%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Duncan Hull at 2006-03-24 08:51:21 +0000 


%% Saved with string encoding ASCII (TeX) 


@book{webservicesbook,
	Author = {Alonso, G. and Casati, F. and Kuno, H. and Machiraju, V.},
	Publisher = {Springer-Verlag},
	Title = {Web Services. Concepts, Architectures and Applications},
	note = {ISBN:3540440089},
	pages={354},
	Year = {2004}}
	
@book{aima,
	Author = {Stuart Russell and Peter Norvig},
	Publisher = {Prentice Hall},
	Title = {Artificial Intelligence: A Modern Approach},
	note = {ISBN:0130803022 \url{http://aima.cs.berkeley.edu/}},
	pages={1080},
	Year = {2003}}
	
@book{longtail,
	Author = {Chris Anderson},
	Publisher = {Hyperion},
	Title = {The Long Tail: Why the Future of Business Is Selling Less of More},
	note = {ISBN:1401302378},
	Year = {2006}}
		
@book{devlin,
	Author = {Keith J. Devlin},
	Title = {The Millenium Problems: The Seven Greatest Unsolved Mathematical Puzzles of Our Time},
	Year = {2002}}


@article{Musen,
	Author = {Mark A. Musen and Suzi Lewis and Barry Smith},
	Doi = {10.1038/nbt0106-21b},
	Journal = {Nature Biotechnol},
	Month = {Jan},
	Number = {1},
	Pages = {21-21},
	Pmid = {16404381},
	Title = {{Wrestling with SUMO and bio-ontologies}},
	Volume = {24},
	Year = {2006}}

@techreport{wsmorelations,
	Author = {Jacek Kopeck\'{y}},
	howpublished = {\url{http://www.w3.org/Submission/WSMO-related/}},
	Title = {{Relationship of WSMO to other relevant technologies}},
	note = {W3C Member Submission 3 June 2005},
	Year = {2005}}	
	
@misc{wsgloss,
	Author = {Hugo Haas and Allen Brown},
	howpublished = {\url{http://www.w3.org/TR/ws-gloss/}},
	Title = {{Web Services Glossary}},
	note = {W3C Working Group Note 11 February 2004},
	Year = {2004}}

@phdthesis{sabouphd,
	Author = {Marta Sabou},
	School = {Vrije Univeristeit, Amsterdam},
	Title = {Building Web Service Ontologies},
	Year = {2005}}

@misc{lawslaws,
	Author = {Andy Law},
	Howpublished = {\url{http://bioinformatics.roslin.ac.uk/lawslaws.html}},
	Note = {Roslin Institute, Edinburgh, Bioinformatics},
	Title = {Law's Laws},
	Year = {2005}}

@misc{luciano,
	Author = {Joanne Luciano},
	Howpublished = {\url{http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jan/0084.html}},
	Title = {{Homologs for yeast proteins}},
	Year = {2006}}
	
	
 
 @Article{hullnarweb2006,
author = {Duncan Hull and Katy Wolstencroft and Robert Stevens and Carole Goble and Matthew R. Pocock and Peter Li and Tom Oinn},
title = {Taverna: a tool for building and running workflows of services},
journal = "Nucleic Acids Research",
year = "2006",
volume = "34",
number = "Web Server issue",
pages = "W729--W732",
month = "Jul",
pmid = "16845108",
}
 

@inproceedings{hulletelaaai,
  author    = {Duncan Hull and Evgeny Zolin and Andrey Bovykin and Ian Horrocks and Ulrike Sattler and Robert Stevens},
  title     = {{Deciding Semantic Matching of Stateless Services}},
  booktitle     = {Proceedings, The Twenty-First National Conference on Artificial
               Intelligence and the Eighteenth Innovative Applications
               of Artificial Intelligence Conference, July 16-20, 2006,
               Boston, Massachusetts, USA},
  year      = {2006},
  crossref  = {DBLP:conf/aaai/2006},
  pages = {1319--1324},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/aaai/2006,
  editor ={James A. Hendler and Kenneth D. Forbus and Yolanda Gil},
  title     = {Proceedings, The Twenty-First National Conference on Artificial
               Intelligence and the Eighteenth Innovative Applications
               of Artificial Intelligence Conference, July 16-20, 2006,
               Boston, Massachusetts, USA},
  booktitle = {AAAI},
  publisher = {AAAI Press, Menlo Park, California},
  year      = {2006},
  ISBN = {978-1-57735-281-5},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
	

@misc{kwebscenarios,
	Author = {Duncan Hull and Jeff Pan},
	Howpublished = {\url{http://knowledgeweb.semanticweb.org}},
	Note = {Knowledge Web deliverable: Workpackage 2.4 Semantic Web Services: In press},
	Title = {{Use Cases for Semantic Web Services from Bioinformatics}},
	Year = {2005}}

@article{HS05,
	Author = {Duncan Hull and Robert Stevens},
	Note = {Third European Summer School on Ontological Engineering and the Semantic Web (SSSW'05), 2005-07-10, Cercedilla, Spain},
	Title = {{Semantic Matching of Biomedical Web Services}},
	Url = {http://www.cs.man.ac.uk/~hulld/papers/matchmaker_madrid.pdf},
	Year = {2005}}

@article{OGA+05,
	Author = {Tom Oinn and Mark Greenwood and Matthew Addis and Justin Ferris and Kevin Glover and Carole Goble and Antoon Goderis and Duncan Hull and Darren Marvin and Peter Li and Phillip Lord and Matthew R Pocock and Martin Senger and Anil Wipat and Chris Wroe},
	Journal = {Concurrency and Computation: Practice and Experience},
	Note = {DOI:10.1002/cpe.993},
	Title = {{Taverna: Lessons in creating a workflow environment for the Life Sciences}},
	Year = {2006},
	Volume ={18},
	Number ={10},
	pages ={1067-1100}}
	

@inproceedings{HSL05,
	Author = {Duncan Hull and Robert Stevens and Phillip Lord},
	Title = {Describing Web Services for user-oriented retrieval},
	booktitle = {W3C Workshop on Frameworks for Semantics in Web Services, June 9-10, 2005 Digital Enterprise Research Institute (DERI), Innsbruck, Austria},
	crossref={W3CFSWS05},
	Year = {2005}}
	
@proceedings{W3CFSWS05,
	Editor={Steve Battle and David Martin},
	Title={W3C Workshop on Frameworks for Semantics in Web Services, June 9-10, 2005 Digital Enterprise Research Institute (DERI), Innsbruck, Austria},
	Booktitle={W3CFSWS},
	year={2005},
	publisher={World Wide Web Consortium (W3C)},
}

@inproceedings{HSL+04,
	Author = {Duncan Hull and Robert Stevens and Phillip Lord and Chris Wroe and Carole Goble},
	Booktitle = {Advanced Knowledge Technologies Semantic Web Services (AKTSWS)},
	Title = {{Treating shimantic web syndrome with ontologies}},
	Year = {2004},
	crossref={AKT-SWS04}}
	

	
	
@proceedings{AKT-SWS04,
	Editor = {John Domingue and Liliana Cabral and Enrico Motta}
	Title = {Proceedings of the First Advanced Knowledge Technologies Workshop on Semantic Web Services, KMi, The Open University, Milton Keynes, UK. },
	Booktitle = {Advanced Knowledge Technologies Semantic Web Services (AKTSWS)},
	year={2004},
	isbn={1613-0073},
	publisher={http://CEUR-WS.org/Vol-122/},
	Volume={122}
}


@misc{LAW+04,
	Author = {Phillip Lord and Pinar Alper and Chris Wroe and Robert Stevens and Carole Goble and Jun Zhao and Duncan Hull and Mark Greenwood},
	Title = {{The Semantic Web: Service discovery and provenance in myGrid}},
	YEAR={2004},
	BOOKtitle={W3C Workshop on Semantic Web for Life Sciences, November 27, Cambridge, Massachusetts USA.},
	Url = {http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0016/semantic_web_for_life_sciences_position.pdf}}

@misc{nada,
	Author = {Nada Hashmi and Sung Lee and Michael P. Cummings},
	Title = {{Abstracting Workflows: Unifying Bioinformatics Task Conceptualization and Specification Through Semantic Web Services}},
	YEAR={2004},
	BOOKtitle={W3C Workshop on Semantic Web for Life Sciences, November 27, Cambridge, Massachusetts USA.},
	Url = {http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0016/semantic_web_for_life_sciences_position.pdf}}

@inproceedings{LBW+04,
  author    = {Phillip W. Lord and Sean Bechhofer and Mark D. Wilkinson and Gary Schiltz and Damian Gessler and Duncan Hull and Carole A. Goble and Lincoln Stein},
  title     = {Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt.},
  booktitle = {International Semantic Web Conference},
  year      = {2004},
  pages     = {350-364},
  crossref  = {DBLP:conf/semweb/2004},
  doi={http://dx.doi.org/10.1007/b102467},
  url={http://biomoby.org/biomoby-comparison-iswc2004.pdf}
}

@proceedings{DBLP:conf/semweb/2004,
  editor    = {Sheila A. McIlraith and Dimitris Plexousakis and Frank van Harmelen},
  title     = {The Semantic Web - ISWC 2004: Third International Semantic Web Conference,Hiroshima, Japan, November 7-11, 2004. Proceedings},
  booktitle = {International Semantic Web Conference},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3298},
  year      = {2004},
  isbn      = {3-540-23798-4},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}	
	
@article{HSL04a,
	Author = {Duncan Hull and Robert Stevens and Phillip Lord and Carole Goble},
	Note = {Poster session, Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB2004) Glasgow, Scotland, UK},
	Title = {Integrating bioinformatics resources using shims},
	Url = {http://www.iscb.org/ismb2004/posters/duncan.hullATcs.man.ac.uk_445.html},
	Year = {2004}}

@mastersthesis{HUL03a,
	Author = {Duncan Hull},
	School = {University of Manchester},
	Title = {{Enabling Semantic Web Services in BioMOBY}},
	Url = {http://www.cs.man.ac.uk/~hulld/papers/masters_thesis.html},
	Year = {2003}}

@article{HUL97,
	Abstract = {Life as we know it is based on carbon. The giant molecules that are characteristic of living things - polysaccharides, proteins and nucleic acids are all long chains of carbon containing units. The small molecules - such as amino acids and ATP - are also made of carbon. But carbon is not a static constituent of life - it travels to and fro throughout the biosphere; its comings and goings are known as the carbon cycle.},
	Author = {Duncan Hull},
	Journal = {Biological Sciences Review},
	Number = {1},
	Pages = {10-13},
	Title = {{A user's guide to the Carbon cycle}},
	Url = {http://www.cs.man.ac.uk/~hulld/papers/users_guide_carbon_cycle.html},
	Volume = {10},
	Year = {1997}}

@unpublished{HUL96,
	Author = {Duncan Hull},
	Note = {Bachelor of Science dissertation, BS3041, University of Manchester},
	Title = {{Signal transduction during embryogenesis in fucoid algae}},
	Url = {http://www.cs.man.ac.uk/~hulld/papers/signal_transduction_during_embryogenesis.html},
	Year = {1996}}

@unpublished{HUL95,
	Author = {Duncan Hull},
	Note = {Bachelor of Science project, BS3030, University of Manchester},
	School = {University of Manchester},
	Title = {{The regulation of Carbon Dioxide efflux from a sub-arctic heathland}},
	Url = {http://www.cs.man.ac.uk/~hulld/papers/users_guide_carbon_cycle.html},
	Year = {1995}}

@article{closingthegap,
	Author = {Lincoln Stein},
	Journal = {Nature},
	Month = {October},
	Number = 431,
	Pages = {915--916},
	Title = {Human Genome: End of the beginning},
	Year = 2004}

@article{LS03,
	Annote = {there are lots of ontologies out there for describing different things some of them are summarised in this conference review},
	Author = {Phillip Lord and Robert Stevens},
	Journal = {Comparative and Functional Genomics},
	Title = {ISMB 2003 bio-ontologies SIG and sixth annual bio-ontologies meeting report},
	Year = {2003}}

@inproceedings{SGG+03,
	Author = {Robert Stevens and Kevin Glover and Chris Greenhalgh and Claire Jennings and Simon Pearce and Peter Li and Melena Radenkovic and Anil Wipat},
	Note = {Proceedings UK e-Science All Hands Meeting 2003 Editors - Simon J Cox 43-50 isbn - 1-904425-11-9},
	Title = {Performing \textit{in silico} Experiments on the Grid: A Users Perspective},
	Year = 2003}

@article{STE01,
	Author = {Robert Stevens and Carole Goble and Patricia Baker and Andy Brass},
	Journal = {Bioinformatics},
	Pages = {180--188},
	Title = {A classification of tasks in bioinformatics},
	Volume = 17,
	Year = {2001}}

@article{MSZ01,
	Author = {Sheila McIlraith and T. Son and H. Zeng},
	Journal = {IEEE Intelligent Systems},
	Month = {March-April},
	Pages = {46--53},
	volume    = {16},
	number    = {2},
	doi ={10.1109/5254.920599},
	Title = {{Semantic Web Services}},
	Year = 2001}
	
	

@article{STE02a,
	Author = {Lincoln Stein},
	Journal = {Nature},
	Month = {May},
	Pages = {119--120},
	Title = {{Creating a bioinformatics nation}},
	doi ={10.1038/417119a},
	Volume = 417,
	Year = 2002}

@misc{swws,
	Howpublished = {\url{http://swws.semanticweb.org/}},
	Note = {{Accessed 20 September 2003}},
	Title = {{Semantic Web enabled Web Services (SWWS)}},
	Year = 2003}

@inproceedings{damls,
	Author = {A Ankolekar and Mark Burstein and J Hobbs and Ora Lassila and David Martin and Sheila McIlraith and S Narayanan and Massimo Paolucci and Terry R Payne and Katia Sycara and H Zeng.},
	Booktitle = {In Proceedings of the International Semantic Web Working Symposium (SWWS)},
	Title = {{\damls: Semantic Markup For Web Services}},
	Year = {2001}}

@misc{myg,
	Howpublished = {\url{http://www.mygrid.org.uk/}},
	Month = {July},
	Title = {{\myg - directly supporting the e-scientist}},
	Year = 2003}

@unpublished{senger,
	Author = {Martin Senger},
	Month = {August},
	Title = {{Personal communication}},
	Year = {2003}}

@mastersthesis{joens93,
	Author = {Scott Joens},
	School = {University of Manchester},
	Title = {{The searching and dissemination of proteomics data}},
	Year = {2003}}

@misc{geneont47,
	Howpublished = {\url{http://www.geneontology.org/}},
	Month = {JULY},
	Title = {{The Gene Ontology Consortium}},
	Year = {2004}}

@unpublished{Hend108,
	Author = {Jim Hendler},
	Month = {July},
	Note = {At Sixth International Protege Workshop \url{http://protege.stanford.edu/workshop_vi/}},
	Title = {{Personal communication}},
	Year = 2003}

@article{Protege,
	Author = {Noy, N F and Crubezy, M and Fergerson, R W and Knublauch, H and Tu, S W and Vendetti, J and Musen, M A},
	Journal = {AMIA Annu Symp Proc},
	Pages = {953-953},
	Pmid = {14728458},
	Title = {Prot{\'e}g{\'e}-2000: an open-source ontology-development and knowledge-acquisition environment},
	Year = {2003}}

@misc{oed31,
	Howpublished = {\url{http://www.oed.com/}},
	Month = {July},
	Title = {{Oxford English Dictionary Online, 2nd edition}},
	Year = 2003}

@misc{wordnet43,
	Howpublished = {\url{http://www.cogsci.princeton.edu/~wn/}},
	Month = {July},
	Note = {Cognitive Science Laboratory, Princeton University.},
	Title = {{WordNet - a lexical database for the English language}},
	Year = 2003}

@techreport{NoyMcG29,
	Author = {Natalya Noy and Deborah McGuinness},
	Institution = {Stanford Medical Informatics},
	Note = {\url{http://protege.stanford.edu/publications/ontology_development/ontology101.pdf}},
	Title = {{Ontology Development 101: A Guide to Creating Your First Ontology}},
	Year = {2003}}

@article{isys96,
	Author = {A Siepel and A Topolko and A Farmer and P Steadman and F Schilkey and B Perry and W Beavis},
	Journal = {IBM Systems Journal},
	Note = {Deep Computing for the Life Sciences},
	Number = {2},
	Pages = {570--591},
	Title = {{An integration platform for heterogeneous bioinformatics software components}},
	Volume = {40},
	Year = {2001}}

@article{Vinoski100,
	Author = {S Vinoski},
	Journal = {IEEE Internet Computing},
	Month = {January},
	Pages = {69--71},
	Title = {{Service discovery 101}},
	Year = {2003}}

@misc{McKeown30,
	Author = {M McKeown},
	Howpublished = {\url{http://www.sve.man.ac.uk/Research/AtoZ/ILCT/OGSI_Lite.ppt}},
	Month = {July},
	Note = {e-Science North West Middleware Discussion},
	Title = {{OGSI::Lite - A Perl hosting environment for Grid Services}},
	Year = 2003}

@inproceedings{Moreau:ABCGRID2003,
	Address = {Tokyo, Japan},
	Author = {Luc Moreau and Simon Miles and Carole Goble and Mark Greenwood and Vijay Dialani and Matthew Addis and Nedim Alpdemir and Rich Cawley and David De Roure and Justin Ferris and Rob Gaizauskas and Kevin Glover and Chris Greenhalgh and Peter Li and Xiaojian Liu and Phillip Lord and Michael Luck and Darren Marvin and Tom Oinn and Norman Paton and Stephen Pettifer and Milena V Radenkovic and Angus Roberts and Alan Robinson and Tom Rodden and Martin Senger and Nick Sharman and Robert Stevens and Brian Warboys and Anil Wipat and Chris Wroe},
	Booktitle = {Proceedings of the Third IEEE/ACM CCGRID'2003 Workshop on Agent Based Cluster and Grid Computing},
	Editor = {Sangsan Lee and Satoshi Sekguchi and Satoshi Matsuoka and Mitsuhisa Sato},
	Month = MAY,
	Pages = {653--661},
	Title = {{On the Use of Agents in a BioInformatics Grid}},
	Url = {http://www.ecs.soton.ac.uk/~lavm/papers/abcgrid2003.ps.gz},
	Year = 2003}

@misc{jena,
	Howpublished = {\url{http://www.hpl.hp.com/semweb/jena.htm}},
	Month = {September},
	Note = {Hewlett Packard Laboratories},
	Title = {{Jena Semantic Web Toolkit}},
	Year = 2003}

@manual{Champion01,
	Author = {M Champion and C Ferris and E Newcomer and D Orchard.},
	Organization = {W3C},
	Title = {{Web Services Architecture W3C Working Draft 14 May 2003}},
	Year = 2003}

@unpublished{goderis03,
	Author = {A Goderis},
	Note = {3 March 2003},
	Title = {{Reasoning support for Semantic Web Services}}}

@article{chicurel04,
	Author = {M Chicurel},
	Journal = {Nature},
	Note = {DOI:10.1038/419751a},
	Number = {6908},
	Pages = {751--757},
	Title = {{Bioinformatics: Bringing it all together}},
	Volume = {419},
	Year = {2002}}

@article{firstdraft,
	Author = {{IHGSC}},
	Journal = {Nature},
	Note = {IHGSC: Intl. Human Genome Sequencing Consortium},
	Number = {6822},
	Pages = {860--921},
	Pmid = {11237011},
	Title = {{Initial sequencing and analysis of the human genome}},
	Volume = {409},
	Year = {2001}}

@article{finishing,
	Annote = {Article mentioned in sanger press release and francis collins about finishing the genome and finding the remaining gaps,   NOTE IHGSC = International Human Genome Sequencing Consortium},
	Author = {{IHGSC}},
	Journal = {Nature},
	Note = {IHGSC: Intl. Human Genome Sequencing Consortium},
	Number = {7011},
	Pages = {931--945},
	Title = {{Finishing the euchromatic sequence of the human genome}},
	Volume = {431},
	Year = {2004}}

@proceedings{Greenwood05,
	Author = {Mark Greenwood and Chris Wroe and Robert Stevens and Carole Goble and Matthew Addis},
	Note = {Euroweb 2002 - The Web and the GRID: from e-science to e-business},
	Title = {{Are bioinformaticians doing e-Business?}},
	Year = {2002}}

@article{timblhype,
	Author = {Tim Berners-Lee and Jim Hendler and Ora Lassila},
	Journal = {Scientific American},
	Month = {May},
	Title = {{The Semantic Web}},
	Year = {2001}}

@misc{wilkinson07,
	Author = {Mark Wilkinson},
	Howpublished = {\url{http://www.BioMOBY.org/overview.html}},
	Note = {Accessed 22 July 2003.},
	Title = {{The MOBY system for the discovery and distribution of biological data}},
	Year = {2003}}

@article{BFM02,
	Author = {C Bussler and D Fensel and A Maedche},
	Journal = {ACM SIGMOD record},
	Number = {4},
	Title = {{A Conceptual Architecture for Semantic Web Enabled Web Services}},
	Volume = {31},
	Year = {2002}}

@proceedings{sabou09,
	Author = {M Sabou and D Richards and S van Splunter},
	Note = {WWW2003, May 20-24, 2003, Budapest, Hungary},
	Title = {{An experience report on using \damls}},
	Year = {2003}}

@article{Wilkinson10,
	Author = {Mark Wilkinson and Matthew Links},
	Journal = {Briefings in Bioinformatics},
	Number = {4},
	Pages = {331--341},
	Title = {{BioMOBY: An Open Source Biological Web Services proposal}},
	Volume = {3},
	Year = 2002}

@article{Hendler12,
	Author = {J Hendler},
	Journal = {IEEE Intelligent Systems},
	Pages = {46--53},
	Title = {{Agents and the Semantic Web}},
	Year = {2001}}

@misc{google14,
	Howpublished = {\url{http://www.google.com/apis}},
	Note = {Accessed 14 July 2003},
	Title = {{Google Web APIs - Develop Your Own Applications Using Google}},
	Year = 2003}

@mastersthesis{matthews15,
	Author = {C Matthews},
	School = {University of Manchester},
	Title = {{Experimenting with a database exposed as a web service}},
	Year = {2002}}

@techreport{wsdl,
	Author = {Erik Christensen and Francisco Curbera and Greg Meredith and Sanjiva Weerawarana},
	Note = {W3C Note 15 March 2001 \url{http://www.w3c.org/TR/wsdl}},
	Organization = {W3C},
	Title = {{Web Services Description Language (WSDL) 1.1}},
	Year = 2001}

@techreport{wsdl2,
	Author = {Roberto Chinnici and Jean-Jacques Moreau and Arthur Ryman and Sanjiva Weerawarana},
	Note = {W3C Candidate Recommendation 6 January 2006 \url{http://www.w3.org/TR/wsdl20/}},
	Organization = {W3C},
	Ttitle = {{Web Services Description Language (WSDL) Version 2.0 Part 1: Core Language}},
	Year = {2006}}

@misc{SOAP17,
	Author = {D Box and D Ehnebuske and G Kakivaya and A Layman and N Mendelsohn and H Nielsen and S Thatte and D Winer},
	howpublished = {\url{http://www.w3.org/TR/2000/NOTE-SOAP-20000508/}},
	Title = {{Simple Object Access Protocol (SOAP) 1.1}},
	Year = 2000}

@inproceedings{wroe18,
	Author = {C Wroe and R Stevens and C Goble and M Ashburner},
	Booktitle = {Pacific Symposium on Biocomputing},
	Editor = {Russ B Altman},
	Publisher = {World Scientific},
	Title = {{A methodology to migrate the gene ontology to a description logic environment using DAML+OIL}},
	Year = {2003}}

@article{lord19,
	Author = {P Lord and C Wroe and R Stevens and C Goble and S Miles and L Moreau and K Decker and T Payne},
	Journal = {???},
	Title = {{Requirements and Views on Semantic Discovery}},
	Year = {????}}

@article{quan20,
	Author = {D Quan and S Martin and D Grossman},
	Journal = {??},
	Title = {{Applying Semantic Web Techniques to Bioinformatics}},
	Year = {????}}

@article{oaks21,
	Author = {P Oaks and A ter Hofstede and D Edmond},
	Journal = {???},
	Title = {{Capabilities: describing what services do}},
	Year = {???}}

@unpublished{peer22,
	Author = {J Peer},
	Note = {???},
	Title = {{Semantic Annotation and Matchmaking of Web Services}}}

@misc{butler23,
	Author = {M Butler},
	Howpublished = {\url{http://www-uk.hpl.hp.com/people/marbut/isTheSemanticWebHype.pdf}},
	Note = {Accessed 14 July 2003. HP Labs Bristol. Digital Media Systems Department},
	Title = {{Is the semantic web hype?}},
	Year = {2003}}

@misc{timbl24,
	Author = {T Berners-Lee},
	Howpublished = {\url{http://www.w3.org/DesignIssues/RDFnot.html}},
	Note = {Accessed 14 July 2003},
	Title = {{Web design issues; What a semantic web can represent}},
	Year = 2003}

