Data Submission/Data Upload - Revision history

JeetVora: /* biomarker_id */

2026-06-17T21:27:03Z

biomarker_id

← Older revision		Revision as of 21:27, 17 June 2026
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	=== biomarker_id ===		=== biomarker_id ===
	A unique identifier assigned to each canonical biomarker concept. The canonical biomarker represents the measured change or observation (e.g. "increased IL6 expression"); disease- or condition-specific records are child records that share the same biomarker_id while differing in condition, specimen, or evidence.		A unique identifier assigned to each canonical biomarker concept. The canonical biomarker represents the measured change or observation (e.g. "increased IL6 expression"); disease- or condition-specific records are child records that share the same biomarker_id while differing in condition, specimen, or evidence. biomarker_id is assigned by the biomarkerKB data processing scripts automatically so the field can be left blank.

	=== biomarker ===		=== biomarker ===

JeetVora at 21:25, 17 June 2026

2026-06-17T21:25:56Z

← Older revision		Revision as of 21:25, 17 June 2026
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	=== condition_id ===		=== condition_id ===
	`condition_id` (from Disease Ontology, MONDO, or SNOMED or ~~NCIT~~) should be provided in the following column.		`condition_id` (from Disease Ontology, MONDO, or SNOMED or NCIt) should be provided in the following column.
	Example: DOID:219		Example: DOID:219

	=== exposure_agent ===		=== exposure_agent ===
	~~A core field.~~ Report in all lowercase. The exposure_agent documents any external stimulus, treatment, environmental factor, or intervention relevant to the biomarker's expression or activity. It provides context for biomarkers that respond to specific exposures rather than intrinsic disease processes (for example, response biomarkers). Leave blank if not applicable.		Report in all lowercase. The exposure_agent documents any external stimulus, treatment, environmental factor, or intervention relevant to the biomarker's expression or activity. It provides context for biomarkers that respond to specific exposures rather than intrinsic disease processes (for example, response biomarkers). Leave blank if not applicable.
	Example: cisplatin		Example: cisplatin

JeetVora at 21:23, 17 June 2026

2026-06-17T21:23:38Z

← Older revision		Revision as of 21:23, 17 June 2026
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	=== assessed_entity_type ===		=== assessed_entity_type ===
	Report in all lowercase.		Report in all lowercase.
			Example: gene

	=== condition ===		=== condition ===
	~~<code>~~condition~~</code>~~ should be reported in all lowercase		`condition` should be reported in all lowercase.
			Example: colon cancer

	=== condition_id ===		=== condition_id ===
	~~<code>~~condition_id~~</code>~~ (from Disease Ontology, MONDO, or SNOMED or NCIT) should be provided in the following column		`condition_id` (from Disease Ontology, MONDO, or SNOMED or NCIT) should be provided in the following column.
			Example: DOID:219

	=== exposure_agent ===		=== exposure_agent ===
	A core field. Report in all lowercase. The exposure_agent documents any external stimulus, treatment, environmental factor, or intervention relevant to the biomarker's expression or activity. It provides context for biomarkers that respond to specific exposures rather than intrinsic disease processes (for example, response biomarkers). Leave blank if not applicable.		A core field. Report in all lowercase. The exposure_agent documents any external stimulus, treatment, environmental factor, or intervention relevant to the biomarker's expression or activity. It provides context for biomarkers that respond to specific exposures rather than intrinsic disease processes (for example, response biomarkers). Leave blank if not applicable.
			Example: cisplatin

	=== exposure_agent_id ===		=== exposure_agent_id ===
	The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.		The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.
			Example: CHEBI:27899

	=== best_biomarker_role ===		=== best_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:		Report in all lowercase. Refer to the [BEST Resource](https://www.ncbi.nlm.nih.gov/books/NBK326791/) to infer the correct biomarker role. Accepted role terms are:
	* ~~'''~~diagnostic~~'''~~: Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.
	* ~~'''~~monitoring~~'''~~: Assesses the status of a disease, medical condition, or exposure to a medical product over time.		* diagnostic: Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.
	* ~~'''~~predictive~~'''~~: Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.		* monitoring: Assesses the status of a disease, medical condition, or exposure to a medical product over time.
	* ~~'''~~prognostic~~'''~~: Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.		* predictive: Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.
	* ~~'''~~response~~'''~~: Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.		* prognostic: Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.
	* ~~'''~~risk~~'''~~: Indicates the potential for an individual to develop a disease or condition in the future.		* response: Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.
	* ~~'''~~safety~~'''~~: Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.		* risk: Indicates the potential for an individual to develop a disease or condition in the future.
			* safety: Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.

