Federating Heterogeneous Biological Resources on the Web: A Case Study on TRP Channel Ontology Construction

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8388)


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.


Ontology SPARQL TRP channel 


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    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)CrossRefGoogle Scholar
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    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)CrossRefGoogle Scholar
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    TRIP Database, http://trpchannel.org/
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    OBO Relation Ontology, http://obofoundry.org/ro/

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Biomedical Knowledge Engineering Lab. (BIKE)Seoul National UniversitySeoulKorea
  2. 2.Dental Research Institute, School of DentistrySeoul National UniversitySeoulKorea
  3. 3.Department of Physiology, College of MedicineSeoul National UniversitySeoulKorea

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