@misc{amazon25,
	Howpublished = {\url{http://www.amazon.com/gp/aws/landing.html}},
	Note = {Accessed 14 July 2003},
	Title = {{Using Amazon web services}},
	Year = 2003}

@misc{lamp26,
	Howpublished = {\url{http://www.onlamp.com}},
	Note = {Accessed 14 July 2003},
	Title = {{LAMP. The Open Source Web Platform}},
	Year = 2003}

@misc{biomoby27,
	Howpublished = {\url{http://www.biomoby.org}},
	Note = {Accessed 14 July 2003},
	Title = {{BioMOBY.org Main Page}},
	Year = 2003}

@misc{semaview28,
	Howpublished = {\url{http://www.semaview.com/c/SW.html}},
	Note = {Accessed 14 July 2003},
	Title = {{Semaview, the semantic web illustrated}},
	Year = 2003}

@manual{uddi31,
	Note = {\url{http://uddi.org/specification.html}},
	Title = {{Universal Description, Discovery and Integration of Web Services}},
	Year = {2003}}

@misc{webservices34,
	Howpublished = {\url{http://www.webservices.org}},
	Note = {Accessed 20 July 2003},
	Title = {{WebServices.Org - The Web Services Industry Portal}},
	Year = 2003}

@misc{omg35,
	Howpublished = {\url{http://www.corba.org}},
	Note = {Accessed 20 July 2003},
	Title = {{The Object Management Groups CORBA Website}},
	Year = 2003}

@misc{timbl36,
	Author = {Tim Berners-Lee},
	Howpublished = {\url{http://www.w3.org/2000/Talks/0906-xmlweb-tbl}},
	Note = {Accessed 20 July 2003},
	Title = {{XML and the web}},
	Year = 2000}

@unpublished{Stevens37,
	Author = {R Stevens and C Wroe and P Lord and C Goble},
	Note = {Chapter 12 of book in press},
	Title = {{Ontologies in bioinformatics}},
	Year = 2003}

@misc{Bray38,
	Author = {Tim Bray},
	Howpublished = {\url{http://www.tbray.org/ongoing/When/200x/2003/06/29/Inflexion}},
	Note = {Accessed 2 July 2003},
	Title = {{On Search: Squirmy Words}},
	Year = 2003}

@article{Lassila39,
	Author = {O Lassila and D McGuinness},
	Journal = {???},
	Note = {\url{http://www.ksl.stanford.edu/people/dlm/etai/etai-abstract.html} Accessed 22 July 2003},
	Title = {{The Role of Frame-Based Representation on the Semantic Web}},
	Year = 2003}

@misc{Booth40,
	Author = {D Booth},
	Howpublished = {\url{http://www.w3.org/2002/Talks/0813-semweb-dbooth/Overview.html}},
	Note = {Accessed 22 July 2003},
	Title = {{Fundamentals of the Semantic Web}},
	Year = 2002}

@misc{oiled42,
	Howpublished = {\url{http://oiled.man.ac.uk/}},
	Note = {Accessed 23 May 2003},
	Title = {{OilEd: The Ontology Editor}},
	Year = 2003}

@misc{protege44,
	Date = 2003,
	Howpublished = {\url{http://protege.stanford.edu/}},
	Note = {Accessed 23 July 2003},
	Title = {{The Prot{\'e}g{\'e} Ontology Editor and Knowledge Acquisition System}}}

@misc{owl45,
	Author = {Deborah L. McGuinness and Frank van Harmelen},
	Howpublished = {\url{http://www.w3.org/TR/owl-features/}},
	Title = {{OWL Web Ontology Language Overview W3C Recommendation}},
	Year = {2004}}

@article{HoPH03a,
	Author = {Ian Horrocks and Peter F. Patel-Schneider and Frank van Harmelen},
	Journal = {Journal of Web Semantics},
	Number = 1,
	Title = {{From {SHIQ} and {RDF} to {OWL}: The Making of a Web Ontology Language}},
	Volume = 1,
	Year = 2003,
	pages     = {7-26}}

@unpublished{Bechhofer46,
	Author = {S. Bechhofer and I. Horrocks and D. Turi},
	Howpublished = {\url{http://instancestore.man.ac.uk/instancestore.pdf}},
	Title = {{Instance Store - Database Support for Reasoning over Individuals}},
	Year = 2003}

@misc{Senger48,
	Author = {M Senger},
	Howpublished = {\url{http://industry.ebi.ac.uk/soaplab/}},
	Note = {Accessed 27 July 2003},
	Title = {{SOAP-based Analysis Web Service}},
	Year = 2003}

@misc{pathport49,
	Howpublished = {\url{http://www.vbi.vt.edu/pathport/services/}},
	Note = {Accessed 27 July 2003},
	Title = {{PathPort: The Pathogen Portal Web Project}}}

@misc{Senger51,
	Author = {Martin Senger},
	Howpublished = {\url{http://industry.ebi.ac.uk/~senger/jMoby/dist/}},
	Title = {{Moby Command Line Client (jMoby-2003-05-09.tar)}},
	Year = 2003}

@misc{gruber52,
	Author = {Tom Gruber},
	Howpublished = {\url{http://www-ksl.stanford.edu/kst/what-is-an-ontology.html}},
	Note = {Accessed 31 July 2003},
	Title = {{What is an Ontology?}},
	Year = 2003}

@article{gruber93,	
	Author = {Tom Gruber},
	Title = {{A translational approach to portable ontology specifications}},
	Journal={{Knowledge Acquisition}},
	Volume ={5},
	Number ={2},
	pages = {199-220},
	Year = 1993}

@misc{goat53,
	Howpublished = {\url{http://goat.man.ac.uk/}},
	Note = {Accessed 31 July 2003},
	Title = {{The Gene Ontology Annotation Tool (GOAT) Project}},
	Year = 2003}

@misc{dublin54,
	Howpublished = {\url{http://www.dublincore.org/}},
	Note = {Accessed 3 August 2003},
	Title = {{Dublin Core Metadata Initiative (DCMI) - Making it easier to find information}},
	Year = 2003}

@misc{w3c55,
	Howpublished = {\url{http://www.w3.org/}},
	Note = {Accessed 3 August 2003},
	Title = {{World Wide Web Consortium}},
	Year = 2003}

@misc{dmoz56,
	Howpublished = {\url{http://www.dmoz.org/}},
	Note = {Accessed 3 August 2003},
	Title = {{DMOZ - Open Directory Project}},
	Year = 2003}

@article{Ferris57,
	Author = {C Ferris and J Farrell},
	Journal = {Communications of the ACM},
	Month = {June},
	Number = {6},
	Pages = {31},
	Title = {{What Are Web Services?}},
	Volume = {46},
	Year = 2003}

@misc{wilkinson58,
	Author = {M Wilkinson},
	Howpublished = {\url{http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI}},
	Note = {Accessed 3 August 2003},
	Title = {{MOBY-S 0.502 API (web-services based)}},
	Year = 2003}

@misc{damloil59,
	Howpublished = {\url{http://www.daml.org/2001/03/daml+oil-index.html}},
	Note = {Accessed 3 August 2003},
	Title = {{DAML+OIL (March 2001)}},
	Year = 2001}

@misc{wilkinson60,
	Author = {M Wilkinson},
	Howpublished = {\url{http://www.biomoby.org/MobyOct2002.ppt}},
	Month = {October},
	Note = {Accessed 3 August 2003},
	Title = {{BioMOBY: Building the Biological Semantic Web}},
	Year = 2002}

@misc{autonomy61,
	Howpublished = {\url{http://www.autonomy.com}},
	Note = {Accessed 5 August 2003},
	Title = {{Autonomy Systems}},
	Year = 2003}

@article{kim62,
	Author = {J Kim},
	Journal = {Computing},
	Month = {July},
	Number = {7},
	Pages = {25--32},
	Title = {{Computers are from Mars, organisms are from Venus}},
	Volume = {35},
	Year = {2002}}

@misc{ncbi63,
	Howpublished = {\url{http://www.ncbi.nlm.nih.gov/Genbank/}},
	Note = {Accessed 7 August 2003},
	Title = {{National Center for Biotechnology Information, GenBank}},
	Year = 2003}

@misc{genbank64,
	Howpublished = {\url{http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html}},
	Note = {Accessed 6 June 2004},
	Title = {{GenBank Growth}},
	Year = 2004}

@article{agresti65,
	Author = {W Agresti},
	Journal = {Communications of the ACM},
	Month = {August},
	Number = {8},
	Title = {{Discovery Informatics}},
	Volume = {46},
	Year = {2003}}

@inproceedings{bechhofer66,
	Author = {Sean Bechhofer and Carole Goble and Ian Horrocks},
	Booktitle = {SWWS-1, Semantic Web working symposium},
	Month = {Jul/Aug},
	Title = {{DAML+OIL is not enough.}},
	Year = 2001}

@misc{gessler67,
	Article = {D Gessler and A Farmer},
	Howpublished = {\url{http://www.biomoby.org/S-MOBY/doc/Requirements/MOBY_Requirements.pdf}},
	Title = {{MOBY-S Requirements Document}},
	Year = 2002}

@misc{biomoby68,
	Howpublished = {\url{http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/Database/?cvsroot=biomoby&hideattic=0#dirlist}},
	Note = {Accessed 12 August 2003 revision 1.4. Modified 7 May 2003.},
	Title = {{BioMOBY relational database schema}}}

@book{Rees69,
	Author = {Martin Rees},
	Publisher = {William Heinemann},
	Title = {{Our Final Century. A Scientist's Warning: How Terror, Error, and Environmental Disaster Threaten Humankind's Future in This Century - On Earth and Beyond}},
	Year = 2003}

@book{lexyacc,
	Author = {John Levine and Tony Mason and Doug Brown},
	Note = {isbn: 1-56592-000-7},
	Publisher = {O'Reilly},
	Title = {{lex & yacc, Second Edition}},
	Year = 1992}

@unpublished{bechhofer70,
	Author = {Sean Bechhofer and Ralf M{\"o}ller and Peter Crowther},
	Note = {To appear in DL2003 International Workshop on Description Logics, Rome, September, 2003},
	Title = {{The DIG Description Logic Interface}},
	Year = 2003}

@misc{google71,
	Howpublished = {\url{http://www.google.com/dirhp}},
	Title = {{Google directory, The web organized by topic into categories}},
	Year = 2003}

@misc{letondal72,
	Author = {C Letondal},
	Howpublished = {\url{http://www.pasteur.fr/~letondal/biomoby/tutorial.html}},
	Note = {Accessed 31 August 2003},
	Title = {{A BioMOBY Perl Tutorial}},
	Year = 2003}

@misc{haarslev74,
	Author = {Volker Haarslev and R Moller},
	Howpublished = {\url{http://www.fh-wedel.de/~mo/racer/}},
	Note = {Accessed 01 September 2003},
	Title = {{RACER: Renamed ABox and Concept Expression Reasoner}},
	Year = 2003}

@misc{flanders75,
	Author = {V Flanders},
	Howpublished = {\url{http://www.fixingyourwebsite.com/googleisgod.html}},
	Note = {Accessed 01 September 2003},
	Title = {{Google is god. Don't piss her off}},
	Year = 2003}

@book{lesk77,
	Author = {Arthur M. Lesk},
	Note = {isbn 0199251967},
	Publisher = {Oxford University Press},
	Title = {{Introduction to Bioinformatics}},
	Year = 2002}

@misc{yellow78,
	Howpublished = {\url{http://www.yell.com}},
	Title = {{Yell.com. Online business directory from Yellow Pages in the UK}},
	Year = 2003}

@misc{wroe:perscomm,
	Author = {Chris Wroe},
	Month = {AUGUST},
	Title = {Personal Communication},
	Year = 2003}

@misc{vogel79,
	Author = {W Vogel},
	Howpublished = {\url{http://weblogs.cs.cornell.edu/AllThingsDistributed/archives/000120.html}},
	Note = {Accessed 02 September 2003},
	Title = {{All Things Distributed: Web Services are NOT Distributed Objects}},
	Year = 2003}

@misc{orfali80,
	Author = {R Orfali and D Harkey and J Edwards},
	Publisher = {John Wiley and Sons Inc.},
	Title = {{Instant CORBA}},
	Year = {1997}}

@misc{blast81,
	Howpublished = {\url{http://www.ebi.ac.uk/blast/index.html}},
	Note = {{Accessed 03 September 2003}},
	Title = {{BLAST @ EBI}},
	Year = {2003}}

@misc{linux82,
	Howpublished = {\url{http://www.linux.org/}},
	Note = {Accessed 03 September},
	Title = {{The Linux Home Page at Linux Online}},
	Year = 2003}

@misc{apache83,
	Howpublished = {\url{http://www.apache.org}},
	Note = {Accessed 03 September 2003},
	Title = {{The Apache Software Foundation}},
	Year = 2003}

@misc{mysql84,
	Howpublished = {\url{http://www.mysql.com/}},
	Note = {Accessed 03 September 2003},
	Title = {{MySQL: The World's Most Popular Open Source Database}},
	Year = 2003}

@misc{linuxplanet86,
	Howpublished = {\url{http://www.linuxplanet.com/linuxplanet/reports/1176/1/}},
	Note = {Accessed 03 September 2003},
	Title = {{LinuxPlanet Reports - Linux at the BBC}},
	Year = 2003}

@misc{netcraft87,
	Howpublished = {\url{http://news.netcraft.com/}},
	Note = {Accessed 03 September 2003},
	Title = {{Netcraft}},
	Year = 2003}

@misc{osi89,
	Howpublished = {\url{http://www.opensource.org/}},
	Note = {Accessed 03 September 2003},
	Title = {{Open Source Initiative OSI}},
	Year = 2003}

@misc{stein90,
	Author = {Lincoln Stein},
	Howpublished = {\url{http://stein.cshl.org/~lstein/}},
	Note = {Accessed 03 September 2003},
	Title = {{Lincoln Stein's Home Page}},
	Year = 2003}

@misc{dyson91,
	Author = {Esther Dyson},
	Howpublished = {\url{http://www.edventure.com/edventure/esther.cfm}},
	Note = {Accessed 03 September 2003},
	Title = {{EDventure holdings Inc}},
	Year = 2003}

@misc{xindice92,
	Howpublished = {\url{http://xml.apache.org/xindice/}},
	Note = {Accessed 03 September 2003},
	Title = {{Apache Xindice}},
	Year = 2003}

@article{kovac94,
	Author = {Caroline Kovac},
	Journal = {IBM Systems Journal},
	Note = {Deep Computing for the Life Sciences},
	Number = {2},
	Title = {{Message from the Vice President, Life Sciences Solutions}},
	Volume = {40},
	Year = {2001}}

@article{goble95,
	Author = {Carole Goble and Robert Stevens and Gary Ng and Sean Bechhofer and Norman Paton and Patricia Baker and Martin Peim and Andy Brass},
	Journal = {IBM Systems Journal},
	Note = {Deep Computing for the Life Sciences},
	Number = {2},
	Pages = {532--551},
	Title = {{Transparent Access to Multiple Bioinformatics Information Sources}},
	Volume = {40},
	Year = {2001}}

@misc{pdb97,
	Howpublished = {\url{http://www.rcsb.org/pdb/}},
	Note = {Accessed 04 September 2003},
	Title = {{The Protein Data Bank}},
	Year = 2003}

@misc{interpro98,
	Howpublished = {\url{http://www.ebi.ac.uk/interpro/}},
	Note = {Accessed 04 September 2003},
	Title = {{Interpro Home}},
	Year = 2003}

@manual{austin99,
	Author = {D Austin and A Barbir and C Ferris and S Garg},
	Note = {\url{http://www.w3.org/TR/wsa-reqs}. W3C Working Draft 14 November 2002. Accessed 04 September},
	Title = {{Web Services Architecture Requirements}},
	Year = 2002}

@misc{uddi101,
	Howpublished = {\url{http://www.uddi.org/pubs/Iru_UDDI_Technical_White_Paper.pdf}},
	Note = {Accessed 03 September 2003},
	Title = {{UDDI Technical White Paper}},
	Year = 2003}

@article{patil102,
	Author = {S Patil and E Newcomer},
	Issue = {?},
	Journal = {IEEE Internet Computing},
	Pages = {?--?},
	Title = {{ebXML and Web Services}},
	Volume = {?},
	Year = {2003}}

@misc{ebxml103,
	Howpublished = {\url{http://www.ebxml.org/}},
	Note = {Accessed 03 September 2003},
	Title = {{ebXML - Enabling A Global Electronic Market}},
	Year = 2003}

@article{filman104,
	Author = {R Filman},
	Journal = {IEEE Internet Computing},
	Month = {July August},
	Title = {{Semantic Services}},
	Year = 2003}

@misc{semweb105,
	Howpublished = {\url{http://www.semanticweb.org/about.html}},
	Note = {Accessed 05 September 2003},
	Title = {{About SemanticWeb.org}},
	Year = 2003}

@misc{sun106,
	Howpublished = {\url{http://developers.sun.com/sw/building/tech_articles/webservice.html}},
	Note = {Accessed 16th September 2003},
	Title = {{Web Services and the Sun ONE Developer Platform}},
	Year = 2003}

@article{hayward107,
	Author = {D Hayward},
	Journal = {Computing},
	Note = {\url{http://www.computing.co.uk}},
	Pages = {26--27},
	Title = {{Software design finds a fresh path to follow}},
	Volume = {4 September 2003},
	Year = 2003}

@misc{nelson109,
	Author = {Ted Nelson},
	Howpublished = {\url{http://xanadu.com.au/ted/}},
	Title = {{Ted Nelson Home Page}},
	Year = 2003}

@misc{naming110,
	Howpublished = {\url{http://www.omg.org/cgi-bin/doc?formal/02-09-02}},
	Title = {{CORBA Naming Service}},
	Year = 2002}

@misc{trading111,
	Howpublished = {\url{http://www.omg.org/cgi-bin/doc?formal/2000-06-27}},
	Title = {{CORBA Trading Object Service}},
	Year = 2000}

@misc{dewey112,
	Howpublished = {\url{http://www.oclc.org/dewey/}},
	Note = {Accessed 18 September 2003},
	Title = {{Dewey services OCLC - Cataloging and Metadata}},
	Year = 2003}

@misc{googlebot113,
	Howpublished = {\url{http://www.google.com/bot.html}},
	Note = {Accessed 18 September 2003},
	Title = {{Googlebot: Google's Web Crawler}},
	Year = 2003}

@misc{auton114,
	Howpublished = {\url{http://www.autonomy.com/Content/Technology/Other_Approaches/Manual_Tagging}},
	Note = {Accessed 18 September 2003},
	Title = {{Manual Tagging}},
	Year = 2003}

@misc{horrocks115,
	Author = {I Horrocks},
	Howpublished = {\url{http://www.cs.man.ac.uk/~horrocks/FaCT/}},
	Title = {{The FaCT System}},
	Year = {Accessed 19 September 2003}}

@misc{hgp116,
	Howpublished = {\url{http://www.wellcome.ac.uk/en/genome/}},
	Note = {Accessed 19 September 2003},
	Title = {{The Human Genome Project}},
	Year = 2003}

@article{genbank,
	Author = {Dennis Benson and Ilene Karsch-Mizrachi and David Lipman and James Ostell and David Wheeler},
	Journal = {Nucleic Acids Research},
	Number = {1},
	Pages = {23--27},
	Title = {{GenBank}},
	Volume = {31},
	Year = 2003}

@misc{rubisco,
	Author = {David Goodsell},
	Howpublished = {\url{http://nist.rcsb.org/pdb/molecules/pdb11_1.html}},
	Title = {{PDB Molecule of the Month: Rubisco (Ribulose Bisphosphate Carboxylase/Oxygenase)}},
	Year = {2003}}

@conference{wilkinson76,
	Author = {Mark Wilkinson and Damian Gessler and Andrew Farmer and Lincoln Stein},
	Booktitle = {Virtual Conference on Genomics and Bioinformatics},
	Note = {\url{http://www.ndsu.edu/virtual-genomics}},
	Title = {{The BioMOBY project explores open source, simple, extensible protocols for enabling biological database interoperability}},
	Year = {2003}}

@article{lordstevens,
	Annote = {there are lots of ontologies out there for describing different things some of them are summarised in this conference review},
	Author = {Phillip Lord and Robert Stevens},
	Journal = {Comparative and Functional Genomics},
	Title = {ISMB 2003 bio-ontologies SIG and sixth annual bio-ontologies meeting report},
	Year = {2003}}

@inbook{Mandell95,
	Author = {Daniel J. Mandell and Sheila A. McIlraith},
	Note = {Proceedings of the Second International Semantic Web Conference (ISWC2003), Sanibel Island, Florida, 2003},
	Title = {Adapting BPEL4WS for the Semantic Web: The Bottom-Up Approach to Web Service Interoperation}}

@article{vinoski_darkmatter,
	Author = {Steve Vinoski},
	Journal = {IEEE Internet Computing},
	Number = {5},
	Pages = {92--95},
	Title = {Middleware dark matter},
	Volume = {6},
	Year = {2002}}

@article{wroe,
	Author = {Chris Wroe and Robert Stevens and Carole Goble and Angus Roberts and Mark Greenwood},
	Journal = {International Journal of Cooperative Information Systems},
	Month = {June},
	Number = 4,
	Pages = {197--224},
	Title = {{A Suite of DAML+OIL Ontologies to Describe Bioinformatics Web Services and Data}},
	Volume = 12,
	Year = {2003},
	URL={http://dx.doi.org/10.1142/S0218843003000711}}

@article{uschold,
	Author = {Michael Uschold},
	Journal = {AI magazine},
	Pages = {25--36},
	Title = {Where Are the Semantics in the Semantic Web},
	Year = {2003}}

@article{miningthebibliome,
	Annote = {text mining, quite useful},
	Author = {bibliome},
	Journal = {Nature Reviews Genetics},
	Pages = {401},
	Title = {Mining the bibliome},
	Volume = {2},
	Year = {2001}}

@article{achard,
	Annote = {Popped up on the radar because it had data integration in title. Doesn't really talk about data integration but has some maybe citable stuff on xml in bioinformatics},
	Author = {Frederic Achard and Guy Vaysseix and Emmanuel Barillot},
	Journal = {Bioinformatics},
	Title = {{XML, bioinformatics and data integration}},
	Volume = {17},
	Year = {2001}}

@article{bruhn,
	Annote = {found searching pubmed for xml and bioinformatics},
	Author = {RE Bruhn and PJ Burton},
	Journal = {Biotechniques},
	Number = {6},
	Pages = {1200--1202},
	Title = {{Designing XML schemas for bioinformatics}},
	Volume = {34},
	Year = {2003}}

@misc{hypershim,
	Author = {{Hyperdictionary}},
	Howpublished = {\url{http://www.hyperdictionary.com/computing/shim}},
	Note = {Accessed 06 August 2004},
	Title = {{Shim - meaning and definition of the word}},
	Year = 2004}

@misc{mysqlbiomoby,
	Author = {Mark Wilkinson},
	Title = {{Personal communication by email}},
	Year = 2007}

	


@misc{absmetalworks,
	Author = {{ABS}},
	Howpublished = {\url{http://www.absmetalworks.com/pages/shims.html}},
	Note = {Accessed 06 August 2004},
	Title = {{ABS Metalworks - Specialty Shims}},
	Year = 2004}

@misc{oed,
	Author = {{OED}},
	Howpublished = {\url{http://www.oed.com/}},
	Title = {{Oxford English Dictionary Online, 2nd edition}},
	Year = {1989}}

@book{zen,
	Author = {Robert M. Pirsig},
	Note = {isbn: 0099322617},
	Publisher = {Vintage},
	Title = {Zen and the Art of Motorcycle Maintenance},
	Year = {1999}}

@article{uniprot,
	Author = {Rolf Apweiler and Amos Bairoch and Cathy Wu and Winona Barker and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger and Hongzhan Huang and Rodrigo Lopez and Michele Magrane and Maria Martin and Darren Natale and Claire O'Donovan and Nicole Redaschi and Lai-Su Yeh},
	Journal = {Nucleic Acids Research},
	Pages = {D115--D119},
	Title = {{UniProt: The Universal Protein knowledgebase}},
	Volume = {32},
	Year = {2004}}

@article{uniprot2005,
	Author = {Amos Bairoch and Rolf Apweiler and Cathy H. Wu and Winona C. Barker and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger and Hongzhan Huang and Rodrigo Lopez and Michele Magrane and Maria J. Martin and Darren A. Natale and Claire O'Donovan and Nicole Redaschi and Lai-Su L. Yeh},
	Journal = {Nucleic Acids Research},
	Note = {Database issue: doi:10.1093/nar/gki070},
	Pages = {D154--D159},
	Title = {{The Universal Protein Resource (UniProt)}},
	Volume = {33},
	Year = {2005}}

@article{bairoch2004,
	Author = {Amos Bairoch and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger},
	Journal = {Briefings in Bioinformatics},
	Month = {March},
	Number = {1},
	Pages = {39-55},
	Title = {Swiss-Prot: Juggling between evolution and stability},
	Volume = {5},
	Year = {2004}}

