https://wiki.biomarkerkb.org/api.php?action=feedcontributions&feedformat=atom&user=JeetVoraBiomarkerKB Wiki - User contributions [en]2026-06-22T20:44:22ZUser contributionsMediaWiki 1.42.3https://wiki.biomarkerkb.org/index.php?title=Data_Submission/Data_Upload&diff=235Data Submission/Data Upload2026-06-17T21:27:03Z<p>JeetVora: /* biomarker_id */</p>
<hr />
<div>==Instructions to submit Biomarker Data==<br />
To submit data for the BiomarkerKB Portal, the biomarker data model must be followed. Instructions on how to format the data for submission, where to send it, and creating a BCO for the data submitted will be provided below.<br />
<br />
# Biomarker data collected should follow the biomarker data model.<br />
# "Core" fields should be filled in from the data source where biomarker data is collected. Core fields:<br />
## <code>biomarker</code><br />
## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code><br />
## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code><br />
## <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.<br />
# 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.<br />
## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).<br />
# Apply the following standards to the data when possible:<br />
## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.<br />
## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.<br />
## <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).<br />
## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code><br />
## 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<br />
# 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 or can be added in the <code>comment</code> field .<br />
## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.<br />
# 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.<br />
## 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.<br />
## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example<br />
# 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<br />
# 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.<br />
<br />
=== Submission === <br />
Once data is formatted and cleaned please send any data to mazumder_lab@gwu.edu.<br />
# Concurrently with submitting data please fill out the BCO Information: Biomarker Data Google Form.<br />
## This will give metadata and description on how biomarker data was collected and is important for adding submitted data to the Biomarker Data page. An example of a previous BCO is provided in the sheet and available on the biomarker data page as well. [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data/BCO_000435 Example]<br />
# If there are any further questions please consult the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for contributing data or reach out to Daniall using the email above.<br />
<br />
==BiomarkerKB dataset datamodel fields==<br />
<br />
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.<br />
=== Biomarker representation framework ===<br />
A biomarker is not simply a gene, protein, metabolite, or other biological entity. A biomarker must include a defined measurement or change concept — such as presence, absence, increase, or decrease — describing what is observed. For example, EGFR alone is not a biomarker, but a specific EGFR mutation used for diagnostic, prognostic, or treatment-selection purposes is. Likewise, "IL6" alone is not a biomarker, but "increased IL6 expression" in a defined clinical context may be.<br />
<br />
The fields below fall into two groups. Core fields directly align with the biomarker definition: <code>biomarker</code>, <code>assessed_biomarker_entity</code>, <code>assessed_biomarker_entity_id</code>, <code>condition</code>, <code>condition_id</code>, <code>exposure_agent</code>, and <code>exposure_agent_id</code>. Contextual fields enrich the representation: <code>specimen</code>, <code>best_biomarker_role</code>, and <code>evidence</code>.<br />
<br />
In the BiomarkerKB accession model, the canonical biomarker concept represents the measured change or observation (e.g. "increased IL6 expression"), and disease- or condition-specific records are represented as child records linked to that canonical biomarker.<br />
<br />
=== biomarker_id ===<br />
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.<br />
<br />
=== biomarker ===<br />
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.<br />
Examples<br />
* Increased level of protein SPP1/UPKB:P10451<br />
* Increased expression of RNA PCA3/HGNC:8637<br />
* Increased expression of gene B2M PCA3/NCBI:567<br />
* Increased methylation in gene VIM/NCBI:7431<br /><br />
For more examples please refer to the [https://data.biomarkerkb.org/ BiomarkerKB Data Page]<br />
<br />
=== assessed_biomarker_entity ===<br />
assessed_biomarker_entity is the entity in which the change is assessed.<br />
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).<br />
If the entity type is anything but a gene the whole name should be typed out.<br />
<br />
=== assessed_biomarker_entity_id ===<br />
{| class="wikitable"<br />
!Assessed Entity Type<br />
!Resource (in order of preference/availability)<br />
|-<br />
|Carbohydrate<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Cell<br />
|Cell Ontology (CO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Chemical Element<br />
|PubChem (PCCID) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|DNA<br />
|National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Gene<br />
|NCBI<br />
|-<br />
|Gene (mutation)<br />
|NCBI dbSNP<br />
|-<br />
|Glycan<br />
|GlyTouCan Accession (GTC) -> PubChem (PCCID)<br />
|-<br />
|Lipoprotein<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Metabolite<br />
|PubChem (PCCID) -> Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Peptide<br />
|Protein Ontology (PRO)<br />
|-<br />
|Protein<br />
|Uniprot (UPKB) -> Protein Data Bank (PDB) -> Protein Ontology (PRO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Protein Complex<br />
|Protein Ontology (PRO) -> Gene Ontology (GO)<br />
|-<br />
|RNA<br />
|HUGO Gene Nomenclature Committee (HGNC) -> RNA Central (RNAC)<br />
|-<br />
|miRNA<br />
|miRBase (MRB)<br />
|}<br />
Refer to the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for the correct resource.<br />
<br />
=== assessed_entity_type ===<br />
Report in all lowercase.<br />
Example: gene<br />
<br />
=== condition ===<br />
`condition` should be reported in all lowercase.<br />
Example: colon cancer<br />
<br />
=== condition_id ===<br />
`condition_id` (from Disease Ontology, MONDO, or SNOMED or NCIt) should be provided in the following column.<br />
Example: DOID:219<br />
<br />
=== exposure_agent ===<br />
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.<br />
Example: cisplatin<br />
<br />
=== exposure_agent_id ===<br />
The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.<br />
Example: CHEBI:27899<br />
<br />
=== best_biomarker_role ===<br />
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:<br />
<br />
* diagnostic: Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.<br />
* monitoring: Assesses the status of a disease, medical condition, or exposure to a medical product over time.<br />
* predictive: Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.<br />
* prognostic: Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.<br />
* response: Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.<br />
* risk: Indicates the potential for an individual to develop a disease or condition in the future.<br />
* safety: Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.<br />
<br />
Example: diagnostic<br />
<br />
=== specimen ===<br />
Report in all lowercase. Leave blank if not applicable.<br />
Example: feces<br />
<br />
=== specimen_id ===<br />
`specimen_id` in the following column should be from UBERON. Leave blank if not applicable.<br />
Example: UBERON:0001988<br />
<br />
=== loinc_code ===<br />
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.<br />
Example: 77354-9</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Submission/Data_Upload&diff=234Data Submission/Data Upload2026-06-17T21:25:56Z<p>JeetVora: </p>
<hr />
<div>==Instructions to submit Biomarker Data==<br />
To submit data for the BiomarkerKB Portal, the biomarker data model must be followed. Instructions on how to format the data for submission, where to send it, and creating a BCO for the data submitted will be provided below.<br />
<br />
# Biomarker data collected should follow the biomarker data model.<br />
# "Core" fields should be filled in from the data source where biomarker data is collected. Core fields:<br />
## <code>biomarker</code><br />
## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code><br />
## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code><br />
## <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.<br />
# 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.<br />
## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).<br />
# Apply the following standards to the data when possible:<br />
## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.<br />
## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.<br />
## <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).<br />
## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code><br />
## 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<br />
# 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 or can be added in the <code>comment</code> field .<br />
## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.<br />
# 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.<br />
## 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.<br />
## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example<br />
# 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<br />
# 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.<br />
<br />
=== Submission === <br />
Once data is formatted and cleaned please send any data to mazumder_lab@gwu.edu.<br />
# Concurrently with submitting data please fill out the BCO Information: Biomarker Data Google Form.<br />
## This will give metadata and description on how biomarker data was collected and is important for adding submitted data to the Biomarker Data page. An example of a previous BCO is provided in the sheet and available on the biomarker data page as well. [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data/BCO_000435 Example]<br />
# If there are any further questions please consult the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for contributing data or reach out to Daniall using the email above.<br />
<br />
==BiomarkerKB dataset datamodel fields==<br />
<br />
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.<br />
=== Biomarker representation framework ===<br />
A biomarker is not simply a gene, protein, metabolite, or other biological entity. A biomarker must include a defined measurement or change concept — such as presence, absence, increase, or decrease — describing what is observed. For example, EGFR alone is not a biomarker, but a specific EGFR mutation used for diagnostic, prognostic, or treatment-selection purposes is. Likewise, "IL6" alone is not a biomarker, but "increased IL6 expression" in a defined clinical context may be.<br />
<br />
The fields below fall into two groups. Core fields directly align with the biomarker definition: <code>biomarker</code>, <code>assessed_biomarker_entity</code>, <code>assessed_biomarker_entity_id</code>, <code>condition</code>, <code>condition_id</code>, <code>exposure_agent</code>, and <code>exposure_agent_id</code>. Contextual fields enrich the representation: <code>specimen</code>, <code>best_biomarker_role</code>, and <code>evidence</code>.<br />
<br />
In the BiomarkerKB accession model, the canonical biomarker concept represents the measured change or observation (e.g. "increased IL6 expression"), and disease- or condition-specific records are represented as child records linked to that canonical biomarker.<br />
<br />
=== biomarker_id ===<br />
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.<br />
<br />
=== biomarker ===<br />
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.<br />
Examples<br />
* Increased level of protein SPP1/UPKB:P10451<br />
* Increased expression of RNA PCA3/HGNC:8637<br />
* Increased expression of gene B2M PCA3/NCBI:567<br />
* Increased methylation in gene VIM/NCBI:7431<br /><br />
For more examples please refer to the [https://data.biomarkerkb.org/ BiomarkerKB Data Page]<br />
<br />
=== assessed_biomarker_entity ===<br />
assessed_biomarker_entity is the entity in which the change is assessed.<br />
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).<br />
If the entity type is anything but a gene the whole name should be typed out.<br />
<br />
=== assessed_biomarker_entity_id ===<br />
{| class="wikitable"<br />
!Assessed Entity Type<br />
!Resource (in order of preference/availability)<br />
|-<br />
|Carbohydrate<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Cell<br />
|Cell Ontology (CO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Chemical Element<br />
|PubChem (PCCID) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|DNA<br />
|National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Gene<br />
|NCBI<br />
|-<br />
|Gene (mutation)<br />
|NCBI dbSNP<br />
|-<br />
|Glycan<br />
|GlyTouCan Accession (GTC) -> PubChem (PCCID)<br />
|-<br />
|Lipoprotein<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Metabolite<br />
|PubChem (PCCID) -> Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Peptide<br />
|Protein Ontology (PRO)<br />
|-<br />
|Protein<br />
|Uniprot (UPKB) -> Protein Data Bank (PDB) -> Protein Ontology (PRO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Protein Complex<br />
|Protein Ontology (PRO) -> Gene Ontology (GO)<br />
|-<br />
|RNA<br />
|HUGO Gene Nomenclature Committee (HGNC) -> RNA Central (RNAC)<br />
|-<br />
|miRNA<br />
|miRBase (MRB)<br />
|}<br />
Refer to the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for the correct resource.<br />
<br />
=== assessed_entity_type ===<br />
Report in all lowercase.<br />
Example: gene<br />
<br />
=== condition ===<br />
`condition` should be reported in all lowercase.<br />
Example: colon cancer<br />
<br />
=== condition_id ===<br />
`condition_id` (from Disease Ontology, MONDO, or SNOMED or NCIt) should be provided in the following column.<br />
Example: DOID:219<br />
<br />
=== exposure_agent ===<br />
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.<br />
Example: cisplatin<br />
<br />
=== exposure_agent_id ===<br />
The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.<br />
Example: CHEBI:27899<br />
<br />
=== best_biomarker_role ===<br />
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:<br />
<br />
* diagnostic: Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.<br />
* monitoring: Assesses the status of a disease, medical condition, or exposure to a medical product over time.<br />
* predictive: Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.<br />
* prognostic: Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.<br />
* response: Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.<br />
* risk: Indicates the potential for an individual to develop a disease or condition in the future.<br />
* safety: Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.<br />
<br />
Example: diagnostic<br />
<br />
=== specimen ===<br />
Report in all lowercase. Leave blank if not applicable.<br />
Example: feces<br />
<br />
=== specimen_id ===<br />
`specimen_id` in the following column should be from UBERON. Leave blank if not applicable.<br />
Example: UBERON:0001988<br />
<br />
=== loinc_code ===<br />
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.<br />
Example: 77354-9</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Submission/Data_Upload&diff=233Data Submission/Data Upload2026-06-17T21:23:38Z<p>JeetVora: </p>
<hr />
<div>==Instructions to submit Biomarker Data==<br />
To submit data for the BiomarkerKB Portal, the biomarker data model must be followed. Instructions on how to format the data for submission, where to send it, and creating a BCO for the data submitted will be provided below.<br />
<br />
# Biomarker data collected should follow the biomarker data model.<br />
# "Core" fields should be filled in from the data source where biomarker data is collected. Core fields:<br />
## <code>biomarker</code><br />
## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code><br />
## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code><br />
## <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.<br />
# 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.<br />
## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).<br />
# Apply the following standards to the data when possible:<br />
## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.<br />
## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.<br />
## <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).<br />
## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code><br />
## 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<br />
# 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 or can be added in the <code>comment</code> field .<br />
## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.<br />
# 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.<br />
## 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.<br />
## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example<br />
# 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<br />
# 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.<br />
<br />
=== Submission === <br />
Once data is formatted and cleaned please send any data to mazumder_lab@gwu.edu.<br />
# Concurrently with submitting data please fill out the BCO Information: Biomarker Data Google Form.<br />
## This will give metadata and description on how biomarker data was collected and is important for adding submitted data to the Biomarker Data page. An example of a previous BCO is provided in the sheet and available on the biomarker data page as well. [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data/BCO_000435 Example]<br />
# If there are any further questions please consult the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for contributing data or reach out to Daniall using the email above.<br />
<br />
==BiomarkerKB dataset datamodel fields==<br />
<br />
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.<br />
=== Biomarker representation framework ===<br />
A biomarker is not simply a gene, protein, metabolite, or other biological entity. A biomarker must include a defined measurement or change concept — such as presence, absence, increase, or decrease — describing what is observed. For example, EGFR alone is not a biomarker, but a specific EGFR mutation used for diagnostic, prognostic, or treatment-selection purposes is. Likewise, "IL6" alone is not a biomarker, but "increased IL6 expression" in a defined clinical context may be.<br />
<br />
The fields below fall into two groups. Core fields directly align with the biomarker definition: <code>biomarker</code>, <code>assessed_biomarker_entity</code>, <code>assessed_biomarker_entity_id</code>, <code>condition</code>, <code>condition_id</code>, <code>exposure_agent</code>, and <code>exposure_agent_id</code>. Contextual fields enrich the representation: <code>specimen</code>, <code>best_biomarker_role</code>, and <code>evidence</code>.<br />
<br />
In the BiomarkerKB accession model, the canonical biomarker concept represents the measured change or observation (e.g. "increased IL6 expression"), and disease- or condition-specific records are represented as child records linked to that canonical biomarker.<br />
<br />
=== biomarker_id ===<br />
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.<br />
<br />
=== biomarker ===<br />
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.<br />
Examples<br />
* Increased level of protein SPP1/UPKB:P10451<br />
* Increased expression of RNA PCA3/HGNC:8637<br />
* Increased expression of gene B2M PCA3/NCBI:567<br />
* Increased methylation in gene VIM/NCBI:7431<br /><br />
For more examples please refer to the [https://data.biomarkerkb.org/ BiomarkerKB Data Page]<br />
<br />
=== assessed_biomarker_entity ===<br />
assessed_biomarker_entity is the entity in which the change is assessed.<br />
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).<br />
If the entity type is anything but a gene the whole name should be typed out.<br />
<br />
=== assessed_biomarker_entity_id ===<br />
{| class="wikitable"<br />
!Assessed Entity Type<br />
!Resource (in order of preference/availability)<br />
|-<br />
|Carbohydrate<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Cell<br />
|Cell Ontology (CO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Chemical Element<br />
|PubChem (PCCID) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|DNA<br />
|National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Gene<br />
|NCBI<br />
|-<br />
|Gene (mutation)<br />
|NCBI dbSNP<br />
|-<br />
|Glycan<br />
|GlyTouCan Accession (GTC) -> PubChem (PCCID)<br />
|-<br />
|Lipoprotein<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Metabolite<br />
|PubChem (PCCID) -> Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Peptide<br />
|Protein Ontology (PRO)<br />
|-<br />
|Protein<br />
|Uniprot (UPKB) -> Protein Data Bank (PDB) -> Protein Ontology (PRO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Protein Complex<br />
|Protein Ontology (PRO) -> Gene Ontology (GO)<br />
|-<br />
|RNA<br />
|HUGO Gene Nomenclature Committee (HGNC) -> RNA Central (RNAC)<br />
|-<br />
|miRNA<br />
|miRBase (MRB)<br />
|}<br />
Refer to the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for the correct resource.<br />
<br />
=== assessed_entity_type ===<br />
Report in all lowercase.<br />
Example: gene<br />
<br />
=== condition ===<br />
`condition` should be reported in all lowercase.<br />
Example: colon cancer<br />
<br />
=== condition_id ===<br />
`condition_id` (from Disease Ontology, MONDO, or SNOMED or NCIT) should be provided in the following column.<br />
Example: DOID:219<br />
<br />
=== exposure_agent ===<br />
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.<br />
Example: cisplatin<br />
<br />
=== exposure_agent_id ===<br />
The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.<br />
Example: CHEBI:27899<br />
<br />
=== best_biomarker_role ===<br />
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:<br />
<br />
* diagnostic: Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.<br />
* monitoring: Assesses the status of a disease, medical condition, or exposure to a medical product over time.<br />
* predictive: Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.<br />
* prognostic: Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.<br />
* response: Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.<br />
* risk: Indicates the potential for an individual to develop a disease or condition in the future.<br />
* safety: Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.<br />
<br />
Example: diagnostic<br />
<br />
=== specimen ===<br />
Report in all lowercase. Leave blank if not applicable.<br />
Example: feces<br />
<br />
=== specimen_id ===<br />
`specimen_id` in the following column should be from UBERON. Leave blank if not applicable.<br />
Example: UBERON:0001988<br />
<br />
=== loinc_code ===<br />
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.<br />
Example: 77354-9</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Submission/Data_Upload&diff=232Data Submission/Data Upload2026-06-17T21:20:07Z<p>JeetVora: </p>
<hr />
<div>==Instructions to submit Biomarker Data==<br />
To submit data for the BiomarkerKB Portal, the biomarker data model must be followed. Instructions on how to format the data for submission, where to send it, and creating a BCO for the data submitted will be provided below.<br />
<br />
# Biomarker data collected should follow the biomarker data model.<br />
# "Core" fields should be filled in from the data source where biomarker data is collected. Core fields:<br />
## <code>biomarker</code><br />
## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code><br />
## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code><br />
## <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.<br />
# 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.<br />
## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).<br />
# Apply the following standards to the data when possible:<br />
## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.<br />
## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.<br />
## <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).<br />
## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code><br />
## 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<br />
# 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 or can be added in the <code>comment</code> field .<br />
## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.<br />
# 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.<br />
## 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.<br />
## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example<br />
# 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<br />
# 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.<br />
<br />
=== Submission === <br />
Once data is formatted and cleaned please send any data to mazumder_lab@gwu.edu.<br />
# Concurrently with submitting data please fill out the BCO Information: Biomarker Data Google Form.<br />
## This will give metadata and description on how biomarker data was collected and is important for adding submitted data to the Biomarker Data page. An example of a previous BCO is provided in the sheet and available on the biomarker data page as well. [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data/BCO_000435 Example]<br />
# If there are any further questions please consult the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for contributing data or reach out to Daniall using the email above.<br />
<br />
==BiomarkerKB dataset datamodel fields==<br />
<br />
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.<br />
=== Biomarker representation framework ===<br />
A biomarker is not simply a gene, protein, metabolite, or other biological entity. A biomarker must include a defined measurement or change concept — such as presence, absence, increase, or decrease — describing what is observed. For example, EGFR alone is not a biomarker, but a specific EGFR mutation used for diagnostic, prognostic, or treatment-selection purposes is. Likewise, "IL6" alone is not a biomarker, but "increased IL6 expression" in a defined clinical context may be.<br />
<br />
The fields below fall into two groups. Core fields directly align with the biomarker definition: <code>biomarker</code>, <code>assessed_biomarker_entity</code>, <code>assessed_biomarker_entity_id</code>, <code>condition</code>, <code>condition_id</code>, <code>exposure_agent</code>, and <code>exposure_agent_id</code>. Contextual fields enrich the representation: <code>specimen</code>, <code>best_biomarker_role</code>, and <code>evidence</code>.<br />
<br />
In the BiomarkerKB accession model, the canonical biomarker concept represents the measured change or observation (e.g. "increased IL6 expression"), and disease- or condition-specific records are represented as child records linked to that canonical biomarker.<br />
<br />
=== biomarker_id ===<br />
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.<br />
<br />
=== biomarker ===<br />
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.<br />
Examples<br />
* Increased level of protein SPP1/UPKB:P10451<br />
* Increased expression of RNA PCA3/HGNC:8637<br />
* Increased expression of gene B2M PCA3/NCBI:567<br />
* Increased methylation in gene VIM/NCBI:7431<br /><br />
For more examples please refer to the [https://data.biomarkerkb.org/ BiomarkerKB Data Page]<br />
<br />
=== assessed_biomarker_entity ===<br />
assessed_biomarker_entity is the entity in which the change is assessed.<br />
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).<br />
If the entity type is anything but a gene the whole name should be typed out.<br />
<br />
=== assessed_biomarker_entity_id ===<br />
{| class="wikitable"<br />
!Assessed Entity Type<br />
!Resource (in order of preference/availability)<br />
|-<br />
|Carbohydrate<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Cell<br />
|Cell Ontology (CO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Chemical Element<br />
|PubChem (PCCID) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|DNA<br />
|National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Gene<br />
|NCBI<br />
|-<br />
|Gene (mutation)<br />
|NCBI dbSNP<br />
|-<br />
|Glycan<br />
|GlyTouCan Accession (GTC) -> PubChem (PCCID)<br />
|-<br />
|Lipoprotein<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Metabolite<br />
|PubChem (PCCID) -> Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Peptide<br />
|Protein Ontology (PRO)<br />
|-<br />
|Protein<br />
|Uniprot (UPKB) -> Protein Data Bank (PDB) -> Protein Ontology (PRO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Protein Complex<br />
|Protein Ontology (PRO) -> Gene Ontology (GO)<br />
|-<br />
|RNA<br />
|HUGO Gene Nomenclature Committee (HGNC) -> RNA Central (RNAC)<br />
|-<br />
|miRNA<br />
|miRBase (MRB)<br />
|}<br />
Refer to the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for the correct resource.<br />
<br />
=== assessed_entity_type ===<br />
Report in all lowercase.<br />
<br />
=== condition ===<br />
<code>condition</code> should be reported in all lowercase <br />
<br />
=== condition_id ===<br />
<code>condition_id</code> (from Disease Ontology, MONDO, or SNOMED or NCIT) should be provided in the following column<br />
<br />
=== exposure_agent ===<br />
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.<br />
<br />
=== exposure_agent_id ===<br />
The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.<br />
<br />
=== best_biomarker_role ===<br />
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:<br />
* '''diagnostic''': Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.<br />
* '''monitoring''': Assesses the status of a disease, medical condition, or exposure to a medical product over time.<br />
* '''predictive''': Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.<br />
* '''prognostic''': Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.<br />
* '''response''': Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.<br />
* '''risk''': Indicates the potential for an individual to develop a disease or condition in the future.<br />
* '''safety''': Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.<br />
<br />
=== specimen ===<br />
Report in all lowercase. Leave blank if not applicable. <br />
<br />
=== specimen_id ===<br />
<code>specimen_id</code> in the following column should be from UBERON. Leave blank if not applicable.<br />
<br />
=== loinc_code ===<br />
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.<br />
<br />
=== evidence_source ===<br />
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).<br />
<br />
=== evidence ===<br />
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.</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Submission/Data_Upload&diff=231Data Submission/Data Upload2026-06-17T21:19:02Z<p>JeetVora: </p>
<hr />
<div>==Instructions to submit Biomarker Data==<br />
To submit data for the BiomarkerKB Portal, the biomarker data model must be followed. Instructions on how to format the data for submission, where to send it, and creating a BCO for the data submitted will be provided below.<br />
<br />
# Biomarker data collected should follow the biomarker data model.<br />
# "Core" fields should be filled in from the data source where biomarker data is collected. Core fields:<br />
## <code>biomarker</code><br />
## <code>assessed_biomarker_entity</code> and <code>assessed_biomarker_entity_id</code><br />
## <code>condition</code> and <code>condition_id</code> OR <code>exposure_agent</code> and <code>exposure_agent_id</code><br />
## <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.<br />
# 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.<br />
## <code>evidence</code> is one or more exact citations from the evidence source (in most cases, it will be the PubMed publication).<br />
# Apply the following standards to the data when possible:<br />
## <code>condition_id</code> = <code>DOID:0080600</code>. Refer to https://disease-ontology.org/do/.<br />
## <code>specimen_id</code> = <code>UBERON:0000178</code>. Refer to https://www.ebi.ac.uk/ols4/ontologies/uberon.<br />
## <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).<br />
## <code>evidence_source</code> = <code>SOURCE:ID</code>, for example <code>PubMed:32677844</code><br />
## 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<br />
# 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 or can be added in the <code>comment</code> field .<br />
## For example: Relevant EHR data/LOINC data for biomarkers/biomarker entities can be included in a separate sheet.<br />
# 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.<br />
## 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.<br />
## The [BiomarkerKB data page] has examples of tsv data submissions and how the data should be formatted with the appropriate biomarker fields. Example<br />
# 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<br />
# 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.<br />
<br />
=== Submission === <br />
Once data is formatted and cleaned please send any data to mazumder_lab@gwu.edu.<br />
# Concurrently with submitting data please fill out the BCO Information: Biomarker Data Google Form.<br />
## This will give metadata and description on how biomarker data was collected and is important for adding submitted data to the Biomarker Data page. An example of a previous BCO is provided in the sheet and available on the biomarker data page as well. [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data/BCO_000435 Example]<br />
# If there are any further questions please consult the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for contributing data or reach out to Daniall using the email above.<br />
<br />
==BiomarkerKB dataset datamodel fields==<br />
<br />
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.<br />
=== Biomarker representation framework ===<br />
A biomarker is not simply a gene, protein, metabolite, or other biological entity. A biomarker must include a defined measurement or change concept — such as presence, absence, increase, or decrease — describing what is observed. For example, EGFR alone is not a biomarker, but a specific EGFR mutation used for diagnostic, prognostic, or treatment-selection purposes is. Likewise, "IL6" alone is not a biomarker, but "increased IL6 expression" in a defined clinical context may be.<br />
<br />
The fields below fall into two groups. Core fields directly align with the biomarker definition: <code>biomarker</code>, <code>assessed_biomarker_entity</code>, <code>assessed_biomarker_entity_id</code>, <code>condition</code>, <code>condition_id</code>, <code>exposure_agent</code>, and <code>exposure_agent_id</code>. Contextual fields enrich the representation: <code>specimen</code>, <code>best_biomarker_role</code>, and <code>evidence</code>.<br />
<br />
In the BiomarkerKB accession model, the canonical biomarker concept represents the measured change or observation (e.g. "increased IL6 expression"), and disease- or condition-specific records are represented as child records linked to that canonical biomarker.<br />
<br />
=== biomarker_id ===<br />
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.<br />
<br />
=== biomarker ===<br />
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.<br />
Examples<br />
* Increased level of protein SPP1/UPKB:P10451<br />
* Increased expression of RNA PCA3/HGNC:8637<br />
* Increased expression of gene B2M PCA3/NCBI:567<br />
* Increased methylation in gene VIM/NCBI:7431<br /><br />
For more examples please refer to the [https://data.biomarkerkb.org/ BiomarkerKB Data Page]<br />
<br />
=== assessed_biomarker_entity ===<br />
assessed_biomarker_entity is the entity in which the change is assessed.<br />
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).<br />
If the entity type is anything but a gene the whole name should be typed out.<br />
<br />
=== assessed_biomarker_entity_id ===<br />
{| class="wikitable"<br />
!Assessed Entity Type<br />
!Resource (in order of preference/availability)<br />
|-<br />
|Carbohydrate<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Cell<br />
|Cell Ontology (CO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Chemical Element<br />
|PubChem (PCCID) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|DNA<br />
|National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Gene<br />
|NCBI<br />
|-<br />
|Gene (mutation)<br />
|NCBI dbSNP<br />
|-<br />
|Glycan<br />
|GlyTouCan Accession (GTC) -> PubChem (PCCID)<br />
|-<br />
|Lipoprotein<br />
|Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Metabolite<br />
|PubChem (PCCID) -> Chemical Entities of Biological Interest (ChEBI)<br />
|-<br />
|Peptide<br />
|Protein Ontology (PRO)<br />
|-<br />
|Protein<br />
|Uniprot (UPKB) -> Protein Data Bank (PDB) -> Protein Ontology (PRO) -> National Cancer Institute Thesaurus (NCIt)<br />
|-<br />
|Protein Complex<br />
|Protein Ontology (PRO) -> Gene Ontology (GO)<br />
|-<br />
|RNA<br />
|HUGO Gene Nomenclature Committee (HGNC) -> RNA Central (RNAC)<br />
|-<br />
|miRNA<br />
|miRBase (MRB)<br />
|}<br />
Refer to the [https://github.com/clinical-biomarkers/biomarker-partnership/blob/main/supplementary_files/documentation/contributing_data.md GitHub Documentation] for the correct resource.<br />
<br />
=== assessed_entity_type ===<br />
Report in all lowercase.<br />
<br />
=== condition ===<br />
<code>condition</code> should be reported in all lowercase <br />
<br />
=== condition_id ===<br />
<code>condition_id</code> (from Disease Ontology, MONDO, or SNOMED or NCIT) should be provided in the following column<br />
<br />
=== exposure_agent ===<br />
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.<br />
<br />
=== exposure_agent_id ===<br />
The ontology identifier for the exposure_agent, provided in the following column. Leave blank if not applicable.<br />
<br />
=== best_biomarker_role ===<br />
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:<br />
* '''diagnostic''': Detects or confirms the presence of a disease or condition, or identifies individuals with a specific disease subtype.<br />
* '''monitoring''': Assesses the status of a disease, medical condition, or exposure to a medical product over time.<br />
* '''predictive''': Identifies which patients are more or less likely to respond favorably or unfavorably to a specific treatment or exposure.<br />
* '''prognostic''': Identifies the likelihood of a clinical event, disease recurrence, or progression in patients with an already established disease or condition.<br />
* '''response''': Shows that a biological response has occurred in a patient after being exposed to a medical product or environmental agent.<br />
* '''risk''': Indicates the potential for an individual to develop a disease or condition in the future.<br />
* '''safety''': Measures or indicates the likelihood, nature, or severity of adverse effects, toxicity, or organ injury.<br />
<br />
=== specimen ===<br />
Report in all lowercase <br />
<br />
=== specimen_id ===<br />
<code>specimen_id</code> in the following column should be from UBERON.<br />
<br />
=== loinc_code ===<br />
Report the Logical Observation Identifiers Names and Codes (LOINC) code corresponding to the test or measurement (e.g. 77354-9).<br />
<br />
=== evidence_source ===<br />
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).<br />
<br />
=== evidence ===<br />
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.</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKG&diff=196BiomarkerKG2026-03-24T18:47:28Z<p>JeetVora: /* BiomarkerKB Knowledge Graph */</p>
<hr />
<div><br />
== BiomarkerKB Knowledge Graph ==<br />
The '''BiomarkerKB Knowledge Graph (BiomarkerKG)''' is a structured, machine-readable representation of the biomarker data contained in BiomarkerKB, organized as a graph of interconnected biological entities and relationships. It is designed to enable complex, multi-hop queries across biomarkers, diseases, anatomical sites, variants, and related biological concepts that go beyond what is possible with traditional tabular data access.<br />
<br />
=== Overview ===<br />
The BiomarkerKG integrates BiomarkerKB data into a Neo4j graph database, exposing relationships such as biomarker–disease associations, specimen types, measurement contexts (via LOINC identifiers), and anatomical locations (via UBERON identifiers). The graph structure is based on the Biolink data model, which provides structured relationship types (such as ''associated_with'', ''expressed_in'', and ''related_to'') to describe associations between entities. This design enables queries that go beyond simple co-occurrence to capture how biomarkers change in relation to specific disease states, treatments, or exposures. The initial release of the BKG contains over 300,000 nodes and 1.2 million edges, reflecting both curated biomarker associations and cross-links to CFDE resources. By representing this knowledge as a graph, the BiomarkerKG supports discovery tasks such as identifying biomarkers shared across multiple diseases, finding diseases characterized by multiple biomarkers, and detecting biomarkers measurable in different specimen types or anatomical locations.<br />
<br />
=== Data Representation & Formats ===<br />
BiomarkerKB data is exported and distributed in two Semantic Web–compatible formats available from the BiomarkerKB data portal:<br />
<br />
* '''RDF N-Triples''' – a standard serialization of RDF (Resource Description Framework) triples, enabling interoperability with SPARQL endpoints and linked data ecosystems. Available as dataset BMK_000019.<br />
* '''OWLNETS''' – a format derived from OWL (Web Ontology Language) that represents ontology-based knowledge as edge lists and node metadata, designed for ingestion into graph databases and machine learning pipelines. Available as dataset BMK_000020.<br />
