TabSQL: a MySQL tool to facilitate mapping user data to public databases
<p>Abstract</p> <p>Background</p> <p>With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases.</p> <p>Results</p> <p>We devel...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-06-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/342 |
| _version_ | 1818750365220208640 |
|---|---|
| author | McClelland Michael Xia Xiao-Qin Wang Yipeng |
| author_facet | McClelland Michael Xia Xiao-Qin Wang Yipeng |
| author_sort | McClelland Michael |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases.</p> <p>Results</p> <p>We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line.</p> <p>Conclusions</p> <p>TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.</p> |
| first_indexed | 2024-12-18T04:18:31Z |
| format | Article |
| id | doaj.art-db9762d8d7d2485a84b8a782cf0c05d0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T04:18:31Z |
| publishDate | 2010-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-db9762d8d7d2485a84b8a782cf0c05d02022-12-21T21:21:18ZengBMCBMC Bioinformatics1471-21052010-06-0111134210.1186/1471-2105-11-342TabSQL: a MySQL tool to facilitate mapping user data to public databasesMcClelland MichaelXia Xiao-QinWang Yipeng<p>Abstract</p> <p>Background</p> <p>With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases.</p> <p>Results</p> <p>We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line.</p> <p>Conclusions</p> <p>TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.</p>http://www.biomedcentral.com/1471-2105/11/342 |
| spellingShingle | McClelland Michael Xia Xiao-Qin Wang Yipeng TabSQL: a MySQL tool to facilitate mapping user data to public databases BMC Bioinformatics |
| title | TabSQL: a MySQL tool to facilitate mapping user data to public databases |
| title_full | TabSQL: a MySQL tool to facilitate mapping user data to public databases |
| title_fullStr | TabSQL: a MySQL tool to facilitate mapping user data to public databases |
| title_full_unstemmed | TabSQL: a MySQL tool to facilitate mapping user data to public databases |
| title_short | TabSQL: a MySQL tool to facilitate mapping user data to public databases |
| title_sort | tabsql a mysql tool to facilitate mapping user data to public databases |
| url | http://www.biomedcentral.com/1471-2105/11/342 |
| work_keys_str_mv | AT mcclellandmichael tabsqlamysqltooltofacilitatemappinguserdatatopublicdatabases AT xiaxiaoqin tabsqlamysqltooltofacilitatemappinguserdatatopublicdatabases AT wangyipeng tabsqlamysqltooltofacilitatemappinguserdatatopublicdatabases |