@misc{leaky,
	Author = {Joel Spolsky},
	Howpublished = {\url{http://www.joelonsoftware.com/articles/LeakyAbstractions.html}},
	Title = {The law of leaky abstractions},
	Year = {2002}}

@misc{shimdotnet,
	Author = {Shim.net},
	Howpublished = {\url{http://www.shim.net/}},
	Note = {Accessed 09 August 2004},
	Title = {Free URL Redirection From Shim.net},
	Year = {2004}}

@misc{seqret,
	Author = {{EMBOSS}},
	Howpublished = {\url{http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/seqret.html}},
	Note = {Accessed 10 August 2004},
	Title = {{The European Molecular Biology Open Software Suite: SeqRet}},
	Year = {2004}}

@conference{Dong04,
	Author = {Xin Dong and Alon Halevy and Jayant Madhavan and Ema Nemes and Jun Zhang},
	Booktitle = {Proceedings of the 30th VLDB Conference, Toronto, Canada 2004},
	Title = {Simililarity Search for Web Services},
	Year = {2004},
	booktitle = {VLDB},
	year      = {2004},
	pages     = {372-383},
  crossref  = {DBLP:conf/vldb/2004}}
	
@proceedings{DBLP:conf/vldb/2004,
  editor    = {Mario A. Nascimento and
               M. Tamer {\"O}zsu and
               Donald Kossmann and
               Ren{\'e}e J. Miller and
               Jos{\'e} A. Blakeley and
               K. Bernhard Schiefer},
  title     = {(e)Proceedings of the Thirtieth International Conference
               on Very Large Data Bases, Toronto, Canada, August 31 - September
               3 2004},
  publisher = {Morgan Kaufmann},
  year      = {2004},
  isbn      = {0-12-088469-0},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
	
		

@conference{Halevy04,
	Author = {Alon Halevy},
	Booktitle = {Proceedings of the 30th VLDB Conference, Toronto, Canada 2004},
	Title = {Structures, Semantics and Statistics},
	Year = {2004}}

@misc{openbio,
	Author = {{OBF}},
	Howpublished = {\url{http://www.open-bio.org/}},
	Note = {Accessed 11 August 2004},
	Title = {The Open Bioinformatics Foundation},
	Year = {2004}}

@misc{pathportwebservices,
	Author = {{Virginia Bioinformatics Institute}},
	Howpublished = {\url{http://staff.vbi.vt.edu/pathport/services/}},
	Note = {Accessed 11 August 2004},
	Title = {ToolBus and PathPort Web Services},
	Year = {2004}}

@article{biocorba,
	Author = {Robert Stevens and Crispin Miller},
	Journal = {Briefings in Bioinformatics},
	Number = {1},
	Pages = {9--21},
	Title = {{Wrapping and Interoperating Bioinformatics Resources Using CORBA}},
	Volume = {1},
	Year = {2000}}

@misc{graphviz,
	Author = {{AT&T laboratories}},
	Howpublished = {\url{http://www.research.att.com/sw/tools/graphviz/}},
	Note = {Accessed 11 August 2004},
	Title = {{Graphviz - open source graph drawing software}},
	Year = {2004}}

@misc{wmc,
	Annote = {a workflows is....The automation of a business process, in whole or parts, where documents, information or tasks are passed from one participant to another to be processed, according to a set of procedural rules},
	Author = {{Workflow Management Coalition}},
	Howpublished = {\url{http://www.wfmc.org/standards/docs/TC-1011_term_glossary_v3.pdf/}},
	Note = {definition appears on page 8},
	Title = {{Terminology and Glossary Document Number WFMC-TC-1011 - Issue 3.0}},
	Year = {1999}}

@article{genscan,
	Author = {Chris Burge and Samuel Karlin},
	Journal = {Journal of Molecular Biology},
	Note = {See also \url{http://genes.mit.edu/GENSCAN.html}},
	Number = {268},
	Pages = {78--94},
	Title = {{Prediction of complete gene structures in human genomic DNA}},
	Year = {1997}}

@article{twinscan,
	Author = {Ian Korf and Paul Flicek and Daniel Duan and Michael R. Brent},
	Journal = {Bioinformatics},
	Note = {See also \url{http://genes.cs.wustl.edu/}},
	Number = {17},
	Pages = {S140--148},
	Title = {{Integrating genomic homology into gene structure prediction}},
	Year = {2001}}

@inproceedings{graves04,
	Author = {Peter Li and Keith Hawyward and Claire Jennings and Kate Owen and Tom Oinn and Robert Stevens and Simon Pearce and Anil Wipat},
	Booktitle = {Proceedings UK e-Science programme All Hands Meeting},
	Title = {{Association of variations in I kappa B-epsilon with Graves' disease using classical myGrid methodologies}},
	Pages = {832--839},
	Year = {2004}
	NOTE={ISBN 1-904425-21-6 }}
	
@inproceedings{graves03,
	Author = {Robert Stevens and Kevin Glover and Chris Greenhalgh and Claire Jennings and Simon Pearce and Peter Li and Melena Radenkovic and Anil Wipat},
	Booktitle = {Proceedings UK e-Science programme All Hands Meeting},
	Note = {2--4 September, Nottingham, UK},
	Pages = {43--50},
	Title = {{Performing in silico Experiments on the Grid: A Users Perspective}},
	Year = {2003}}

@misc{swfsurvey,
	Author = {Aleksander Slominski and Gregor von Laszewski},
	Howpublished = {\url{http://www.extreme.indiana.edu/swf-survey/}},
	Note = {Accessed 18 August 2004},
	Title = {{Scientific Workflows Survey}},
	Year = {2004}}

@inproceedings{berger96supporting,
	Address = {Drymen, Scotland},
	Author = {F. C. Berger and A. H. M. ter Hofstede and Th.P. van der Weide},
	Booktitle = {Information retrieval: New systems and current research, Proceedings of the 16th Research Colloquium of the British Computer Society Information Retrieval Specialists Group},
	Editor = {R. Leon},
	Pages = {26--46},
	Publisher = {Taylor Graham},
	Title = {{Supporting Query by Navigation}},
	Url = {citeseer.ist.psu.edu/berger94supporting.html},
	Year = {1996}}

@misc{monet,
	Author = {Sarah Turner},
	Howpublished = {\url{http://monet.nag.co.uk/}},
	Note = {Accessed 19 August 2004},
	Title = {MONET Home Page Mathematics on the Net}}

@misc{damlshome,
	Author = {Defense Advanced Research Projects Agency},
	Howpublished = {http://www.daml.org/services/owl-s/},
	Note = {Accessed 19 August 2004},
	Title = {DAML Services Home Page}}

@misc{stein_bioit,
	Author = {Lincoln Stein},
	Howpublished = {\url{http://www.bio-itworld.com/news/040703_report2278.html}},
	Note = {Bio-IT world: technology for the life sciences. Special report: 50/50 reflections on the double-helix},
	Title = {Data Sharing Is Key to Understanding the Genome},
	Year = {2004}}

@article{varmusdatabases,
	Author = {Harold Varmus},
	Journal = {Nature Genetics},
	Note = {{A user's guide to the human genome: supplement to Nature Genetics. doi:10.1038/ng963}},
	Pages = {3},
	Title = {Genomic empowerment: the importance of public databases},
	Volume = {32},
	Year = {2002}}

@inbook{raymondart,
	Annote = {Rule of Representation: Fold knowledge into data, so program logic can be stupid and robust. It follows that where you see a choice between complexity in data structures and complexity in code, choose the former. basics of unix philosophy},
	Author = {Eric S. Raymond},
	Chapter = {1: Philosophy},
	Editor = {Eric S. Raymond},
	Note = {isbn 0131429019 also available online at \url{http://www.faqs.org/docs/artu/philosophychapter.html}},
	Publisher = {Addison Wesley Professional Computing Series},
	Title = {The Art of UNIX Programming},
	Year = {2004}}

@misc{genbanksample,
	Author = {Anon},
	Howpublished = {\url{http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html}},
	Month = {July},
	Note = {Accessed 23 August 2004},
	Title = {Sample NCBI GenBank Record},
	Year = {2004}}

@article{genbank2004,
	Author = {Dennis A. Benson and Ilene Karsch-Mizrachi and David J. Lipman and James Ostell and David L. Wheeler},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D23--D26},
	Title = {{GenBank: update}},
	Volume = {32},
	Year = {2004}}

@article{genbank2005,
	Author = {Dennis A. Benson and Ilene Karsch-Mizrachi and David J. Lipman and James Ostell and David L. Wheeler},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D34--D38},
	Title = {{GenBank}},
	Volume = {33},
	Year = {2005}}

@article{ddbj2005,
	Author = {Y. Tateno and N. Saitou and K. Okubo and H. Sugawara and T. Gojobori},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D25--D28},
	Title = {{DDBJ in collaboration with mass-sequencing teams on annotation}},
	Volume = {33},
	Year = {2005}}

@article{obbujirdf,
	Author = {Uche Ogbuji},
	Howpublished = {http://www-106.ibm.com/developerworks/library/w-rdf/},
	Journal = {IBM Developerworks},
	Pages = {557--572},
	Title = {{An introduction to RDF: Exploring the standard for Web-based metadata}},
	Year = {2000}}

@article{biostar,
	Author = {Harry Mangalam},
	Issue = {3},
	Journal = {{Briefings in Bioinformatics}},
	Number = {3},
	Pages = {296--302},
	Title = {{The Bio* toolkits--a brief overview.}},
	Year = {2003}}

@misc{wmc,
	Annote = {a workflows is....The automation of a business process, in whole or parts, where documents, information or tasks are passed from one participant to another to be processed, according to a set of procedural rules},
	Author = {{Workflow Management Coalition}},
	Howpublished = {\url{http://www.wfmc.org/standards/docs/TC-1011_term_glossary_v3.pdf/}},
	Note = {definition appears on page 8},
	Title = {{Terminology and Glossary Document Number WFMC-TC-1011 - Issue 3.0}},
	Year = {1999}}

@article{nar2004,
	Annote = {548 databases},
	Author = {Michael Y. Galperin},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D3--D22},
	Title = {The Molecular Biology Database Collection: 2004 update},
	Volume = {32},
	Year = {2004}}

@article{nar2003,
	Annote = {386 databases},
	Author = {Andreas D. Baxevanis},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Number = {1},
	Pages = {1--12},
	Title = {The Molecular Biology Database Collection: 2003 update},
	Volume = {31},
	Year = {2003}}

@article{nar2002,
	Annote = {335 databases},
	Author = {Andreas D. Baxevanis},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Number = {1},
	Pages = {1--12},
	Title = {The Molecular Biology Database Collection: 2002 update},
	Volume = {30},
	Year = {2002}}

@article{nar2001,
	Annote = {281 databases},
	Author = {Andreas D. Baxevanis},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Number = {1},
	Pages = {1--10},
	Title = {The Molecular Biology Database Collection: an updated compilation of biological database resources},
	Volume = {29},
	Year = {2001}}

@article{nar2000,
	Annote = {227 databases by my count, there isn't an official figure},
	Author = {Andreas D. Baxevanis},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Number = {1},
	Pages = {1--7},
	Title = {The Molecular Biology Database Collection: an online compilation of relevant database resources},
	Volume = {28},
	Year = {2000}}

@article{nar1999,
	Annote = {201 databases by my count, there isn't an official figure},
	Author = {Christian Burks},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Number = {1},
	Pages = {1--9},
	Title = {Molecular Biology Database List},
	Volume = {27},
	Year = {1999}}

@article{nar1998,
	Annote = {93 databases by my count},
	Author = {Anon.},
	Howpublished = {\url{http://nar.oupjournals.org/content/vol26/issue1/}},
	Journal = {Nucleic Acids Research},
	Month = {January},
	Number = {1},
	Title = {Table of Contents},
	Volume = {26},
	Year = {1998}}

@article{nar1997,
	Annote = {64 databases by my count},
	Author = {Anon.},
	Howpublished = {\url{http://nar.oupjournals.org/content/vol25/issue1/}},
	Journal = {Nucleic Acids Research},
	Month = {January},
	Number = {1},
	Title = {Table of Contents},
	Volume = {25},
	Year = {1997}}

@article{nar1996,
	Annote = {58 databases by my count},
	Author = {Anon},
	Howpublished = {\url{http://nar.oupjournals.org/content/vol24/issue1/}},
	Journal = {Nucleic Acids Research},
	Month = {January},
	Number = {1},
	Title = {Table of Contents},
	Volume = {24},
	Year = {1996}}

@article{puttingittogether,
	Author = {Tyra G. Wolfsberg and Kris A. Wetterstrand and Mark S. Guyer and Francis S. Collins and Andreas D. Baxevanis},
	Journal = {Nature Genetics},
	Note = {{A user's guide to the human genome: supplement to Nature Genetics. doi:10.1038/ng965}},
	Pages = {5--8},
	Title = {Introduction: putting it together},
	Volume = {32},
	Year = {2002}}

@article{steinannotation,
	Abstract = {The genome sequence of an organism is an information resource unlike any that biologyists have previously had access to. But the value of the genome is only as good as its annotation. It is the annotation that bridges the gap from the sequcence to the biology of the organism. The aim of high-quality annotation is to idetnify the key features of the genome - in particular, the genes and their products. The tools and resources fot annotation are developing rapidly, and the scientific community is becoming increasingly reliant on this information for all aspects of biological research.},
	Annote = {Annotation = Metadata: a good review of genome annotation tools, mapping, finding genomic landmarks, gene finding, identifying non-coding RNAs and regulatory regions},
	Author = {Lincoln Stein},
	Journal = {Nature Reviews Genetics},
	Pages = {493--503},
	Title = {Genome annotation: from sequence to biology},
	Volume = {2},
	Year = {2001}}

@article{rambauthiv,
	Author = {Andrew Rambaut and D Posasa and KA Crandall and EC Holmes},
	Journal = {Nature Reviews Genetics},
	Pages = {52--61},
	Title = {{The causes and consequences of HIV evolution}},
	Volume = {5},
	Year = {2004}}

@misc{gff,
	Author = {Richard Durbin and David Haussler},
	Howpublished = {\url{http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml}},
	Note = {Accessed 26 August 2004},
	Title = {GFF (General Feature Format) Specifications Document},
	Year = {2003}}

@misc{bsml,
	Author = {{LabBook}},
	Howpublished = {\url{http://www.bsml.org}},
	Note = {Accessed 26 August 2004},
	Title = {{Bioinformatic Sequence Markup Language}},
	Year = {2004}}

@misc{fasta,
	Author = {Rolf Huehne and K Aumann},
	Howpublished = {\url{http://ngfnblast.gbf.de/docs/fasta.html}},
	Note = {Accessed 26 August 2004},
	Title = {FASTA Format description},
	Year = {2004}}

@misc{agave,
	Author = {{DoubleTwist}},
	Howpublished = {\url{http://www.agavexml.org/}},
	Note = {Accessed 26 August 2004},
	Title = {AGAVE - Architecture for Genomic Annotation, Visualization, and Exchange},
	Year = 2004}

@misc{das,
	Author = {Lincoln D. Stein and Sean Eddy and Robin Dowell},
	Howpublished = {http://biodas.org/documents/spec.html},
	Title = {{Distributed Sequence Annotation System (DAS) version 1.53}},
	Year = {2002}}

@misc{featuretable,
	Author = {{EMBL}},
	Howpublished = {\url{http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html}},
	Note = {Version 6.1 Apr 15 2004},
	Title = {The DDBJ/EMBL/GenBank Feature Table: Definition},
	Year = {2004}}

@misc{gamexml,
	Annote = {Genome Annotation Markup Elements (GAME) is a syntax for the exchange of genomic annotation. It will enable genome centres, model organism databases, and individual researchers to specify the conclusions they have drawn from their analyses of primary sequence data and share these XML descriptions with one another.},
	Author = {{bioxml.org}},
	Howpublished = {\url{http://www.bioxml.org/Projects/game/game.dtd.html}},
	Title = {GAME DTD (Genome Annotation Markup Elements)},
	Year = {2000}}

@misc{fan,
	Author = {Jun Fan},
	Note = {Continuation report, School of Biological Sciences, University of Manchester},
	Title = {Design and implementation of an analytical bioinformatics database},
	Year = {2004}}

@inbook{beginningperl,
	Author = {James Tisdall},
	Chapter = {Introduction},
	Note = {isbn: 0-596-00080-4},
	Pages = {384},
	Publisher = {O'Reilly},
	Title = {Beginning Perl for Bioinformatics},
	Year = {2001}}

@article{dowel_das,
	Annote = {main reference for das},
	Author = {Robin D Dowel and Rodney M. Jokerst and Allen Day and Sean R. Eddy and Lincoln Stein},
	Journal = {BMC Bioinformatics},
	Number = {1},
	Title = {The Distributed Annotation System},
	Volume = {2},
	Year = {2001}}

@article{knikker_choreography,
	Annote = {reckons that 'Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application' but I wouldn't necessarily agree. Whats wrong with BPEL?},
	Author = {Remko de Knikker and Youjun Guo and Jin-long Li and Albert KH Kwan and Kevin Y Yip and David W Cheung and Kei-Hoi Cheung},
	Journal = {BMC Bioinformatics},
	Note = {doi:10.1186/1471-2105-5-25},
	Number = {25},
	Title = {A web services choreography scenario for interoperating bioinformatics applications},
	Volume = {5},
	Year = {2004}}

@article{gims_yeast,
	Author = {Mike Cornell and Norman M Paton and Cornelia Hedeler and Paul Kirby and D Delneri and A Hayes and S.G. Oliver},
	Journal = {Yeast},
	Number = {15},
	Pages = {1291-1306},
	Title = {{GIMS: A Data Warehouse for Storage and Analysis of Genome Sequence and Functional Data}},
	Volume = {20},
	Year = {2003}}

@article{gims_bioinformatics,
	Author = {Norman W Paton and S.A. Khan and A. Hayes and F Moussouni and Andy Brass and K Eilbeck and Carole A Goble and S Hubbard and Stephen G. Oliver},
	Journal = {Bioinformatics},
	Number = {6},
	Pages = {548--558},
	Title = {{Conceptual Modelling of Genomic Information}},
	Volume = {16},
	Year = {2000}}

@misc{w3clifesciences,
	Author = {{W3C}},
	Howpublished = {\url{http://www.w3.org/2004/07/swls-cfp.html}},
	Note = {27-28 October 2004, Cambridge, Massachusetts USA},
	Title = {{CFP: Call For Participation: W3C Workshop on Semantic Web for Life Sciences}},
	Year = {2004}}

@article{blast,
	Author = {Stephen F. Altschul and Warren Gish and Webb Miller and Eugene W. Meyers and David J. Lipman},
	Journal = {Journal of Molecular Biology},
	Pages = {403--410},
	Title = {{Basic Local Alignment Search Tool}},
	Volume = {215},
	Year = {1990}}

@article{gblast,
	Author = {Stephen F. Altschul and Thomas L. Madden and Alejandro A. Schaffer and Jinghui Zhang and Zheng Zhang and Webb Miller and David J. Lipman},
	Journal = {Nucleic Acids Research},
	Pages = {3389--3402},
	Title = {{Gapped BLAST and PSI-BLAST: a new generation of protein database search programs}},
	Volume = {25},
	Year = {1997}}

@misc{linkup,
	Author = {Carole Goble},
	Howpublished = {\url{http://www.mygrid.org.uk/linkup/}},
	Title = {LinkUp Project},
	Year = {2004}}

@misc{sofg,
	Author = {{Jackson Laboratory}},
	Howpublished = {\url{http://www.sofg.org/}},
	Note = {Oct 23-26, 2004, The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania},
	Title = {{Standards and Ontologies For Functional Genomics}},
	Year = {2004}}

@article{OFM+04,
	Author = {Tom Oinn and Matthew Addis and Justin Ferris and Darren Marvin and Mark Greenwood and Tim Carver and Matthew R. Pocock and Anil Wipat and Peter Li},
	Journal = {Bioinformatics},
	Number = 17,
	Title = {Taverna: a tool for the composition and enactment of bioinformatics workflows},
	Volume = 20,
	Year = {2004}}

@misc{monet1,
	Author = {Olga Caprotti and Mike Dewar and Daniele Turi},
	Howpublished = {\url{http://monet.nag.co.uk/cocoon/monet/publicdocs/monetonts.pdf}},
	Title = {Mathematical Service Matching Using Description Logic and OWL},
	Year = {2004}}

@article{srsebi,
	Author = {Evgeni M. Zdobnov and Rodrigo Lopez and Rolf Apweiler and Thure Etzold},
	Journal = {Bioinformatics},
	Number = {2},
	Pages = {368--373},
	Title = {{The EBI SRS Server-recent developments}},
	Volume = {18},
	Year = {2002}}
	
	

@book{wattprog,
	Annote = {recommended by Alvaro},
	Author = {David A. Watt},
	Note = {ISBN:0137288743},
	Publisher = {Prentice-Hall},
	Title = {Programming language concepts and paradigms},
	Year = {1990}}

@inproceedings{matchmaker,
	Author = {Massimo Paolucci and Takahiro Kawamura and Terry R. Payne and Katia Sycara},
	Booktitle = {{First International Semantic Web Conference (ISWC2002)}},
	Pages = {333--347},
	Title = {{Semantic Matching of Web Services Capabilities}},
	Year = {2002},
	  crossref  = {DBLP:conf/semweb/2002},
}
	
@proceedings{DBLP:conf/semweb/2002,
  editor    = {Ian Horrocks and James A. Hendler},
  title     = {The Semantic Web - ISWC 2002, First International Semantic Web Conference, Sardinia, Italy, June 9-12, 2002, Proceedings},
  booktitle = {International Semantic Web Conference},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {2342},
  year      = {2002},
  isbn      = {3-540-43760-6},
}	
	

@article{uschold,
	Author = {Michael Uschold},
	Journal = {AI magazine},
	Pages = {25--36},
	Title = {Where Are the Semantics in the Semantic Web},
	Year = {2003}}

@article{lordstevens,
	Annote = {there are lots of ontologies out there for describing different things some of them are summarised in this conference review},
	Author = {Phillip Lord and Robert Stevens},
	Journal = {Comparative and Functional Genomics},
	Title = {ISMB 2003 bio-ontologies SIG and sixth annual bio-ontologies meeting report},
	Year = {2003}}

@inproceedings{Bracciali,
	Author = {Bracciali},
	Year = 2002}

@inbook{Mandell95,
	Author = {Daniel J. Mandell and Sheila A. McIlraith},
	Note = {Proceedings of the Second International Semantic Web Conference (ISWC2003), Sanibel Island, Florida, 2003},
	Title = {Adapting BPEL4WS for the Semantic Web: The Bottom-Up Approach to Web Service Interoperation}}

@article{vinoski_darkmatter,
	Author = {Steve Vinoski},
	Journal = {IEEE Internet Computing},
	Number = {5},
	Pages = {92--95},
	Title = {Middleware dark matter},
	Volume = {6},
	Year = {2002}}

@article{uschold,
	Author = {Michael Uschold},
	Journal = {AI magazine},
	Pages = {25--36},
	Title = {Where Are the Semantics in the Semantic Web},
	Year = {2003}}

@misc{hypershim,
	Author = {{Hyperdictionary}},
	Howpublished = {\url{http://www.hyperdictionary.com/computing/shim}},
	Note = {Accessed 06 August 2004},
	Title = {{Shim - meaning and definition of the word}},
	Year = 2004}

@misc{absmetalworks,
	Author = {{ABS}},
	Howpublished = {\url{http://www.absmetalworks.com/pages/shims.html}},
	Note = {Accessed 06 August 2004},
	Title = {{ABS Metalworks - Specialty Shims}},
	Year = 2004}

@misc{oed,
	Author = {{OED}},
	Howpublished = {\url{http://www.oed.com/}},
	Title = {{Oxford English Dictionary Online, 2nd edition}},
	Year = {1989}}

@book{zen,
	Author = {Robert M. Pirsig},
	Note = {isbn: 0099322617},
	Publisher = {Vintage},
	Title = {Zen and the Art of Motorcycle Maintenance},
	Year = {1999}}

@article{uniprot,
	Author = {Rolf Apweiler and Amos Bairoch and Cathy Wu and Winona Barker and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger and Hongzhan Huang and Rodrigo Lopez and Michele Magrane and Maria Martin and Darren Natale and Claire O'Donovan and Nicole Redaschi and Lai-Su Yeh},
	Journal = {Nucleic Acids Research},
	Pages = {D115--D119},
	Title = {{UniProt: The Universal Protein knowledgebase}},
	Volume = {32},
	Year = {2004}}

@article{bairoch2004,
	Author = {Amos Bairoch and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger},
	Journal = {Briefings in Bioinformatics},
	Month = {March},
	Number = {1},
	Pages = {39-55},
	Title = {Swiss-Prot: Juggling between evolution and stability},
	Volume = {5},
	Year = {2004}}

@misc{leaky,
	Author = {Joel Spolsky},
	Howpublished = {\url{http://www.joelonsoftware.com/articles/LeakyAbstractions.html}},
	Title = {The law of leaky abstractions},
	Year = {2002}}

