Dr Alejandra Gonzalez-Beltran
PhD

Research Lecturer

alejandra.gonzalezbeltran@oerc.ox.ac.uk

 

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Bio  | Selected Publications | Recent talks and meetings | News  | Scholarly Service | Teaching

Bio     Back to Top

Alejandra is a Research Lecturer in the Oxford e-Research Centre (OeRC), University of Oxford, UK, working in the Data Sharing Infrastructure team. The main projects are the Investigation/Study/Assay (ISA) infrastructure ( http://www.isa-tools.org ) and the BioSharing catalogue ( http://biosharing.org ).

Before joining OeRC, Alejandra was Senior Research Associate in Computational and Systems Medicine at University College London (UCL). At UCL, she was previously at the Department of Computer Science , working on knowledge management for cancer research data.

She was awarded a PhD in Computer Science from Queen's University Belfast, UK and a Licentiateship (5-year degree with final research project) from Universidad Nacional de Rosario, Argentina .

Selected News             Back to Top

  • See the SOAPdenovo2 case study , relying on Galaxy workflows and data models such as ISA, RO and nanpublications.
  • See the STATistic Ontology (STATO) website
  • See blog post by Scott Edmunds (GigaScience) about our collaboration presented at the ISMB workshop on Digital Publishing beyond the PDF
  • Winner of the ORCID codefest. See blog post in  Elsevier Connect .

Selected Scholarly Service       Back to Top

  • Bio-Ontologies 2015, Programme Committee member
  • Co-chair of 'Big data in healthcare' session of the UK-Brazil Frontiers of Engineering Symposium organised by the Royal Academy of Engineering (RAEng) and the São Paulo Research Foundation (FAPESP).
  • Programme Committee Member of the 4th International Workshop on Semantic Digital Archives (SDA 2014)
  • Programme Committee Member of the  XV Argentine Symposium on Artificial Intelligence (ASAI 2014)
  • Member of the Scientific Committee of the 4th Argentine Congress on Bioinformatics and Computational Biology and the 4th International Conference of the Iberoamerican Society of Bioinformatics , Rosario, Argentina. October 2013.
  • Member of the Informatics Advisory Board for the Cancer Research UK Stratified Medicine programme

Teaching         Back to Top

  • Data Carpentry instructor at the First UK Data Carpentry workshop. See details here.
  • Course at the European Bioinformatics Institute on "Metagenomics Bioinformatics" , September 2014. Find the training material here .
  • Course at the European Bioinformatics Institute on "Metagenomics: Managing, Analysing and Visualising Data" , September 2013. Find the training material here .

For my previous teaching experience, please visit my old website .

Selected publications     Back to Top

See also DBLP , Google Scholar , Microsoft Academic Search  or PubMed .

Alejandra Gonzalez-Beltran, Peter Li, Jun Zhao, Maria Susana Avila-Garcia, Marco Roos, Mark Thompson Eelke van der Horst, Rajaram Kaliyaperumal, Ruibang Luo, Tin-Lap Lee,Tak-wah Lam, Scott C. Edmunds, Susanna-Assunta Sansone, Philippe Rocca-Serra.  "From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics". PLoS ONE. DOI: 10.1371/journal.pone.0127612

Philippe Rocca-Serra, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna Sansone, Alejandra Gonzalez-Beltran. "Modeling microbial community and biodiversity assay with OBO Foundry ontologies OBI and PCO: the interoperability gains of a modular approach". Database 2015. doi: 10.1093/database/bau132

Alejandra Gonzalez-Beltran, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra. linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinformatics 2014.

 

Risa-workflow.png Alejandra Gonzalez-Beltran , Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra. The Risa R/Bioconductor package: integrative data analysis   from experimental metadata and back again. BMC Bioinformatics 2014, 15 (Suppl 1):S11 [ HTML ]


  • Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra Gonzalez-Beltran , Christopher Hunter,  Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Masien, Alex Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radhakrishnan, Philippe Rocca-Serra, Maxim Scheremetjew, Peter Sterk, Daniel Vaughan, Guy Cochrane, Dawn Field and Susanna-Assunta Sansone. EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Research 2013. [ HTML ]
  • Alejandra Gonzalez-Beltran , Eamonn Maguire, Pavlos Georgiou, Susanna-Assunta Sansone, Philippe Rocca-Serra. Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data. NETTAB 2013 . [ HTML ]
  • Eamonn Maguire,  Alejandra Gonzalez-Beltran , Philippe Rocca-Serra, Susanna-Assunta Sansone. "Reproducible, Open Data Science in the Life Sciences ".  Digital Research 2013 , 9-11 September 2013, Oxford, UK. See Eamonn's slides following  this link .
  • Eamonn Maguire, Alejandra Gonzalez-Beltran,  Patricia Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra  OntoMaton:  Google spreadsheets meet NCBO BioPortal services.     4th   International Conference on Biomedical Ontologies (ICBO) 2013 Highlights Track. Montreal, Canada. [ HTML ]

