Data Release Notes - Revision history

MariaKim: /* Version 3.5.1 */

2026-08-20T21:12:17Z

Version 3.5.1

← Older revision		Revision as of 21:12, 20 August 2026
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	Planned: Aug 20th, 2026		Planned: Aug 20th, 2026
	=== Data Updates ===		=== Data Updates ===
	* The [https://data.biomarkerkb.org/BMK_000003 BMK_000003] dataset (<code>biomarkers_llm_glycan.tsv</code>) has been retired and replaced by ~~the bGSL~~ dataset (BioCompute Object TBA).		* The [https://data.biomarkerkb.org/BMK_000003 BMK_000003] dataset (<code>biomarkers_llm_glycan.tsv</code>) has been retired and replaced by a new LLM-mined glycan dataset (BioCompute Object TBA).

	== Version 3.4.2 ==		== Version 3.4.2 ==

MariaKim at 17:59, 17 August 2026

2026-08-17T17:59:16Z

← Older revision		Revision as of 17:59, 17 August 2026
Line 4:		Line 4:
	* The second digit (Y) increments when new data is added.		* The second digit (Y) increments when new data is added.
	* The third digit (Z) is updated for bug fixes or minor changes.		* The third digit (Z) is updated for bug fixes or minor changes.

			== Version 3.5.1 ==
			Planned: Aug 20th, 2026
			=== Data Updates ===
			* The [https://data.biomarkerkb.org/BMK_000003 BMK_000003] dataset (<code>biomarkers_llm_glycan.tsv</code>) has been retired and replaced by the bGSL dataset (BioCompute Object TBA).

	== Version 3.4.2 ==		== Version 3.4.2 ==

MariaKim at 11:40, 10 August 2026

2026-08-10T11:40:47Z

← Older revision		Revision as of 11:40, 10 August 2026
Line 4:		Line 4:
	* The second digit (Y) increments when new data is added.		* The second digit (Y) increments when new data is added.
	* The third digit (Z) is updated for bug fixes or minor changes.		* The third digit (Z) is updated for bug fixes or minor changes.

			== Version 3.4.2 ==
			Date: Aug 6th, 2026
			=== Biomarker Knowledge Graph ===
			* Fixed an issue where biomarker labels in the KG did not reflect standardized biomarker terminology.
			* The JSON-to-NT conversion script now uses controlled vocabulary terms for biomarkers instead of original biomarker names.
			* Expanded and corrected edge predicate mappings (<code>biomarker_change</code>, <code>best_biomarker_role</code>, <code>specimen_sampled_from</code>, <code>condition_role_indicator</code>) to use standardized 9-digit OBCI URIs; previously missing predicates have been added, resolving cases where not all biomarker types appeared in "Select Relation."
			=== Biomarker Ontology ===
			* Updated Metadata > Details page: "Biomarker Ontology" now displays as "Ontology for Biomarkers of Clinical Importance (OBCI)."
			* Ontology nodes are now sorted alphanumerically.
			* Updated hierarchy view instructional text to "Please click on a term on left side to explore more."
			* Published a new hierarchy-display-specific ontology version that resolves the multiple-parent issue.

	== Version 3.4.1 ==		== Version 3.4.1 ==
	~~Planned~~: July 23rd, 2026		Date: July 23rd, 2026
			=== Data Updates ===
			* Added the caDSR ([https://cadsr.cancer.gov/onedata/Home.jsp NCI Cancer Data Standards Registry and Repository]) dataset: a pilot set of ~30 manually curated, standardized biomarker entries derived from caDSR permissible values, mapped to the BiomarkerKB schema. Conditions are broadly mapped to general cancer (DOID:162) pending future organ/tissue-specific enrichment. Extraction code and mapping scripts are available on [https://github.com/clinical-biomarkers/biomarker-extraction GitHub].
			=== Backend Updates ===
			* Added a new [https://api.biomarkerkb.org/ Global Search API] (<code>/biomarker/search_global/</code>) enabling search results to be broken out by section (Biomarker Entity, Biomarker Term, Condition/Disease, Specimen, Cross-References, Biomarker ID).
			* Each result section now includes an <code>order</code> attribute to control display order on the frontend, standardized as:
			1. Biomarker Entity
			2. Biomarker ID
			3. Biomarker Term
			4. Condition/Disease
			5. Specimen
			6. Cross-References
			* Relabeled "crossref" section to "Cross-References" in the UI.

