Federating heterogeneous biological resources on the web: A case study on TRP channel ontology construction

Se Jin Nam; Jinhyun Ahn; Jin Muk Lim; Jae Hong Eom; Ju Hong Jeon; Hong Gee Kim

doi:10.1007/978-3-319-06826-8_9

Federating heterogeneous biological resources on the web: A case study on TRP channel ontology construction

Se Jin Nam, Jinhyun Ahn, Jin Muk Lim, Jae Hong Eom, Ju Hong Jeon, Hong Gee Kim

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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.

Original language	English
Title of host publication	Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers
Publisher	Springer Verlag
Pages	103-109
Number of pages	7
ISBN (Print)	9783319068251
DOIs	https://doi.org/10.1007/978-3-319-06826-8_9
State	Published - 2014
Event	3rd Joint International Semantic Technology Conference, JIST 2013 - Seoul, Korea, Republic of Duration: 28 Nov 2013 → 30 Nov 2013

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	8388 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	3rd Joint International Semantic Technology Conference, JIST 2013
Country/Territory	Korea, Republic of
City	Seoul
Period	28/11/13 → 30/11/13

Keywords

Ontology
SPARQL
TRP channel

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/978-3-319-06826-8_9

Cite this

Nam, S. J., Ahn, J., Lim, J. M., Eom, J. H., Jeon, J. H., & Kim, H. G. (2014). Federating heterogeneous biological resources on the web: A case study on TRP channel ontology construction. In Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers (pp. 103-109). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8388 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-06826-8_9

Nam, Se Jin ; Ahn, Jinhyun ; Lim, Jin Muk et al. / Federating heterogeneous biological resources on the web : A case study on TRP channel ontology construction. Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers. Springer Verlag, 2014. pp. 103-109 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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.",

keywords = "Ontology, SPARQL, TRP channel",

author = "Nam, {Se Jin} and Jinhyun Ahn and Lim, {Jin Muk} and Eom, {Jae Hong} and Jeon, {Ju Hong} and Kim, {Hong Gee}",

note = "Funding Information: 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). ; null ; Conference date: 28-11-2013 Through 30-11-2013",

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language = "English",

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series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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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 Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8388 LNCS, Springer Verlag, pp. 103-109, 3rd Joint International Semantic Technology Conference, JIST 2013, Seoul, Korea, Republic of, 28/11/13. https://doi.org/10.1007/978-3-319-06826-8_9

Federating heterogeneous biological resources on the web : A case study on TRP channel ontology construction. / Nam, Se Jin; Ahn, Jinhyun; Lim, Jin Muk et al.

Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers. Springer Verlag, 2014. p. 103-109 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8388 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Federating heterogeneous biological resources on the web

AU - Nam, Se Jin

AU - Ahn, Jinhyun

AU - Lim, Jin Muk

AU - Eom, Jae Hong

AU - Jeon, Ju Hong

AU - Kim, Hong Gee

N1 - Funding Information: 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).

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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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KW - SPARQL

KW - TRP channel

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AN - SCOPUS:84902594851

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers

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ER -

Nam SJ, Ahn J, Lim JM, Eom JH, Jeon JH, Kim HG. Federating heterogeneous biological resources on the web: A case study on TRP channel ontology construction. In Semantic Technology - Third Joint International Conference, JIST 2013, Revised Selected Papers. Springer Verlag. 2014. p. 103-109. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-06826-8_9

Federating heterogeneous biological resources on the web: A case study on TRP channel ontology construction

Abstract

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Keywords

UN SDGs

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