Katy Wolstencroft
Assistant professor
- Name
- Dr. K.J. Wolstencroft
- Telephone
- +31 71 527 8926
- k.j.wolstencroft@liacs.leidenuniv.nl
- ORCID iD
- 0000-0002-1279-5133
Katy Wolstencroft works in data and knowledge integration, applying cutting-edge computer science technologies to bioinformatics and Systems Biology research.
I lead the Semantic Systems Bioinformatics group at the Leiden Institute of Advanced Computer Science. My group focuses on research methods and workflows for analysing, modelling and semantically integrating biomedical data. By exploring and exploiting the wealth of research results already in the public domain, we can address the growing analysis bottleneck and produce new insights that increase the economic and scientific value of research results. We are particularly interested in Systems Biology and Systems Medicine, where multiple types of multi-scale, heterogeneous and distributed information can potentially be integrated and modelled to further our understanding of dynamic interactions in biological systems.
Current research projects involve; ontologies and semantic modelling for automated data extraction (Making Sense of Illustrated Handwritten Archives), bioinformatics workflows for omics research and diagnostics, and FAIR (Findable, Accessible, Interoperable and Reusable) data management and methodologies, particularly in Systems Biology with the FAIRDOM project and the FAIRDOMHub.
Assistant professor
- Science
- Leiden Inst. Advanced Computer Sciences
- Stork L., Weber A., Gassó Miracle E., Verbeek F.J., Plaat A., Herik H.J. van den & Wolstencroft K.J. (2019), Semantic annotation of natural history collections, Journal of Web Semantics 59: 100462.
- Stork L., Weber A., Herik H.J. van den, Plaat A., Verbeek F.J. & Wolstencroft K.J. (2018), From Handwritten Manuscripts to Linked Data. In: Méndez E., Crestani F., Ribeiro C., David G., Lopes J. (Eds.) Digital Libraries for Open Knowledge. no. Lecture Notes in Computer Science, volume 11057 Cham: Springer. 330-334.
- Stork L., Weber A., Gasso Miracle E. & Wolstencroft K.J. (2018), Linking Natural History Collections. In: 2018 IEEE 14th International Conference on e-Science (e-Science).: IEEE. 388-389.
- Weber A., Ameryan M., Wolstencroft K.J., Stork L., Heerlien M. & Schomaker L. (2018), Towards a digital infrastructure for illustrated handwritten archives. In: M. Loannides (Ed.) Digital Cultural Heritage. no. Lecture Notes in Computer Science, volume 10605 Cham: Springer International Publishing. 155-166.
- McMurry J.A., Juty N., Blomberg N., Burdett T., Conlin T., Conte N., Courtot M., Deck J., Dumontier M., Fellows D.K., Gonzalez-Beltran A., Gormanns P., Grethe J., Hastings J., Heriche J.-K., Hermjakob H., Ison J.C., Jimenez R.C., Jupp S., Kunze J., Laibe C., Novere N. Le, Malone J., Martin M.J., McEntyre J.R., Morris C., Muilu J., Mueller W., Rocca-Serra P., Sansone S.-A., Sariyar M., Snoep J.L., Soiland-Reyes S., Stanford N.J., Swainston N., Washington N., Williams A.R., Wimalaratne S.M., Winfree L.M., Wolstencroft K.J., Goble C., Mungall C.J., Haendel M.A. & Parkinson H. (2017), Identifiers for the 21st century: how to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data, PLOS BIOLOGY 15(6): e2001414.
- Wilkins J.J., Chan P.L.S., Chard J., Smith G., Smith M.K., Beer M., Dunn A., Flandorfer C., Franklin C., Gomeni R., Harnisch L., Kaye R., Moodie S., Sardu M.L., Wang E., Watson E., Wolstencroft K.J. & Cheung S.Y.A. (2017), Thoughtflow: Standards and Tools for Provenance Capture and Workflow Definition to Support Model-Informed Drug Discovery and Development, CPT: Pharmacometrics & Systems Pharmacology 6(5): 285-292.