	== Version 3.3.1 ==		== Version 3.3.1 ==
	Date: July 13th, 2026		Date: July 13th, 2026
	=== Data Updates ===		=== Data Updates ===
	* Split merged datasets back into their original four separate outputs to match the legacy pipeline structure and restore BCO consistency. Affected datasets: BMK_000001, BMK_000005, BMK_000014, BMK_000015.		* Split merged datasets back into their original four separate outputs to match the legacy pipeline structure and restore BCO consistency. Affected datasets: [https://data.biomarkerkb.org/BMK_000001 BMK_000001], [https://data.biomarkerkb.org/BMK_000005 BMK_000005], [https://data.biomarkerkb.org/BMK_000014 BMK_000014], [https://data.biomarkerkb.org/BMK_000015 BMK_000015].
	* Reverted Biomarker ID generation back to the original format (<code>XX1234</code>, two-letter prefix + four-digit numeric ID, e.g., <code>AN6256</code>, <code>AN6256-1</code>), correcting a regression that had introduced a non-standard format (e.g., <code>BMKB151581-1</code>).		* Reverted Biomarker ID generation back to the original format (<code>XX1234</code>, two-letter prefix + four-digit numeric ID, e.g., <code>AN6256</code>, <code>AN6256-1</code>), correcting a regression that had introduced a non-standard format (e.g., <code>BMKB151581-1</code>).
	=== Backend Updates ===		=== Backend Updates ===

MariaKim at 20:07, 21 July 2026

2026-07-21T20:07:00Z

@@ Line 4: / Line 4: @@
 * The second digit (Y) increments when new data is added.
 * The third digit (Z) is updated for bug fixes or minor changes.
 == Version 3.2.2 ==
@@ Line 10: / Line 24: @@
 * The Ontology page has been updated to the latest version.
 * The Knowledge Graph files, <all-biomarkers-nt.tar.gz> and <owlnets.tar.gz>, are now up-to-date with the current data.
 === Bug Fixes ===
 * All data sources are now displayed correctly under "Data Source" in the Advanced Search.

MariaKim at 18:06, 7 July 2026

2026-07-07T18:06:39Z

← Older revision		Revision as of 18:06, 7 July 2026
Line 4:		Line 4:
	* The second digit (Y) increments when new data is added.		* The second digit (Y) increments when new data is added.
	* The third digit (Z) is updated for bug fixes or minor changes.		* The third digit (Z) is updated for bug fixes or minor changes.

			== Version 3.2.2 ==
			Date: June 22nd, 2026
			=== Data Updates ===
			* The Ontology page has been updated to the latest version.
			* The Knowledge Graph files, <all-biomarkers-nt.tar.gz> and <owlnets.tar.gz>, are now up-to-date with the current data.
			=== Bug Fixes ===
			* All data sources are now displayed correctly under "Data Source" in the Advanced Search.

	== Version 3.2.1 ==		== Version 3.2.1 ==

MariaKim at 14:40, 11 May 2026

2026-05-11T14:40:32Z

← Older revision		Revision as of 14:40, 11 May 2026
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	* Added a new dataset containing user-submitted biomarkers.		* Added a new dataset containing user-submitted biomarkers.
	* Added a new manually curated dataset of biomarkers with exposure agents.		* Added a new manually curated dataset of biomarkers with exposure agents.
			=== Bug Fixes ===
			* Publications and exposure agents are now displayed correctly on the biomarker details pages.

	== Version 3.1.1 ==		== Version 3.1.1 ==

MariaKim at 15:27, 29 April 2026

2026-04-29T15:27:03Z

← Older revision		Revision as of 15:27, 29 April 2026
Line 5:		Line 5:
	* The third digit (Z) is updated for bug fixes or minor changes.		* The third digit (Z) is updated for bug fixes or minor changes.