<br />
These formats serve as the basis for constructing the graph: N-Triples are first generated from BiomarkerKB JSON records, then converted to OWLNETS edge list and node metadata files using the nt-owlnets-kg-converter, and finally ingested into Neo4j via a CSV-based Extract-Transform-Load (ETL) pipeline. The serialization CSV files generated during the build process are available for download with instructions for integrating the BKG with the CFDE Data Distillery Knowledge Graph (see ubkg.docs.xconsortia.org). The graph can be queried using Cypher to identify subgraphs within BiomarkerKB and to integrate it with other compatible knowledgebases.<br />
<br />
=== Integration with External Knowledge Graphs ===<br />
The BiomarkerKG is designed to be integrated into larger biomedical knowledge graph ecosystems:<br />
<br />
* '''CFDE Unified Biomedical Knowledge Graph (UBKG):''' The BiomarkerKB data is structured to be compatible with the Data Distillery / UBKG framework, maintained by the NIH Common Fund Data Ecosystem (CFDE). Integration follows the UBKG ETL and build processes, allowing BiomarkerKB nodes and edges to be co-queried with data from other CFDE programs including drug targets, therapeutic agents, and cross-disease treatment connections.<br />
* '''Proto-OKN Knowledge Graph:''' The BiomarkerKG is also integrated into the Proto Open Knowledge Network (Proto-OKN), a national initiative funded by the NSF to build an open, interconnected network of knowledge graphs spanning multiple scientific domains beyond biomedicine, including environmental, social, and geospatial data. Within this broader multi-domain network, BiomarkerKB contributes biomarker knowledge that can be linked to molecular entities such as metabolite-to-protein sequence connections, interacting genes and proteins, and biological pathway and reaction information relevant to disease processes.<br />
<br />
=== BiomarkerKG Explorer ===<br />
An interactive web interface for the BiomarkerKG is available at '''[https://biomarker-kg.maayanlab.cloud/ biomarker-kg.maayanlab.cloud]''', developed by the Ma'ayan Laboratory at the Icahn School of Medicine at Mount Sinai. The explorer is built on the open-source Knowledge-Graph-UI framework and provides:<br />
<br />
* '''BKG Explorer:''' Visual graph navigation supporting Cypher-based queries to view immediate neighbors of any node and compute shortest paths between two entities.<br />
* '''Downloads:''' Access to downloadable graph dumps and data files.<br />
* '''Tutorials:''' Guided instructions for querying and interpreting the knowledge graph.<br />
<br />
The interface is implemented in TypeScript/Next.js and backed by a Neo4j database. Source code is publicly available on GitHub.<br />
<br />
=== Links ===<br />
{| class="wikitable"<br />
!Resource<br />
!URL<br />
|-<br />
|BiomarkerKG Explorer<br />
|<nowiki>https://biomarker-kg.maayanlab.cloud/</nowiki><br />
|-<br />
|GitHub (KG build)<br />
|<nowiki>https://github.com/clinical-biomarkers/Knowledge-Graph</nowiki><br />
|-<br />
|GitHub (KG UI)<br />
|<nowiki>https://github.com/MaayanLab/Biomarker-KG-UI</nowiki><br />
|-<br />
|RDF N-Triples dataset (BMK_000019)<br />
|<nowiki>https://data.biomarkerkb.org/BMK_000019</nowiki><br />
|-<br />
|OWLNETS dataset (BMK_000020)<br />
|<nowiki>https://data.biomarkerkb.org/BMK_000020</nowiki><br />
|}</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKG&diff=195BiomarkerKG2026-03-24T18:35:21Z<p>JeetVora: Created page with " == BiomarkerKB Knowledge Graph == The '''BiomarkerKB Knowledge Graph (BiomarkerKG)''' is a structured, machine-readable representation of the biomarker data contained in BiomarkerKB, organized as a graph of interconnected biological entities and relationships. It is designed to enable complex, multi-hop queries across biomarkers, diseases, anatomical sites, variants, and related biological concepts that go beyond what is possible with traditional tabular data access. =..."</p>
<hr />
<div><br />
== BiomarkerKB Knowledge Graph ==<br />
The '''BiomarkerKB Knowledge Graph (BiomarkerKG)''' is a structured, machine-readable representation of the biomarker data contained in BiomarkerKB, organized as a graph of interconnected biological entities and relationships. It is designed to enable complex, multi-hop queries across biomarkers, diseases, anatomical sites, variants, and related biological concepts that go beyond what is possible with traditional tabular data access.<br />
<br />
=== Overview ===<br />
The BiomarkerKG integrates BiomarkerKB data into a Neo4j graph database, exposing relationships such as biomarker–disease associations, specimen types, measurement contexts (via LOINC identifiers), and anatomical locations (via UBERON identifiers). By representing this knowledge as a graph, the BiomarkerKG supports discovery tasks such as identifying biomarkers shared across multiple diseases, finding diseases characterized by multiple biomarkers, and detecting biomarkers measurable in different specimen types or anatomical locations.<br />
<br />
=== Data Representation & Formats ===<br />
BiomarkerKB data is exported and distributed in two Semantic Web–compatible formats available from the BiomarkerKB data portal:<br />
<br />
* '''RDF N-Triples''' – a standard serialization of RDF (Resource Description Framework) triples, enabling interoperability with SPARQL endpoints and linked data ecosystems. Available as dataset BMK_000019.<br />
* '''OWLNETS''' – a format derived from OWL (Web Ontology Language) that represents ontology-based knowledge as edge lists and node metadata, designed for ingestion into graph databases and machine learning pipelines. Available as dataset BMK_000020.<br />
<br />
These formats serve as the basis for constructing the graph: N-Triples are first generated from BiomarkerKB JSON records, then converted to OWLNETS edge list and node metadata files using the nt-owlnets-kg-converter, and finally ingested into Neo4j via a CSV-based Extract-Transform-Load (ETL) pipeline.<br />
<br />
=== Integration with External Knowledge Graphs ===<br />
The BiomarkerKG is designed to be integrated into larger biomedical knowledge graph ecosystems:<br />
<br />
* '''CFDE Unified Biomedical Knowledge Graph (UBKG):''' The BiomarkerKB data is structured to be compatible with the Data Distillery / UBKG framework, maintained by the NIH Common Fund Data Ecosystem (CFDE). Integration follows the UBKG ETL and build processes, allowing BiomarkerKB nodes and edges to be co-queried with data from other CFDE programs including drug targets, therapeutic agents, and cross-disease treatment connections.<br />
* '''Proto-OKN Knowledge Graph:''' The BiomarkerKG is also integrated into the Proto Open Knowledge Network (Proto-OKN), a national initiative funded by the NSF to build an open, interconnected network of knowledge graphs spanning multiple scientific domains beyond biomedicine, including environmental, social, and geospatial data. Within this broader multi-domain network, BiomarkerKB contributes biomarker knowledge that can be linked to molecular entities such as metabolite-to-protein sequence connections, interacting genes and proteins, and biological pathway and reaction information relevant to disease processes.<br />
<br />
=== BiomarkerKG Explorer ===<br />
An interactive web interface for the BiomarkerKG is available at '''[https://biomarker-kg.maayanlab.cloud/ biomarker-kg.maayanlab.cloud]''', developed by the Ma'ayan Laboratory at the Icahn School of Medicine at Mount Sinai. The explorer is built on the open-source Knowledge-Graph-UI framework and provides:<br />
<br />
* '''BKG Explorer:''' Visual graph navigation supporting Cypher-based queries to view immediate neighbors of any node and compute shortest paths between two entities.<br />
* '''Downloads:''' Access to downloadable graph dumps and data files.<br />
* '''Tutorials:''' Guided instructions for querying and interpreting the knowledge graph.<br />
<br />
The interface is implemented in TypeScript/Next.js and backed by a Neo4j database. Source code is publicly available on GitHub.<br />
<br />
=== Links ===<br />
{| class="wikitable"<br />
!Resource<br />
!URL<br />
|-<br />
|BiomarkerKG Explorer<br />
|<nowiki>https://biomarker-kg.maayanlab.cloud/</nowiki><br />
|-<br />
|GitHub (KG build)<br />
|<nowiki>https://github.com/clinical-biomarkers/Knowledge-Graph</nowiki><br />
|-<br />
|GitHub (KG UI)<br />
|<nowiki>https://github.com/MaayanLab/Biomarker-KG-UI</nowiki><br />
|-<br />
|RDF N-Triples dataset (BMK_000019)<br />
|<nowiki>https://data.biomarkerkb.org/BMK_000019</nowiki><br />
|-<br />
|OWLNETS dataset (BMK_000020)<br />
|<nowiki>https://data.biomarkerkb.org/BMK_000020</nowiki><br />
|}</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Biomarker_Partnership&diff=188Biomarker Partnership2026-03-04T21:04:46Z<p>JeetVora: </p>
<hr />
<div>Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.<br />
<br />
== About the Partnership Project ==<br />
The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
The scope of this project includes the following:<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
* Disseminating the results of this project to the research community.<br />
<br />
<br />
The project will use a variety of methods to achieve its goals, including:<br />
<br />
* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.<br />
* Software development: The project will develop software tools to support the management and analysis of biomarker data.<br />
* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project. Xy<br />
<br />
== Benefits ==<br />
The benefits of this project include:<br />
<br />
<br />
This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.<br />
<br />
== Relevant Publications ==<br />
<br />
# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: [https://academic.oup.com/glycob/article/32/10/855/6655823?login=true /glycob/cwac046]. PMID: [https://pubmed.ncbi.nlm.nih.gov/35925813/ 35925813].<br />
# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: [https://academic.oup.com/bib/article/22/6/bbab191/6278606?login=true /bib/bbab191]. PMID: [https://pubmed.ncbi.nlm.nih.gov/34015823/ 34015823].<br />
# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; [https://ceur-ws.org/ ceur-ws.org].<br />
# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: [https://ascopubs.org/doi/10.1200/CCI.19.00117 10.1200/CCI.19.00117]. PMID: [https://pubmed.ncbi.nlm.nih.gov/32142370/ 32142370].<br />
<br />
The [https://commonfund.nih.gov/dataecosystem CFDE] Biomarker Partnership is funded by the [https://commonfund.nih.gov/ National Institutes of Health Office of Strategic Coordination - The Common Fund] under the grant # 1OT2OD032092.<br />
<br />
== Collaborators ==<br />
<br />
===== [https://www.glygen.org/ GlyGen - The George Washington University] =====<br />
* Raja Mazumder (Principal Investigator)<br />
* Jeet Vora (Program Manager)<br />
* Daniall Masood (Ph.D. student | Data Curator)<br />
* Maria Kim (Backend Developer)<br />
* Sean Kim (Backend Developer)<br />
<br />
===== [https://www.glygen.org/ GlyGen - CCRC The University of Georgia, Athens] =====<br />
* Rene Ranzinger (Subrecipient PI | Project Manager)<br />
* Michael Tiemeyer (Co-Investigator)<br />
* Sujeet Kulkarni (Full Stack Develoepr)<br />
<br />
===== [https://www.metabolomicsworkbench.org/ Metabolomics Workbench (MW) - University of California, San Diego] =====<br />
* Shankar Subramaniam (Subrecipient PI)<br />
* Srinivasan Ramachandran (Project Manager)<br />
* Mano Maurya (Software Developer)<br />
* Shakti Gupta (Bioinformatics Researcher)<br />
<br />
===== [https://edrn.cancer.gov/ Early Detection Research Network (EDRN) - NASA JPL - California Institute of Technology] =====<br />
<br />
* Ashish Mahabal (Subrecipient PI)<br />
* Daniel Crichton (Project Manager)<br />
* Sean Kelly (Software Developer)<br />
* Heather Kincaid (Bioinformatics Researcher)<br />
<br />
===== [https://commonfund.nih.gov/idg Illuminating Druggable Genome (IDG) - University of New Mexico] =====<br />
<br />
* Jeremy Yang (Subrecipient PI)<br />
* Christophe Lambert (Subrecipient PI)<br />
* Vincent Metzger (Co-Investigator) <br />
* Cristian Bologa (Co-Investigator) <br />
* Noah Reboul (Student Research Assistant)</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Xrefs_and_annotations&diff=185Xrefs and annotations2026-02-25T17:42:01Z<p>JeetVora: </p>
<hr />
<div>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.<br />
<br />
<br />
BiomarkerKB Xrefs (Currently Added)<br />
<br />
* UniProtKB<br />
* GTEx<br />
* Pharos<br />
* Reactome<br />
* Undiagnosed Diseases Network<br />
* Illuminating the Druggable Genome (IDG) Reactome Portal<br />
* Metabolomics Workbench<br />
* SigCom LINCS<br />
* Metabolomics Workbench<br />
* ENCODE (Encyclopedia of DNA Elements)<br />
* ClinGen (Clinical Genome Resource)<br />
* MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration)<br />
* GeneVA (Gene Variation Analysis)<br />
* GeneCards<br />
* BioGPS<br />
* HGNC (HUGO Gene Nomenclature Committee)<br />
* GWAS Catalog<br />
* PDBe-KB<br />
* PCRP<br />
* IDG Reactome<br />
* Bgee<br />
* NCBI Gene<br />
* KEGG<br />
* SigCom LINCS<br />
* Gene Ontology<br />
* Reactome<br />
* GeneMANIA<br />
* Human Protein Atlas<br />
* AlphaFold<br />
* Open Targets<br />
* UCSC Genome Browser<br />
* Undiagnosed Diseases Network<br />
* BioMuta<br />
* GlyGen Protein<br />
* UniProtKB<br />
* Protein Ontology<br />
* PubChem<br />
* dbSNP<br />
* LOINC<br />
* Cell Ontology<br />
* ChEBI<br />
* NCI Thesaurus<br />
* GlyGen Glycan<br />
* Protein Data Bank<br />
* RNAcentral<br />
* Monarch Initiative<br />
* GlyTouCan<br />
* miRBase<br />
<br />
<br />
Xrefs to be added<br />
<br />
* Bgee<br />
* Kegg<br />
* MIM<br />
* HMDB ID<br />
* Ensembl<br />
* RefSeq<br />
* MONDO<br />
* DisGeNET<br />
* Orphanet<br />
<br />
== Annotations ==<br />
BiomarkerKB contains additional information called which is termed as 'Annotations' that complements the biomarker information in different sections of the BiomarkerKB details page<br />
<br />
<br />
Annotations in BiomarkerKB (Current)<br />
