Cross-references to other resources from BiomarkerKB. BiomarkerKB from it cross-reference section provides cross-reference links to other protein, gene, glycan, metabolite databases and resources for further exploration.

BiomarkerKB Xrefs (Currently Added)

* UniProtKB
* GTEx
* Pharos
* Reactome
* Undiagnosed Diseases Network
* Illuminating the Druggable Genome (IDG) Reactome Portal
* Metabolomics Workbench
* SigCom LINCS
* Metabolomics Workbench
* ENCODE (Encyclopedia of DNA Elements)
* ClinGen (Clinical Genome Resource)
* MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration)
* GeneVA (Gene Variation Analysis)
* GeneCards
* BioGPS
* HGNC (HUGO Gene Nomenclature Committee)
* GWAS Catalog
* PDBe-KB
* PCRP
* IDG Reactome
* Bgee
* NCBI Gene
* KEGG
* SigCom LINCS
* Gene Ontology
* Reactome
* GeneMANIA
* Human Protein Atlas
* AlphaFold
* Open Targets
* UCSC Genome Browser
* Undiagnosed Diseases Network
* BioMuta
* GlyGen Protein
* UniProtKB
* Protein Ontology
* PubChem
* dbSNP
* LOINC
* Cell Ontology
* ChEBI
* NCI Thesaurus
* GlyGen Glycan
* Protein Data Bank
* RNAcentral
* Monarch Initiative
* GlyTouCan
* miRBase

Xrefs to be added

* Bgee
* Kegg
* MIM
* HMDB ID
* Ensembl
* RefSeq
* MONDO
* DisGeNET
* Orphanet

== Annotations ==
BiomarkerKB contains additional information called which is termed as 'Annotations' that complements the biomarker information in different sections of the BiomarkerKB details page

Annotations in BiomarkerKB (Current)

* Normal range data for BiomarkerKB entity from the Electronic Health Data from GWDC and Oracle Health.

Annotations to be added

* General (Name, description, class for Gene, Protein, Glycan and Metabolite)
* Function information about Gene, Protein and Metabolite
* Phenotype Data for Genes and Proteins that complement condition information
* Information about variant from dbSNP
* 3D structures for Gene, Protein, Glycan and Metabolite
For current and upcoming data and data resources list please visit - [[BiomarkerKB Resource Integration]]

2025-12-08T22:44:57Z

JeetVora: Created page with "The Biomarker Ontology Working Group is a collaborative effort dedicated to developing, refining, and maintaining standardized ontological frameworks that support the representation, integration, and interoperability of biomarker-related data. The group brings together ontology experts, data curators, biomarker experts, to establish consistent terminologies, formal relationships, and semantic structures that enhance the discoverability and reuse of biomarker information..."

The Biomarker Ontology Working Group is a collaborative effort dedicated to developing, refining, and maintaining standardized ontological frameworks that support the representation, integration, and interoperability of biomarker-related data. The group brings together ontology experts, data curators, biomarker experts, to establish consistent terminologies, formal relationships, and semantic structures that enhance the discoverability and reuse of biomarker information across diverse biomedical resources. By aligning with community standards and promoting transparent, open development practices, the working group plays a central role in ensuring that biomarker data can be reliably linked, compared, and analyzed within translational research, clinical informatics, and computational biology applications.

The Biomarker Ontology Working Group have jointly developed '''Ontology for Biomarkers of Clinical Interest (OBCI)'''. A fully functioning ontology in OWL format can be found at https://proteininformationresource.org/staff/nataled/OBCI/core/obci_core_full.owl

The Ontology Working Group has also created a '''Controlled Vocabularies (CV)''' for standardizing the representation of the biomarker values and the biomarker entity types. The CV can be found at [[Controlled Vocabulary and Keywords]]

Biomarker Ontology Working Group currently contains the members:
{| class="wikitable"
|'''Name'''
|'''ORCID'''
|-
|'''Darren A. Natale'''
|0000-0001-5809-9523
|-
|'''Raja Mazumder'''
|0000-0001-8823-9945
|-
|'''Daniall Masood'''
|0000-0001-7441-1628
|-
|'''Hande Küçük McGinty'''
|0000-0002-9025-5538
|-
|'''Marc E. Gillespie'''
|0000-0002-5766-1702
|-
|'''Astghik Sargsyan'''
|0000-0002-5860-6369
|-
|'''Soheil Abadifard'''
|0000-0002-2980-4251
|-
|'''Jeet K. Vora'''
|0000-0002-5317-1458
|}

Main Page

2025-12-08T22:31:32Z

JeetVora:

Data Release Notes

2025-11-14T18:12:10Z

JeetVora:

== 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 with each new release.
* The third digit (Z) is updated for bug fixes or minor changes.

== Version 2.0.0 ==
=== Data Updates ===
* The biomarker field is now standardized using controlled vocabulary terms.
* Added metabolite as an <code>assessed_entity_type</code> to <code>mw_loinc_biomarkers.tsv</code>.
* Added [https://rnacentral.org/ 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 (<code>mw_loinc_biomarkers.tsv</code>).
* Added [https://ncithesaurus.nci.nih.gov/ National Cancer Institute Thesaurus] and [https://www.rcsb.org/ Protein Data Bank] cross-references.
=== Backend and Infrastructure Updates ===
* Added the <code>display_name</code> field to the <code>format-converter</code> so data source names appear with correct casing.

== Version 1.0.5 ==
=== Data Updates ===
* Updated the Troponin biomarker value <code>assessed_biomarker_entity</code> 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 <code>data_source.conf</code> 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: [https://www.ebi.ac.uk/chebi/backend/api/docs ChEBI REST API docs]
** New data products and beta interface available at [https://www.ebi.ac.uk/chebi/beta/ ChEBI 2.0].
== 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.

2025-03-11T20:54:00Z

JeetVora:

The BiomarkerKB portal was first released on XXX. A new update is released every XXX months.

==Version 1.0==
{{main|Portal release notes/1.0}}
This version was released on XX.

* XX

API Release Notes

2025-03-11T20:52:28Z

JeetVora: Created page with "cc"

Data Release Notes

2025-03-11T20:52:19Z

JeetVora: Created page with "cc"

2024-12-20T18:28:49Z

JeetVora:

Main Page

2024-12-20T18:28:29Z

JeetVora:

Main Page

2024-12-20T18:27:50Z

JeetVora: