Data Release Notes

Versioning Format

The versioning format follows a three-digit structure: X.Y.Z.

• The first digit (X) changes when a major update is introduced, such as changes in the data model.
• The second digit (Y) increments when new data is added.
• The third digit (Z) is updated for bug fixes or minor changes.

Version 2.1.0

Date: December 11, 2025

Data Updates

• Added the LLM-extracted glycan biomarker dataset provided by Cyrus Chun Hong Au Yeung.

Backend and Infrastructure Updates

• The incorrect download links on the Data Portal have been fixed.
• LOINC codes are no longer tied to specimen IDs.

Version 2.0.2

Date: December 4, 2025

Bug Fixes

• LOINC codes are no longer tied to specimen (UBERON) IDs.
• For biomarkers that could not be mapped to Controlled Vocabulary the original biomarker name is displayed, followed by "in review".

Version 2.0.1

Data Updates

• Added cross-references to the Common Fund Data Ecosystem (CFDE) Data Coordinating Centers and other resources:
  • GTEx
  • Pharos
  • Reactome
  • Undiagnosed Diseases Network
  • Illuminating the Druggable Genome (IDG) Reactome Portal
  • Metabolomics Workbench
  • SigCom LINCS

Version 2.0.0

Data Updates

• The biomarker field is now standardized using controlled vocabulary terms.
• Added metabolite as an assessed_entity_type to mw_loinc_biomarkers.tsv.
• Added RNAcentral cross-reference support.
• Added Electronic Health Records Normal ranges data from Oracle Health for Troponin I as an example.

Version 1.0.6

Data Updates

• Added a new dataset: MW LOINC biomarkers (mw_loinc_biomarkers.tsv).
• Added National Cancer Institute Thesaurus and Protein Data Bank cross-references.

Backend and Infrastructure Updates

• Added the display_name field to the format-converter so data source names appear with correct casing.

Version 1.0.5

Data Updates

• Updated the Troponin biomarker value assessed_biomarker_entity for consistency.
• Added normal ranges from Electronic Health Records provided by the University of New Mexico for Troponin biomarkers.
• Added Cell Ontology and Protein Ontology cross-references.

Backend and Infrastructure Updates

• Updated all script paths to use data_source.conf and validated data source names.

Version 1.0.4

This release introduces new datasets, cross-references, and bug fixes.

Data Updates

• Added Cancer Genome Interpreter data on cancer biomarkers from MetaKB.
• Added Metabolomics Workbench LOINC data on metabolite biomarkers.
• Added Cell Ontology and Protein Ontology cross-references.

Bug Fixes

• Fixed issue where cookie preferences weren't being saved when selecting "Allow".

Version 1.0.3

This release introduces new cross-references and updates to ensure compatibility with external resources.

Data Updates

• NCBI cross-references added across gene biomarker entries.
• ChEBI cross-references integrated for small molecules and metabolites.

Backend and Infrastructure Updates

• ChEBI API migration: Updated all programmatic links from the legacy SOAP services to the new REST API endpoints, following ChEBI’s platform migration.
  • Old services retired 1 September 2025.
  • New stable API: ChEBI REST API docs
  • New data products and beta interface available at ChEBI 2.0.

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_source database 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_source 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 _suggest_header_corrections to flag and propose fixes for misspelled headers.
• Enhanced _stream_tsv with a call to _check_header_spelling to prevent invalid headers from being processed.

Version 1.0.1

Data Updates

• Added xrefs.tsv to 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.