{ "bcoid": "GLY_000737", "title": "Glycan Biomarkers (Biomarker Database)", "description": "The Glycan Biomarkers dataset contains glycan biomarker information, including cross-mapped GlyTouCan ...", "filename_list": "glycan_biomarkers.csv", "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": [ [ "G78959US...", "AN6708..." ], [ "G36521AS...", "AN6709..." ] ], "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" } ], [ "G78959US", "AN6708", "AN6708-1", "increased antigen level", "Sialylated tumor-related antigen", "GTC:G78959US", "glycan", "", "", "predictive", "", "Furthermore, a blood-plasma test for the sTRA glycan identified the PDACs that showed rapid relapse following neoadjuvant chemotherapy. This research demonstrates the use of the sTRA glycan to identify the PDAC cases that are highly resistant to chemotherapy.", "pancreatic cancer", "assessed_biomarker_entity; biomarker; specimen", "best_biomarker_role; condition", "both_levels", "", "0000178", "blood", "1793", "", "An endocrine gland cancer located_in the pancreas.", "Ca body of pancreas|Ca head of pancreas|Ca tail of pancreas|malignant neoplasm of body of pancreas|malignant neoplasm of head of pancreas|malignant neoplasm of tail of pancreas|pancreas neoplasm|pancreatic neoplasm|pancreatic tumor", "glycan_xref_pubmed", "33093149", "glycan_xref_biomarkerkb", "AN6708-1" ], [ "G36521AS", "AN6709", "AN6709-1", "increased N-glycan level", "Lewis x fucosylated monogalactosylated triantennary N-glycan", "GTC:G36521AS", "glycan", "", "", "prognostic", "", "Following digestion with sialidase and beta-galactosidase, the alpha1,3-fucosylated trisialylated triantennary structure (A3FG3S3, GU 10.75) digested to form the alpha1,3-fucosylated monogalactosylated triantennary structure (A3FG1). We observed a significant difference in the trends of both A3FG1 and CA 15-3 in all 10 patients. Interestingly, we found that A3FG1 increased in all the second samples, clearly consistent with breast cancer progression and/or metastasis. This preliminary result suggests that compared to the commonly measured CA 15-3 and CEA, the glycan marker A3FG1, quantified from whole serum of breast cancer patients, could be more reliable for detecting disease progression and metastasis.", "breast cancer", "assessed_biomarker_entity; biomarker; specimen", "best_biomarker_role; condition", "both_levels", "", "0000178", "blood", "1612", "", "An organ system cancer that originates in the mammary gland.", "breast tumor|malignant neoplasm of breast|malignant tumor of the breast|mammary cancer|mammary tumor|primary breast cancer", "glycan_xref_pubmed", "18818422", "glycan_xref_biomarkerkb", "AN6709-1" ] ] }, "readme": "Name\n - Glycan Biomarkers (Biomarker Database)\n\nVersion\n - v-2.10.1\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-2.10.1/reviewed/glycan_masterlist.csv\n Name: glycan_names.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_names.csv\n Name: protein_disease_names.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/protein_disease_names.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/sample_mapping.csv\n Name: oncomx.tsv\n URI: https:/data.glygen.org/ln2downloads/biomarkerdb/2025_10_09/oncomx.tsv\n Output Subdomain\n Name: glycan_biomarkers.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_biomarkers.csv\n Name: glycan_biomarkers.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/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: \"18\"\n Name: \"biomarker_canonical_id\"\n Description: \"\"\n Unique Values: \"18\"\n Name: \"biomarker_id\"\n Description: \"\"\n Unique Values: \"18\"\n Name: \"biomarker\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"assessed_biomarker_entity\"\n Description: \"\"\n Unique Values: \"18\"\n Name: \"assessed_biomarker_entity_id\"\n Description: \"\"\n Unique Values: \"18\"\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: \"4\"\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: \"7\"\n Name: \"condition\"\n Description: \"\"\n Unique Values: \"4\"\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: \"2\"\n Name: \"anatomical_entity\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"4\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"do_desc\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"do_syn\"\n Description: \"\"\n Unique Values: \"4\"\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: \"7\"\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: \"18\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/glycan_biomarkers.csv" }