Beyond access to structures and workflows via the Dashboard, future functionality of the Dashboard will allow for users to upload structure files and receive back the MS-Ready version of the structures of interest, increasing standardization across database searching and compound identification. Alterations to the output format (as described in the Methods) will enable other in silico fragmentation and compound identification tools, methods, and software to use the work described here. Further flexibility in file formats will be implemented to achieve broader usability. As with any chemical structure standardization workflow, algorithms are modified to deal with edge cases as they are identified. As the database content continues to expand, the algorithm is improved as failures are identified. While the MS-Ready approach may lead to potentially confusing results sets containing structures with different formulae and masses than specified in the original search parameters, communication, education, and transparency within the Dashboard interface, download files, and publications will serve to clarify and provide guidance. Finally, to facilitate access to the underlying data for structure identification on the broadest scale, an application programming interface (API) and associated web services to allow instrument software integration is forthcoming. These will enable access via applications such as Python, R, and Matlab to facilitate integration of Dashboard data into user-specific applications.
Database searching is a vital part of NTA and SSA workflows. The accurate mapping of MS-Ready structures to chemical substances improves accessibility to structure metadata and improves searching of the represented chemical space. By providing access to MS-Ready data from DSSTox, both via the Dashboard and as downloadable datasets, users of HRMS instrumentation who perform NTA/SSA experiments will benefit from this approach as an enhancement to other online databases that do not support MS-Ready structural forms. The integration into the in silico fragmenter MetFrag lets users further explore the use of this approach in identification of unknowns. The openly available workflow for generation of MS-Ready structures allows others to process their own data for preparation of MS-Ready data files and extend the data handling to account for errors and specific cases that we have not yet identified.
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The PCAWG-generated alignments, somatic variant calls, annotations and derived datasets are available for general research use for browsing and download at (Box 1 and Supplementary Table 4). In accordance with the data access policies of the ICGC and TCGA projects, most molecular, clinical and specimen data are in an open tier which does not require access approval. To access potentially identifying information, such as germline alleles and underlying read data, researchers will need to apply to the TCGA Data Access Committee (DAC) via dbGaP ( =login) for access to the TCGA portion of the dataset, and to the ICGC Data Access Compliance Office (DACO; ) for the ICGC portion. In addition, to access somatic single nucleotide variants derived from TCGA donors, researchers will also need to obtain dbGaP authorization. 2ff7e9595c
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