<br />
* Normal range data for BiomarkerKB entity from the Electronic Health Data from GWDC and Oracle Health.<br />
<br />
<br />
Annotations to be added<br />
<br />
* General (Name, description, class for Gene, Protein, Glycan and Metabolite)<br />
* Function information about Gene, Protein and Metabolite<br />
* Phenotype Data for Genes and Proteins that complement condition information<br />
* Information about variant from dbSNP<br />
* 3D structures for Gene, Protein, Glycan and Metabolite<br />
For current and upcoming data and data resources list in BiomarkerKB please visit - [[BiomarkerKB Resource Integration]]</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKB_Resource_Integration&diff=184BiomarkerKB Resource Integration2026-02-25T17:41:38Z<p>JeetVora: </p>
<hr />
<div>BiomarkerKB collects data from many different resources. The data that is collected is not always directly integrated into the data model and data from a resource is sometimes just added as valuable contextual annotations or cross references.<br />
<br />
Other resources to be explored: [https://cadsr.cancer.gov/onedata/Home.jsp CADSR Cancer], https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB, https://glycanage.com/publications, [https://www.cancergenomeinterpreter.org/biomarkers https://www.c], [https://github.com/issues/assigned?issue=clinical-biomarkers%7Cbiomarker-issue-repo%7C248 Glycan Biomarkers] ([https://github.com/glygener/CarboCurator code]), [https://www.alliancegenome.org/ Alliance Genome]<br />
<br />
<br />
<br />
Please contact us at mazumder_lab@gwu.edu and daniallmasood@gwu.edu if you have any other resources that may contain biomarker data <br />
<br />
= GWAS =<br />
Status: Direct Integration into Data Model<br />
<br />
* Published genome-wide association studies (GWAS).<br />
* Provides biomarkers in form of SNPs.<br />
* GWAS Catalog contains SNPs for a vast amount of diseases.<br />
** Preliminary curation only focused on cancer.<br />
** All available biomarkers for conditions in GWAS Catalog are integrated 12/11<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
= MetaKB =<br />
Status: Direct Integration into Data Model<br />
<br />
* Provides harmonized associations between cancer genomic variants, diseases, and therapeutic evidence.<br />
* Aggregates and standardizes variant interpretation data from six major knowledgebases:<br />
** CIViC (Clinical Interpretation of Variants in Cancer) [Already Integrated Directly]<br />
** OncoKB [Yet to be integrated]<br />
** JAX-CKB (The Jackson Laboratory Clinical Knowledgebase) [Yet to be integrated]<br />
** MolecularMatch [Yet to be integrated]<br />
** PMKB (Precision Medicine Knowledgebase) [Yet to be integrated]<br />
** Cancer Genome Interpreter (CGI) – through its ''Cancer Biomarkers Database'' component .[Integrated]<br />
* Enables mapping of variant–disease–drug relationships with supporting evidence levels, citations, and ontology alignment (e.g., genes, variants, diseases, and drugs).<br />
* Data integration requires review to ensure harmonized entity mappings consistent with the BiomarkerKB data model.<br />
* Focused on somatic variant–based biomarkers; contextual attributes such as tissue type, therapy response, or evidence type can be inferred or imputed where not directly specified.<br />
* Manual curation may be required for entries with incomplete evidence annotation or lacking standard ontology references.<br />
* Integration approach: direct mapping of variant, condition, and evidence entities; cross-references retained to original data sources.<br />
* License: Aggregated data are available for non-commercial, research use only, respecting constituent licenses:<br />
** CIViC – CC0 (Public Domain)<br />
** PMKB – CC-BY 4.0<br />
** CGI – CC0 for biomarkers database, CC-BY-NC 4.0 for tool<br />
** JAX-CKB – CC-BY-NC-SA 4.0<br />
** OncoKB – custom non-commercial license<br />
** MolecularMatch – restricted commercial use<br />
** MetaKB codebase – MIT license<br />
* Overall usage requires adherence to non-commercial research terms; commercial use needs separate permissions from individual data providers.<br />
<br />
= Glycan LLM Biomarkers =<br />
* LangChain LLM method used to collect biomarkers from PubMed Central abstracts<br />
* Method identifies glycan entities and changes mentioned in them associated to disease<br />
<br />
= Top 50 Biomarkers =<br />
Status: Direct Integration into Data Model<br />
* Biomarkers collected during Summer Volunteership<br />
* Volunteers identified top 50 biomarker entities from BiomarkerKB<br />
* Using this information the top 50 biomarker entities were searched in PubMed<br />
* 100 biomarkers were manually curated<br />
<br />
*<br />
<br />
= EDRN =<br />
Status: Sample Integration into Data Model<br />
<br />
* Cancer biomarkers.<br />
* Sample of EDRN Biomarkers provided from EDRN LLM method<br />
* Biomarkers are extracted from free text in EDRN publicly available biomarkers<br />
<br />
= LOINC =<br />
Status: Cross-Reference<br />
<br />
''Data provided by Metabolomics Workbench''<br />
<br />
= OncoKB =<br />
Status: Cross-Reference<br />
<br />
* Provides useful information on drugs and therapy options for different biomarker entities.<br />
* Also provides information based on what condition the entity is related to.<br />
* License: A license is required to use OncoKB for commercial and/or clinical purposes, and to access OncoKB data programmatically for academic purposes.<br />
* Paid license is required<br />
* Cross-reference from biomarkers in BiomarkerKB to the appropriate drug information and therapy information is the best solution.<br />
<br />
=HPO=<br />
<br />
Status: Cross-Reference<br />
<br />
* HPO provides disease and entity associations.<br />
* Does not provide a change within the entity so we cannot collect biomarker data from here.<br />
* However we can use it as a cross-reference within our cross-referencing section.<br />
* Provides cross-reference to OMIM, SNOMED, and MONDO.<br />
<br />
= UniProtKB =<br />
Status: Direct Integration into Data Model<br />
<br />
* Can provide biomarker (change in entity), entity, condition, and sampling data.<br />
* This data is in a text file that has to be reviewed fully and to make sure it will be able to be automatically extracted.<br />
* Contextual information can be imputed if necessary.<br />
* In UniProt there are found_in and entries that are actual biomarkers:<br />
** found_in will get a cross-reference;<br />
** actual biomarkers will be directly integrated.<br />
* Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file.<br />
* License is Creative Commons Attribution 4.0 International (CC BY 4.0).<br />
<br />
= CIViC =<br />
Status: Direct Integration into Data Model<br />
<br />
* Clinical Interpretation of Variants in Cancer (CIViC).<br />
* Provides cancer biomarkers in form of DNA mutations (dbSNPs).<br />
* Platform provides clinicians treatment options for patients based on unique tumor profile.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=ClinVar=<br />
Status: Direct Integration into Data Model<br />
<br />
* Public archive of reports of human variations classified for diseases and drug responses.<br />
* Provides biomarkers for all disease, but we have only curated cancer biomarkers for now.<br />
** dbSNPs<br />
** File is really big but will go back and use existing script to map all biomarkers from here into the data model.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
= MarkerDB =<br />
Status: Direct Integration into Data Model<br />
<br />
* Provides a lot of useful biomarker data and cross-references other resources as well.<br />
* Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc.<br />
* Annotations that can be cross-referenced include the above.<br />
* By cross-referencing, BiomarkerKB will allow users to find more information for specific biomarkers and move towards the goal of being a comprehensive resource for biomarkers.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=Metabolomics Workbench=<br />
Status: Direct Integration into Data Model<br />
<br />
''Data provided by Metabolomics Workbench''<br />
<br />
* Metabolite biomarkers utilized in the uniform newborn screening program.<br />
* Detect treatable disorders that are life threatening or having long-term morbidity, before they become symptomatic.<br />
<br />
=OncoMX=<br />
Status: Direct Integration into Data Model<br />
<br />
* integrated cancer mutation and expression resource for exploring cancer biomarkers<br />
* Manual curation effort by GWU and JPL<br />
* Over 600 single and panel biomarkers<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=OpenTargets=<br />
Status: Direct Integration into Data Model<br />
<br />
* Collects potential drug targets and therapeutic targets.<br />
* Some effort was required to find the correct biomarker data.<br />
* 1200 biomarkers collected.<br />
** dbSNPs related to cancer and other disease<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=PubMed Central Biomarker Gene Set Curation=<br />
Status: Direct Integration into Data Model<br />
<br />
''Data provided by Avi Ma'ayan's LINCS group''<br />
<br />
* This data set was created through manual curation of biomarker gene sets on Pubmed Central using the results of gene sets returned from Rummagene. <br />
* Using the outputted search results within the Rummagene web server, we manually identified publications that associated different conditions and environmental exposures to biomarker gene sets. <br />
* The biomarker gene sets were retrieved through the validation of the gene mentioned within each of the publications. <br />
* The primary use case for this data is to identify biomarker panels/ gene sets associated with conditions.<br />
<br />
= SenNet Biomarker Data =<br />
Status: Direction Integration Into Data Model<br />
<br />
* Cell senescence biomarkers from SenNet group<br />
* Biomarker data was collected and incorporated however biomarker field was incomplete and data integrated was given a score of -2<br />
* Data is still valuable as contextual data and can be revisited to complete biomarker field in future<br />
For infomation about Cross-references and Annotations in BiomarkerKB please visit - [[Xrefs and annotations]]</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Xrefs_and_annotations&diff=183Xrefs and annotations2026-02-25T17:40:55Z<p>JeetVora: </p>
<hr />
<div>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.<br />
<br />
<br />
BiomarkerKB Xrefs (Currently Added)<br />
<br />
* UniProtKB<br />
* GTEx<br />
* Pharos<br />
* Reactome<br />
* Undiagnosed Diseases Network<br />
* Illuminating the Druggable Genome (IDG) Reactome Portal<br />
* Metabolomics Workbench<br />
* SigCom LINCS<br />
* Metabolomics Workbench<br />
* ENCODE (Encyclopedia of DNA Elements)<br />
* ClinGen (Clinical Genome Resource)<br />
* MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration)<br />
* GeneVA (Gene Variation Analysis)<br />
* GeneCards<br />
* BioGPS<br />
* HGNC (HUGO Gene Nomenclature Committee)<br />
* GWAS Catalog<br />
* PDBe-KB<br />
* PCRP<br />
* IDG Reactome<br />
* Bgee<br />
* NCBI Gene<br />
* KEGG<br />
* SigCom LINCS<br />
* Gene Ontology<br />
* Reactome<br />
* GeneMANIA<br />
* Human Protein Atlas<br />
* AlphaFold<br />
* Open Targets<br />
* UCSC Genome Browser<br />
* Undiagnosed Diseases Network<br />
* BioMuta<br />
* GlyGen Protein<br />
* UniProtKB<br />
* Protein Ontology<br />
* PubChem<br />
* dbSNP<br />
* LOINC<br />
* Cell Ontology<br />
* ChEBI<br />
* NCI Thesaurus<br />
* GlyGen Glycan<br />
* Protein Data Bank<br />
* RNAcentral<br />
* Monarch Initiative<br />
* GlyTouCan<br />
* miRBase<br />
<br />
<br />
Xrefs to be added<br />
<br />
* Bgee<br />
* Kegg<br />
* MIM<br />
* HMDB ID<br />
* Ensembl<br />
* RefSeq<br />
* MONDO<br />
* DisGeNET<br />
* Orphanet<br />
<br />
== Annotations ==<br />
BiomarkerKB contains additional information called which is termed as 'Annotations' that complements the biomarker information in different sections of the BiomarkerKB details page<br />
<br />
<br />
Annotations in BiomarkerKB (Current)<br />
<br />
* Normal range data for BiomarkerKB entity from the Electronic Health Data from GWDC and Oracle Health.<br />
<br />
<br />
Annotations to be added<br />
<br />
* General (Name, description, class for Gene, Protein, Glycan and Metabolite)<br />
* Function information about Gene, Protein and Metabolite<br />
* Phenotype Data for Genes and Proteins that complement condition information<br />
* Information about variant from dbSNP<br />
* 3D structures for Gene, Protein, Glycan and Metabolite<br />
For current and upcoming data and data resources list please visit - [[BiomarkerKB Resource Integration]]</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Xrefs_and_annotations&diff=182Xrefs and annotations2026-02-25T17:39:39Z<p>JeetVora: </p>
<hr />
<div>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.<br />
<br />
<br />
BiomarkerKB Xrefs (Currently Added)<br />
<br />
* UniProtKB<br />
* GTEx<br />
* Pharos<br />
* Reactome<br />
* Undiagnosed Diseases Network<br />
* Illuminating the Druggable Genome (IDG) Reactome Portal<br />
* Metabolomics Workbench<br />
* SigCom LINCS<br />
* Metabolomics Workbench<br />
* ENCODE (Encyclopedia of DNA Elements)<br />
* ClinGen (Clinical Genome Resource)<br />
* MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration)<br />
* GeneVA (Gene Variation Analysis)<br />
* GeneCards<br />
* BioGPS<br />
* HGNC (HUGO Gene Nomenclature Committee)<br />
* GWAS Catalog<br />
* PDBe-KB<br />
* PCRP<br />
* IDG Reactome<br />
* Bgee<br />
* NCBI Gene<br />
* KEGG<br />
* SigCom LINCS<br />
* Gene Ontology<br />
* Reactome<br />
* GeneMANIA<br />
* Human Protein Atlas<br />
* AlphaFold<br />
* Open Targets<br />
* UCSC Genome Browser<br />
* Undiagnosed Diseases Network<br />
* BioMuta<br />
* GlyGen Protein<br />
* UniProtKB<br />
* Protein Ontology<br />
* PubChem<br />
* dbSNP<br />
* LOINC<br />
* Cell Ontology<br />
* ChEBI<br />
* NCI Thesaurus<br />
* GlyGen Glycan<br />
* Protein Data Bank<br />
* RNAcentral<br />
* Monarch Initiative<br />
* GlyTouCan<br />
