diff --git a/README.md b/README.md index 3022b49..9972f49 100644 --- a/README.md +++ b/README.md @@ -21,4 +21,4 @@ QUERY BUILDERS - QueryBuilder - Class to support creation of cypher queries to work with data in Neo4j Dependencies: -- https://mygithub.gsk.com/gsk-tech/neointerface +- https://github.com/GSK-Biostatistics/neointerface diff --git a/data_loaders/azure_data_loader.py b/data_loaders/azure_data_loader.py index 5c6973d..70a0384 100644 --- a/data_loaders/azure_data_loader.py +++ b/data_loaders/azure_data_loader.py @@ -46,7 +46,7 @@ def listdir(self, path: str) -> [str]: Lists all files (full path) in a directory on Azure blob storage :param path: A list of strings - # EXAMPLE of list item: "rd/space/test_compound/117106/testing_01/sdtm/gsk_117106_vs.sas7bdat" + # EXAMPLE of list item: "rd/space/test_compound/trial_01/testing_01/sdtm/vs.sas7bdat" """ return [path.name for path in self.fs.get_paths(path=path)] diff --git a/data_loaders/sql_server_data_loader.py b/data_loaders/sql_server_data_loader.py index fd12c77..7d21e00 100644 --- a/data_loaders/sql_server_data_loader.py +++ b/data_loaders/sql_server_data_loader.py @@ -15,13 +15,8 @@ def __init__(self, self._con = f"jdbc:sqlserver://{sqldburl};databaseName={self.sqldbname};user={self.sqluser};password={self._sqlpassword};" super().__init__(*args, **kwargs) if self.autoconnect: - self.remove_apoc_custom("load_tables_from_sql") - self.setup_apoc_custom_load_tables_from_sql() self.query("call db.clearQueryCaches()") - self.create_index("Source Data Row", "_study_") - self.create_index("Source Data Row", "_domain_") - def sql_query(self, sqlq:str): q = "CALL apoc.load.jdbc($con, $sqlq) YIELD row RETURN row" params = { diff --git a/data_providers/archive/data_provider.py b/data_providers/archive/data_provider.py deleted file mode 100644 index cc71a13..0000000 --- a/data_providers/archive/data_provider.py +++ /dev/null @@ -1,396 +0,0 @@ -import re -import pandas as pd -from neointerface import NeoInterface -from query_builders.query_builder import QueryBuilder - - -class DataProvider(NeoInterface): - """ - To use the data already in the database (such as the data after the transformations with ModelApplier), - for various purposes - such as to feed the User Interface. - - Also for future data transformation, data enrichment, etc. - """ - - def __init__(self, mode='schema_PROPERTY', allow_optional_classes=True, *args, **kwargs): - """ - :param mode: if 'schema_PROPERTY': determines matching based on Class-Property schema \ - if 'schema_CLASS' - determines matching based on Class schema - (where columns are mapped to Classes and no Property nodes defined) - if 'noschema': determines matching based on all relationships in the database - if 'noschema': NOTE: all the interrelationships should consistently exits for all classes - :param allow_optional_classes If True then classes in the list with postfix ** will be considered optional - (OPTIONAL MATCH will be used to fetch data for those classes - see example test_get_data_noschema_optional_class ) - :param args: - :param kwargs: - """ - assert mode in ['schema_PROPERTY', 'schema_CLASS', 'noschema'] - self._mode = mode - self.qb = QueryBuilder(mode=self._mode, allow_optional_classes=allow_optional_classes, *args, **kwargs) - super().__init__(*args, **kwargs) - if self.verbose: - print(f"---------------- {self.__class__} initialized -------------------") - - @property - def mode(self): - return self._mode - - def set_mode(self, mode:str): - assert mode in ['schema_PROPERTY', 'schema_CLASS', 'noschema'] - self._mode = mode - self.qb.mode = mode - - ############################################################# - # DATA RETRIEVAL # - ############################################################# - - def get_data(self, classes: list, where_map=None, limit=20, return_q_and_dict=False): - """ - Assembles into a Pandas dataframe the Property values from the data nodes with the specified Classes. - Simplified version of get_data_generic() - - :param classes: List of strings with Class names. EXAMPLE: ['Study', 'Site', 'Subject'] - :param where_map: Used to restrict the data (by default, no restriction.) - A dictionary whose keys are Classes to apply restrictions to, - and whose values are dictionaries specifying conditions on Property values. - An implicit AND is understood among all the clauses. - EXAMPLE: - { - 'SUBJECT': { - 'USUBJID': '01-001', - 'SUBJID': '001', - 'PATIENT GROUP': [3, 5] - }, - 'SEX': { - 'ASEX': 'Male' - } - } - Notes: - - The keys in the outer dictionary are expected to be node labels. - - The (key/values) in the inner dictionary entries - are meant to be (attribute names : desired values) - that are applicable to the node with their corresponding label. - - The values may be various data type, incl. strings, integers and lists. - - :param limit: Either None or an integer. If specified, it restricts the maximum number of rows - in the returned dataframe. Defaults to 20 - - :return: pd.DataFrame A Pandas dataframe containing all the (direct and indirect) Property values - of the data points from the requested Classes, plus their Neo4j IDs. - The Property names are prefixed with the Class names - """ - return self.get_data_generic( - classes=classes, - where_map=where_map, - allow_unrelated_subgraphs=False, - return_nodeid=True, - return_properties="*", - prefix_keys_with_label=True, - order=None, - limit=limit, - return_q_and_dict=return_q_and_dict - ) - - def get_data_generic(self, - classes: list, - where_map=None, - allow_unrelated_subgraphs: bool = False, - return_nodeid: bool = True, - return_properties: str = "*", - prefix_keys_with_label: bool = True, - order=None, - limit=20, - return_q_and_dict=False): - """ - Assembles into a Pandas dataframe the Property values from the data nodes with the specified Classes. - Use this instead of get_data() when you need a full set of options. - - Used when we have a schema with Classes and Properties (in self.mode == 'schema_PROPERTY') - or on graph data as is (if self.mode == 'noschema') - - TODO: it cannot handle different classes with the same property name - it may produce wrong results; - use prefix_keys_with_label = True in this case - - :param classes: List of strings. EXAMPLE: ['Study', 'Site', 'Subject'] - :param where_map: Used to restrict the data (default, no restriction.) - A dictionary of dictionaries. SEE explanation in get_data() - :param return_nodeid: Boolean - :param return_properties: Either a list of Property names to include in the dataframe, or the string "*" (meaning, "all") - EXAMPLE: ["STUDYID", "SITEID"] - :param prefix_keys_with_label: If True adds a prefix (corresponding node label) to each column name of the returned dataframe - :param order: Either None (default) or a list or a string - :param limit: Either None or an integer. Defaults to 20 - :return: pd.DataFrame(): nodes in path, merged with apoc.map.mergeList and converted to pd.DataFrame() - """ - if self.verbose: - print("-- Getting data --") - if self.debug: - print("classes: ", classes) - print("where_map: ", where_map) - assert order is None or type(order) == list or type(order) == str - assert limit is None or type(limit) == int - - (q, data_dict) = self._get_data_generic_helper(classes=classes, where_map=where_map, - allow_unrelated_subgraphs=allow_unrelated_subgraphs, - return_nodeid=return_nodeid, - return_properties=return_properties, - prefix_keys_with_label=prefix_keys_with_label, - order=order, limit=limit) - - if self.debug: - print("q : ", q, "\n | data_dict : ", data_dict) - - df = self.convert_qb_result_to_df( - self.query(q, data_dict) - ) - if self._mode in ['schema_PROPERTY', 'schema_CLASS']: - # Re-ordering columns (in the order of classes provided in the query) - expected_cols = [] - for class_ in classes: - class_pure = class_ - if self.qb.allow_optional_classes and class_.endswith(self.qb.OCLASS_MARKER): - class_pure = class_[:(len(class_) - len(self.qb.OCLASS_MARKER))] - for cols in self.qb.mm.get_class_properties(class_pure).values(): - for col in cols: - col_name = (class_pure + "." if prefix_keys_with_label else "") + col - if not col_name in expected_cols: - expected_cols.append(col_name) - if return_nodeid: - expected_cols.append(class_pure) - if self._mode == "schema_CLASS": - all_classes = [(class_[:-len(self.qb.OCLASS_MARKER)] if class_.endswith(self.qb.OCLASS_MARKER) else class_) - for class_ in classes] - short_labels = self.qb.mm.get_class_short_labels(classes=all_classes) - if prefix_keys_with_label: - expected_cols += [f"{label}.{short_label}" for label, short_label in short_labels.items() if - not f"{label}.{short_label}" in expected_cols] - else: - expected_cols += [short_label for short_label in short_labels.values() if not short_label in expected_cols] - - df = df[[col for col in expected_cols if col in df.columns]] - if return_q_and_dict: - return df, q, data_dict - return df - - def _get_data_generic_helper(self, - classes: list, - where_map=None, - allow_unrelated_subgraphs: bool = False, - return_nodeid: bool = True, - return_properties: str = "*", - prefix_keys_with_label: bool = True, - order=None, - limit=20): - """ - Helper function, to produce the Cypher query and data binding for get_data_generic(). - - It's implemented with a Cypher query whose MAIN BODY originates from qb.generate_query_body(), - and whose RETURN statement originates from qb.generate_return() - - Parameters - Same as for get_data_generic() - :return: The pair (Cypher query string, Cypher data binding dictionary) - """ - if type(classes) == str: - classes = [classes] - if not where_map: - where_map = {} - (cypher, data_dict) = self.qb.generate_query_body(classes, where_map, allow_unrelated_subgraphs) - - if self.debug: - print("In _get_data_generic_helper() :") - print(" cypher: ", cypher) - print(" data_dict: ", data_dict) - print(" where_map: ", where_map) - - (q_return, data_dict2) = self.qb.generate_return( - labels=classes, - return_disjoint=False, - return_nodeid=return_nodeid, - return_properties=return_properties, - prefix_keys_with_label=prefix_keys_with_label, - ) - if order: - q_return = re.sub(r'^RETURN', 'WITH', q_return) - q = " ".join( - [cypher, - q_return, - ] + - ([f"ORDER BY {', '.join([f'all.`{o}`' for o in order] if type(order) == list else [f'all.`{order}`'])}"] if order else []) + - ([f"LIMIT {str(limit)}"] if limit else []) + - ["RETURN *"] - ) - else: - q = " ".join( - [cypher, - q_return - ] + - ([f"LIMIT {str(limit)}"] if limit else []) - ) - - # Extend the Cypher data dictionary, to also include a value for the key "labels" - data_dict["labels"] = list(classes) - return (q, {**data_dict, **data_dict2}) - - ############################################################# - # FILTERS # - ############################################################# - - def get_filters(self, classes: list, where_map=None, return_q_and_dict=False) -> dict: - """ - Useful to build a dropdown menu in a UI. - Simplified version of get_filters_generic() - - :param classes: A string or list of strings with Class names. EXAMPLE: ['Study', 'Site', 'Subject'] - :param where_map: See explanation in get_data() - :param return_q_and_dict: Optionally return query and data_dict - :return: A (possibly empty) Python dictionary. For example, see get_filters_generic() - """ - return self.get_filters_generic( - classes=classes, - where_map=where_map, - allow_unrelated_subgraphs=False, - return_nodeid=True, - return_properties="*", - prefix_keys_with_label=True, - return_q_and_dict=return_q_and_dict, - ) - - def get_filters_generic(self, - classes, - where_map=None, - allow_unrelated_subgraphs=False, - return_nodeid=True, - return_properties="*", - prefix_keys_with_label=True, - return_q_and_dict=False): - """ - Useful to build a dropdown menu in a UI - - :param classes: A string or list of strings with Class names. EXAMPLE: ['Study', 'Site', 'Subject'] - :param where_map: See explanation in get_data() - :param return_nodeid: Boolean - :param return_properties: Either a list of Property names to include in the dataframe, or the string "*" (meaning, "all") - EXAMPLE: ["STUDYID", "SITEID"] - :param return_q_and_dict: Optionally return query and data_dict - :param prefix_keys_with_label: If True adds a prefix (corresponding node label) to each column name of the returned data - :return: A (possibly empty) Python dictionary - EXAMPLE: - { - Label1: pd.DataFrame( - [ - {prop1: value11, prop2: value21}, - {prop2: value21, prop2: value22}, - ... - ] - ), - Label3: pd.DataFrame( - [ - {prop3: value11}, - {prop3: value21}, - ... - ] - ) - } - """ - results, q, data_dict = self._get_filters_helper(classes, - where_map=where_map, - allow_unrelated_subgraphs=allow_unrelated_subgraphs, - return_nodeid=return_nodeid, - return_properties=return_properties, - prefix_keys_with_label=prefix_keys_with_label) - - if return_q_and_dict: - return {k: pd.DataFrame(i) for k, i in results.items()}, q, data_dict - return {k: pd.DataFrame(i) for k, i in results.items()} - - def _get_filters_helper(self, - classes: list, - where_map=None, - allow_unrelated_subgraphs=False, - return_nodeid=True, - return_properties="*", - prefix_keys_with_label=True, - ): - """ - Helper function for get_filters_generic() - - Look for nodes whose relationships among them conform to the "CLASS_RELATES_TO" - relationships among `Class`-labeled nodes with "label" attributes matching the given classes. - EXAMPLE: if classes consists of ["apple", "fruit"] then look for `apple` labeled nodes and - `fruit` labeled nodes, with a "HAS_FRUIT" relationship between them. - - :param classes: A string or list of strings. EXAMPLE: ['Study', 'Site', 'Subject'] - :param where_map: Used to restrict the data (default, no restriction.) - A dictionary of dictionaries. SEE explanation in qb_list_where_conditions_per_dict() - :param return_nodeid: Boolean - :param return_properties: Either a list of Property names to include in the dataframe, or the string "*" (meaning, "all") - EXAMPLE: ["STUDYID", "SITEID"] - :param prefix_keys_with_label: If True adds a prefix (corresponding node label) to each column name of the returned data - """ - if self.verbose: - print("-- Getting filters --") - if type(classes) == str: - # Intercept empty strings because they lead to faulty Cypher such as: MATCH (``:``) RETURN collect(distinct ``{.*}) as `` - assert classes.strip() != "", "ERROR in _get_filters_helper(): the argument `classes` cannot be an empty string" - classes = [classes] - - if not where_map: - where_map = {} - - if self.debug: - print("classes : ", classes) - print("where_map : ", where_map) - - (cypher, data_dict) = self.qb.generate_query_body(classes, where_map, allow_unrelated_subgraphs) - (return_cypher, data_dict2) = self.qb.generate_return( - labels=classes, - return_disjoint=True, - return_nodeid=return_nodeid, - return_properties=return_properties, - prefix_keys_with_label=prefix_keys_with_label, - ) - q = " ".join([cypher, return_cypher]) - if self.debug: - print("Inside _get_filters_helper(). q : ", q, " | data_dict : ", data_dict) - - # Extend the Cypher data dictionary, to also include a value for the key "labels" - data_dict["labels"] = list(classes) - - query_result = self.qb.query(q, {**data_dict, **data_dict2}) - try: - results = query_result[0] - except KeyError: - results = {} - - return results, q, data_dict - - ############################################################# - # PANDAS SUPPORT # - ############################################################# - - def convert_qb_result_to_df(self, neoresult, hstack=True): # TODO: add tests - """ - - :param neoresult: - :param hstack: If hstack == True returns 1 dataframe (properties of all returned neo4j variables are concatenated horizontally) - if hstack == False returns a dictionary of dataframes (1 per returned unit) - - :return: Either a Pandas dataframe or a dictionary of dataframes - """ - - dct_of_lists = {} - keys = [] - for i, res in enumerate(neoresult): - if i == 0: - keys = res.keys() - for prop in keys: - if i == 0: - dct_of_lists[prop] = [] - dct_of_lists[prop].append(res[prop]) - if hstack: - if len(dct_of_lists) > 0: - return pd.concat([pd.DataFrame(lst) for lst in dct_of_lists.values()], axis=1) - else: - return pd.DataFrame() - else: - return {k: pd.DataFrame(dct_of_lists[k]) for k in keys} diff --git a/data_providers/archive/sdtm_data_provider.py b/data_providers/archive/sdtm_data_provider.py deleted file mode 100644 index a02c319..0000000 --- a/data_providers/archive/sdtm_data_provider.py +++ /dev/null @@ -1,225 +0,0 @@ -import datacompy - -from data_providers import DataProvider -import logging - - -class SDTMDataProvider(DataProvider): - """ - A wrapper-class over DataProvider to extract specifically SDTM data - """ - - def __init__(self, check_for_refarctored=True, *args, **kwargs): - self.check_for_refarctored = check_for_refarctored - super().__init__(*args, **kwargs) - - def get_data_sdtm(self, standard: str, domain: str, study=None, where_map=None, user_role=None): - assert where_map is None or isinstance(where_map, dict) - if not where_map: - where_map = {} - assert study is None or isinstance(study, str) - if study: - where_map = {**where_map, **{ - 'Study': {('STUDYID' if self.mode == "schema_PROPERTY" else self.mm.RDFSLABEL): study}}} - # TODO: add assert statements to check prerequisites - e.g. extraction model contains all required nodes and properties - meta = self.neo_get_meta(standard=standard, table=domain) - if self.debug: - print("meta", meta) - if meta: - classes = (['Study'] if 'Study' not in meta[0]['classes'] else []) + meta[0]['classes'] - if self.check_for_refarctored: - classes, non_valid = self.neo_validate_classes_to_extract(classes) - if non_valid: - print( - f"ERROR: the following classes were excluded as those were never created during refactoring: {non_valid}") - if user_role: - classes, no_access = self.neo_validate_access(classes, user_role=user_role) - print( - f"WARNING: the following classes were excluded as the user_role {user_role} access is restricted: {no_access}") - if meta[0]['req_classes']: - classes = [(class_ + self.OCLASS_MARKER if class_ not in meta[0]['req_classes'] else class_) for - class_ in classes] - if self.debug: - print(f"Getting classes: {classes}") - df = self.get_data_generic(labels=classes, - where_map=where_map, - infer_rels=True, - return_nodeid=False, - limit=None) - - # renaming and re-ordering columns (according to metadata): - rename_dct = {} - for key, item in meta[0]['rename_dct'].items(): - if not item in rename_dct.values(): # to avoid 2 columns with the same name - rename_dct[key] = item - df = df.rename(rename_dct, axis=1) - col_order = [k for k, v in sorted(meta[0]['order_dct'].items(), key=lambda item: item[1])] - for col in col_order: - if col not in df.columns: - df[col] = None - df = df[col_order] - - # Sorting - # check that variables for sorting in meta actaully exist - sorting, sorting_excluded = [], [] - if meta[0]['sorting']: - for col in meta[0]['sorting']: - if col in df.columns: - sorting.append(col) - else: - sorting_excluded.append(col) - if sorting_excluded: - print( - f"ERROR: the following columns were excluded from sort-by-group as those have not been extracted" - f"from the graph: {sorting_excluded}") - - # sorting dataframe: - if sorting: - df = df.sort_values(by=sorting, ignore_index=True) - else: - print(f"WARNING: no sort-by-group metadata(`Source Data Table`.SortOrder) was provided") - return df - - def neo_get_meta(self, standard: str, table: str): - if self.mode == "schema_PROPERTY": - q = """ - MATCH (sdf:`Data Extraction Standard`{_tag_:$standard})-[:HAS_TABLE]->(sdt:`Source Data Table`{_domain_:$table}), - (sdt)-[:HAS_COLUMN]->(sdc:`Source Data Column`), (class:Class) - WHERE - EXISTS( - (sdc)-[:MAPS_TO_PROPERTY]->(:Property)<-[:HAS_PROPERTY]-(class) - ) - OR - EXISTS( - (sdt)-[:MAPS_TO_CLASS]->(class) - ) - WITH * - OPTIONAL MATCH (sdc)-[r:MAPS_TO_PROPERTY]->(property:Property)<-[:HAS_PROPERTY]-(class) - WITH * - ORDER BY sdf, sdt, sdc.Order, sdc - RETURN - collect(distinct class.label) as classes, - apoc.coll.toSet([triple in [triple in collect([class.label, sdc.Core, class.CoreClass]) where triple[1] = "Required" or triple[2]] | triple[0]]) - as req_classes, - apoc.map.fromPairs( - [y in - [x in collect(distinct {class:class, sdc:sdc, property:property, r:r}) - WHERE NOT