Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2014-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/276.pdf |
| _version_ | 1797420207851962368 |
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| author | Anabel Usie Hiren Karathia Ivan Teixidó Rui Alves Francesc Solsona |
| author_facet | Anabel Usie Hiren Karathia Ivan Teixidó Rui Alves Francesc Solsona |
| author_sort | Anabel Usie |
| collection | DOAJ |
| description | One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this ‘up-to-dateness’ came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains ‘up-to-dateness’ of the results. Availability: http://metres.udl.cat/index.php/downloads, Contact: metres.cmb@gmail.com. |
| first_indexed | 2024-03-09T06:59:18Z |
| format | Article |
| id | doaj.art-9cc5b5a304fd404eb4ad9c497c410a4a |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:59:18Z |
| publishDate | 2014-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-9cc5b5a304fd404eb4ad9c497c410a4a2023-12-03T09:56:50ZengPeerJ Inc.PeerJ2167-83592014-02-012e27610.7717/peerj.276276Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documentsAnabel Usie0Hiren Karathia1Ivan Teixidó2Rui Alves3Francesc Solsona4Department of Basic Medical Sciences, Edifici Recerca Biomedica I, Universitat de Lleida and IRBLleida, Lleida, SpainDepartment of Basic Medical Sciences, Edifici Recerca Biomedica I, Universitat de Lleida and IRBLleida, Lleida, SpainDepartment of Computer Science, Escola Politècnica Superior and INSPIRES, Universitat de Lleida, Lleida, SpainDepartment of Basic Medical Sciences, Edifici Recerca Biomedica I, Universitat de Lleida and IRBLleida, Lleida, SpainDepartment of Computer Science, Escola Politècnica Superior and INSPIRES, Universitat de Lleida, Lleida, SpainOne way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this ‘up-to-dateness’ came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities. We show that the performance of Biblio-MetReS in identifying gene co-occurrence is as least as good as that of other comparable applications (STRING and iHOP). In addition, we also show that the identification of GO processes is on par to that reported in the latest BioCreAtIvE challenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from documents that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains ‘up-to-dateness’ of the results. Availability: http://metres.udl.cat/index.php/downloads, Contact: metres.cmb@gmail.com.https://peerj.com/articles/276.pdfNetwork reconstructionSystems biologyLiterature analysis |
| spellingShingle | Anabel Usie Hiren Karathia Ivan Teixidó Rui Alves Francesc Solsona Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents PeerJ Network reconstruction Systems biology Literature analysis |
| title | Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents |
| title_full | Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents |
| title_fullStr | Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents |
| title_full_unstemmed | Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents |
| title_short | Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents |
| title_sort | biblio metres for user friendly mining of genes and biological processes in scientific documents |
| topic | Network reconstruction Systems biology Literature analysis |
| url | https://peerj.com/articles/276.pdf |
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