Data Submission/Data Upload - Revision history

MariaKim: /* assessed_entity_type */

2026-09-18T16:53:35Z

assessed_entity_type

@@ Line 109: / Line 109: @@
 === assessed_entity_type ===
 Report in all lowercase.
 Example: gene
 === condition ===

MariaKim at 14:09, 27 August 2026

2026-08-27T14:09:18Z

MariaKim at 12:05, 27 August 2026

2026-08-27T12:05:34Z

@@ Line 17: / Line 17: @@
 === Headers ===
 Your file must contain the following headers:
-* <code>biomarker_index</code> ('''required'''): biomarker counter - integer (1, 2, 3...)
+* <code>biomarker_index</code> ('''required'''): biomarker counter - integer (1, 2, 3...).
-** <code>component_index</code> ('''required'''): component counter within each biomarker (integer). In most cases, a biomarker would have only one component, unless it is a multicomponent biomarker. A multicomponent biomarker is a group of biological markers tested together to provide a comprehensive assessment of health, e.g., a lipid panel (blood test) that measures total cholesterol, LDL, HDL, and triglycerides. These four entities would occupy four rows with the <code>component_index</code> from 1 to 4 (see example table in the "Examples" section).
+** <code>component_index</code> ('''required'''): sub-index within <code>biomarker_index</code>. Component counter within each biomarker (integer). To learn the difference between single and multicomponent biomarkers, see [[Single biomarker]] and [[Multicomponent biomarker]].
-*** <code>entity_index</code> ('''required'''): entity counter within each component (integer). This index is used to represent complex entities such as glycoforms or protein complexes. E.g., in a biomarker where a glycoprotein is being measured, within one component entity 1 is a glycan, while entity 2 is a protein (see example in the "Examples" section).
+*** <code>entity_index</code> ('''required'''): sub-index within <code>component_index</code>. Entity counter within each component (integer). This index is used to represent complex entities such as glycoforms or protein complexes. E.g., in a biomarker where a glycoprotein is being measured, within one component entity 1 is a glycan, while entity 2 is a protein. See [[Multi-entity biomarker]].
 *** <code>assessed_biomarker_entity_id</code> ('''required'''): entity ID for each entity_index
 *** <code>assessed_biomarker_entity</code> ('''required'''): see [[Data Submission/Data Upload#assessed_biomarker_entity|assessed_biomarker_entity]]
@@ Line 33: / Line 33: @@
 * <code>evidence_source</code>: see [[Data Submission/Data Upload#evidence_source|evidence_source]]
 * <code>evidence</code>: see [[Data Submission/Data Upload#evidence|evidence]]
 === Biomarker representation framework ===

MariaKim at 11:52, 27 August 2026

2026-08-27T11:52:41Z

Show changes

MariaKim at 11:16, 27 August 2026

2026-08-27T11:16:26Z

← Older revision		Revision as of 11:16, 27 August 2026
Line 21:		Line 21:
	## 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 [BiomarkerKB 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.
	# 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.

	=== Submission ===		=== Submission ===
Line 98:		Line 97:

	=== biomarker ===		=== biomarker ===
	~~The biomarker field is the most important as follows~~ the [https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary BiomarkerKB Controlled Vocabulary] for standardized reporting. There are several distinctions here and changes are made based on the entity being reported. The text should be in lowercase except when a gene name appears then it should remain all uppercase.		Follow the [https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary BiomarkerKB Controlled Vocabulary] for standardized reporting. There are several distinctions here and changes are made based on the entity being reported. The text should be in lowercase except when a gene name appears then it should remain all uppercase.
	Examples		Examples
	* Increased level of protein SPP1/UPKB:P10451		* Increased level of protein SPP1/UPKB:P10451
Line 195:		Line 194:
	=== specimen ===		=== specimen ===
	Report in all lowercase. Leave blank if not applicable.		Report in all lowercase. Leave blank if not applicable.
	Example: feces		* Example: feces

