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Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

Gavrielides M, Furney SJ, Yates T, Miller CJ, Marais R - Source Code Biol Med (2014)

Bottom Line: Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective.The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data.Hence it is suitable for laboratories that do not require a commercial system.

View Article: PubMed Central - PubMed

Affiliation: Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.

ABSTRACT

Background: Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments.

Results: The current work presents a sample tracking system for oncogenomic studies (Onco-STS) to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database. The web application development programming framework Grails was used for the development and implementation of the system.

Conclusions: The resulting Onco-STS solution is efficient, secure and easy to use and is intended to replace the manual data handling of text records. Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective. The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data. Onco-STS is based on open-source software, is easy to develop and can be modified according to a research group's needs. Hence it is suitable for laboratories that do not require a commercial system.

No MeSH data available.


Related in: MedlinePlus

Summary of the database schema with thesample,patient,projectand the six experiments tables (WGS, WES, RNASeq, aCGH, SNPx mRNA) and their connections. The User, Role tables and their connection through the UserRole table are also shown. The Sample table is connected with one-to-many relationship to the User, Patient and Project tables.
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Fig1: Summary of the database schema with thesample,patient,projectand the six experiments tables (WGS, WES, RNASeq, aCGH, SNPx mRNA) and their connections. The User, Role tables and their connection through the UserRole table are also shown. The Sample table is connected with one-to-many relationship to the User, Patient and Project tables.

Mentions: Onco-STS is a sample driven application. The Sample table (FigureĀ 1) is connected with a one-to-one (1:1) relationship to six tables that correspond to the six different oncogenomic experiments: WGS, WES, SNP, RNA-Seq, mRNA and aCGH. A one-to-one relationship denotes that each sample record is linked with foreign keys to one particular record from each of the experiment tables.Figure 1


Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

Gavrielides M, Furney SJ, Yates T, Miller CJ, Marais R - Source Code Biol Med (2014)

Summary of the database schema with thesample,patient,projectand the six experiments tables (WGS, WES, RNASeq, aCGH, SNPx mRNA) and their connections. The User, Role tables and their connection through the UserRole table are also shown. The Sample table is connected with one-to-many relationship to the User, Patient and Project tables.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4288629&req=5

Fig1: Summary of the database schema with thesample,patient,projectand the six experiments tables (WGS, WES, RNASeq, aCGH, SNPx mRNA) and their connections. The User, Role tables and their connection through the UserRole table are also shown. The Sample table is connected with one-to-many relationship to the User, Patient and Project tables.
Mentions: Onco-STS is a sample driven application. The Sample table (FigureĀ 1) is connected with a one-to-one (1:1) relationship to six tables that correspond to the six different oncogenomic experiments: WGS, WES, SNP, RNA-Seq, mRNA and aCGH. A one-to-one relationship denotes that each sample record is linked with foreign keys to one particular record from each of the experiment tables.Figure 1

Bottom Line: Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective.The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data.Hence it is suitable for laboratories that do not require a commercial system.

View Article: PubMed Central - PubMed

Affiliation: Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.

ABSTRACT

Background: Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments.

Results: The current work presents a sample tracking system for oncogenomic studies (Onco-STS) to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database. The web application development programming framework Grails was used for the development and implementation of the system.

Conclusions: The resulting Onco-STS solution is efficient, secure and easy to use and is intended to replace the manual data handling of text records. Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective. The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data. Onco-STS is based on open-source software, is easy to develop and can be modified according to a research group's needs. Hence it is suitable for laboratories that do not require a commercial system.

No MeSH data available.


Related in: MedlinePlus