From 4a855061b2813f3f6c2f77f80774d85334f14ed3 Mon Sep 17 00:00:00 2001 From: yuanzhou Date: Wed, 6 Nov 2024 13:39:27 -0500 Subject: [PATCH] Delete dev assay directory --- dev/.gitignore | 2 - dev/Dockerfile | 13 - dev/README.md | 95 - dev/app.py | 125 - dev/assayclasses.json | 5248 ---------------------------------- dev/docker-compose.yml | 13 - dev/instance/app.cfg.example | 3 - dev/requirements.txt | 1 - dev/test_api.sh | 52 - 9 files changed, 5552 deletions(-) delete mode 100644 dev/.gitignore delete mode 100644 dev/Dockerfile delete mode 100644 dev/README.md delete mode 100644 dev/app.py delete mode 100644 dev/assayclasses.json delete mode 100644 dev/docker-compose.yml delete mode 100644 dev/instance/app.cfg.example delete mode 100644 dev/requirements.txt delete mode 100755 dev/test_api.sh diff --git a/dev/.gitignore b/dev/.gitignore deleted file mode 100644 index 2dc5e5d..0000000 --- a/dev/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -#config file -instance/app.cfg \ No newline at end of file diff --git a/dev/Dockerfile b/dev/Dockerfile deleted file mode 100644 index 0cdd64a..0000000 --- a/dev/Dockerfile +++ /dev/null @@ -1,13 +0,0 @@ -FROM hubmap/api-base-image:1.0.0 - -LABEL description="DEV Server for Assayclasses" - -WORKDIR /usr/src/app - -COPY . . - -RUN pip install --upgrade pip -r requirements.txt - -EXPOSE 8181 - -CMD [ "python", "-m" , "app"] diff --git a/dev/README.md b/dev/README.md deleted file mode 100644 index 606a7ad..0000000 --- a/dev/README.md +++ /dev/null @@ -1,95 +0,0 @@ -# Development AssayClasses RESTful service - -## Dev Service -This simple, standalone service is designed for quick changes to the assay class/rule chain information during development to allow for quick testing. The service two endpoints: - - /assayclasses?application_context=HUBMAP - - assayclasses/?application_context=HUBMAP - -## JSON backing file and releasing to UBKG -The [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/dev-integrate/dev/assayclasses.json) file is read directly by this service to form the responses. This file can be changed directly in GitHub (in the dev-integrate branch only) to test changes to the associated rule chain/assay class information that normally is sourced from UBKG. To develop using this service and eventually release to UBKG follow this procedure: - - Update the [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/dev-integrate/dev/assayclasses.json) directly by merging changes into the `dev-integrate` branch. Test locally or using the HuBMAP DEV infrastructure where this dev service has been put in place. - - After successful tests on the DEV infrastructure make a PR to `main` with the changes in assayclasses.json. Add Alan Simmons as a reviewer on the PR. - - The changes will be added to UBKG and released to the UBKG DEV instance. - - Test the changes on the HuBMAP TEST infrastructure (TEST infrastructure is connected to UBKG DEV instance). - - After successful testing on TEST the changes to UBKG will be released to PROD. - - -### Running the service locally -To run this service, in this directory: - - copy instance/app.cfg.example to instance/app.cfg - - create a python virtual environment with the contents of requirements.txt imported into the environment - - source/activate the virtual environment - - execute `python app.py` -The service will be available on port 8181. -See below for instructions to run with Docker - - -Both endpoints require the `application_context=HUBMAP` parameter. (A future version will allow SENNET context as well, which will read results from a different file). - -### Endpoints -The `/assayclasses` endpoint simply returns the contents of the [assayclasses.json file](https://github.com/x-atlas-consortia/hs-ontology-api/blob/main/dev/assayclasses.json) as a json response. - -The `/assayclasses/` endpoint searches the same [assayclasses.json file](https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json) for an assayclass item matching `rule_description.code` and returns the full matching assayclass item as a json response. If the code is not found a 404 is returned. For example if `/assayclasses/C200001?application_context=HUBMAP` is called the return value is: - -``` -{ - "rule_description": { - "application_context": "HUBMAP", - "code": "C200150", - "name": "non-DCWG primary IMC2D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry", - "dir_schema": "imc-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "HUBMAP:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "OBI:0003096", - "term": "imaging mass cytometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "imc-v", - "vitessce_hints": [] - } -} -``` - -### Docker Deployment on DEV VM - -First build a new docker image -``` -docker-compose build -``` - -Then spin up the container -``` -docker-compose up -d -``` - -Once the container is up running correctly, you can access at `http://gateway.dev.hubmapconsortium.org:8181/assayclasses` diff --git a/dev/app.py b/dev/app.py deleted file mode 100644 index 481cd76..0000000 --- a/dev/app.py +++ /dev/null @@ -1,125 +0,0 @@ -import os -import json -from flask import Flask, request, Response, abort -from urllib.request import urlopen -from urllib.error import HTTPError -import logging - -# -# This is a RESTful service that exposes two endpoints: -# /assayclasses?application_context=HUBMAP -# /assayclasses/?application_context=HUBMAP -# -# Both endpoints require the application_context=HUBMAP parameter to be included, otherwise they return a 400. -# -# This service is intended to be for development purposes only, so a developer can easily control the output by -# changing the [assayclasses.json file in GitHub], specified in the ASSAYCLASSES_JSON_URL app.conf parameter. -# -# It is intended to mimic the services: -# https://ontology-api.dev.hubmapconsortium.org/assayclasses?application_context=HUBMAP -# https://ontology-api.dev.hubmapconsortium.org/assayclasses/C200150?application_context=HUBMAP -# -# Please see Issue: https://github.com/orgs/hubmapconsortium/projects/40/views/1?filterQuery=kollar&visibleFields=%5B%22Title%22%2C%22Assignees%22%2C%22Status%22%2C%22Labels%22%2C117184707%5D&pane=issue&itemId=74945308 - - -logging.basicConfig(format='[%(asctime)s] %(levelname)s in %(module)s: %(message)s', - level=logging.DEBUG, - datefmt='%Y-%m-%d %H:%M:%S' - ) -logger = logging.getLogger() - - -app = Flask(__name__, - instance_path=os.path.join(os.path.abspath(os.path.dirname(__file__)), 'instance'), - instance_relative_config=True) -app.config.from_pyfile('app.cfg') - - -def get_assayclasses() -> dict: - """ - Download the assayclasses information and return it as a dict. - Since this is done at startup time, on error it will log an error and exit as the app cannot recover from this. - """ - if "ASSAYCLASSES_JSON_URL" not in app.config: - logger.error("app.cfg must contain ASSAYCLASSES_JSON_URL") - exit(1) - assayclasses_json_url: str = app.config["ASSAYCLASSES_JSON_URL"] - try: - response = urlopen(assayclasses_json_url) - data: str = response.read().decode("utf-8") - except HTTPError as he: - logger.error(f"Could not read ASSAYCLASSES_JSON_URL: {assayclasses_json_url}, error: {he}") - exit(1) - try: - json_dict: dict = json.loads(data) - except json.JSONDecodeError as jde: - logger.error(f"Invalid JSON syntax: {jde}") - exit(1) - logger.info(f"successfully downloaded app.cfg:ASSAYCLASSES_JSON_URL={assayclasses_json_url} json as dict") - return json_dict - - -assayclasses_list: dict = get_assayclasses() - - -def find_assayclass_with_rule_description_code(code: str): - """ - Find the assayclass corresponding the rule_description code given or return None. - """ - for ad in assayclasses_list: - if "rule_description" in ad and "code" in ad["rule_description"] and ad["rule_description"]["code"] == code: - return ad - return None - - -def check_for_valid_application_context() -> None: - """ - Check for a valid auery parameter application_context, and if not found abort with a 400. - """ - application_context = request.args.get('application_context') - if application_context is None or application_context.upper() != "HUBMAP": - abort(Response(json.dumps({"message": "A query parameter of application_context=HUBMAP must be specified"}), - 400, - mimetype='application/json')) - - -@app.route('/', methods=['GET']) -def index(): - return "Hello! This is the DEV AssayClass service :)" - - -@app.route('/assayclasses/', methods=['GET']) -def assayclasses_by_code(code): - """ - This endpoint searches the same assayclasses.json file for an assayclass item matching - rule_description.code and returns the full matching assayclass