@misc{shimdotnet,
	Author = {Shim.net},
	Howpublished = {\url{http://www.shim.net/}},
	Note = {Accessed 09 August 2004},
	Title = {Free URL Redirection From Shim.net},
	Year = {2004}}

@conference{Dong04,
	Author = {Xin Dong and Alon Halevy and Jayant Madhavan and Ema Nemes and Jun Zhang},
	Booktitle = {Proceedings of the 30th VLDB Conference, Toronto, Canada 2004},
	Title = {Simililarity Search for Web Services},
	Year = {2004}}

@conference{Halevy04,
	Author = {Alon Halevy},
	Booktitle = {Proceedings of the 30th VLDB Conference, Toronto, Canada 2004},
	Title = {Structures, Semantics and Statistics},
	Year = {2004}}

@misc{openbio,
	Author = {{OBF}},
	Howpublished = {\url{http://www.open-bio.org/}},
	Note = {Accessed 11 August 2004},
	Title = {The Open Bioinformatics Foundation},
	Year = {2004}}

@misc{pathportwebservices,
	Author = {{Virginia Bioinformatics Institute}},
	Howpublished = {\url{http://staff.vbi.vt.edu/pathport/services/}},
	Note = {Accessed 11 August 2004},
	Title = {ToolBus and PathPort Web Services},
	Year = {2004}}

@article{biocorba,
	Author = {Robert Stevens and Crispin Miller},
	Journal = {Briefings in Bioinformatics},
	Number = {1},
	Pages = {9--21},
	Title = {{Wrapping and Interoperating Bioinformatics Resources Using CORBA}},
	Volume = {1},
	Year = {2000}}

@article{STW+04,
	Author = {Robert D. Stevens and Hannah J. Tipney and Chris Wroe and Tom Oinn and Martin Senger and Phillip W Lord and Carole A. Goble and Andy Brass and May Tassabehji},
	Issue = {1},
	Journal = {Bioinformatics},
	Pages = {i303--i310},
	Title = {{Exploring Williams-Beuren Syndrome Using myGrid}},
	Volume = {20},
	Year = {2004}}

@misc{graphviz,
	Author = {{AT & T laboratories}},
	Howpublished = {\url{http://www.research.att.com/sw/tools/graphviz/}},
	Note = {Accessed 11 August 2004},
	Title = {{Graphviz - open source graph drawing software}},
	Year = {2004}}

@article{genscan,
	Author = {Chris Burge and Samuel Karlin},
	Journal = {Journal of Molecular Biology},
	Note = {See also \url{http://genes.mit.edu/GENSCAN.html}},
	Number = {268},
	Pages = {78--94},
	Title = {{Prediction of complete gene structures in human genomic DNA}},
	Year = {1997}}

@article{nar2004,
	Author = {Michael Y. Galperin},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D3--D22},
	Title = {The Molecular Biology Database Collection: 2004 update},
	Volume = {32},
	Year = {2004}}

@article{karp95,
	Author = {Karp, P.},
	Journal = {Journal of Computational Biology},
	Number = {4},
	Pages = {573--586},
	Title = {{A Strategy for Database Interoperation}},
	Volume = {2},
	Year = {1995}}

@misc{hgmpemboss,
	Author = {Gary Williams},
	Howpublished = {\url{http://emboss.sourceforge.net/docs/themes/SequenceFormats.html}},
	Title = {{EMBOSS sequence formats}},
	Year = {2003}}

@article{chen95,
	Author = {Chen, I.A. and Markowitz, V.M.},
	Journal = {Information Systems},
	Number = {5},
	Pages = {393--418},
	Title = {{A}n {O}verview of the {O}bject-{P}rotocol {M}odel ({OPM}) and the {OPM} {D}ata {M}anagement {T}ools},
	Volume = {20},
	Year = {1995}}

@article{davidson95,
	Author = {Davidson, S.B. and Overton, C. and Buneman, P.},
	Journal = {Journal of Computational Biology},
	Number = {4},
	Pages = {557--572},
	Title = {{C}hallenges in {I}ntegrating {B}iological {D}ata {S}ources},
	Volume = {2},
	Year = {1995}}

@inbook{sicp,
	Annote = {Some useful stuff based around LISP},
	Author = {Harold Abelson and Gerald Jay Sussman},
	Chapter = {2.5.2 Combining Data of Different Types},
	Edition = {Second edition},
	Note = {isbn: 0262510871 also available from \url{http://mitpress.mit.edu/sicp/full-text/book/book-Z-H-18.html#%_sec_2.5.2}},
	Pages = {??--??},
	Publisher = {MIT Press},
	Title = {Structure and Interpretation of Computer Programs},
	Year = {1996}}

@article{Chagoyen2004,
	Annote = {From Monica, first read suggests that motivating examples might be useful},
	Author = {M. Chagoyen and M. E. Kurul and P. A. De-Alarcon and J. M. Carazo and A. Gupta},
	Journal = {Bioinformatics},
	Number = {13},
	Pages = {2092--2100},
	Title = {Designing and executing scientific workflows with a programmable integrator},
	Volume = {20},
	Year = {2004}}

@article{SteinIntegrating,
	Annote = {Useful overview, Talks about BioMOBY and Mygrid. Points out problems of data modelling, e.g. Implies that  mygrid too complex, service providers won't use it. BioMOBY too simple and limited in its ability to describe web services},
	Author = {Lincoln Stein},
	Journal = {Nature Reviews Genetics},
	Pages = {337--345},
	Title = {Integrating Biological Databases},
	Volume = {4},
	Year = {2003}}

@inproceedings{saboujapan,
	Address = {Hiroshima, Japan},
	Annote = {Describes some of the preliminary work to Martas talk in Manchester titled Learning Web Service Ontologies from the mygrid service collection},
	Author = {Marta Sabou},
	Booktitle = {Proc.\ of the Third International Semantic Web Conference (ISWC2004)},
	Note = {November, 2004},
	Title = {From Software APIs to Web Service Ontologies: a Semi-Automatic Extraction Method},
	Year = 2004}

@inproceedings{SWG+05,
	Address = {Chiba, Japan},
	Author = {Marta Sabou and Chris Wroe and Carole Goble and Gilad Mishne},
	Booktitle = {Proc.\ of the 14th International World Wide Web Conference (WWW2005)},
	Note = {10-14 May, 2005},
	Title = {{Learning Domain Ontologies for Web Service Descriptions: an Experiment in Bioinformatics}},
	Year = 2005}

@article{sabouvalencia,
	Annote = {learning ontologies},
	Author = {Marta Sabou},
	Note = {In Proceedings of the ECAI-2004 Workshop on Ontology Learning and Population (ECAI-OLP), Valencia, Spain, August 2004},
	Title = {Extracting Ontologies from Software Documentation: a Semi-Automatic Method and its Evaluation},
	Year = {2004}}

@article{blythe,
	Annote = {The paper that Jim referenced in his slides at the shims breakout session of sisters linkup},
	Author = {Jim Blythe and Ewa Deelman and Yolanda Gil},
	Journal = {IEEE Intelligent Systems},
	Number = {4},
	Pages = {16--23},
	Title = {Automatically Composed Workflows for Grid Environments},
	Volume = {19},
	Year = {2004}}

@inproceedings{owlrules,
	Author = {Ian Horrocks and Peter F. Patel-Schneider},
	Booktitle = {Thirteenth International World Wide Web Conference (WWW 2004)},
	Pages = {723--731},
	Title = {A Proposal for an OWL Rules Language},
	Year = {2004}}

@misc{SWRL,
	Author = {Ian Horrocks and Peter F. Patel-Schneider and Harold Boley and Said Tabet and Benjamin Grosof and Mike Dean},
	Howpublished = {\url{http://www.w3.org/Submission/SWRL/}},
	Note = {W3C Member Submission 21 May 2004},
	Title = {SWRL: A Semantic Web Rule Language: Combining OWL and RuleML},
	Year = {2004}}

@article{garwoodpedro,
	Annote = {Most up to date description of Pedro, makes comparisons to XML spy and emphasises support for ontology use},
	Author = {Kevin L. Garwood and Chris F. Taylor and Kai J. Runte and Andy Brass and Stephen G. Oliver and Norman W. Paton},
	Journal = {Bioinformatics},
	Note = {Application note},
	Number = {15},
	Pages = {2463--2465},
	Title = {Pedro: a configurable data entry tool for XML},
	Volume = {20},
	Year = {2004}}

@inproceedings{KimandGil,
	Author = {Jihie Kim and Yolanda Gil},
	Booktitle = {Second International Semantic Web Conference (ISWC 2003), Sanibel Island, Florida, USA},
	Pages = {??--??},
	Title = {Towards Interactive Composition of Semantic Web Services},
	Year = {2004}}

@inproceedings{KimGilSpraragen,
	Author = {Jihie Kim and Yolanda Gil and Marc Spraragen},
	Booktitle = {In Workshop: Planning and Scheduling for Web and Grid Services, at the 14th International Conference on Automatic Planning and Scheduling (ICAPS 04); Whistler, Candada},
	Title = {A Knowledge-Based Approach to Interactive Workflow Composition},
	Year = {2004}}

@misc{OntologiesvsSchemas,
	Annote = {references living in a schemaless web},
	Author = {Roger Costello},
	Howpublished = {\url{http://lists.xml.org/archives/xml-dev/200309/msg00256.html}},
	Note = {xml-dev mailign},
	Title = {xml-dev - Ontologies vs Schemas vs Transformation},
	Year = {2003}}
	
	
@Article{Stevens:2003:Bioinformatics:12855473,
author = "Stevens, R D and Robinson, A J and Goble, C A",
title = {myGrid: personalised bioinformatics on the information grid},
journal = "Bioinformatics",
year = "2003",
volume = "19 Suppl 1",
number = "",
pages = "302-304",
month = "",
pmid = "12855473",
}

@misc{mygridtype,
	Annote = {Has useful pointers to type inference in mygrid},
	Author = {M.Nedim Alpdemir and Alvaro A. Fernandes},
	Howpublished = {\url{http://twiki.mygrid.org.uk/twiki/pub/Mygrid/MyGridInformationRepository/myGridTypes-thoughts.pdf}},
	Note = {Some unfinished notes on type systems in mygrid},
	Title = {Thoughts on myGrid Type System and MIR},
	Year = {2003}}

@inproceedings{Radetzki,
	Author = {Uwe Radetzki and A. B. Cremers},
	Booktitle = {2004 IEEE International Conference on Web Services (ICWS 2004)},
	Note = {July 6-9, 2004, San Diego, California.},
	Pages = {752--755},
	Title = {IRIS: A Framework for Mediator-Based Composition of Service-Oriented Software.},
	Year = {2004}}

@article{ZRK+04,
	Annote = {referred to in Excel ate my DNA article on the register: Some type transformations are unsafe },
	Author = {Barry R Zeeberg and Joseph Riss and David W Kane and Kimberly J Bussey and Edward Uchio and W Marston Linehan and Carl Barrett and John N Weinstein},
	Journal = {BMC Bioinformatics},
	Number = {80},
	Title = {Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics},
	Volume = {5},
	Year = {2004}}

@article{ARN+04,
	Annote = {flagged by aktsws workshop review},
	Author = {J F Aldana and M Roldan and I Navas and A J Perez and O Trelles},
	Journal = {Proceedings of the 2004 ACM Symposium on Applied Computing},
	Title = {Integrating Biological Data Sources and Data Analysis Tools through Mediator},
	Year = {2004}}

@article{PSS04,
	Author = {Massimo Paolucci and Naveen Srinivasan and Katia Sycara},
	Journal = {International Semantic Web Conference 2004},
	Note = {Workshop notes VI: Semantic Web Services},
	Pages = {120--134},
	Title = {{Expressing WSMO Mediators in OWL-S}},
	Volume = {W6},
	Year = {2004}}

@misc{LB04a,
	Author = {Shawn Bowers and Bertram Lud\"{a}scher},
	Note = {Intl. Workshop on Data Integration in the Life Sciences (DILS'04), March 25-26, 2004 Leipzig, Germany, LNCS 2994.},
	Title = {An Ontology-Driven Framework for Data Transformation in Scientific Workflows},
	Year = {2004}}

@misc{HUL05a,
	Author = {Chris Wroe and Jim Blythe},
	Howpublished = {\url{http://www.cs.man.ac.uk/~hulld/images/IMGP1269.jpg}},
	Note = {Picture of whiteboard from sisters link-up in San Diego},
	Title = {San Diego Scenario},
	Year = {2005}}

@misc{HUL05b,
	Author = {Duncan Hull},
	Howpublished = {\url{http://www.cs.man.ac.uk/~hulld/pres/20050223_querying_bioinformatics_data.pdf}},
	Note = {IMG seminar presentation},
	Title = {Querying bioinformatics data: where can semantic web services help?},
	Year = {2005}}

@article{CaW85,
	Annote = {Alvaro, a paper that everybody cites but I find not actually very useful as a starting point},
	Author = {Luca Cardelli and Peter Wegner},
	Journal = {ACM Computing Surveys},
	Number = {4},
	Pages = {471--522},
	Title = {On understanding Types, Data Abstraction and Polymorphism},
	Volume = {17},
	Year = {1985}}

@article{LOS02,
	Annote = {Alvaro, a recent paper, not studied whic *may* be useful in spite of its very narrow foxus on (loosely coupled) OOPL},
	Author = {Yuri Leontiev and M Tamer Ozsu and Duane Safron},
	Journal = {ACM Computing Surveys},
	Number = {4},
	Pages = {409--449},
	Title = {On type systems for object-oriented database programming languages},
	Volume = {34},
	Year = {2002}}

@conference{RSH97,
	Annote = {Seminal paper on wrapping},
	Author = {Mary Tork Roth and Peter Schwarz},
	Booktitle = {Proceedings of the 2rd VLDB Conference, Athens, Greece},
	Pages = {266--275},
	Title = {Don't Scrap It, Wrap It! A Wrapper Architecture for Legacy Data Sources},
	Year = {1997}}

@incollection{old-jdm,
	Author = {Robert Stevens and Carole Goble and Norman W. Paton and Sean Bechhofer and Gary Ng and Patricia Baker and Andy Brass},
	Booktitle = {Bioinformatics: Managing Scientific Data},
	Editor = {Zoe Lacroix and Terence Critchlow},
	Isbn = {1-55860-829-X},
	Key = {ontology,stevens},
	Month = {May},
	Publisher = {Morgan Kaufmann},
	Title = {{Complex Query Formulation Over Diverse Information Sources in TAMBIS}},
	Year = 2003}

@inproceedings{ssmdb02,
	Author = {M. Peim and E. Franconi and N.W. Paton and C.A. Goble},
	Booktitle = {Proc. 14th International Conference on Scientific and Statistical Database Management (SSDBM)},
	Editor = {J. Kennedy},
	Pages = {27-36},
	Publisher = {EEE Computer Society},
	Title = {{Query Processing with Description Logic Ontologies Over Object-Wrapped Databases}},
	Year = {2002}}

@article{goble01,
	Author = {Carole Goble and Robert Stevens and Gary Ng and Sean Bechhofer and Norman Paton and Patricia Baker and Martin Peim and Andy Brass},
	Journal = {IBM Systems Journal Special issue on deep computing for the life sciences},
	Number = {2},
	Pages = {532 -- 552},
	Title = {{Transparent Access to Multiple Bioinformatics Information Sources}},
	Url = {http://dx.doi.org/10.1147/sj.402.0532},
	Volume = {40},
	Year = {2001}}

@article{briefings2,
	Author = {Stevens, R. and Goble, C.A. and Bechhofer, S.},
	Journal = {Briefings in Bioinformatics},
	Month = {November},
	Number = {4},
	Pages = {398--416},
	Title = {{Ontology-based Knowledge Representation for Bioinformatics}},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/briefings-ontology.pdf},
	Volume = {1},
	Year = {2000}}

@article{bio-queries,
	Author = {Stevens, R.D. and Goble, C.A. and Baker, P. and Brass, A.},
	Journal = {Bioinformatics},
	Key = {stevens,ontology},
	Number = {2},
	Pages = {180--188},
	Title = {{A Classification of Tasks in Bioinformatics}},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/bio-queries.pdf},
	Volume = {17},
	Year = {2001}}

@article{briefings1,
	Author = {Stevens, R. and Miller, C.},
	Journal = {Briefings in Bioinformatics},
	Number = {1},
	Pages = {9--21},
	Title = {{Wrapping and Interoperating Bioinformatics Resources Using CORBA}},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/briefings-corba.pdf},
	Volume = {1},
	Year = {2000}}

@misc{final-report,
	Author = {C.A. Goble and Norman W. Paton and Andy Brass},
	Title = {{TAMBIS Final Report to the BBSRC Bioinformatics Panel}},
	Url = {papers/TAMBISReport formatted.doc},
	Year = {2000}}

@inproceedings{eml99,
	Author = {Stevens, R. and Goble, C.A. and Paton, N.W. and Bechhofer, S. and Ng, G. and Baker, P. and Brass, A.},
	Booktitle = {Workshop on Computation of Biochemical Pathways and Genetic Networks},
	Editor = {Bornberg-Bauer, E. and {De Beuckelaer}, A. and Kummer, U. and Rost, U.},
	Location = {European Media Lab, Heidelberg, Germany},
	Month = {August},
	Pages = {83--88},
	Publisher = {European Media Lab (EML)},
	Title = {{Complex Query Formulation Over Diverse Information Sources Using an Ontology}},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/eml99.pdf},
	Year = {1999}}

@article{tambis_appnote,
	Author = {Stevens, R. and Baker, P. and Bechhofer, S. and Ng, G. and Jacoby, A. and Paton, N.W. and Goble, C.A. and Brass, A.},
	Journal = {Bioinformatics},
	Number = {2},
	Pages = {184--186},
	Title = {{TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources}},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/application-note.ps},
	Volume = {16},
	Year = {2000}}

@inproceedings{uidis99,
	Author = {Sean Bechhofer and Robert Stevens and Gary Ng and Alex Jacoby and Carole Goble},
	Booktitle = {Proc. User Interfaces to Data Intensive Systems (UIDIS99)},
	Day = {5--6},
	Editor = {Norman W. Paton and Tony Griffiths},
	Location = {Edinburgh, UK},
	Month = {September},
	Pages = {158--161},
	Publisher = {{IEEE} Press},
	Title = {{G}uiding the {U}ser: {A}n {O}ntology {D}riven {I}nterface},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/uidis99.pdf},
	Year = {1999}}

@inproceedings{paton99,
	Address = {Los Alamitos, California},
	Author = {Paton, N.W. and Stevens, R.D. and Baker, P.G. and Goble, C.A. and Bechhofer, S. and Brass, A.},
	Booktitle = {Proc. 11th Int. Conf. on Scientific and Statistical Database Management ({SSDBM})},
	Editor = {Z.M. Ozsoyoglo, \emph{et al}.},
	Location = {Cleveland},
	Month = {July},
	Pages = {138--147},
	Publisher = {{IEEE} Press},
	Title = {{Q}uery {P}rocessing in the {TAMBIS} {B}ioinformatics {S}ource {I}ntegration {S}ystem},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/ssdb.ps},
	Year = {1999}}

@article{baker99,
	Author = {Baker, P.G. and Goble, C.A. and Bechhofer, S. and Paton, N.W. and Stevens, R. and Brass, A},
	Journal = {Bioinformatics},
	Key = {stevens,ontology},
	Number = {6},
	Pages = {510--520},
	Title = {{A}n {O}ntology for {B}ioinformatics {A}pplications},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/bioinformatics-ontology99.doc},
	Volume = {15},
	Year = {1999}}

@inproceedings{baker98,
	Address = {Menlow Park, California},
	Author = {Baker, P.G. and Brass, A. and Bechhofer, S. and Goble, C. and Paton, N. and Stevens, R.},
	Booktitle = {{Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB'98)}},
	Location = {Montreal, Canada},
	Month = {June 28-July 1},
	Pages = {25--34},
	Publisher = {AAAI Press},
	Title = {{TAMBIS}: {T}ransparent {A}ccess to {M}ultiple {B}ioinformatics {I}nformation {S}ources. {A}n {O}verview},
	Url = {http://www.cs.man.ac.uk/~stevensr/papers/baker98.pdf},
	Year = {1998}}

@article{GWr05,
	Author = {Carole Goble and Chris Wroe},
	Journal = {Comparative and Functional Genomics},
	Pages = {623--632},
	Title = {The Montagues and the Capulets},
	Volume = {5},
	Year = {2004},
	url{http://dx.doi.org/10.1002/cfg.442}}

@inproceedings{LRP+04,
	Author = {Rub{\'e}n Lara and Dumitru Roman and Axel Polleres and Dieter Fensel},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {ECOWS},
	Crossref = {DBLP:conf/ecows/2004},
	Ee = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}issn=0302-9743{\&}volume=3250{\&}spage=254},
	Pages = {254-269},
	Title = {A Conceptual Comparison of WSMO and OWL-S.},
	Year = {2004}}

@proceedings{ecows04,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {ECOWS},
	Editor = {Liang-Jie Zhang},
	Isbn = {3-540-23202-8},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Web Services, European Conference, ECOWS 2004, Erfurt, Germany, September 27-30, 2004, Proceedings},
	Volume = {3250},
	Year = {2004}}

@techreport{BMLSW-LTCS-05-02,
	Address = {Germany},
	Author = {F.~Baader and M.~Milicic and C.~Lutz and U.~Sattler and F.~Wolter},
	Institution = {Chair for Automata Theory, Institute for Theoretical Computer Science, Dresden University of Technology},
	Note = {See \url{ http://lat.inf.tu-dresden.de/research/reports.html.}},
	Number = {LTCS-05-02},
	Title = {Integrating Description Logics and Action Formalisms for Reasoning about Web Services},
	Type = {LTCS-Report},
	Year = 2005}

@article{WIE92,
  Annote = {Original paper cited by Lara in the knowledge web deliverable also cited by wsmo paper},
  author    = {Gio Wiederhold},
  title     = {Mediators in the Architecture of Future Information Systems.},
  journal   = {IEEE Computer},
  volume    = {25},
  number    = {3},
  year      = {1992},
  pages     = {38-49},
}
	
	
@article{HHH05,
	Annote = {Summary:  A case study demonstrates that Web services could be the key to coordinating and standardizing incompatible applications in bioinformatics, an effort that is becoming increasingly critical to meaningful research. The paper describes a relatively modest case study integrating several analyzers to investigate some microarray data.  It also mentions several moves towards standardization of Web services. The authors do not, however, make any mention of Stds-1953. sI wonder if this might be a timely opportunity to draw attention to our mission.  I think a timely response or follow-up in the magazine's letter column might be valuable.  Unfortunately, I don't think I'm the right person to do this......  Perhaps our esteemed committee President might be able to do so?   Or maybe delegate the task to some influential voice?  :-)
Regards,
John Murray, jxm@sri.com
SRI International
333 Ravenswood Ave, 301-58
Menlo Park, CA 94025
+1-650-859-5186 (phone)
+1-650-859-3919 (fax) },
	Author = {Hong Tina Gao and Hayes, J.H. and Henry Cai;},
	Journal = {IEEE Computer},
	Month = {March},
	Number = 3,
	Pages = {26--31},
	Title = {{Integrating Biological Research through Web Services}},
	Volume = 38,
	Year = 2005}

@techreport{LARD242,
	Author = {Rub\'{e}n Lara},
	Institution = {Universit\"{a}t Innsbruck},
	Note = {Knowledge web deliverable available from \url{http://kw.dia.fi.upm.es/semanticportal/home.jsp?content=deliverable_list.jsp}},
	Number = {D2.4.2},
	Title = {Semantics for Web Service Discovery and Composition},
	Year = 2004}

@techreport{CMR+05,
	Author = {Emilia Cimpian and Adrian Mocan and Dumitru Roman and Francois Scharffe and James Scicluna},
	Editor = {Francois Scharffe},
	Howpublished = {\url{http://www.wsmo.org/TR/d29/v0.1/}},
	Institution = {DERI},
	Note = {WSMO Working Draft 05 August 2005},
	Number = {D29v0.1},
	Title = {D29v0.1 WSMO Mediators},
	Year = 2005}

@techreport{SPR+06,
	Author = {James Scicluna and Axel Polleres and Dumitru Roman and Dieter Fensel},
	Howpublished = {\url{http://www.wsmo.org/TR/d14/v0.2/}},
	Note = {WSMO Working Draft 13 January 2006},
	Title = {D14v0.2. Ontology-based Choreography and Orchestration of WSMO Services},
	Year = 2006}

@techreport{KMR+05,
	Author = {Jacek Kopeck\'{y} and Matthew Moran and Dumitru Roman and Adrian Mocan},
	Howpublished = {\url{http://www.wsmo.org/TR/d24/v0.1/}},
	Note = {WSMO Working Draft 16 September 2005},
	Title = {D24.2v0.1 WSMO Grounding},
	Year = 2005}

@techreport{KOP05,
	Author = {Jacek Kopeck\'{y}},
	Howpublished = {\url{http://www.wsmo.org/TR/d30/v0.1/}},
	Note = {WSMO Working Draft 5 August 2005},
	Title = {D30v0.1 Aligning WSMO and WSDL-S},
	Year = 2005}