* miRBase<br />
<br />
<br />
Xrefs to be added<br />
<br />
* Bgee<br />
* Kegg<br />
* MIM<br />
* HMDB ID<br />
* Ensembl<br />
* RefSeq<br />
* MONDO<br />
* DisGeNET<br />
* Orphanet<br />
<br />
== Annotations ==<br />
BiomarkerKB contains additional information called which is termed as 'Annotations' that complements the biomarker information in different sections of the BiomarkerKB details page<br />
<br />
<br />
Annotations in BiomarkerKB (Current)<br />
<br />
* Normal range data for BiomarkerKB entity from the Electronic Health Data from GWDC and Oracle Health.<br />
<br />
<br />
Annotations to be added<br />
<br />
* General (Name, description, class for Gene, Protein, Glycan and Metabolite)<br />
* Function information about Gene, Protein and Metabolite<br />
* Phenotype Data for Genes and Proteins that complement condition information<br />
* Information about variant from dbSNP<br />
* 3D structures for Gene, Protein, Glycan and Metabolite</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Xrefs_and_annotations&diff=180Xrefs and annotations2026-02-25T14:17:03Z<p>JeetVora: Created page with "Cross-references to other resources"</p>
<hr />
<div>Cross-references to other resources</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Frequently_Asked_Questions&diff=173Frequently Asked Questions2026-01-30T17:04:38Z<p>JeetVora: </p>
<hr />
<div>'''1. Where can I find more information on the project?''' The project webpage can be found [https://biomarkerkb.org/about/ here].<br />
<br />
'''2. Is the project repository publicly available?''' You can view all the project repositories [https://github.com/clinical-biomarkers here].<br />
<br />
'''3. What are the biomarker scores and how are scores assigned for the biomarkers?''' The biomarker-score-calculator and default scoring algorithm can be found [https://github.com/clinical-biomarkers/biomarker-score-calculator here]. The biomarker scores can be seen on the full JSON data model responses from the API.<br />
<br />
'''4. Why are some biomarkers assigned a score of 0?''' Biomarkers with a default score of 0 are manually assigned a 0 score and are pending a manual review. The review of the biomarker can include a spot check, full manual quality checking, NLP based methods, and discussions with the submitter/resource. Until the review is complete the biomarker will keep a score of 0 and after the review is complete the biomarker will be scored using the biomarker score calculator tool.<br />
<br />
'''5. How to download all the 'current' dataset files using CLI?''' The BiomarkerKB dataset can be downloaded using command - <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKB_Partnership_(Previous)&diff=165BiomarkerKB Partnership (Previous)2026-01-22T20:29:04Z<p>JeetVora: </p>
<hr />
<div>THE BIOMARKER PARTNERSHIP PROJECT CONCLUDED IN SEPTEMBER 2024. This page contains the description of the BIOMARKER PARTNERSHIP PROJECT from https://hivelab.biochemistry.gwu.edu/biomarker-partnership/<br />
<br />
== Biomarker Partnership Project ==<br />
Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.<br />
<br />
The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
The scope of this project includes the following:<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
* Disseminating the results of this project to the research community.<br />
<br />
The benefits of this project include:<br />
<br />
This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.<br />
<br />
The project will use a variety of methods to achieve its goals, including:<br />
<br />
* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.<br />
* Software development: The project will develop software tools to support the management and analysis of biomarker data.<br />
* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.<br />
<br />
== Useful Links (Some links could be outdated) ==<br />
<br />
* [https://biomarkerkb.org Biomarker Portal] - Visit the Biomarker platform that allows researchers to search, filter, and explore a vast repository of biomarker data<br />
* [https://github.com/clinical-biomarkers/biomarker-partnership Biomarker Partnership Github Page] - Explore the project's source code, documentation, and development updates.<br />
* [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data Biomarker-Partnership Data Page] - Access the dataset and tools for biomarker data integration and analysis.<br />
* [https://github.com/clinical-biomarkers/biomarker-backend-api/blob/main/api/biomarker/README.md REST API] - Utilize the API to programmatically query and retrieve biomarker data.<br />
* [https://hivelab.biochemistry.gwu.edu/fda_biomarker_definitions FDA Biomarker Definitions] - Find official biomarker definitions and guidelines provided by the FDA.<br />
* [https://proteininformationresource.org/staff/nataled/OBCI/obci.owl Biomarker Ontology] - Explore the structured vocabulary for biomarker research and data categorization.<br />
* [https://github.com/biomarker-ontology/biomarker-partnership/blob/main/supplementary_files/documents/Master_Biomarker_Partnership_Data_Model_RFC.pdf Biomarker Data Model RFC] - Review the proposed biomarker data model.<br />
* [https://hivelab.biochemistry.gwu.edu/biomarker_data_submission Biomarker Data Submission Instructions] - Learn how to submit biomarker data to the partnership's database.<br />
<br />
== Relevant Publications ==<br />
<br />
# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: /glycob/cwac046. PMID: 35925813.<br />
# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: /bib/bbab191. PMID: 34015823.<br />
# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; ceur-ws.org.<br />
# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: 10.1200/CCI.19.00117. PMID: 32142370.The CFDE Biomarker Partnership is funded by the National Institutes of Health Office of Strategic Coordination - The Common Fund under the grant # 1OT2OD032092.<br />
<br />
==== Collaborators ====<br />
<br />
===== Principal Investigators =====<br />
<br />
* Raja Mazumder (GlyGen)<br />
* Michael Tiemeyer (GlyGen)<br />
* Christophe Lambert (IDG)<br />
* Jeremy Yang (IDG)<br />
* Shankar Subramaniam (MW)<br />
* Avi Ma'ayan (LINCS)<br />
* Jonathan Silverstein (SN/HuBMAP)<br />
* Nicola Neretti (SN/HuBMAP)<br />
<br />
===== Project Managers =====<br />
<br />
* Daniall Masood (GlyGen)<br />
* Sean Kim (GlyGen)<br />
* Grace Faustino (IDG)<br />
* Mano Maurya (MW)<br />
* Sherry Jenkins (LINCS)<br />
* Jesse Helfer (SN/HuBMAP)<br />
<br />
===== Consultants =====<br />
<br />
* Darren Natale<br />
* Nikolai Daraselia</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKB_Partnership_(Previous)&diff=164BiomarkerKB Partnership (Previous)2026-01-22T20:27:45Z<p>JeetVora: Created page with "THE BIOMARKER PARTNERSHIP PROJECT CONCLUDED IN SEPTEMBER 2024. This page contains the description of the BIOMARKER PARTNERSHIP PROJECT from https://hivelab.biochemistry.gwu.edu/biomarker-partnership/ ==== Biomarker Partnership Project ==== Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual informat..."</p>
<hr />
<div>THE BIOMARKER PARTNERSHIP PROJECT CONCLUDED IN SEPTEMBER 2024. This page contains the description of the BIOMARKER PARTNERSHIP PROJECT from https://hivelab.biochemistry.gwu.edu/biomarker-partnership/<br />
<br />
==== Biomarker Partnership Project ====<br />
Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.<br />
<br />
The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
The scope of this project includes the following:<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
* Disseminating the results of this project to the research community.<br />
<br />
The benefits of this project include:<br />
<br />
This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.<br />
<br />
The project will use a variety of methods to achieve its goals, including:<br />
<br />
* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.<br />
* Software development: The project will develop software tools to support the management and analysis of biomarker data.<br />
* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.<br />
<br />
== Useful Links (Some links could be outdated) ==<br />
<br />
* [https://biomarkerkb.org Biomarker Portal] - Visit the Biomarker platform that allows researchers to search, filter, and explore a vast repository of biomarker data<br />
* [https://github.com/clinical-biomarkers/biomarker-partnership Biomarker Partnership Github Page] - Explore the project's source code, documentation, and development updates.<br />
* [https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data Biomarker-Partnership Data Page] - Access the dataset and tools for biomarker data integration and analysis.<br />
* [https://github.com/clinical-biomarkers/biomarker-backend-api/blob/main/api/biomarker/README.md REST API] - Utilize the API to programmatically query and retrieve biomarker data.<br />
* [https://hivelab.biochemistry.gwu.edu/fda_biomarker_definitions FDA Biomarker Definitions] - Find official biomarker definitions and guidelines provided by the FDA.<br />
* [https://proteininformationresource.org/staff/nataled/OBCI/obci.owl Biomarker Ontology] - Explore the structured vocabulary for biomarker research and data categorization.<br />
* [https://github.com/biomarker-ontology/biomarker-partnership/blob/main/supplementary_files/documents/Master_Biomarker_Partnership_Data_Model_RFC.pdf Biomarker Data Model RFC] - Review the proposed biomarker data model.<br />
* [https://hivelab.biochemistry.gwu.edu/biomarker_data_submission Biomarker Data Submission Instructions] - Learn how to submit biomarker data to the partnership's database.<br />
<br />
== Relevant Publications ==<br />
<br />
# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: /glycob/cwac046. PMID: 35925813.<br />
# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: /bib/bbab191. PMID: 34015823.<br />
# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; ceur-ws.org.<br />
# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: 10.1200/CCI.19.00117. PMID: 32142370.The CFDE Biomarker Partnership is funded by the National Institutes of Health Office of Strategic Coordination - The Common Fund under the grant # 1OT2OD032092.<br />
<br />
==== Collaborators ====<br />
<br />
===== Principal Investigators =====<br />
<br />
* Raja Mazumder (GlyGen)<br />
* Michael Tiemeyer (GlyGen)<br />
* Christophe Lambert (IDG)<br />
* Jeremy Yang (IDG)<br />
* Shankar Subramaniam (MW)<br />
* Avi Ma'ayan (LINCS)<br />
* Jonathan Silverstein (SN/HuBMAP)<br />
* Nicola Neretti (SN/HuBMAP)<br />
<br />
===== Project Managers =====<br />
<br />
* Daniall Masood (GlyGen)<br />
* Sean Kim (GlyGen)<br />
* Grace Faustino (IDG)<br />
* Mano Maurya (MW)<br />
* Sherry Jenkins (LINCS)<br />
* Jesse Helfer (SN/HuBMAP)<br />
<br />
===== Consultants =====<br />
<br />
* Darren Natale<br />
* Nikolai Daraselia</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=163Main Page2026-01-22T20:20:13Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div><br />
<br />
<div style="text-align:left;"><br />
'''<u>What is BiomarkerKB?</u>'''<br />
[https://biomarkerkb.org/about/ BiomarkerKB] is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that is organized and integrates biomarker data from different public sources. The motivation for this project is to improve the harmonization and organization of biomarker data. This is being done by mapping biomarkers from public sources to, and across, Common Fund data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines..<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
*Provide computational and informatics resources and tools for biomarker research.<br />
<br />
*Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
*Mapping biomarkers from public sources to relevant data elements.<br />
<br />
*Mapping contextual data from participating CFDE DCCs.<br />
<br />
*Developing a framework for organizing biomarker data.<br />
<br />
*Creating tools for querying and exploring biomarker data.<br />
<br />
*Disseminating the results of this project to the research community.<br />
<br />
<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomaker Ontology Working Group]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomaker Ontology Working Group]]'' <br><br />
</div><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Partnership (Previous)]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Partnership (Previous)]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Frequently_Asked_Questions&diff=160Frequently Asked Questions2026-01-13T18:27:54Z<p>JeetVora: </p>
<hr />
<div>1) How to download all the 'current' dataset files using CLI<br />
<br />
> The BiomarkerKB dataset can be downloaded using command - <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code><br />
<br />
2)</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Frequently_Asked_Questions&diff=159Frequently Asked Questions2026-01-13T18:27:35Z<p>JeetVora: </p>
<hr />
<div>How to download all the 'current' dataset files using CLI<br />
<br />
> The BiomarkerKB dataset can be downloaded using command - <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=MediaWiki:Common.css&diff=153MediaWiki:Common.css2025-12-16T18:20:51Z<p>JeetVora: Created page with "/* Custom monospace font */ .courier-new { font-family: "Courier New", Courier, monospace; }"</p>
<hr />
<div>/* Custom monospace font */<br />
.courier-new {<br />
font-family: "Courier New", Courier, monospace;<br />
}</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Frequently_Asked_Questions&diff=152Frequently Asked Questions2025-12-16T18:15:15Z<p>JeetVora: </p>
<hr />
<div>How to download all the 'current' dataset files using CLI<br />
<br />
> The BiomarkerKB dataset can be downloaded using command - <code>wget -r -l1 -np -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Biomarker_Ontology_Working_Group&diff=138Biomarker Ontology Working Group2025-12-08T22:44:57Z<p>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..."</p>
<hr />
<div>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.<br />
<br />
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<br />
<br />
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]]<br />