item as a json response. - If the code is not found a 404 is returned. - """ - check_for_valid_application_context() - - assayclass_dict = find_assayclass_with_rule_description_code(code) - - if assayclass_dict is not None: - return Response(json.dumps(assayclass_dict), 200, mimetype='application/json') - - return Response(json.dumps({"message": f"No assayclass corresponding the rule_description code:{code} was found"}), - 404, mimetype='application/json') - - -@app.route('/assayclasses', methods=['GET']) -def assayclass(): - """ - This endpoint returns the contents of the ASSAYCLASSES_JSON_URL as a json response. - """ - check_for_valid_application_context() - - return Response(json.dumps(assayclasses_list), 200, mimetype='application/json') - - -# For development/testing only -if __name__ == '__main__': - try: - port = 8181 - app.run(port=port, host='0.0.0.0') - finally: - pass diff --git a/dev/assayclasses.json b/dev/assayclasses.json deleted file mode 100644 index b2227cc..0000000 --- a/dev/assayclasses.json +++ /dev/null @@ -1,5248 +0,0 @@ -[ - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200001", - "name": "non-DCWG primary AF" - }, - "value": { - "active_status": "active", - "assaytype": "AF", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Auto-fluorescence", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Auto-fluorescence Microscopy", - "dir_schema": "af-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "OBI:0003088", - "term": "autofluorescence microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "af-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200010", - "name": "derived AF_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "AF_pyramid", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Auto-fluorescence", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Auto-fluorescence Microscopy [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200020", - "name": "non-DCWG primary ATACseq-bulk" - }, - "value": { - "active_status": "active", - "assaytype": "ATACseq-bulk", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "Bulk ATACseq", - "dir_schema": "bulkatacseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "OBI:0002039", - "term": "assay for transposase-accessible chromatin using sequencing" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "bulkatacseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200030", - "name": "derived bulk_atacseq" - }, - "value": { - "active_status": "active", - "assaytype": "bulk_atacseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "Bulk ATAC-seq [BWA + MACS2]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "BWA + MACS2", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200040", - "name": "non-DCWG primary cell-dive" - }, - "value": { - "active_status": "active", - "assaytype": "cell-dive", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "Cell DIVE", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Cell DIVE", - "dir_schema": "celldive-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "HUBMAP:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "OBI:0003092", - "term": "Cell DIVE multiplexed imaging assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200050", - "name": "derived celldive_deepcell" - }, - "value": { - "active_status": "active", - "assaytype": "celldive_deepcell", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "Cell DIVE", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Cell DIVE [DeepCell + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "DeepCell + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_tiled", - "is_image", - "anndata", - "sprm" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200060", - "name": "non-DCWG primary CODEX" - }, - "value": { - "active_status": "active", - "assaytype": "CODEX", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX", - "dir_schema": "codex-v1", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "HUBMAP:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "OBI:0003093", - "term": "co-detection by indexing assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "codex-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200070", - "name": "non-DCWG primary CODEX2" - }, - "value": { - "active_status": "active", - "assaytype": "CODEX2", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX (CODEX2 assay type)", - "dir_schema": "codex-v1", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "HUBMAP:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "OBI:0003093", - "term": "co-detection by indexing assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "codex-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200080", - "name": "derived codex_cytokit_v1" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "anndata", - "codex", - "is_tiled", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200090", - "name": "derived codex_cytokit_v1 json-based" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "json-based", - "codex", - "is_tiled", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200100", - "name": "derived codex_cytokit" - }, - "value": { - "active_status": "active", - "assaytype": "codex_cytokit_v1", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX [Cytokit + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Cytokit + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_tiled", - "is_image", - "anndata", - "sprm" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200110", - "name": "non-DCWG primary DART-FISH" - }, - "value": { - "active_status": "active", - "assaytype": "DART-FISH", - "dataset_type": { - "PDR_category": null, - "dataset_type": "DARTFish", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "DART-FISH", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006701", - "term": "Decoding Amplified taRgeted Transcripts with Fluorescence In Situ Hybridization (DARTFish) Measurement Assay" - }, - { - "code": "HUBMAP:C006701", - "term": "Decoding Amplified taRgeted Transcripts with Fluorescence In Situ Hybridization (DARTFish) Measurement Assay" - }, - { - "code": "OBI:0003095", - "term": "decoding amplified targeted transcripts with fluorescence in situ hybridization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200120", - "name": "non-DCWG primary DESI" - }, - "value": { - "active_status": "active", - "assaytype": "DESI", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "DESI", - "dir_schema": "ims-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "HUBMAP:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "OBI:0003101", - "term": "nanospray desorption electrospray ionization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "ims-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200130", - "name": "derived DESI_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "DESI_pyramid", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "DESI [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200140", - "name": "derived image_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "image_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Image Pyramid", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200150", - "name": "non-DCWG primary IMC2D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry", - "dir_schema": "imc-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "HUBMAP:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "OBI:0003096", - "term": "imaging mass cytometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "imc-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200160", - "name": "non-DCWG primary IMC3D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC3D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "3D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "3D Imaging Mass Cytometry", - "dir_schema": "imc3d-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "HUBMAP:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "OBI:0003096", - "term": "imaging mass cytometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "imc3d-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200170", - "name": "derived IMC2D_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D_pyramid", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200180", - "name": "derived IMC3D_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "IMC3D_pyramid", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "3D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "3D Imaging Mass Cytometry [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200190", - "name": "non-DCWG primary lc-ms_label-free" - }, - "value": { - "active_status": "active", - "assaytype": "lc-ms_label-free", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Label-free