A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations]
The 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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2020-07-01
|
| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/8-1822/v2 |
| _version_ | 1811313860972380160 |
|---|---|
| author | Ana Claudia Sima Christophe Dessimoz Kurt Stockinger Monique Zahn-Zabal Tarcisio Mendes de Farias |
| author_facet | Ana Claudia Sima Christophe Dessimoz Kurt Stockinger Monique Zahn-Zabal Tarcisio Mendes de Farias |
| author_sort | Ana Claudia Sima |
| collection | DOAJ |
| description | The 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. |
| first_indexed | 2024-04-13T11:02:07Z |
| format | Article |
| id | doaj.art-7f453f24685b48fba6af40688d93dfb7 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-13T11:02:07Z |
| publishDate | 2020-07-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-7f453f24685b48fba6af40688d93dfb72022-12-22T02:49:22ZengF1000 Research LtdF1000Research2046-14022020-07-01810.12688/f1000research.21027.227892A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations]Ana Claudia Sima0Christophe Dessimoz1Kurt Stockinger2Monique Zahn-Zabal3Tarcisio Mendes de Farias4Department of Computational Biology, University of Lausanne, Lausanne, Vaud, SwitzerlandDepartment of Computational Biology, University of Lausanne, Lausanne, Vaud, SwitzerlandZHAW Zurich University of Applied Sciences, Winterthur, Zurich, SwitzerlandDepartment of Computational Biology, University of Lausanne, Lausanne, Vaud, SwitzerlandDepartment of Computational Biology, University of Lausanne, Lausanne, Vaud, SwitzerlandThe 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.https://f1000research.com/articles/8-1822/v2 |
| spellingShingle | Ana Claudia Sima Christophe Dessimoz Kurt Stockinger Monique Zahn-Zabal Tarcisio Mendes de Farias A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] F1000Research |
| title | A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_full | A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_fullStr | A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_short | A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 1 approved, 2 approved with reservations] |
| title_sort | hands on introduction to querying evolutionary relationships across multiple data sources using sparql version 2 peer review 1 approved 2 approved with reservations |
| url | https://f1000research.com/articles/8-1822/v2 |
| work_keys_str_mv | AT anaclaudiasima ahandsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT christophedessimoz ahandsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT kurtstockinger ahandsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT moniquezahnzabal ahandsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT tarcisiomendesdefarias ahandsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT anaclaudiasima handsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT christophedessimoz handsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT kurtstockinger handsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT moniquezahnzabal handsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations AT tarcisiomendesdefarias handsonintroductiontoqueryingevolutionaryrelationshipsacrossmultipledatasourcesusingsparqlversion2peerreview1approved2approvedwithreservations |