Acquire: an open-source comprehensive cancer biobanking system
| Autor: | Lauren B. Becnel, Benjamin Pew, Heidi Dowst, Shijing Qu, Christopher M. Watkins, Jonathan Barney, Apollo McOwiti |
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| Rok vydání: | 2015 |
| Předmět: |
Quality Control
Statistics and Probability Databases Factual Computer science Databases and Ontologies Information Storage and Retrieval Genomics Cancer Biobank Biochemistry World Wide Web User-Computer Interface 03 medical and health sciences 0302 clinical medicine Neoplasms Data Mining Humans Resource allocation (computer) Molecular Biology Biological Specimen Banks 030304 developmental biology 0303 health sciences Genomic sequencing Computational Biology Original Papers Biobank 3. Good health Computer Science Applications Computational Mathematics Computational Theory and Mathematics 030220 oncology & carcinogenesis Database Management Systems Software |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btv012 |
| Popis: | Motivation: The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research. Results: To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute ‘scoreboard’ and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens’ progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen. Availability and Implementation: Acquire implements standard controlled vocabularies, ontologies and objects from the NCI, CDISC and others. Here we describe the functionality of the system, its technological stack and the processes it supports. A test version Acquire is available at https://tcrbacquire-stg.research.bcm.edu; software is available in https://github.com/BCM-DLDCC/Acquire; and UML models, data and workflow diagrams, behavioral specifications and other documents are available at https://github.com/BCM-DLDCC/Acquire/tree/master/supplementaryMaterials. Contact: becnel@bcm.edu |
| Databáze: | OpenAIRE |
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