LC-MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200200", - "name": "non-DCWG primary lc-ms_labeled" - }, - "value": { - "active_status": "active", - "assaytype": "lc-ms_labeled", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Labeled LC-MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200210", - "name": "non-DCWG primary lc-ms-ms_label-free" - }, - "value": { - "active_status": "active", - "assaytype": "lc-ms-ms_label-free", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Label-free LC-MS/MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200220", - "name": "non-DCWG primary lc-ms-ms_labeled" - }, - "value": { - "active_status": "active", - "assaytype": "lc-ms-ms_labeled", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Labeled LC-MS/MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200230", - "name": "non-DCWG primary LC-MS-untargeted" - }, - "value": { - "active_status": "active", - "assaytype": "LC-MS-untargeted", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Untargeted LC-MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200240", - "name": "non-DCWG primary Lightsheet" - }, - "value": { - "active_status": "active", - "assaytype": "Lightsheet", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Light Sheet", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Light Sheet Microscopy", - "dir_schema": "lightsheet-v1", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200243", - "term": "Lightsheet fluorescence microscopy measurement assay" - }, - { - "code": "HUBMAP:C200243", - "term": "Lightsheet fluorescence microscopy measurement assay" - }, - { - "code": "OBI:0003098", - "term": "lightsheet fluorescence microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lightsheet-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200250", - "name": "non-DCWG primary MALDI-IMS" - }, - "value": { - "active_status": "active", - "assaytype": "MALDI-IMS", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "MALDI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "MALDI IMS", - "dir_schema": "ims-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C007701", - "term": "Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) Measurement Assay" - }, - { - "code": "HUBMAP:C007701", - "term": "Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) Measurement Assay" - }, - { - "code": "OBI:0003099", - "term": "matrix assisted laser desorption ionization imaging mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "ims-v", - "vitessce_hints": [ - "maldi" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200260", - "name": "derived MALDI-IMS_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "MALDI-IMS_pyramid", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "MALDI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "MALDI IMS [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "maldi", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200270", - "name": "non-DCWG primary MIBI" - }, - "value": { - "active_status": "active", - "assaytype": "MIBI", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "MIBI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Multiplex Ion Beam Imaging", - "dir_schema": "mibi-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C007801", - "term": "Multiplex Ion Beam Imaging (MIBI) Measurement Assay" - }, - { - "code": "HUBMAP:C007801", - "term": "Multiplex Ion Beam Imaging (MIBI) Measurement Assay" - }, - { - "code": "OBI:0003100", - "term": "multiplexed ion beam imaging assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "mibi-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200280", - "name": "derived mibi_deepcell" - }, - "value": { - "active_status": "active", - "assaytype": "mibi_deepcell", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "MIBI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Multiplex Ion Beam Imaging [DeepCell + SPRM]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "DeepCell + SPRM", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "anndata", - "sprm", - "is_tiled", - "is_image" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200290", - "name": "non-DCWG primary NanoDESI" - }, - "value": { - "active_status": "active", - "assaytype": "NanoDESI", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "NanoDESI", - "dir_schema": "nano-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "HUBMAP:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "OBI:0003101", - "term": "nanospray desorption electrospray ionization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "nano-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200300", - "name": "derived NanoDESI_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "NanoDESI_pyramid", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "NanoDESI [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200310", - "name": "non-DCWG primary NanoPOTS" - }, - "value": { - "active_status": "active", - "assaytype": "NanoPOTS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "NanoPOTS", - "dir_schema": "nano-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C201063", - "term": "nanoSPLITS Measurement Assay" - }, - { - "code": "SENNET:C008101", - "term": "Nanodroplet Processing in One POt for Trace Samples (NanoPOTS) Measurement Assay" - }, - { - "code": "HUBMAP:C201063", - "term": "nanoSPLITS Measurement Assay" - }, - { - "code": "HUBMAP:C008101", - "term": "Nanodroplet Processing in One POt for Trace Samples (NanoPOTS) Measurement Assay" - }, - { - "code": "OBI:0003102", - "term": "nanodroplet processing in one pot for trace samples assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "nano-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200320", - "name": "derived NanoPOTS_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "NanoPOTS_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "NanoPOTS [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200330", - "name": "non-DCWG primary MxIF" - }, - "value": { - "active_status": "active", - "assaytype": "MxIF", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Multiplexed IF Microscopy", - "dir_schema": "mxif-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008201", - "term": "Multiplexed Immunofluorescence Microscopy (MxIF) Measurement Assay" - }, - { - "code": "HUBMAP:C008201", - "term": "Multiplexed Immunofluorescence Microscopy (MxIF) Measurement Assay" - }, - { - "code": "NCI:C181928", - "term": "Multiplexed Immunofluorescence" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "mxif-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200340", - "name": "derived MxIF_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "MxIF_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Multiplexed IF Microscopy [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200350", - "name": "non-DCWG primary PAS" - }, - "value": { - "active_status": "active", - "assaytype": "PAS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Histology", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Brightfield microscopy" - } - }, - "description": "PAS Stained Microscopy", - "dir_schema": "stained-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008301", - "term": "Period Acid Schiff (PAS) Stained Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C008301", - "term": "Period Acid Schiff (PAS) Stained Microscopy Measurement Assay" - }, - { - "code": "OBI:0600020", - "term": "histological assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "stained-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200360", - "name": "derived PAS_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "PAS_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Histology", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Brightfield microscopy" - } - }, - "description": "PAS Stained Microscopy [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200370", - "name": "derived pas_ftu_segmentation" - }, - "value": { - "active_status": "active", - "assaytype": "pas_ftu_segmentation", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Histology", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Brightfield microscopy" - } - }, - "description": "PAS Stained Microscopy [Kaggle-1 Glomerulus Segmentation]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Kaggle-1 Glomerulus Segmentation", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200380", - "name": "derived publication" - }, - "value": { - "active_status": "active", - "assaytype": "publication", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Publication