{ "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": "human_protein_biomarkers.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tags": [ "Cancer Biomarker (BiomarkerDB)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P05231-1...", "A0001..." ], [ "P05231-1...", "A0001..." ] ], "headers": [ "uniprotkb_ca...", "biomarker_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "biomarker_id" }, { "type": "string", "label": "assessed_biomarker_entity" }, { "type": "string", "label": "biomarker" }, { "type": "string", "label": "best_biomarker_type" }, { "type": "string", "label": "loinc_code" }, { "type": "string", "label": "notes" }, { "type": "string", "label": "anatomical_entity" }, { "type": "string", "label": "uberon_id" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "assessed_entity_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_biomarkerdb", "A0001", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32259560", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32428990", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32677844", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32438331", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32475810", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32234467", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32442528", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32161940", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32425269", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "monitoring", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", 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"9351", "", "protein", "protein_xref_pubmed", "31772933", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "safety", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "9351", "", "protein", "protein_xref_biomarkerdb", "A0001", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "safety", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "9351", "", "protein", "protein_xref_pubmed", "32430456", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "safety", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "9351", "", "protein", "protein_xref_pubmed", "28848164", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "safety", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "9351", "", 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"2531", "", "protein", "protein_xref_pubmed", "32479790", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well|lymphoma (DOID:8584)", "", "0000178", "2531", "", "protein", "protein_xref_pubmed", "32369209", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "DOID:3571 / Liver Cancer", "0000178", "3571", "DOID:3571 / Liver Cancer", "protein", "protein_xref_biomarkerdb", "A0001", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "DOID:3571 / Liver Cancer", "0000178", "3571", "DOID:3571 / Liver Cancer", "protein", "protein_xref_pubmed", "32479790", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 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"protein_xref_pubmed", "32369209", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "4362", "", "protein", "protein_xref_biomarkerdb", "A0001", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "4362", "", "protein", "protein_xref_pubmed", "32479790", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "", "0000178", "4362", "", "protein", "protein_xref_pubmed", "32369209", "protein_xref_biomarkerdb", "A0001" ], [ "P05231-1", "A0001", "Interleukin-6 (IL6)", "increased IL6 level", "prognostic", "26881-3", "Measured in serum (UN:0001977) as well.", "DOID:1781 / Thyroid Gland Cancer", 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"monitoring", "71426-1", "Measured in serum (UN:0001977) and plasma (UN:0001969) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32475810", "protein_xref_biomarkerdb", "A0009" ], [ "P02741-1", "A0009", "C-reactive protein (CRP)", "increased CRP level", "monitoring", "71426-1", "Measured in serum (UN:0001977) and plasma (UN:0001969) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32296824", "protein_xref_biomarkerdb", "A0009" ], [ "P02741-1", "A0009", "C-reactive protein (CRP)", "increased CRP level", "monitoring", "71426-1", "Measured in serum (UN:0001977) and plasma (UN:0001969) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_doi", "10.1101/2020.03.10.20033613", "protein_xref_biomarkerdb", "A0009" ], [ "P02741-1", "A0009", "C-reactive protein (CRP)", "increased CRP level", "monitoring", "71426-1", "Measured in serum (UN:0001977) and plasma (UN:0001969) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32281668", "protein_xref_biomarkerdb", "A0009" ], [ "P02741-1", "A0009", "C-reactive protein (CRP)", "increased CRP level", "monitoring", "71426-1", "Measured in serum (UN:0001977) and plasma (UN:0001969) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_pubmed", "32243911", "protein_xref_biomarkerdb", "A0009" ], [ "P02741-1", "A0009", "C-reactive protein (CRP)", "increased CRP level", "prognostic", "71426-1", "Measured in serum (UN:0001977) as well.", "", "0000178", "0080600", "", "protein", "protein_xref_biomarkerdb", "A0009", "protein_xref_biomarkerdb", "A0009" ] ] }, "readme": "Name\n - Human Protein Biomarkers (Biomarker Database)\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2022-03-29T11:06:26.279356\n\nModified on\n - 2023-03-14T16:22:16.567Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Biomarker DB [], Jingyue Wu [jingyue.wu@email.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: doid2uberonid_mapping_v5.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/doid2uberonid_mapping_v5.csv\n Name: allbiomarkers-all.csv\n URI: /data/shared/glyds/downloads/biomarkerdb/2023_04_13/allbiomarkers-all.csv\n Output Subdomain\n Name: human_protein_biomarkers.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_biomarkers.csv\n Name: human_protein_biomarkers.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_biomarkers.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"219\"\n Name: \"biomarker_id\"\n Description: \"\"\n Unique Values: \"225\"\n Name: \"assessed_biomarker_entity\"\n Description: \"\"\n Unique Values: \"224\"\n Name: \"biomarker\"\n Description: \"\"\n Unique Values: \"221\"\n Name: \"best_biomarker_type\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"loinc_code\"\n Description: \"\"\n Unique Values: \"55\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"158\"\n Name: \"anatomical_entity\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"uberon_id\"\n Description: \"\"\n Unique Values: \"18\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"21\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"16\"\n Name: \"assessed_entity_type\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"555\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"225\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/human_protein_biomarkers.csv" }