Keynote talk at Bioinformatics Open Source Conference (BOSC) Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007 by Carole Goble, University of Manchester.

1. The Seven Deadly Sins of Bioinformatics Professor Carole Goble [email_address] The University of Manchester, UK The myGrid project OMII-UK

3. Intractable Problems in Bioinformatics. Have we sinned? Are these part of the intractable problem?

7. They came up with more than seven. But I beat them into submission. Many are highly inter-related. Hopefully they are all too familiar.

11. Comparative Genomics? Tisk! Its Comparative Bioinformatics Bioinformatics is about mapping one schema to another, one format to another, one id scheme to another. What a waste of time. What a handy distraction from doing some Real Science™.

20. The “Oh No” OBO Pragmatists Aesthetics Philosophers Life Scientists Capulets Knowledge Representation Montagues A means to an end Content providers Theoreticians The end Mechanism providers Spiritual guides The Montagues and The Capulets …SOFG 2004, KCap 2005, Comparative and Functional Genomics 2004 Endurants, Perdurants, Being, Substance, Event

31. A few months in the laboratory (or the computer) can save a few hours in the library (or on Google). Westheimer's Law (with additions).

34. Not just bioinformatics Computer Science is Guilty!

35. Why don’t biologists modularise OWL ontologies properly? Er, well, like how should we do it “properly” and where are the tools to help us? We don’t know and we haven’t got any. But here are some vague guidelines. W3C Semantic Web for Life Sciences mailing list, 2005

36. “ I don't blame them [MGED/PSI community] because to truly comprehend RDF/OWL is not an easy task, it takes not just the understand of technology itself but more so the vision on how things should and can work in SW.” “ One thing we have to remember is that biologists are building ontologies to do a job of work. They are not produced as some end of CS or SW research” “ Principles are all well and good, but we should know from decades of software engineering that saying "do it properly" isn't a solution. We need tooling and methodologies that do not in themselves hinder a domain specialist. In many cases it is easier to re-develop than re-use or even cut-and-paste from an existing ontology than it is to muck around “doing it properly”” “ There is actually a gap between the view of ontology for CS people and for biological people. The ontology in biologist's eyes are more of a treaty than logical representation, that in CS view is on the reverse of that view. It needs dialog to bring the view to a middle ground and mechanisms to stretch to both directions.”

40. Trust I don’t trust your code I don’t trust your data I don’t trust you will still be around in 1 year

53. The myGrid Semantic Sweatshop notice how tired they look Franck Tanoh Katy Wolstencroft

59. A good User Experience outweighs smart features. Can I use it? Is the user interface familiar? Does it fit with my needs?

66. Distributed Annotation System Mash-Up http://www.biodas.org Reference Server AC003027 AC005122 M10154 Annotation Server Annotation Server AC003027 M10154 WI1029 AFM820 AFM1126 WI443 AC005122 Annotation Server

73. “ No experiment is reproducible.” Wyszowski's Law “ An experiment is reproducible until another laboratory tries to repeat it.” Alexander Kohn

76. “ I am sure one could reuse large parts of re-annotation for building transcriptome maps, if they only used workflows and ontologies”. Marco Roos A Biologist and Bioinformatician VL-e Project, Amsterdam

77. “ Bioinformaticians have reached the standards of the 1980s, while computer scientists are working on the standards of the 2020s, leaving roughly 40 years to bridge. Marco Roos A Biologist and Bioinformatician VL-e Project, Amsterdam

82. Sin Summary Maybe only one “original sin” in bioinformatics. Parochialism and Insularity Exceptionalism Autonomy or death! Vanity: Pride and Narcissism Monolith Meglomania Scientific method Sloth Instant Gratification Reinvention Churn

83. Can we become less sinful? Why do these sins exist? Are bioinformaticians particularly naughty? No naughtier than Computer Scientists. And its all very hard. Though they are naughty…

88. FaceBook & Bazaar for Workflow e-Scientists myexperiment.org Trials start August 2007!

89. Delivery Bulge

94. The Final Word Sin writes histories, goodness is silent. Thomas Fuller