{ "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" ], "tag": [ "Cancer Biomarker (BiomarkerDB)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P05231-1...", "AA4686..." ], [ "P05231-1...", "AA4686..." ] ], "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" } ], [ "P05231-1", "AA4686", "AA4686-1", "increased IL6 level", "Interleukin-6", "UPKB:P05231", "protein", "", "", "prognostic", "26881-3", "Univariate analysis of all patients demonstrated that an extent of disease (EOD) on bone scanning > or = 1, IL-6 > or = 7 pg/ml, PS > or = 1, PSA > 100 ng/ml, and ALP > 620 IU/liter were associated with a significantly lower survival rate than their respective counterparts. In multivariate analysis, however, the only two significant prognostic factors were EOD and IL-6. These results indicate that the serum IL-6 level is a significant prognostic factor for prostate cancer as well as EOD.", "prostate cancer", "biomarker; assessed_biomarker_entity; assessed_biomarker_entity_id; assessed_entity_type", "condition", "both_levels", "IL-6|B-cell stimulatory factor 2|BSF-2|CTL differentiation factor|CDF|Hybridoma growth factor|Interferon beta-2|IFN-beta-2", "0000178", "blood", "10283", "DOID:10283 / Prostate Cancer", "A male reproductive organ cancer that is located_in the prostate.", "prostate neoplasm|NGP - new growth of prostate|tumor of the prostate|prostate cancer, familial|prostatic neoplasm|malignant tumor of the prostate|hereditary prostate cancer|prostatic cancer", "protein_xref_pubmed", "10914713", "protein_xref_glygen_ds", "GLY_000625" ], [ "P05231-1", "AA4686", "AA4686-1", "increased IL6 level", "Interleukin-6", "UPKB:P05231", "protein", "", "", "prognostic", "26881-3", "IL-6 plays multifaceted roles in regulation of vascular leakage, complement activation, and coagulation pathways, which ultimately causes poor outcomes for acute respiratory distress syndrome, multiple organ dysfunction syndrome, and SARS.", "prostate cancer", "biomarker; assessed_biomarker_entity; assessed_biomarker_entity_id; assessed_entity_type", "condition", "both_levels", "IL-6|B-cell stimulatory factor 2|BSF-2|CTL differentiation factor|CDF|Hybridoma growth factor|Interferon beta-2|IFN-beta-2", "0000178", "blood", "10283", "DOID:10283 / Prostate Cancer", "A male reproductive organ cancer that is located_in the prostate.", "prostate neoplasm|NGP - new growth of prostate|tumor of the prostate|prostate cancer, familial|prostatic neoplasm|malignant tumor of the prostate|hereditary prostate cancer|prostatic cancer", "protein_xref_pubmed", "32479790", "protein_xref_glygen_ds", "GLY_000625" ] ] }, "readme": "Name\n - Human Protein Biomarkers (Biomarker Database)\n\nVersion\n - v-2.5.1\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: doid2uberonid_mapping_v5.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/doid2uberonid_mapping_v5.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/sample_mapping.csv\n Name: allbiomarkers.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2024_04_19/allbiomarkers.tsv\n Output Subdomain\n Name: human_protein_biomarkers.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/human_protein_biomarkers.csv\n Name: human_protein_biomarkers.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/human_protein_biomarkers.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"308\"\n Name: \"biomarker_canonical_id\"\n Description: \"\"\n Unique Values: \"274\"\n Name: \"biomarker_id\"\n Description: \"\"\n Unique Values: \"383\"\n Name: \"biomarker\"\n Description: \"\"\n Unique Values: \"264\"\n Name: \"assessed_biomarker_entity\"\n Description: \"\"\n Unique Values: \"263\"\n Name: \"assessed_biomarker_entity_id\"\n Description: \"\"\n Unique Values: \"308\"\n Name: \"assessed_entity_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"exposure_agent\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"exposure_agent_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"best_biomarker_role\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"loinc_code\"\n Description: \"\"\n Unique Values: \"59\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"424\"\n Name: \"condition\"\n Description: \"\"\n Unique Values: \"22\"\n Name: \"component_level_tags\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"top_level_tags\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"evidence_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"component_synonyms\"\n Description: \"\"\n Unique Values: \"276\"\n Name: \"uberon_id\"\n Description: \"\"\n Unique Values: \"24\"\n Name: \"anatomical_entity\"\n Description: \"\"\n Unique Values: \"24\"\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: \"do_desc\"\n Description: \"\"\n Unique Values: \"21\"\n Name: \"do_syn\"\n Description: \"\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"357\"\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: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.5.1/reviewed/human_protein_biomarkers.csv" }