- Wolstencroft K.J., Krebs O., Snoep J.L., Stanford N.J., Bacall F., Golebiewski M., Kuzyakiv R., Owen S., Soiland-Reyes S., Straszewski J., Niekerk D.D. van, Williams A.R., Malmstrom L., Rinn B., Mueller W. & Goble C. (2017), FAIRDOMHub: a repository and collaboration environment for sharing systems biology research, Nucleic Acids Research 45(D1): D404-D407.
- Thomas S., Wolstencroft K., Bono B. de & Hunter P.J. (2016), A physiome interoperability roadmap for personalized drug development, INTERFACE FOCUS 6(2): 20150094.
- Hartogh S.C. den, Wolstencroft K.J., Mummery C.L. & Passier R. (2016), A comprehensive gene expression analysis at sequential stages of in vitro cardiac differentiation from isolated MESP1-expressing-mesoderm progenitors, SCIENTIFIC REPORTS 6: 19386.
- Schomaker L., Weber A., Thijssen M., Heerlien M., Plaat A., Nijssen S.G.R., Verbeek F.J., Lew M.S.K., Gasso Micacle E., Wolstencroft K., Suyver E., Verheij B., Wiering M., Dekker M., Kok J., Roberts L. & Herik H.J. van den (2016), Making Sense of Illustrated Handwritten Archives. In: Digital Humanities 2016 Conference Abstracts. Krakow: Jagiellonian University and Pedagogical University. 674-676.
- Wilkinson M.D., Dumontier M., Aalbersberg IJ.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J-W., Silva Santos L.B. da, Bourne P.E., Bouwman J., Brookes A.J., Clark T., Crosas M., Dillo I., Dumon O., Edmunds S., Evelo C.T., Finkers R., Gonzalez-Beltran A., Gray A.J.G., Groth P., Goble C., Grethe J.S., Heringa J., Hoen P.A.C. ‘t, Hooft R., Kuhn T., Kok R., Kok J.N., Lusher S.J., Martone M.E., Mons A., Packer A.L., Persson B., Rocca-Serra P., Roos M., Schaik R. van, Sansone S-A., Schultes E., Sengstag T., Slater T., Strawn G., Swertz M.A., Thompson M., Lei J. van der, Mulligen. E. van, Velterop J., Waagmeester A., Wittenburg P., Wolstencroft K.J., Zhao J. & Mons B. (2016), The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data 2016(3): 160018.
- Mina E., Thompson M., Hettne K.M., Roon-Mom W.M.C. van, Kaliyaperumal R., Horst E. van der, Wolstencroft K.J., Mons B. & Roos M. (2015), Multidisciplinary Collaboration to Facilitate Hypotheses Generation in Huntington's Disease. In: 2015 IEEE 11th International Conference on e-Science.: IEEE. 118-125.
- Wolstencroft K.J., Owen S., Krebs O., Nguyen Q., Stanford N.J., Golebiewski M., Weidemann A., Bittkowski M., An L., Shockley D., Snoep J.L., Mueller W. & Goble C.A. (2015), SEEK: a systems biology data and model management platform, BMC Systems Biology 9: 33.
- Stanford N.J., Wolstencroft K.J., Golebiewski M., Kania R., Juty N., Tomlinson C., Owen S., Butcher S., Hermjakob H., Novère N. Le, Mueller W., Snoep J. & Goble C. (2015), The evolution of standards and data management practices in systems biology, Molecular Systems Biology 11(12): 851.
- Vanschoren J., Bischl B., Hutter F., Sebag M., Kegl B., Schmid M., Napolitano G., Wolstencroft K.J., Williams A.R. & Lawrence N. (2015), Towards a Data Science Collaboratory. In: Fromont E., De Bie T., Leeuwen M. van (Eds.) Proceedings of Advances in Intelligent Data Analysis XIV (IDA 2015). no. LNCS 9385 Cham: Springer. IX-XXI.