x['r'] IS NULL] | //filtering for existing Column MAPS_TO_PROPERTY relationship - [ - y['class'].label + '.' + y['property'].label, //to be used as key of the dict - y['sdc']._columnname_ //to be used as value of the dict - ] - ] - ) as rename_dct, - apoc.map.fromPairs(collect([sdc._columnname_, sdc.Order])) as order_dct, - apoc.text.split(sdt['SortOrder'],',') as sorting - """ - elif self.mode == "schema_CLASS": - q = """ - MATCH (sdf:`Data Extraction Standard`{_tag_:$standard})-[:HAS_TABLE]->(sdt:`Source Data Table`{_domain_:$table}), - (sdt)-[:HAS_COLUMN]->(sdc:`Source Data Column`), (class:Class) - WHERE - EXISTS( - (sdc)-[:MAPS_TO_CLASS]->(class) - ) - OR - EXISTS( - (sdt)-[:MAPS_TO_CLASS]->(class) - ) - WITH * - OPTIONAL MATCH (sdc)-[r:MAPS_TO_CLASS]->(class) - WITH * - ORDER BY sdf, sdt, sdc.Order, sdc - RETURN - collect(distinct class.label) as classes, - apoc.coll.toSet([triple in [triple in collect([class.label, sdc.Core, class.CoreClass]) where triple[1] = "Required" or triple[2]] | triple[0]]) - as req_classes, - apoc.map.fromPairs( - [y in - [x in collect(distinct {class:class, sdc:sdc, r:r}) WHERE NOT x['r'] IS NULL] | //filtering for classes with existing Column MAPS_TO_CLASS relationship - [ - y['class'].label + '.' + y['class'].short_label, //to be used as key of the dict - y['sdc']._columnname_ // to be used as value of the dict - ] - ] - ) as rename_dct, - apoc.map.fromPairs(collect([sdc._columnname_, sdc.Order])) as order_dct, - apoc.text.split(sdt['SortOrder'],',') as sorting - """ - params = {'standard': standard, 'table': table} - if self.debug: - logging.debug(f""" - query: {q} - parameters: {params} - """) - res = self.query(q, params) - return res - - def neo_get_mapped_classes(self): - q = """ - MATCH (sdf:`Source Data Folder`)-[:HAS_TABLE]->(sdt:`Source Data Table`), - (sdt)-[:HAS_COLUMN]->(sdc:`Source Data Column`), - (sdc)-[:MAPS_TO_PROPERTY]->(property:Property), - (class:Class)-[:HAS_PROPERTY]->(property:Property) - RETURN DISTINCT class.label as Class - """ - params = {} - if self.debug: - logging.debug(f""" - query: {q} - parameters: {params} - """) - res = self.query(q, params) - if res: - return [r['Class'] for r in res] - else: - return [] - - def neo_validate_classes_to_extract(self, classes: list) -> ([], []): - """ - :param classes: list of classes to validate (nodes with labels Class and property label must exist) - :return: [], [] - list of valid classes and list if invalid classes - Identifies non-valid classes with count==0 or no count property (at least 1 instance got extracted during reshaping) - """ - q = """ - MATCH (n:Class) - WHERE n.count = 0 OR NOT EXISTS (n.count) - RETURN DISTINCT n.label as class - """ - pre_non_valid = [res['class'] for res in self.query(q, {'classes': classes})] - non_valid = [] - for class_ in pre_non_valid: - if class_ in classes: - non_valid.append(class_) - - valid = [class_ for class_ in classes if class_ not in non_valid] - return valid, non_valid - - def neo_validate_access(self, classes: list, user_role=None) -> ([], []): - """ - :param classes: list of classes to validate (nodes with labels Class and property label must exist) - :param user_role: when None no access restrictions are accounted for, otherwise the classes with - (:`User Role`{name:$user_role})-[:RESTRICTED_ACCESS]->(:Class) would be considered invalid - :return: - Identifies non-valid classes to which the user_role(if provided does not have access to) - """ - no_access = [] - if user_role: - q = """ - MATCH (role:`User Role`{name:$user_role}) - OPTIONAL MATCH (role)-[:ACCESS_RESTRICTED]->(c:Class) - RETURN DISTINCT role.name as role, c.label as class - """ - pre_no_access = [res['class'] for res in self.query(q, {'user_role': user_role})] - if pre_no_access == []: - raise Exception(f"User Role {user_role} does not exist") - for class_ in pre_no_access: - if class_ in classes: - no_access.append(class_) - has_access = [class_ for class_ in classes if class_ not in no_access] - return has_access, no_access - - @staticmethod - def check_dataframes_equal(df1, df2): - compare = datacompy.Compare(df1.reset_index(), df2.reset_index(), join_columns=['index']) - return compare.report() diff --git a/data_providers/data_provider.py b/data_providers/data_provider.py index e30283d..5f23d57 100644 --- a/data_providers/data_provider.py +++ b/data_providers/data_provider.py @@ -25,7 +25,7 @@ def __init__(self, *args, **kwargs): def check_schema(self, labels: list, rels: list): for label in labels: - q = "MATCH " + self.qb.generate_1match_schema_check(label) + " RETURN *" + q = "MATCH " + self.qb.generate_1match_schema_check(label=label) + " RETURN *" res = self.query(q) assert res, f"Class {label} not found in the schema" for rel in rels: diff --git a/examples/refactor_all.py b/examples/refactor_all.py deleted file mode 100644 index 20f396b..0000000 --- a/examples/refactor_all.py +++ /dev/null @@ -1,4 +0,0 @@ -from model_appliers.model_applier import ModelApplier - -ma = ModelApplier() -ma.refactor_all() \ No newline at end of file diff --git a/examples/refactor_sdtm_metadata.py b/examples/refactor_sdtm_metadata.py deleted file mode 100644 index 41fd864..0000000 --- a/examples/refactor_sdtm_metadata.py +++ /dev/null @@ -1,48 +0,0 @@ -import neointerface -from model_managers import model_manager -from model_appliers import model_applier -import time - -start_time = time.time() - -#neo = neointerface.NeoInterface(host = "neo4j://10.40.225.48:17687", credentials = None) -neo = neointerface.NeoInterface() - -groupings = { - "SDTM-3-2-EXCEL":{ - "Observation Class": ["Observation_Class"], - "Domain": ["Domain_Prefix"], - "Variable": ["Domain_Prefix", "Variable_Name", "Seq_For_Order"], - "Variable Name": ["Variable_Name"], - "Variable Label": ["Variable_Label"], - "Variable Role": ["Role"], - } -} - -class_relationships = [ - ["Observation Class", "Domain"], - ["Domain", "Variable"], - ["Domain", "Variable Name"], - ["Variable", "Variable Name"], - ["Variable", "Variable Label"], - ["Variable", "Variable Role"] -] - - -neo.clean_slate(keep_labels=["Message", "Source Data Row", "Source Data Table", "Source Data Folder", "Source Data Column"]) - -#mm = model_managers.ModelManager(host = "neo4j://10.40.225.48:17687", credentials = None) -mm = model_manager.ModelManager() -mm.create_custom_mappings_from_dict(groupings) -mm.create_custom_rels_from_list(class_relationships) - -mod_a = model_applier.ModelApplier() -mod_a.define_refactor_indexes() -# IMPORTANT !!! in order to make it work make sure latest apoc is installed and procedures must be whitelisted: -# in neo4j.conf: -# dbms.security.procedures.unrestricted=jwt.security.*,apoc.* -# dbms.security.procedures.allowlist=apoc.* -# dbms.security.procedures.whitelist=apoc.* -mod_a.refactor_all() - -print(f"--- {(time.time() - start_time):.3f}' seconds ---") \ No newline at end of file diff --git a/install_from_local_repos.bat b/install_from_local_repos.bat deleted file mode 100644 index b8f3ed2..0000000 --- a/install_from_local_repos.bat +++ /dev/null @@ -1 +0,0 @@ -venv\Scripts\python.exe -m pip install -e ..\neointerface \ No newline at end of file diff --git a/model_appliers/_archive_model_applier.py b/model_appliers/_archive_model_applier.py deleted file mode 100644 index db6c1ea..0000000 --- a/model_appliers/_archive_model_applier.py +++ /dev/null @@ -1,447 +0,0 @@ -import re -from neointerface import NeoInterface -from data_providers.data_provider import DataProvider -from query_builders.query_builder import QueryBuilder - - -class ModelApplier(NeoInterface): - """ - The purpose of the class is to refactor the data in the graph, extract_entities (create new nodes using data from other nodes) - and link_entities (create relationships between existing nodes based on certain condition. - The methods in the class utilize metadata nodes with labels Class and Property to get information on how to extract_entities - and link_entities - """ - RDFSLABEL = 'rdfs:label' - def __init__(self, mode="schema_PROPERTY", *args, **kwargs): - """ - :param mode: mode of MethodApplier to work either with schema_PROPERTY schema or MAPS_TO_CLASS schema - :param args: - :param kwargs: - """ - assert mode is None or mode in ["schema_PROPERTY", "schema_CLASS"] - super().__init__(*args, **kwargs) - if not mode: - res = self.query("MATCH (p:Property)<-[:MAPS_TO_PROPERTY]-() RETURN p LIMIT 1") - if res: - self.mode = "schema_PROPERTY" - else: - self.mode = "schema_CLASS" - if self.debug: - print(f"Setting ModelApplier mode to {self.mode}") - else: - self.mode = mode - - - def delete_classes_entities(self, delete_rawdata=False) -> None: - """ - Delete all nodes with labels corresponding to the existing Class Entities (such as - 'Study', 'Site', 'Race', 'Treatment', etc) - - If the flag delete_rawdata is True, then also eliminate all nodes with the label "Source Data Row". - - Note: all the relationships to the deleted nodes are deleted as well. - - :param delete_rawdata: Flag indicating whether to also delete the nodes with the label "Source Data Row" - :return: None - """ - # Get a list of all the values of the field "label" in nodes labeled "Class" - list_of_labels_to_delete = self.get_single_field(field_name="label", labels="Class") # List of Class entities - - if delete_rawdata: - list_of_labels_to_delete.append("Source Data Row") # Also mark "Source Data Row" nodes for deletion - - # print(list_of_labels_to_delete) # EXAMPLE: ["Study", "Site", "Race", etc, possibly including "Source Data Row"] - - self.delete_nodes_by_label(delete_labels=list_of_labels_to_delete) - - if self.verbose: - print("Nodes with the following labels have been deleted:", list_of_labels_to_delete) - - def define_refactor_indexes(self, where_map:dict = None) -> None: - """ - Read classes and properties, and create index for most of them (except for some) - - In order to improve refactoring query performance indexes on the class_/properties need to be defined - getting the list of labels and properties to define indexes on. - - :return: None - """ - wh_list = [] - if not (where_map): - where_map = {} - else: - wh_list, where_map = QueryBuilder.list_where_conditions_per_dict(where_map) - wh = (("WHERE " + " AND ".join(wh_list)) if wh_list else "") - if self.mode == "schema_PROPERTY": - q = f""" - MATCH (`Source Data Table`:`Source Data Table`)-[:HAS_COLUMN]->(`Source Data Column`:`Source Data Column`), - (`Source Data Column`)-[:MAPS_TO_PROPERTY]->(Property:Property)<-[:HAS_PROPERTY]-(Class:Class) - {wh} - RETURN DISTINCT Class.label as label, Class.create as create, Property.label as property - """ - elif self.mode == "schema_CLASS": - q = f""" - MATCH (`Source Data Table`:`Source Data Table`)-[:HAS_COLUMN]->(`Source Data Column`:`Source Data Column`), - (`Source Data Column`)-[:MAPS_TO_CLASS]->(Class:Class) - {wh} - RETURN DISTINCT Class.label as label, Class.create as create, '{self.RDFSLABEL}' as property - """ - res = self.query(q, where_map) - for data in res: - # handling Labels that are exceptions e.g. labels most likely to have many distinct values therefore does not make sense to create an index - if not (data["create"] == True): - self.create_index(data['label'], data['property']) - - def replace_class_relates_to(self): - q = """ - MATCH (c1:Class)-[r:CLASS_RELATES_TO]->(c2:Class) - WITH *, - CASE WHEN r.relationship_type IS NULL THEN - 'HAS_' + toUpper(c2.label) - ELSE - r.relationship_type - END as type - MERGE (c1)<-[:FROM]-(rn:Relationship{type:type})-[:TO]->(c2) - DELETE r - """ - self.query(q) - - def refactor_all(self, where_map=None) -> None: - """ - Running full pipleline of refactoring the data (i.e. extract_entities, link_entities, etc.) - :param where_map a dictionary to be passed to extract_class_entities - :return: None - """ - self.define_refactor_indexes() - self.extract_class_entities(where_map=where_map) - self.link_classes() - #TODO: to move the below temporary hardcoded metadata update to the ttls and update ModelApplier processing - self.replace_class_relates_to() - - def refactor_selected(self, domains=None, classes=None) -> None: - """ - Running a selective pipleline of refactoring the data (i.e. extract_entities, link_entities, etc.). - Either Domains or Classes should not be None. - :param where_map a dictionary to be passed to extract_class_entities - :param domains a list of domains to be refactored - :param classes a list of classes to be refactored - :return: None - """ - assert domains is not None or classes is not None, "No Domains or Classes were passed. To run a full pipeline of " \ - "refactoring, use refactor_all()" - - where_map = {} - if domains: - where_map['Source Data Table'] = {'_domain_': domains} - if classes: - where_map['Class'] = {'label': classes} - - self.define_refactor_indexes(where_map=where_map) - self.extract_class_entities(where_map=where_map) - self.link_classes(domains=domains, classes=classes) - - def extract_class_entities(self, where_map=None, store_counts=True) -> None: - """ - The 2 parts of the function are explained separately - :param where_map a dictionary to be passed to _extract_class_entities_part_1 - :return: None - """ - qres = self._extract_class_entities_part_1(where_map=where_map) - self._extract_class_entities_part_2(qres) - # only when store_counts=True we store counts of instances of classes on node with label 'Class' - if store_counts: - for lbl in set([lbl for res in qres for lbl in res['lbl']]): - q = f""" - MATCH (x:`{lbl}`) - WITH count(x) as cnt - MATCH (c:Class{{label:$lbl}}) - SET c.count = cnt - """ - self.query(q, {'lbl': lbl}) - - def _extract_class_entities_part_1(self, where_map=None) -> [{}]: - """ - Helper function to locate paths traversing the Neo4j graph from `Source Data Table` nodes to `Class` nodes, - by way of `Source Data Column` and `Property` nodes, - following the relationships `HAS_COLUMN`, `MAPS_TO_PROPERTY` and `HAS_PROPERTY`, - but avoiding scenarios where an alternate path exists with a `MAPS_TO` relationship. - - In essence, this is a traversal from the lower-lever domain of "source tables" to - the higher-level domain of "classes". - - The results of the traversal are compiled as a list of dictionaries, with a mix of gathered and created values - - :param where_map a dictionary to be passed to QueryBuilder.list_where_conditions_per_dict to extend where condition - applied to meta-model nodes in the query. - - - - :return: A list of dictionaries. EXAMPLES of individual entries: - {'mode': 'merge', 'domain': 'ADSL', 'coll': [['STUDYID', 'STUDYID']], 'lbl': 'Study'} - {'mode': 'merge', 'domain': 'ADSL', 'coll': [['RACE', 'RACE'], ['RACEN', 'RACEN']], 'lbl': 'Race'} - {'mode': 'merge', 'domain': 'ADAE', 'coll': [['ASTDT', 'ASTDT'], ['ASTTM', 'ASTTM'], ['AETERM', 'AETERM']], 'lbl': 'Adverse Event'} - - DICTIONARY KEYS: - 'mode': the string "apoc.create.node" if the 'lbl' value (see below) occurs in the list self.labels_to_always_create; - otherwise, "apoc.merge.node" - 'domain': the value of the "_domain_" attribute in the `Source Data Table` node - 'coll': a 2-element list comprising the value of "_columnname_" in the `Source Data Column` node, - and the value of "label" in the `Property` node - 'lbl': a list of "label" attributes in the `Class` node (along with labels of the classes to which the class is SUBCLASS_OF) - """ - if self.verbose: - print(" ------ Refactoring loaded data per graph class_ definition. EXECUTING PART 1 --------- ") - wh_list = [] - if not (where_map): - where_map = {} - else: - wh_list, where_map = QueryBuilder.list_where_conditions_per_dict(where_map) - ### Processing MAPS_TO_PROPERTY - # The MATCH part locates paths on the graph, from `Source Data Table` nodes to `Class` nodes; - # the WHERE part excludes some of those paths based on the where_map paramtere; - # the second WITH statement extracts some variables, and packages 2 variables as a "coll" pair; - # the third WITH statement aliases "mode" - - if self.mode == "schema_PROPERTY": - q_match = f""" - MATCH (`Source Data Folder`:`Source Data Folder`)-[:HAS_TABLE]->(`Source Data Table`:`Source Data Table`), - (`Source Data Table`)-[:HAS_COLUMN]->(`Source Data Column`:`Source Data Column`), - (`Source Data Column`)-[:MAPS_TO_PROPERTY]->(property:Property)<-[:HAS_PROPERTY]-(Class:Class), - p_classes=(Class)-[:SUBCLASS_OF*0..10]->(parent) - WHERE NOT ( ()-[:SUBCLASS_OF]->(Class) OR (parent)-[:SUBCLASS_OF]->() ) - {("AND " + " AND ".join(wh_list) if wh_list else "")} - """ - else: - q_match = f""" - MATCH (`Source Data Folder`:`Source Data Folder`)-[:HAS_TABLE]->(`Source Data Table`:`Source Data Table`), - (`Source Data Table`)-[:HAS_COLUMN]->(`Source Data Column`:`Source Data Column`), - (`Source Data Column`)-[:MAPS_TO_CLASS]->(Class:Class), - p_classes=(Class)-[:SUBCLASS_OF*0..10]->(parent) - WHERE NOT ( ()-[:SUBCLASS_OF]->(Class) OR (parent)-[:SUBCLASS_OF]->() ) - {("AND " + " AND ".join(wh_list) if wh_list else "")} - WITH *, {{label:'{self.RDFSLABEL}'}} as property - """ - q = f""" - {q_match} - WITH *, CASE WHEN Class.create = True THEN - 'create' - ELSE - 'merge' - END AS mode - ORDER BY `Source Data Table`, Class, `Source Data Column` - WITH mode, `Source Data Table`, [c in nodes(p_classes) | c.label] as lbl, - collect([`Source Data Column`._columnname_, property.label]) as coll - RETURN mode, `Source Data Table`._domain_ as domain, coll, lbl - """ - params = where_map - if self.debug: - print(q, params) - qres = self.query(q, params) - - if self.debug: - print("_extract_class_entities_part_1() created a list with the following ", len(qres), " elements: ") - for r in qres: - print(" ", r) - ### Processing `Source Data Table` MAPS_TO_CLASS (extraction of 1 node per `Source Data Row` with no properties (CoreClass to link to) - q2 = f""" - MATCH (`Source Data Folder`:`Source Data Folder`)-[:HAS_TABLE]->(`Source Data Table`:`Source Data Table`), - (`Source Data Table`)-[:MAPS_TO_CLASS]->(Class:Class), - p_classes=(Class)-[:SUBCLASS_OF*0..10]->(parent) - WHERE NOT ( ()-[:SUBCLASS_OF]->(Class) OR (parent)-[:SUBCLASS_OF]->() ) - {("AND " + " AND ".join(wh_list) if wh_list else "")} - RETURN - CASE WHEN Class.create = True THEN - 'create' - ELSE - 'merge' - END AS mode, - `Source Data Table`._domain_ as domain, - [] as coll, - [c in nodes(p_classes) | c.label] as lbl - """ - qres_no_columns = self.query(q2, params) - return qres + qres_no_columns - - def _extract_class_entities_part_2(self, qres) -> None: - """ - Create new nodes connected to `Source Data Row` with "FROM_DATA" relationships as needed. - - For each dictionary in the list qres, look for `Source Data Table` nodes that have a "_domain_" attribute - with a value matching that of the "domain" key in the dictionary, - and connected to `Source Data Row` nodes with a ":HAS_DATA" relationship; - also, require that the properties of the `Source Data Row` node overlap with the zero-th elements - in the dictionary value for "coll". - Whenever the above conditions are met, create a new node with label(s) specified - by in "lbl", with the same attributes/value as the overlapping attributes - found in the `Source Data Row` node, and pointing to the `Source Data Row` node with a - relationship named "FROM_DATA" - - :param qres: A list of dictionaries. For details, see _extract_class_entities_part_1() - :return: None - """ - if self.verbose: - print(" ------ Refactoring loaded data per graph class_ definition. EXECUTING PART 2 --------- ") - print(" LOOPING OVER ", len(qres), " entries in helper list:") - - for i, r in enumerate(qres): - if self.debug: - print(f"{i} Processing {r}") - self.extract_entities( - mode=r['mode'], - label='Source Data Row', - cypher=''' - MATCH (f:`Source Data Table`{_domain_:$domain})-[:HAS_DATA]->(node:`Source Data Row`) - RETURN id(node) - ''', - cypher_dict={'domain': r['domain']}, - target_label=r["lbl"], - property_mapping={x[0]: x[1] for x in r["coll"]}, - relationship='FROM_DATA', - direction='<' - ) - - def link_classes(self, domains=None, classes=None) -> None: - """ - Establish, among data nodes, relationships that echo the relationships - among their corresponding (metadata) classes. - - Look for all pairs of "Class"-labeled nodes linked by a "CLASS_RELATES_TO" relationship; - if (left_c, right_c) is such a pair, then look for all triples of nodes fulfilling some requirements - (described below) - and to all the found node, add