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x-atlas-consortia / ubkg-etl

A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
MIT License
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update HUBMAP and SENNET assay classifications with new rules from assayclasses.json #159

Open AlanSimmons opened 1 month ago

AlanSimmons commented 1 month ago

Re: https://github.com/x-atlas-consortia/hs-ontology-api/pull/138

AlanSimmons commented 1 month ago

EPIC dataset segmentation mask

from /assayclasses endpoint, running against a local instance of UBKG


    "rule_description": {
        "application_context": "HUBMAP",
        "code": "C202020",
        "name": "EPIC dataset segmentation mask"
    },
    "value": {
        "active_status": "active",
        "assaytype": "segmentation-mask",
        "dataset_type": {
            "PDR_category": null,
            "dataset_type": "Segmentation Mask",
            "fig2": {
                "aggregated_assaytype": null,
                "category": "imaging",
                "modality": null
            }
        },
        "description": "Segmentation Mask",
        "dir_schema": "segmentation-mask-v",
        "is_multiassay": false,
        "measurement_assay": {
            "codes": [],
            "contains_full_genetic_sequences": false
        },
        "must_contain": [],
        "pipeline_shorthand": null,
        "process_state": "epic",
        "tbl_schema": null,
        "vitessce_hints": [
            "pyramid",
            "is_image",
            "segmentation-mask"
        ]
    }
}
AlanSimmons commented 1 month ago

DCWG RNAseq-geomx-with-probes

response from/assayclasses endpoint running against local instance of UBKG.


    "rule_description": {
        "application_context": "HUBMAP",
        "code": "C202030",
        "name": "DCWG RNAseq-geomx-with-probes"
    },
    "value": {
        "active_status": "active",
        "assaytype": "geomx-rnaseq-with-probes",
        "dataset_type": {
            "PDR_category": "RNA Sequencing",
            "dataset_type": "RNAseq (with probes)",
            "fig2": {
                "aggregated_assaytype": "RNAseq",
                "category": "bulk",
                "modality": "Transcriptomics"
            }
        },
        "description": "GeoMx RNAseq (with probes)",
        "dir_schema": "rnaseq-with-probes-v2",
        "is_multiassay": false,
        "measurement_assay": {
            "codes": [
                {
                    "code": "SENNET:C014201",
                    "term": "GeoMX Digital Spatial Profiler Measurement Assay"
                },
                {
                    "code": "HUBMAP:C014201",
                    "term": "GeoMX Digital Spatial Profiler Measurement Assay"
                },
                {
                    "code": "NCI:C181933",
                    "term": "GeoMx Digital Spatial Profiler"
                }
            ],
            "contains_full_genetic_sequences": true
        },
        "must_contain": [],
        "pipeline_shorthand": null,
        "process_state": "primary",
        "tbl_schema": null,
        "vitessce_hints": []
    }
}
AlanSimmons commented 1 month ago

DCWG scRNAseq-with probes

from /assayclasses endpoint running against local instance of UBKG


    "rule_description": {
        "application_context": "HUBMAP",
        "code": "C202040",
        "name": "DCWG scRNAseq-with-probes"
    },
    "value": {
        "active_status": "active",
        "assaytype": "scRNAseq-with-probes",
        "dataset_type": {
            "PDR_category": "RNA Sequencing",
            "dataset_type": "RNAseq (with probes)",
            "fig2": {
                "aggregated_assaytype": "RNAseq",
                "category": "bulk",
                "modality": "Transcriptomics"
            }
        },
        "description": "RNAseq (with probes)",
        "dir_schema": "rnaseq-with-probes-v",
        "is_multiassay": false,
        "measurement_assay": {
            "codes": [
                {
                    "code": "SENNET:C001022",
                    "term": "Single-cell RNA sequencing (scRNA-seq) Assay"
                },
                {
                    "code": "HUBMAP:C001022",
                    "term": "Single-cell RNA sequencing (scRNA-seq) Assay"
                },
                {
                    "code": "OBI:0002631",
                    "term": "single-cell RNA sequencing assay"
                }
            ],
            "contains_full_genetic_sequences": true
        },
        "must_contain": [],
        "pipeline_shorthand": null,
        "process_state": "primary",
        "tbl_schema": null,
        "vitessce_hints": []
    }
}
AlanSimmons commented 1 month ago

DCWG xenium

from /assayclasses endpoint running against local instance of UBKG.


    "rule_description": {
        "application_context": "HUBMAP",
        "code": "C202050",
        "name": "DCWG xenium"
    },
    "value": {
        "active_status": "active",
        "assaytype": "xenium",
        "dataset_type": {
            "PDR_category": null,
            "dataset_type": "Xenium",
            "fig2": {
                "aggregated_assaytype": null,
                "category": "imaging",
                "modality": "Spatial Transcriptomics"
            }
        },
        "description": "Xenium",
        "dir_schema": "xenium-v",
        "is_multiassay": false,
        "measurement_assay": {
            "codes": [
                {
                    "code": "HUBMAP:C202053",
                    "term": "Xenium measurement assay"
                }
            ],
            "contains_full_genetic_sequences": false
        },
        "must_contain": [],
        "pipeline_shorthand": null,
        "process_state": "primary",
        "tbl_schema": null,
        "vitessce_hints": []
    }
}