{ "bcoid": "GLY_000625", "title": "Human Protein Biomarkers (Biomarker Database)", "description": "This is a Human Protein Biomarkers dataset. It contains human [taxonomy:9606] protein biomarker information, ...", "filename_list": "human_protein_biomarkers.csv", "filename": "human_protein_biomarkers.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "Cancer Biomarker (BiomarkerDB)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "others" ] }, "minitable": { "content": [ [ "P05783-1...", "BD0291..." ], [ "P05783-1...", "BD0291..." ] ], "headers": [ "uniprotkb_ca...", "biomarker_ca..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "biomarker_canonical_id" }, { "type": "string", "label": "biomarker_id" }, { "type": "string", "label": "biomarker" }, { "type": "string", "label": "assessed_biomarker_entity" }, { "type": "string", "label": "assessed_biomarker_entity_id" }, { "type": "string", "label": "assessed_entity_type" }, { "type": "string", "label": "exposure_agent" }, { "type": "string", "label": "exposure_agent_id" }, { "type": "string", "label": "best_biomarker_role" }, { "type": "string", "label": "loinc_code" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "condition" }, { "type": "string", "label": "component_level_tags" }, { "type": "string", "label": "top_level_tags" }, { "type": "string", "label": "evidence_type" }, { "type": "string", "label": "component_synonyms" }, { "type": "string", "label": "uberon_id" }, { "type": "string", "label": "anatomical_entity" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "do_desc" }, { "type": "string", "label": "do_syn" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P05783-1", "BD0291", "BD0291-1", "increased level of K18-M65", "Keratin, type I cytoskeletal 18", "UPKB:P05783", "peptide", "", "", "diagnostic", "", "High levels of K18-M65 characterized AUD patients with early ALD while levels in the minimal ALD group were similar to those in healthy controls. Serum K18-M65 can be used as a biomarker to detect early ALD stages with an excellent predictive value.", "alcohol-associated liver disease", "assessed_biomarker_entity; biomarker; specimen", "best_biomarker_role; condition", "both_levels", "Keratin-18|K18||Cytokeratin-18|CK-18|Cell proliferation-inducing gene 46 protein", "0001977", "blood serum", "0070658", "alcohol-associated liver disease", "A liver disease resulting from excessive alcohol intake.", "ALD|alcohol-related liver disease|alcoholic liver disease", "protein_xref_pubmed", "37060262", "protein_xref_biomarkerkb", "BD0291-1" ], [ "P05783-1", "BD0291", "BD0291-1", "increased level of K18-M65", "Keratin, type I cytoskeletal 18", "UPKB:P05783", "peptide", "", "", "diagnostic", "", "Total (K18-M65) and caspase-cleaved K18 (K18-M30) were quantified in pretreatment sera... K18 fragments were markedly elevated in severe AH and strongly predicted steatohepatitis (alcoholic steatohepatitis)... In a large cohort of patients with severe AH, serum K18 strongly correlated with histological severity, independently associated with 90-day mortality, and predicted response to prednisolone therapy. Quantification of serum K18 levels could assist in clinical decision-making.", "alcohol-associated liver disease", "assessed_biomarker_entity; biomarker; specimen", "best_biomarker_role; condition", "both_levels", "Keratin-18|K18||Cytokeratin-18|CK-18|Cell proliferation-inducing gene 46 protein", "0001977", "blood serum", "0070658", "alcohol-associated liver disease", "A liver disease resulting from excessive alcohol intake.", "ALD|alcohol-related liver disease|alcoholic liver disease", "protein_xref_pubmed", "33156105", "protein_xref_biomarkerkb", "BD0291-1" ] ] }, "readme": "Name\n - Human Protein Biomarkers (Biomarker Database)\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2022-03-29T11:06:26.279356\n\nModified on\n - 2024-05-17T11:24:07.032Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Biomarker DB [], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - This is a Human Protein Biomarkers dataset. It contains human [taxonomy:9606] protein biomarker information, including cross-mapped UniProtKB or Protein Ontology accessions, assessed biomarker entity, biomarker status, biomarker type, specimen type, LOINC code, disease name, and source evidence from the cancer biomarker portal (https://data.oncomx.org/cancerbiomarkers). This dataset can be used to obtain biomarker information for 19 cancer types and COVID-19. If you use this dataset, please provide proper attribution to OncoMX and GlyGen. Cite: PMID:32142370, PMID:34015823, and PMID:31616925. The dataset was earlier called as human_protein_cancer_biomarkers.csv\n\nDescription Domain\n Keywords\n - biomarker\n - cancer\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accession from the source file to UniProtKB canonical accession. The script extracts the other fields as is from the source input file.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: human_protein_altnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_altnames.csv\n Name: human_protein_submittednames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_submittednames.csv\n Name: protein_disease_names.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/protein_disease_names.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/sample_mapping.csv\n Name: biomarkers_cadsr.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_cadsr.tsv\n Name: biomarkers_cgi.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_cgi.tsv\n Name: biomarkers_civic_metakb.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_civic_metakb.tsv\n Name: biomarkers_civic.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_civic.tsv\n Name: biomarkers_clinvar.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_clinvar.tsv\n Name: biomarkers_edrn.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_edrn.tsv\n Name: biomarkers_exposure_agents.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_exposure_agents.tsv\n Name: biomarkers_gwas.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_gwas.tsv\n Name: biomarkers_llm_glycan.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_llm_glycan.tsv\n Name: biomarkers_microplastics.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_microplastics.tsv\n Name: biomarkers_mw_loinc.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_mw_loinc.tsv\n Name: biomarkers_mw_newborn_screening.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_mw_newborn_screening.tsv\n Name: biomarkers_oncomx.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_oncomx.tsv\n Name: biomarkers_opentargets.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_opentargets.tsv\n Name: biomarkers_PMC_biomarker_sets.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_PMC_biomarker_sets.tsv\n Name: biomarkers_sennet.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_sennet.tsv\n Name: biomarkers_top_50.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_top_50.tsv\n Name: biomarkers_upkb_reviewed_v2.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_upkb_reviewed_v2.tsv\n Name: biomarkers_user_submitted.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2026_08_10/biomarkers_user_submitted.tsv\n Output Subdomain\n Name: human_protein_biomarkers.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_biomarkers.csv\n Name: human_protein_biomarkers.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_biomarkers.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"236\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_protein_biomarkers.csv" }