Data", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200390", - "name": "derived publication_ancillary" - }, - "value": { - "active_status": "active", - "assaytype": "publication_ancillary", - "dataset_type": { - "PDR_category": null, - "dataset_type": "UNKNOWN", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Publication Data [ancillary]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "ancillary", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "json" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200400", - "name": "non-DCWG primary bulk-RNA" - }, - "value": { - "active_status": "active", - "assaytype": "bulk-RNA", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "Bulk RNAseq", - "dir_schema": "bulkrnaseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008401", - "term": "Bulk RNAseq Measurement Assay" - }, - { - "code": "HUBMAP:C008401", - "term": "Bulk RNAseq Measurement Assay" - }, - { - "code": "OBI:0003090", - "term": "bulk RNA-seq assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "bulkrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200410", - "name": "derived salmon_rnaseq_bulk" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_rnaseq_bulk", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "Bulk RNAseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200420", - "name": "non-DCWG primary SNARE-ATACseq2" - }, - "value": { - "active_status": "active", - "assaytype": "SNARE-ATACseq2", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq (SNAREseq2)", - "dir_schema": "scatacseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "HUBMAP:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "OBI:0003108", - "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scatacseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200430", - "name": "non-DCWG primary SNARE-RNAseq2" - }, - "value": { - "active_status": "active", - "assaytype": "SNARE-RNAseq2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v3)", - "dir_schema": "scrnaseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "HUBMAP:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "OBI:0003108", - "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200440", - "name": "derived sc_atac_seq_snare_lab" - }, - "value": { - "active_status": "active", - "assaytype": "sc_atac_seq_snare_lab", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq (SNAREseq2) [Lab Processed]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": "external", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200450", - "name": "derived sc_rna_seq_snare_lab" - }, - "value": { - "active_status": "active", - "assaytype": "sc_rna_seq_snare_lab", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (SNAREseq2) [Lab Processed]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": "external", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200460", - "name": "derived salmon_rnaseq_snareseq" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_rnaseq_snareseq", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (SNAREseq2) [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200470", - "name": "derived sc_atac_seq_snare" - }, - "value": { - "active_status": "active", - "assaytype": "sc_atac_seq_snare", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq (SNAREseq2) [SnapATAC]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "SnapATAC", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "atac", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200480", - "name": "non-DCWG primary scRNAseq-10xGenomics-v2" - }, - "value": { - "active_status": "active", - "assaytype": "scRNAseq-10xGenomics-v2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "scRNAseq (10x Genomics v2)", - "dir_schema": "scrnaseq-v0", - "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", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200490", - "name": "non-DCWG primary scRNAseq-10xGenomics-v3" - }, - "value": { - "active_status": "active", - "assaytype": "scRNAseq-10xGenomics-v3", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": null, - "dir_schema": "scrnaseq-v0", - "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", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200500", - "name": "derived salmon_rnaseq_10x" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_rnaseq_10x", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "scRNAseq (10x Genomics) [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200510", - "name": "non-DCWG primary sciATACseq" - }, - "value": { - "active_status": "active", - "assaytype": "sciATACseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "sciATACseq", - "dir_schema": "scatacseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010301", - "term": "Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing (sciATAC-seq) Assay" - }, - { - "code": "HUBMAP:C010301", - "term": "Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing (sciATAC-seq) Assay" - }, - { - "code": "OBI:0003104", - "term": "single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scatacseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200520", - "name": "derived sc_atac_seq_sci" - }, - "value": { - "active_status": "active", - "assaytype": "sc_atac_seq_sci", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "sciATACseq [SnapATAC]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "SnapATAC", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "atac", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200530", - "name": "non-DCWG primary sciRNAseq" - }, - "value": { - "active_status": "active", - "assaytype": "sciRNAseq", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "sciRNAseq", - "dir_schema": "scrnaseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010501", - "term": "Single-cell combinatorial indexing RNA sequencing (sciRNAseq) assay" - }, - { - "code": "HUBMAP:C010501", - "term": "Single-cell combinatorial indexing RNA sequencing (sciRNAseq) assay" - }, - { - "code": "OBI:0003105", - "term": "single-cell combinatorial indexing RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200540", - "name": "derived salmon_rnaseq_sciseq" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_rnaseq_sciseq", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "sciRNAseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200550", - "name": "non-DCWG primary seqFish" - }, - "value": { - "active_status": "active", - "assaytype": "seqFish", - "dataset_type": { - "PDR_category": null, - "dataset_type": "seqFISH", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "seqFISH", - "dir_schema": "seqfish-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010701", - "term": "Sequential fluorescence in-situ hybridization (seqFISH) Measurement Assay" - }, - { - "code": "HUBMAP:C010701", - "term": "Sequential fluorescence in-situ hybridization (seqFISH) Measurement Assay" - }, - { - "code": "OBI:0003106", - "term": "sequential fluorescence in-situ hybridization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "seqfish-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200560", - "name": "derived seqFish_pyramid" - }, - "value": { - "active_status": "active", - "assaytype": "seqFish_pyramid", - "dataset_type": { - "PDR_category": null, - "dataset_type": "seqFISH", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "seqFISH [Image Pyramid]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Image Pyramid", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "is_support", - "pyramid" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200570", - "name": "derived seqFish_lab_processed" - }, - "value": { - "active_status": "active", - "assaytype": "seqFish_lab_processed", - "dataset_type": { - "PDR_category": null, - "dataset_type": "seqFISH", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "seqFISH [Lab Processed]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "derived", - "provider": "external", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200580", - "name": "non-DCWG primary SIMS-IMS" - }, - "value": { - "active_status": "active", - "assaytype": "SIMS-IMS", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "SIMS", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "SIMS-IMS", - "dir_schema": "ims-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C013001", - "term": "SIMS-IMS Measurement Assay" - }, - { - "code": "HUBMAP:C013001", - "term": "SIMS-IMS Measurement Assay" - }, - { - "code": "LCH_NW:sh85119424", - "term": "Secondary ion mass spectrometry" - }, - { - "code": "NCI:C154790", - "term": "Secondary Ion Mass