<br />
Biomarker Ontology Working Group currently contains the members:<br />
{| class="wikitable"<br />
|'''Name'''<br />
|'''ORCID'''<br />
|-<br />
|'''Darren A. Natale'''<br />
|0000-0001-5809-9523<br />
|-<br />
|'''Raja Mazumder'''<br />
|0000-0001-8823-9945<br />
|-<br />
|'''Daniall Masood'''<br />
|0000-0001-7441-1628<br />
|-<br />
|'''Hande Küçük McGinty'''<br />
|0000-0002-9025-5538<br />
|-<br />
|'''Marc E. Gillespie'''<br />
|0000-0002-5766-1702<br />
|-<br />
|'''Astghik Sargsyan'''<br />
|0000-0002-5860-6369<br />
|-<br />
|'''Soheil Abadifard'''<br />
|0000-0002-2980-4251<br />
|-<br />
|'''Jeet K. Vora'''<br />
|0000-0002-5317-1458<br />
|}</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=137Main Page2025-12-08T22:31:32Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div><br />
<br />
<div style="text-align:left;"><br />
'''<u>What is BiomarkerKB?</u>'''<br />
[https://biomarkerkb.org/about/ BiomarkerKB] is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that is organized and integrates biomarker data from different public sources. The motivation for this project is to improve the harmonization and organization of biomarker data. This is being done by mapping biomarkers from public sources to, and across, Common Fund data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines..<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
*Provide computational and informatics resources and tools for biomarker research.<br />
<br />
*Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
*Mapping biomarkers from public sources to relevant data elements.<br />
<br />
*Mapping contextual data from participating CFDE DCCs.<br />
<br />
*Developing a framework for organizing biomarker data.<br />
<br />
*Creating tools for querying and exploring biomarker data.<br />
<br />
*Disseminating the results of this project to the research community.<br />
<br />
<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomaker Ontology Working Group]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomaker Ontology Working Group]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Release_Notes&diff=132Data Release Notes2025-11-14T18:12:10Z<p>JeetVora: </p>
<hr />
<div>== Versioning Format ==<br />
The versioning format follows a three-digit structure: X.Y.Z.<br />
* The first digit (X) changes when a major update is introduced, such as changes in the data model.<br />
* The second digit (Y) increments with each new release.<br />
* The third digit (Z) is updated for bug fixes or minor changes.<br />
<br />
== Version 2.0.0 ==<br />
=== Data Updates ===<br />
* The biomarker field is now standardized using controlled vocabulary terms.<br />
* Added metabolite as an <code>assessed_entity_type</code> to <code>mw_loinc_biomarkers.tsv</code>.<br />
* Added [https://rnacentral.org/ RNAcentral] cross-reference support.<br />
* Added Electronic Health Records Normal ranges data from Oracle Health for Troponin I as an example.<br />
<br />
== Version 1.0.6 ==<br />
=== Data Updates ===<br />
* Added a new dataset: MW LOINC biomarkers (<code>mw_loinc_biomarkers.tsv</code>).<br />
* Added [https://ncithesaurus.nci.nih.gov/ National Cancer Institute Thesaurus] and [https://www.rcsb.org/ Protein Data Bank] cross-references.<br />
=== Backend and Infrastructure Updates ===<br />
* Added the <code>display_name</code> field to the <code>format-converter</code> so data source names appear with correct casing.<br />
<br />
== Version 1.0.5 ==<br />
=== Data Updates ===<br />
* Updated the Troponin biomarker value <code>assessed_biomarker_entity</code> for consistency.<br />
* Added normal ranges from Electronic Health Records provided by the University of New Mexico for Troponin biomarkers.<br />
* Added Cell Ontology and Protein Ontology cross-references.<br />
=== Backend and Infrastructure Updates ===<br />
* Updated all script paths to use <code>data_source.conf</code> and validated data source names.<br />
<br />
== Version 1.0.4 ==<br />
This release introduces new datasets, cross-references, and bug fixes.<br />
=== Data Updates ===<br />
* Added Cancer Genome Interpreter data on cancer biomarkers from MetaKB.<br />
* Added Metabolomics Workbench LOINC data on metabolite biomarkers.<br />
* Added Cell Ontology and Protein Ontology cross-references.<br />
=== Bug Fixes ===<br />
* Fixed issue where cookie preferences weren't being saved when selecting "Allow".<br />
<br />
== Version 1.0.3 ==<br />
This release introduces new cross-references and updates to ensure compatibility with external resources.<br />
=== Data Updates ===<br />
* NCBI cross-references added across gene biomarker entries.<br />
* ChEBI cross-references integrated for small molecules and metabolites.<br />
=== Backend and Infrastructure Updates ===<br />
* ChEBI API migration: Updated all programmatic links from the legacy SOAP services to the new REST API endpoints, following ChEBI’s platform migration.<br />
** Old services retired 1 September 2025.<br />
** New stable API: [https://www.ebi.ac.uk/chebi/backend/api/docs ChEBI REST API docs]<br />
** New data products and beta interface available at [https://www.ebi.ac.uk/chebi/beta/ ChEBI 2.0].<br />
== Version 1.0.2 ==<br />
=== Data Updates ===<br />
* Published updated [https://www.metabolomicsworkbench.org/ Metabolomics Workbench] data.<br />
* Published sample data from the [https://edrn.nci.nih.gov/ Early Detection Research Network].<br />
=== Backend and Infrastructure Updates ===<br />
* <code>evidence_source</code> database names now retain their original casing for accuracy and consistency.<br />
* EDRN identifiers were added to the [https://github.com/clinical-biomarkers/format-converter/blob/main/mapping_data/namespace_map.json namespace map].<br />
* [https://www.genenames.org/ HUGO Gene Nomenclature Committee] (HGNC) was added to the cross-reference JSON file.<br />
* Fixed an issue where <code>evidence_source</code> values without tags were previously dropped; these are now preserved.<br />
* Added a user-guided spelling correction function to improve data entry quality.<br />
* The TSV-to-JSON converter now automatically checks for header spelling errors.<br />
* Introduced <code>_suggest_header_corrections</code> to flag and propose fixes for misspelled headers.<br />
* Enhanced <code>_stream_tsv</code> with a call to <code>_check_header_spelling</code> to prevent invalid headers from being processed.<br />
<br />
== Version 1.0.1 ==<br />
=== Data Updates ===<br />
* Added <code> xrefs.tsv</code> to the list of datasets.<br />
=== Backend & Infrastructure Updates ===<br />
* 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.<br />
* Merged assessed entity type synonyms.<br />
<br />
== Version 1.0.0 ==<br />
* BiomarkerKB data portal available with OncoMX, OpenTargets, MarkerDB, ClinVar, PubMed Central Biomarker Gene Set Curation, MW, UniProtKB, GWAS, CIViC biomarker data.</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=127Main Page2025-11-11T19:46:32Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div><br />
<br />
<div style="text-align:left;"><br />
'''<u>What is BiomarkerKB?</u>'''<br />
[https://biomarkerkb.org/about/ BiomarkerKB] is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that is organized and integrates biomarker data from different public sources. The motivation for this project is to improve the harmonization and organization of biomarker data. This is being done by mapping biomarkers from public sources to, and across, Common Fund data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines..<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
*Provide computational and informatics resources and tools for biomarker research.<br />
<br />
*Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
*Mapping biomarkers from public sources to relevant data elements.<br />
<br />
*Mapping contextual data from participating CFDE DCCs.<br />
<br />
*Developing a framework for organizing biomarker data.<br />
<br />
*Creating tools for querying and exploring biomarker data.<br />
<br />
*Disseminating the results of this project to the research community.<br />
<br />
<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=126Main Page2025-11-11T19:45:35Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div><br />
<br />
<div style="text-align:left;"><br />
'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
*Provide computational and informatics resources and tools for biomarker research.<br />
<br />
*Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
*Mapping biomarkers from public sources to relevant data elements.<br />
<br />
*Mapping contextual data from participating CFDE DCCs.<br />
<br />
*Developing a framework for organizing biomarker data.<br />
<br />
*Creating tools for querying and exploring biomarker data.<br />
<br />
*Disseminating the results of this project to the research community.<br />
<br />
<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=125Main Page2025-11-11T19:43:46Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki<br />
<br />
<div style="text-align:left;"><br />
'''<u>What is BiomarkerKB?'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<div style="text-align:left;"><br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
* Provide computational and informatics resources and tools for biomarker research.<br />
* Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating CFDE DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
<br />
</div><br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=124Main Page2025-11-11T19:43:06Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki<br />
<div style="text-align:left;"><br />
</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<div style="text-align:left;"><br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
* Provide computational and informatics resources and tools for biomarker research.<br />
* Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating CFDE DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
<br />
</div><br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=123Main Page2025-11-11T19:42:22Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<div style="text-align:left;"><br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
* Provide computational and informatics resources and tools for biomarker research.<br />
* Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
* Mapping biomarkers from public sources to relevant data elements.<br />
* Mapping contextual data from participating CFDE DCCs.<br />
* Developing a framework for organizing biomarker data.<br />
* Creating tools for querying and exploring biomarker data.<br />
<br />
</div><br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Releases]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Resource Integration]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Resource Integration]]'' <br><br />
</div><br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=BiomarkerKB_Resource_Integration&diff=119BiomarkerKB Resource Integration2025-10-23T20:26:12Z<p>JeetVora: </p>
<hr />
<div>BiomarkerKB collects data from many different resources. The data that is collected is not always directly integrated into the data model and data from a resource is sometimes just added as valuable contextual annotations or cross references.<br />
<br />
Other resources to be explored: [https://cadsr.cancer.gov/onedata/Home.jsp CADSR Cancer], https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB, https://glycanage.com/publications, [https://www.cancergenomeinterpreter.org/biomarkers https://www.c], [https://github.com/issues/assigned?issue=clinical-biomarkers%7Cbiomarker-issue-repo%7C248 Glycan Biomarkers] ([https://github.com/glygener/CarboCurator code])<br />
<br />
<br />
Please contact us at mazumder_lab@gwu.edu and daniallmasood@gwu.edu if you have any other resources that may contain biomarker data <br />
<br />
=CIViC=<br />
Status: Direct Integration into Data Model<br />
<br />
* Clinical Interpretation of Variants in Cancer (CIViC).<br />
* Provides cancer biomarkers in form of DNA mutations (dbSNPs).<br />
* Platform provides clinicians treatment options for patients based on unique tumor profile.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=ClinVar=<br />
Status: Direct Integration into Data Model<br />
<br />
* Public archive of reports of human variations classified for diseases and drug responses.<br />
* Provides biomarkers for all disease, but we have only curated cancer biomarkers for now.<br />
** dbSNPs<br />
** File is really big but will go back and use existing script to map all biomarkers from here into the data model.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=EDRN=<br />
Status: Sample Integration into Data Model<br />
<br />
* Cancer biomarkers.<br />
<br />
=GWAS=<br />
Status: Direct Integration into Data Model<br />
<br />
* Published genome-wide association studies (GWAS).<br />
* Provides biomarkers in form of SNPs.<br />
* GWAS Catalog contains SNPs for a vast amount of diseases.<br />
** Preliminary curation only focused on cancer.<br />
** Will use existing script to map all biomarkers into data model.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=HPO=<br />
<br />
Status: Cross-Reference<br />
<br />
* HPO provides disease and entity associations.<br />
* Does not provide a change within the entity so we cannot collect biomarker data from here.<br />
* However we can use it as a cross-reference within our cross-referencing section.<br />
* Provides cross-reference to OMIM, SNOMED, and MONDO.<br />
<br />
=LOINC=<br />
Status: Cross-Reference<br />
<br />
''Data provided by Metabolomics Workbench''<br />
<br />
=MarkerDB=<br />
Status: Direct Integration into Data Model<br />
<br />
* Provides a lot of useful biomarker data and cross-references other resources as well.<br />
* Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc.<br />
* Annotations that can be cross-referenced include the above.<br />
* By cross-referencing, BiomarkerKB will allow users to find more information for specific biomarkers and move towards the goal of being a comprehensive resource for biomarkers.<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=Metabolomics Workbench=<br />
