Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-20358
Full metadata record
DC FieldValueLanguage
dc.contributor.authorSima, Ana-Claudia-
dc.contributor.authorDessimoz, Christophe-
dc.contributor.authorStockinger, Kurt-
dc.contributor.authorZahn-Zabal, Monique-
dc.contributor.authorMendes de Farias, Tarcisio-
dc.date.accessioned2020-08-17T08:37:52Z-
dc.date.available2020-08-17T08:37:52Z-
dc.date.issued2020-08-
dc.identifier.issn2046-1402de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/20358-
dc.description.abstractThe increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple data sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the equivalent SPARQL constructs required to benefit from this data - in particular, recursive property paths. In this article, we provide a hands-on introduction to querying evolutionary data across several data sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different data sources can be compared, through the use of federated SPARQL queries.de_CH
dc.language.isoende_CH
dc.publisherFaculty of 1000de_CH
dc.relation.ispartofF1000Researchde_CH
dc.rightshttp://creativecommons.org/licenses/by/4.0/de_CH
dc.subjectComparative Genomicsde_CH
dc.subjectOrthologyde_CH
dc.subjectResource Description Framework (RDF)de_CH
dc.subjectSPARQLde_CH
dc.subjectSequence Homologyde_CH
dc.subject.ddc005: Computerprogrammierung, Programme und Datende_CH
dc.titleA hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQLde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementSchool of Engineeringde_CH
zhaw.organisationalunitInstitut für Informatik (InIT)de_CH
dc.identifier.doi10.12688/f1000research.21027.2de_CH
dc.identifier.doi10.21256/zhaw-20358-
dc.identifier.pmid32612807de_CH
zhaw.funding.euNode_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.start1822de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume8de_CH
zhaw.publication.reviewOpen peer reviewde_CH
zhaw.funding.snf167149de_CH
zhaw.webfeedDatalabde_CH
zhaw.webfeedInformation Engineeringde_CH
zhaw.webfeedZHAW digitalde_CH
zhaw.funding.zhawSNF NRP 75 "Big Data": Bio-SODA - Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Datade_CH
zhaw.author.additionalNode_CH
zhaw.display.portraitYesde_CH
Appears in collections:Publikationen School of Engineering

Files in This Item:
File Description SizeFormat 
2020_Sima_A_hands-on_introduction_to_querying_evolutionary_relationships_F1000Research.pdf1.1 MBAdobe PDFThumbnail
View/Open
Show simple item record
Sima, A.-C., Dessimoz, C., Stockinger, K., Zahn-Zabal, M., & Mendes de Farias, T. (2020). A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. F1000Research, 8, 1822. https://doi.org/10.12688/f1000research.21027.2
Sima, A.-C. et al. (2020) ‘A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL’, F1000Research, 8, p. 1822. Available at: https://doi.org/10.12688/f1000research.21027.2.
A.-C. Sima, C. Dessimoz, K. Stockinger, M. Zahn-Zabal, and T. Mendes de Farias, “A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL,” F1000Research, vol. 8, p. 1822, Aug. 2020, doi: 10.12688/f1000research.21027.2.
SIMA, Ana-Claudia, Christophe DESSIMOZ, Kurt STOCKINGER, Monique ZAHN-ZABAL und Tarcisio MENDES DE FARIAS, 2020. A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. F1000Research. August 2020. Bd. 8, S. 1822. DOI 10.12688/f1000research.21027.2
Sima, Ana-Claudia, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, and Tarcisio Mendes de Farias. 2020. “A Hands-on Introduction to Querying Evolutionary Relationships across Multiple Data Sources Using SPARQL.” F1000Research 8 (August): 1822. https://doi.org/10.12688/f1000research.21027.2.
Sima, Ana-Claudia, et al. “A Hands-on Introduction to Querying Evolutionary Relationships across Multiple Data Sources Using SPARQL.” F1000Research, vol. 8, Aug. 2020, p. 1822, https://doi.org/10.12688/f1000research.21027.2.


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.