relationships. - - Requirement for the sought triplets (left, sdr, right) of nodes, given the (left_c, right_c) pair above: - 1. the label of (left) equals the value of the "label" attribute of the node left_c - 2. the label of (right) equals the value of the "label" attribute of the node right_c - 3. the label of (sdr) is `Source Data Row` - 4. there's a relationship named FROM_DATA from (left) to (sdr), as well as from (right) to (sdr) - - The added relationship, if all the above requirements are met, is: - A relationship from (left) to (right), named HAS_XYZ , where XYZ is the (upper-case version) of the - value of the "label" attribute of the node right_c - - SEE DIAGRAM in repository: docs/link_classes.png - - NOTE: a plan under consideration (but NOT implemented) is to - perhaps exclude CLASS_RELATES_TO relationships that have properties defined on them; - that could be attained by inserting the clause WHERE size(keys(r)) = 0 - after the initial MATCH - The CLASS_RELATES_TO relationships with properties defined on them would be processed in a different manner - - :param classes an optional list of classes to pass to _link_classes_part_1, in order to limit qres to specific classes - :param domains an optional list of domains to pass to _link_classes_part_1, in order to limit qres to specific domains - :return: None - """ - qres = self._link_classes_part_1(domains=domains, classes=classes) - self._link_classes_part_2(qres) - - def _link_classes_part_1(self, domains=None, classes=None): - """ - :param classes an optional list of classes to define WHERE condition, to only return specified classes for linking - :param domains an optional list of domains to define WHERE condition, to only return specified domains for linking - """ - - conditions = [] - if domains: - conditions.append(""" ( apoc.coll.intersection(apoc.text.split(left_c.from_domains,","), $domains) OR - apoc.coll.intersection(apoc.text.split(right_c.from_domains,","), $domains) ) - """) - - if classes: - conditions.append("(left_c.label in $classes OR right_c.label in $classes)") - - selection = "WHERE " + " and ".join(conditions) if conditions else "" - - q = f""" - MATCH (left_c:Class)-[r:CLASS_RELATES_TO]->(right_c:Class) - {selection} - RETURN DISTINCT left_c.label as left_class, right_c.label as right_class, r.relationship_type as relationship - """ - - params = {"domains": domains, "classes": classes} - if self.debug: - print(q, params) - - qres = self.query(q, params) - - if self.debug: - print("_link_classes_part_1() created a list with the following ", len(qres), " elements: ") - for r in qres: - print(" ", r) - - return qres - - def _link_classes_part_2(self, qres: list) -> None: - if self.verbose: - print("--------------- Linking classes ----------------------") - for res in qres: - self.link_entities( - left_class=res['left_class'], - right_class=res['right_class'], - relationship=(res['relationship'] if res['relationship'] is not None else "_default_"), - cond_via_node="Source Data Row", - cond_left_rel="FROM_DATA>", - cond_right_rel="", "", None] - d1 = ("<" if cond_via_rel_direction == "<" else "") - d2 = (">" if cond_via_rel_direction == ">" else "") - periodic_part1 = f""" - MATCH (`{class_.lower()}`:`{class_}`){d1}-[:`{cond_via_rel}`]-{d2}(`{add_label['Class'].lower()}`:`{ - add_label['Class']}`) - RETURN {class_.lower()}, {add_label['Class'].lower()} - """ - q = f""" - call apoc.periodic.iterate( - '{periodic_part1}', - 'CALL apoc.create.addLabels(`{class_.lower()}`, [' + $property + ']) YIELD node RETURN node', - {{batchSize:10000, parallel:false, params: {{cypher: $cypher, cypher_dict: $cypher_dict}}}}) - YIELD total, batches, failedBatches - RETURN total, batches, failedBatches - """ - params = {'cypher': cond_cypher, 'cypher_dict': cond_cypher_dict, - 'property': "`" + add_label['Class'].lower() + "`.`" + add_label['Property'] + "`" - } - if self.debug: - print(" Query : ", q) - print(" Query parameters: ", params) - self.query(q, params) \ No newline at end of file diff --git a/model_appliers/model_applier.py b/model_appliers/model_applier.py index e3ca1c1..0f2915a 100644 --- a/model_appliers/model_applier.py +++ b/model_appliers/model_applier.py @@ -545,7 +545,7 @@ def delete_reshaped(self, batch_size=10000): def label_entities(self, class_='Observation', - add_label={'Class': 'Category', 'Property': 'name'}, + add_label=None, cond_via_rel='HAS_OBSERVATION', cond_via_rel_direction='<', cond_cypher=None, @@ -570,6 +570,8 @@ def label_entities(self, assert type(add_label) == dict assert "Class" in add_label.keys() assert "Property" in add_label.keys() + if not add_label: + add_label = {'Class': 'Category', 'Property': 'name'} if cond_cypher: assert re.search(f'RETURN.*{class_.lower()}', cond_cypher) assert re.search(f'RETURN.*{add_label["Class"].lower()}', cond_cypher) diff --git a/model_managers/archive/model_manager.py b/model_managers/archive/model_manager.py deleted file mode 100644 index 4b74282..0000000 --- a/model_managers/archive/model_manager.py +++ /dev/null @@ -1,591 +0,0 @@ -from neointerface import NeoInterface -import pandas as pd -import logging - -class ModelManager(NeoInterface): - """ - Python class to manage metadata nodes (such as nodes with label Class and Property) along with relationships between them - as well as to return information about them - """ - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - if self.verbose: - print (f"---------------- {self.__class__} initialized -------------------") - - - - #################### TO CREATE/DELETE Classes or Properties #################### - - def create_class(self, classes, merge=True) -> [list]: - """ - :param classes: Name, or list of names, to give to the new class(es) created - :param merge: boolean - if True use MERGE statement to create nodes to avoid duplicate classes - TODO: address question "would we want to ever allow multiple classes with the same name??" - :return: A list of lists that contain a single dictionary with keys 'label', 'neo4j_id' and 'neo4j_labels' - EXAMPLE: [ [{'label': 'A', 'neo4j_id': 0, 'neo4j_labels': ['Class']}], - [{'label': 'B', 'neo4j_id': 1, 'neo4j_labels': ['Class']}] - ] - """ - assert type(merge)==bool - - if not type(classes) == list: - classes = [classes] - - if merge: - q = "WITH $classes as classes UNWIND classes as class_name CALL apoc.merge.node(['Class'], {label: class_name}, {}, {}) YIELD node RETURN node as class" - else: - q = "WITH $classes as classes UNWIND classes as class_name CALL apoc.create.node(['Class'], {label: class_name}) YIELD node RETURN node as class" - - params = {'classes': classes} - - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - - return self.query_expanded(q, params) - - - - def delete_class(self, class_:str): - #TODO: add check EXISTS ( (class:Class{{label:$class_}})-[:HAS_PROPERTY]->() ), return -1 - q = "MATCH (class:Class{{label:$class_}}) DELETE class" - params = {'label': class_} - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) - - - - def create_property(self, class_:str, property:str, merge=True) -> None: - """ - Add the given Property to the specified Class - - :param class_: Name of the Class to which the new Property is attached - :param property: Name of the new Property. It must be a non-empty string. - :param merge: If True, then the Class is created if not present, - and the Property is only created if not already present; - if False, then the Class must be already present (or nothing will be added), - and the Property is always created - :return: None - """ - if not class_: - return # Whether a Class node is matched or created, the Class name must always be present - - if not property: - return # Validate property to be a non-empty string - - op1 = ('MERGE' if merge else 'MATCH') - op2 = ('MERGE' if merge else 'CREATE') - q = f""" - {op1} (class:Class {{label:$class_}}) - WITH * - {op2} (class)-[:HAS_PROPERTY]->(property:Property{{label:$property}}) - """ - params = { - 'class_': class_, - 'property': property - } - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) - - - - def delete_property(self, class_:str, property:str): - q = """ - MATCH (class:Class{{label:$class_}})-[:HAS_PROPERTY]->(property:Property{{label:$property}}) - DELETE property - """ - params = { - 'class_': class_, - 'property': property - } - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) - - - - #################### TO RENAME Classes or Properties #################### - - def rename_class(self, class_:str, new_class_label:str): - q = """ - MATCH (class:Class {{label:$class_}}) - set class.label = $new_class_label - """ - params = { - 'class_': class_, - 'new_class_label': new_class_label - } - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) - #currently existing instances of nodes with label of class.label will not be renamed (the method to be called before refactoring) - #TODO: consider adding calling apoc.refactor.rename.label withing apoc.periodic.iterate to allow for renaming instances of the class_ - - - - def rename_classes_by_ids(self, name_mapping: list) -> list: - """ - Bulk-rename one or more Class nodes using the given mapping, - a list of pairs which provides the new names for the nodes with the specified Neo4j IDs - - :param name_mapping: EXAMPLE: [[123, 'new name for node 123'], [88, 'new name for node 88']] - - :return: A list of dictionaries explaining the operations performed. - EXAMPLE: [{'mod': 'Class: A=>A new'}, {'mod': 'Class: B=>B new'}, {'mod': 'Class: C=>C new'}] - """ - q = """ - WITH $name_mapping as name_mapping - UNWIND name_mapping as single_rename - MATCH (class :Class) WHERE id(class) = single_rename[0] - WITH class, class.label as old_label, single_rename - SET class.label = single_rename[1] - RETURN 'Class: ' + old_label + '=>' + class.label as mod - """ - params = {'name_mapping': name_mapping} - - if self.debug: - logging.debug(f""" - query: {q} - parameters: {params} - """) - - return self.query(q, params) - - - - def rename_property(self, class_:str, property:str, new_property_label:str): - q = """ - MATCH (class:Class{{label:$class_}})-[:HAS_PROPERTY]->(property:Property{{label:$property}}) - set property.label = $new_property_label - """ - params = { - 'class_': class_, - 'property': property, - 'new_property_label': new_property_label - } - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) - #currently existing instances of nodes with label of class.label will not be renamed (the method to be called before refactoring) - #TODO: consider adding calling apoc.refactor.rename.nodeProperty withing apoc.periodic.iterate to allow for renaming properties of instances of the class_ - - - - #################### TO CREATE RELATIONSHIPS #################### - - def create_class_relationship(self, from_class: str, to_class: str, rel_name = "CLASS_RELATES_TO") -> None: - """ - Add a relationship between the 2 specified classes, by default named "CLASS_RELATES_TO", - provided that it doesn't already exists. - For bulk-creation of relationships, see create_custom_rels_from_list() - - :param from_class: Name of the 1st Class - :param to_class: Name of the 2nd Class - :param rel_name: Name of the relationship to create from the 1st to the 2nd Class - :return: None - """ - cypher = f''' - MATCH (from:`Class` {{label: $from_class}}), (to:`Class` {{label: $to_class}}) - MERGE (from)-[:{rel_name}]->(to) - ''' - - self.query(cypher, {"from_class": from_class, "to_class": to_class}) - - - - def create_custom_rels_from_list(self, rels: [[str, str]], create_if_absent = False) -> None: - """ - Adds "CLASS_RELATES_TO" relationships to pairs of nodes with "Class" label, - based on the list passed as the argument "rels". - Matches occur based on node attributes named "label". - Optionally, create the Class nodes if needed. - To create just a single relationship, see create_class_relationship() - - NOTE: this is a more general version of the method create_related_classes_from_list() - - :param rels: A list of 2-element lists, indicating a relationship among nodes of type `Class` - EXAMPLE: [ - ["Study", "Site"], - ["Study", "Subject"], - ["Subject", "Race"] - ] - :param create_if_absent: If True, the Class nodes specified in the argument "rel" get created as needed; - otherwise, no relationships get created whenever their start or end class is missing - :return: None - """ - if rels is None or rels == []: - return # There's nothing to do - - if create_if_absent: - q = f""" - UNWIND $rels as rel - WITH rel[0] as left, rel[1] as right - WHERE apoc.meta.type(left) = apoc.meta.type(right) = 'STRING' - MERGE (ln:Class {{label:left}}) - MERGE (rn:Class {{label:right}}) - MERGE (ln)-[:CLASS_RELATES_TO]->(rn) - """ - else: # The Class nodes MUST be present, or no relationship gets created - q = f""" - UNWIND $rels as rel - WITH rel[0] as left, rel[1] as right - WHERE apoc.meta.type(left) = apoc.meta.type(right) = 'STRING' - MATCH (ln:Class {{label:left}}), (rn:Class {{label:right}}) - MERGE (ln)-[:CLASS_RELATES_TO]->(rn) - """ - - params = {"rels": rels} - self.query(q, params) - - - - def create_related_classes_from_list(self, rel_list: [[str, str]]) -> [str]: - """ - Create `Class` nodes and "CLASS_RELATES_TO" relationships among them, as specified by rel_list - - Given a list of name pairs, perform 2 operations: - 1) Identify all the unique names, and create new nodes labeled "Class", - each new node has one of the unique names stored in an attribute named "label" - 2) Adds "CLASS_RELATES_TO" relationships to pairs of the newly-created nodes, - as specified by the pairs in the elements of rel_list - - EXAMPLE: if rel_list is [ ["Study", "Site"], ["Study", "Subject"] ] - then 3 new `Class`-labeled nodes will be created, with "label" attributes respectively - valued "Study", "Site" and "Subject", - plus a CLASS_RELATES_TO" relationship from "Study" to "Site", and one from "Study" to "Subject" - - NOTE: if some of the Class` nodes might already exist, use create_custom_rels_from_list() instead - - :param rel_list: A list of 2-element lists, indicating a relationship among nodes of type `Class` - EXAMPLE: [ - ["Study", "Site"], - ["Study", "Subject"], - ["Subject", "Race"] - ] - :return: List of all the class names; repeated ones are taken out - """ - - # Identify all the unique names in inner elements of rel_list - class_set = set() # Empty set - for rel in rel_list: - class_set = class_set.union(rel) # The Set Union operation will avoid duplicates - - class_list = sorted(list(class_set)) # Convert the final set back to list - - # Create the new nodes - self.query( - "UNWIND $classes as class CREATE (:Class {label:class})", - {'classes': class_list} - ) - - # Create the desired relationships among them - self.create_custom_rels_from_list(rel_list) - - return class_list - - - - def create_custom_mappings_from_dict(self, groupings = None) -> None: - """ - Create a set of nodes labeled "Class", all taken from the groupings dictionary; their names are - stored in an attribute named "label". EXAMPLES: "Study", "Site", "Race", "Adverse Event". - - Also, create a set of nodes labeled "Property"; likewise, their names are - stored in an attribute named "label". EXAMPLES: "RACE", "RACEN", "SITEID". - - In addition, create relationships named "HAS_PROPERTY", from each of the "Class" nodes to the appropriate - "Property" nodes. EXAMPLE: The "Race" node (labeled "Class") links to the "RACE", "RACEN" nodes - (labeled "Property") - - Finally, create relationships named "MAPS_TO_PROPERTY", from `Source Data Column` nodes to `Property` nodes. - These relationships are created based on matches between the "_columnname_" attribute on `Source Data Column` nodes - and entries in the lists contained in groupings (e.g., "RACEN"); in some cases, further restrictions are applied, - requiring the `Source Data Column` node to be linked to a particular `Source Data Table` node. - - :param groupings: A dictionary. The keys are either "*" (meaning no `Source Data Table` restriction) - or the name of a specific `Source Data Table`. - The values are dictionaries such as {"Race": ["RACE", "RACEN"]} - :return: None - """ - if not groupings: - groupings = {} - - # Loop over all the keys/values of the groupings dictionary - for table, groupping in groupings.items(): - # EXAMPLES of table: "ADSL" or "*" (the star indicates "all tables") - # groupping is a dictionary with entries such as "Race": ["RACE", "RACEN"] - - # Define the Cypher query, which depends on the value of the "table" variable in the outer loop; - # for examples of how the query shapes up, see below (inside inner loop) - q = f""" - MERGE (class:Class {{label:$class}}) - WITH * UNWIND $properties as property - MERGE (class)-[:HAS_PROPERTY]->(p:Property {{label:property}}) - WITH * - MATCH (sdc:`Source Data Column` {{_columnname_:property}}) - { - "" if table == "*" else "<-[:HAS_COLUMN]-(sdt:`Source Data Table` {_domain_:$table})" - } - MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) - """ - - for class_, properties in groupping.items(): - # EXAMPLE of class_ : "Race" - # EXAMPLE of properties: ["RACE", "RACEN"] - - params = {"table":table, "class": class_, "properties": properties} - self.query(q, params) - - # EXAMPLE1 of query (involving a specific table, such as "ADSL") - """ - MERGE (class:Class {label:$class}) - WITH * UNWIND $properties as property - MERGE (class)-[:HAS_PROPERTY]->(p:Property {label:property}) - WITH * - MATCH (sdc:`Source Data Column` {_columnname_:property}) - <-[:HAS_COLUMN]-(sdt:`Source Data Table` {_domain_:$table}) - MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) - """ - - # EXAMPLE2 of query (involving any table, indicated by the "*" value of the table variable) - """ - MERGE (class:Class {label:$class}) - WITH * UNWIND $properties as property - MERGE (class)-[:HAS_PROPERTY]->(p:Property {label:property}) - WITH * - MATCH (sdc:`Source Data Column` {_columnname_:property}) - MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) - """ - # EXAMPLE of params: {'table': 'ADSL', 'class': 'Race', 'properties': ['RACE', 'RACEN']} - - - - #################### TO DELETE RELATIONSHIP #################### - - def delete_rels(self, data) -> None: - """ - Bulk-delete the "CLASS_RELATES_TO" relationship (if present) from node pairs specified by their Neo4j IDs. - Return status information - - :param data: A list of dictionaries that contain the keys '_id_Class1' (FROM node) and '_id_Class2' (TO node) - EXAMPLE: [{'_id_Class1': 777, '_id_Class2': 123}, - {'_id_Class1': 111, '_id_Class2': 888}] - :return: None - """ - q = """ - WITH $data as data UNWIND data as row - MATCH (class1), (class2) - WHERE id(class1) = row['_id_Class1'] and id(class2) = row['_id_Class2'] - OPTIONAL MATCH (class1)-[r:CLASS_RELATES_TO]->(class2) - DELETE r - RETURN class1.label + '-->' + class2.label as mod - """ - - params = {'data': data} - - self.query(q, params) - - - - - #################### TO RETRIEVE #################### - - def get_all_classes(self, include_id=False, sort=False) -> [dict]: - """ - Get all the existing Class names, optionally including their Neo4j ID, and optionally sorted - :param include_id: If True, also include the Neo4j ID's - :param sort: If True, sort the results by name - :return: A list of dictionaries, with keys "Class" (for the name) and "_id_Class" - EXAMPLE, with include_id=False: - [{'Class': 'car'}, {'Class': 'boat'}] - EXAMPLE, with include_id=True: - [{'Class': 'car', "_id_Class": 88}, {'Class': 'boat', "_id_Class": 91}] - """ - q = ''' - MATCH (class:Class) - RETURN class.label as Class - ''' - - if include_id: - q += " , id(class) as _id_Class " - - if sort: - q += " ORDER BY class.label" - - return self.query(q) - - - - def get_label_by_id(self, neo4j_id: int) -> str: - """ - Return the value of the "label" attribute of the node with the given ID. - In case of error, return "NA" - - :param neo4j_id: Neo4j internal numeric ID to identify a node - :return: The value of the "label" attribute - """ - if type(neo4j_id) != int: - return "NA" - - q = f"MATCH (n) WHERE id(n) = {neo4j_id} RETURN n.label AS label" - result = self.query(q) - - return result[0]["label"] - - - - def get_class_properties(self, classes = None): - """ - Given a string, or list of strings, locate all the `Class` nodes with a "label" attribute matching one of those values, - and that are connected to `Property` nodes thru HAS_PROPERTY relationships. - Collect