The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics.

Paula de Matos

Paula de Matos Jennifer A. Cham Hong Cao Rafael Alcántara Francis Rowland Rodrigo Lopez Christoph Steinbeck The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics. 103 2013 14 BMC Bioinform. https://doi.org/10.1186/1471-2105-14-103 https://www.wikidata.org/entity/Q28709108 db/journals/bmcbi/bmcbi14.html#MatosCCARLS13

Janna Hastings Paula de Matos Adriano Dekker Marcus Ennis Bhavana Harsha Namrata Kale Venkatesh Muthukrishnan Gareth I. Owen Steve Turner Mark Williams 0002 Christoph Steinbeck The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. 456-463 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1146 https://www.wikidata.org/entity/Q28710191 db/journals/nar/nar41.html#HastingsMDEHKMOTWS13

Rafael Alcántara Joseph Onwubiko Hong Cao Paula de Matos Jennifer A. Cham Julius O. B. Jacobsen Gemma L. Holliday Julia D. Fischer Syed Asad Rahman Bijay Jassal Mickael Goujon Francis Rowland Sameer Velankar Rodrigo Lopez John P. Overington Gerard J. Kleywegt Henning Hermjakob Claire O'Donovan Maria Jesus Martin Janet M. Thornton Christoph Steinbeck The EBI enzyme portal. 773-780 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1112 https://www.wikidata.org/entity/Q34313323 db/journals/nar/nar41.html#AlcantaraOCMCJHFRJGRVLOKHOMTS13

Kenneth Haug Reza M. Salek Pablo Conesa Janna Hastings Paula de Matos Mark Rijnbeek Tejasvi Mahendraker Mark Williams 0002 Steffen Neumann Philippe Rocca-Serra Eamonn Maguire Alejandra N. González-Beltrán Susanna-Assunta Sansone Julian L. Griffin Christoph Steinbeck MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. 781-786 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1004 https://www.wikidata.org/entity/Q27818909 db/journals/nar/nar41.html#HaugSCHMRMWNRMBSGS13

Lian Duan Janna Hastings Paula de Matos Marcus Ennis Christoph Steinbeck Structured chemical class definitions and automated matching for chemical ontology evolution. 5 2012 4 J. Cheminformatics S-1 https://doi.org/10.1186/1758-2946-4-S1-P5 https://www.wikidata.org/entity/Q45789375 db/journals/jcheminf/jcheminf4S.html#DuanHMES12

Rafael Alcántara Kristian B. Axelsen Anne Morgat Eugeni Belda Elisabeth Coudert Alan J. Bridge Hong Cao Paula de Matos Marcus Ennis Steve Turner Gareth I. Owen Lydie Bougueleret Ioannis Xenarios Christoph Steinbeck Rhea - a manually curated resource of biochemical reactions. 754-760 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr1126 https://www.wikidata.org/entity/Q35630899 db/journals/nar/nar40.html#AlcantaraAMBCBCMETOBXS12

Katrina Pavelin Jennifer A. Cham Paula de Matos Catherine Brooksbank Graham Cameron Christoph Steinbeck Bioinformatics Meets User-Centred Design: A Perspective. 2012 8 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1002554 https://www.wikidata.org/entity/Q28727218 db/journals/ploscb/ploscb8.html#PavelinCMBCS12

Janna Hastings Paula de Matos Adriano Dekker Marcus Ennis Venkatesh Muthukrishnan Steve Turner Gareth I. Owen Christoph Steinbeck Modular Extensions to the ChEBI Ontology. 2012 ICBO https://ceur-ws.org/Vol-897/poster_7.pdf conf/icbo/2012 db/conf/icbo/icbo2012.html#HastingsMDEMTOS12 Janna Hastings Paula de Matos Adriano Dekker Marcus Ennis Kenneth Haug Zara Josephs Gareth I. Owen Steve Turner Christoph Steinbeck Recent Developments in the ChEBI Ontology. 2011 ICBO https://ceur-ws.org/Vol-833/paper38.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#HastingsMDEHJOTS11

Paula de Matos Adriano Dekker Marcus Ennis Janna Hastings Kenneth Haug Steve Turner Christoph Steinbeck ChEBI: a chemistry ontology and database. 6 2010 2 J. Cheminformatics S-1 https://doi.org/10.1186/1758-2946-2-S1-P6 https://www.wikidata.org/entity/Q28752271 db/journals/jcheminf/jcheminf2S.html#MatosDEHHTS10

Paula de Matos Rafael Alcántara Adriano Dekker Marcus Ennis Janna Hastings Kenneth Haug Inmaculada Spiteri Steve Turner Christoph Steinbeck Chemical Entities of Biological Interest: an update. 249-254 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp886 https://www.wikidata.org/entity/Q24644887 db/journals/nar/nar38.html#MatosADEHHSTS10

Nico Adams Paula de Matos Adriano Dekker Marcus Ennis Janna Hastings Kenneth Haug Duncan Hull Zara Josephs Pablo A. Moreno Steve Turner Christoph Steinbeck Semantic access to chemistry data with the ChEBI ontology and web services. 2009 SWAT4LS https://ceur-ws.org/Vol-559/Poster1.pdf conf/swat4ls/2009 db/conf/swat4ls/swat4ls2009.html#AdamsMDEHHHJMTS09

Kirill Degtyarenko Paula de Matos Marcus Ennis Janna Hastings Martin Zbinden Alan McNaught Rafael Alcántara Michael Darsow Mickaël Guedj Michael Ashburner ChEBI: a database and ontology for chemical entities of biological interest. 344-350 2008 36 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkm791 https://www.wikidata.org/entity/Q24650818 db/journals/nar/nar36.html#DegtyarenkoMEHZMADGA08

Janna Hastings Kirill Degtyarenko Paula de Matos Marcus Ennis Christoph Steinbeck The ChEBI Ontology: An Ontology for Chemistry within a Biological Context. 2008 SWAT4LS https://ceur-ws.org/Vol-435/poster04.pdf conf/swat4ls/2008 db/conf/swat4ls/swat4ls2008.html#HastingsDMES08 Nico Adams Rafael Alcántara Michael Ashburner Kristian B. Axelsen Eugeni Belda Lydie Bougueleret Alan J. Bridge Catherine Brooksbank Graham Cameron Hong Cao Jennifer A. Cham Pablo Conesa Elisabeth Coudert Michael Darsow Kirill Degtyarenko Adriano Dekker Lian Duan Marcus Ennis Julia D. Fischer Alejandra N. González-Beltrán Mickael Goujon Julian L. Griffin Mickaël Guedj Bhavana Harsha Janna Hastings Kenneth Haug Henning Hermjakob Gemma L. Holliday Duncan Hull Julius O. B. Jacobsen Bijay Jassal Zara Josephs Namrata Kale Gerard J. Kleywegt Rodrigo Lopez Eamonn Maguire Tejasvi Mahendraker Maria Jesus Martin Alan McNaught Pablo A. Moreno Anne Morgat Venkatesh Muthukrishnan Steffen Neumann Claire O'Donovan Joseph Onwubiko John P. Overington Gareth I. Owen Katrina Pavelin Syed Asad Rahman Mark Rijnbeek Philippe Rocca-Serra Francis Rowland Reza M. Salek Susanna-Assunta Sansone Inmaculada Spiteri Christoph Steinbeck Janet M. Thornton Steve Turner Sameer Velankar Mark Williams 0002 Ioannis Xenarios Martin Zbinden