- Kok J.N., Lamprecht A, Turner K.J. & Wolstencroft K.J (2014), Track Introduction: Scientific Workflows, LEVERAGING APPLICATIONS OF FORMAL METHODS, VERIFICATION AND VALIDATION: SPECIALIZED TECHNIQUES AND APPLICATIONS, PT II 8803: 404-406.
- Hettne KM, Dharuri H, Zhao J, Wolstencroft K, Belhajjame K, Soiland-Reyes S, Mina E, Thompson M, Cruickshank D, Verdes-Montenegro L, Garrido J, de Roure D, Corcho O, Klyne G, van Schouwen R, 't Hoen PA, Bechhofer S, Goble C & Roos M. (2014), Structuring research methods and data with the research object model: genomics workflows as a case study, Journal Biomedical Semantics 15(1): paper number 41.
- Wolstencroft K.J., Owen S., Krebs O., Mueller W. Nguyen Q., Snoep J.L. & Goble C. (2013), Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform. In: The Semantic Web-ISWC 2013.: Springer-Verlag. 212-227.
- Goble C, Bechhofer S & Wolstencroft K (2013), Semantic Web, Interoperability. In: Encyclopedia of Systems Biology.: Springer New York. 1921--1925.
- Wolstencroft K, Owen S, Horridge M, Jupp S, Krebs O, Snoep JL, Preez F, Mueller W, Stevens R & Goble CA (2013), Stealthy annotation of experimental biology by spreadsheets, Concurrency and Computation: Practice and Experience 25(4): 467-480.
- Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P & others (2013), The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud, Nucleic Acids Research 41(W1): W557--W561.
- Sansone Susanna-Assunta, Rocca-Serra Philippe, Field Dawn, Maguire Eamonn, Taylor Chris, Hofmann Oliver, Fang Hong, Neumann Steffen, Tong Weida, Amaral-Zettler Linda, Begley Kimberly, Booth Tim, Bougueleret Lydie, Burns Gully, Chapman Brad, Clark Tim, Coleman Lee-Ann, Copeland Jay, Das Sudeshna, de Daruvar Antoine, de Matos Paula, Dix Ian, Edmunds Scott, Evelo Chris T., Forster Mark J., Gaudet Pascale, Gilbert Jack, Goble Carole, Griffin Julian L., Jacob Daniel, Kleinjans Jos, Harland Lee, Haug Kenneth, Hermjakob Henning, Sui Shannan J. Ho, Laederach Alain, Liang Shaoguang, Marshall Stephen, McGrath Annette, Merrill Emily, Reilly Dorothy, Roux Magali, Shamu Caroline E., Shang Catherine A., Steinbeck Christoph, Trefethen Anne, Williams-Jones Bryn, Wolstencroft Katherine, Xenarios Ioannis & Hide Winston (2012), Toward interoperable bioscience data, NATURE GENETICS 44(2): 121-126.
- Hettne KM, Wolstencroft K, Belhajjame K, Goble CA, Mina E, Dharuri H, Roure DD, Verdes-Montenegro L, Garrido J & Roos M (2012), Best Practices for Workflow Design: How to Prevent Workflow Decay. In: SWAT4LS..
- David DCAW, ROURE D, GOBLE C, ROOS M & Wolstencroft K (2012), Opening new gateways to workflows for life scientists, 175: 131.
- Jupp S., Horridge M., Iannone L., Klein J., Owen S., Schanstra J., Wolstencroft K.J. & Stevens R. (2012), Populous: a tool for building OWL ontologies from templates, BMC bioinformatics 13((Suppl 1)): S5.
- Wolstencroft K, Owen S, Horridge M, Müller W, Bacall F, Snoep JL, Preez F, Nguyen Q, Krebs O & Goble CA (2012), RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets. In: EKAW.. 438-441.