	== Version 2.4.3 ~~(draft)~~ ==		== Version 3.2.1 ==
			Date: April 23rd, 2026
			=== Data Updates ===
			* Added a new dataset containing user-submitted biomarkers.
			* Added a new manually curated dataset of biomarkers with exposure agents.

			== Version 3.1.1 ==
			Date: April 9th, 2026
			=== Backend Updates ===
			Complete overhaul of the backend data pipeline architecture:
			* Improved ETL processes for greater reliability and scalability
			* Enhanced data validation and error handling across pipeline stages
			* Optimized performance for faster data processing and reduced runtime
			* Refactored codebase for maintainability and extensibility

			== Version 2.4.3 ==
	Date: February 26th, 2026		Date: February 26th, 2026
	=== Data Updates ===		=== Data Updates ===
	* An image biomarker ~~was added to~~ OncoMX ~~data~~.		* Added a new image-based biomarker from the OncoMX dataset.
	* ~~Fix UPKB~~ biomarkers ~~containing~~ exposure agents.		* Fixed UniProtKB biomarkers that incorrectly included exposure agents.
	=== Backend Updates ===		=== Backend Updates ===
	* ~~Read~~ ChEBI API ~~response which is in~~ JSON ~~format~~		* Updated ChEBI API integration to properly parse JSON responses.

	== Version 2.4.2 ==		== Version 2.4.2 ==

MariaKim at 15:57, 25 February 2026

2026-02-25T15:57:29Z

← Older revision		Revision as of 15:57, 25 February 2026
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	Date: February 19th, 2026		Date: February 19th, 2026
	=== Data Updates ===		=== Data Updates ===
	* An archive file of all biomarker NTriples is now available for download at [https://data.biomarkerkb.org/ data.biomarkerkb.org].		* An archive file of all biomarker NTriples is now available for download at [https://data.biomarkerkb.org/BMK_000019 data.biomarkerkb.org/BMK_000019].

	== Version 2.4.1 ==		== Version 2.4.1 ==
	Date: February 12th, 2026		Date: February 12th, 2026
	=== Data Updates ===		=== Data Updates ===
	* A master list of all biomarkers present in BiomarkerKB is now available for download at [https://data.biomarkerkb.org/ data.biomarkerkb.org].		* A master list of all biomarkers present in BiomarkerKB is now available for download at [https://data.biomarkerkb.org/BMK_000007 data.biomarkerkb.org/BMK_000007].

	== Version 2.4.0 ==		== Version 2.4.0 ==

MariaKim at 22:22, 24 February 2026

2026-02-24T22:22:17Z

← Older revision		Revision as of 22:22, 24 February 2026
Line 4:		Line 4:
	* The second digit (Y) increments when new data is added.		* The second digit (Y) increments when new data is added.
	* The third digit (Z) is updated for bug fixes or minor changes.		* The third digit (Z) is updated for bug fixes or minor changes.

			== Version 2.4.3 (draft) ==
			Date: February 26th, 2026
			=== Data Updates ===
			* An image biomarker was added to OncoMX data.
			* Fix UPKB biomarkers containing exposure agents.
			=== Backend Updates ===
			* Read ChEBI API response which is in JSON format

	== Version 2.4.2 ==		== Version 2.4.2 ==

MariaKim: /* Version 2.4.1 */

2026-02-24T19:12:24Z

Version 2.4.1

← Older revision		Revision as of 19:12, 24 February 2026
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	== Version 2.4.1 ==		== Version 2.4.1 ==
	Date: February 12th, 2026		Date: February 12th, 2026
	=== ~~Backend~~ Updates ===		=== Data Updates ===
	* A master list of all biomarkers present in BiomarkerKB is now available for download at [https://data.biomarkerkb.org/ data.biomarkerkb.org].		* A master list of all biomarkers present in BiomarkerKB is now available for download at [https://data.biomarkerkb.org/ data.biomarkerkb.org].