Best Use of Experimental Data in Cancer Informatics

Yong, May; Begent, R. H. J.

doi:10.2217/fon.10.108

Cited by 3 publications

(2 citation statements)

References 41 publications

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“…More details on the GIATE notebook and its use for the ADEPT therapeutic investigation applied to an animal model [39] were presented in [28]. …”

Section: Resultsmentioning

confidence: 99%

“…At a later stage, GIATE was extended to support other therapeutic approaches [28], while focusing on the importance and necessity of sharing data and data standards as required precursors of effective data sharing. Additionally, [29] showed how GIATE enables the establishment of a knowledge trail from molecular experiments to clinical trials, reflecting the steps of therapy development.…”

Section: Introductionmentioning

confidence: 99%

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Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy

et al. 2012

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BackgroundBiology, biomedicine and healthcare have become data-driven enterprises, where scientists and clinicians need to generate, access, validate, interpret and integrate different kinds of experimental and patient-related data. Thus, recording and reporting of data in a systematic and unambiguous fashion is crucial to allow aggregation and re-use of data. This paper reviews the benefits of existing biomedical data standards and focuses on key elements to record experiments for therapy development. Specifically, we describe the experiments performed in molecular, cellular, animal and clinical models. We also provide an example set of elements for a therapy tested in a phase I clinical trial.FindingsWe introduce the Guidelines for Information About Therapy Experiments (GIATE), a minimum information checklist creating a consistent framework to transparently report the purpose, methods and results of the therapeutic experiments. A discussion on the scope, design and structure of the guidelines is presented, together with a description of the intended audience. We also present complementary resources such as a classification scheme, and two alternative ways of creating GIATE information: an electronic lab notebook and a simple spreadsheet-based format. Finally, we use GIATE to record the details of the phase I clinical trial of CHT-25 for patients with refractory lymphomas. The benefits of using GIATE for this experiment are discussed.ConclusionsWhile data standards are being developed to facilitate data sharing and integration in various aspects of experimental medicine, such as genomics and clinical data, no previous work focused on therapy development. We propose a checklist for therapy experiments and demonstrate its use in the 131Iodine labeled CHT-25 chimeric antibody cancer therapy. As future work, we will expand the set of GIATE tools to continue to encourage its use by cancer researchers, and we will engineer an ontology to annotate GIATE elements and facilitate unambiguous interpretation and data integration.

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“…More details on the GIATE notebook and its use for the ADEPT therapeutic investigation applied to an animal model [39] were presented in [28]. …”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy

et al. 2012

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Establishing a knowledge trail from molecular experiments to clinical trials

2011

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Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop

Kettner

Field²,

Sansone³

et al. 2010

Stand. Genomic Sci.

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This report summarizes the proceedings of the second workshop of the ‘Minimum Information for Biological and Biomedical Investigations’ (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institut. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/.

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Best Use of Experimental Data in Cancer Informatics

Cited by 3 publications

References 41 publications

Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy

Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy

Establishing a knowledge trail from molecular experiments to clinical trials

Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop

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