Metabolights-database Reza M. Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Susanna-Assunta Sansone and Christoph Steinbeck   The MetaboLights repository: curation challenges in metabolomics. Database 2013. [ Abstract ][ HTML ]   [ PDF ]

 

OntoMaton Eamonn Maguire,  Alejandra Gonzalez-Beltran , Patricia L. Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets  Bioinformatics 2013.   [ DOI ][ PDF ]



Metabolights-nar Kenneth Haug, Reza M. Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire,  Alejandra González-Beltrán , Susanna-Assunta Sansone, Jules L. Griffin, Christoph Steinbeck.  MetaboLights: An open-access general-purpose repository for Metabolomics studies and associated meta-data   Nucleic Acids Research (2013) . (available online )

 

 

  • Shannan Ho Sui, Emily Merrill, Nils Gehlenborg, Psalm Haseley, Ilya Sytchev, Richard Park, Philippe Rocca-Serra, Stephane Corlosquet,  Alejandra Gonzalez-Beltran , Eamonn Maguire, Oliver Hofmann, Peter Park, Sudeshna Das, Susanna-Assunta Sansone, Winston Hide. The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework . AMIA Summit on Translational Bioinformatics (TBI) 2013.  http://proceedings.amia.org/T2013-nav/

nettab2012 Alejandra González-Beltrán,  Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone. The open source ISA software suite and its international user community: knowledge management of experimental data EMBnet.journal, Bioinformatics in Action, NETTAB 2012. (available online)

 

Philippe Rocca-Serra, Eamonn Maguire, Chris Taylor, Dawn Field, Timo Wittenberger, Annapaola Santarsiero, Alejandra Gonzalez-Beltran, Susanna-Assunta Sansone. Investigation-Study-Assay, a toolkit for standardizing data capture and sharing. In book "Open Source Software in Life Science Research: Practical Solutions to Common Challenges in Pharmaceutical Industry and Beyond". Elsevier 2012. (available online)

 

GIATE Alejandra González-Beltrán , May Yong, Gairin Dancey, Richard Begent

Guidelines for Information About Therapy Experiments: A proposal on best practice for recording experimental data on cancer therapy
BMC Research Notes  2012 (available online )
 
 
 
 
 
 
New Biotechnology 2011 May Yee Yong,  Alejandra González-Beltrán , Richard Begent
  Establishing a knowledge trail from molecular experiments to clinical trials
  New Biotechnology (2011)   [ HTML ][ PDF ]
 
 
 
 
 
 

COnQueST Alejandra González-Beltrán , Ben Tagger, Anthony Finkelstein

 
Federated Ontology-based Queries over Cancer Data
 
BMC Bioinformatics Volume 13 Supplement 1, Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010.  (available online )
 
 
 
  • Best paper award: Alejandra González-Beltrán , Ben Tagger, Anthony Finkelstein. Ontology-based queries over cancer data . In Adrian Paschke, Albert Burger, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS 2010), Berlin, Germany, December 8-10, 2010. [ PDF ]

amia2010

 
 
 
Joshua Phillips,  Alejandra González-Beltrán , Anthony Finkelstein, Jyotishman Pathak. Exposing caGrid Data Services as Linked Data. In the proceedings of the  2010 AMIA Summit on Clinical Research Informatics (AMIA CRI 2010). San Francisco, CA, USA. March 12-13, 2010. [ PDF ]
 
 
 
  • Carsten Kettner, Dawn Field, Susanna Sansone, Chris Taylor, Jan Aerts, Nigel Binns, Andrew Black, Cedrik M. Britten, Ario de Marco, Jennifer Fostel, Pascale Gaudet,  Alejandra González-Beltrán , Nigel Hardy, Jan Hellmans, Hennin Hermjakob, Nick Juty, Jim Leebens-Mack, Eamonn Maguire, Steffen Neumann, Sandra Orchard, Helen Parkinson, William Piel, Shoba Ranganathan, Philippe Rocca-Serra, Annapaola Santarsiero, David Shotton, Peter Sterk, Andreas Untergasser, Patricia L. Whetzel   Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop  Standards in Genomic Sciences, Vol 3, No 3 (2010)           [ HTML ] [ PDF ]