Spectrometry" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "ims-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200590", - "name": "non-DCWG primary snATACseq" - }, - "value": { - "active_status": "active", - "assaytype": "snATACseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq", - "dir_schema": "scatacseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "OBI:0002762", - "term": "single-nucleus ATAC-seq" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scatacseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200600", - "name": "derived sn_atac_seq" - }, - "value": { - "active_status": "active", - "assaytype": "sn_atac_seq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq [SnapATAC]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "SnapATAC", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "atac", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200610", - "name": "non-DCWG primary snRNAseq-10xGenomics-v2" - }, - "value": { - "active_status": "active", - "assaytype": "snRNAseq-10xGenomics-v2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v2)", - "dir_schema": "scrnaseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "HUBMAP:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "OBI:0003109", - "term": "single-nucleus RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200620", - "name": "non-DCWG primary snRNAseq-10xGenomics-v3" - }, - "value": { - "active_status": "active", - "assaytype": "snRNAseq-10xGenomics-v3", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v3)", - "dir_schema": "scrnaseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "HUBMAP:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "OBI:0003109", - "term": "single-nucleus RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "scrnaseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200630", - "name": "derived salmon_sn_rnaseq_10x" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_sn_rnaseq_10x", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200640", - "name": "non-DCWG primary Slide-seq" - }, - "value": { - "active_status": "active", - "assaytype": "Slide-seq", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Slideseq", - "fig2": { - "aggregated_assaytype": null, - "category": "single-cell", - "modality": "Single-cell omics" - } - }, - "description": "Slideseq", - "dir_schema": "slideseq-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C011401", - "term": "Slideseq Measurement Assay" - }, - { - "code": "HUBMAP:C011401", - "term": "Slideseq Measurement Assay" - }, - { - "code": "OBI:0003107", - "term": "slide-seq assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "slideseq-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200650", - "name": "derived salmon_rnaseq_slideseq" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_rnaseq_slideseq", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Slideseq", - "fig2": { - "aggregated_assaytype": null, - "category": "single-cell", - "modality": "Single-cell omics" - } - }, - "description": "Slideseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200660", - "name": "non-DCWG primary Targeted-Shotgun-LC-MS" - }, - "value": { - "active_status": "active", - "assaytype": "Targeted-Shotgun-LC-MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "Targeted Shotgun / Flow-injection LC-MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200670", - "name": "non-DCWG primary TMT-LC-MS" - }, - "value": { - "active_status": "active", - "assaytype": "TMT-LC-MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "TMT LC-MS", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200680", - "name": "non-DCWG primary WGS" - }, - "value": { - "active_status": "active", - "assaytype": "WGS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "WGS", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "Whole Genome Sequencing", - "dir_schema": "wgs-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C011801", - "term": "Whole Genome Sequencing (WGS) Measurement Assay" - }, - { - "code": "HUBMAP:C011801", - "term": "Whole Genome Sequencing (WGS) Measurement Assay" - }, - { - "code": "OBI:0002117", - "term": "whole genome sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "wgs-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200690", - "name": "non-DCWG primary LC-MS" - }, - "value": { - "active_status": "active", - "assaytype": "LC-MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "LC-MS", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200700", - "name": "non-DCWG primary LC-MS_bottom_up" - }, - "value": { - "active_status": "active", - "assaytype": "LC-MS_bottom_up", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "LC-MS Bottom Up", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200710", - "name": "non-DCWG primary MS_bottom_up" - }, - "value": { - "active_status": "active", - "assaytype": "MS_bottom_up", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "MS Bottom Up", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0000470", - "term": "mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200720", - "name": "non-DCWG primary LC-MS_top_down" - }, - "value": { - "active_status": "active", - "assaytype": "LC-MS_top_down", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "LC-MS Top Down", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200730", - "name": "non-DCWG primary MS_top_down" - }, - "value": { - "active_status": "active", - "assaytype": "MS_top_down", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "MS Top Down", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0000470", - "term": "mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200740", - "name": "DCWG visium-no-probes" - }, - "value": { - "active_status": "active", - "assaytype": "visium-no-probes", - "dataset_type": { - "PDR_category": "Spatial Transcriptomics", - "dataset_type": "Visium (no probes)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "Visium (no probes)", - "dir_schema": "visium-no-probes-v2", - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "HUBMAP:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "EFO:0010961", - "term": "Visium Spatial Gene Expression" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [ - "RNAseq", - "Histology" - ], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200750", - "name": "DCWG visium-with-probes" - }, - "value": { - "active_status": "active", - "assaytype": "visium-with-probes", - "dataset_type": { - "PDR_category": "Spatial Transcriptomics", - "dataset_type": "Visium (with probes)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "Visium (with probes)", - "dir_schema": null, - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "HUBMAP:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "EFO:0010961", - "term": "Visium Spatial Gene Expression" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [ - "RNAseq (with probes)", - "Histology" - ], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200760", - "name": "DCWG geomx_ngs?" - }, - "value": { - "active_status": "active", - "assaytype": "geomx_ngs?", - "dataset_type": { - "PDR_category": null, - "dataset_type": "GeoMx (NGS)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "GeoMx (NGS)", - "dir_schema": "geomx-ngs-v2", - "is_multiassay": true, - "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": [ - "RNAseq" - ], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200770", - "name": "DCWG 10x-multiome" - }, - "value": { - "active_status": "active", - "assaytype": "10x-multiome", - "dataset_type": { - "PDR_category": "Multiome Sequencing", - "dataset_type": "10X Multiome", - "fig2": { - "aggregated_assaytype": null, - "category": "single-cell", - "modality": "Single-cell multiomics" - } - }, - "description": "10x Multiome", - "dir_schema": "10x-multiome-v2", - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200772", - "term": "10x Multiome Measurement Assay" - }, - { - "code": "HUBMAP:C200772", - "term": "10x Multiome Measurement Assay" - }, - { - "code": "EFO:0030059", - "term": "10x multiome" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [ - "ATACseq", - "RNAseq" - ], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200780", - "name": "DCWG multiome-snare-seq2" - }, - "value": { - "active_status": "active", - "assaytype": "multiome-snare-seq2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "SNARE-seq2", - "fig2": { - "aggregated_assaytype": "sc/snATAC+RNA-seq (SNARE)", - "category": "single-cell", - "modality": "Single-cell multiomics" - } - }, - "description": "SNAREseq2", - "dir_schema": "snareseq2-v2", - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "HUBMAP:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "OBI:0003108", - "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [ - "ATACseq", - "RNAseq" - ], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200790", - "name": "DCWG sciRNAseq" - }, - "value": { - "active_status": "active", - "assaytype": "sciRNAseq", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "sciRNAseq", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010501", - "term": "Single-cell combinatorial indexing RNA sequencing (sciRNAseq) assay" - }, - { - "code": "HUBMAP:C010501", - "term": "Single-cell combinatorial indexing RNA sequencing (sciRNAseq) assay" - }, - { - "code": "OBI:0003105", - "term": "single-cell combinatorial indexing RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200800", - "name": "DCWG SNARE-RNAseq2" - }, - "value": { - "active_status": "active", - "assaytype": "SNARE-RNAseq2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v3)", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "HUBMAP:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "OBI:0003108", - "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200810", - "name": "DCWG rnaseq-visium-no-probes" - }, - "value": { - "active_status": "active", - "assaytype": "rnaseq-visium-no-probes", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "Capture bead RNAseq (10x Genomics v3)", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "HUBMAP:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "EFO:0010961", - "term": "Visium Spatial Gene Expression" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200820", - "name": "DCWG scRNAseq-visium-with-probes" - }, - "value": { - "active_status": "active", - "assaytype": "scRNAseq-visium-with-probes", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq (with probes)", - "fig2": { - "aggregated_assaytype": "RNAseq", - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "Visium RNAseq with probes", - "dir_schema": "rnaseq-with-probes-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "HUBMAP:C200743", - "term": "Visium Measurement Assay" - }, - { - "code": "EFO:0010961", - "term": "Visium Spatial Gene Expression" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200830", - "name": "DCWG scRNAseq-10xGenomics-v2" - }, - "value": { - "active_status": "active", - "assaytype": "scRNAseq-10xGenomics-v2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "scRNAseq (10x Genomics v2)", - "dir_schema": "rnaseq-v2", - "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", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200840", - "name": "DCWG snRNAseq-10xGenomics-v2" - }, - "value": { - "active_status": "active", - "assaytype": "snRNAseq-10xGenomics-v2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v2)", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "HUBMAP:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "OBI:0003109", - "term": "single-nucleus RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200850", - "name": "DCWG scRNAseq-10xGenomics-v3" - }, - "value": { - "active_status": "active", - "assaytype": "scRNAseq-10xGenomics-v3", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": null, - "dir_schema": "rnaseq-v2", - "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", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200860", - "name": "DCWG snRNAseq-10xGenomics-v3" - }, - "value": { - "active_status": "active", - "assaytype": "snRNAseq-10xGenomics-v3", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq (10x Genomics v3)", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "HUBMAP:C001023", - "term": "Single-nucleus RNA sequencing (snRNA-seq) Assay" - }, - { - "code": "OBI:0003109", - "term": "single-nucleus RNA sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200870", - "name": "DCWG snATACseq" - }, - "value": { - "active_status": "active", - "assaytype": "snATACseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq", - "dir_schema": "atacseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "OBI:0002762", - "term": "single-nucleus ATAC-seq" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200880", - "name": "DCWG SNARE-ATACseq2" - }, - "value": { - "active_status": "active", - "assaytype": "SNARE-ATACseq2", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq (SNAREseq2)", - "dir_schema": "atacseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "OBI:0002762", - "term": "single-nucleus ATAC-seq" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200890", - "name": "DCWG sn_atac_seq?" - }, - "value": { - "active_status": "active", - "assaytype": "sn_atac_seq?", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "snATACseq-multiome", - "dir_schema": "atacseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C010901", - "term": "snATACseq Measurement Assay" - }, - { - "code": "OBI:0002762", - "term": "single-nucleus ATAC-seq" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200900", - "name": "DCWG bulk-RNA" - }, - "value": { - "active_status": "active", - "assaytype": "bulk-RNA", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "Bulk RNAseq", - "dir_schema": "rnaseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008401", - "term": "Bulk RNAseq Measurement Assay" - }, - { - "code": "HUBMAP:C008401", - "term": "Bulk RNAseq Measurement Assay" - }, - { - "code": "OBI:0003090", - "term": "bulk RNA-seq assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200910", - "name": "DCWG ATACseq-bulk" - }, - "value": { - "active_status": "active", - "assaytype": "ATACseq-bulk", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "Bulk ATACseq", - "dir_schema": "atacseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "HUBMAP:C200023", - "term": "ATACseq Measurement Assay" - }, - { - "code": "OBI:0002039", - "term": "assay for transposase-accessible chromatin using sequencing" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200920", - "name": "DCWG sciATACseq" - }, - "value": { - "active_status": "active", - "assaytype": "sciATACseq", - "dataset_type": { - "PDR_category": "ATAC Sequencing", - "dataset_type": "ATACseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Epigenomics" - } - }, - "description": "sciATACseq", - "dir_schema": "atacseq-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C010301", - "term": "Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing (sciATAC-seq) Assay" - }, - { - "code": "HUBMAP:C010301", - "term": "Single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing (sciATAC-seq) Assay" - }, - { - "code": "OBI:0003104", - "term": "single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200930", - "name": "DCWG PAS" - }, - "value": { - "active_status": "active", - "assaytype": "PAS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Histology", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Brightfield microscopy" - } - }, - "description": "PAS Stained Microscopy", - "dir_schema": "histology-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008301", - "term": "Period Acid Schiff (PAS) Stained Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C008301", - "term": "Period Acid Schiff (PAS) Stained Microscopy Measurement Assay" - }, - { - "code": "OBI:0600020", - "term": "histological assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200940", - "name": "DCWG h-and-e" - }, - "value": { - "active_status": "active", - "assaytype": "h-and-e", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Histology", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Brightfield microscopy" - } - }, - "description": "H&E Stained Microscopy", - "dir_schema": "histology-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200943", - "term": "Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C200943", - "term": "Microscopy Measurement Assay" - }, - { - "code": "OBI:0002119", - "term": "microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200950", - "name": "DCWG CODEX" - }, - "value": { - "active_status": "active", - "assaytype": "CODEX", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CODEX", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CODEX", - "dir_schema": "codex-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "HUBMAP:C006501", - "term": "CO-detection by inDEXing (CODEX) Measurement Assay" - }, - { - "code": "OBI:0003093", - "term": "co-detection by indexing assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200960", - "name": "DCWG phenocycler" - }, - "value": { - "active_status": "active", - "assaytype": "phenocycler", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "PhenoCycler", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "PhenoCycler", - "dir_schema": "phenocycler-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200962", - "term": "PhenoCycler