Data Release Notes: Difference between revisions
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Version 1.0 |
Expanded 1.0.2; introduced Data Updates and Backed & Infrastructure Updates headers |
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== Versioning Format == | |||
The versioning format follows a three-digit structure: X.Y.Z. | |||
* The first digit (X) changes annually, typically at the start of a new project year. | |||
* The second digit (Y) increments with each new release. | |||
* The third digit (Z) is updated for bug fixes or minor changes. | |||
== Version 1.0 == | == Version 1.0.2 == | ||
=== Data Updates === | |||
* Published updated [https://www.metabolomicsworkbench.org/ Metabolomics Workbench] data. | |||
* Published sample data from the [https://edrn.nci.nih.gov/ Early Detection Research Network]. | |||
=== Backend and Infrastructure Updates === | |||
* <code>evidence_source</code> database names now retain their original casing for accuracy and consistency. | |||
* EDRN identifiers were added to the [https://github.com/clinical-biomarkers/format-converter/blob/main/mapping_data/namespace_map.json namespace map]. | |||
* [https://www.genenames.org/ HUGO Gene Nomenclature Committee] (HGNC) was added to the cross-reference JSON file. | |||
* Fixed an issue where <code>evidence_source</code> values without tags were previously dropped; these are now preserved. | |||
* Added a user-guided spelling correction function to improve data entry quality. | |||
* The TSV-to-JSON converter now automatically checks for header spelling errors. | |||
* Introduced <code>_suggest_header_corrections</code> to flag and propose fixes for misspelled headers. | |||
* Enhanced <code>_stream_tsv</code> with a call to <code>_check_header_spelling</code> to prevent invalid headers from being processed. | |||
== Version 1.0.1 == | |||
=== Data Updates === | |||
* Added <code> xrefs.tsv</code> to the list of datasets. | |||
=== Backend & Infrastructure Updates === | |||
* Fixed ID formatting issues in NCBI and UniProt references within <code> oncomx.tsv</code>, removing erroneous spaces (e.g., <code> NCBI: 3288</code> → <code> NCBI:3288</code>) and extraneous text (e.g., <code>"(composition)"</code>). Affected biomarkers included AN6295-1, AN6756-1, AN6728-1, and others. | |||
* Merged assessed entity type synonyms. | |||
== Version 1.0.0 == | |||
* BiomarkerKB data portal available with OncoMX, OpenTargets, MarkerDB, ClinVar, PubMed Central Biomarker Gene Set Curation, MW, UniProtKB, GWAS, CIViC biomarker data. | * BiomarkerKB data portal available with OncoMX, OpenTargets, MarkerDB, ClinVar, PubMed Central Biomarker Gene Set Curation, MW, UniProtKB, GWAS, CIViC biomarker data. | ||
Latest revision as of 15:26, 29 August 2025
Versioning Format
The versioning format follows a three-digit structure: X.Y.Z.
- The first digit (X) changes annually, typically at the start of a new project year.
- The second digit (Y) increments with each new release.
- The third digit (Z) is updated for bug fixes or minor changes.
Version 1.0.2
Data Updates
- Published updated Metabolomics Workbench data.
- Published sample data from the Early Detection Research Network.
Backend and Infrastructure Updates
evidence_sourcedatabase names now retain their original casing for accuracy and consistency.- EDRN identifiers were added to the namespace map.
- HUGO Gene Nomenclature Committee (HGNC) was added to the cross-reference JSON file.
- Fixed an issue where
evidence_sourcevalues without tags were previously dropped; these are now preserved. - Added a user-guided spelling correction function to improve data entry quality.
- The TSV-to-JSON converter now automatically checks for header spelling errors.
- Introduced
_suggest_header_correctionsto flag and propose fixes for misspelled headers. - Enhanced
_stream_tsvwith a call to_check_header_spellingto prevent invalid headers from being processed.
Version 1.0.1
Data Updates
- Added
xrefs.tsvto the list of datasets.
Backend & Infrastructure Updates
- Fixed ID formatting issues in NCBI and UniProt references within
oncomx.tsv, removing erroneous spaces (e.g.,NCBI: 3288→NCBI:3288) and extraneous text (e.g.,"(composition)"). Affected biomarkers included AN6295-1, AN6756-1, AN6728-1, and others. - Merged assessed entity type synonyms.
Version 1.0.0
- BiomarkerKB data portal available with OncoMX, OpenTargets, MarkerDB, ClinVar, PubMed Central Biomarker Gene Set Curation, MW, UniProtKB, GWAS, CIViC biomarker data.