MUTATIONAL DATA LOADING ROUTINES FOR HUMAN GENOME DATABASES - The BRCA1 Case

Matthijs van der Kroon, Ignacio Lereu Ramirez, Ana M. Levin, Óscar Pastor, Sjaak Brinkkemper

Abstract

The last decades a large amount of research has been done in the genomics domain which has and is generating terabytes, if not exabytes, of information stored globally in a very fragmented way. Different databases use different ways of storing the same data, resulting in undesired redundancy and restrained information transfer. Adding to this, keeping the existing databases consistent and data integrity maintained is mainly left to human intervention which in turn is very costly, both in time and money as well as error prone. Identifying a fixed conceptual dictionary in the form of a conceptual model thus seems crucial. This paper presents an effort to integrating the mutational data from the established genomic data source HGMD into a conceptual model driven database HGDB, thereby providing useful lessons to improve the already existing conceptual model of the human genome.

References

  1. Ashburner, M., Ball, C., and Blake, J. (2000). Gene ontology: tool for the unification of biology. Nature genetics, 25(1):25-30.
  2. Langston, A., Stanford, J., Wicklund, K., Thompson, J., Blazej, R., and Ostrander, E. (1996). Germ-line brca1 mutations in selected men with prostate cancer. American Journal of Human Genetics, 58:881-885.
  3. Okayama, T., Tamura, T., Gojobori, T., Tateno, Y., Ikeo, K., Miyazaki, S., Fukami-Kobayashi, K., and Sugawara, H. (1998). Formal design and implementation of an improved ddbj dna database with a new schema and object-oriented library. Bioinformatics, 14(6):472.
  4. Panguluri, R., Dunston, G., Brody, L., Modali, R., Utley, K., Adams-Campbell, L., Day, A., and WhitfieldBroome, C. (1999). Brca1 mutations in african americans. Human Genetics, 105(1-2):28-31.
  5. Pastor, O. (2008). Conceptual modeling meets the human genome. In Conceptual modeling - ER 2008, volume 5231 of Lecture Notes in Computer Science, pages 1- 11. Springer-Verlag Berling Heidelberg.
  6. Pastor, O., Levin, A., Casamayor, J., Celma, M., Virrueta, A., and Eraso, L. (2009). The Evolution of Conceptual Modeling, chapter Model driven-based engineering applied to the interpretation of the human genome. Springer-Verlag.
  7. Pastor, O., Levin, A., Celma, M., Casamayor, J., Schattka, L. E., Villanueva, M., and Perez-Alonso, M. (2010a). Proceedings of the IVth Int. Conference on Research Challenges in Information Science, chapter Enforcing Conceptual Modeling to Improve the Understanding of Human Genome. IEEE Press.
  8. Pastor, O., Pastor, M., and Burriel, V. (2010b). Conceptual modeling of human genome mutations: a dichotomy between what we have and what we should have. In Proceedings of Bioinformatics 2010, pages 160-166. BIOSTEC Bioinformatics.
  9. Paton, N., Khan, S., Hayes, A., Moussouni, F., Brass, A., Eilbeck, K., Goble, C., Hubbard, S., and Oliver, S. (2000). Conceptual modeling of genomic information. Bioinformatics, 16(6):548-557.
  10. Smith, T., Lee, M., Jerome, N., McEuen, M., Taylor, M., Hood, L., and King, M. (1996). Complete genomic sequence and analysis of 117 kb of human dna containing the gene brca1. Genome Research, 6:1029- 1049.
  11. van der Kroon, M., Ramirez, I. L., Levin, A., Pastor, O., and Brinkkemper, S. (2009). Mutational data loading routines for human genome databases: the brca1 case. Report UUCS2009020, Utrecht University.
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Paper Citation


in Harvard Style

van der Kroon M., Lereu Ramirez I., M. Levin A., Pastor Ó. and Brinkkemper S. (2011). MUTATIONAL DATA LOADING ROUTINES FOR HUMAN GENOME DATABASES - The BRCA1 Case . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 266-269. DOI: 10.5220/0003130902660269


in Bibtex Style

@conference{bioinformatics11,
author={Matthijs van der Kroon and Ignacio Lereu Ramirez and Ana M. Levin and Óscar Pastor and Sjaak Brinkkemper},
title={MUTATIONAL DATA LOADING ROUTINES FOR HUMAN GENOME DATABASES - The BRCA1 Case},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={266-269},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003130902660269},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - MUTATIONAL DATA LOADING ROUTINES FOR HUMAN GENOME DATABASES - The BRCA1 Case
SN - 978-989-8425-36-2
AU - van der Kroon M.
AU - Lereu Ramirez I.
AU - M. Levin A.
AU - Pastor Ó.
AU - Brinkkemper S.
PY - 2011
SP - 266
EP - 269
DO - 10.5220/0003130902660269