Measurement Assay" - }, - { - "code": "HUBMAP:C200962", - "term": "PhenoCycler Measurement Assay" - }, - { - "code": "EFO:0700002", - "term": "PhenoCycler" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200970", - "name": "DCWG cycif" - }, - "value": { - "active_status": "active", - "assaytype": "cycif", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "CyCIF", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "CyCIF", - "dir_schema": "cycif-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200972", - "term": "CyCIF Measurement Assay" - }, - { - "code": "HUBMAP:C200972", - "term": "CyCIF Measurement Assay" - }, - { - "code": "NCI:C181929", - "term": "Tissue-Based Cyclic Immunofluorescence" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200980", - "name": "DCWG merfish" - }, - "value": { - "active_status": "active", - "assaytype": "merfish", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "MERFISH", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "MERFISH", - "dir_schema": "merfish-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200982", - "term": "MERFISH Measurement Assay" - }, - { - "code": "HUBMAP:C200982", - "term": "MERFISH Measurement Assay" - }, - { - "code": "EFO:0008992", - "term": "MERFISH" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C200990", - "name": "DCWG cell-dive" - }, - "value": { - "active_status": "active", - "assaytype": "cell-dive", - "dataset_type": { - "PDR_category": "cell", - "dataset_type": "Cell DIVE", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Cell DIVE", - "dir_schema": "celldive-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "HUBMAP:C006301", - "term": "Cell DIVE Measurement Assay" - }, - { - "code": "OBI:0003092", - "term": "Cell DIVE multiplexed imaging assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201000", - "name": "DCWG MALDI-IMS" - }, - "value": { - "active_status": "active", - "assaytype": "MALDI-IMS", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "MALDI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "MALDI IMS", - "dir_schema": "maldi-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C007701", - "term": "Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) Measurement Assay" - }, - { - "code": "HUBMAP:C007701", - "term": "Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) Measurement Assay" - }, - { - "code": "OBI:0003099", - "term": "matrix assisted laser desorption ionization imaging mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201010", - "name": "DCWG SIMS-IMS" - }, - "value": { - "active_status": "active", - "assaytype": "SIMS-IMS", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "SIMS", - "fig2": { - "aggregated_assaytype": null, - "category": null, - "modality": null - } - }, - "description": "SIMS-IMS", - "dir_schema": "sims-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C013001", - "term": "SIMS-IMS Measurement Assay" - }, - { - "code": "HUBMAP:C013001", - "term": "SIMS-IMS Measurement Assay" - }, - { - "code": "LCH_NW:sh85119424", - "term": "Secondary ion mass spectrometry" - }, - { - "code": "NCI:C154790", - "term": "Secondary Ion Mass Spectrometry" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201020", - "name": "DCWG DESI-IMS" - }, - "value": { - "active_status": "active", - "assaytype": "DESI-IMS", - "dataset_type": { - "PDR_category": "IMS", - "dataset_type": "DESI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "DESI", - "dir_schema": "desi-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "HUBMAP:C008001", - "term": "Nanospray Desorption ElectroSpray Ionization (NanoDESI) Measurement Assay" - }, - { - "code": "OBI:0003101", - "term": "nanospray desorption electrospray ionization assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201030", - "name": "DCWG MIBI" - }, - "value": { - "active_status": "active", - "assaytype": "MIBI", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "MIBI", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Multiplex Ion Beam Imaging", - "dir_schema": "mibi-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C007801", - "term": "Multiplex Ion Beam Imaging (MIBI) Measurement Assay" - }, - { - "code": "HUBMAP:C007801", - "term": "Multiplex Ion Beam Imaging (MIBI) Measurement Assay" - }, - { - "code": "OBI:0003100", - "term": "multiplexed ion beam imaging assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201040", - "name": "DCWG IMC2D" - }, - "value": { - "active_status": "active", - "assaytype": "IMC2D", - "dataset_type": { - "PDR_category": "MxNF", - "dataset_type": "2D Imaging Mass Cytometry", - "fig2": { - "aggregated_assaytype": "LC-MS", - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "2D Imaging Mass Cytometry", - "dir_schema": "imc-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "HUBMAP:C006901", - "term": "Imaging Mass Cytometry Measurement Assay" - }, - { - "code": "OBI:0003096", - "term": "imaging mass cytometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201050", - "name": "DCWG LC-MS" - }, - "value": { - "active_status": "active", - "assaytype": "LC-MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "LC-MS", - "dir_schema": "lcms-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C200205", - "term": "Liquid Chromatography Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0003097", - "term": "liquid chromatography mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201060", - "name": "DCWG nano-splits" - }, - "value": { - "active_status": "active", - "assaytype": "nano-splits", - "dataset_type": { - "PDR_category": "LC-MS", - "dataset_type": "nanoSPLITS", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "MS-based imaging" - } - }, - "description": "nanoSPLITS", - "dir_schema": "nano-splits-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "HUBMAP:C201063", - "term": "nanoSPLITS Measurement Assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201070", - "name": "DCWG AF" - }, - "value": { - "active_status": "active", - "assaytype": "AF", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Auto-fluorescence", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Auto-fluorescence Microscopy", - "dir_schema": "af-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "HUBMAP:C006002", - "term": "Auto-fluorescence Microscopy Measurement Assay" - }, - { - "code": "OBI:0003088", - "term": "autofluorescence microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201080", - "name": "DCWG Lightsheet" - }, - "value": { - "active_status": "active", - "assaytype": "Lightsheet", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Light Sheet", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Light Sheet Microscopy", - "dir_schema": "lightsheet-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200243", - "term": "Lightsheet fluorescence microscopy measurement assay" - }, - { - "code": "HUBMAP:C200243", - "term": "Lightsheet fluorescence microscopy measurement assay" - }, - { - "code": "OBI:0003098", - "term": "lightsheet fluorescence microscopy assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201090", - "name": "DCWG confocal" - }, - "value": { - "active_status": "active", - "assaytype": "confocal", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Confocal", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Confocal Microscopy", - "dir_schema": "confocal-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001007", - "term": "Confocal Microscopy Assay" - }, - { - "code": "HUBMAP:C001007", - "term": "Confocal Microscopy Assay" - }, - { - "code": "PDQ:CDR0000538218", - "term": "confocal microscopy" - }, - { - "code": "NCI:C17753", - "term": "Confocal Microscopy" - }, - { - "code": "LCH_NW:sh90001543", - "term": "Confocal microscopy" - }, - { - "code": "CHV:0000025004", - "term": "confocal microscopy" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201100", - "name": "DCWG thick-section-multiphoton-mxif" - }, - "value": { - "active_status": "active", - "assaytype": "thick-section-multiphoton-mxif", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Thick section Multiphoton MxIF", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Antibody-based imaging" - } - }, - "description": "Thick section Multiphoton MxIF", - "dir_schema": "thick-section-multiphoton-mxif-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C008201", - "term": "Multiplexed Immunofluorescence Microscopy (MxIF) Measurement Assay" - }, - { - "code": "HUBMAP:C008201", - "term": "Multiplexed Immunofluorescence Microscopy (MxIF) Measurement Assay" - }, - { - "code": "NCI:C181928", - "term": "Multiplexed