete genome collection III. Comparative and Functional Genomics, 2007.
20. A. L. Lister, A. R. Jones, M. Pocock, O. Shaw, and A. Wipat. CS-TR number 1016: Implementing the FuGE object model: a systems biology data portal and integrator. Technical report, Newcastle University, April 2007.

Bibliography

[1]

The UniProt Consortium. The Universal Protein Resource (UniProt). Nucl. Acids Res., 36(suppl_1):D190–195, January 2008.

[2]

Andrew R. Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A. Ball, Alvis Brazma, James DeGreef, Nigel Hardy, Henning Hermjakob, Simon J. Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K. Julian, Kent Laursen, Stephen G. Oliver, Norman W. Paton, Susanna-Assunta Sansone, Ugis Sarkans, Christian J. Stoeckert, Chris F. Taylor, Patricia L. Whetzel, Joseph A. White, Paul Spellman, and Angel Pizarro. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology, 25(10):1127–1133, October 2007.

[3]

Andrew R. Jones and Allyson L. Lister. Managing experimental data using FuGE. Methods in molecular biology (Clifton, N.J.), 604:333–343, 2010.

[4]

Andrew R. Jones, Allyson L. Lister, Leandro Hermida, Peter Wilkinson, Martin Eisenacher, Khalid Belhajjame, Frank Gibson, Phil Lord, Matthew Pocock, Heiko Rosenfelder, Javier Santoyo-Lopez, Anil Wipat, and Norman W. W. Paton. Modeling and managing experimental data using FuGE. Omics : a journal of integrative biology, 13(3):239–251, June 2009.

[5]

Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. The OWL of Biomedical Investigations. In OWLED 2008, October 2008.

[6]

The OBI Consortium. Modeling biomedical experimental processes with OBI. In Phillip Lord, Susanna-Assunta Sansone, Nigam Shah, Susie Stephens, and Larisa Soldatova, editors, The 12th Annual Bio-Ontologies Meeting, ISMB 2009, pages 41+, June 2009.

[7]

Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. MIREOT: The minimum information to reference an external ontology term. Applied Ontology, 6(1):23–33, January 2011.

[8]

Susanna-Assunta Sansone, Philippe R. Serra, Marco Brandizi, Alvis Brazma, Dawn Field, Jennifer Fostel, Andrew G. Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister, Michael Miller, Norman Morrison, Tim Rayner, Nataliya Sklyar, Chris Taylor, Weida Tong, Guy Warner, and Stefan Wiemann. The First RSBI (ISA-TAB) Workshop: “Can a Simple Format Work for Complex Studies?”. OMICS: A Journal of Integrative Biology, 12(2):143–149, 2008.

[9]

Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J. Allen, Samuel V. Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude dePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank O. Glockner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E. Lewis, Kelvin Li, Allyson L. Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, and Anil Wipat. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26(5):541–547, May 2008.

[10]

Dagmar Waltemath, Neil Swainston, Allyson Lister, Frank Bergmann, Ron Henkel, Stefan Hoops, Michael Hucka, Nick Juty, Sarah Keating, Christian Knuepfer, Falko Krause, Camille Laibe, Wolfram Liebermeister, Catherine Lloyd, Goksel Misirli, Marvin Schulz, Morgan Taschuk, and Nicolas Le Novère. SBML Level 3 Package Proposal: Annotation. Nature Precedings, (713), January 2011.