			If reporting more than one, use separate rows. Example:
			{\| class="wikitable"
			\|-
			! <code>biomarker_index</code> !! <code>component_index</code> !! <code>entity_index</code> !! <code>biomarker</code> !! ... !! <code>specimen</code> !! <code>specimen_id</code>
			\|-
			\| 1 \|\| 1 \|\| 1 \|\| increased protein X \|\| ... \|\| blood \|\| UBERON:0000178
			\|-
			\| 1 \|\| 1 \|\| 1 \|\| increased protein X \|\| ... \|\| urine \|\| UBERON:0001088
			\|}

	=== specimen_id ===		=== specimen_id ===

MariaKim: /* BiomarkerKB dataset datamodel fields */

2026-08-27T11:03:14Z

BiomarkerKB dataset datamodel fields

← Older revision		Revision as of 11:03, 27 August 2026
Line 34:		Line 34:
	This is the standard way to report biomarker data. This section covers how biomarkers should be reported and how other fields should be filled out.		This is the standard way to report biomarker data. This section covers how biomarkers should be reported and how other fields should be filled out.

	~~Biomarker data must be reported using dedicated~~ templates with color-coded mandatory ~~(orange)~~ and optional ~~(green) columns~~.		To make reporting easier, please use these templates with color-coded fields: orange for mandatory and green for optional.
	* Disease Biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/disease_biomarker_template.xlsx Download the Disease Biomarker Template]		* Disease Biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/disease_biomarker_template.xlsx Download the Disease Biomarker Template]
	* Exposure Agent Biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/exposure_agent_biomarker_template.xlsx Download the Exposure Agent Biomarker Template]		* Exposure Agent Biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/exposure_agent_biomarker_template.xlsx Download the Exposure Agent Biomarker Template]

MariaKim: /* assessed_biomarker_entity */

2026-08-27T11:00:31Z

assessed_biomarker_entity

← Older revision		Revision as of 11:00, 27 August 2026
Line 107:		Line 107:

	=== assessed_biomarker_entity ===		=== assessed_biomarker_entity ===
	assessed_biomarker_entity is the entity in which the change is assessed.		<code>assessed_biomarker_entity</code> is the entity in which the change is assessed.
	Should start off with a capital letter but if it is just a gene then it should remain in all capitals (e.g Myosin-binding protein H-like or IL6).		Should start off with a capital letter but if it is just a gene then it should remain in all capitals (e.g Myosin-binding protein H-like or IL6).
	If the entity type is anything but a gene the whole name should be typed out.		If the entity type is anything but a gene the whole name should be typed out.

MariaKim: /* condition_id */

2026-08-27T11:00:16Z

condition_id

← Older revision		Revision as of 11:00, 27 August 2026
Line 169:		Line 169:

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

MariaKim: /* condition */

2026-08-27T11:00:02Z

condition

← Older revision		Revision as of 11:00, 27 August 2026
Line 165:		Line 165:

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

MariaKim: /* specimen_id */

2026-08-27T10:59:44Z

specimen_id

← Older revision		Revision as of 10:59, 27 August 2026
Line 198:		Line 198:

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

← Older revision		Revision as of 14:09, 27 August 2026
Line 12:		Line 12:

	To make reporting easier, please use these templates with color-coded fields: orange for mandatory and green for optional.		To make reporting easier, please use these templates with color-coded fields: orange for mandatory and green for optional.
	* Disease ~~Biomarkers~~: [https://data.biomarkerkb.org/ln2downloads/templates/current/disease_biomarker_template.xlsx Download the Disease Biomarker Template]		* Disease biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/disease_biomarker_template.xlsx Download the Disease Biomarker Template]
	* Exposure ~~Agent Biomarkers~~: [https://data.biomarkerkb.org/ln2downloads/templates/current/exposure_agent_biomarker_template.xlsx Download the Exposure Agent Biomarker Template]		** Example of a disease biomarker: [https://biomarkerkb.org/biomarker/AN5370-8 AN5370-8]
			* Exposure agent biomarkers: [https://data.biomarkerkb.org/ln2downloads/templates/current/exposure_agent_biomarker_template.xlsx Download the Exposure Agent Biomarker Template]
			** Example of an exposure agent biomarker: [https://biomarkerkb.org/biomarker/BMKB151582-1 BMKB151582-1]

