Data Submission/Data Upload

MariaKim — Thu, 07 May 2026 22:18:27 GMT

Standardized and Controlled Vocabulary

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	## <code>component_group</code> containing integers (1, 2, 3...). A multicomponent biomarker must have the same integer in all rows related to that biomarker.		## <code>component_group</code> containing integers (1, 2, 3...). A multicomponent biomarker must have the same integer in all rows related to that biomarker.
	# Other fields and annotations may also be collected from the data source, however if data is missing it can also be inferred or mapped from other sources.		# Other fields and annotations may also be collected from the data source, however if data is missing it can also be inferred or mapped from other sources.
			## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).
	# Apply the following standards to the data when possible:		# Apply the following standards to the data when possible:
	## <code>condition_id</code> = <code>DOID:0080600</code>		## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.
	## <code>specimen_id</code> = <code>UBERON:0000178</code>		## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.
			## <code>loinc_code</code> = <code>LOINC:100153-6</code>. Refer to https://loinc.org/ (you may need to create an account to access the search functionality).
	## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code>		## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code>
	## For <code>assessed_biomarker_entity_id</code> please refer to ~~this~~ GitHub documentation for which standards to follow		## For <code>assessed_biomarker_entity_id</code> please refer to the [https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary GitHub documentation] for which standards to follow
	# Provide extra annotations from your DCC/data with the agreed upon standards from the Biomarker Annotation RFC. This data does not have to follow the data model and can be submitted in a separate file.		# Provide extra annotations from your DCC/data with the agreed upon standards from the Biomarker Annotation RFC. This data does not have to follow the data model and can be submitted in a separate file.
	## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.		## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.
	# Create a tsv/json file with the agreed upon fields which correspond to the biomarker data model. The data dictionary provides details on what the different fields represent.		# Create a tsv/json file with the agreed upon fields which correspond to the biomarker data model. The data dictionary provides details on what the different fields represent.
	## The preferred method for data submission is a json file as it will help ingest the data into the existing data efficiently. However, tsv file submissions are ok as well. In the GitHub, <code>data_conversion.py</code> script exists in the Data Conversion Folder and it will handle tsv to json file conversion and json to tsv file conversion as well.		## The preferred method for data submission is a json file as it will help ingest the data into the existing data efficiently. However, tsv file submissions are ok as well. In the GitHub, <code>data_conversion.py</code> script exists in the Data Conversion Folder and it will handle tsv to json file conversion and json to tsv file conversion as well.
	## The ~~biomarker~~ data page has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example		## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example
	# For panel biomarkers, if the biomarkers are part of the same panel, the biomarker_id value for each biomarker should be any string value that can uniquely identify which rows are part of the same biomarker panel. Documentation		# For panel biomarkers, if the biomarkers are part of the same panel, the biomarker_id value for each biomarker should be any string value that can uniquely identify which rows are part of the same biomarker panel. Documentation
	# If curating data in tsv format: If biomarker rows are part of the same biomarker entry but differ on specimen, evidence, or role, then the biomarker_id for each row should be any string value that can uniquely identify which rows are part of the same biomarker.		# If curating data in tsv format: If biomarker rows are part of the same biomarker entry but differ on specimen, evidence, or role, then the biomarker_id for each row should be any string value that can uniquely identify which rows are part of the same biomarker.
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	There is a standard way to report some biomarker data. This section covers how the actual biomarker should be reported and how other fields should be filled out.		There is a standard way to report some biomarker data. This section covers how the actual biomarker should be reported and how other fields should be filled out.

	=== ~~Condition~~ ===		=== condition ===
	~~Condition~~ should be reported in all lowercase and <code>condition_id</code> (from Disease Ontology, MONDO, or SNOMED) should be provided in the following column		<code>condition</code> should be reported in all lowercase and <code>condition_id</code> (from Disease Ontology, MONDO, or SNOMED) should be provided in the following column

	=== assessed_biomarker_entity ===		=== assessed_biomarker_entity ===
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	=== best_biomarker_role ===		=== best_biomarker_role ===
	Report in all lowercase. Refer to the [https://www.ncbi.nlm.nih.gov/books/NBK326791/ BEST Resource] ~~for~~ the correct biomarker role.		Report in all lowercase. Refer to the [https://www.ncbi.nlm.nih.gov/books/NBK326791/ BEST Resource] to infer the correct biomarker role. Accepted role terms are:
			* diagnostic
			* monitoring
			* predictive
			* prognostic
			* response
			* risk
			* safety

	=== specimen ===		=== specimen ===

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