Status: Direct Integration into Data Model<br />
<br />
''Data provided by Metabolomics Workbench''<br />
<br />
* Metabolite biomarkers utilized in the uniform newborn screening program.<br />
* Detect treatable disorders that are life threatening or having long-term morbidity, before they become symptomatic.<br />
<br />
=OncoKB=<br />
Status: Cross-Reference<br />
<br />
* Provides useful information on drugs and therapy options for different biomarker entities.<br />
* Also provides information based on what condition the entity is related to.<br />
* License: A license is required to use OncoKB for commercial and/or clinical purposes, and to access OncoKB data programmatically for academic purposes.<br />
* Paid license is required<br />
* Cross-reference from biomarkers in BiomarkerKB to the appropriate drug information and therapy information is the best solution.<br />
<br />
=OncoMX=<br />
Status: Direct Integration into Data Model<br />
<br />
* integrated cancer mutation and expression resource for exploring cancer biomarkers<br />
* Manual curation effort by GWU and JPL<br />
* Over 600 single and panel biomarkers<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=OpenTargets=<br />
Status: Direct Integration into Data Model<br />
<br />
* Collects potential drug targets and therapeutic targets.<br />
* Some effort was required to find the correct biomarker data.<br />
* 1200 biomarkers collected.<br />
** dbSNPs related to cancer and other disease<br />
* License: Creative Commons Attribution-NonCommercial 4.0 International License.<br />
<br />
=PubMed Central Biomarker Gene Set Curation=<br />
Status: Direct Integration into Data Model<br />
<br />
''Data provided by Avi Ma'ayan's LINCS group''<br />
<br />
* This data set was created through manual curation of biomarker gene sets on Pubmed Central using the results of gene sets returned from Rummagene. <br />
* Using the outputted search results within the Rummagene web server, we manually identified publications that associated different conditions and environmental exposures to biomarker gene sets. <br />
* The biomarker gene sets were retrieved through the validation of the gene mentioned within each of the publications. <br />
* The primary use case for this data is to identify biomarker panels/ gene sets associated with conditions.<br />
<br />
=UniProtKB=<br />
<br />
Status: Direct Integration into Data Model<br />
<br />
* Can provide biomarker (change in entity), entity, condition, and sampling data.<br />
* This data is in a text file that has to be reviewed fully and to make sure it will be able to be automatically extracted.<br />
* Contextual information can be imputed if necessary.<br />
* In UniProt there are found_in and entries that are actual biomarkers:<br />
** found_in will get a cross-reference;<br />
** actual biomarkers will be directly integrated.<br />
* Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file.<br />
* License is Creative Commons Attribution 4.0 International (CC BY 4.0).<br />
=MetaKB=<br />
<br />
Status: Direct Integration into Data Model<br />
<br />
* Provides harmonized associations between cancer genomic variants, diseases, and therapeutic evidence.<br />
* Aggregates and standardizes variant interpretation data from six major knowledgebases:<br />
** CIViC (Clinical Interpretation of Variants in Cancer) [Already Integrated Directly]<br />
** OncoKB [Yet to be integrated]<br />
** JAX-CKB (The Jackson Laboratory Clinical Knowledgebase) [Yet to be integrated]<br />
** MolecularMatch [Yet to be integrated]<br />
** PMKB (Precision Medicine Knowledgebase) [Yet to be integrated]<br />
** Cancer Genome Interpreter (CGI) – through its ''Cancer Biomarkers Database'' component .[Integrated]<br />
* Enables mapping of variant–disease–drug relationships with supporting evidence levels, citations, and ontology alignment (e.g., genes, variants, diseases, and drugs).<br />
* Data integration requires review to ensure harmonized entity mappings consistent with the BiomarkerKB data model.<br />
* Focused on somatic variant–based biomarkers; contextual attributes such as tissue type, therapy response, or evidence type can be inferred or imputed where not directly specified.<br />
* Manual curation may be required for entries with incomplete evidence annotation or lacking standard ontology references.<br />
* Integration approach: direct mapping of variant, condition, and evidence entities; cross-references retained to original data sources.<br />
* License: Aggregated data are available for non-commercial, research use only, respecting constituent licenses:<br />
** CIViC – CC0 (Public Domain)<br />
** PMKB – CC-BY 4.0<br />
** CGI – CC0 for biomarkers database, CC-BY-NC 4.0 for tool<br />
** JAX-CKB – CC-BY-NC-SA 4.0<br />
** OncoKB – custom non-commercial license<br />
** MolecularMatch – restricted commercial use<br />
** MetaKB codebase – MIT license<br />
* Overall usage requires adherence to non-commercial research terms; commercial use needs separate permissions from individual data providers.</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=API_Release_Notes&diff=65API Release Notes2025-03-11T21:07:17Z<p>JeetVora: </p>
<hr />
<div>== Version 2.7.1 ==<br />
Main article: Data release notes/2.7.1<br />
<br />
* New datasets for organism Bovine (''Bos taurus'') added</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Release_Notes&diff=64Data Release Notes2025-03-11T21:06:59Z<p>JeetVora: </p>
<hr />
<div><br />
== Version 1.0 ==<br />
Main article: Data release notes/2.7.1<br />
<br />
* New datasets for organism Bovine (''Bos taurus'') added</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Portal_Release_Notes&diff=63Portal Release Notes2025-03-11T21:05:55Z<p>JeetVora: /* Version 1.0 */</p>
<hr />
<div>The BiomarkerKB portal was first released on XXX. A new update is released every XXX months.<br />
<br />
==Version 1.0==<br />
*</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Template:Main&diff=62Template:Main2025-03-11T21:04:04Z<p>JeetVora: </p>
<hr />
<div>{{#invoke:main|main}}<noinclude><br />
{{documentation}}<br />
<!-- Categories go on the /doc subpage, and interwikis go on Wikidata. --><br />
</noinclude></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Template:Main&diff=61Template:Main2025-03-11T21:03:30Z<p>JeetVora: </p>
<hr />
<div>Main Article</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Template:Main&diff=60Template:Main2025-03-11T20:57:43Z<p>JeetVora: Created page with "MAIN"</p>
<hr />
<div>MAIN</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Portal_Release_Notes&diff=59Portal Release Notes2025-03-11T20:54:00Z<p>JeetVora: </p>
<hr />
<div>The BiomarkerKB portal was first released on XXX. A new update is released every XXX months.<br />
<br />
==Version 1.0==<br />
{{main|Portal release notes/1.0}}<br />
This version was released on XX.<br />
<br />
* XX</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=API_Release_Notes&diff=58API Release Notes2025-03-11T20:52:28Z<p>JeetVora: Created page with "cc"</p>
<hr />
<div>cc</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Data_Release_Notes&diff=57Data Release Notes2025-03-11T20:52:19Z<p>JeetVora: Created page with "cc"</p>
<hr />
<div>cc</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Portal_Release_Notes&diff=56Portal Release Notes2025-03-11T20:52:01Z<p>JeetVora: Created page with "cc"</p>
<hr />
<div>cc</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Releases&diff=55Releases2025-03-11T20:51:35Z<p>JeetVora: </p>
<hr />
<div></div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Portal Release Notes]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Portal Release Notes]]'' <br><br />
</div><br />
</div><br />
<br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Data Release Notes]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Release Notes]]'' <br><br />
</div><br />
</div><br />
<br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[API Release Notes]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[API Release Notes]]'' <br><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=33Main Page2024-12-20T19:22:40Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br>...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Releases&diff=32Releases2024-12-20T19:22:06Z<p>JeetVora: Created page with "Release info"</p>
<hr />
<div>Release info</div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=31Main Page2024-12-20T19:21:38Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload|Releases]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
<br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br>...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=30Main Page2024-12-20T19:20:42Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Portal]]'' <br><br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Data Repository]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[BiomarkerKB Web Services API]]'' <br><br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Frequently Asked Questions]]'' <br><br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Workflow & Data Model]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Workflow & Data Model]]'' <br><br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Data Submission/Data Upload]]'' <br><br />
</div><br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
&nbsp;&nbsp;&nbsp;&nbsp;'''''Main article:''' [[Biomarker About]]'' <br>...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=15Main Page2024-12-20T18:39:31Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB portal}}<br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB data repository}}...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>Data Workflow | Data Model</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Web Services API|Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB Web Services API}}<br />
...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=14Main Page2024-12-20T18:38:58Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB portal}}<br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB data repository}}...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>Data workflow | Data Model</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Web Services API|Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB Web Services API}}<br />
...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=13Main Page2024-12-20T18:38:07Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB portal}}<br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB data repository}}...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>Data workflow | Data Model</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[BiomarkerKB Web Services API|Biomarker About]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB Web Services API}}<br />
...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=12Main Page2024-12-20T18:36:12Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB portal}}<br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB data repository}}...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>Data Model</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Web Services API|BiomarkerKB Web Services API]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB Web Services API}}<br />
...<br />
</div><br />
</div><br />
</div></div>JeetVorahttps://wiki.biomarkerkb.org/index.php?title=Main_Page&diff=10Main Page2024-12-20T18:35:21Z<p>JeetVora: </p>
<hr />
<div>__NOTOC__<br />
<!--BANNER ACROSS TOP OF PAGE--><div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;"><div style="margin:0.4em; text-align:center;"><div style="font-size:160%; padding:.1em;">Welcome to [https://biomarkerkb.org/ BiomarkerKB] Wiki</div>'''<u>What is BiomarkerKB?</u>'''<br />
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers. The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.<br />
<br />
'''<u>Our Mission:</u>'''<br />
<br />
Provide computational and informatics resources and tools for biomarker research.<br />
<br />
Integrate biomarker data and knowledge from diverse resources.<br />
<br />
'''<u>Our Goals:</u>'''<br />
<br />
Mapping biomarkers from public sources to relevant data elements.<br />
<br />
Mapping contextual data from participating CFDE DCCs.<br />
<br />
Developing a framework for organizing biomarker data.<br />
<br />
Creating tools for querying and exploring biomarker data.<br />
<br />
Disseminating the results of this project to the research community.<div style="font-size:100%;"></div></div></div><div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB portal|BiomarkerKB Portal]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB portal}}<br />
The [[BiomarkerKB portal]] is the web interface allowing browser based access to the Biomarker data... <br />
</div><br />
</div><br />
<br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB data repository|BiomarkerKB Data Repository]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB data repository}}...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
=== [[Frequently Asked Questions|BiomarkerKB Web Services API]] ===<br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
The FAQ section contains ...<br />
</div><br />
</div><br />
<div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>Data Model</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
<br />
</div><br />
</div><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[Frequently Asked Questions|Data Submission/Data Upload]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|Frequently Asked Questions}}<br />
...<br />
</div><br />
</div><br />
<div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;"><div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC; padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;"><br />
<h3>[[BiomarkerKB Web Services API|BiomarkerKB Web Services API]]</h3><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><br />
{{main|BiomarkerKB Web Services API}}<br />
...<br />
</div><br />
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</div></div>JeetVora