@techreport{KER+05,
	Author = {Mick Kerrigan},
	Howpublished = {\url{http://www.wsmo.org/TR/d9/d9.1/v0.1/20050127/}},
	Institution = {DERI},
	Note = {WSMX Working Draft 27 January 2005},
	Number = {D9.1v0.1},
	Title = {D9.1v0.1 Web Service Modeling Toolkit (WSMT)},
	Year = 2005}

@article{EMBL2005,
	Author = {Carola Kanz \emph{et al.}},
	Journal = {Nucleic Acids Research},
	Pages = {D29-D33},
	Title = {{The EMBL Nucleotide Sequence Database}},
	Volume = 33,
	Year = 2005}
	
@Article{EMBL2007,
author = "Kulikova, T and Akhtar, R and Aldebert, P and Althorpe, N and Andersson, M and Baldwin, A and Bates, K and Bhattacharyya, S and Bower, L and Browne, P and Castro, M and Cochrane, G and Duggan, K and Eberhardt, R and Faruque, N and Hoad, G and Kanz, C and Lee, C and Leinonen, R and Lin, Q and Lombard, V and Lopez, R and Lorenc, D and McWilliam, H and Mukherjee, G and Nardone, F and Pastor, M P and Plaister, S and Sobhany, S and Stoehr, P and Vaughan, R and Wu, D and Zhu, W and Apweiler, R",
title = {{EMBL Nucleotide Sequence Database in 2006}},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "Database issue",
pages = "16-20",
month = "Jan",
pmid = "17148479",
doi = "10.1093/nar/gkl913"
}

@article{UniProt2005,
	Author = {Amos Bairoch and Rolf Apweiler and Cathy H. Wu and Winona C. Barker and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger and Hongzhan Huang and Rodrigo Lopez and Michele Magrane and Maria J. Martin and Darren A. Natale and Claire O'Donovan and Nicole Redaschi and Lai-Su L. Yeh},
	Journal = {Nucleic Acids Research},
	Pages = {D154-D159},
	Title = {{The Universal Protein Resource (UniProt)}},
	Volume = 33,
	Year = 2005}

@Article{UniProt2007,
Author = {{UniProt Consortium}},
title = {{The Universal Protein Resource (UniProt)}},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "Database issue",
pages = "193-197",
pmid = "17142230",
doi = "10.1093/nar/gkl929"
}

@article{GSG+05,
	Author = {Dov Greenbaum and Andrew Smith and Mark Gerstein},
	Journal = {Nucleic Acids Research},
	Pages = {D3-D4},
	Title = {{Editorial: Impediments to database interoperation: legal issues and security concerns}},
	Volume = 33,
	Year = 2005}

@article{discoverieee,
	Author = {C. Wroe and C. Goble and M. Greenwood and P. Lord and S. Miles and J. Papay and T. Payne and L. Moreau},
	Journal = {IEEE Intelligent Systems},
	Link = {http://csdl.computer.org/comp/mags/ex/2004/01/x1048abs.htm},
	Number = 1,
	Pages = {48-55},
	Title = {Automating Experiments Using Semantic Data on a Bioinformatics Grid.},
	Volume = {19},
	Year = 2004}

@article{bioinf-simil,
	Author = {P.W.Lord and R.D. Stevens and A. Brass and C.A.Goble},
	F1000 = {http://www.f1000biology.com/article/12835272/evaluation},
	Journal = {Bioinformatics},
	Link = {http://bioinformatics.oupjournals.org/cgi/content/abstract/19/10/1275?ijkey=35y5NKFGceWLQ&keytype=ref},
	Number = 10,
	Pages = {1275-83},
	Pdf = {download/publications/bioinf-sim-2002.pdf},
	Title = {Investigating semantic similarity measures across the {Gene Ontology}: the relationship between sequence and annotation.},
	Volume = 19,
	Year = 2003}

@article{bioinf-cinema,
	Author = {P.W.Lord and J.N.Selley and T.K.Attwood},
	Journal = {Bioinformatics},
	Number = 10,
	Pages = {1402-03},
	Pdf = {download/publications/cinema-paper.pdf},
	Title = {{CINEMA-MX}: A modular multiple alignment editor},
	Volume = 18,
	Year = 2002}

@article{sofg03,
	Author = {Robert Stevens and Chris Wroe and Sean Bechhofer and Phillip Lord and Alan Rector and Carole Goble},
	Journal = {Comparative and Functional Genomics},
	Link = {http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=102531153},
	Number = 1,
	Title = {Building ontologies in {DAML + OIL}},
	Volume = 4,
	Year = 2003}

@incollection{ggbp-description-logics-2004,
	Author = {Phillip Lord and Robert D. Stevens and Carole A. Goble and Ian Horrocks},
	Booktitle = {Genetics, Genomics, Proteomics, and Bioinformatics},
	Link = {http://www.wiley.com/ggpb/},
	Note = {Invited Article In Press},
	Pdf = {download/publications/wiley_gggb_encyc.pdf},
	Publisher = {Wiley},
	Title = {{Description Logics: OWL and DAML+OIL}},
	Year = 2004}

@inproceedings{pedro-eswc,
	Author = {Kevin Garwood and Phillip Lord and Helen Parkinson and Norman W. Paton and Carole Goble},
	Booktitle = {European Semantic Web Conference},
	Note = {Accepted for Publication},
	Title = {Pedro Ontology Services: A framework for rapid ontology markup},
	Year = 2005}

@inproceedings{feta-eswc,
	Author = {Phillip Lord and Pinar Alper and Chris Wroe and Carole Goble},
	Booktitle = {Proceedings of the European Semantic Web Conference 2005},
	Publisher = {Springer-Verlag},
	Title = {Feta: A light-weight architecture for user oriented semantic service discovery},
	Year = {2005},
	pages     = {17-31},
	crossref  = {DBLP:conf/esws/2005},
	}


@proceedings{DBLP:conf/esws/2005,
  editor    = {Asunci{\'o}n G{\'o}mez-P{\'e}rez and J{\'e}r{\^o}me Euzenat},
  title     = {The Semantic Web: Research and Applications, Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May 29 - June 1, 2005, Proceedings},
  booktitle = {ESWC},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3532},
  year      = {2005},
  note      = {isbn:3-540-26124-9},
}	
	
	

@misc{escience,
	Author = {Research Councils UK},
	Howpublished = {\url{http://www.rcuk.ac.uk/escience/}},
	Title = {{About the UK e-Science Programme}},
	Year = 2004}

@techreport{wsmlfinaldraft,
	Author = {Jos de Bruijn and Holger Lausen and Reto Krummenacher and Axel Polleres and Livia Predoiu and Michael Kifer and Dieter Fensel},
	Institution = {Universit\"{a}t Innsbruck},
	Note = {WSML Final Draft 20 March 2005 available from \url{http://www.wsmo.org/TR/d16/d16.1/v0.2/}},
	Title = {D16.1v0.2 The Web Service Modeling Language WSML},
	Year = 2005}

@techreport{wsmldiscovery,
	Author = {David Aiken},
	Institution = {Universit\"{a}t Innsbruck},
	Note = {WSMO Working Draft 13 April 2005},
	Title = {{D10.1v0.1 Focused Crawler for Web Service Discovery}},
	Year = 2005}

@techreport{wsmt,
	Author = {Mick Kerrigan},
	Institution = {Universit\"{a}t Innsbruck},
	Note = {WSMX Working Draft 27 January 2005 available from \url{http://www.wsmo.org/TR/d9/d9.1/v0.1/}},
	Title = {D9.1v0.1 Web Service Modeling Toolkit (WSMT)},
	Year = 2005}

@misc{biologyfordummies,
	Author = {Alvis Brazma and Helen Parkinson and Thomas Schlitt and Mohammadreza Shojatalab},
	Howpublished = {\url{http://www.ebi.ac.uk/microarray/biology_intro.html}},
	Note = {Published by the European Bioinformatics Institute (EBI)},
	Title = {{A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays}},
	Year = 2001}

@misc{swfsurvey,
	Author = {Aleksander Slominski and Gregor von Laszewski},
	Howpublished = {\url{http://www.extreme.indiana.edu/swf-survey/}},
	Title = {{Scientific Workflows Survey}},
	Year = 2005}
	
@article{Galperin06,
	annote={858 databases},
	Author = {Galperin, MY},
	Doi = {10.1093/nar/gkj162},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {3--5},
	Pmid = {16381871},
	Title = {The Molecular Biology Database Collection: 2006 update},
	Volume = {34},
	Year = {2006}}


@article{nar2005,
	Annote = {719 databases},
	Author = {Michael Y. Galperin},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D5--D24},
	Title = {The Molecular Biology Database Collection: 2005 update},
	Volume = {33},
	Year = {2005}}
	
@article{nar2007,
	Annote = {968 databases},
	author = "Galperin, M Y",
title = {The Molecular Biology Database Collection: 2007 update},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "Database issue",
pages = "3-4",
month = "Jan",
doi = "10.1093/nar/gkl1008"
}	
	
	
	

@inproceedings{ZWG+04,
	Address = {Hiroshima, Japan},
	Author = {Jun Zhao and Chris Wroe and Carole Goble and Robert Stevens and Dennis Quan and Mark Greenwood},
	Booktitle = {Proc.\ of the Third International Semantic Web Conference},
	Note = {November 7 - 11, 2004.},
	Title = {Using Semantic Web Technologies for Representing e-Science Provenance},
	Year = 2004}

@inproceedings{kifer,
	Address = {Hiroshima, Japan},
	Author = {Michael Kifer and Rub{\'e}n Lara and Axel Polleres and Chang Zhao and Uwe Keller and Holger Lausen and Dieter Fensel},
	Booktitle = {Proc.\ of the Third International Semantic Web Conference},
	Note = {November 7 - 11, 2004.},
	Title = {A logical framework for Web Service Discovery},
	Year = 2004}

@inproceedings{HJK05,
	Address = {Hiroshima, Japan},
	Author = {Andreas Hess and Eddie Johnston and Nicholas Kushmerick},
	Booktitle = {Proc.\ of the Third International Semantic Web Conference},
	Note = {November 7 - 11, 2004.},
	Title = {ASSAM: A Tool for Semi-Automatically Annotating Semantic Web Services},
	Year = 2004}
	
	
@inproceedings{DBLP:conf/semweb/HessJK04,
  author    = {Andreas He{\ss} and Eddie Johnston and Nicholas Kushmerick},
  title     = {ASSAM: A Tool for Semi-automatically Annotating Semantic Web Services.},
  booktitle = {International Semantic Web Conference},
  year      = {2004},
  pages     = {320-334},
  url        = {http://www.few.vu.nl/~andreas/publications/hess-iswc04.pdf},
  crossref  = {DBLP:conf/semweb/2004},
}	
	
	

@misc{GR/R67743/01,
	Author = {Carole Goble},
	Howpublished = {\url{http://gow.epsrc.ac.uk/ViewGrant.aspx?Grant=GR/R67743/01}},
	Title = {{myGRID: Directly supporting the e-Scientist}},
	Year = 2001}

@misc{SCH04,
	Author = {Gary Schlitz},
	Howpublished = {\url{http://www.w3.org/2004/10/swls/schiltz.pdf}},
	Note = {W3C workshop on Semantic Web for Life Sciences},
	Title = {{Semantic MOBY Overview}},
	Year = 2004}

@misc{semanticmoby,
	Author = {Lincoln Stein and Damian Gessler and Gary Schiltz},
	Howpublished = {\url{http://biomoby.org/S-MOBY.htm}},
	Title = {{Semantic BioMOBY (S-MOBY)}},
	Year = 2003}

@book{conceptsofgenetics,
	Author = {William S Klug and Michael R Cummings},
	Note = {isbn:0-13-121449-7},
	Publisher = {Prentice Hall},
	Title = {{Concepts of Genetics}},
	Year = 2003}

@incollection{computationalgenomics,
	Annote = {Haven't read this in detail yet},
	Author = {Mark D Wilkinson},
	Booktitle = {Computational Genomics Theory and Application},
	Editor = {Richard P Grant},
	Note = {isbn:1904933017},
	Pages = {???--??},
	Publisher = {Horizon Bioscience, Wymondham, U.K},
	Title = {BioMOBY - the MOBY-S Platform for Interoperable Data Service Provision},
	Year = {2004}}

@article{macneil,
	Annote = {newsy article about biomoby},
	Author = {Jane Salodof MacNeil},
	Journal = {The Scientist},
	Number = {24},
	Pages = {25--27},
	Title = {Coding a Bridge Across the Data Divide},
	Volume = {18},
	Year = {2004}}

@book{cherfasgenome,
	Author = {Jeremy Cherfas},
	Note = {Essential Science Series: isbn:0751337161},
	Publisher = {Dorling Kindersley},
	Title = {{The Human Genome: A beginner's guide to the chemical code of life}},
	Year = 2002}

@book{attwoodintro,
	Author = {Teresa K Attwood and David J Parry-Smith},
	Note = {isbn:0582327881},
	Publisher = {Prentice Hall},
	Title = {{Introduction to Bioinformatics}},
	Year = 2001}

@misc{openbqs,
	Author = {Martin Senger},
	Howpublished = {\url{http://industry.ebi.ac.uk/openBQS/}},
	Title = {{Bibliographic Query Service}},
	Year = 2002}

@article{interpro2005,
	Author = {Nicola J. Mulder and Rolf Apweiler and Teresa K. Attwood and Amos Bairoch and Alex Bateman and David Binns and Paul Bradley and Peer Bork and Phillip Bucher and Lorenzo Cerutti and Richard Copley and Emmanuel Courcelle and Ujjwal Das and Richard Durbin and Wolfgang Fleischmann and Julian Gough and Daniel Haft and Nicola Harte and Nicolas Hulo and Daniel Kahn and Alexander Kanapin and Maria Krestyaninova and David Lonsdale and Rodrigo Lopez and Ivica Letunic and Martin Madera and John Maslen and Jennifer McDowall and Alex Mitchell and Anastasia N. Nikolskaya and Sandra Orchard and Marco Pagni and Chris P. Ponting and Emmanuel Quevillon and Jeremy Selengut and Christian J. A. Sigrist and Ville Silventoinen and David J. Studholme and Robert Vaughan and Cathy H. Wu},
	Journal = {Nucleic Acids Research},
	Note = {Database issue},
	Pages = {D201--D205},
	Title = {InterPro, progress and status in 2005},
	Volume = {33},
	Year = {2005}}

@article{interproscan,
	Author = {Quevillon, E and Silventoinen, V and Pillai, S and Harte, N and Mulder, N and Apweiler, R and Lopez, R},
	Doi = {10.1093/nar/gki442},
	Journal = {Nucleic Acids Research},
	Month = {Jul},
	Number = {Web Server issue},
	Pages = {116-120},
	Pmid = {15980438},
	Title = {InterProScan: protein domains identifier},
	Volume = {33},
	Year = {2005}}

@inproceedings{CYS+05,
	Annote = {A data warehouse built from RDF using Sesame. Paper contains some factual inaccuracies about OWL, XML and RDF and is not clear what and why they've chosen to use RSS},
	Author = {Kei-Hoi Cheung and Kevin Y Yip and Andrew Smith and Remko deKnikker and Andy Masiar and Mark Gerstein},
	Booktitle = {{Intelligent Systems for Molecular Biology 2005, Michigan.}},
	Issue = {?},
	Journal = {Bioinformatics},
	Note = {issn ????-????},
	Title = {{YeastHub: a semantic web use case for integrating data in the life sciences domain}},
	Volume = {??},
	Year = 2005}

@article{OukselS99,
	Annote = {from Robert Stevens},
	Author = {Aris M. Ouksel and Amit P. Sheth},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Ee = {db/journals/sigmod/OukselS99.html},
	Journal = {SIGMOD Record},
	Number = {1},
	Pages = {5-12},
	Title = {Semantic Interoperability in Global Information Systems: A Brief Introduction to the Research Area and the Special Section.},
	Volume = {28},
	Year = {1999}}

@techreport{OUZ04,
	Author = {Christos Ouzounis},
	Institution = {EMBL Research Reports},
	Note = {\url{http://www.ebi.ac.uk/Groups/reports/current/ouzounis.pdf}},
	Pages = {370--372},
	Title = {{Computational Genomics}},
	Year = {2004}}

@article{JANS03,
	Annote = {via Ouzounis, searching for 200 genomes},
	Author = {Paul Janssen and Benjamin Audit and Ildefonso Cases and Nikos Darzentas and Leon Goldovsky and Victor Kunin and Nuria Lopez-Bigas and Jos\'e Manuel Peregrin-Alvarez and \'e Pereira-Leal and Sophia Tsoka and Christos A Ouzounis},
	Journal = {Genome Biology},
	Pages = {402},
	Title = {Beyond 100 genomes},
	Volume = {4},
	Year = {2003}}

@incollection{DL4DB,
	Annote = {useful comparison of description logic and database technology. chapter 16 (last)},
	Author = {Alex Borgida and Maurizio Lenzerini and Riccardo Rosati},
	Booktitle = {The Description Logic Handbook: Theory, Implementation, and Applications},
	Editor = {Franz Baader and Diego Calvanese and Deborah McGuinness and Daniele Nardi and Peter F.~Patel-Schneider},
	Note = {isbn:0521781760},
	Pages = {462--484},
	Publisher = {Cambridge University Press},
	Title = {Description Logics for Databases},
	Year = {2003}}

@incollection{DL4DB2,
	Annote = {Chapter ? has a comparison of DLs with other formalisms e.g. ER schemas},
	Author = {???},
	Booktitle = {The Description Logic Handbook: Theory, Implementation, and Applications},
	Editor = {Franz Baader and Diego Calvanese and Deborah McGuinness and Daniele Nardi and Peter F.~Patel-Schneider},
	Note = {isbn:0521781760},
	Pages = {???--???},
	Publisher = {Cambridge University Press},
	Title = {Relationship with other formalisms???},
	Year = {2003}}

@incollection{corcho,
	Annote = {Chapter ? has a comparison of DLs with other formalisms e.g. ER schemas shelfmark: 	Blue,Floor 2: 006.33/G2},
	Author = {Asunci\'on G\'omez-P\'erez and Mariano Fern\'andez-L\'opez and Oscar Corcho},
	Booktitle = {Ontological engineering : with examples from the areas of knowledge management, e-commerce and the semantic Web},
	Editor = {editors},
	Note = {isbn:0521781760},
	Pages = {???--???},
	Publisher = {Springer},
	Title = {chaptertitle},
	Year = {2004}}

@article{Horrocks01j,
	Annote = {useful comparison on ontologies vs schemas},
	Author = {Michaels Klein and Dieter Fensel and Frank van Harmelen and Ian Horrocks},
	Journal = {Electronic Transactions on Artificial Intelligence},
	Note = {Special Issue on the 1st International Workshop ``Semantic Web: Models, Architectures and Management''},
	Title = {The relation between ontologies and XML schemas},
	URL={http://www.cs.man.ac.uk/~horrocks/Publications/download/2000/ECAI00-WS2.pdf},
	Year = {2001}}

@article{ILI00,
	Annote = {via Ouzounis, searching for 200 genomes},
	Author = {Ioannis Iliopoulos and Sophia Tsoka and Miguel A Andrade and Paul Janssen and Benjamin Audit and Anna Tramontano and Alfonso Valencia and Christophe Leroy and Chris Sander and Christos A Ouzounis},
	Journal = {Genome Biology},
	Number = {1},
	Pages = {0001.1--0001.3},
	Title = {Genome sequences and great expectations},
	Volume = {2},
	Year = {2000}}

@article{200genomes,
	Annote = {via Ouzounis, searching for 200 genomes},
	Author = {Paul Janssen and Leon Goldovsky and Victor Kunin and Nikos Darzentas and Christos A Ouzounis},
	Journal = {EMBO reports},
	Number = {5},
	Pages = {397--399},
	Title = {Genome coverage, literally speaking: The challenge of annotating 200 genomes with 4 million publications},
	Volume = {6},
	Year = {2005}}

@article{buetowscience,
	Annote = {mentions mygrid},
	Author = {Kenneth H Buetow},
	Journal = {Science},
	Pages = {821--824},
	Title = {Cyberinfrastructure: Empowering a Third Way in Biomedical Research},
	Volume = {308},
	Year = {2005}}

@article{heyscience,
	Annote = {mentions mygrid},
	Author = {Tony Hey and Anne E Trefethen},
	Journal = {Science},
	Pages = {817--821},
	Title = {Cyberinfrastructure for e-Science},
	Volume = {308},
	Year = {2005}}

@article{fosterscience,
	Annote = {mentions mygrid},
	Author = {Ian Foster},
	Journal = {Science},
	Pages = {814--817},
	Title = {Service-Oriented Science},
	Volume = {308},
	Year = {2005}}

@article{AitkenFMA,
	Annote = {talks about part-whole relations in the Anatomy Context Ontology which has been extended with a developmental mouse anatomy (Kaufmann, Bard and Davidson, MRC HGU) and a human anatomy (Bard) to illustrate its use},
	Author = {Stuart Aitken},
	Journal = {Bioinformatics},
	Number = {11},
	Pages = {2773--2779},
	Title = {Formalizing concepts of species, sex and developmental stage in anatomical ontologies},
	Volume = {21},
	Year = {2005}}

@article{bardontologies,
	Annote = {Biological knowledge is inherently complex and so cannot readily be integrated into existing databases of molecular (for example, sequence) data. An ontology is a formal way of representing knowledge in which concepts are described both by their meaning and their relationship to each other. Unique identifiers that are associated with each concept in biological ontologies (bio-ontologies) can be used for linking to and querying molecular databases. This article reviews the principal bio-ontologies and the current issues in their design and development: these include the ability to query across databases and the problems of constructing ontologies that describe complex knowledge, such as phenotypes.},
	Author = {Jonathan B. L. Bard and Seung Y. Rhee},
	Journal = {Nature Reviews Genetics},
	Pages = {213--222},
	Title = {ONTOLOGIES IN BIOLOGY: DESIGN, APPLICATIONS AND FUTURE CHALLENGES},
	Volume = {5},
	Year = {2004}}

@article{sequenceontology,
	Annote = {The sequence ontology is a mereonomy, part-whole relations},
	Author = {Karen Eilbeck and Suzanna E Lewis and Christopher J Mungall and Mark Yandell and Lincoln Stein and Richard Durbin and Michael Ashburner},
	Journal = {Genome Biology},
	Number = {5},
	Pages = {R44},
	Title = {The Sequence Ontology: a tool for the unification of genome annotations},
	Volume = {6},
	Year = {2005}}

@article{barryrelations,
	Annote = {outlines the relations that exist in biomedical ontolgies isa, partof etc and proposes how they should be standardised and formalised},
	Author = {Barry Smith and Werner Ceusters and Bert Klagges and Jacob Kohler and Anand Kumar and Jane Lomax and Chris Mungall and Fabian Neuhaus and Alan Rector and Cornelius Rosse},
	Journal = {Genome Biology},
	Pages = {R46},
	Title = {Relations in biomedical ontologies},
	Volume = {6},
	Year = {2005}}

@article{planet,
	Annote = {srong statement in abstract: Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem.},
	Author = {Mark Wilkinson and Heiko Schoof and Rebecca Ernst and Dirk Haase},
	Journal = {Plant Physiology},
	Month = MAY,
	Number = {1},
	Pages = {5--17},
	Title = {{BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case}},
	Volume = {138},
	Year = {2005}}

@misc{bundychecklist,
	Author = {Alan Bundy},
	Howpublished = {\url{http://homepages.inf.ed.ac.uk/bundy/how-tos/note1144.pdf}},
	Title = {{A Scientific Checklist}},
	Year = 1997}

@misc{bundybible,
	Author = {Alan Bundy and Ben du Boulay and Jim Howe and Gordon Plotkin},
	Howpublished = {\url{http://homepages.inf.ed.ac.uk/bundy/how-tos/resbible.html}},
	Title = {{The Researcher's Bible}},
	Year = 1985}

@misc{bundyquestions,
	Author = {Alan Bundy},
	Howpublished = {\url{http://homepages.inf.ed.ac.uk/bundy/how-tos/questions.pdf}},
	Title = {{Questions to Ask of Artificial Intelligence Research}},
	Year = 1995}

@inproceedings{bechhofer99:classification,
	Address = {Rotorua, New Zealand},
	Author = {Sean Bechhofer and Carole Goble},
	Booktitle = {IFIP WG2.6 Conference on Data Semantics, DS8},
	Month = {January},
	Title = {{Classification Based Navigation and Retrieval for Picture Archives}},
	Year = 1999}

@article{pubcrawler1,
	Annote = {More recent pubcrawler article},
	Author = {Karsten Hokamp and Kenneth H Wolfe},
	Journal = {Nucleic Acids Research},
	Note = {Web Server Issue},
	Pages = {W16--W19},
	Title = {{PubCrawler: keeping up comfortably with PubMed and GenBank}},
	Volume = {32},
	Year = {2004}}

@article{pubcrawler2,
	Annote = {original pubcrawler article},
	Author = {Karsten Hokamp and Kenneth H Wolfe},
	Journal = {Trends in Genetics},
	Number = {11},
	Pages = {471--472.},
	Title = {{What's new in the library? What's new in GenBank? let PubCrawler tell you}},
	Volume = {15},
	Year = {1999}}