the values of the "label" attributes of all the `Property` nodes, and - turn them into a dictionary, indexed by the value of the "label" attribute of the `Class` nodes. - - :param classes: A string or list of strings. EXAMPLE: ['Study', 'Site', 'Subject'] - :return: A dictionary - """ - if self.verbose: - print (f"-- Getting class properties {classes}--") - - # If the passed argument was a string, turn into a 1-element list - if type(classes) == str: - classes = [classes] - - # Prepare a WHERE clause - wh = (f"WHERE class.label in $classes" if classes else "") - - q = f""" - MATCH (class:Class)-[:HAS_PROPERTY]->(property:Property) - {wh} - WITH * ORDER BY class, id(property) - WITH class, collect(property) as coll - RETURN apoc.map.fromPairs(collect([class.label, [x in coll | x.label]])) as mp - """ - # EXAMPLE of Cypher query constructed above: - """ - MATCH (class:Class)-[:HAS_PROPERTY]->(property:Property) - WHERE class.label in $classes - WITH * ORDER BY class, id(property) - WITH class, collect(property) as coll - RETURN apoc.map.fromPairs(collect([class.label, [x in coll | x.label]])) as mp - """ - - qres = self.query(q, {"classes": classes}) - if qres: - return qres[0]['mp'] - else: - return {} - - def get_class_short_labels(self, classes=None): - """ - Return a dictionary with class.label as keys and - values of non-NULL class.short_label values of the corresponding class as items - :param classes: - :return: - """ - q = """ - MATCH (c:Class) - WHERE c.label in $labels and c.short_label IS NOT NULL - WITH collect([c.label, c.short_label]) as coll - RETURN apoc.map.fromPairs(coll) as map - """ - res = self.query(q, {'labels': classes}) - if res: - return res[0]['map'] - else: - return {} - - - ######################### PANDAS-RELATED ######################### - - - def get_related_classes(self) -> pd.DataFrame: - """ - Locate all pairs of Classes (class1, class2) such that there is a "CLASS_RELATES_TO" - from class1 to class2. - Return their names and Neo4j ID's, as a Pandas dataframe, - with columns named _id_Class1, Class1, _id_Class2 Class2. - - :return: A Pandas dataframe - EXAMPLE: if the relationships are A->B->C and A->C, it may return - _id_Class1 Class1 _id_Class2 Class2 - 0 381 A 382 B - 1 381 A 383 C - 2 382 B 383 C - """ - q = """ - MATCH (class1:Class)-[:CLASS_RELATES_TO]->(class2:Class) - RETURN id(class1) as _id_Class1, class1.label as Class1, - id(class2) as _id_Class2, class2.label as Class2 - """ - if self.debug: - logging.debug(f""" - query: {q} - """) - - result = self.query(q) - - return pd.DataFrame(result) - - - - def load_mappings_from_df(self, df_mappings:pd.DataFrame): - """ - The method can be used for batch-loading (Class)-[]-(Property) mapping to (Source Data Column)<-[]-(Source Data Table) - with [:MAPS_TO_PROPERTY] relationship - NOTE: - - if specified Class or Property do not exist they will be created - - if values of (Source Data Table)._domain_ = '*' then columns with specified name of all datasets will be mapped - - if values of (Source Data Table)._domain_ and (Source Data Column)._columnname_ are None the Class and Property will just be created/merged - EXAMPLE input data frame - pd.DataFrame([ - {'Class':'ZZZ', 'Property':None}, - {'Class':'ZZZ', 'Property':'abc'}, - {'Class':'ZZZ', 'Property':'zyx', 'Source Data Table':'adsl', 'Source Data Column':'country'}, - {'Class':'ZZZ', 'Property':'new_property_no_mapping', 'Source Data Table':None, 'Source Data Column':'country'} - ]) - :return: - """ - q = """ - WITH $mappings as mappings UNWIND mappings as mapping - WITH mapping['Class'] as class_, collect(mapping) as class_mappings - MERGE (class:Class{label:class_}) - WITH * UNWIND class_mappings as mapping - WITH class, mapping['Property'] as property_, collect(mapping) as class_property_mappings - WHERE NOT property_ IS NULL - MERGE (class)-[:HAS_PROPERTY]->(property:Property{label:property_}) - WITH * UNWIND class_property_mappings as mapping - WITH class, property, mapping - WHERE NOT mapping['Source Data Table'] IS NULL AND NOT mapping['Source Data Column'] IS NULL - MATCH (sdt:`Source Data Table`)-[:HAS_COLUMN]->(sdc:`Source Data Column`) - WHERE sdt._domain_ = mapping['Source Data Table'] AND sdc._columnname_ = mapping['Source Data Column'] - MERGE (sdc)-[:MAPS_TO_PROPERTY]->(property) - """ - params = { - 'mappings': df_mappings.to_dict(orient='records') - } - if self.debug: - print(f""" - query: {q} - parameters: {params} - """) - self.query(q, params) diff --git a/model_managers/model_manager.py b/model_managers/model_manager.py index 4b1cdd3..911bd0b 100644 --- a/model_managers/model_manager.py +++ b/model_managers/model_manager.py @@ -529,6 +529,125 @@ def export_model_ttl(self, folder: str, filename: str, include_mappings=False): with open(rdf_file_path, "w") as file: file.write(rdf) + def create_custom_mappings_from_dict(self, groupings = None) -> None: + """ + Function to support MethodApplier(mode="schema_PROPERTY") + + Create a set of nodes labeled "Class", all taken from the groupings dictionary; their names are + stored in an attribute named "label". EXAMPLES: "Study", "Site", "Race", "Adverse Event". + + Also, create a set of nodes labeled "Property"; likewise, their names are + stored in an attribute named "label". EXAMPLES: "RACE", "RACEN", "SITEID". + + In addition, create relationships named "HAS_PROPERTY", from each of the "Class" nodes to the appropriate + "Property" nodes. EXAMPLE: The "Race" node (labeled "Class") links to the "RACE", "RACEN" nodes + (labeled "Property") + + Finally, create relationships named "MAPS_TO_PROPERTY", from `Source Data Column` nodes to `Property` nodes. + These relationships are created based on matches between the "_columnname_" attribute on `Source Data Column` nodes + and entries in the lists contained in groupings (e.g., "RACEN"); in some cases, further restrictions are applied, + requiring the `Source Data Column` node to be linked to a particular `Source Data Table` node. + + :param groupings: A dictionary. The keys are either "*" (meaning no `Source Data Table` restriction) + or the name of a specific `Source Data Table`. + The values are dictionaries such as {"Race": ["RACE", "RACEN"]} + :return: None + """ + if not groupings: + groupings = {} + + # Loop over all the keys/values of the groupings dictionary + for table, groupping in groupings.items(): + # EXAMPLES of table: "ADSL" or "*" (the star indicates "all tables") + # groupping is a dictionary with entries such as "Race": ["RACE", "RACEN"] + + # Define the Cypher query, which depends on the value of the "table" variable in the outer loop; + # for examples of how the query shapes up, see below (inside inner loop) + q = f""" + MERGE (class:Class {{label:$class}}) + WITH * UNWIND $properties as property + MERGE (class)-[:HAS_PROPERTY]->(p:Property {{label:property}}) + WITH * + MATCH (sdc:`Source Data Column` {{_columnname_:property}}) + { + "" if table == "*" else "<-[:HAS_COLUMN]-(sdt:`Source Data Table` {_domain_:$table})" + } + MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) + """ + + for class_, properties in groupping.items(): + # EXAMPLE of class_ : "Race" + # EXAMPLE of properties: ["RACE", "RACEN"] + + params = {"table":table, "class": class_, "properties": properties} + self.query(q, params) + + # EXAMPLE1 of query (involving a specific table, such as "ADSL") + """ + MERGE (class:Class {label:$class}) + WITH * UNWIND $properties as property + MERGE (class)-[:HAS_PROPERTY]->(p:Property {label:property}) + WITH * + MATCH (sdc:`Source Data Column` {_columnname_:property}) + <-[:HAS_COLUMN]-(sdt:`Source Data Table` {_domain_:$table}) + MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) + """ + + # EXAMPLE2 of query (involving any table, indicated by the "*" value of the table variable) + """ + MERGE (class:Class {label:$class}) + WITH * UNWIND $properties as property + MERGE (class)-[:HAS_PROPERTY]->(p:Property {label:property}) + WITH * + MATCH (sdc:`Source Data Column` {_columnname_:property}) + MERGE (sdc)-[:MAPS_TO_PROPERTY]->(p) + """ + # EXAMPLE of params: {'table': 'ADSL', 'class': 'Race', 'properties': ['RACE', 'RACEN']} + + def create_custom_rels_from_list(self, rels: [[str, str]], create_if_absent = False) -> None: + """ + Adds "CLASS_RELATES_TO" relationships to pairs of nodes with "Class" label, + based on the list passed as the argument "rels". + Matches occur based on node attributes named "label". + Optionally, create the Class nodes if needed. + To create just a single relationship, see create_class_relationship() + + NOTE: this is a more general version of the method create_related_classes_from_list() + + :param rels: A list of 2-element lists, indicating a relationship among nodes of type `Class` + EXAMPLE: [ + ["Study", "Site"], + ["Study", "Subject"], + ["Subject", "Race"] + ] + :param create_if_absent: If True, the Class nodes specified in the argument "rel" get created as needed; + otherwise, no relationships get created whenever their start or end class is missing + :return: None + """ + if rels is None or rels == []: + return # There's nothing to do + + if create_if_absent: + q = f""" + UNWIND $rels as rel + WITH rel[0] as left, rel[1] as right + WHERE apoc.meta.type(left) = apoc.meta.type(right) = 'STRING' + MERGE (ln:Class {{label:left}}) + MERGE (rn:Class {{label:right}}) + MERGE (ln)-[:CLASS_RELATES_TO]->(rn) + """ + else: # The Class nodes MUST be present, or no relationship gets created + q = f""" + UNWIND $rels as rel + WITH rel[0] as left, rel[1] as right + WHERE apoc.meta.type(left) = apoc.meta.type(right) = 'STRING' + MATCH (ln:Class {{label:left}}), (rn:Class {{label:right}}) + MERGE (ln)-[:CLASS_RELATES_TO]->(rn) + """ + + params = {"rels": rels} + self.query(q, params) + def create_model_from_data( self, data_label: str = "Source Data Row", diff --git a/query_builders/archive/query_builder.py b/query_builders/archive/query_builder.py deleted file mode 100644 index 1387099..0000000 --- a/query_builders/archive/query_builder.py +++ /dev/null @@ -1,600 +0,0 @@ -from neointerface import NeoInterface -from model_managers.model_manager import ModelManager -import pandas as pd - - -class QueryBuilder(NeoInterface): - """ - To support creation of cypher queries to work with data in Neo4j - - Supports 2 modes: - 'schema_PROPERTY' - generating query for fetching data based on definitions and relationships between metadata - nodes(such as Class and Property) - 'schema_CLASS' - generating query for fetching data based on definitions and relationships between metadata - nodes(where columns are mapped to Classes and no Property nodes defined) - 'noschema' - generating query for fetching data based on all existing nodes and relationships in the database - """ - OCLASS_MARKER = "**" - RDFSLABEL = "rdfs:label" - def __init__(self, mode='schema_PROPERTY', allow_optional_classes=True, *args, **kwargs): - """ - :param mode: 'schema_PROPERTY' or 'schema_CLASS' or 'noschema' - :param args: - :param kwargs: - """ - assert mode in ['schema_PROPERTY', 'schema_CLASS', 'noschema'] - self.mode = mode - self.allow_optional_classes = allow_optional_classes - if self.mode in ['schema_PROPERTY', 'schema_CLASS']: - self.mm = ModelManager(*args, **kwargs) - else: - self.mm = None - # self.bindings = {} - super().__init__(*args, **kwargs) - if self.verbose: - print(f"---------------- {self.__class__} initialized -------------------") - - # ----------------------------------------------------------- - # ------------------------ Core Method ---------------------- - # ----------------------------------------------------------- - def generate_query_body(self, classes: list, where_map=None, allow_unrelated_subgraphs=False): - """ - Generates query body based on self.mode - Takes care about optional classes - :param classes: - :param where_map: - :return: - """ - if not where_map: - where_map = {} - # classes with a postfix ** are considered optional for matching - separating general and optional classes - g_classes, g_opt_classes = self.split_out_optional_classes(classes) - # separating classes that are in where clause (to go first if the query) - wg_classes = [class_ for class_ in g_classes if class_ in where_map.keys()] - - if self.mode in ['schema_PROPERTY', 'schema_CLASS']: - f = self.qb_generate_query_body - else: - f = self.qbns_generate_query_body - - if self.allow_optional_classes and g_opt_classes: - # first part - classes from the where statement - (wg_cypher, wg_data_dict) = ("", {}) - if wg_classes: - wg_where_map = {k: i for k, i in where_map.items() if k in wg_classes} - (wg_cypher, wg_data_dict) = f(classes=wg_classes, where_map=wg_where_map) - - # second part - all other non-optional classes - (g_cypher, g_data_dict) = f(classes=[class_ for class_ in g_classes if class_ not in wg_classes], - classes_for_rel=g_classes, - where_map={}) - # case when all classes are present also in the where_map - if g_cypher.strip() == "MATCH": - g_cypher = "" - - # third part - optional classes - o_cyphers = [] - o_data_dict = {} - # 1 OPTIONAL MATCH statement per optional class (considering they are all allow to exist/non-exist independently) - for oc in g_opt_classes: - oc_where_map = ({oc: where_map[oc]} if oc in where_map.keys() else {}) - (oc_cypher, oc_data_dict) = f(classes=[oc], - classes_for_rel=g_classes + [oc], - where_map=oc_where_map) - o_cyphers.append(oc_cypher) - o_data_dict = {**o_data_dict, **oc_data_dict} - # building query and dictionaries together - return ( - (wg_cypher.strip() + ' \n' + 'WITH * \n' if wg_cypher else "") + - g_cypher.strip() + ' \n' + - ''.join(['OPTIONAL ' + c_chunk.strip() + ' \n' for c_chunk in o_cyphers]), - {**wg_data_dict, **o_data_dict} - ) - else: - (wg_cypher, wg_data_dict) = ("", {}) - if wg_classes: - wg_where_map = {k: i for k, i in where_map.items() if k in wg_classes} - (wg_cypher, wg_data_dict) = f(classes=wg_classes, where_map=wg_where_map) - - (g_cypher, g_data_dict) = f(classes=[class_ for class_ in g_classes if class_ not in wg_classes], - classes_for_rel=g_classes, - where_map={}) - # case when all classes are present also in the where_map - if g_cypher.strip() == "MATCH": - g_cypher = "" - return ( - (wg_cypher.strip() + ' \n' + 'WITH * \n' if wg_cypher else "") + g_cypher.strip(), - {**wg_data_dict, **g_data_dict} - ) - - # ----------------------------------------------------------- - # ----------- General methods (regardless of mode) --------- - # ----------------------------------------------------------- - def split_out_optional_classes(self, classes: list) -> (list, list): - """ - Checks if class name ends with optional class marker and splits classes into usual and optional - :param classes: list of class names - :return: tuple of lists ([normal classes], [optional classes]) - """ - c, oc = [], [] - for class_ in classes: - if class_.endswith(self.OCLASS_MARKER): - oc.append(class_[:-(len(self.OCLASS_MARKER))]) - else: - c.append(class_) - return c, oc - - # # TODO: implement list dict of bindings instead of using lower-case label (for cases when different bindings need to be assinged to the same class - # def append_binding(self, label): - # if label not in self.bindings.keys(): - # self.bindings[label] = 'b' + str(len(self.bindings)) - - def list_data_labels(self, classes: list) -> list: - """ - Helper function, to produce a list that will be used to form the "MATCH" part of a Cypher query. - - EXAMPLE: The input list ['Class 1', '$$$'] results in ['(`class 1`:`Class 1`)', '(`$$$`:`$$$`)'] - The lower-case versions of the class names are meant to be placeholder for Neo4j nodes, - in a downstream Cypher query. - - :param classes: List of strings (class names) - :return: A list of strings (meant to be later used to form a Cypher query) - """ - # for label in classes: - # self.append_binding(label) - # return [f"(`{self.bindings[label]}`:`{label}`)" for label in classes] - return [f"(`{label.lower()}`:`{label}`)" for label in classes] - - def list_where_conditions_per_dict(self, mp: dict) -> ([], {}): - """ - Given a dictionary of dictionaries (see below for example), loop thru all the entries - and produce a list of strings, each of them suitable for inclusion in WHERE clauses in Cypher, - together with a data-binding dictionary. - - The keys in the outer dictionary are expected to be node labels. - The (key/values) in the inner dictionary entries are meant to be (attribute names/desired values) that - are applicable to the node with their corresponding label. - - EXAMPLE - if the argument is: - { - 'CAR': { - 'year': 2021 - }, - 'BOAT': { - 'make': 'Jeanneau' - } - } - - then the goal is to enforce that the 'year' property for 'CAR' nodes has a value of 2021, - and that the 'make' property for 'BOAT' nodes has a value of 'Jeanneau'. - The above requirements are encoded in the following list of strings: - - ["`car`.`year` = $par_1", "`boat`.`make` = $par_2"] - - in conjunction with the following data dictionary: - - {"par_1": 2021 , "par_2": 'Jeanneau'} - - Notice that the label names are turned to lower case, - and that backticks are used in all the label and attributes names - (which allows for blank spaces in the final Cypher code). - - :param mp: A dictionary of dictionaries. EXAMPLE: - { - 'SUBJECT': { - 'USUBJID': '01-001', - 'SUBJID': '001', - 'PATIENT GROUP': [3, 5] - }, - 'SEX': { - 'ASEX': 'Male' - } - } - - - The keys in the outer dictionary are expected to be node labels. - - The (key/values) in the inner dictionary entries are meant to be (attribute names : desired values) - that are applicable to the node with their corresponding label. - - The values may be various data type, incl. strings, integers and lists. - - :return: The pair (list_of_Cypher_strings , data_dictionary) - - Each string in the list is of the form - "`label_name`.`attribute_name` = $par_N" - - where label_name is always in lower case, and N is an integer. - EXAMPLE: ["`subject`.`USUBJID` = $par_1", - "`subject`.`SUBJID` = $par_2", - "`subject`.`PATIENT GROUP` in $par_3", <- NOTE: it's "in" rather than equal because $par3 is a list - "`sex`.`ASEX` = $par_4"] - - EXAMPLE of data dictionary: {"par_1": "01-001" , "par_2": "001", "par_3": [3, 5], "par_4": "Male"} - """ - cypher_list = [] - data_dictionary = {} - - def parameter_labels(): # Generates sequential integers used in the data dictionary, such as "par_1", "par_2", etc. - k = 1 - while True: - yield f"par_{k}" - k += 1 - - parameter_token_stack = parameter_labels() - - # Loop over the outer dictionary - for label, property_dict in mp.items(): - # EXAMPLE: label = 'SUBJECT' , property_dict = {'USUBJID': '01-001','SUBJID': '001', 'PATIENT GROUP': [3, 5]} - - # Loop over the inner dictionary - for property_name, property_value in property_dict.items(): - # EXAMPLE: property_name = 'USUBJID' , property_value = '01-001' - - # Handle ranges - # EXAMPLE: {"Age": {"AGE": {"min": 18, "max": 65, "max_include": False, "min_include": True, "incl_null": True}}} - if isinstance(property_value, dict) and set(property_value.keys()).intersection( - {"min", "max", "min_include", "max_include", "incl_null"}): - - max_include = property_value.get("max_include", False) - min_include = property_value.get("min_include", False) - incl_null = property_value.get("incl_null") #if None then the clause is not included at all - - t1, t2 = next(parameter_token_stack), next(parameter_token_stack) - data_dictionary[t1], data_dictionary[t2] = property_value.get("min"), property_value.get("max") - min_max_subclause_list = [] - if data_dictionary[t1]: - min_max_subclause_list.append(f"${t1} {'<=' if min_include else '<'}") - if data_dictionary[t1] or data_dictionary[t2]: - min_max_subclause_list.append(f"`{label.lower()}`.`{property_name}`") - if data_dictionary[t2]: - min_max_subclause_list.append(f"{'<=' if max_include else '<'} ${t2}") - - if incl_null is None: - include_nulls_list = [] - elif incl_null: - include_nulls_list = [f"`{label.lower()}`.`{property_name}` IS NULL"] - if min_max_subclause_list: - include_nulls_list.append("OR") - else: - include_nulls_list = [f"`{label.lower()}`.