- Wolstencroft K, Owen S, Goble C, Nguyen, Q, Krebs O & Muller W (2012), RightField: Semantic enrichment of Systems Biology data using spreadsheets. In: Proceedings 8th International Conference on E-science.: IEEE Computer Society. 1-8.
- Wolstencroft K, Owen S, Goble CA, Nguyen Q, Krebs O & Müller W (2012), RightField: Semantic enrichment of Systems Biology data using spreadsheets. In: eScience.. 1-8.
- Wolstencroft K (2012), The Taverna Workbench: Integrating and analysing biological and clinical data with computerised workflows, EMBnet. journal 18(B): p--18.
- Wolstencroft Katy, Owen Stuart, du Preez Franco, Krebs Olga, Mueller Wolfgang, Goble Carole & Snoep Jacky L. (2011), THE SEEK: A PLATFORM FOR SHARING DATA AND MODELS IN SYSTEMS BIOLOGY, METHODS IN ENZYMOLOGY 500: 629-655.
- Wolstencroft Katy, Owen Stuart, Horridge Matthew, Krebs Olga, Mueller Wolfgang, Snoep Jacky L., du Preez Franco & Goble Carole (2011), RightField: embedding ontology annotation in spreadsheets, BIOINFORMATICS 27(14): 2021-2022.
- Neudecker C, Schlarb S, Dogan ZM, Missier P, Sufi S, Williams A & Wolstencroft K (2011), An experimental workflow development platform for historical document digitisation and analysis. In: Proceedings of the 2011 workshop on historical document imaging and processing.. 161--168.
- Du Preez FB, Owen S, Wolstencroft K, Krebs O, Müller W, Goble C & Snoep JL (2011), OneStop: JWS Online’s access point to SBML, SBGN and MIRIAM compliant annotation: Nature Publishing Group.
- Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K & Stevens R (2011), Populous: A Tool for Populating an Ontology. In: ICBO..
- Krebs O, Wolstencroft K, Owen S, Mueller W, Goble C & Snoep JL (2011), The Just Enough Results Model (JERM) for Systems Biology Data, : 178.
- Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S & others (2010), BioCatalogue: a universal catalogue of web services for the life sciences, Nucleic Acids Research 38(suppl 2): W689--W694.
- Moeller S, Krabbenhoeft H, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C & Plessy C (2010), Community-driven computational biology with debian and taverna. In: BOSC 2010..
- Missier P, Wolstencroft K, Tanoh F, Li P, Bechhofer S, Belhajjame K, Pettifer S & Goble CA (2010), Functional Units: Abstractions for Web Service Annotations. In: SERVICES.. 306-313.
- Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Stevens R & Wolstencroft K (2010), Populous: A tool for populating ontology templates.
- Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Stevens R & Wolstencroft K (2010), Populous: A Tool for Populating Templates for OWL Ontologies.. In: SWAT4LS..
- Wolstencroft K, Horridge M, Owen S, Mueller W, Bacall F, Snoep J, Krebs O & Goble C (2010), RightField: Embedding Ontology Term Selection into Spreadsheets for the Annotation of Biological Data. In: 9th International Semantic Web Conference.. 141.
- Roure DD, Goble CA, Aleksejevs S, Bechhofer S, Bhagat J, Cruickshank D, Fisher P, Kollara N, Michaelides DT, Missier P, Newman DR, Ramsden M, Roos M, Wolstencroft K, Zaluska E & Zhao J (2010), The Evolution of myExperiment. In: eScience.. 153-160.
- Swertz MA, Velde vdKJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K & others (2010), XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments, Genome Biol 11(3): R27.
- Wassink IHC, Vet PE, Wolstencroft K, Neerincx PBT, Roos M, Rauwerda H & Breit TM (2009), Analysing Scientific Workflows: Why Workflows Not Only Connect Web Services. In: SERVICES I.. 314-321.