@book{ceramixml,
	Author = {Ethan Cerami},
	Note = {isbn:0387230289},
	Publisher = {Springer},
	Title = {{XML for Bioinformatics}},
	Year = 2005}

@book{ec,
	Annote = {gene ontology comments on EC: Similar considerations suggested that a static hierarchical system, such as the Enzyme Commission (EC) hierarchy, although computationally tractable, was also likely to be inadequate to describe the role of a gene or a protein in biology in a manner that would be either intuitive or helpful for biologists. The hierarchical EC numbering system for enzymes is the standard resource for classifying enzymatic chemical reactions. The EC system does not address the classification of non-enzymatic proteins or the ability to describe the role of a gene product within a cell; also, the system has little facility for describing diverse protein interactions. The vagueness of the term 'function' when applied to genes or proteins emerged as a particular problem, as this term is colloquially used to describe biochemical activities, biological goals and cellular structure. It is commonplace today to refer to the function of a protein such as tubulin as 'GTPase' or 'constituent of the mitotic spindle'. For all these reasons, we are constructing three independent ontologies.},
	Author = {Edwin C. Webb},
	Note = {isbn:0122271645},
	Publisher = {Academic Press},
	Title = {{Enzyme Nomenclature. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enyzmes.}},
	Year = 1992}

@book{Wragg,
	Author = {Ted Wragg},
	Note = {isbn:?},
	Publisher = {publisher},
	Title = {{Education, Education, Education: subtitle?}},
	Year = 2004}

@book{GrandChallenges,
	Author = {Tony Hoare and Robin Miller},
	Howpublished = {\url{http://www.ukcrc.org.uk/gcresearch.pdf}},
	Note = {isbn:190250562X},
	Publisher = {British Computer Society},
	Title = {{Grand Challenges in Computing Research}},
	Year = 2004}

@inbook{ivis,
	Author = {Ronan Sleep},
	Chapter = {GC1: In Vivo-In Silico (iVis): The virtual worm, weed, bug},
	Howpublished = {\url{http://www.ukcrc.org.uk/gcresearch.pdf}},
	Note = {isbn:190250562X},
	Publisher = {British Computer Society},
	Title = {{Grand Challenges in Computing Research}},
	Year = {2004}}

@inbook{lengauer,
	Author = {Robert Stevens and Phillip Lord and Duncan Hull},
	Chapter = {45: Using Distributed Data and Tools in bioinformatics Applications},
	Editor = {Thomas Lengauer},
	Note = {in press},
	Publisher = {Wiley-VCH},
	Title = {{Bioinformatics - From Genomes to Therapies}},
	Year = {2006}}

@article{Brewster:IS04,
	Author = {Christopher Brewster and Kieron O'Hara},
	Journal = {IEEE Intelligent Systems},
	Month = {January/February},
	Note = {Trends and controversies},
	Number = {1},
	Pages = {72-73},
	Title = {Knowledge Representation with Ontologies: The Present and Future},
	Volume = {19},
	Year = {2004}}

@inproceedings{Brewster:Dagstuhl05,
	Address = {Dagstuhl},
	Author = {Christopher Brewster and Jose Iria and Fabio Ciravegna and Yorick Wilks},
	Booktitle = {Proceedings of the Dagstuhl Seminar Machine Learning for the Semantic Web},
	Month = {February},
	Title = {The Ontology: Chimaera or Pegasus},
	Url = {http://www.dagstuhl.de/05071/},
	Year = {2005}}

@misc{eee,
	Author = {Tony Blair},
	Note = {BBC News article, updated 2004-07-20},
	Title = {In quotes: Blair's leadership},
	Url = {http://news.bbc.co.uk/1/hi/uk_politics/3750847.stm},
	Year = {1996}}

@article{collins03,
	Author = {Francis S. Collins and Eric D. Green and Alan E. Guttmacher and Mark S. Guyer},
	Journal = {Nature},
	Note = {on behalf of the US National Human Genome Research Institute},
	Number = {6934},
	Pages = {835--847},
	Pmid = {12695777},
	Title = {{{A vision for the future of genomics research: A blueprint for the genomic era}}},
	Volume = {422},
	Year = {2003}}

@article{deepweb,
	Author = {Michael K Bergman},
	Howpublished = {http://www.press.umich.edu/jep/07-01/bergman.html},
	Journal = {Journal of Electronic Publishing},
	Note = {issn:0146-5422},
	Number = {1},
	Title = {{{The Deep Web: Surfacing Hidden Value}}},
	Volume = {7},
	Year = {2000}}

@inproceedings{icapturer,
	Author = {Benjamin M. Good and E. Tranfield and P.C. Tan and M. Shehata and G.K. Singhera and J Gosselink and E.B. Okon and Mark D. Wilkinson},
	Booktitle = {Pacific Symposium on Biocomputing (PSB2006)},
	Note = {Accepted for publication},
	Title = {{Fast, cheap and out of control: A Zero Curation Model for Ontology Development}},
	Year = {2006}}

@article{gasteiger01,
	Annote = {according to the Uniprot swissprot release notes, more details on Swiss-Prot cross-references, implicit and explicit can be found in this article.},
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	Journal = {Current Issues in Molecular Biology},
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	Pmid = {11488411},
	Title = {{SWISS-PROT: connecting biomolecular knowledge via a protein database}},
	Volume = {3},
	Year = {2001}}

@article{geneontology,
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	Pmid = {10802651},
	Title = {{Gene ontology: tool for the unification of biology. The Gene Ontology Consortium}},
	Volume = {25},
	Year = {2000}}

@article{watts98,
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	Journal = {Nature},
	Number = {6684},
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	Pmid = {9623998},
	Title = {{Collective dynamics of 'small-world' networks}},
	Volume = {393},
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@inproceedings{handschuhdeep,
	Address = {Budapest, Hungary},
	Author = {Siegfried Handschuh and Steffen Staab and Raphael Volz},
	Booktitle = {Tweltfth International World Wide Web Conference (WWW2003)},
	Title = {On deep annotation},
	Year = 2003}

@inproceedings{RDBMS4B,
	Author = {Aaron J. Mackey and William R. Pearson},
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	Year = {2002}}
	
@inproceedings{racer,
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  booktitle = {Description Logics},
  year      = {2001},
  crossref  = {DBLP:conf/dlog/2001},
}

@proceedings{DBLP:conf/dlog/2001,
  editor    = {Carole A. Goble and Deborah L. McGuinness and Ralf M{\"o}ller and Peter F. Patel-Schneider},
  title     = {Working Notes of the 2001 International Description Logics Workshop (DL-2001), Stanford, CA, USA, August 1-3, 2001},
  booktitle = {Description Logics},
  publisher = {CEUR-WS.org},
  series    = {CEUR Workshop Proceedings},
  volume    = {49},
  year      = {2001},
}

@article{whatisaisandisnt,
	Author = {Ronald J. Brachman},
	Journal = {IEEE Computer},
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	Volume = {16},
	Year = {1983}}

@article{soldatova05,
	Annote = {a personal attack on the mged ontology by the russian postdoc Larisa Soldotova},
	Author = {Larisa N Soldatova and Ross D King},
	Journal = {Nature Biotechnology},
	Number = {9},
	Pages = {1095--1098},
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@book{designpatterns,
	Author = {Erich Gamma and Richard Helm and Ralph Johnson and John Vissides},
	Note = {isbn:0201633612},
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	Title = {{Design Patterns: Elements of Reusable Object-Oriented Software}},
	Year = 2003}

@article{chimp,
	Author = {CSAC},
	Journal = {Nature},
	Note = {CSAC: The Chimpanzee Sequencing and Analysis Consortium},
	Number = {7055},
	Pages = {69-87},
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	Title = {{Initial sequence of the chimpanzee genome and comparison with the human genome}},
	Volume = {437},
	Year = {2005}}

	
@inproceedings{MPM+04,
  author    = {David L. Martin and Massimo Paolucci and Sheila A. McIlraith and Mark H. Burstein and Drew V. McDermott and Deborah L. McGuinness and Bijan Parsia and Terry R. Payne and Marta Sabou and Monika Solanki and Naveen Srinivasan and Katia P. Sycara},
  title     = {{Bringing Semantics to Web Services: The OWL-S Approach}},
  booktitle = {Semantic Web Services and Web Process Composition, First International Workshop, SWSWPC 2004, San Diego, CA, USA, July 6, 2004},
  year      = {2004},
  pages     = {26-42},
  ee        = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}issn=0302-9743{\&}volume=3387{\&}spage=26},
  crossref  = {DBLP:conf/semweb/2004swswpc},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@misc{wsmocomments,
	Author = {Carine Bournez},
	Howpublished = {\url{http://www.w3.org/Submission/2005/06/Comment}},
	Title = {{Team Comment on Web Service Modeling Ontology (WSMO) Submission}},
	Year = {2005}}
	
@misc{owlscomments,
	Author = {Carine Bournez and Sandro Hawke},
	Howpublished = {\url{http://www.w3.org/Submission/2004/07/Comment}},
	Title = {{Team Comment on the OWL-S Submission}},
	Year = {2004}}
	
@misc{owlsrelationship,
	Author = {Anupriya Ankolekar and David Martin and Deborah McGuinness and Sheila McIlraith and Massimo Paolucci and Bijan Parsia},
	Howpublished = {\url{http://www.w3.org/Submission/OWL-S-related}},
	Title = {{OWL-S' Relationship to Selected Other Technologies}},
	note={W3C Member Submission 22 November 2004},
	Year = {2005}}	


@proceedings{DBLP:conf/semweb/2004swswpc,
  editor    = {Jorge Cardoso and Amit P. Sheth},
  title     = {Semantic Web Services and Web Process Composition, First
               International Workshop, SWSWPC 2004, San Diego, CA, USA,
               July 6, 2004},
  booktitle = {SWSWPC},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3387},
  year      = {2004},
  isbn      = {3-540-24328-3},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}	
	
@inproceedings{PPS01,
	Author = {Terry R. Payne and Massimo Paolucci and Katia Sycara},
	Booktitle = {Semantic Web Working Symposium (SWWS 2001)},
	Title = {{Advertising and Matching DAML-S Service Descriptions}},
	Year = {2001}}

@book{javalanguagespec,
	Author = {James Gosling and Bill Joy and Guy Steele and Gilad Bracha},
	Note = {isbn:0321246780},
	Publisher = {Addison-Wesley},
	Title = {{The Java Language Specification: Third Edition}},
	Year = 2005}

@article{databasesinperil,
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	Journal = {Nature},
	Number = {7045},
	Pages = {1010--1011},
	Pmid = {15973369},
	Title = {{Databases in peril}},
	Volume = {435},
	Year = {2005}}

@article{owlimitations,
	Author = {Robert Stevens and Mikel Egana Aranguren and Katy Wolstencroft and Ulrike Sattler and Nick Drummond and Matthew Horridge and Alan Rector},
	Journal = {International Journal of Human Computer Studies},
	Note = {Submitted for publication, Special Issue: Knowledge representation with ontologies: present challenges - future possibilities},
	Number = {???},
	Pages = {???--???},
	Title = {{Managing OWL's Limitations in Modelling Biomedical Knowledge}},
	Volume = {???},
	Year = {2006}}

@inproceedings{goderisbottle,
	Address = {Galway, Ireland},
	Author = {Antoon Goderis and Ulrike Sattler and Phillip Lord and Carole Goble},
	Booktitle = {Proc.\ of the Fourth International Semantic Web Conference (ISWC2005)},
	Note = {November 6 - 10, 2003.},
	Pages = {???--??},
	Title = {Seven bottlenecks to workflow reuse and repurposing},
	Year = {2005}}

@inproceedings{katylongway,
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	Author = {Katy Wolstencroft and Andy Brass and Ian Horrocks and Phillip Lord and Ulrike Sattler and Daniele Turi and Robert Stevens},
	Booktitle = {Proc.\ of the Fourth International Semantic Web Conference (ISWC2005)},
	Note = {November 6 - 10, 2003.},
  pages     = {786-800},
	Title = {{A Little Semantic Web Goes a Long Way in Biology}},
	Year = {2005},
	url        = {http://dx.doi.org/10.1007/11574620_56},
	}	
	
	
	

@inproceedings{semanticsearch,
	Address = {Budapest, Hungary},
	Author = {Ramanathan Guha and Rob McCool and Eric Miller},
	Booktitle = {Proc.\ of the Twelfth International Conference on World Wide Web (WWW2003)},
	Note = {May 20 - 24, 2004.},
	Pages = {700--709},
	Title = {Semantic search},
	Year = {2003}}

@inproceedings{archwww,
	Author = {Ian Jacobs and Norman Walsh},
	Booktitle = {???},
	Pages = {???},
	Title = {Architecture of the World Wide Web, Volume One},
	Year = {2005}}

@article{DAMLSSubsume,
	Author = {Terry R. Payne and Massimo Paolucci and Katia Sycara},
	Journal = {Semantic Web Working Symposium (SWWS)},
	Title = {{Advertising and Matching DAML-S Service Descriptions}},
	Year = {2001}}

@inproceedings{RomansTR,
	Author = {Diego Calvanese and G. {De Giacomo} and D. Lembo and M. Lenzerini and R. Rosati},
	Booktitle = {Proc. of DL'05)},
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	Volume = {147},
	Year = {2005}}

@inproceedings{CalvaPODS98,
	Author = {D. Calvanese and G. {De Giacomo} and M. Lenzerini},
	Booktitle = {Proc. of PODS'98},
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	Title = {On the decidability of query containment under constraints},
	Year = {1998}}

@inproceedings{hstt2000,
	Author = {Ian Horrocks and Ulrike Sattler and Sergio Tessaris and S Tobies},
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	Publisher = {Springer-Verlag},
	Series = {Lecture Notes in Artificial Intelligence},
	Title = {How to decide query containment under constraints using a description logic},
	Year = {2000}}

@phdthesis{tessarisPhD,
	Author = {Sergio Tessaris},
	School = {University of Manchester},
	Title = {Questions and answers: reasoning and querying in Description Logic},
	Year = {2001}}

@techreport{AndrEvgTR,
	Author = {Andrey Bovykin and Evgeny Zolin},
	Institution = {University of Manchester},
	Note = {Available at \url{http://dynamo.man.ac.uk/publications/services_as_queries_TR.pdf}},
	Title = {Describing information providing services},
	Year = {2005}}

@techreport{HullTR,
	Author = {Duncan Hull},
	Institution = {University of Manchester},
	Note = {Available at \url{http://cs.man.ac.uk/~hulld/sws-usecases.pdf}},
	Title = {Semantic Web Services: Use cases from Biomedicine},
	Year = {2005}}

@techreport{TR-FUB-2005-07,
	Author = {Ortiz de la Fuente, Maria Magdalena and Diego Calvanese and Thomas Eiter and Enrico Franconi},
	Institution = {Faculty of Computer Science, Free University of Bozen-Bolzano},
	Title = {{Data Complexity of Answering Conjunctive Queries over {SHIQ} Knowledge Bases}},
	Year = {2005}}

@inproceedings{BLMSW-AAAI05,
	Author = {F. Baader and C. Lutz and M. Milicic and U. Sattler and F. Wolter},
	Booktitle = {Proc. of AAAI-05},
	Editor = {{AAAI} Press/The {MIT} Press},
	Title = {Integrating Description Logics and Action Formalisms: First Results},
	Url = {http://www.cs.man.ac.uk/~sattler/publications/aaai05.pdf},
	Year = 2005}

@book{biomedicalinformatics,
	Author = {Edward H. Shortliffe and James J. Cimino},
	Note = {Third edition, ISBN:0387289860},
	Publisher = {Springer Verlag},
	Title = {{Biomedical Informatics: Computer Applications in Health Care And Biomedicine}},
	Year = 2006}

@article{luciano05,
	Author = {Joanne S Luciano},
	Journal = {Drug Discovery Today},
	Number = {13},
	Pages = {937--942},
	Title = {{PAX of mind for pathway researchers}},
	Volume = {10},
	Year = {2005}}

@article{pillai,
	Author = {Sharma Pillai and V Silventoinen and K Kallio and M Senger and S Sobhany and J Tate and S Valenkar and A Golovin and K Henrick and P Rice and P Stoehr and R Lopez},
	Journal = {Nucleic Acids Research},
	Note = {Web Server Issue},
	Pages = {W25--W28},
	Title = {{SOAP-based services provided by the European Bioinformatics Institute}},
	Volume = {33},
	Year = {2005}}

@article{narweb2005,
	Author = {Fox, JA and Butland, SL and McMillan, S and Campbell, G and Ouellette, BF},
	Doi = {10.1093/nar/gki594},
	annote ={166 servers},
	Journal = {Nucleic Acids Research},
	Month = {Jul},
	Number = {Web Server issue},
	Pages = {3--24},
	Pmid = {15980476},
	Title = {{The Bioinformatics Links Directory: a compilation of molecular biology web servers}},
	Volume = {33},
	Year = {2005}}

@article{narweb2004,
	Author = {Anon},
	doi = {10.1093/nar/gkh487},
	Journal = {Nucleic Acids Research},
	Number = {Web Server issue},
	Pages = {W1},
	Title = {{Editorial}},
	Volume = {32},
	Year = {2004}}

@article{wsmo,
	Author = {Dumitru Roman and Uwe Keller and Holger Lausen and Jos de Bruijn and Rub{\'e}n Lara and Michael Stollberg and Axel Polleres and Cristina Feier and Cristoph Bussler and Dieter Fensel},
	Journal = {Applied Ontology},
	Number = {1},
	Pages = {77--106},
	Title = {{Web Service Modeling Ontology}},
	Volume = {1},
	Year = {2005},}

@article{guarino,
	Author = {Nicola Guarino and Mark A. Musen},
	Journal = {Applied Ontology},
	Number = {1},
	Pages = {1--5},
	Title = {{Applied Ontology: Focusing on content}},
	Volume = {1},
	Year = {2005},
	url={http://iospress.metapress.com/openurl.asp?genre=article&issn=1570-5838&volume=1&issue=1&spage=1}}

	
@article{lenat,
	Author = {Douglas B. Lenat},
	Journal = {Applied Ontology},
	Number = {1},
	Pages = {9--12},
	Title = {{Applied Ontology Issues}},
	Volume = {1},
	Year = {2005}}

@article{uschold,
	Author = {Mike Uschold},
	Journal = {Applied Ontology},
	Number = {1},
	Pages = {9--12},
	Title = {{An ontology research pipeline}},
	Volume = {1},
	Year = {2005},
	url={http://iospress.metapress.com/openurl.asp?genre=article&issn=1570-5838&volume=1&issue=1&spage=13}}
	
@article{weltyandersen,
	Author = {Christopher Welty and William Andersen},
	Journal = {Applied Ontology},
	Number = {1},
	Pages = {107--116},
	Title = {{Towards OntoClean 2.0: A framework for rigidity}},
	Volume = {1},
	Year = {2005},
	url={http://iospress.metapress.com/openurl.asp?genre=article&issn=1570-5838&volume=1&issue=1&spage=107}}
	
@misc{wsdls,
	Author = {Rama Akkiraju and Joel Farrell and John Miller and Meenakshi Nagarajan and Marc-Thomas Schmidt and Amit Sheth and Kunal Verma},
	Howpublished = {\url{http://www.w3.org/Submission/WSDL-S/}},
	Note = {W3C Member Submission 7 November 2005},
	Title = {{Web Service Semantics - WSDL-S}},
	Year = {2005}}


@article{Birney06,
	Author = {Birney, E and Andrews, D and Caccamo, M and Chen, Y and Clarke, L and Coates, G and Cox, T and Cunningham, F and Curwen, V and Cutts, T and Down, T and Durbin, R and Fernandez-Suarez, XM and Flicek, P and Gr{\"a}f, S and Hammond, M and Herrero, J and Howe, K and Iyer, V and Jekosch, K and K{\"a}h{\"a}ri, A and Kasprzyk, A and Keefe, D and Kokocinski, F and Kulesha, E and London, D and Longden, I and Melsopp, C and Meidl, P and Overduin, B and Parker, A and Proctor, G and Prlic, A and Rae, M and Rios, D and Redmond, S and Schuster, M and Sealy, I and Searle, S and Severin, J and Slater, G and Smedley, D and Smith, J and Stabenau, A and Stalker, J and Trevanion, S and Ureta-Vidal, A and Vogel, J and White, S and Woodwark, C and Hubbard, TJ},
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	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {556-561},
	Pmid = {16381931},
	Title = {Ensembl 2006},
	Volume = {34},
	Year = {2006}}

@article{Wheeler06,
	Author = {Wheeler, DL and Barrett, T and Benson, DA and Bryant, SH and Canese, K and Chetvernin, V and Church, DM and Dicuccio, M and Edgar, R and Federhen, S and Geer, LY and Helmberg, W and Kapustin, Y and Kenton, DL and Khovayko, O and Lipman, DJ and Madden, TL and Maglott, DR and Ostell, J and Pruitt, KD and Schuler, GD and Schriml, LM and Sequeira, E and Sherry, ST and Sirotkin, K and Souvorov, A and Starchenko, G and Suzek, TO and Tatusov, R and Tatusova, TA and Wagner, L and Yaschenko, E},
	Doi = {10.1093/nar/gkj158},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {173-180},
	Pmid = {16381840},
	Title = {Database resources of the National Center for Biotechnology Information},
	Volume = {34},
	Year = {2006}}
	
@Article{Wheeler07,
author = "Wheeler, D L and Barrett, T and Benson, D A and Bryant, S H and Canese, K and Chetvernin, V and Church, D M and DiCuccio, M and Edgar, R and Federhen, S and Geer, L Y and Kapustin, Y and Khovayko, O and Landsman, D and Lipman, D J and Madden, T L and Maglott, D R and Ostell, J and Miller, V and Pruitt, K D and Schuler, G D and Sequeira, E and Sherry, S T and Sirotkin, K and Souvorov, A and Starchenko, G and Tatusov, R L and Tatusova, T A and Wagner, L and Yaschenko, E",
title = {Database resources of the National Center for Biotechnology Information},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "Database issue",
pages = "5-12",
}

@article{GenBank06,
	Author = {Benson, DA and Karsch-Mizrachi, I and Lipman, DJ and Ostell, J and Wheeler, DL},
	Doi = {10.1093/nar/gkj157},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {16-20},
	Pmid = {16381837},
	Title = {GenBank},
	Volume = {34},
	Year = {2006}}

@article{Kanehisa:2006:Nucleic-Acids-Res:16381885,
	Author = {Kanehisa, M and Goto, S and Hattori, M and Aoki-Kinoshita, K F and Itoh, M and Kawashima, S and Katayama, T and Araki, M and Hirakawa, M},
	Doi = {10.1093/nar/gkj102},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {354-357},
	Pmid = {16381885},
	Title = {From genomics to chemical genomics: new developments in KEGG},
	Volume = {34},
	Year = {2006}}

@article{Hu:2004:Nucleic-Acids-Res:15215387,
	Author = {Hu, Z and Fu, Y and Halees, A S and Kielbasa, S M and Weng, Z},
	Doi = {10.1093/nar/gkh483},
	Journal = {Nucleic Acids Res},
	Month = {Jul},
	Number = {Web Server issue},
	Pages = {235-241},
	Pmid = {15215387},
	Title = {SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation},
	Url = {http://www.hubmed.org/display.cgi?uids=15215387},
	Volume = {32},
	Year = {2004}}

@article{Okubo:2006:Nucleic-Acids-Res:16381940,
	Author = {Okubo, K and Sugawara, H and Gojobori, T and Tateno, Y},
	Doi = {10.1093/nar/gkj111},
	Journal = {Nucleic Acids Res},
	Month = {Jan},
	Number = {Database issue},
	Pages = {6-9},
	Pmid = {16381940},
	Title = {DDBJ in preparation for overview of research activities behind data submissions},
	Url = {http://www.hubmed.org/display.cgi?uids=16381940},
	Volume = {34},
	Year = {2006}}

@article{Kinoshita:2004:Bioinformatics:14871866,
	Author = {Kinoshita, K and Nakamura, H},
	Doi = {10.1093/bioinformatics/bth073},
	Journal = {Bioinformatics},
	Month = {May},
	Number = {8},
	Pages = {1329-1330},
	Pmid = {14871866},
	Title = {eF-site and PDBjViewer: database and viewer for protein functional sites},
	Url = {http://www.hubmed.org/display.cgi?uids=14871866},
	Volume = {20},
	Year = {2004}}

@article{Nakamura:2002:Tanpakushitsu-Kakusan-Koso:12099029,
	Author = {Nakamura, H and Ito, N and Kusunoki, M},
	Journal = {Tanpakushitsu Kakusan Koso},
	Month = {Jun},
	Number = {8 Suppl},
	Pages = {1097-1101},
	Pmid = {12099029},
	Title = {[Development of PDBj: Advanced database for protein structures]},
	Url = {http://www.hubmed.org/display.cgi?uids=12099029},
	Volume = {47},
	Year = {2002}}