`{property_name}` IS NOT NULL"] - if min_max_subclause_list: - include_nulls_list.append("AND") - - full_str = " ".join(include_nulls_list + ( - ['(' + " ".join(min_max_subclause_list) + ')'] if min_max_subclause_list else [])) - if include_nulls_list and min_max_subclause_list: - full_str = f"({full_str})" - if full_str: - cypher_list.append(full_str) - else: - operator = ("in" if type( - property_value) == list else "=") # For list inclusions, use "in"; in all other case check for equality - - # Extend the list of Cypher strings and their corresponding data dictionary - t = next(parameter_token_stack) - if label.startswith("!"): # ! is NOT operator - cypher_list.append(f"""NOT (`{label.lower()[1:]}`.`{property_name}` {operator} ${t})""") # The $ refers to the data binding - else: - cypher_list.append(f"`{label.lower()}`.`{property_name}` {operator} ${t}") - data_dictionary[t] = property_value - - return cypher_list, data_dictionary - - def generate_return(self, - classes: list, - return_disjoint: bool = False, - return_nodeid: bool = False, - return_properties: str = "*", - prefix_keys_with_label:bool = False, - ) -> (str, dict): - """ - Helper function for get_data() and for _get_filters_helper(). - Compose and return a string suitable for the RETURN statement of a Cypher query to populate tables and menus on the dashboard. - Used when we have a schema with Classes and Properties. - - EXAMPLES - all based on the class list ['Study', 'Site'], with various arguments: - - "RETURN apoc.map.mergeList([`study`, `site`]) as all" - "RETURN id(`study`) as `Study`, id(`site`) as `Site`, apoc.map.mergeList([`study`, `site`]) as all" - "RETURN collect(distinct `study`{.*}) as `Study`, collect(distinct `site`{.*}) as `Site`" - "RETURN collect(distinct {`Study`:id(`study`)}) as `Study`, collect(distinct {`Site`:id(`site`)}) as `Site`" - - :param classes: List of strings. EXAMPLE: ['Study', 'Site']. If empty, an Exception is raised. - :param return_disjoint: If True, the result will contain a term for each class, such as "collect(distinct `study`{.*}) as `Study`" - The final goal is a Cypher query to produce a dictionary of dataframes, to populate the - menus in the dashboard. - EXAMPLE: "RETURN collect(distinct `study`{.*}) as `Study`, collect(distinct `site`{.*}) as `Site`" - If False, the result contains the apoc.map.mergeList function, to produce data - for the tables in the dashboard - EXAMPLE: "RETURN apoc.map.mergeList([`study`, `site`]) as all" - - :param return_nodeid: If True, also include in the result, just after the "RETURN " part, - a string used to return the id's of all the classes. - EXAMPLE: "id(`study`) as `Study`, id(`site`) as `Site`" - :param return_properties: A string (default value "*") TODO: only the "*" option is currently implemented - :param prefix_keys_with_label: If True adds a prefix (corresponding node label) to each column name of the returned data - :param rename_rdfslabel: If True renames all properties named rdfs:label to value of corresponding Class.short_label - :return: A string - """ - assert type(classes) == list, "ERROR in qb_generate_return(): the argument `classes` must be a list" - assert classes != [], "ERROR in qb_generate_return(): empty lists are not an acceptable argument for `classes`" - assert return_properties == "*" or type(return_properties) == list - data_dictionary = {} - all_classes = [(class_[:-len(self.OCLASS_MARKER)] if class_.endswith(self.OCLASS_MARKER) else class_) - for class_ in classes] - if self.mode == 'schema_CLASS': - short_labels = self.mm.get_class_short_labels(classes=all_classes) - data_dictionary = {**data_dictionary, **{'rename_keys': short_labels}} - if self.allow_optional_classes: - classes = all_classes - return_items = {key: [] for key in classes} - for label in classes: - if return_nodeid: - item_str = f"{{`{label}`:id(`{label.lower()}`)}}" - return_items[label].append(item_str) - item_str = f'`{label.lower()}`{{.*}}' - # item_str = f'apoc.map.clean({item_str},[],[NULL])' - item_str = f'CASE WHEN {item_str} IS NULL THEN {{}} ELSE {item_str} END' - if self.mode == 'schema_CLASS' and prefix_keys_with_label: - item_str = f''' - apoc.map.fromPairs( - [key in keys({item_str}) | - [ - "{label}." + CASE WHEN key = 'rdfs:label' THEN $rename_keys["{label}"] ELSE key END - , - ({item_str})[key] - ] - ] - ) - ''' - elif self.mode == 'schema_CLASS': - item_str = f''' - apoc.map.fromPairs([key in keys({item_str}) | [ - CASE WHEN key = '{self.RDFSLABEL}' THEN $rename_keys['{label}'] ELSE key END, {item_str}[key]]]) - ''' - elif prefix_keys_with_label: - item_str = f'apoc.map.fromPairs([key in keys({item_str}) | ["{label}." + key, {item_str}[key]]])' - if return_properties != "*": - submap_keys = "[" + ", ".join([f"'{key}'" for key in return_properties]) + "]" - item_str = f'apoc.map.clean(apoc.map.submap({item_str}, {submap_keys}, NULL, False),[],[NULL])' - return_items[label].append(item_str) - - if return_disjoint: # Note: this is the branch followed when this function is used by _get_filters_helper() - return "RETURN " + "\n, ".join([f"collect(distinct apoc.map.mergeList([{', '.join(item)}])) as `{label}`" - for label, item in return_items.items()]), data_dictionary - else: # return_disjoint is False - items = [item for key, item in return_items.items()] - items_flat = [item for sublist in items for item in sublist] - if self.debug: - print(items_flat) - return "RETURN apoc.map.mergeList([" + '\n, '.join(items_flat) + "]) as all", data_dictionary - - # ----------------------------------------------------------- - # ------------- Methods for mode == 'schema_PROPERTY' ---------------- - # ----------------------------------------------------------- - def qb_list_data_relationships_per_schema(self, - classes: list, - classes_in_pair=None, - opt_rel_postix=None, - allow_unrelated_subgraphs=False): - """ - Adapted from DataProvider._generate_match_relationships_per_schema() - - From the given list of Classes, and the "CLASS_RELATES_TO" relationships among them in the database, - - - It looks for `Class`-labeled nodes with "label" attributes having the values in the passed "classes" list, - and for "CLASS_RELATES_TO" relationships among them... - then it creates and returns a list of strings meant for later use in a Cypher query. - - EXAMPLE: if there are 2 `Class`-labeled nodes, - one with a "label" attribute whose value is "car", and one "vehicle", - as well as a "CLASS_RELATES_TO" relationship from the car to the vehicle node... - then it returns the list - ['(`car`)-[:`HAS_VEHICLE`]->(`vehicle`)', - '(`car`)', - '(`vehicle`)'] - - :param classes: List of strings. EXAMPLE: ['Study', 'Site', 'Subject'] - :param classes_in_pair: None or list of strings. If the parameter is set then the specified classes must be - present in each pair of classes in (a:Class)-[r:CLASS_RELATES_TO]->(b:Class) relationship - :param opt_rel_postix: Optional postfix to be added to relationship type name - :param allow_unrelated_subgraphs: - :return: A (possibly empty) list of strings (meant to be later used to form a Cypher query) - """ - relpostfix = "+ '`|`' + 'HAS_' + toUpper(coll[1]) + f'_{opt_rel_postix}'" if opt_rel_postix else "" - # e.g. opt_rel_postix = 'POOLED' is used for Data Displays metadata - - if not allow_unrelated_subgraphs: - q_unrel = """ - MATCH (c1:Class), (c2:Class) - WHERE - c1.label in $labels and c2.label in $labels - AND - id(c1)>id(c2) - WITH collect([c1,c2]) AS coll UNWIND coll AS item - WITH coll, item[0] as c1, item[1] as c2 - CALL apoc.path.expandConfig( - c1, - { - uniqueness:'RELATIONSHIP_GLOBAL', - relationshipFilter:'CLASS_RELATES_TO|0 - WITH coll, collect([c1,c2]) AS coll2 - WITH apoc.coll.subtract(coll,coll2) AS sub UNWIND sub AS unrelated - RETURN unrelated[0]['label'] as c1, unrelated[1]['label'] as c2 - """ - param_unrel = {"labels": list(classes)} - res_unrel = self.query(q_unrel, param_unrel) - assert len(res_unrel) == 0, f"Provided classes are not all related: {classes}" - - # generating the match relationship part of the query (for that we need to subquery) - ##optional part - q_classes_in_pair = ("AND (a.label in $rightLabels or b.label in $rightLabels)" if classes_in_pair else "") - dict_classes_in_pair = ({"rightLabels": classes_in_pair} if classes_in_pair else {}) - ##mandatory part - subq0 = f""" - //extracting from schema which classes($labels provided) are related to each other - //if a subclass of a class is related to another class in means that the parent class is also related - MATCH (a:Class), (b:Class) - WHERE a.label in $labels and b.label in $labels {q_classes_in_pair} - AND EXISTS ( (a)-[:SUBCLASS_OF*0..50]->()-[:CLASS_RELATES_TO]->()<-[:SUBCLASS_OF*0..50]-(b)) - MATCH p = (a)-[:SUBCLASS_OF*0..50]->()-[r:CLASS_RELATES_TO]->()<-[:SUBCLASS_OF*0..50]-(b) - WITH [a.label, b.label, r.relationship_type] as coll - ORDER BY coll[0], coll[1] - WITH collect(coll) as collp - RETURN collp - """ - collp = self.query(subq0, {**{"labels": list(classes)}, **dict_classes_in_pair})[0]['collp'] - - if collp: - subq = f""" - WITH - reduce( - acc=[], - coll in $collp | - //acc + ['(`' + $bindings[coll[0]] + '`' + ')' + - acc + ['(`' + toLower(coll[0]) + '`' + ')' + - case when size(coll) = 3 then '-[:`' + - CASE WHEN coll[2] IS NULL THEN ('HAS_' + toUpper(coll[1]) {relpostfix}) ELSE coll[2] END + - '`]->(`' + toLower(coll[1]) + '`)' - else '' end] - ) as q - // looping over the list of lists and accumulating the query step by step - // WARNING! it is possible that it actually needs to loop over Cartesian product as this way not all schema relationship may be captured - return q - """ - # return self.query(subq, {"collp": collp, "bindings": self.bindings})[0]['q'] - return self.query(subq, {"collp": collp})[0]['q'] - else: - return [] - - def qb_generate_query_body(self, - classes: list, - classes_for_rel="*", - where_map=None, - allow_unrelated_subgraphs=False) -> (str, {}): - """ - Helper function for get_data() - Compose and return a string suitable for the MATCH (and optionally the WHERE) part of a Cypher string - exclusive - of the RETURN statement. - Used when we have a schema with Classes and Properties. - - EXAMPLE: 2 `Class` nodes ['Study', 'Site'] and a "CLASS_RELATES_TO" relationship between them, - will result in the following string: - "MATCH (`site`:`Site`), (`study`:`Study`), (`site`), (`study`)-[:`HAS_SITE`]->(`site`), (`study`)" - - NOTE about the redundant part about having (`site`:`Site`) as well as (`site`): - "was just easier to implement it this way and it does not impact the result. Can be updated in the future" - - :param classes: List of strings. EXAMPLE: ['Study', 'Site'] - :param classes_for_rel: '*' or list of strings. if '*' then classes_for_rel considered to be equal to classes. - classes_for_rel are used for generation of relationships via qb_list_data_relationships_per_schema. - typical use-case with classes_for_rel != '*' - for generation of OPTIONAL MATCH chunks of query - :param where_map: A dictionary of dictionaries. SEE explanation in list_where_conditions_per_dict() - :return: A pair consisting of a Cypher string and a data dictionary to run that Cypher query - """ - assert (classes_for_rel == "*") or (type(classes_for_rel) == list) - if classes_for_rel == "*": - classes_for_rel = classes - - match_node_list = self.list_data_labels(classes) - # EXAMPLE: ['(`study`:`Study`)', '(`site`:`Site`)', '(`subject`:`Subject`)'] - - match_relationships_per_schema = \ - self.qb_list_data_relationships_per_schema( - classes=classes_for_rel, - # the set of classes for relationships is usually larger the one for matching nodes in the OPTIONAL MATCH statement folloing MATCH statement - classes_in_pair=classes, - # one of these classes must be present in each pair of CLASS_RELATES_TO to relationship - allow_unrelated_subgraphs=allow_unrelated_subgraphs - ) - # EXAMPLE: ['(`site`)-[:`HAS_SUBJECT`]->(`subject`)', - # '(`site`)', - # '(`study`)-[:`HAS_SITE`]->(`site`)', - # '(`study`)-[:`HAS_SUBJECT`]->(`subject`)', - # '(`study`)', - # '(`subject`)'] - - wh = "" - data_dictionary = {} - if where_map: - (list_of_Cypher_strings, data_dictionary) = self.list_where_conditions_per_dict(where_map) - wh = f"WHERE {' AND '.join(list_of_Cypher_strings)}" - - q = "MATCH " + "\n,".join(match_node_list + match_relationships_per_schema) + " \n" + wh - return (q, data_dictionary) - - # ----------------------------------------------------------- - # ------------- Methods for mode == 'noschema' -------------- - # ----------------------------------------------------------- - def qbns_get_label_relationships_df(self, classes: list): - """ - :param classes: list of labels to process - :return: pd.DataFrame(columns=['souce_lbl', 'rel', 'target_lbl']) with all existing relationships between - nodes having labels provided in classes list - """ - # TODO: assess risk that sample = 100000 is not enough - q = """ - CALL apoc.meta.data({includeLabels:$classes, sample:100000}) - YIELD label as souce_lbl, type, elementType, property as rel, other - WHERE elementType = "node" and type = "RELATIONSHIP" - UNWIND other as target_lbl - WITH souce_lbl, rel, target_lbl - WHERE target_lbl in $classes and souce_lbl in $classes - RETURN * - """ - params = {'classes': classes} - if self.debug: - print(" Query : ", q) - print(" Query parameters: ", params) - return pd.DataFrame(self.query(q, params)) - - def qbns_list_data_relationships(self, classes: list, allow_unrelated_subgraphs=False): - assert allow_unrelated_subgraphs == False # TODO implement for allow_unrelated_subgraphs==False - # for label in classes: - # self.append_binding(label) - res = [] - for i, row in self.qbns_get_label_relationships_df(classes).iterrows(): - # res.append(f"(`{self.bindings[row['souce_lbl']]}`:`{row['souce_lbl']}`)-" - # f"[:`{row['rel']}`]->(`{self.bindings[row['target_lbl']]}`:`{row['target_lbl']}`)") - res.append(f"(`{row['souce_lbl'].lower()}`:`{row['souce_lbl']}`)-" - f"[:`{row['rel']}`]->(`{row['target_lbl'].lower()}`:`{row['target_lbl']}`)") - return res - - def qbns_generate_query_body(self, - classes: list, - classes_for_rel='*', - where_map=None, - allow_unrelated_subgraphs=False): - assert classes_for_rel == "*" or type(classes_for_rel) == list - if classes_for_rel == "*": - classes_for_rel = classes - - wh = "" - data_dictionary = {} - if where_map: - (list_of_Cypher_strings, data_dictionary) = self.list_where_conditions_per_dict(where_map) - wh = f"WHERE {' AND '.join(list_of_Cypher_strings)}" - - match_node_list = self.list_data_labels(classes) - # EXAMPLE: ['(`study`:`Study`)', '(`site`:`Site`)', '(`subject`:`Subject`)'] - - match_relationships = self.qbns_list_data_relationships(classes_for_rel) - # EXAMPLE: ['(`site`)-[:`HAS_SUBJECT`]->(`subject`)', - # '(`study`)-[:`HAS_SITE`]->(`site`)'] - - q = "MATCH " + "\n,".join(match_node_list + match_relationships) + " \n" + wh - - wh = "" - data_dictionary = {} - if where_map: - (list_of_Cypher_strings, data_dictionary) = self.list_where_conditions_per_dict(where_map) - wh = f"WHERE {' AND '.join(list_of_Cypher_strings)}" - - return (q, data_dictionary) diff --git a/setup.py b/setup.py index 5c988d8..d8a5157 100644 --- a/setup.py +++ b/setup.py @@ -32,7 +32,7 @@ def read_text(file_name: str): name="tab2neo", # This is the name of the package version="1.1.0.0", # Release.Major Feature.Minor Feature.Bug Fix author="Alexey Kuznetsov", # Full name of the author - description="Clinical Linked Data: High-level Python classes to load, model and fetch and enrich data in Neo4j database", + description="Clinical Linked Data: High-level Python classes to load, model and reshape tabular data imported into Neo4j database", long_description=long_description, # Long description read from the the readme file long_description_content_type="text/markdown", packages=setuptools.find_packages(include=[ diff --git a/tests/test_data_providers/_archive_test_data_provider.py b/tests/test_data_providers/_archive_test_data_provider.py deleted file mode 100644 index 0d466c5..0000000 --- a/tests/test_data_providers/_archive_test_data_provider.py +++ /dev/null @@ -1,494 +0,0 @@ -import json -import os -filepath = os.path.dirname(__file__) -import pytest -from data_providers import data_provider -import pandas as pd -from utils.utils import compare_unordered_lists - - -# Provide a DataProvider object (which contains a database connection) -# that can be used by the various tests that need it -@pytest.fixture(scope="module") -def dp(): - dp = data_provider.DataProvider(verbose=False) - yield dp - - - -###################### TESTS FOR DATA RETRIEVAL ###################### - - -def test_get_data(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['Subject', 'Treatment']]) - assert my_classes == ['Subject', 'Treatment'] - - dp.qb.mm.create_property('Subject', 'USUBJID') - # This time, we have 2 Properties for Treatment - dp.qb.mm.create_property('Treatment', 'TRT01A') - dp.qb.mm.create_property('Treatment', 'TRT01AN', merge=False) - cypher = "CREATE (:Subject {USUBJID:'1234'})-[:`HAS_TREATMENT`]->(:Treatment {TRT01A:'Placebo', TRT01AN:2.0})" - dp.query(cypher) - - df = dp.get_data(my_classes) - # Note: the new defaults are now return_nodeid=True, and prefix_keys_with_label=True - - # It returns a dataframe such as (where 23 is the Neo4j of the `Subject` node, and 24 that of the `Treatment` node): - ''' - Subject.USUBJID Subject Treatment.TRT01A Treatment.TRT01AN Treatment - 0 1234 23 Placebo 2.0 24 - ''' - assert len(df) == 1 - result = dp.get_nodes("Subject", return_nodeid=True) - subject0_id = result[0]["neo4j_id"] - result = dp.get_nodes("Treatment", return_nodeid=True) - treatment0_id = result[0]["neo4j_id"] - - expected_df = pd.DataFrame( [["1234", "Placebo", 2.0, subject0_id, treatment0_id]], - columns = ["Subject.USUBJID", "Treatment.TRT01A", "Treatment.TRT01AN", "Subject", "Treatment"]) - - assert df.sort_index(axis=1).equals(expected_df.sort_index(axis=1)) # Compare regardless of column order - - - # Add a 2nd data point, with the same schema - cypher = "CREATE (:Subject {USUBJID:'9876'})-[:`HAS_TREATMENT`]->(:Treatment {TRT01A:'Active', TRT01AN:1.0})" - dp.query(cypher) - df = dp.get_data(my_classes) - # Dataframe such as (the numbers in the Subject and Treatment columns will vary): - ''' - Subject.USUBJID Subject Treatment.TRT01A Treatment.TRT01AN Treatment - 0 1234 23 Placebo 2.0 24 - 1 9876 25 Active 1.0 26 - ''' - assert len(df) == 2 - result = dp.get_nodes("Subject", return_nodeid=True, properties_condition={"USUBJID": "9876"}) - subject1_id = result[0]["neo4j_id"] - - result = dp.get_nodes("Treatment", return_nodeid=True, properties_condition={"TRT01A": "Active"}) - treatment1_id = result[0]["neo4j_id"] - - expected_df.loc[1] = ["9876", "Active", 1.0, subject1_id, treatment1_id] - assert df.sort_index(axis=1).equals(expected_df.sort_index(axis=1)) # Compare regardless of column order - - - # Now retrieve the same data, but with conditions - - df = dp.get_data(my_classes, where_map = {'Treatment': {'TRT01A': 'Active'}}) - ''' - Subject.USUBJID Subject Treatment.TRT01A Treatment.TRT01AN Treatment - 0 9876 25 Active 1.0 26 - ''' - assert len(df) == 1 - - expected_df = pd.DataFrame( [["9876", subject1_id, "Active", 1.0, treatment1_id]], - columns = ["Subject.USUBJID", "Subject", "Treatment.TRT01A", "Treatment.TRT01AN", "Treatment"]) - # Use the IDs from the 2nd row of the previous dataset - - assert df.sort_index(axis=1).equals(expected_df.sort_index(axis=1)) # Compare regardless of column order - - - # Add a 3rd data point, with the same schema - cypher = "CREATE (:Subject {USUBJID:'555'})-[:`HAS_TREATMENT`]->(:Treatment {TRT01A:'Active', TRT01AN:1.0})" - dp.query(cypher) - df = dp.get_data(my_classes) - # Dataframe such as (the numbers in the Subject and Treatment columns will vary): - ''' - Subject.USUBJID Subject Treatment.TRT01A Treatment.TRT01AN Treatment - 0 1234 122 Placebo 2.0 123 - 1 9876 124 Active 1.0 125 - 2 555 126 Active 1.0 127 - ''' - # Retrieve the same data with a double condition that leads back to the same row from the last data fetch - df = dp.get_data(my_classes, where_map = {'Treatment': {'TRT01A': 'Active'}, 'Subject': {'USUBJID': '9876'}}) - assert len(df) == 1 - assert df.sort_index(axis=1).equals(expected_df.sort_index(axis=1)) # Compare regardless of column order - - - -def test_get_data_generic_prefix_label(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['Appl e', 'fruit']]) - dp.query("MATCH (c:Class) MERGE (c)-[:HAS_PROPERTY]->(:Property{label:'label'})") - - # Now expand the database just created above - cypher = "CREATE (a:`Appl e` {label:'app le'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'}) RETURN id(a) as a_id, id(f) as f_id" - dp.debug=True - nodeids = dp.query(cypher) - - result = dp.get_data_generic(my_classes, prefix_keys_with_label=True, return_nodeid=False) - print('result:', result) - df = pd.DataFrame({ - 'Appl e.label': ['app le'], - 'fruit.label': ['fruit']}) - assert df.equals(result) - - - -def test_get_data_generic_prefix_label_and_nodeid(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['Appl e', 'fruit']]) - dp.query("MATCH (c:Class) MERGE (c)-[:HAS_PROPERTY]->(:Property{label:'label'})") - - # Now expand the database just created above - cypher = "CREATE (a:`Appl e` {label:'app le'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'}) RETURN id(a) as a_id, id(f) as f_id" - dp.debug=True - nodeids = dp.query(cypher) - - result = dp.get_data_generic(my_classes) - print('result:', result) - df = pd.DataFrame({ - 'Appl e.label': ['app le'], - 'Appl e': [nodeids[0]['a_id']], - 'fruit.label': ['fruit'], - 'fruit': [nodeids[0]['f_id']]}) - assert df.equals(result) - - - -def test_get_data_generic_helper(dp): - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - - # Add 2 Class nodes, with a relationship between them - my_classes = dp.qb.mm.create_related_classes_from_list([['apple', 'fruit']]) - - (cypher, data_dict) = dp._get_data_generic_helper(my_classes, return_nodeid=False, prefix_keys_with_label=False) - expected = '''MATCH (`apple`:`apple`) -,(`fruit`:`fruit`) -,(`apple`)-[:`HAS_FRUIT`]->(`fruit`) RETURN apoc.map.mergeList([CASE WHEN `apple`{.