	=== Headers ===		=== Headers ===
Line 24:		Line 26:
	*** <code>assessed_entity_type</code> ('''required'''): see [[Data Submission/Data Upload#assessed_entity_type\|assessed_entity_type]]		*** <code>assessed_entity_type</code> ('''required'''): see [[Data Submission/Data Upload#assessed_entity_type\|assessed_entity_type]]
	* <code>biomarker_controlled_vocab</code> ('''required'''): this replaces the field "biomarker" (see below) to emphasize that controlled vocabulary is expected. This field is going to be broken down into three items: change, aspect, and entity.		* <code>biomarker_controlled_vocab</code> ('''required'''): this replaces the field "biomarker" (see below) to emphasize that controlled vocabulary is expected. This field is going to be broken down into three items: change, aspect, and entity.
	* <code>taxonomy_id</code>: taxonomy ID of the organism in which the biomarker has been measured (human, mouse, zebrafish...)		* <code>taxonomy_id</code> (optional): taxonomy ID of the organism in which the biomarker has been measured (human, mouse, zebrafish...)
	* <code>condition</code> or <code>exposure_agent</code> (optional): see [[Data Submission/Data Upload#condition\|condition]] or [[Data Submission/Data Upload#exposure_agent\|exposure_agent]]		* <code>condition</code> or <code>exposure_agent</code> (optional): see [[Data Submission/Data Upload#condition\|condition]] or [[Data Submission/Data Upload#exposure_agent\|exposure_agent]]
	* <code>condition_id</code> or <code>exposure_agent_id</code> ('''required'''): see [[Data Submission/Data Upload#condition_id\|condition_id]] or [[Data Submission/Data Upload#exposure_agent_id\|exposure_agent_id]]		* <code>condition_id</code> or <code>exposure_agent_id</code> ('''required'''): see [[Data Submission/Data Upload#condition_id\|condition_id]] or [[Data Submission/Data Upload#exposure_agent_id\|exposure_agent_id]]
	* <code>best_biomarker_role</code>: see [[Data Submission/Data Upload#best_biomarker_role\|best_biomarker_role]]		* <code>best_biomarker_role</code> (optional): see [[Data Submission/Data Upload#best_biomarker_role\|best_biomarker_role]]
	* <code>specimen</code> (optional): see [[Data_Submission/Data_Upload#specimen\|specimen]]		* <code>specimen</code> (optional): see [[Data_Submission/Data_Upload#specimen\|specimen]]
	* <code>specimen_id</code> ('''required'''): see [[Data Submission/Data Upload#specimen_id\|specimen_id]]		* <code>specimen_id</code> ('''required'''): see [[Data Submission/Data Upload#specimen_id\|specimen_id]]
	* <code>loinc_code</code>: see [[Data Submission/Data Upload#loinc_code\|loinc_code]]		* <code>loinc_code</code> (optional): see [[Data Submission/Data Upload#loinc_code\|loinc_code]]
	* <code>evidence_source</code>: see [[Data Submission/Data Upload#evidence_source\|evidence_source]]		* <code>evidence_source</code> (optional): see [[Data Submission/Data Upload#evidence_source\|evidence_source]]
	* <code>evidence</code>: see [[Data Submission/Data Upload#evidence\|evidence]]		* <code>evidence</code> (optional): see [[Data Submission/Data Upload#evidence\|evidence]]

	=== Biomarker representation framework ===		=== Biomarker representation framework ===