@article{Eckart:2003:OMICS:12831562,
	Author = {Eckart, J D and Sobral, B W},
	Doi = {10.1089/153623103322006661},
	Journal = {OMICS},
	Number = {1},
	Pages = {79-88},
	Pmid = {12831562},
	Title = {A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework},
	Url = {http://www.hubmed.org/display.cgi?uids=12831562},
	Volume = {7},
	Year = {2003}}

@article{Bader:2003:Nucleic-Acids-Res:12519993,
	Author = {Bader, G D and Betel, D and Hogue, C W},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {1},
	Pages = {248-250},
	Pmid = {12519993},
	Title = {BIND: the Biomolecular Interaction Network Database},
	Url = {http://www.hubmed.org/display.cgi?uids=12519993},
	Volume = {31},
	Year = {2003}}

@article{biomart,
	Author = {S Durinck and Y Moreau and Arek Kasprzyk and S Davis and B De Moor and Alvis Brazma and Wolfgang Huber},
	Journal = {Bioinformatics},
	Number = {16},
	Pages = {3439--40},
	Pmid = {16082012},
	Title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.},
	Volume = {21},
	Year = {2005}}

@article{pfam,
	Author = {Finn RD and Mistry J and Schuster-Bockler B and Griffiths-Jones S and Hollich V and Lassmann T and Moxon S and Marshall M and Khanna A and Durbin R and Eddy SR and Sonnhammer EL and Bateman A.},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {1},
	Pages = {D247--51},
	Pmid = {16381856},
	Title = {Pfam: clans, web tools and services},
	Url = {http://www.hubmed.org/display.cgi?uids=12519993},
	Volume = {34},
	Year = {2006}}

@article{godatabase,
	Author = {Harris, M A and Clark, J and Ireland, A and Lomax, J and Ashburner, M and Foulger, R and Eilbeck, K and Lewis, S and Marshall, B and Mungall, C and Richter, J and Rubin, G M and Blake, J A and Bult, C and Dolan, M and Drabkin, H and Eppig, J T and Hill, D P and Ni, L and Ringwald, M and Balakrishnan, R and Cherry, J M and Christie, K R and Costanzo, M C and Dwight, S S and Engel, S and Fisk, D G and Hirschman, J E and Hong, E L and Nash, R S and Sethuraman, A and Theesfeld, C L and Botstein, D and Dolinski, K and Feierbach, B and Berardini, T and Mundodi, S and Rhee, S Y and Apweiler, R and Barrell, D and Camon, E and Dimmer, E and Lee, V and Chisholm, R and Gaudet, P and Kibbe, W and Kishore, R and Schwarz, E M and Sternberg, P and Gwinn, M and Hannick, L and Wortman, J and Berriman, M and Wood, V and de la Cruz, N and Tonellato, P and Jaiswal, P and Seigfried, T and White, R and ,},
	Doi = {10.1093/nar/gkh036},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {258-261},
	Pmid = {14681407},
	Title = {The Gene Ontology (GO) database and informatics resource},
	Volume = {32},
	Year = {2004}}

@article{go2006,
	Author = {Gene Ontology Consortium},
	Doi = {10.1093/nar/gkj021},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {322-326},
	Pmid = {16381878},
	Title = {The Gene Ontology (GO) project in 2006},
	Volume = {34},
	Year = {2006}}

@article{inparanoid,
	Author = {O'Brien, K P and Remm, M and Sonnhammer, E L},
	Doi = {10.1093/nar/gki107},
	Journal = {Nucleic Acids Research},
	Month = {Jan},
	Number = {Database issue},
	Pages = {476-480},
	Pmid = {15608241},
	Title = {Inparanoid: a comprehensive database of eukaryotic orthologs},
	Volume = {33},
	Year = {2005}}

@article{bioperl,
	Author = {Stajich, J E and Block, D and Boulez, K and Brenner, S E and Chervitz, S A and Dagdigian, C and Fuellen, G and Gilbert, J G and Korf, I and Lapp, H and Lehv{\"a}slaiho, H and Matsalla, C and Mungall, C J and Osborne, B I and Pocock, M R and Schattner, P and Senger, M and Stein, L D and Stupka, E and Wilkinson, M D and Birney, E},
	Doi = {10.1101/gr.361602},
	Journal = {Genome Res},
	Month = {Oct},
	Number = {10},
	Pages = {1611-1618},
	Pmid = {12368254},
	Title = {The Bioperl toolkit: Perl modules for the life sciences},
	Volume = {12},
	Year = {2002}}

@techreport{shims,
	Author = {Duncan Hull},
	Institution = {University of Manchester},
	Note = {Available from \url{http://www.cs.man.ac.uk/~hulld/shims.html}},
	Title = {Description and classification of some shims in myGrid},
	Year = {2006}}
	
@misc{hegaret,	
	Author = {Philippe Le H\'{e}garet},
	Year={2003},
	title={{Introduction to Web Services}},
	Howpublished={\url{http://www.w3.org/2003/Talks/0317-ws-intro/}}}
	
	
@TECHREPORT{services,
  Author = {Duncan Hull},
  Institution = {University of Manchester},
  Note = {Available from \url{http://taverna.sourceforge.net/index.php?doc=services.html}},
  Title = {{Biological Web Services}},
  Year = {2006}}
	
@inproceedings{khalid,
  author    = {Khalid Belhajjame and Suzanne M. Embury and Norman W. Paton},
  title     = {On Characterising and Identifying Mismatches in Scientific Workflows.},
  booktitle = {Proceedings of Data Integration in the Life Sciences (DILS'06),  European Bioinformatics Institute (EBI), Hinxton, UK 20-22 July 2006},
  year      = {2006},
  pages     = {240-247},
  url        = {http://dx.doi.org/10.1007/11799511_22},
  crossref  = {DBLP:conf/dils/2006},
}

@proceedings{DBLP:conf/dils/2006,
  editor    = {Ulf Leser and Felix Naumann and Barbara A. Eckman},
  title     = {Data Integration in the Life Sciences, Third International
               Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006, Proceedings},
  booktitle = {DILS},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {4075},
  year      = {2006},
  isbn      = {3-540-36593-1},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
	
@inproceedings{owlpizzas,
	Author = {Alan Rector and Nick Drummond and Matthew Horridge and Jeremy Rogers and Holger Knublauch and Robert Stevens and Hai Wang and Chris Wroe},
  title     = {OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors and Common Patterns.},
  booktitle = {Proc. of European Conference on Knowledge Acquistion (EKAW'04)},
  year      = {2004},
  pages     = {63-81},
  url        = {http://www.co-ode.org/resources/papers/ekaw2004.pdf},
  crossref  = {DBLP:conf/ekaw/2004},
}

@proceedings{DBLP:conf/ekaw/2004,
  editor    = {Enrico Motta and Nigel Shadbolt and Arthur Stutt and Nicholas Gibbins},
  title     = {Engineering Knowledge in the Age of the Semantic Web, 14th International Conference, EKAW 2004, Whittlebury Hall, UK, October 5-8, 2004, Proceedings},
  booktitle = {EKAW},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3257},
  year      = {2004},
  isbn      = {3-540-23340-7},
}	
	

@techreport{howlrridge,
	Author = {Matthew Horridge and Holger Knublauch and Alan Rector and Robert Stevens and Chris Wroe},
	Institution = {University of Manchester},
	Note = {available from \url{http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf}},
	Title = {{A Practical Guide To Building OWL Ontologies Using The Protege-OWL Plugin and CO-ODE Tools}},
	Year = {2004}}

@inproceedings{PaHo03b,
	Author = {Jeff Pan and Ian Horrocks},
	Booktitle = {Proc.\ of the 2003 International Semantic Web Conference (ISWC 2003)},
	Editor = {Dieter Fensel and Katia Sycara and John Mylopoulos},
	Isbn = {3-540-20362-1},
	Number = 2870,
	Pages = {30--46},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {{RDFS(FA)} and {RDF MT}: Two Semantics for {RDFS}},
	Year = 2003}
	
	
@inproceedings{rdfqlcf,
  author    = {Peter Haase and
               Jeen Broekstra and
               Andreas Eberhart and
               Raphael Volz},
  title     = {A Comparison of RDF Query Languages.},
  booktitle = {International Semantic Web Conference},
  year      = {2004},
  pages     = {502-517},
  crossref  = {DBLP:conf/semweb/2004},
}
	
	
	
	
	@Article{Hancock:2005:BMC-Bioinformatics:16269077,
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title = {maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination},
journal = "BMC Bioinformatics",
year = "2005",
volume = "6",
number = "",
pages = "264-264",
month = "",
pmid = "16269077",
doi = "10.1186/1471-2105-6-264"
}

@ARTICLE{R:Ihaka+Gentleman:1996,
  AUTHOR = {Ross Ihaka and Robert Gentleman},
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@inproceedings{panoply,
	Author = {Katy Wolstencroft and Tom Oinn and Carole Goble and Justin Ferris and Chris Wroe and Phillip Lord and Kevin Glover and Robert Stevens},
	Booktitle = {First International Conference on e-Science and Grid Computing (e-Science'05)},
	Title = {Panoply of Utilities in Taverna},
	pages = {156--162},
	Year = {2005}}
	
	
@Article{Miyazaki:2004:Nucleic-Acids-Res:14681352,
author = "Miyazaki, S and Sugawara, H and Ikeo, K and Gojobori, T and Tateno, Y",
title = {{DDBJ in the stream of various biological data}},
journal = "Nucleic Acids Research",
year = "2004",
volume = "32",
number = "Database issue",
pages = "31--34",
month = "Jan",
pmid = "14681352",
doi = "10.1093/nar/gkh127"
}

@Article{Clark:2004:Brief-Bioinform:15153306,
author = "Tim Clark and Sean Martin and Ted Liefeld",
title = {Globally distributed object identification for biological knowledgebases},
journal = "Brief Bioinform",
year = "2004",
volume = "5",
number = "1",
pages = "59--70",
month = "Mar",
pmid = "15153306",
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}


@Article{Butler:2006:Nature:16397468,
author = "Declan Butler",
title = {Mashups mix data into global service},
journal = "Nature",
year = "2006",
volume = "439",
number = "7072",
pages = "6--7",
month = "Jan",
pmid = "16397468",
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}

@Article{Radetzki:2006:Bioinformatics:16481335,
author = "Radetzki, U and Leser, U and Schulze-Rauschenbach, S C and Zimmermann, J and L{\"u}ssem, J and Bode, T and Cremers, A B",
title = {Adapters, shims, and glue - service interoperability for in silico experiments},
journal = "Bioinformatics",
year = "2006",
volume = "22",
number = "9",
pages = "1137--1143",
month = "Feb",
pmid = "16481335",
doi = "10.1093/bioinformatics/btl054"
}

@INPROCEEDINGS{WBHL+05,
  AUTHOR = {Katherine Wolstencroft and Andy Brass and Ian
                  Horrocks and Phil Lord and Ulrike Sattler and Robert
                  Stevens and Daniele Turi},
  TITLE = {A Little Semantic Web Goes a Long Way in Biology},
  BOOKTITLE = {Proc.\ of the 2005 International Semantic Web
                   Conference (ISWC 2005)},
  YEAR = 2005,
  SERIES = {Lecture Notes in Artificial Intelligence},
  PUBLISHER = {Springer},
  URL = {download/2005/WBHL05.pdf},
  NOTE = {To appear}
}


@inproceedings{LermanPK06,
  author    = {Kristina Lerman and Anon Plangprasopchok and Craig A. Knoblock},
  title     = {Automatically Labeling the Inputs and Outputs of Web Services.},
  booktitle = {AAAI'06},
  year      = {2006},
  crossref  = {DBLP:conf/aaai/2006},
  url = {http://www.isi.edu/~lerman/papers/AAAI0610LermanK.pdf}
}

@inproceedings{DBLP:conf/www/HalpinT06,
  author    = {Harry Halpin and Henry S. Thompson},
  title     = {{One Document to Bind Them: Combining XML, Web Services, and the Semantic Web}},
  booktitle = {Proceedings of the 15th international conference on World Wide Web, WWW 2006, Edinburgh, Scotland, UK, May 23-26, 2006},
  year      = {2006},
  pages     = {679-686},
  ee        = {http://doi.acm.org/10.1145/1135777.1135877},
  crossref  = {DBLP:conf/www/2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@Article{BernersLee:2006:Science:16902115,
author = "Tim Berners-Lee and Wendy Hall and James Hendler and Nigel Shadbolt and Daniel J. Weitzner",
title = {Computer science. Creating a science of the Web},
journal = "Science",
year = "2006",
volume = "313",
number = "5788",
pages = "769-771",
month = "Aug",
pmid = "16902115",
doi = "10.1126/science.1126902"
}
@Article{BernersLee:2001:Nature:11323639,
author = "Tim Berners-Lee and James Hendler",
title = {Publishing on the semantic web},
journal = "Nature",
year = "2001",
volume = "410",
number = "6832",
pages = "1023-1024",
month = "Apr",
pmid = "11323639",
doi = "10.1038/35074206"
}

@Article{HendlerWebOfScience,
author = "Jim Hendler",
title = {Communication. Science and the semantic web},
journal = "Science",
year = "2003",
volume = "299",
number = "5606",
pages = "520-521",
month = "Jan",
pmid = "12543958",
doi = "10.1126/science.1078874"
}


@inproceedings{querycontainment,
  author    = {Diego Calvanese and Giuseppe De Giacomo and Maurizio Lenzerini and Moshe Y. Vardi},
  title     = {View-based query containment.},
  booktitle = {PODS},
  year      = {2003},
  pages     = {56-67},
  crossref  = {DBLP:conf/pods/2003},
}

@proceedings{DBLP:conf/pods/2003,
  title     = {Proceedings of the Twenty-Second ACM SIGACT-SIGMOD-SIGART
               Symposium on Principles of Database Systems (PODS), June 9-12,
               2003, San Diego, CA, USA},
  publisher = {ACM},
  year      = {2003},
  isbn      = {1-58113-670-6},}
}

@article{owlqlfikes,
  author    = {Richard Fikes and Patrick J. Hayes and Ian Horrocks},
  title     = {OWL-QL - a language for deductive query answering on the Semantic Web.},
  journal   = {Journal of Web Semantics},
  volume    = {2},
  number    = {1},
  year      = {2004},
  pages     = {19-29},
  ee        = {http://dx.doi.org/10.1016/j.websem.2004.07.002},
}

@proceedings{DLhandbook,
  editor    = {Franz Baader and Diego Calvanese and Deborah L. McGuinness and Daniele Nardi and Peter F. Patel-Schneider},
  title     = {The Description Logic Handbook: Theory, Implementation and Applications},
  booktitle = {Description Logic Handbook},
  publisher = {Cambridge University Press},
  year      = {2003},
  isbn      = {0-521-78176-0},
}

@inproceedings{DBLP:conf/dlog/Sattler03,
  author    = {Ulrike Sattler and Diego Calvanese and Ralf Molitor},
  title     = {Description Logic: Relationships with other Formalisms.},
  booktitle = {Description Logic Handbook},
  year      = {2003},
  pages     = {137-177},
  crossref  = {DLhankbook},
}





@article{DBLP:journals/aim/DavisSS93,
  author    = {Randall Davis and Howard E. Shrobe and Peter Szolovits},
  title     = {What Is a Knowledge Representation?},
  journal   = {AI Magazine},
  volume    = {14},
  number    = {1},
  year      = {1993},
  pages     = {17-33},
  url = {http://groups.csail.mit.edu/medg/ftp/psz/k-rep.html}
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@inproceedings{DBLP:conf/www/Patel-SchneiderH06,
  author    = {Peter F. Patel-Schneider and Ian Horrocks},
  title     = {Position paper: a comparison of two modelling paradigms in the Semantic Web.},
  booktitle = {WWW2006 Proceedings},
  year      = {2006},
  pages     = {3-12},
  url        = {http://dx.doi.org/10.1145/1135777.1135784},
  crossref  = {DBLP:conf/www/2006},
}

@proceedings{DBLP:conf/www/2006,
  editor    = {Les Carr and David De Roure and Arun Iyengar and Carole A. Goble and Michael Dahlin},
  title     = {Proceedings of the 15th international conference on World Wide Web, WWW 2006, Edinburgh, Scotland, UK, May 23-26, 2006},
  booktitle = {WWW2006 Proceedings},
  publisher = {ACM},
  year      = {2006},
  isbn      = {1-59593-323-9},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@inproceedings{DBLP:conf/www/LiH03,
  author    = {Lei Li and Ian Horrocks},
  title     = {A software framework for matchmaking based on semantic web technology},
  booktitle = {WWW2003},
  year      = {2003},
  pages     = {331-339},
}

@inproceedings{DBLP:conf/www/HorrocksP03,
  author    = {Ian Horrocks and Peter F. Patel-Schneider},
  title     = {Three theses of representation in the semantic web.},
  booktitle = {WWW2003},
  year      = {2003},
  pages     = {39-47},
  url        = {http://dx.doi.org/10.1145/775152.775159},
}

@inbook{IRevaluation,
	Author = {C.J. van Rijsbergen},
	Title={Information Retrieval},
	Chapter = {Seven: Evaluation},
	Year = {1979},
	publisher={Butterworths},
	isbn      = {0-408-70929-4},
	note={isbn:0408709294},
	url={http://www.dcs.gla.ac.uk/Keith/Preface.html}	
}


@article{badaboy,
  author    = {Michael Bada and Robert Stevens and Carole A. Goble and Yolanda Gil and Michael Ashburner and Judith A. Blake and J. Michael Cherry and Midori A. Harris and Suzanna Lewis},
  title     = {A short study on the success of the Gene Ontology.},
  journal   = {Journal of Web Semantics},
  volume    = {1},
  number    = {2},
  year      = {2004},
  pages     = {235-240},
  url        = {http://dx.doi.org/10.1016/j.websem.2003.12.003},
}

@misc{owlsoverview,
  author    = {David Martin and Mark Burstein and Jerry Hobbs and Ora Lassila and Drew McDermott and Sheila McIlraith and Srini Narayanan and Massimo Paolucci and Bijan Parsia and Terry Payne and Evren Sirin and Naveen Srinivasan and Katia Sycara},
  title     = {OWL-S: Semantic Markup for Web Services},
  note = {W3C Member Submission 22 November 2004},
  howpublished = {\url{http://www.w3.org/Submission/OWL-S}},
  year      = {2004},
}

@inproceedings{currencyconverter,
  author    = {Enrico Motta and John Domingue and Liliana Cabral and Mauro Gaspari},
  title     = {{IRS-II: A Framework and Infrastructure for Semantic Web Services}},
  booktitle = {International Semantic Web Conference},
  year      = {2003},
  pages     = {306-318},
  crossref  = {DBLP:conf/semweb/2003},
}

@proceedings{DBLP:conf/semweb/2003,
  editor    = {Dieter Fensel and Katia P. Sycara and John Mylopoulos},
  title     = {Second International Semantic Web Conference (ISWC 2003), Sanibel Island, FL, USA, October 20-23, 2003, Proceedings},
  booktitle = {International Semantic Web Conference},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {2870},
  year      = {2003},
  isbn      = {3-540-20362-1},
}



@article{DBLP:journals/ws/BechhoferSL06,
  author    = {Sean Bechhofer and Robert D. Stevens and Phillip W. Lord},
  title     = {GOHSE: Ontology driven linking of biology resources.},
  journal   = {Journal of Web Semantics},
  volume    = {4},
  number    = {3},
  year      = {2006},
  pages     = {155-163},
  url        = {http://dx.doi.org/10.1016/j.websem.2005.09.003},
}

@misc{secretsws,
  author    = {David Martin},
  year      = {2006},
  title ={Commercial/Real-world Semantic Web Services?},
  note={W3C public mailing list archive for the Semantic Web Services Interest Group.}
  url        = {http://lists.w3.org/Archives/Public/public-sws-ig/2006Oct/0060.html},
}

@article{DBLP:journals/vldb/ThakkarAK05,
  author    = {Snehal Thakkar and Jose Luis Ambite and Craig A. Knoblock},
  title     = {Composing, optimizing, and executing plans for bioinformatics web services.},
  journal   = {Very Large DataBases Journal},
  volume    = {14},
  number    = {3},
  year      = {2005},
  pages     = {330-353},
  url        = {http://dx.doi.org/10.1007/s00778-005-0158-4},
}


@inproceedings{DBLP:conf/esws/PotterA05,
  author    = {Stephen Potter and
               J. Stuart Aitken},
  title     = {A Semantic Service Environment: A Case Study in Bioinformatics.},
  booktitle = {ESWC},
  year      = {2005},
  pages     = {694-709},
  url        = {http://dx.doi.org/10.1007/11431053_47},
  crossref  = {DBLP:conf/esws/2005},
}

@proceedings{DBLP:conf/esws/2005,
  editor    = {Asunci{\'o}n G{\'o}mez-P{\'e}rez and
               J{\'e}r{\^o}me Euzenat},
  title     = {The Semantic Web: Research and Applications, Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May 29 - June 1, 2005, Proceedings},
  booktitle = {ESWC},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3532},
  year      = {2005},
  isbn      = {3-540-26124-9},
}


@inproceedings{DBLP:conf/iccS/ByunMH06,
  author    = {Yanga Byun and
               Sanghoon Moon and
               Kyungsook Han},
  title     = {Web Service for Finding Ribosomal Frameshifts.},
  booktitle = {International Conference on Computational Science (1)},
  year      = {2006},
  pages     = {284-291},
  url        = {http://dx.doi.org/10.1007/11758501_41},
  crossref  = {DBLP:conf/iccS/2006-1},
}

@proceedings{DBLP:conf/iccS/2006-1,
  editor    = {Vassil N. Alexandrov and
               G. Dick van Albada and
               Peter M. A. Sloot and
               Jack Dongarra},
  title     = {Computational Science - ICCS 2006, 6th International Conference,
               Reading, UK, May 28-31, 2006, Proceedings, Part I},
  booktitle = {International Conference on Computational Science (1)},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3991},
  year      = {2006},
  isbn      = {3-540-34379-2},
}
@MISC{yorick,
	author={Yorick Wilks},
	title={What is the Semantic Web and what will it do for eScience?},
	note={Oxford Internet Institute Research Report No. 12},
	URL={http://www.oii.ox.ac.uk/research/publications/RR12.pdf}
}


@article{turingtest,
  author    = {Alan Turing},
  title     = {Computing Machinery and Intelligence: The Turing Test},
  journal   = {Mind},
  volume    = {59},
  number    = {236},
  year      = {1950},
  pages     = {433-460},
  url        = {http://cogprints.org/499/00/turing.html},
}

@inproceedings{identitycrisis,
	author={Jun Zhao and Carole Goble and Robert Stevens},
	booktitle={IPAW'06 International Provenance and Annotation Workshop, Chicago, Illinois, USA May 3-5, 2006},
	title={An Identity Crisis in The Life Sciences},
	publisher={Springer Verlag},
	year={2006},
	url={http://www.ipaw.info/ipaw06/proceedings/CameraReady_s9_1.pdf}
}

@inproceedings{DBLP:conf/ijcai/CarmanK07,
  author    = {Mark James Carman and Craig A. Knoblock},
  title     = {Learning Semantic Descriptions of Web Information Sources.},
  booktitle = {IJCAI},
  year      = {2007},
  pages     = {2695-2700},
  crossref  = {DBLP:conf/ijcai/2007},
}

@proceedings{DBLP:conf/ijcai/2007,
  editor    = {Manuela M. Veloso},
  title     = {IJCAI 2007, Proceedings of the 20th International Joint
               Conference on Artificial Intelligence, Hyderabad, India,
               January 6-12, 2007},
  booktitle = {IJCAI},
  year      = {2007},
}



@article{DBLP:journals/bioinformatics/RoccoC03,
  author    = {Daniel Rocco and Terence Critchlow},
  title     = {Automatic discovery and classification of bioinformatics Web sources.},
  journal   = {Bioinformatics},
  volume    = {19},
  number    = {15},
  year      = {2003},
  pages     = {1927-1933},
  bibsource = {DBLP, http://dblp.uni-trier.de}
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@Article{Fox2006,
author="Joanne A. Fox and Scott McMillan and B. F. Francis Ouellette",
title="A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory.",
journal="Nucleic acids research.",
year="2006",
volume="34",
issue="Web Server issue",
pages="3--5",
}


@Article{tavernabiomoby,
author = "Edward Kawas and Martin Senger and Mark D. Wilkinson",
title = {{BioMoby extensions to the Taverna workflow management and enactment software}},
journal = {{BMC Bioinformatics}},
year = "2006",
volume = "7",
pages = "523",
}


@book{bakercheung,
editor = "Christopher J.O. Baker and Kei-Hoi Cheung",
booktitle="Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences",
year="2006",
publisher="Springer",
isbn ={978038748465},
}

@inbook{sembowser,
	Author = {Satya S. Sahoo and Amith Sheth and Blake Hunter and William S. York},
	Chapter = {Sembowser: Semantic Biological Web Services Registry},
	crossref  = {bakercheung},
	Year = {2006}}
	
