Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses
Abstract Background Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology...
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| Format: | Article |
| Language: | English |
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BMC
2017-12-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1981-5 |
| _version_ | 1818887271551598592 |
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| author | Edison Ong Jiangan Xie Zhaohui Ni Qingping Liu Sirarat Sarntivijai Yu Lin Daniel Cooper Raymond Terryn Vasileios Stathias Caty Chung Stephan Schürer Yongqun He |
| author_facet | Edison Ong Jiangan Xie Zhaohui Ni Qingping Liu Sirarat Sarntivijai Yu Lin Daniel Cooper Raymond Terryn Vasileios Stathias Caty Chung Stephan Schürer Yongqun He |
| author_sort | Edison Ong |
| collection | DOAJ |
| description | Abstract Background Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the default ontology for LINCS cell line representation and integration. Results CLO has consistently represented all 1097 LINCS cell lines and included information extracted from the LINCS Data Portal and ChEMBL. Using MCF 10A cell line cells as an example, we demonstrated how to ontologically model LINCS cellular signatures such as their non-tumorigenic epithelial cell type, three-dimensional growth, latrunculin-A-induced actin depolymerization and apoptosis, and cell line transfection. A CLO subset view of LINCS cell lines, named LINCS-CLOview, was generated to support systematic LINCS cell line analysis and queries. In summary, LINCS cell lines are currently associated with 43 cell types, 131 tissues and organs, and 121 cancer types. The LINCS-CLO view information can be queried using SPARQL scripts. Conclusions CLO was used to support ontological representation, integration, and analysis of over a thousand LINCS cell line cells and their cellular responses. |
| first_indexed | 2024-12-19T16:34:35Z |
| format | Article |
| id | doaj.art-0d2ffb7e1a624ac4bc3f83d3763c86a3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T16:34:35Z |
| publishDate | 2017-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-0d2ffb7e1a624ac4bc3f83d3763c86a32022-12-21T20:14:00ZengBMCBMC Bioinformatics1471-21052017-12-0118S17435310.1186/s12859-017-1981-5Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responsesEdison Ong0Jiangan Xie1Zhaohui Ni2Qingping Liu3Sirarat Sarntivijai4Yu Lin5Daniel Cooper6Raymond Terryn7Vasileios Stathias8Caty Chung9Stephan Schürer10Yongqun He11Department of Computational Medicine and Bioinformatics, University of MichiganUnit of Laboratory Animal Medicine and Department of Micro biology and Immunology, University of MichiganUnit of Laboratory Animal Medicine and Department of Micro biology and Immunology, University of MichiganUnit of Laboratory Animal Medicine and Department of Micro biology and Immunology, University of MichiganSamples, Phenotypes and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryDepartment of Molecular and Cellular Pharmacology, University of MiamiDepartment of Molecular and Cellular Pharmacology, University of MiamiDepartment of Molecular and Cellular Pharmacology, University of MiamiDepartment of Molecular and Cellular Pharmacology, University of MiamiBD2K LINCS Data Coordination and Integration Center, University of MiamiDepartment of Molecular and Cellular Pharmacology, University of MiamiDepartment of Computational Medicine and Bioinformatics, University of MichiganAbstract Background Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the default ontology for LINCS cell line representation and integration. Results CLO has consistently represented all 1097 LINCS cell lines and included information extracted from the LINCS Data Portal and ChEMBL. Using MCF 10A cell line cells as an example, we demonstrated how to ontologically model LINCS cellular signatures such as their non-tumorigenic epithelial cell type, three-dimensional growth, latrunculin-A-induced actin depolymerization and apoptosis, and cell line transfection. A CLO subset view of LINCS cell lines, named LINCS-CLOview, was generated to support systematic LINCS cell line analysis and queries. In summary, LINCS cell lines are currently associated with 43 cell types, 131 tissues and organs, and 121 cancer types. The LINCS-CLO view information can be queried using SPARQL scripts. Conclusions CLO was used to support ontological representation, integration, and analysis of over a thousand LINCS cell line cells and their cellular responses.http://link.springer.com/article/10.1186/s12859-017-1981-5Cell lineLincsData integrationOntologyCell line ontologyChEMBL |
| spellingShingle | Edison Ong Jiangan Xie Zhaohui Ni Qingping Liu Sirarat Sarntivijai Yu Lin Daniel Cooper Raymond Terryn Vasileios Stathias Caty Chung Stephan Schürer Yongqun He Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses BMC Bioinformatics Cell line Lincs Data integration Ontology Cell line ontology ChEMBL |
| title | Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses |
| title_full | Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses |
| title_fullStr | Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses |
| title_full_unstemmed | Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses |
| title_short | Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses |
| title_sort | ontological representation integration and analysis of lincs cell line cells and their cellular responses |
| topic | Cell line Lincs Data integration Ontology Cell line ontology ChEMBL |
| url | http://link.springer.com/article/10.1186/s12859-017-1981-5 |
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