*} IS NULL THEN {} ELSE `apple`{.*} END -, CASE WHEN `fruit`{.*} IS NULL THEN {} ELSE `fruit`{.*} END]) as all LIMIT 20''' - - assert cypher.strip() == expected - assert data_dict == {'labels': ['apple', 'fruit']} - - - # Add 2 data nodes, with a relationship between them - cypher = "CREATE (:apple {label:'apple'})-[:`HAS_FRUIT`]->(:fruit {label:'fruit'})" - dp.query(cypher) - - (cypher, data_dict) = dp._get_data_generic_helper(my_classes, return_nodeid=False, prefix_keys_with_label=False) - - expected = '''MATCH (`apple`:`apple`),(`fruit`:`fruit`),(`apple`)-[:`HAS_FRUIT`]->(`fruit`) RETURN apoc.map.mergeList([CASE WHEN `apple`{.*} IS NULL THEN {} ELSE `apple`{.*} END, CASE WHEN `fruit`{.*} IS NULL THEN {} ELSE `fruit`{.*} END]) as all LIMIT 20''' - - assert cypher.replace("\n", "").strip() == expected - assert data_dict == {'labels': ['apple', 'fruit']} - - - -def test_get_data_generic(dp): - # Preparing data, part 1 : create 2 `Class` nodes, with a "CLASS_RELATES_TO" relationship between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['EMPLOYEE', 'DEPARTMENT']]) - df = dp.get_data(my_classes) - assert df.empty # Too soon in the data-building process - - # Preparing data, part 2 : attach a property node to each of the Class nodes - dp.qb.mm.create_property('EMPLOYEE', 'Name') - dp.qb.mm.create_property('DEPARTMENT', 'Budget') - df = dp.get_data(my_classes) - assert df.empty # Still too soon in the data-building process - - # Preparing data, part 3 : add 2 data nodes (instances of the above classes), with a suitable relationship between them - cypher = "CREATE (:EMPLOYEE {Name:'John Brown'})-[:`HAS_DEPARTMENT`]->(:DEPARTMENT {Budget:150000})" - dp.query(cypher) - - df = dp.get_data_generic(my_classes, return_nodeid=False, prefix_keys_with_label=False) - print(df) - expected_df = pd.DataFrame([[150000, "John Brown"]], columns = ["Budget", "Name"]) - assert df.equals(expected_df) - - - -def test_get_data_generic_2(dp): - # Prepare the data, as in test_get_data() - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['Subject', 'Treatment']]) - dp.qb.mm.create_property('Subject', 'USUBJID') - # This time, we have 2 Properties for Treatment - dp.qb.mm.create_property('Treatment', 'TRT01A') - dp.qb.mm.create_property('Treatment', 'TRT01AN', merge=False) - cypher = "CREATE (:Subject {USUBJID:'1234'})-[:`HAS_TREATMENT`]->(:Treatment {TRT01A:'Placebo', TRT01AN:2.0})" - dp.query(cypher) - - df = dp.get_data_generic(my_classes, return_nodeid=False, prefix_keys_with_label=False) - # Dataframe: - ''' - USUBJID TRT01A TRT01AN - 0 1234 Placebo 2.0 - ''' - expected_df = pd.DataFrame([["1234", "Placebo", 2.0]], columns = ["USUBJID", "TRT01A", "TRT01AN"]) - assert df.equals(expected_df) - - # Add a 2nd data point, with the same schema - cypher = "CREATE (:Subject {USUBJID:'9876'})-[:`HAS_TREATMENT`]->(:Treatment {TRT01A:'Active', TRT01AN:1.0})" - dp.query(cypher) - df = dp.get_data_generic(my_classes, return_nodeid=False, prefix_keys_with_label=False) - # Dataframe: - ''' - USUBJID TRT01A TRT01AN - 0 1234 Placebo 2.0 - 1 9876 Active 1.0 - ''' - expected_df.loc[1] = ["9876", "Active", 1.0] - assert df.equals(expected_df) - -def test_get_data_generic_rename_rdfs(dp): - dp.clean_slate() - #loading metadata (Class/Property from json created in arrows.app) - with open(os.path.join(filepath, 'data', 'test_get_data_generic_rename_rdfs_01.json')) as jsonfile: - dct = json.load(jsonfile) - dp.load_arrows_dict(dct) - - #for testing purposes we don't reshapre the data with ModelApplier, just creating it as if it was reshaped - cypher = """ - CREATE (subj:Subject {`rdfs:label`:'1234'})-[:`HAS_PLANNED TREATMENT PERIOD 1`]->(:`Planned Treatment Period 1` {`rdfs:label`:'Placebo'}), - (subj)-[:HAS_SEX]->(:Sex{`rdfs:label`:'F'}) - """ - dp.query(cypher) - # dp.debug=True - dp.set_mode("schema_CLASS") - - #Test case #1 - df = dp.get_data_generic(['Subject', 'Planned Treatment Period 1', 'Sex'], - return_nodeid=False, - prefix_keys_with_label=False) - expected_df = pd.DataFrame([["1234", "Placebo", "F"]], columns = ["USUBJID", "TRT01P", "SEX"]) - print(df) - print(expected_df) - assert df.equals(expected_df) - - #Test case #2 with prefix_keys_with_label=True - df2 = dp.get_data_generic(['Subject', 'Planned Treatment Period 1', 'Sex'], - return_nodeid=False, - prefix_keys_with_label=True) - expected_df2 = pd.DataFrame( - [["1234", "Placebo", "F"]], - columns=["Subject.USUBJID", "Planned Treatment Period 1.TRT01P", "Sex.SEX"] - ) - # print(df2) - # print(expected_df2) - assert df2.equals(expected_df2) - - #Test case 3 - the Subject node will have a property MYSUBJID rather than rdfs:label - #this should be reflected in the metadata: - dp.query("MATCH (c:Class{label:'Subject'})-[:HAS_PROPERTY]->(prop:Property) SET prop.label = 'MYSUBJID'") - #and data: - dp.query("MATCH (s:Subject) SET s.MYSUBJID = s.`rdfs:label` REMOVE s.`rdfs:label`") - #dp.debug=True - df = dp.get_data_generic(['Subject', 'Planned Treatment Period 1', 'Sex'], - return_nodeid=False, - prefix_keys_with_label=False, - ) - expected_df = pd.DataFrame([["1234", "Placebo", "F"]], columns = ["MYSUBJID", "TRT01P", "SEX"]) - print(df) - print(expected_df) - assert df.equals(expected_df) - dp.set_mode("schema_PROPERTY") #return to schema mode - - -###################### TESTS RELATED TO get_filters() ###################### - - -def test_get_filters_helper(dp): - # Verify that an exception is raised in some pathological cases - with pytest.raises(Exception): - assert dp._get_filters_helper("") # "ERROR in _get_filters_helper(): the argument `classes` cannot be an empty string" - assert dp._get_filters_helper([]) # "ERROR in qb_generate_return(): empty lists are not an acceptable argument for `classes`" - - - result, _, _ = dp._get_filters_helper("Non_existent_node") - assert result == {'Non_existent_node': []} - result, _, _ = dp._get_filters_helper(["List_with_Non_existent_node"]) - assert result == {'List_with_Non_existent_node': []} - - result, _, _ = dp._get_filters_helper(["cls1", "cls2"], return_nodeid=False, prefix_keys_with_label=False) - assert result == {'cls1': [], 'cls2': []} - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['apple', 'fruit']]) - result, _, _ = dp._get_filters_helper(my_classes, return_nodeid=True, prefix_keys_with_label=False) - assert result == {'apple': [], 'fruit': []} - # Now expand the database just created above - cypher = "CREATE (a:`apple` {label:'apple'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'})" - dp.query(cypher) - - result, _, _ = dp._get_filters_helper(my_classes, return_nodeid=False, prefix_keys_with_label=False) - """ - Note: the internal query run by _get_filters_helper is: - MATCH (`fruit`:`fruit`), (`apple`:`apple`), (`apple`)-[:`HAS_FRUIT`]->(`fruit`), (`apple`), (`fruit`) - RETURN collect(distinct `fruit`{.*}) as `fruit`, collect(distinct `apple`{.*}) as `apple` - """ - assert result == {'fruit': [{'label': 'fruit'}], 'apple': [{'label': 'apple'}]} - - - -def test_get_filters_helper_return_nodeid(dp): - - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['apple', 'fruit']]) - cypher = "CREATE (a:`apple` {label:'apple'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'})" - dp.query(cypher) - - # Extract the Neo4j ID's of the newly-created `apple` and `fruit` nodes - apple_node_data = dp.get_nodes("apple", return_nodeid=True) - apple_id = apple_node_data[0]["neo4j_id"] # There's only 1 node labeled "apple" - - fruit_node_data = dp.get_nodes("fruit", return_nodeid=True) - fruit_id = fruit_node_data[0]["neo4j_id"] # There's only 1 node labeled "fruit" - - # Repeat the last function call, but this time asking for the node IDs to be returned - result, _, _ = dp._get_filters_helper(my_classes, return_nodeid=True, prefix_keys_with_label=False) - """ - Note: the internal query run by _get_filters_helper is: - MATCH (`fruit`:`fruit`), (`apple`:`apple`), (`apple`)-[:`HAS_FRUIT`]->(`fruit`), (`apple`), (`fruit`) - RETURN collect(distinct {`fruit`:id(`fruit`)}) as `fruit`, collect(distinct {`apple`:id(`apple`)}) as `apple` - """ - assert result == {'fruit': [{'fruit': fruit_id, 'label': 'fruit'}], 'apple': [{'apple': apple_id, 'label': 'apple'}]} - - - -def test_get_filters_generic_prefix_label(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['Appl e', 'fruit']]) - - # Now expand the database just created above - cypher = "CREATE (a:`Appl e` {label:'app le'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'})" - dp.query(cypher) - - result = dp.get_filters_generic(my_classes, prefix_keys_with_label=True, return_nodeid = False) - """ - Note: the internal query run by _get_filters_helper is: - MATCH (`fruit`:`fruit`), (`appl e`:`Appl e`), (`appl e`)-[:`HAS_FRUIT`]->(`fruit`), (`appl e`), (`fruit`) - RETURN collect(distinct `fruit`{.*}) as `fruit`, collect(distinct `appl e`{.*}) as `appl e` - """ - df1 = pd.DataFrame({'fruit.label': ['fruit']}) # A 1x1 table with data "fruit" and column name "label" - df2 = pd.DataFrame({'Appl e.label': ['app le']}) - assert df1.equals(result['fruit']) - assert df2.equals(result['Appl e']) - - #print("result : ", result) - - -def test_get_filters_generic(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['apple', 'fruit']]) - - # Now expand the database just created above - cypher = "CREATE (a:`apple` {label:'apple'})-[:HAS_FRUIT]->(f:`fruit` {label:'fruit'})" - dp.query(cypher) - - result = dp.get_filters_generic(my_classes, return_nodeid = False, prefix_keys_with_label=False) - """ - Note: the internal query run by _get_filters_helper is: - MATCH (`fruit`:`fruit`), (`apple`:`apple`), (`apple`)-[:`HAS_FRUIT`]->(`fruit`), (`apple`), (`fruit`) - RETURN collect(distinct `fruit`{.*}) as `fruit`, collect(distinct `apple`{.*}) as `apple` - """ - df1 = pd.DataFrame({'label': ['fruit']}) # A 1x1 table with cell value "fruit" and column name "label" - df2 = pd.DataFrame({'label': ['apple']}) - assert df1.equals(result['fruit']) - assert df2.equals(result['apple']) - - - -def test_get_filters(dp): - - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - dp.clean_slate() - my_classes = dp.qb.mm.create_related_classes_from_list([['patient', 'gender']]) - - # Now expand the database by adding data points of Classes 'patient' and 'gender' - q = ''' - CREATE (:`patient` {label:'Jack'})-[:HAS_GENDER]->(:`gender` {label:'M'}), - (:`patient` {label:'Jill'})-[:HAS_GENDER]->(:`gender` {label:'F'}) - ''' - dp.query(q) - - result = dp.get_filters_generic(my_classes) - # A dict with 2 keys, 'patient' and 'gender', and Pandas data frames for values - assert len(result) == 2 - expected_keys = ['patient', 'gender'] - returned_keys = list(result) # List of all the keys in the result dict - assert compare_unordered_lists(expected_keys, returned_keys) - - Jack_id = dp.query("MATCH (n:patient {label:'Jack'}) RETURN id(n) as nodeid")[0]["nodeid"] - Jill_id = dp.query("MATCH (n:patient {label:'Jill'}) RETURN id(n) as nodeid")[0]["nodeid"] - - male_id = dp.query("MATCH (n:gender {label:'M'}) RETURN id(n) as nodeid")[0]["nodeid"] - female_id = dp.query("MATCH (n:gender {label:'F'}) RETURN id(n) as nodeid")[0]["nodeid"] - - df1 = pd.DataFrame([[Jack_id, "Jack"], [Jill_id, "Jill"]], columns=["patient", "patient.label"]) # A 2x2 dataframe - df2 = pd.DataFrame([[male_id, "M"], [female_id, "F"]], columns=["gender", "gender.label"]) # A 2x2 dataframe - assert df1.equals(result['patient']) - assert df2.equals(result['gender']) - - - - -###################### TESTS FOR convert_qb_result_to_df() ###################### - -def test_convert_qb_result_to_df(dp): - # Test one form of the input - neoresult = [{'Study': {'studyid':'ABC'}, 'Site': {'siteid':1, 'sitename':'SITE1'}}, - {'Study': {'studyid':'ABC'}, 'Site': {'siteid':2, 'sitename':'SITE2'}}] - result = dp.convert_qb_result_to_df(neoresult) - '''It returns the following Pandas dataframe: - studyid siteid sitename - 0 ABC 1 SITE1 - 1 ABC 2 SITE2 - ''' - expected_result = pd.DataFrame([["ABC", 1, "SITE1"] , ["ABC", 2, "SITE2"]], - columns=['studyid', 'siteid', 'sitename']) - assert result.equals(expected_result) - - result_dict = dp.convert_qb_result_to_df(neoresult, hstack=False) - # It returns a dictionary with keys 'Study' and 'Site' - assert len(result_dict) == 2 - # The value of 'Study' is the data frame - ''' - studyid - 0 ABC - 1 ABC - ''' - pd1 = pd.DataFrame({"studyid": ["ABC","ABC"]}) - assert result_dict['Study'].equals(pd1) - # and the value of 'Site' is the data frame - ''' - siteid sitename - 0 1 SITE1 - 1 2 SITE2 - ''' - pd2 = pd.DataFrame({"siteid": [1,2], "sitename": ["SITE1","SITE2"]}) - assert result_dict['Site'].equals(pd2) - - - # Test an alternate form of the input - neoresult = [{'all': {'studyid':'ABC', 'siteid':1, 'sitename':'SITE1'}}, - {'all': {'studyid':'ABC', 'siteid':2, 'sitename':'SITE2'}}] - result = dp.convert_qb_result_to_df(neoresult) - # It returns the same Pandas dataframe as the first run - assert result.equals(expected_result) - - result_dict = dp.convert_qb_result_to_df(neoresult, hstack=False) - # It returns a dictionary with a single key 'all', whose value is the above Pandas dataframe - assert len(result_dict) == 1 - assert result_dict['all'].equals(expected_result) - - - # Tests of pathological scenarios - result = dp.convert_qb_result_to_df([]) - assert result.empty - - result_dict = dp.convert_qb_result_to_df([], hstack=False) - assert result_dict == {} \ No newline at end of file diff --git a/tests/test_data_providers/_archive_test_data_provider_noschema.py b/tests/test_data_providers/_archive_test_data_provider_noschema.py deleted file mode 100644 index de30aa0..0000000 --- a/tests/test_data_providers/_archive_test_data_provider_noschema.py +++ /dev/null @@ -1,71 +0,0 @@ -import pytest -from data_providers import data_provider -import pandas as pd - - -# Provide a DataProvider object (which contains a database connection) -# that can be used by the various tests that need it -@pytest.fixture(scope="module") -def dp(): - dp = data_provider.DataProvider(mode='noschema') - dp.clean_slate() - yield dp - - -def test_get_data_noschema(dp): - dp.clean_slate() - q = """ - UNWIND $data AS row - CALL apoc.create.node([row['label']], row['properties']) YIELD node - RETURN id(node) - """ - params = {'data': [ - {'label': 'Z', 'properties': {'z':1, 'zz':2.1}}, - {'label': 'B', 'properties': {'b b':'xYz'}}, - {'label': 'C', 'properties': {}}, - {'label': 'D', 'properties': {'d':3}}, - {'label': 'E', 'properties': {'e':4}}, - {'label': 'Z', 'properties': {'z':2}}, - {'label': 'B', 'properties': {'b b': 'AbC'}}, - {'label': 'C', 'properties': {}}, - {'label': 'D', 'properties': {'d': 33}}, - ]} - nodeids = [res['id(node)'] for res in dp.query(q, params)] - dp.link_nodes_by_ids(nodeids[0], nodeids[1], 'REL1') - dp.link_nodes_by_ids(nodeids[2], nodeids[1], 'REL2') - dp.link_nodes_by_ids(nodeids[3], nodeids[1], 'REL3') - dp.link_nodes_by_ids(nodeids[5], nodeids[6], 'REL1') - dp.link_nodes_by_ids(nodeids[7], nodeids[6], 'REL2') - dp.link_nodes_by_ids(nodeids[8], nodeids[6], 'REL3') - result = dp.get_data_generic(classes=['Z', 'B', 'C', 'D', 'E'], return_nodeid=False, prefix_keys_with_label=False) - expected_result = pd.DataFrame([ - {'zz':2.1, 'z':1, 'd':3, 'b b':'xYz','e':4}, - {'z': 2, 'd': 33, 'b b': 'AbC', 'e': 4}, - ]) - assert result.equals(expected_result) - - -def test_get_data_noschema_optional_class(dp): - dp.clean_slate() - ia = dp.create_node_by_label_and_dict('Strain', {'type':'apple'}) - io = dp.create_node_by_label_and_dict('Strain', {'type': 'orange'}) - if_ = dp.create_node_by_label_and_dict('Fruit', {'n_types':9999}) - iarel = dp.create_node_by_label_and_dict('AdditionalInfo', {'desc': 'blah-blah'}) - dp.link_nodes_by_ids(ia,if_,'IS_A') - dp.link_nodes_by_ids(io, if_, 'IS_A') - dp.link_nodes_by_ids(ia, iarel, 'HAS') - #1 - result = dp.get_data_generic( - classes = ['Strain', 'Fruit', 'AdditionalInfo'], - prefix_keys_with_label = True, return_nodeid=False - ) - assert len(result) == 1 - # print(result) - #2 - result = dp.get_data_generic( - classes=['Strain', 'Fruit', 'AdditionalInfo**'], - prefix_keys_with_label=True, return_nodeid=False - ) - assert len(result) == 2 - # print(result) - diff --git a/tests/test_data_providers/_archive_test_sdtm_data_provider.py b/tests/test_data_providers/_archive_test_sdtm_data_provider.py deleted file mode 100644 index 1b5f322..0000000 --- a/tests/test_data_providers/_archive_test_sdtm_data_provider.py +++ /dev/null @@ -1,199 +0,0 @@ -import pytest -from data_providers import sdtm_data_provider -from data_loaders import file_data_loader -from model_appliers import model_applier -import pandas as pd -import os - - -# Provide a DataProvider object (which contains a database connection) that can be used by the various tests that need it -@pytest.fixture(scope="module") -def dp(): - dp = sdtm_data_provider.SDTMDataProvider(debug = True, check_for_refarctored = True) - yield dp - -@pytest.fixture(scope="module") -def data_folder(): - testfile_path = os.path.dirname(__file__) - data_folder = os.path.join(testfile_path, "data") - yield data_folder - - -# Test case 1 -def test_get_data_sdtm_output(dp, data_folder): - dp.set_mode("schema_PROPERTY") - # checking content of columns - df_extracted=prepare_get_data_sdtm(dp, data_folder, metadata_version = "v4") - result1= df_extracted[['STUDYID', 'USUBJID', 'AGE', 'SITEID', 'RFSTDTC', 'SEX']] - dl = file_data_loader.FileDataLoader(domain_dict={'testdata.xls': 'DM'}) - df = dl.read_file(folder=data_folder, filename="testdata.xls")[0] - assert df.equals(result1), "Values in ['STUDYID', 'USUBJID', 'AGE', 'SITEID', 'RFSTDTC', 'SEX'] are different in the result returned" \ - "from the dataframe loaded to neo4j" - - # checking columns names - q = f""" - MATCH (c:`Source Data Column`) where c.uri CONTAINS '#Metadata' and c._domain_='DM' - Return c.`_columnname_` as column order by c.Order - """ - params = {} - meta_col = pd.DataFrame(dp.query(q, params)) - data_col = pd.DataFrame(df_extracted.columns.values.tolist(), columns=['column']) - assert data_col.equals(meta_col), "Set of columns is different" - -#Test case 2 (with schema_CLASS mode (req v5 metadata) ) -def test_get_data_sdtm_output_maps_to_class(dp, data_folder): - dp.set_mode("schema_CLASS") - # checking content of columns - df_extracted=prepare_get_data_sdtm(dp, data_folder, metadata_version = "v5") - result1= df_extracted[['STUDYID', 'USUBJID', 'AGE', 'SITEID', 'RFSTDTC', 'SEX']] - dl = file_data_loader.FileDataLoader(domain_dict={'testdata.xls': 'DM'}) - df = dl.read_file(folder=data_folder, filename="testdata.xls")[0] - print(result1.compare(df)) - # assert df.equals(result1), "Values in ['STUDYID', 'USUBJID', 'AGE', 'SITEID', 'RFSTDTC', 'SEX'] are different in the result returned" \ - # "from the dataframe loaded to neo4j" - - # checking columns names - q = f""" - MATCH (c:`Source Data Column`) where c.uri CONTAINS '#Metadata' and c._domain_='DM' - Return c.