Initial commit

api/python/src/cellxgene_ontology_guide/__init__.py

@@ -1,3 +1,3 @@
-import _version
+import cellxgene_ontology_guide._version as _version
 
 __version__ = _version.__version__

api/python/src/cellxgene_ontology_guide/supported_versions.py

@@ -4,9 +4,9 @@
 import os
 from typing import Any, Dict, List, Optional
 
-from constants import DATA_ROOT, ONTOLOGY_FILENAME_SUFFIX, ONTOLOGY_INFO_FILENAME
 from semantic_version import Version
 
+from cellxgene_ontology_guide.constants import DATA_ROOT, ONTOLOGY_FILENAME_SUFFIX, ONTOLOGY_INFO_FILENAME
 from cellxgene_ontology_guide.entities import Ontology
 
 

tools/ontology-builder/src/compute_descendent_mappings.py

@@ -0,0 +1,279 @@
+#!/usr/bin/env python
+"""
+# Descendant Mappings for Tissues and Cell Types
+
+## Overview
+
+The ontology-aware tissue and cell type filters in the Single Cell Data Portal each require artifacts generated
+by this script.
+
+#### Descendant Mappings
+To facilitate in-filter, cross-panel restriction of filter values, a descendant hierarchy dictionary is required by
+the Single Cell Data Portal frontend. For example, if a user selects `hematopoietic system` in the tissue filter's
+`System` panel, the values in the tissue filter's `Organ` and `Tissue` panels must be restricted by `hematopoietic
+system`.
+
+This script generates a dictionary of descendants keyed by tissue or cell type ontology term ID. The dictionary
+is stored as a JSON file and copied to cellxgene-ontology-guide/ontology_assets directory. A versioned github release is
+ created to simplify referencing in the Single Cell Data Portal.
+
+The descendant mappings should be updated when:
+
+1. The ontology version is updated,
+2. A new tissue or cell type is added to the production corpus, or,
+3. The hand-curated systems, organs, cell classes or cell subclasses are updated.
+"""
+
+import json
+import os
+from typing import Any, Dict, List
+from urllib.request import urlopen
+
+import env
+from cellxgene_ontology_guide.ontology_parser import OntologyParser
+
+
+def load_prod_datasets() -> Any:
+    """
+    Request datasets the production corpus.
+    """
+    response = urlopen("https://api.cellxgene.cziscience.com/dp/v1/datasets/index").read().decode("utf-8")
+    return json.loads(response)
+
+
+def extract_cell_types(datasets: List[Dict[str, Any]]) -> List[str]:
+    """
+    List the set of cell type values for the given datasets.
+
+    :param datasets: a list of datasets from the production corpus.
+    :return: a list formated of cell type values
+    """
+    cell_types = set()
+    for dataset in datasets:
+        for cell_type in dataset["cell_type"]:
+            cell_types.add(cell_type["ontology_term_id"].replace("_", ":", False))
+    return list(cell_types)
+
+
+def extract_tissues(datasets: List[Dict[str, Any]]) -> List[str]:
+    """
+    List the set of tissue values for the given datasets.
+
+    :param datasets: a list of datasets from the production corpus.
+    :return: a list of formated tissue values with tags for tissue type.
+    """
+    tissues = set()
+    for dataset in datasets:
+        for tissue in dataset["tissue"]:
+            formatted_entity_name = tissue["ontology_term_id"].replace("_", ":", False)
+            tissue_type = tissue.get("tissue_type")
+            tissues.add(tag_tissue_type(formatted_entity_name, tissue_type))
+
+    return list(tissues)
+
+
+def tag_tissue_type(entity_name: str, tissue_type: str) -> str:
+    """
+    Append the tissue type to the given entity name if the tissue type is cell
+    culture or organoid, otherwise return the entity name as is.
+
+    :param entity_name: str entity name
+    :param tissue_type: str tissue type
+    :return: str entity name with tissue type appended
+    """
+    # Tissue types
+    tissue_type_cell_culture = "cell culture"
+    tissue_type_organoid = "organoid"
+
+    # Handle error case (possible if tissue has not been migrated to 4.0.0+ schema).
+    if tissue_type is None:
+        return entity_name
+
+    if tissue_type == tissue_type_cell_culture:
+        # true if the given tissue type is "cell culture".
+        return f"{entity_name} ({tissue_type_cell_culture})"
+
+    if tissue_type == tissue_type_organoid:
+        # true if the given tissue type is "organoid".
+        return f"{entity_name} ({tissue_type_organoid})"
+
+    return entity_name
+
+
+def key_organoids_by_ontology_term_id(entity_names: List[str]) -> Dict[str, str]:
+    """
+    Returns a dictionary of organoid ontology term IDs by stem ontology term ID.
+
+    :param entity_names: List of entity names
+    :return: Dict of organoid ontology term IDs by ontology term ID
+    """
+
+    organoids_by_ontology_term_id = {}
+    for entity_name in entity_names:
+        if "(organoid)" in entity_name:
+            """
+            Historically (i.e. before schema 4.0.0 and the introduction of
+            `tissue_type`), tissues of type "organoid" were tagged with "(organoid)"
+            in their labels and ontology IDs. The post-4.0.0 `tissue_type` value is
+            mapped to this tagged version in order to minimize downstream updates to
+            the filter functionality.
+            """
+            ontology_term_id = entity_name.replace(" (organoid)", "")
+            organoids_by_ontology_term_id[ontology_term_id] = entity_name
+
+    return organoids_by_ontology_term_id
+
+
+def build_descendants_by_entity(
+    entity_hierarchy: List[List[str]], ontology_parser: OntologyParser
+) -> Dict[str, List[str]]:
+    """
+    Create descendant relationships between the given entity hierarchy.
+
+    :param entity_hierarchy: List of lists of entity names
+    :param ontology_parser: OntologyParser instance
+    :return: Dict of descendants by term_id
+    """
+    all_descendants = {}
+    for idx, entity_set in enumerate(entity_hierarchy):
+        # Create the set of descendants that can be included for this entity set.
+        # For example, systems can include organs or tissues,
+        # organs can only include tissues, tissues can't have descendants.
+        accept_lists = entity_hierarchy[idx + 1 :]
+
+        # Tissue or cell type for example will not have any descendants.
+        if not accept_lists:
+            continue
+
+        accept_list = [i for sublist in accept_lists for i in sublist]
+        organoids_by_ontology_term_id = key_organoids_by_ontology_term_id(accept_list)
+
+        # List descendants of entity in this set.
+        for entity_name in entity_set:
+            descendants = set(ontology_parser.get_terms_descendants(entity_name)[entity_name])
+            # TODO: change get_terms_descendants return an iterator or add a single term version.
+
+            # Determine the set of descendants that be included.
+            descendant_accept_list = []
+            for descendant in descendants:
+                # Include all entities in the accept list.
+                if descendant in accept_list:
+                    descendant_accept_list.append(descendant)
+
+                # Add organoid descendants, if any.
+                if descendant in organoids_by_ontology_term_id:
+                    descendant_accept_list.append(organoids_by_ontology_term_id[descendant])
+
+            # Add organoid entity, if any.
+            if entity_name in organoids_by_ontology_term_id:
+                descendant_accept_list.append(organoids_by_ontology_term_id[entity_name])
+
+            if not descendant_accept_list:
+                continue
+
+            # Add descendants to dictionary.
+            all_descendants[entity_name] = descendant_accept_list
+    return all_descendants
+
+
+def generate_cell_descendant_mapping(ontology_parser: OntologyParser, datasets: List[Dict[str, Any]]) -> None:
+    """
+    Extracts a descendant mapping of CL starting with a set of hand-curated cell classes and subclasses. Cell types
+    from the production corpus are also included in the mapping. The resulting mapping is saved to a JSON file.
+
+    :param ontology_parser: OntologyParser instance
+    :param datasets: a list of datasets from the production corpus.
