Abstract
TRP (Transient receptor potential) channel is a biological component which could be of factors in severe diseases such as heart attack and cancer. In order for researchers to easily search for protein-protein interactions for mammalian TRP channel, TRIP Database was created. However, TRIP Database does not contain information about proteins in details, making researchers in turn visit other database services such as UniProt and PDB. In this paper, we propose a semantic TRP Ontology made from TRIP Database, allowing users to be given the collected contents from other relevant databases as well using a single request. As a practical scenario, we generate RDF triples from TRIP Database by referring to TRP Ontology designed to have links with UniProt. A federated way of collecting contents from two different services is proposed.
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References
Shin, Y.-C., Shin, S.-Y., So, I., Kwon, D., Jeon, J.-H.: TRIP Database: a manually curated database of protein–protein interactions for mammalian TRP channels. Nucleic Acids Re. 39(Suppl. 1), D356–D361 (2011)
Shin, Y.-C., Shin, S.-Y., Chun, J.N., Cho, H.S., Lim, J.M., Kim, H.-G., So, I., Kwon, D., Jeon, J.-H.: TRIP Database 2.0: a manually curated information hub for accessing TRP channel interaction network. PloS ONE 7(10), e47165 (2012)
SPARQL 1.1, http://www.w3.org/TR/sparql11-query/
UniProt, http://www.UniProt.org/
TRIP Database, http://trpchannel.org/
OBO Relation Ontology, http://obofoundry.org/ro/
Acknowledgement(s)
This work was supported by the Industrial Strategic Technology Development Program (10044494, WiseKB: Big data based self-evolving knowledge base and reasoning platform) funded by the Ministry of Science, ICT & Future Planning (MSIP, Korea).
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© 2014 Springer International Publishing Switzerland
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Nam, SJ., Ahn, J., Lim, JM., Eom, JH., Jeon, JH., Kim, HG. (2014). Federating Heterogeneous Biological Resources on the Web: A Case Study on TRP Channel Ontology Construction. In: Kim, W., Ding, Y., Kim, HG. (eds) Semantic Technology. JIST 2013. Lecture Notes in Computer Science(), vol 8388. Springer, Cham. https://doi.org/10.1007/978-3-319-06826-8_9
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DOI: https://doi.org/10.1007/978-3-319-06826-8_9
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