Immunofluorescence" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201110", - "name": "DCWG second-harmonic-generation" - }, - "value": { - "active_status": "active", - "assaytype": "second-harmonic-generation", - "dataset_type": { - "PDR_category": "Single-cycle Flourescence Microscopy", - "dataset_type": "Second Harmonic Generation (SHG)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Second Harmonic Generation (SHG)", - "dir_schema": "second-harmonic-generation-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "HUBMAP:C201113", - "term": "Second Harmonic Generation Microscopy Measurement Assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201120", - "name": "DCWG enhanced-srs" - }, - "value": { - "active_status": "active", - "assaytype": "enhanced-srs", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Enhanced Stimulated Raman Spectroscopy (SRS)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Label free imaging" - } - }, - "description": "Enhanced Stimulated Raman Spectroscopy (SRS)", - "dir_schema": "enhanced-srs-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C201123", - "term": "Enhanced Stimulated Raman Spectroscopy Measurement Assay" - }, - { - "code": "HUBMAP:C201123", - "term": "Enhanced Stimulated Raman Spectroscopy Measurement Assay" - }, - { - "code": "CHV:0000011571", - "term": "raman spectroscopy" - }, - { - "code": "LCH_NW:sh85111278", - "term": "Raman spectroscopy" - }, - { - "code": "NCI:C17157", - "term": "Raman Spectroscopy" - }, - { - "code": "CSP:0633-0213", - "term": "Raman spectrometry" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201130", - "name": "DCWG molecular-cartography" - }, - "value": { - "active_status": "active", - "assaytype": "molecular-cartography", - "dataset_type": { - "PDR_category": null, - "dataset_type": "Molecular Cartography", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "Molecular Cartography", - "dir_schema": "mc-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "HUBMAP:C201133", - "term": "Molecular Cartography Measurement Assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": null, - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201140", - "name": "derived visium-no-probes" - }, - "value": { - "active_status": "active", - "assaytype": "visium-no-probes", - "dataset_type": { - "PDR_category": "Spatial Transcriptomics", - "dataset_type": "Visium (no probes)", - "fig2": { - "aggregated_assaytype": null, - "category": "imaging", - "modality": "Spatial Transcriptomics" - } - }, - "description": "Visium (no probes) [Salmon + Scanpy]", - "dir_schema": null, - "is_multiassay": true, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon + Scanpy", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "spatial", - "anndata", - "is_image", - "rna" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201150", - "name": "derived multiome snare-seq2" - }, - "value": { - "active_status": "active", - "assaytype": "multiome-snare-seq2", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "SNAREseq2 [Salmon + ArchR + Muon]", - "dir_schema": null, - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "HUBMAP:C001024", - "term": "Single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq) assay" - }, - { - "code": "OBI:0003108", - "term": "single-nucleus chromatin accessibility and mRNA expression sequencing assay" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": "Salmon + ArchR + Muon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "atac", - "spatial", - "anndata", - "is_image", - "rna" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201160", - "name": "derived multiome 10x" - }, - "value": { - "active_status": "active", - "assaytype": "10x-multiome", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "10x Multiome [Salmon + ArchR + Muon]", - "dir_schema": null, - "is_multiassay": true, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C200772", - "term": "10x Multiome Measurement Assay" - }, - { - "code": "HUBMAP:C200772", - "term": "10x Multiome Measurement Assay" - }, - { - "code": "EFO:0030059", - "term": "10x multiome" - } - ], - "contains_full_genetic_sequences": true - }, - "must_contain": [], - "pipeline_shorthand": "Salmon + ArchR + Muon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "anndata", - "atac", - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201170", - "name": "DCWG music" - }, - "value": { - "active_status": "active", - "assaytype": "music", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "MUSIC", - "dir_schema": "music-v2", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "HUBMAP:C201172", - "term": "MUSIC Measurement Assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C201190", - "name": "non-DCWG primary MS" - }, - "value": { - "active_status": "active", - "assaytype": "MS", - "dataset_type": { - "PDR_category": null, - "dataset_type": "LC-MS", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Proteomics" - } - }, - "description": "MS", - "dir_schema": "lcms-v0", - "is_multiassay": false, - "measurement_assay": { - "codes": [ - { - "code": "SENNET:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "HUBMAP:C001001", - "term": "Mass Spectrometry Measurement Assay" - }, - { - "code": "OBI:0000470", - "term": "mass spectrometry assay" - } - ], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": null, - "process_state": "primary", - "provider": "IEC", - "tbl_schema": "lcms-v", - "vitessce_hints": [] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C202000", - "name": "derived salmon_sn_rnaseq_10x json-based" - }, - "value": { - "active_status": "active", - "assaytype": "salmon_sn_rnaseq_10x", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "snRNAseq [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "json-based", - "rna", - "is_sc" - ] - } - }, - { - "rule_description": { - "application_context": "HUBMAP", - "code": "C202010", - "name": "derived salmon_rnaseq_10x json-based" - }, - "value": { - "active_status": "active", - "asssaytype": "salmon_rnaseq_10x", - "dataset_type": { - "PDR_category": "RNA Sequencing", - "dataset_type": "RNAseq", - "fig2": { - "aggregated_assaytype": null, - "category": "bulk", - "modality": "Transcriptomics" - } - }, - "description": "scRNAseq (10x Genomics) [Salmon]", - "dir_schema": null, - "is_multiassay": false, - "measurement_assay": { - "codes": [], - "contains_full_genetic_sequences": false - }, - "must_contain": [], - "pipeline_shorthand": "Salmon", - "process_state": "derived", - "provider": "IEC", - "tbl_schema": null, - "vitessce_hints": [ - "rna", - "is_sc", - "json_based" - ] - } - } -] diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml deleted file mode 100644 index 906423f..0000000 --- a/dev/docker-compose.yml +++ /dev/null @@ -1,13 +0,0 @@ -services: - - assayclasses-dev-server: - build: - context: . - container_name: assayclasses-dev-server - ports: - - "8181:8181" - init: true - restart: always - volumes: - - "./instance:/usr/src/app/instance" - \ No newline at end of file diff --git a/dev/instance/app.cfg.example b/dev/instance/app.cfg.example deleted file mode 100644 index 2a9da04..0000000 --- a/dev/instance/app.cfg.example +++ /dev/null @@ -1,3 +0,0 @@ -# URL to the json file containing the assay class information -ASSAYCLASSES_JSON_URL = 'https://raw.githubusercontent.com/x-atlas-consortia/hs-ontology-api/dev-integrate/dev/assayclasses.json' - diff --git a/dev/requirements.txt b/dev/requirements.txt deleted file mode 100644 index 95fef4e..0000000 --- a/dev/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -Flask==3.0.3 diff --git a/dev/test_api.sh b/dev/test_api.sh deleted file mode 100755 index 7d3b9e8..0000000 --- a/dev/test_api.sh +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/bash -set -e -set -u - -ASSAYCLASS_URL_LOCAL=http://localhost:8181 -ASSAYCLASS_URL=$ASSAYCLASS_URL_LOCAL - - -curl --request GET \ - --url "${ASSAYCLASS_URL}" -echo -echo - - -echo "Only the last one in the group should succeed..." -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses?application_context=Wrong" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses?application_context=HUBMAp" \ - --header "Accept: application/json" -echo -echo - - -echo "Only the last one in the group should succeed..." -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/C200010" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/xyzzy?application_context=NoMap" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/xyzzy?application_context=huBMAP" \ - --header "Accept: application/json" -echo - -curl --request GET \ - --url "${ASSAYCLASS_URL}/assayclasses/C200010?application_context=HUbmAP" \ - --header "Accept: application/json" -echo