Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data.

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We use as our implementation example a breast cancer database linking RNA expression measurements (by microarray) and clinical variables, such as survival metrics and tumor size. Such an endeavor involves integrating across different microarray datasets as well as clinical parameters. To this end, we created a data curation and processing pipeline, formal database ontology, and SQL schema to optimally query, analyze and visualize data from over 30 publicly available breast cancer microarray studies listed in the Gene Expression Omnibus (GEO). We demonstrate several pilot examples using this database. This methodology serves as a model for future meta-analyses of complex public clinical datasets, in particular those in the field of cancer.", "claims": [{"id": "claim-data-access", "statement": "The majority of RNA microarray datasets were collected from the National Center for Biotechnology (NCBI) Gene Expression Omnibus (GEO), a public functional genomics data repository that supports standardized data following the Minimum Information About a Microarray Experiment (MIAME) protocol11.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24303324", "locator": "sections[3] \"Gene Expression Processing\" paragraph 2", "quote": "The majority of RNA microarray datasets were collected from the National Center for Biotechnology (NCBI) Gene Expression Omnibus (GEO), a public functional genomics data repository that supports standardized data following the Minimum Information About a Microarray Experiment (MIAME) protocol11."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The authors created a MySQL meta-database integrating clinical variables with microarray data from over 30 GEO studies and performed a preliminary gene-expression analysis using False Discovery Rate (FDR), yielding significant FDR values but insignificant p-values for over- or under-expression across all datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24303324", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To this end, we created a data curation and processing pipeline, formal database ontology, and SQL schema to optimally query, analyze and visualize data from over 30 publicly available breast cancer microarray studies listed in the Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:24303324", "locator": "sections[5] \"Results\" paragraph 4", "quote": "Our database currently contains 4923 patient records; 592 patients have pCR records recording treatment response immediately after all therapy was completed, and 4331 have long-term relapse and/or disease-free survival records for at least 3 years."}, {"asset": "source:pmid:24303324", "locator": "sections[5] \"Results\" paragraph 5", "quote": "A preliminary gene expression analysis across all patients provided genes with significant False Discovery Rate (FDR) values, but insignificant p-values for over- or under-expression across all datasets."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "partial", "objective": "The authors created a MySQL meta-database integrating clinical variables with microarray data from over 30 GEO studies and performed a preliminary gene-expression analysis using False Discovery Rate (FDR), yielding significant FDR values but insignificant p-values for over- or under-expression across all datasets.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:24303324"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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