			Example: diagnostic

	=== specimen ===		=== specimen ===
	Report in all lowercase. Leave blank if not applicable.		Report in all lowercase. Leave blank if not applicable.
			Example: feces

	=== specimen_id ===		=== specimen_id ===
	~~<code>~~specimen_id~~</code>~~ in the following column should be from UBERON. Leave blank if not applicable.		`specimen_id` in the following column should be from UBERON. Leave blank if not applicable.
			Example: UBERON:0001988

	=== loinc_code ===		=== loinc_code ===
	Report the Logical Observation Identifiers Names and Codes (LOINC) code corresponding to the test or measurement (e.g. 77354-9). Leave blank if not applicable.		Report the Logical Observation Identifiers Names and Codes (LOINC) code corresponding to the test or measurement (e.g. 77354-9). Leave blank if not applicable.
			Example: 77354-9
	~~=== evidence_source ===~~
	~~The source of the supporting evidence, reported as the resource followed by the identifier within that resource (e.g. a PubMed ID such as 16077070, or a resource~~-~~prefixed accession such as EDRN: 107).~~

	~~=== evidence ===~~
	A contextual field capturing the supporting documentation, literature references, experimental findings, or curated assertions that justify the biomarker's inclusion and characterization. It provides transparency and traceability back to primary sources.

JeetVora at 21:20, 17 June 2026

2026-06-17T21:20:07Z

← Older revision		Revision as of 21:20, 17 June 2026
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	=== specimen ===		=== specimen ===
	Report in all lowercase		Report in all lowercase. Leave blank if not applicable.

	=== specimen_id ===		=== specimen_id ===
	<code>specimen_id</code> in the following column should be from UBERON.		<code>specimen_id</code> in the following column should be from UBERON. Leave blank if not applicable.

	=== loinc_code ===		=== loinc_code ===
	Report the Logical Observation Identifiers Names and Codes (LOINC) code corresponding to the test or measurement (e.g. 77354-9).		Report the Logical Observation Identifiers Names and Codes (LOINC) code corresponding to the test or measurement (e.g. 77354-9). Leave blank if not applicable.

	=== evidence_source ===		=== evidence_source ===

JeetVora at 21:19, 17 June 2026

2026-06-17T21:19:02Z

Show changes

MariaKim: /* Instructions to submit Biomarker Data */

2026-05-26T01:24:59Z

Instructions to submit Biomarker Data

← Older revision		Revision as of 01:24, 26 May 2026
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	## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code>		## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code>
	## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code>		## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code>
	## <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...) from 1 to N where N is the number of components. Normally N would simply be equal to the number of rows, unless your data contains multicomponent biomarkers. 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).		## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).

MariaKim: best_biomarker_role

2026-05-19T14:29:18Z

best_biomarker_role

← Older revision		Revision as of 14:29, 19 May 2026
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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] to infer the correct biomarker role. Accepted role terms are:		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		* '''diagnostic''': Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.
	* monitoring		* '''monitoring''': Assesses the status of a disease, medical condition, or exposure to a medical product over time.
	* predictive		* '''predictive''': Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.
	* prognostic		* '''prognostic''': Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.
	* response		* '''response''': Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.
	* risk		* '''risk''': Indicates the potential for an individual to develop a disease or condition in the future.
	* safety		* '''safety''': Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.

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

MariaKim: /* Standardized and Controlled Vocabulary */

2026-05-07T22:18:27Z

Standardized and Controlled Vocabulary

← Older revision		Revision as of 22:18, 7 May 2026
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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 ===

MariaKim at 22:14, 7 May 2026

2026-05-07T22:14:57Z

MariaKim at 22:52, 30 April 2026

2026-04-30T22:52:12Z

← Older revision		Revision as of 22:52, 30 April 2026
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	=== Condition ===		=== Condition ===
	Condition should be reported in all lowercase and ~~condition ID~~ (from Disease Ontology ID) should be provided in the following column		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

	=== assessed_biomarker_entity ===		=== assessed_biomarker_entity ===
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	=== specimen ===		=== specimen ===
	Report in all lowercase and ~~specimen_ID~~ in the following column should be from UBERON.		Report in all lowercase and <code>specimen_id</code> in the following column should be from UBERON.

	=== biomarker ===		=== biomarker ===

← Older revision		Revision as of 22:14, 7 May 2026
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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 ===