@inbook{kdtaverna,
	Author = {Carole Goble and Katy Wolstencroft and Antoon Goderis and Duncan Hull and Jun Zhao and Pinar Alper and Phillip Lord and Chris Wroe and Khalid Belhajjame and Daniele Turi and Robert Stevens and Tom Oinn and David De Roure},
	Chapter = {Knowledge Discovery for Biology with Taverna: Producing and Consuming Semantics on the Web of Science},
	crossref  = {bakercheung},
	Year = {2006}}	
	
@inproceedings{Sahoowww06,
  author    = {Satya Sanket Sahoo and Christopher Thomas and Amit P. Sheth and William S. York and Samir Tartir},
  title     = {Knowledge modeling and its application in life sciences: a tale of two ontologies.},
  booktitle = {Proceedings of WWW2006},
  year      = {2006},
  pages     = {317-326},
  doi        = {http://dx.doi.org/10.1145/1135777.1135826},
  crossref  = {DBLP:conf/www/2006},
}

@Article{Batemen,
author = "Alex Bateman",
title = {Editorial: What makes a good database?},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "1",
pages = "1-1",
pmid = "17202158",
}

@Article{fisherp,
author = "Paul Fisher and Cornelia Hedeler and Katy Wolstencroft and David Withers and Stuart Owen and Helen Hulme and Harry Noyes and Steve Kemp and Robert Stevens and Andy Brass",
title = {A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations},
journal = "Bioinformatics",
year = "2007",
volume = "??",
number = "?",
pages = "??",
note={submitted for publication}
}

@Article{EMBOSS,
author = "Rice, P and Longden, I and Bleasby, A",
title = {EMBOSS: the European Molecular Biology Open Software Suite},
journal = "Trends in Genetics",
year = "2000",
volume = "16",
number = "6",
pages = "276-277",
month = "Jun",
pmid = "10827456",
}


@Article{Clustalw,
author = "Thompson, J D and Higgins, D G and Gibson, T J",
title = {CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
journal = "Nucleic Acids Research",
year = "1994",
volume = "22",
number = "22",
pages = "4673-4680",
month = "Nov",
pmid = "7984417",
}


@inproceedings{wsmonutshell,
  author    = {Dumitru Roman and
               Jos de Bruijn and
               Adrian Mocan and
               Holger Lausen and
               John Domingue and
               Christoph Bussler and
               Dieter Fensel},
  title     = {WWW: WSMO, WSML, and WSMX in a Nutshell.},
  booktitle = {ASWC},
  year      = {2006},
  pages     = {516-522},
  ee        = {http://dx.doi.org/10.1007/11836025_49},
  crossref  = {DBLP:conf/aswc/2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/aswc/2006,
  editor    = {Riichiro Mizoguchi and
               Zhongzhi Shi and
               Fausto Giunchiglia},
  title     = {The Semantic Web - ASWC 2006, First Asian Semantic Web Conference,
               Beijing, China, September 3-7, 2006, Proceedings},
  booktitle = {ASWC},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {4185},
  year      = {2006},
  isbn      = {3-540-38329-8},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{utopia,
	Author = {Steven R. Pettifer and James R. Sinnott and Terri K. Attwood},
	Journal = {Comparative and Functional Genomics},
	Pages = {56--60},
	Title = {UTOPIA: User-friendly Tools for OPerating Informatics Applications},
	Volume = {5},
	Year = {2004},
}


@conference{utopia2 ,
	title = {An Architecture for Visualisation and Interactive Analysis of Proteins},
	year = {2006},
	pages = {55--68},
	publisher = {IEEE Computer Society},
	type = {inproceedings},
	address = {Washington, DC, USA},
	ISBN = {0-7695-2605-5},
	author = { P. McDermott and  J. Sinnott and  D. Thorne and  S. Pettifer and  T. Attwood}
}

@Article{GenBank07,
author = "Benson, D A and Karsch-Mizrachi, I and Lipman, D J and Ostell, J and Wheeler, D L",
title = {GenBank},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",                                                                                            
number = "Database issue",
pages = "21-25",
month = "Jan",
pmid = "17202161",
}

@Article{ijbra,
author = "Katy Wolstencroft and Pinar Alper and Duncan Hull and Chris Wroe and Phillip Lord and Robert Stevens and Carole Goble",
title = {The myGrid Ontology: Bioinformatics Service Discovery },
journal = "International Journal of Bioinformatics Research and Applications",
year = "2007",
volume = "3",
number = {3},
note = "Accepted for publication",
}


@article{srs,
title={{SRS: Information Retrieval System for Molecular Biology Data Banks}},
author={Thure Etzold and Anatoly Ulyanov and Patrick Argos},
journal="Methods in Enzymology", 
volume="266",
pages="114",
year="1996"}

@article{etzold,
  author    = {Thure Etzold and Patrick Argos},
  title     = {SRS - an indexing and retrieval tool for flat file data libraries.},
  journal   = {Computer Applications in the Biosciences},
  volume    = {9},
  number    = {1},
  year      = {1993},
  pages     = {49-57},
}

@Article{DragIdentity,
author = "Draghici, S and Sellamuthu, S and Khatri, P",
title = {Babel's tower revisited: a universal resource for cross-referencing across annotation databases},
journal = "Bioinformatics",
year = "2006",
volume = "22",
number = "23",
pages = "2934-2939",
month = "Dec",
pmid = "17068090",
doi = "10.1093/bioinformatics/btl372"
}

@Article{connotea,
author="Bend Lund and Tony Hammond and Martin Flack and Timo Hannay",
title="Social Bookmarking Tools (II): A Case Study - Connotea",
journal="D-Lib Magazine",
year="2005",
volume="11",
issue="4",
doi="10.1045/april2005-lund",
issn="1082-9873",
}

@Article{doicrossref,
author = "Renn, O",
title = {DOI, CrossRef, LINK, and the future of scientific publishing},
journal = "J Orofac Orthop",
year = "2001",
volume = "62",
number = "6",
pages = "408-409",
month = "Nov",
pmid = "11765704",
}

@misc{wsmoprimer,
Author = {Cristina Feier and Sinuhe Arroyo and Emilia Cimpian and John Domingue and Cristina Feier and Dieter Fensel and Birgitta Kšnig-Ries and Holger Lausen and Axel Polleres and Michael Stollberg},
Howpublished = {\url{http://www.w3.org/Submission/WSMO-primer/}},
Note = {W3C Member Submission 3 June 2005},
Title = {Web Service Modeling Ontology Primer},
Year = {2005}
}

@misc{astronauts,
Author = {Joel Spolsky},
Howpublished = {\url{http://www.joelonsoftware.com/articles/fog0000000018.html}},
Title = {Don't Let Architecture Astronauts Scare You},
Year = {2001}
}

@inproceedings{citation-needed,
Author = {A. Bluffer},
Title = {A real citation is needed here instead of this dummy placeholder},
Year = {2003},
Booktitle="BINS2003",
pages ={5--7},
crossref={DBLP:conf/bins/2003},
}


@proceedings{DBLP:conf/bins/2003,
  editor    = {Boris Ullshitter and Justin Hotair},
  title     = {{Proceedings of the 784th Boring Incomprehensible Nonsense Society}},
  booktitle = {BINS2007},
  publisher = {BIN},
  year      = {2003},
}










@book{weaving,
	Author = {Tim Berners-Lee and Mark Fischetti},
	Publisher = {Texere Publishing, USA},
	Title = {{Weaving the Web: The original design and ultimate destiny of the World Wide Web, by its inventor}},
	note = {ISBN:006251587X},
	pages={288},
	Year = {1999}}
	
@misc{xmlschema,
	Author = {David C. Fallside and Priscilla Walmsley},
	Title={{XML Schema Part 0: Primer Second Edition}},
	Howpublished={\url{http://www.w3.org/TR/2004/REC-xmlschema-0-20041028/}},
	Note ={W3C Recommendation 28 October 2004},
	Year={2004}}
   
@inproceedings{geertjanbex,
  author    = {Geert Jan Bex and Wim Martens and Frank Neven and Thomas Schwentick},
  title     = {{Expressiveness of XSDs: from practice to theory, there and back again}},
  booktitle = {WWW2005},
  year      = {2005},
  pages     = {712-721},
  crossref  = {DBLP:conf/www/2005},
}

@proceedings{DBLP:conf/www/2005,
  editor    = {Allan Ellis and Tatsuya Hagino},
  title     = {{Proceedings of the 14th international conference on World Wide Web, WWW 2005, Chiba, Japan, May 10-14, 2005}},
  booktitle = {WWW2005},
  publisher = {ACM},
  year      = {2005},
  isbn      = {1-59593-046-9},
}

@article{Studer98,
  author    = {Rudi Studer and V. Richard Benjamins and Dieter Fensel},
  title     = {Knowledge Engineering: Principles and Methods.},
  journal   = {Data and Knowledge Engineering},
  volume    = {25},
  number    = {1-2},
  year      = {1998},
  pages     = {161-197},
  doi        = {10.1016/S0169-023X(97)00056-6},
}

@article{suddi,
  author    = {Marta Sabou and Jeff Pan},
  title     = {Towards semantically enhanced Web service repositories},
  journal   = {Journal of Web Semantics},
  year      = {2007},
  note        = {DOI:10.1016/j.websem.2006.11.004},
}

@book{kellylogic,
	author ={John J Kelly},
	title={The Essence of Logic},
	note={ISBN:0133963756},
	publisher={Prentice Hall},
	pages={273},
	year={1996}	
	}

@book{lfol,
	author ={Jon Barwise and John Etchemendy},
	title={The Language of First-Order Logic},
	note={Third Edition, ISBN:0937073903},
	publisher={Center for the Study of Language and Information (CLSI) Stanford University},
	pages={320},
	year={1992}	
	}
	
@Article{ensembl2007,
author = "Hubbard, T J and Aken, B L and Beal, K and Ballester, B and Caccamo, M and Chen, Y and Clarke, L and Coates, G and Cunningham, F and Cutts, T and Down, T and Dyer, S C and Fitzgerald, S and Fernandez-Banet, J and Graf, S and Haider, S and Hammond, M and Herrero, J and Holland, R and Howe, K and Howe, K and Johnson, N and Kahari, A and Keefe, D and Kokocinski, F and Kulesha, E and Lawson, D and Longden, I and Melsopp, C and Megy, K and Meidl, P and Ouverdin, B and Parker, A and Prlic, A and Rice, S and Rios, D and Schuster, M and Sealy, I and Severin, J and Slater, G and Smedley, D and Spudich, G and Trevanion, S and Vilella, A and Vogel, J and White, S and Wood, M and Cox, T and Curwen, V and Durbin, R and Fernandez-Suarez, X M and Flicek, P and Kasprzyk, A and Proctor, G and Searle, S and Smith, J and Ureta-Vidal, A and Birney, E",
title = {Ensembl 2007},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "Database issue",
pages = "610--617",
pmid = "17148474",
doi = "10.1093/nar/gkl996"
}

@article{BrinPage98,
  author    = {Sergey Brin and Lawrence Page},
  title     = {The Anatomy of a Large-Scale Hypertextual Web Search Engine.},
  journal   = {Computer Networks},
  volume    = {30},
  number    = {1-7},
  year      = {1998},
  pages     = {107-117},
  DOI        = {10.1016/S0169-7552(98)00110-X},
}

@inproceedings{stackortwotowers,
  author    = {Ian Horrocks and Bijan Parsia and Peter F. Patel-Schneider and James A. Hendler},
  title     = {Semantic Web Architecture: Stack or Two Towers?},
  booktitle = {PPSWR},
  year      = {2005},
  pages     = {37-41},
  DOI        = {10.1007/11552222_4},
  crossref  = {DBLP:conf/ppswr/2005},

}

@proceedings{DBLP:conf/ppswr/2005,
  editor    = {Fran\c{c}ois Fages and Sylvain Soliman},
  title     = {Principles and Practice of Semantic Web Reasoning, Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings},
  booktitle = {PPSWR},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3703},
  year      = {2005},
  isbn      = {3-540-28793-0},
}


@misc{sparql,
	Author = {Eric Prud'hommeaux and Andy Seaborne},
	howpublished = {\url{http://www.w3.org/TR/rdf-sparql-query/}},
	Title = {{SPARQL Query Language for RDF}},
	note = {W3C Working Draft 4 October 2006},
	Year = {2006}}
	
	
@incollection{DBLP:books/sp/staabS2004/McBride04,
  author    = {Brian McBride},
  title     = {The Resource Description Framework (RDF) and its Vocabulary
               Description Language RDFS.},
  booktitle = {Handbook on Ontologies},
  year      = {2004},
  pages     = {51-66},
  crossref  = {DBLP:books/sp/StaabS04},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@incollection{mcbride,
	Author = {Brian McBride},
	Booktitle = {Handbook on Ontologies},
	Editor = {Steffen Staab and Rudi Studer},
	Pages = {51--66},
	Publisher = {Springer},
	Title = {{The Resource Description Framework (RDF) and its Vocabulary Description Language RDFS}},
	Year = {2004}}

@book{DBLP:books/sp/StaabS04,
  editor    = {Steffen Staab and
               Rudi Studer},
  title     = {Handbook on Ontologies},
  booktitle = {Handbook on Ontologies},
  publisher = {Springer},
  series    = {International Handbooks on Information Systems},
  year      = {2004},
  isbn      = {3-540-40834-7},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@incollection{onto-handbook-chap:03,
	Author = {Robert Stevens and Chris Wroe and Phillip Lord and Carole Goble},
	Booktitle = {Handbook on Ontologies},
	Editor = {Steffen Staab and Rudi Studer},
	Pages = {635-657},
	Publisher = {Springer},
	Title = {Ontologies in Bioinformatics},
	Year = 2003}

@misc{notahealthysign,
	Author = {Bijan Parsia},
	howpublished = {\url{http://lists.w3.org/Archives/Public/public-sws-ig/2006Oct/0015.html}},
	Title = {{Are there any commercial or real-world Semantic Web Services?}},
	note = {post to W3C mailing list for the Semantic Web Services Interest Group (SWSIG) public-sws-ig@w3.org},
	Year = {2006}}	

@misc{nofreelunch,
		Author = {Alan Rector},
		howpublished = {\url{http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jul/0054.html}},
		Title = {{Ontology specifications for self-publishing experiment}},
		note = {post to W3C mailing list for the Semantic Web Services Interest Group (SWSIG) public-sws-ig@w3.org},
		Year = {2006}}

@misc{rdfnot,
	Author = {Tim Berners-Lee},
	howpublished = {\url{http://www.w3.org/DesignIssues/RDFnot.html}},
	Title = {{What the Semantic Web can represent}},
	Note = {World Wide Web Consortium Design Issues},
	Year = {1998}}	
	
@misc{flyingpigs,
  author    = {Michael Stollberg and Emilia Cimpian and Liliana Cabral and John Domingue},
  title     = {{MAP4: Semantic Web Services}},
  note     = {Tutorial delivered at the Twenty-First National Conference on Artificial
               Intelligence and the Eighteenth Innovative Applications
               of Artificial Intelligence Conference, July 16-20, 2006,
               Boston, Massachusetts, USA},
  year      = {2006},
}

@article{vogels,
	Author = {James N. Gray},
	Journal ={ACM Queue},
	Volume = {4},
	Number={4},
	Title = {{A Conversation with Werner Vogels: Learning from the Amazon technology platform}},
	note = {May issue},
	Year = {2006}}	
	
@article{biomoby-tootbrush,
	Author = {Mark Wilkinson and A.N. Other},
	Journal ={PLOS Computational Biology},
	Title = {{Interoperability with Moby 1.0 - It's Better Than Sharing Your Toothbrush}},
	note ={in submission},
	Year = {2007}}		

@book{topdownbottomup,
	Author = {Douglas Bell and Ian Morrey and John Pugh},
	Publisher = {Prentice Hall},
	Title = {The Essence of Program Design},
	note = {Essence of Computing Series, ISBN:0133678067},
	pages={354},
	Year = {2004}}

@inproceedings{soaplab,
	Author = {Martin Senger and Peter Rice and Tom Oinn},
	Booktitle = {Proceedings UK e-Science programme All Hands Meeting},
	Title = {{Soaplab - a unified Sesame door to analysis tools}},
	Pages = {509--513},
	Year = {2003}
	NOTE={ISBN 1-904425-11-9 }}
	
	
@Article{seqhound,
author = "Michalickova, K and Bader, G D and Dumontier, M and Lieu, H and Betel, D and Isserlin, R and Hogue, C W",
title = {{SeqHound: biological sequence and structure database as a platform for bioinformatics research}},
journal = "BMC Bioinformatics",
year = "2002",
volume = "3",
number = "",
pages = "32-32",
month = "Oct",
pmid = "12401134",
}

@Article{talisman,
author = "Oinn, T M",
title = {Talisman--rapid application development for the grid},
journal = "Bioinformatics",
year = "2003",
volume = "19 Suppl 1",
pages = "212-214",
pmid = "12855460",
}
@misc{hockney,
	Author = {David Hockney},
	Note = {Sunday 10th July edition, via \url{http://www.oxfordreference.com/views/ENTRY.html?entry=t93.e851}},
	Title = {{The Observer newspaper}},
	Year = {1994}}
	
	
@inproceedings{DBLP:conf/iccS/BlowerHH06,
  author    = {J. D. Blower and A. B. Harrison and K. Haines},
  title     = {Styx Grid Services: Lightweight, Easy-to-Use Middleware for Scientific Workflows.},
  booktitle = {International Conference on Computational Science (3)},
  year      = {2006},
  pages     = {996-1003},
  ee        = {http://dx.doi.org/10.1007/11758532_135},
  crossref  = {DBLP:conf/iccS/2006-3},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/iccS/2006-3,
  editor    = {Vassil N. Alexandrov and G. Dick van Albada and Peter M. A. Sloot and Jack Dongarra},
  title     = {Computational Science - ICCS 2006, 6th International Conference, Reading, UK, May 28-31, 2006, Proceedings, Part III},
  booktitle = {International Conference on Computational Science (3)},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {3993},
  year      = {2006},
  isbn      = {3-540-34383-0},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

 @misc{ wiki:unixpipe,
   author = "Wikipedia",
   title = "Pipeline (Unix) --- Wikipedia{,} The Free Encyclopedia",
   year = "2007",
   url = "\url{http://en.wikipedia.org/w/index.php?title=Pipeline_%28Unix%29&oldid=117308783}",
   note = "[Online; accessed 27-March-2007]"
 }
 
 @inproceedings{whytaggingworks,
  author    = {George W. Furnas and
               Caterina Fake and
               Luis von Ahn and
               Joshua Schachter and
               Scott A. Golder and
               Kevin Fox and
               Marc Davis and
               Cameron Marlow and
               Mor Naaman},
  title     = {Why do tagging systems work?},
  booktitle = {CHI Extended Abstracts},
  year      = {2006},
  pages     = {36-39},
  ee        = {http://doi.acm.org/10.1145/1125451.1125462},
  crossref  = {DBLP:conf/chi/2006a},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/chi/2006a,
  editor    = {Gary M. Olson and
               Robin Jeffries},
  title     = {Extended Abstracts Proceedings of the 2006 Conference on
               Human Factors in Computing Systems, CHI 2006, Montr{\'e}al,
               Qu{\'e}bec, Canada, April 22-27, 2006},
  booktitle = {CHI Extended Abstracts},
  publisher = {ACM},
  year      = {2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}



@proceedings{codecomplete,
	Author = {Steven C. McConnell},
	Publisher = {Microsoft},
	Title = {Code Complete: A Practical Handbook of Software Construction },
	note = {ISBN:1556154844},
	pages={857},
	Year = {2004}}



 
@inproceedings{metaphor,
	Author = {Steven C. McConnell},
	Title = {Metaphors for a Richer Understanding of Programming},
	crossref  = {codecomplete},
	year={2004}
	}
	
	
@misc{jamesclark,
	Author ={James J. Clark},
	Title = {Do we need a new kind of schema language?},
	howpublished = {\url{http://blog.jclark.com/2007/04/do-we-need-new-kind-of-schema-language.html}},
	Year = {2007}}
	

@Article{agentshims,
author = "Merelli, E and Armano, G and Cannata, N and Corradini, F and d'Inverno, M and Doms, A and Lord, P and Martin, A and Milanesi, L and M{\"o}ller, S and Schroeder, M and Luck, M",
title = {Agents in bioinformatics, computational and systems biology},
journal = "Briefings in Bioinformatics",
year = "2007",
volume = "8",
number = "1",
pages = "45-59",
month = "Jan",
pmid = "16772270",
doi = "10.1093/bib/bbl014"
}	


@inproceedings{ambite,
  author    = {Jos{\'e} Luis Ambite and
               Dipsy Kapoor and
               Mountu Jinwala},
  title     = {Data processing workflows in the social sciences: representation
               and automatic generation.},
  booktitle = {DG.O},
  year      = {2006},
  pages     = {321-322},
  ee        = {http://doi.acm.org/10.1145/1146598.1146685},
  crossref  = {DBLP:conf/dgo/2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/dgo/2006,
  editor    = {Jos{\'e} A. B. Fortes and
               Ann Macintosh},
  title     = {Proceedings of the 7th Annual International Conference on
               Digital Government Research, DG.O 2006, San Diego, California,
               USA, May 21-24, 2006},
  booktitle = {DG.O},
  publisher = { Digital Government Research Center},
  year      = {2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{jwebsemplan1,
  author    = {Ugur Kuter and
               Evren Sirin and
               Bijan Parsia and
               Dana S. Nau and
               James A. Hendler},
  title     = {Information gathering during planning for Web Service composition.},
  journal   = {J. Web Sem.},
  volume    = {3},
  number    = {2-3},
  year      = {2005},
  pages     = {183-205},
  ee        = {http://dx.doi.org/10.1016/j.websem.2005.07.001},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
 
@article{jwebsemplan2,
  author    = {Evren Sirin and
               Bijan Parsia and
               Dan Wu and
               James A. Hendler and
               Dana S. Nau},
  title     = {HTN planning for Web Service composition using SHOP2.},
  journal   = {J. Web Sem.},
  volume    = {1},
  number    = {4},
  year      = {2004},
  pages     = {377-396},
  ee        = {http://dx.doi.org/10.1016/j.websem.2004.06.005},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@Article{PhysRevE.66.067103,
  title = {From gene families and genera to incomes and internet file sizes: Why power laws are so common in nature},
  author = {William J. Reed and Barry D. Hughes},
  journal = {Physical Review E},
  volume = {66},
  number = {6},
  pages = {067103},
  numpages = {4},
  year = {2002},
  month = {Dec},
  doi = {10.1103/PhysRevE.66.067103},
  publisher = {American Physical Society}
}

@Article{Su:2007:Genome-Biol:17472739,
author = "Su, A I and Hogenesch, J B",
title = {Power-law-like distributions in biomedical publications and research funding},
journal = "Genome Biol",
year = "2007",
volume = "8",
number = "4",
pages = "404-404",
month = "Apr",
pmid = "17472739",
url = "http://www.hubmed.org/display.cgi?uids=17472739",
doi = "10.1186/gb-2007-8-4-404"
}

@Article{Davies:2007:BMC-Dev-Biol:17472742,
author = "Davies, J A",
title = {Developmental biologists choice of subjects approximates to a power law, with no evidence for the existence of a special group of model organisms},
journal = "BMC Dev Biol",
year = "2007",
volume = "7",
number = "1",
pages = "40-40",
month = "May",
pmid = "17472742",
url = "http://www.hubmed.org/display.cgi?uids=17472742",
doi = "10.1186/1471-213X-7-40"
}


@book{DBLP:books/el/Kent1978,
  editor    = {William Kent},
  title     = {Data and Reality, 1st edition.},
  publisher = {North-Holland},
  year      = {1978},
  isbn      = {0-444-85187-9},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@book{DBLP:books/ph/Tanenbaum81,
  author    = {Andrew S. Tanenbaum},
  title     = {Computer Networks},
  publisher = {Prentice-Hall},
  year      = {2003},
}

@misc{swfaq,
	Author = {Ivan Herman},
	Howpublished = {\url{http://www.w3.org/2001/sw/SW-FAQ}},
	Title = { W3C Semantic Web Frequently Asked Questions},
	Year = {2007}}
	

@misc{sawsdl,
	Author = {Joel Farrell and Holger Lausen},
	Howpublished = {\url{http://www.w3.org/TR/sawsdl/}},
	Title = {Semantic Annotations for WSDL and XML Schema},
	note = {W3C Working Draft},
	Year = {2007}}
	

	
	
@Article{Ruttenberg,
author = "Ruttenberg, A and Clark, T and Bug, W and Samwald, M and Bodenreider, O and Chen, H and Doherty, D and Forsberg, K and Gao, Y and Kashyap, V and Kinoshita, J and Luciano, J and Marshall, M S and Ogbuji, C and Rees, J and Stephens, S and Wong, G T and Wu, E and Zaccagnini, D and Hongsermeier, T and Neumann, E and Herman, I and Cheung, K H",
title = {Advancing translational research with the Semantic Web},
journal = "BMC Bioinformatics",
year = "2007",
volume = "8",
number = "s3",
pmid = "17493285",
doi = "10.1186/1471-2105-8-S3-S2"
}