+
+    """
+    # Load curated list of cell classes and cell subclasses.
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, "cell_class_list.json"), "r") as f:
+        cell_classes = json.load(f)
+
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, "cell_subclass_list.json"), "r") as f:
+        cell_subclasses = json.load(f)
+
+    # extract the cell types from the datasets in the production corpus
+    prod_cell_types = extract_cell_types(datasets)
+    # establish the hierarchy of terms
+    heirarchy = [cell_classes, cell_subclasses, prod_cell_types]
+    # build the descendants mapping
+    descendent_mapping = build_descendants_by_entity(heirarchy, ontology_parser)
+    # save the mapping to a file
+    file_name = os.path.join(env.ONTOLOGY_ASSETS_DIR, "tissue_descendants.json")
+    save_json(descendent_mapping, file_name)
+
+
+def generate_tissue_descendant_mapping(ontology_parser: OntologyParser, datasets: List[Dict[str, Any]]) -> None:
+    """
+    Extracts a descendant mapping of UBERON starting with a set of hand-curated system and organ tissue. Tissues types
+    from the production corpus are also included in the mapping. The resulting mapping is saved to a JSON file.
+
+    :param ontology_parser: OntologyParser instance
+    :param datasets: a list of datasets from the production corpus.
+    :return:
+    """
+    # Load curated list of systems and organ tissues.
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, "system_list.json"), "r") as f:
+        system_tissues = json.load(f)
+
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, "organ_list.json"), "r") as f:
+        organ_tissues = json.load(f)
+
+    # extract the tissue types from the datasets in the production corpus
+    prod_tissues = extract_tissues(datasets)
+    # establish the hierarchy of terms
+    heirarchy = [system_tissues, organ_tissues, prod_tissues]
+    # build the descendants mapping
+    descendent_mapping = build_descendants_by_entity(heirarchy, ontology_parser)
+    # save the mapping to a file
+    file_name = os.path.join(env.ONTOLOGY_ASSETS_DIR, "tissue_descendants.json")
+    save_json(descendent_mapping, file_name)
+
+
+def compare_descendant_mappings(file_1: str, file_2: str) -> None:
+    # Testing
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, file_1), "r") as f:
+        mapping_1 = json.load(f)
+
+    with open(os.path.join(env.ONTOLOGY_ASSETS_DIR, file_2), "r") as f:
+        mapping_2 = json.load(f)
+
+    print(f"In {file_1} not in {file_2}")
+    print(mapping_1.keys() - mapping_2.keys())
+
+    print(f"In {file_2} not in {file_1}")
+    print(mapping_2.keys() - mapping_1.keys())
+
+    matching_keys = mapping_1.keys() & mapping_2.keys()
+    print(f"Not in {file_2}")
+    for key in matching_keys:
+        decendents_1 = set(mapping_1[key])
+        decendents_2 = set(mapping_2[key])
+        if decendents_1 != decendents_2:
+            print(key, decendents_2 - decendents_1)
+
+    print(f"Not in {file_1}")
+    for key in matching_keys:
+        decendents_1 = set(mapping_1[key])
+        decendents_2 = set(mapping_2[key])
+        if decendents_1 != decendents_2:
+            print(key, decendents_1 - decendents_2)
+
+
+def save_json(data: Any, file_name: str) -> None:
+    """
+    Save the given data to a JSON file.
+    :param data: Any data compatiblewith JSON
+    :param file_name: The name of the file to save the data to.
+    """
+    with open(file_name, "w") as f:
+        json.dump(data, f, indent=2)
+
+
+if __name__ == "__main__":
+    ONTOLOGY_PARSER = OntologyParser("v5.0.0")  # TODO: this should default to the latest supported schema version
+    PROD_DATASETS = load_prod_datasets()
+    generate_cell_descendant_mapping(ONTOLOGY_PARSER, PROD_DATASETS)
+    compare_descendant_mappings("cell_type_descendants.json", "cell_type_descendants_cxg.json")
+    generate_tissue_descendant_mapping(ONTOLOGY_PARSER, PROD_DATASETS)
+    compare_descendant_mappings("tissue_descendants.json", "tissue_descendants_cxg.json")