 Semantic web datawarehousing for caGrid James P. McCusker, Joshua A. Phillips,  Alejandra González-Beltrán , Anthony Finkelstein, Michael Krauthammer  

“Semantic web data warehousing for caGrid” 
BMC Bioinformatics, Vol 10, Supp 10, 2009.
[ PDF ] [ HTML ]
 
 
  • Alejandra González-Beltrán , Anthony Finkelstein, J. Max Wilkinson, Jeff Kramer. Domain Concept-Based Queries for Cancer Research Data Sources . Proceedings of the 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2009) on August 3-4, 2009 in Albuquerque, NM, USA. [ PDF ]


  • Giulio Napolitano,  Alejandra González-Beltrán , Colin Fox, A Marshall, Anthony Finkelstein, P. McCarron. Biomedical Ontologies and Grid Computing As New Resources for Cancer Registries . In Proceedings of HealthInf (International Conference on Health Informatics), Porto, Portugal, 14-17 January, 2009. [ PDF ]

STG-rangequeries2

Alejandra González-Beltrán , Peter Milligan, Paul Sage
“Range queries over skip tree graphs”  
Journal of Computer Communications, Volume 31 Issue 2, pp 358-374, February 2008. 

Special Issue: Foundation of Peer-to-Peer Computing. 

[ DOI ][ PDF ]

 
 
  • Alejandra González-Beltrán , Paul Sage, Peter Milligan.  Skip Tree Graph: a Distributed and Balanced Search Tree for Peer-to-Peer Networks . Proceedings of IEEE International Conference on Communication (ICC 2007). Glasgow, UK, 24th June - 28th June 2007 [ DOI ][ PDF ]
  • Alejandra González-Beltrán , Peter Milligan, Paul Sage.  Heterogeneity-Aware Distributed Access Structure . Proceedings of Fifth IEEE International Conference on Peer-to-Peer Computing (P2P 2005). Konstanz, Germany, 31th August - 2th September 2005. [ DOI ][ PDF ]

Recent talks and meetings      Back to Top The slides from my talks are available on SlideShare: http://www.slideshare.net/agbeltran/ Also, see some of the slides and posters below.

        • EBI Metagenomics Bioinfomatics Course, September 2014, Hinxton, UK
Metagenomic Data Provenance and Management using the ISA infrastructure --- overview, implementation patterns & software tools from Alejandra Gonzalez-Beltran

 

        • ISBM Workshop 2014, Boston, USA
ISMB Workshop 2014 from Alejandra Gonzalez-Beltran
      • BioMedBridges Workshop 2014, Amsterdam, The Netherlands
BioSharing.org - mapping the landscape of community standards, databases, data policies and their interrelations from Alejandra Gonzalez-Beltran
      • UKON 2014, Birmingham, UK
UKON 2014 from Alejandra Gonzalez-Beltran
    • 4A2B2C 2013, October 29th, 2013, Rosario, Argentina
4A2B2C-2013 from Alejandra Gonzalez-Beltran
    • NETTAB 2013, October 18th, 2013, Venice Lido, Italy
NETTAB 2013 from Alejandra Gonzalez-Beltran
  • OpenTox Europe, September 30th, 2013, Mainz, Germany
OpenTox Europe 2013 from Alejandra Gonzalez-Beltran
 
  • 4th International Conference on Biomedical Ontology 2013
Ontomaton icbo2013-alternative order-t_wv3 from Philippe Rocca-Serra

 

  • Biocuration, 2013, Cambridge, UK.
 
  • Beyond the PDF 2, 2013, Amsterdam, The Netherlands.
 
Beyond the PDF 2, 2013 from Alejandra Gonzalez-Beltran
 
  • CSHALS 2013, Cambridge, MA, USA.
 
CSHALS 2013 from Alejandra Gonzalez-Beltran
  • NETTAB 2012, Como, Italy.
 
NETTAB 2012 from Alejandra Gonzalez-Beltran
  • Drug Discovery, ELRIG 2012
Drug Discovery- ELRIG -2012 from Alejandra Gonzalez-Beltran

 

  • Web Valley School, 2012, Italy.
    • Website:  http://webv.fbk.eu/
    • Blog: http://dashnanowebgis.blog.com/collaborators/

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