NEWS

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curatedOvarianData 1.52.0

SIGNIFICANT USER-VISIBLE CHANGES

• The 30 datasets are no longer stored inside the package: they are hosted on Zenodo and downloaded individually on first use, then cached locally with BiocFileCache. This shrinks the installed package from ~400 MB to a few MB.
• New exported function curatedOvarianData(): call it with no arguments to list available datasets, with one dataset name to get an ExpressionSet, or with several names to get a named list. test = TRUE loads small offline subsets bundled with the package (used by examples, tests, and the vignette).
• Legacy data(TCGA_eset) access still works (it downloads through the same cache, deferred until the object is first used) but is deprecated and will be removed in a future release.
• inst/extdata/createEsetList.R now loads datasets through the getter; a new test.mode option in the patientselection config files selects the offline subsets.
• The cache is package-specific (tools::R_user_dir("curatedOvarianData", "cache")); delete that directory to reclaim disk space. Downloads are verified against md5 checksums recorded in inst/extdata/zenodo-manifest.csv.

INTERNAL

• inst/scripts/data-integrity-report.Rmd now verifies size_bytes as well as md5. R/getData.R compares size_bytes against the cached file on every cache hit, so a wrong size in the manifest would have silently evicted and re-downloaded a valid file on every call. Caught by Copilot review on lima1/curatedBladderData#3.

• Replaced the never-executed RUnit scaffolding with testthat tests.

• Explicit NAMESPACE exporting only curatedOvarianData().

• Replaced the dead DFCI URL with the GitHub repository URL and added BugReports; removed the committed build/ PDF.

DOCUMENTATION AND METADATA

• Repaired UTF-8 transcoding damage ("??" artifacts) in 7 dataset man pages (author names, copyright marks, and statistical symbols).
• biocViews extended to ExpressionData, OvarianCancerData, miRNAData, ArrayExpress, and GEO for better discoverability.

Changes in version 1.49.1

• Modernized package for current Bioconductor standards.
• Updated DESCRIPTION with Authors@R, standard version and correct biocViews.
• Converted legacy CITATION to bibentry() format.
• Consolidated NEWS into NEWS.md.

Changes in version 1.5.2

• Fixed bugs in createEsets.R

Changes in version 1.3.2

• Updated all gene maps

Changes in version 1.3.1

• Added missing grade to GSE26913
• Improved order of gene filtering in createEsetList.R

Changes in version 1.3.0

• Added datasets: GSE26193, GSE49997, GSE44104, GSE51088
• Curated debulking status for Mok (GSE18520)
• Added sample_type classifications
• Refined platform_accession and metadata column names
• Upgraded to Ensembl release 76 for gene maps

Changes in version 1.2.2

• Added "Non-unique gene symbols" section to vignette
• Updated createEsetList.R and patient selection config

Changes in version 1.2.1

• Fixed curation of TCGA sample type "11"

Changes in version 1.2.0

• Added RNA-seq TCGA data
• Updated gene maps

Changes in version 1.1.1

• Added options remove.retracted and remove.subsets to createEsets.R

Changes in version 1.1.0

• Added p-values to figure captions
• Renamed package variants in inst/extdata/*
• Updated metadata for GSE18520
• Added GSE8842 (Agilent array)
• Added DATABASE publication citation

Changes in version 1.0.1

• Curated grade for GSE17260

Changes in version 1.0.0

• Automated per-dataset documentation
• Expanded vignette
• Added missing grade/summarygrade fields
• Enriched ExpressionSets with metadata
• Fixed TCGA experiment name typo
• Fixed featureData in FULLV version

Changes in version 0.99.21

• Improved merging logic for technical replicate metadata

Changes in version 0.99.20

• Added stromal/tumor/normal cell percentages
• Added uncurated_author_metadata
• Removed obsolete metadata fields
• Renamed metadata fields
• Defined TCGA optimal debulking as <10mm

Changes in version 0.99.10

• Added TCGA-mirna-8x15kv2 and GSE30161

Changes in version 0.99.2

• Added tumorstage and summarystage to GSE26712

Changes in version 0.99.1

• Fixed expO short title
• Updated staging system in template
• Curated stage/grade fields in multiple datasets
• Added tumorstage to GSE2109
• Removed curation files for uncurated datasets
• Fixed stage data in GSE6008
• Updated BLAST reference genome to GRCh37.68
• Updated BioMart gene maps
• Addressed missing publication metadata
• Made test_counts.R work
• Handled metadata disagreement in technical replicates
• Added batch variable to GSE17290060

Changes in version 0.5.0

• Disallowed "unknown" in templates; use NA instead
• Added syntax-checking unit test

Changes in version 0.4.2

• Actually included ages for GSE26712

Changes in version 0.4.1

• Added ages to GSE26712
• Used getPlatformsBiomaRt for GSE6822

Changes in version 0.4.0

• Added GSE30009 (Taqman qPCR dataset)

Changes in version 0.3.0

• Added GSE32062.GPL6480 and GSE32063
• GSE13876: removed redundant recurrence status
• Resolved missing ExperimentData for GSE2109 and GSE6822
• Added subtype information to multiple datasets
• Converted dataset check test to R CMD check unit test

Changes in version 0.2.4

• TCGA: replaced missing batch variable
• GSE9891: corrected survival data for three patients

Changes in version 0.2.3

• Renamed batch variables for consistency
• Consistently label missing debulking status as NA
• Replaced missing probesets in FULL version
• Added unit test for sample counts (not yet functional)

Changes in version 0.2.2

• Replace GSE17260, which was missing in 0.2.1

Changes in version 0.2.1

• In the TCGA dataset, about 40 censored patients had days_to_death and days_to_recurrence labelled as NA instead of follow-up time.
• TCGA released updated clinical information for six patients
• Minor changes to GSE18520 based on a review, including updates to debulking status, stage, and grade.

Changes in version 0.2.0

• Added E-MTAB-386 (FFPE samples with survival data)
• Put MaxMean probe mappings in eset@featureData
• Put official Bioconductor platform names in eset@annotation

Initial Release

curatedOvarianData is a comprehensive resource for clinically-oriented investigation of the ovarian cancer transcriptome. It provides clinically-annotated expression data for 2,970 patients as 24 expression datasets including The Cancer Genome Atlas (TCGA) microRNA and Affymetrix mRNA microarray datasets. Probesets are mapped to official gene symbols using up-to-date maps. All clinical annotations are hand-curated and machine-checked to ensure consistent syntax and maximum retention of available clinical variables, resulting in nearly 1,500 patients in which overall survival, stage, grade and histology are available. ExpressionSet slots are populated with numerous metadata including PubMed IDs, citations, abstracts, study-specific warnings for retractions and duplicated samples, and probeset <--> gene maps. The package vignette provides examples for selecting patients and datasets based on flexible rules, performing meta-analysis of potential biomarkers, creating publication-ready tables from ExpressionSet metadata, and simple exporting of data tables for non R-users.