{ "bcoid": "GLY_000737", "title": "Glycan Biomarkers (Biomarker Database)", "description": "The Glycan Biomarkers dataset contains glycan biomarker information, including cross-mapped GlyTouCan ...", "filename": "glycan_biomarkers.csv", "filetype": "csv", "categories": { "molecule": [ "Glycan" ], "tag": [ "Glycan Biomarker (BiomarkerDB)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "species": [ "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Sus scrofa", "Rattus", "Rattus norvegicus", "Severe acute respiratory syndrome coronavirus 2", "Saccharomyces cerevisiae", "Dictyostelium discoideum", "Hepacivirus C" ] }, "minitable": { "content": [ [ "G00053MO...", "AN4074..." ], [ "G00053MO...", "AN4074..." ] ], "headers": [ "glytoucan_ac...", "biomarker_ca..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_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" } ], [ "G00053MO", "AN4074", "AN4074-1", "increased CA199 level", "Carbohydrate antigen 199", "GTC:G00053MO", "glycan", "", "", "monitoring;prognostic", "", "Increases in levels of Human epididymis protein 4 (HE4), Cytokeratin-19 fragment (CYFRA21-1) Carcinoembryonic antigen (CEA), Carbohydrate antigen 125 (CA125), Carbohydrate antigen 153 (CA153), Squamous cell carcinoma antigen (SCC), Carbohydrate antigen 199 (CA199). There were positive associations between levels of C-reactive protein and levels of HE4 (R= 0.631, p<0.001), CYFRA21-1(R= 0.431, p<0.001), CEA (R= 0.316, p<0.001), SCC (R= 0.351, p<0.001), CA153 (R= 0.359, p<0.001) and CA125 (R= 0.223, p=0.031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute lung injuries.", "COVID-19", "biomarker; assessed_biomarker_entity; assessed_biomarker_entity_id; assessed_entity_type", "condition", "both_levels", "", "0000178", "blood", "0080600", "", "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "SARS-CoV-2 infection|Wuhan coronavirus infection|COVID19|Wuhan seafood market pneumonia virus infection|2019-nCoV infection|2019 Novel Coronavirus (2019-nCoV)", "glycan_xref_pubmed", "32347972", "glycan_xref_glygen_ds", "GLY_000737" ], [ "G00053MO", "AN4074", "AN4074-1", "increased CA199 level", "Carbohydrate antigen 199", "GTC:G00053MO", "glycan", "", "", "monitoring;prognostic", "", "Significant increases in levels of human epididymis protein 4 (HE4), cytokeratin-19 fragment (CYFRA21-1), carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125 , and 153. Squamous cell carcinoma antigen (SCC) and CA199 increased significantly.", "COVID-19", "biomarker; assessed_biomarker_entity; assessed_biomarker_entity_id; assessed_entity_type", "condition", "both_levels", "", "0000178", "blood", "0080600", "", "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.", "SARS-CoV-2 infection|Wuhan coronavirus infection|COVID19|Wuhan seafood market pneumonia virus infection|2019-nCoV infection|2019 Novel Coronavirus (2019-nCoV)", "glycan_xref_pubmed", "32347972", "glycan_xref_glygen_ds", "GLY_000737" ] ] }, "readme": "Name\n - Glycan Biomarkers (Biomarker Database)\n\nVersion\n - v-2.5.1\n\nCreated on\n - 2023-03-14T20:00:08.127Z\n\nModified on\n - 2024-05-17T11:24:11.261Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Dan Lyman [danlyman@gwu.edu], 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 - The Glycan Biomarkers dataset contains glycan biomarker information, including cross-mapped GlyTouCan accessions, assessed biomarker entity, biomarker type, specimen type, LOINC code, disease name, and source evidence from the biomarker portal (https://data.oncomx.org/allbiomarkers). If you use this dataset, please provide proper attribution to OncoMX and GlyGen. Cite: PMID:32142370, PMID:34015823, and PMID:31616925.\n\nDescription Domain\n Keywords\n - biomarker\n - cancer\n\n Pipeline Steps\n - Step-1: \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\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: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/glycan_masterlist.csv\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: glycan_biomarkers.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/glycan_biomarkers.csv\n Name: glycan_biomarkers.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/glycan_biomarkers.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"79\"\n Name: \"biomarker_canonical_id\"\n Description: \"\"\n Unique Values: \"33\"\n Name: \"biomarker_id\"\n Description: \"\"\n Unique Values: \"36\"\n Name: \"biomarker\"\n Description: \"\"\n Unique Values: \"33\"\n Name: \"assessed_biomarker_entity\"\n Description: \"\"\n Unique Values: \"33\"\n Name: \"assessed_biomarker_entity_id\"\n Description: \"\"\n Unique Values: \"79\"\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: \"6\"\n Name: \"loinc_code\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"22\"\n Name: \"condition\"\n Description: \"\"\n Unique Values: \"11\"\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: \"1\"\n Name: \"uberon_id\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"anatomical_entity\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"11\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"11\"\n Name: \"do_desc\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"do_syn\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\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/glycan_biomarkers.csv" }