ArticleJournal of biomedical semantics2014
Structuring research methods and data with the research object model: genomics workflows as a case study.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Biosemantics guided gene expression profiling of Sjögren's syndrome: a comparative analysis with systemic lupus erythematosus and rheumatoid arthritis.Arthritis research & therapy · 2017Pooled it
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- Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.GigaScience · 2019Article
- Enabling precision medicine via standard communication of HTS provenance, analysis, and results.PLoS biology · 2018Article
- Genetic variants including markers from the exome chip and metabolite traits of type 2 diabetes.Scientific reports · 2017Article
- RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Knowledge Representation and Management: a Linked Data Perspective.Yearbook of medical informatics · 2016Review
- Consent Codes: Upholding Standard Data Use Conditions.PLoS genetics · 2016Article
- Combining computational models, semantic annotations and simulation experiments in a graph database.Database : the journal of biological databases and curation · 2015Article
- COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.BMC bioinformatics · 2014Article
- Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.PDA journal of pharmaceutical science and technologyArticle
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.
resultsWe present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?".
conclusionsApplying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. AVAILABILITY: The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.