- Goderis A, Fisher P, Gibson A, Tanoh F, Wolstencroft K, Roure DD & Goble CA (2009), Benchmarking workflow discovery: a case study from bioinformatics, Concurrency and Computation: Practice and Experience 21(16): 2052-2069.
- Goble CA, Belhajjame K, Tanoh F, Bhagat J, Wolstencroft K, Stevens R, Nzuobontane E, McWilliam H, Laurent T & Lopez R (2009), BioCatalogue: a curated web service registry for the life science community Nature Precedings: Nature Publishing Group.
- Wolstencroft K, Fisher P, De Roure D & Goble C (2009), Scientific Workflows. In: Voss A., Vander Meer E., Fergusson D (Eds.) Research In a Connected World..
- Goble C, Wolstencroft K, Owen S, Aleksejevs S, Snoep J, Krebs O, Mueller W & Rojas I (2009), SysMO-DB: A pragmatic approach to sharing information amongst Systems Biology projects in Europe. In: Proceedings of the UK e-Science All Hand Meeting..
- Gibson A, Gamble M, Wolstencroft K, Oinn T, Goble CA, Belhajjame K & Missier P (2009), The data playground: An intuitive workflow specification environment, Future Generation Comp. Syst. 25(4): 453-459.
- Goble Carole, Stevens Robert, Hull Duncan, Wolstencroft Katy & Lopez Rodrigo (2008), Data curation process curationdata integration science, BRIEFINGS IN BIOINFORMATICS 9(6): 506-517.
- Smedley Damian, Swertz Morris A., Wolstencroft Katy, Proctor Glenn, Zouberakis Michael, Bard Jonathan, Hancock John M. & Schofield Paul (2008), Solutions for data integration in functional genomics: a critical assessment and case study, BRIEFINGS IN BIOINFORMATICS 9(6): 532-544.
- Belhajjame K, Goble C, Tanoh F, Bhagat J, Wolstencroft K, Stevens R, Nzuobontane E, McWilliam H, Laurent T & Lopez R (2008), Biocatalogue: A curated web service registry for the life science community, .
- Swertz MA, Smedley D, Wolstencroft K, Alberts R, Zouberakis M, Aidinis V, Schughart K, Schofield PN & Jansen RC (2008), in volume 8th IEEE International Conference on BioInformatics and BioEngineering, 2008. BIBE 2008, .
- Belhajjame K, Wolstencroft K, Corcho Ó, Oinn T, Tanoh F, Williams A & Goble CA (2008), Metadata Management in the Taverna Workflow System. In: CCGRID.. 651-656.
- Swertz MA, Smedley D, Wolstencroft K, Alberts R, Zouberakis M, Aidinis V, Schughart K, Schofield PN & Jansen RC (2008), Towards dynamic database infrastructures for mouse genetics. In: BIBE.. 1-7.
- Pettifer Steve, Wolstencroft Katy, Alper Pinar, Attwood Teresa, Coletta Alain, Goble Carole, Li Peter, McDermott Philip, Marsh James, Oinn Tom, Sinnott James & Thorne David (2007), (my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences, 4544: 59-70.
- Fisher Paul, Hedeler Cornelia, Wolstencroft Katherine, Hulme Helen, Noyes Harry, Kemp Stephen, Stevens Robert & Brass Andrew (2007), A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis, Nucleic Acids Research 35(16): 5625-5633.
- Stevens Robert, Aranguren Mikel Egana, Wolstencroft Katy, Sattler Ulrike, Drummond Nick, Horridge Matthew & Rector Alan (2007), Using OWL to model biological knowledge, INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES 65(7): 583-594.
- Wolstencroft K, Stevens R & Haarslev V (2007), Applying OWL reasoning to genomic data. In: Semantic Web.: Springer US. 225--248.
- Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp S, Stevens R & Brass A (2007), A systematic strategy for large-scale analysis of genotype--phenotype correlations: identification of candidate genes involved in African trypanosomiasis, Nucleic Acids Research 35(16): 5625--5633.
