Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project

E Antezana; W {Blondé}; M {Egaña}; A Rutherford; R Stevens; B {De Baets}; V Mironov; M Kuiper; A Burger; A Paschke; P Romano; A Splendiani

Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project

E Antezana, W {Blondé}, M {Egaña}, A Rutherford, R Stevens, B {De Baets}, V Mironov, M Kuiper, A Burger (Editor), A Paschke (Editor), P Romano (Editor), A Splendiani (Editor)

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

Abstract

The application of Semantic Web technologies in the life sci- ences for data integration is still nascent. We have recently built Bio- Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio- Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider accep- tance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.

Original language	English
Title of host publication	{Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}
Editors	A Burger, A Paschke, P Romano, A Splendiani
Publisher	RWTH Aachen University
Volume	435
Publication status	Published - 2008

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Name	CEUR Workshop Proceedings

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Antezana, E., {Blondé}, W., {Egaña}, M., Rutherford, A., Stevens, R., {De Baets}, B., Mironov, V., Kuiper, M., Burger, A. (Ed.), Paschke, A. (Ed.), Romano, P. (Ed.), & Splendiani, A. (Ed.) (2008). Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. In A. Burger, A. Paschke, P. Romano, & A. Splendiani (Eds.), {Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}} (Vol. 435). (CEUR Workshop Proceedings). RWTH Aachen University. http://ceur-ws.org/Vol-435/paper04.pdf

Antezana, E ; {Blondé}, W ; {Egaña}, M et al. / Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. {Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}. editor / A Burger ; A Paschke ; P Romano ; A Splendiani. Vol. 435 RWTH Aachen University, 2008. (CEUR Workshop Proceedings).

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title = "Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project",

abstract = "The application of Semantic Web technologies in the life sci- ences for data integration is still nascent. We have recently built Bio- Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio- Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider accep- tance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.",

author = "E Antezana and W {Blond{\'e}} and M {Ega{\~n}a} and A Rutherford and R Stevens and {{De Baets}}, B and V Mironov and M Kuiper and A Burger and A Paschke and P Romano and A Splendiani",

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volume = "435",

series = "CEUR Workshop Proceedings",

publisher = "RWTH Aachen University",

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Antezana, E, {Blondé}, W, {Egaña}, M, Rutherford, A, Stevens, R, {De Baets}, B, Mironov, V, Kuiper, M, Burger, A (ed.), Paschke, A (ed.), Romano, P (ed.) & Splendiani, A (ed.) 2008, Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. in A Burger, A Paschke, P Romano & A Splendiani (eds), {Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}. vol. 435, CEUR Workshop Proceedings, RWTH Aachen University. <http://ceur-ws.org/Vol-435/paper04.pdf>

Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. / Antezana, E; {Blondé}, W; {Egaña}, M et al.
{Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}. ed. / A Burger; A Paschke; P Romano; A Splendiani. Vol. 435 RWTH Aachen University, 2008. (CEUR Workshop Proceedings).

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

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T1 - Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project

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AU - {Egaña}, M

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AU - Stevens, R

AU - {De Baets}, B

AU - Mironov, V

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A2 - Burger, A

A2 - Paschke, A

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N2 - The application of Semantic Web technologies in the life sci- ences for data integration is still nascent. We have recently built Bio- Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio- Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider accep- tance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.

AB - The application of Semantic Web technologies in the life sci- ences for data integration is still nascent. We have recently built Bio- Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio- Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider accep- tance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.

M3 - Conference contribution

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T3 - CEUR Workshop Proceedings

BT - {Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}

PB - RWTH Aachen University

ER -

Antezana E, {Blondé} W, {Egaña} M, Rutherford A, Stevens R, {De Baets} B et al. Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project. In Burger A, Paschke A, Romano P, Splendiani A, editors, {Proceedings of the Workshop on Semantic Web Applications and Tools for the Life Sciences: {(SWAT4LS'08)}}. Vol. 435. RWTH Aachen University. 2008. (CEUR Workshop Proceedings).

Structuring the life science resourceome for Semantic Systems Biology: lessons from the BioGateway project

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