- Fisher P., Hedeler C., Wolstencroft K.J., Hulme H., Noyes H., Kemp S., Stevens R. & Brass A. (2007), A systematic strategy for the discovery of candidate genes responsible for phenotypic variation, BMC bioinformatics 8((Suppl 8)): P7.
- Goble C, Wolstencroft K, Goderis A, Hull D, Zhao J, Alper P, Lord P, Wroe C, Belhajjame K, Turi D & others (2007), Knowledge discovery for biology with Taverna. In: Semantic Web.: Springer US. 355--395.
- Gibson A, Wolstencroft K & Stevens R (2007), Promotion of Ontological Comprehension: Exposing Terms and Metadata with Web 2.0. In: CKC..
- Gibson A, Gamble M, Wolstencroft K, Oinn T & Goble CA (2007), The Data Playground: An Intuitive Workflow Specification Environment. In: eScience.. 59-68.
- Wolstencroft K, Alper P, Hull D, Wroe C, Lord PW, Stevens RD & Goble CA (2007), The my Grid ontology: bioinformatics service discovery, International Journal of Bioinformatics Research and Applications 3(3): 303--325.
- Wolstencroft K.J. (2007), Third International Conference on e-Science and Grid Computing, e-Science 2007, 10-13 December 2007, Bangalore, India: IEEE Computer Society.
- Goble C, Wolstencroft K, Goderis A, Hull D, Zhao J, Alper P, Lord P, Belhajjame K, Turi D, Stevens R & others (2006), Knowledge Discovery for in silico Experiments with Taverna, Semantic web: revolutionizing knowledge discovery in the life sciences .
- Wolstencroft K, Lord P, Tabernero L, Brass A & Stevens R (2006), Protein classification using ontology classification, BIOINFORMATICS 22(14): e530--e538.
- Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P & Oinn T (2006), Taverna: a tool for building and running workflows of services, Nucleic Acids Research 34(suppl 2): W729--W732.
- Rose C, Turi D, Williams A, Wolstencroft K & Taylor CJ (2006), Web Services for the DDSM and Digital Mammography Research. In: Digital Mammography / IWDM.. 376-383.
- Wolstencroft K, McEntire R, Stevens R, Tabernero L & Brass A (2005), Constructing ontology-driven protein family databases, BIOINFORMATICS 21(8): 1685-1692.
- Wolstencroft K, Brass A, Horrocks I, Lord PW, Sattler U, Turi D & Stevens R (2005), A Little Semantic Web Goes a Long Way in Biology. In: International Semantic Web Conference.. 786-800.
- Wolstencroft K, Stevens R & Haarslev V (2005), Chapter\# APPLYING OWL REASONING TO GENOMIC DATA, Semantic web: revolutionizing knowledge discovery in the life sciences .
- Taylor C, Rose C, Turi D, Williams A & Wolstencroft K (2005), MIAS-Grid: An e-Science Workbench for Medical Images and Signals Research, : 59.
- Wolstencroft K (2005), Ontological methods for structuring and managing protein family resources (PhD thesis. The University of Manchester).
- Wolstencroft K, Oinn TM, Goble CA, Ferris J, Wroe C, Lord PW, Glover K & Stevens R (2005), Panoply of Utilities in Taverna. In: e-Science.. 156-162.
- Wolstencroft K, Stevens R, Tabernero L & Brass A (2005), PhosphaBase: An ontology-driven database resource for protein phosphatases, 58(2): 290--294.
- Wolstencroft K, Lord P, Tabernero L, Brass A & Stevens R (2005), Using ontology reasoning to classify protein phosphatases. In: 8th Annual Bio-Ontologies Meeting.. 2005.
- Rose C, Turi D, Williams AR, Wolstencroft K & Taylor C (2005), Web Services for Digital Mammography Research. In: Proceedings of Medical Image Understanding and Analysis 2.. 196--200.
No relevant ancillary activities