`_columnname_` as column order by c.Order - """ - params = {} - meta_col = pd.DataFrame(dp.query(q, params)) - data_col = pd.DataFrame(df_extracted.columns.values.tolist(), columns=['column']) - assert data_col.equals(meta_col), "Set of columns is different" - dp.set_mode("schema_PROPERTY") - - -# helper functions -def prepare_get_data_sdtm(dp, data_folder, metadata_version): - dp.clean_slate() - dl = file_data_loader.FileDataLoader(domain_dict={'testdata.xls': 'DM'}) - df = dl.load_file(folder=data_folder, filename="testdata.xls") - - # Refactor data - neo = model_applier.ModelApplier( - rdf=True, - mode=("schema_PROPERTY" if metadata_version == "v4" else "schema_CLASS") - ) - import_reshaping_metadata_ttl(data_folder, metadata_version) - neo.define_refactor_indexes() - neo.delete_classes_entities() - neo.refactor_all() - - # Extract data - import_extracting_metadata_ttl(data_folder, metadata_version) - df_extracted = dp.get_data_sdtm(standard='MDR3_2', domain='DM', where_map=None) - return df_extracted - -def import_reshaping_metadata_ttl(data_folder:str, metadata_version): - uri_dct = { - "Class": {"properties": "label"}, - "Property": {"properties": ["Class.label", "label"]}, - "Source Data Table": { - "properties": "_domain_", - "where": "WHERE NOT (exists(x.uri) and x.uri CONTAINS '#Metadata')" - }, - "Source Data Column": { - "properties": ["_domain_", "_columnname_"], - "where": "WHERE NOT (exists(x.uri) and x.uri CONTAINS '#Metadata')" - } - } - - neo = model_applier.ModelApplier(rdf=True) - with open(os.path.join(data_folder, f'Map Columns to Properties_{metadata_version}_example_2domains_117106.ttl'), "r", encoding='utf-8') as f: - neo.rdf_generate_uri(uri_dct) - rdf = f.read() - neo.delete_nodes_by_label(delete_labels=['Class', 'Property']) - res = neo.rdf_import_subgraph_inline(rdf) - print("Importing metadata:", res) - classes = uri_dct.keys() - for class_ in classes: - q = f""" - MATCH (x:`{class_}`:Resource) - remove x:Resource - """ - params = {} - neo.query(q, params) - - -def import_extracting_metadata_ttl(data_folder:str, metadata_version): - URI_MAP = { - "Class": {"properties": "label"}, - "Property": {"properties": ["Class.label", "label"]}, - "Data Extraction Standard": { - "properties": "_tag_", - "where": "WHERE (exists(x.uri) and x.uri CONTAINS '#Metadata')"}, - "Source Data Folder": {"properties": "_folder_"}, - "Source Data Table": { - "properties": "_domain_", - "where": "WHERE (exists(x.uri) and x.uri CONTAINS '#Metadata')" - }, - "Source Data Column": { - "properties": ["_domain_", "_columnname_"], - "where": "WHERE (exists(x.uri) and x.uri CONTAINS '#Metadata')" - } - } - neo = model_applier.ModelApplier(rdf=True) - with open(os.path.join(data_folder, f'export_sdtm_{metadata_version}_2domains.ttl'), "r", encoding='utf-8') as f: - neo.rdf_generate_uri(dct={k: i for k, i in URI_MAP.items() if k in ['Class', 'Property']}) - rdf = f.read() - res =neo.rdf_import_subgraph_inline(rdf) - print("Importing metadata:", res) - classes = URI_MAP - for class_ in classes: - q = f""" - MATCH (x:`{class_}`:Resource) - remove x:Resource - """ - params = {} - neo.query(q, params) - f.close() - -def test_neo_validate_access(dp): - dp.clean_slate() - classes = ["End Date/Time of Observation", "Date/Time of Reference Time Point", "Date/Time of Collection", - "Subject", "Race"] - dp.query( - """ - UNWIND $classes as class - MERGE (c:Class{label:class}) - """, - {'classes': classes} - ) - dp.query(""" - WITH [['ak956494', 'Study Lead'], ['external', 'External Researcher']] as coll - UNWIND coll as pair - WITH pair[0] as user_id, pair[1] as role_name - MERGE (user:User{id:user_id})-[r1:HAS_ROLE]->(role:`User Role`{name:role_name}) - WITH * - WHERE role.name = 'External Researcher' - MATCH (class:Class) - WHERE class.label in $rclasses - MERGE (role)-[:ACCESS_RESTRICTED]->(class) - """, - {'rclasses': classes[:3]} - ) - #External Researcher - res_has_access, res_no_access = dp.neo_validate_access(classes=classes, user_role="External Researcher") - print(res_has_access, res_no_access) - assert set(res_has_access) == {'Subject', 'Race'} - assert set(res_no_access) == {'Date/Time of Reference Time Point', 'Date/Time of Collection', 'End Date/Time of Observation'} - #Study Lead - res_has_access, res_no_access = dp.neo_validate_access(classes=classes, user_role="Study Lead") - assert set(res_has_access) == {'Subject', 'Race', 'Date/Time of Reference Time Point', 'Date/Time of Collection', - 'End Date/Time of Observation'} - assert len(res_no_access) == 0 - #Not specified - res_has_access, res_no_access = dp.neo_validate_access(classes=classes) - assert set(res_has_access) == {'Subject', 'Race', 'Date/Time of Reference Time Point', 'Date/Time of Collection', - 'End Date/Time of Observation'} - assert len(res_no_access) == 0 - #Role does not exist - try: - dp.neo_validate_access(classes=classes, user_role="Directors") - except Exception as e: - print(e) - - - - diff --git a/tests/test_data_providers/data/Map Columns to Properties_v007_example_2domains_117106.ttl b/tests/test_data_providers/data/Map Columns to Properties_v007_example_2domains_117106.ttl deleted file mode 100644 index c696524..0000000 --- a/tests/test_data_providers/data/Map Columns to Properties_v007_example_2domains_117106.ttl +++ /dev/null @@ -1,4537 +0,0 @@ -@prefix n4sch: . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study"; - n4sch:short_label "STUDYID"; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,IS,LB,VS"; - n4sch:CoreClass false . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "FACE"; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EG"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "STUDYID" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "1"^^ . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required"; - n4sch:Order "1"^^; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "EX" . - - a ; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DS"; - n4sch:Core "Required"; - n4sch:Order "1"^^ . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "IS"; - n4sch:Order "1"^^; - n4sch:Core "Required" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "LB" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "VS" . - - a n4sch:Class; - n4sch:label "Adverse Events Domain Abbreviation"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:short_label "DOMAIN"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - a n4sch:Class; - n4sch:short_label "DOMAIN"; - n4sch:create false; - n4sch:from_domains "EG,EX,AE,LB,DM,IS,VS,FACE,DS"; - n4sch:CoreClass false; - n4sch:label "Domain Abbreviation" . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,IS,LB,VS"; - n4sch:short_label "USUBJID"; - n4sch:create false . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS" . - - a ; - n4sch:Core "Required"; - n4sch:Order "3"^^; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID"; - n4sch:Core "Required"; - n4sch:_domain_ "IS"; - n4sch:Order "3"^^ . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "USUBJID" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:Core "Required" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:_domain_ "FACE"; - n4sch:Core "Required" . - - a ; - n4sch:Order "3"^^; - n4sch:_domain_ "LB"; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID" . - - a ; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "3"^^; - n4sch:Core "Required" . - - a ; - n4sch:Order "3"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "USUBJID"; - n4sch:Core "Required" . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - a - n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a - n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - a - n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - a - n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:create false; - n4sch:short_label "SUBJID"; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,IS,LB,VS"; - n4sch:CoreClass false . - - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - - 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n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true . - - a ; - n4sch:SortOrder "STYDYID,USUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:short_label "DM"; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:create true . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:MAPS_TO_CLASS . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Timing"; - n4sch:from_domains "EG,EX,AE,LB,DM,IS,VS,FACE,DS"; - n4sch:CoreClass false; - n4sch:short_label "T" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:SUBCLASS_OF ; - n4sch:label "Date/Time of Reference Time Point"; - n4sch:CoreClass false; - n4sch:from_domains "EG,LB,IS,VS"; - n4sch:create false; - n4sch:short_label "--RFTDTC" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Class; - n4sch:create false; - n4sch:from_domains "EG,EX,AE,LB,DM,IS,VS,FACE,DS"; - n4sch:short_label "DY"; - n4sch:label "Study Day"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - a n4sch:Relationship; - n4sch:relationship_type "IS_A"; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES"; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES"; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES"; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES"; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:relationship_type "HAS_SUBCATEGORY"; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - a n4sch:Relationship; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "IS_A" . - - - a n4sch:Relationship; - n4sch:relationship_type "IS_A"; - n4sch:TO . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:relationship_type "QUALIFIES"; - n4sch:TO ; - n4sch:FROM . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES"; - n4sch:FROM . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - a n4sch:Relationship; - n4sch:TO ; - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO . - - n4sch:FROM - . - - - n4sch:FROM . - - n4sch:FROM - . - - n4sch:FROM - . - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM - . - - n4sch:FROM - . - - - n4sch:FROM . - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM . - - n4sch:FROM - . - - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM - . - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM - . - - n4sch:FROM . - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO . - - - n4sch:TO . - - - n4sch:TO . - - - n4sch:TO . - - - n4sch:TO . - - - n4sch:TO . - - n4sch:TO - . - - - n4sch:TO . - - n4sch:TO . - - - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO . - - - n4sch:TO . - - n4sch:TO . - - - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM . - - - n4sch:FROM . - - - n4sch:FROM . - - n4sch:FROM - . - - n4sch:FROM . - - n4sch:FROM . - - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO . - - - n4sch:TO . - - n4sch:TO . - - n4sch:TO - . - - n4sch:FROM - ; - n4sch:TO . diff --git a/tests/test_data_providers/data/Map Columns to Properties_v4_example_2domains_117106.ttl b/tests/test_data_providers/data/Map Columns to Properties_v4_example_2domains_117106.ttl deleted file mode 100644 index 0634512..0000000 --- a/tests/test_data_providers/data/Map Columns to Properties_v4_example_2domains_117106.ttl +++ /dev/null @@ -1,3157 +0,0 @@ -@prefix n4sch: . - - a n4sch:Class; - n4sch:label "Study"; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:create true; - n4sch:label "Exposure"; - n4sch:from_domains "EX"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , - , - , , - , , - , , - , - , - , , - , , - , , - , , - , - , , - , , - , , - , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , - ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:create true; - n4sch:label "Findings About Clinical Events"; - n4sch:CLASS_RELATES_TO , ; - n4sch:CoreClass true; - n4sch:from_domains "FACE" . - - a n4sch:Class; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , - , , - , , - , - , - , - , , - , , - , , - , - , , - , , - , - , , - , , - , - , - , , - , , - , , - , , - , - ; - n4sch:create true; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - ; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:create true . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:from_domains "LB"; - n4sch:CLASS_RELATES_TO , , - ; - n4sch:label "Laboratory Test Results"; - n4sch:create true . - - a n4sch:Class; - n4sch:label "Vital Signs"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , ; - n4sch:create true; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:label "Disposition"; - n4sch:CoreClass true; - n4sch:create true; - n4sch:CLASS_RELATES_TO , ; - n4sch:from_domains "DS" . - - a n4sch:Class; - n4sch:label "ECG Test Results"; - n4sch:create true; - n4sch:CLASS_RELATES_TO , ; - n4sch:from_domains "EG"; - n4sch:CoreClass true . - - a n4sch:Property; - n4sch:Class.label "Study"; - n4sch:label "STUDYID" . - - a n4sch:Class; - n4sch:create true; - n4sch:CoreClass false; - n4sch:label "Adverse Events Identifiers"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY , - , , - , . - - a n4sch:Property; - n4sch:label "--GRPID"; - n4sch:Class.label "Adverse Events Identifiers" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "--SPID" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "--REFID" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Adverse Events Identifiers" . - - a n4sch:Property; - n4sch:Class.label "Subject"; - n4sch:label "USUBJID" . - - a n4sch:Class; - n4sch:label "Adverse Events Epoch"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Relative to Reference Time Point"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Medically Important Serious Event"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Lowest Level Term"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Relationship to Non-Study Treatment"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pre-Specified Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a - n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Primary System Organ Class"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Congenital Anomaly or Birth Defect"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Occurred with Overdose"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:label "Adverse Events Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Is Life Threatening"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Concomitant or Additional Trtmnt Given"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Modified Reported Term"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Results in Death"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Standard Toxicity Grade"; - n4sch:from_domains "AE,LB"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Duration of Adverse Event"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events Persist or Signif Disability/Incapacity"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Category for Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Action Taken with Study Treatment"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Causality"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "End Date/Time of Adverse Event"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Subcategory for Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Primary System Organ Class Code"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Severity/Intensity"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Dictionary-Derived Term"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Adverse Event"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Day of Start of Adverse Event"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Reference Time Point"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Involves Cancer"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Outcome of Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Start Date/Time of Adverse Event"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:label "Adverse Events End Relative to Reference Period"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Study Day of End of Adverse Event"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events Preferred Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Location of Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Reported Term for the Adverse Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events Serious Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Action Taken"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a - n4sch:Property; - n4sch:Class.label "Subject Identifier for the Study"; - n4sch:label "SUBJID" . - - - a n4sch:Property; - n4sch:label "--TERM"; - n4sch:Class.label "Reported Term for the Adverse Event" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Reported Term"; - n4sch:from_domains "AE,DS" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Modified Reported Term"; - n4sch:label "--MODIFY" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Modified Reported Term" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Lowest Level Term"; - n4sch:label "--LLT" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Lowest Level Term" . - - - a n4sch:Property; - n4sch:label "--LLTCD"; - n4sch:Class.label "Adverse Events Lowest Level Term Code" . - - a n4sch:Class; - n4sch:label "Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Dictionary-Derived Term"; - n4sch:label "--DECOD" . - - a n4sch:Class; - n4sch:label "Dictionary-Derived Term"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DS" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Preferred Term Code"; - n4sch:label "--PTCD" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events High Level Term"; - n4sch:label "--HLT" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term Code" . - - - a n4sch:Property; - n4sch:label "--HLTCD"; - n4sch:Class.label "Adverse Events High Level Term Code" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--HLGT"; - n4sch:Class.label "Adverse Events High Level Group Term" . - - - a n4sch:Property; - n4sch:label "--HLGTCD"; - n4sch:Class.label "Adverse Events High Level Group Term Code" . - - a n4sch:Class; - n4sch:label "High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:from_domains "EG,AE,LB,VS,FACE,DS"; - n4sch:CoreClass false; - n4sch:label "Category" . - - a n4sch:Property; - n4sch:label "--CAT"; - n4sch:Class.label "Category for Adverse Event" . - - a n4sch:Class; - n4sch:label "Subcategory"; - n4sch:from_domains "EG,AE,LB,VS,FACE,DS"; - n4sch:CoreClass false . - - a n4sch:Property; - n4sch:Class.label "Subcategory for Adverse Event"; - n4sch:label "--SCAT" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Pre-specified" . - - a n4sch:Property; - n4sch:Class.label "Pre-Specified Adverse Event"; - n4sch:label "--PRESP" . - - a n4sch:Class; - n4sch:label "Body System or Organ Class"; - n4sch:CoreClass false; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--BODSYS"; - n4sch:Class.label "Adverse Events Body System or Organ Class" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Body System or Organ Class Code"; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Adverse Events Body System or Organ Class Code" . - - a n4sch:Class; - n4sch:label "Primary System Organ Class"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Primary System Organ Class"; - n4sch:label "--SOC" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Primary System Organ Class Code"; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Adverse Events Primary System Organ Class Code" . - - a n4sch:Class; - n4sch:label "Location of Event"; - n4sch:from_domains "AE,LB,VS,FACE"; - n4sch:CoreClass false . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Adverse Events Location of Event" . - - a n4sch:Class; - n4sch:label "Severity"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity/Intensity" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Serious Event"; - n4sch:label "--SER" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Serious Event" . - - a n4sch:Class; - n4sch:label "Action Taken with Study Treatment"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - a n4sch:Class; - n4sch:label "Other Action Taken"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Other Action Taken"; - n4sch:label "--ACNOTH" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Causality"; - n4sch:label "--REL" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Causality"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Relationship to Non-Study Treatment" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Relationship to Non-Study Treatment"; - n4sch:label "--RELNST" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Adverse Event" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Outcome of Event" . - - a n4sch:Property; - 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- n4sch:HAS_PROPERTY - . - - a ; - n4sch:Order "24"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESOC"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESOCCD"; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "25"^^ . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "26"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AELOC" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESEV"; - n4sch:Order "27"^^; - n4sch:Core "Permissible" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_columnname_ "AESER"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "28"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected" . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AEACN"; - n4sch:Order "29"^^; - n4sch:Core "Expected" . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "30"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEACNOTH" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "31"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AEREL"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected" . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE"; - n4sch:Order "32"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AERELNST" . - - a ; - n4sch:Order "33"^^; - n4sch:_columnname_ "AEPATT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "34"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AEOUT" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "35"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESCAN" . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "36"^^; - n4sch:_columnname_ "AESCONG" . - - - n4sch:HAS_PROPERTY . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "37"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESDISAB" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Order "38"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESDTH"; - n4sch:MAPS_TO_PROPERTY . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "AESHOSP"; - n4sch:Order "39"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "40"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESLIFE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "41"^^; - n4sch:_columnname_ "AESOD"; - n4sch:_domain_ "AE" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "42"^^; - n4sch:_columnname_ "AESMIE" . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AECONTRT"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "43"^^; - n4sch:_domain_ "AE" . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "AETOXGR"; - n4sch:Core "Permissible"; - n4sch:Order "44"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "45"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "EPOCH"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESTDTC"; - n4sch:Order "46"^^ . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:Order "47"^^; - n4sch:_columnname_ "AEENDTC" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESTDY"; - n4sch:Order "48"^^; - n4sch:Core "Permissible" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AEENDY"; - n4sch:_domain_ "AE"; - n4sch:Order "49"^^; - n4sch:Core "Permissible" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "50"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AEDUR" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "51"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENRF"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible" . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:Order "52"^^; - n4sch:_columnname_ "AEENRTPT"; - n4sch:_domain_ "AE" . - - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "53"^^; - n4sch:_columnname_ "AEENTPT"; - n4sch:_domain_ "AE" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DOMAIN" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:Order "5"^^; - n4sch:_columnname_ "RFSTDTC" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "RFENDTC"; - n4sch:Order "6"^^; - n4sch:Core "Expected" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM"; - n4sch:Order "7"^^ . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "RFXENDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:Order "8"^^; - n4sch:_domain_ "DM" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "9"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:Core "Expected" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "RFPENDTC"; - n4sch:Order "10"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected" . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:Order "11"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "DTHDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "12"^^; - n4sch:_columnname_ "DTHFL" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "14"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "INVID" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "15"^^; - n4sch:_columnname_ "INVNAM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "16"^^ . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AGE"; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:Order "17"^^ . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "AGEU"; - n4sch:Order "18"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "20"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "RACE"; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "21"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "ETHNIC" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "ARMCD"; - n4sch:Order "22"^^ . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ARM"; - n4sch:Core "Required" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ACTARMCD"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Required"; - n4sch:Order "24"^^ . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:Core "Required"; - n4sch:Order "25"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "26"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "COUNTRY" . - - a ; - n4sch:_columnname_ "DMDTC"; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM" . - - a ; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:Order "28"^^ . - - a ; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:SortOrder "STUDYID,USUBJID"; - n4sch:_domain_ "DM"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - a n4sch:Class; - n4sch:from_domains "EG,LB,VS"; - n4sch:SUBCLASS_OF ; - n4sch:label "Date/Time of Reference Time Point"; - n4sch:CoreClass false . - - a n4sch:Property; - n4sch:label "--RFTDTC"; - n4sch:Class.label "Date/Time" . - - n4sch:HAS_PROPERTY , - , , - , , - , , - , , - , , - ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Timing"; - n4sch:CoreClass false; - n4sch:from_domains "EG,EX,AE,LB,DM,VS,FACE,DS" . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:label "--ENDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "BRTHDTC" . - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time" . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFPENDTC" . - - a n4sch:Property; - n4sch:label "RFXENDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "--STDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFENDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "DTHDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "--DTC" . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "EG,EX,AE,LB,DM,VS,FACE,DS"; - n4sch:label "Study Day"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY , , - ; - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day" . - - a n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day" . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - . - - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "Reported Term"; - n4sch:label "--TERM" . - - a n4sch:Property; - n4sch:label "--MODIFY"; - n4sch:Class.label "Modified Reported Term" . - - n4sch:SUBCLASS_OF - . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--LLT"; - n4sch:Class.label "Lowest Level Term" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "Lowest Level Term Code"; - n4sch:label "--LLTCD" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--DECOD"; - n4sch:Class.label "Dictionary-Derived Term" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "Preferred Term Code"; - n4sch:label "--PTCD" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--HLT"; - n4sch:Class.label "High Level Term" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "High Level Term Code"; - n4sch:label "--HLTCD" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term"; - n4sch:label "--HLGT" . - - - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term Code"; - n4sch:label "--HLGTCD" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "HAS_SUBCATEGORY" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:CLASS_RELATES_TO , ; - n4sch:CoreClass false; - n4sch:label "Name of Treatment" . - - a - n4sch:Class; - n4sch:CLASS_RELATES_TO , ; - n4sch:CoreClass false; - n4sch:from_domains "EG,LB,VS,FACE"; - n4sch:label "Name of Measurement, Test or Examination" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:Class.label "Category"; - n4sch:label "--CAT" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SCAT"; - n4sch:Class.label "Subcategory" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - n4sch:HAS_PROPERTY - . - - n4sch:SUBCLASS_OF - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - n4sch:HAS_PROPERTY - . - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - n4sch:HAS_PROPERTY - . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - n4sch:HAS_PROPERTY - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - n4sch:HAS_PROPERTY - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - n4sch:SUBCLASS_OF - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - n4sch:HAS_PROPERTY - . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - n4sch:HAS_PROPERTY - . - - - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:label "Toxicity"; - n4sch:from_domains "LB" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY , - , , - , , - , , - , , - , , - , , - , . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--STDY" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--ENDTC" . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY , , - , , - , , - , , - , , - , . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFPENDTC" . - - a n4sch:Property; - n4sch:label "--DTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--STDTC" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFENDTC" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "BRTHDTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFXSTDTC" . - - a n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Timing" . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFICDTC" . - - a n4sch:Property; - n4sch:label "RFXENDTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--RFTDTC" . - - a n4sch:Property; - n4sch:label "DTHDTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , - , , - , , - , , - , - , - , , - , , - , , - , , - , , - , , - , - , , - , , - , , - , , - , - , , - , , - , . - - n4sch:CLASS_RELATES_TO , - , , . - - n4sch:MAPS_TO_CLASS . - - n4sch:CLASS_RELATES_TO , - . - - n4sch:CLASS_RELATES_TO , - . - - n4sch:MAPS_TO_CLASS . diff --git a/tests/test_data_providers/data/Map Columns to Properties_v5_example_2domains_117106.ttl b/tests/test_data_providers/data/Map Columns to Properties_v5_example_2domains_117106.ttl deleted file mode 100644 index 9fbbfde..0000000 --- a/tests/test_data_providers/data/Map Columns to Properties_v5_example_2domains_117106.ttl +++ /dev/null @@ -1,3145 +0,0 @@ -@prefix n4sch: . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study"; - n4sch:short_label "STUDYID"; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , - , - , , - , , - , , - , , - , - , , - , , - , , - , - , , - , - , , - , - , , - , - , , - , , - , - , , - , ; - n4sch:create false; - n4sch:label "Subject"; - n4sch:short_label "USUBJID" . - - a n4sch:Class; - n4sch:short_label "FACE"; - n4sch:create false; - n4sch:label "Findings About Clinical Events"; - n4sch:CLASS_RELATES_TO , ; - n4sch:CoreClass true; - n4sch:from_domains "FACE" . - - a n4sch:Class; - n4sch:short_label "LB"; - n4sch:CoreClass true; - n4sch:from_domains "LB"; - n4sch:CLASS_RELATES_TO , ; - n4sch:label "Laboratory Test Results"; - n4sch:create false . - - a n4sch:Class; - n4sch:label "Disposition"; - n4sch:CoreClass true; - n4sch:create true; - n4sch:CLASS_RELATES_TO , ; - n4sch:short_label "DS"; - n4sch:from_domains "DS" . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Vital Signs"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , ; - n4sch:short_label "VS"; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:create true; - n4sch:label "Exposure"; - n4sch:from_domains "EX"; - n4sch:CoreClass true; - n4sch:short_label "EX"; - n4sch:CLASS_RELATES_TO , . - - a n4sch:Class; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , - , - , - , - , , - , , - , , - , - ; - n4sch:short_label "AE"; - n4sch:create true; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:short_label "DM"; - n4sch:CLASS_RELATES_TO , ; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:create true . - - a n4sch:Class; - n4sch:create false; - n4sch:label "ECG Test Results"; - n4sch:CLASS_RELATES_TO , ; - n4sch:short_label "EG"; - n4sch:from_domains "EG"; - n4sch:CoreClass true . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EG"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "STUDYID" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "LB" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "1"^^ . - - a ; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DS"; - n4sch:Core "Required"; - n4sch:Order "1"^^ . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required"; - n4sch:Order "1"^^; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "EX" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "FACE"; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "VS" . - - a n4sch:Class; - n4sch:label "Adverse Events Domain Abbreviation"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:short_label "DOMAIN"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:from_domains "EG,EX,AE,LB,DM,VS,FACE,DS"; - n4sch:short_label "DOMAIN"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Domain Abbreviation" . - - a ; - n4sch:Order "3"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "USUBJID"; - n4sch:Core "Required" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:_domain_ "FACE"; - n4sch:Core "Required" . - - a ; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "3"^^; - n4sch:Core "Required" . - - a ; - n4sch:Order "3"^^; - n4sch:_domain_ "LB"; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "USUBJID" . - - a ; - n4sch:Core "Required"; - n4sch:Order "3"^^; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:Core "Required" . - - a n4sch:Class; - n4sch:label "Adverse Events Results in Death"; - n4sch:create false; - n4sch:short_label "AESDTH"; - n4sch:CoreClass false; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term Code"; - n4sch:short_label "AEHLTCD"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events End Relative to Reference Period"; - n4sch:CoreClass false; - n4sch:short_label "AEENRF"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Reference Time Point"; - n4sch:CoreClass false; - n4sch:short_label "AEENTPT"; - n4sch:create false . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:create false; - n4sch:from_domains "AE,DM,DS,EG,EX,FACE,LB,VS"; - n4sch:short_label "SUBJID"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:short_label "AEENDTC"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:label "End Date/Time of Adverse Event"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AEPRESP"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pre-Specified Adverse Event"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Standard Toxicity Grade"; - n4sch:short_label "AETOXGR"; - n4sch:create false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AEOUT"; - n4sch:label "Outcome of Adverse Event"; - n4sch:create false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:short_label "AEHLGT"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Epoch"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:short_label "EPOCH" . - - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:short_label "AESHOSP" . - - a n4sch:Class; - n4sch:short_label "AEDECOD"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Dictionary-Derived Term"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study Day of Start of Adverse Event"; - n4sch:short_label "AESTDY"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - 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n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Location of Event"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term"; - n4sch:short_label "AEHLT"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Preferred Term Code"; - n4sch:CoreClass false; - n4sch:short_label "AEPTCD"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AECAT"; - n4sch:create false; - n4sch:label "Category for Adverse Event"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Start Date/Time of Adverse Event"; - n4sch:short_label "AESTDTC"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Reference ID"; - n4sch:from_domains "AE"; - 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- a - n4sch:Class; - n4sch:CLASS_RELATES_TO , ; - n4sch:create false; - n4sch:short_label "--TEST"; - n4sch:CoreClass false; - n4sch:from_domains "EG,LB,VS,FACE"; - n4sch:label "Name of Measurement, Test or Examination" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:create false; - n4sch:CLASS_RELATES_TO , ; - n4sch:short_label "--TRT"; - n4sch:CoreClass false; - n4sch:label "Name of Treatment" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:CLASS_RELATES_TO - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:short_label "--TOX"; - n4sch:create false; - n4sch:CLASS_RELATES_TO ; - n4sch:label "Toxicity"; - n4sch:from_domains "LB" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , - , - , , - , , - , - , , - , - , , - , , - , , - , - , , - , , - , - , , - , , - , - , , - , - , , - , - , , - , , - , , - , . - - n4sch:CLASS_RELATES_TO , - . - - n4sch:CLASS_RELATES_TO , - . diff --git a/tests/test_data_providers/data/export_sdtm_v007_2domains.ttl b/tests/test_data_providers/data/export_sdtm_v007_2domains.ttl deleted file mode 100644 index 18a0a2c..0000000 --- a/tests/test_data_providers/data/export_sdtm_v007_2domains.ttl +++ /dev/null @@ -1,3291 +0,0 @@ -@prefix n4sch: . - - a ; - n4sch:SortOrder "STYDYID,USUBJID"; - n4sch:_domain_ "DM" . - - a ; - n4sch:_filename_ "export_sdtm_2domains.ttl"; - n4sch:HAS_TABLE , ; - n4sch:_tag_ "MDR3_2" . - - a ; - n4sch:_domain_ "AE"; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ" . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study"; - n4sch:short_label "STUDYID"; - n4sch:from_domains "AE,DM"; - n4sch:CoreClass false . - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "AE" . - - a n4sch:Class; - n4sch:label "Adverse Events Domain Abbreviation"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:short_label "DOMAIN"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO ; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE" . - - a n4sch:Class; - n4sch:from_domains "AE,DM"; - n4sch:short_label "DOMAIN"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Domain Abbreviation" . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:short_label "USUBJID"; - n4sch:create false . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM" . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a - n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a - n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a - n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a - n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:FROM ; - n4sch:TO . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:create false; - n4sch:short_label "SUBJID"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM" . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "SUBJID"; - n4sch:Order "4"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required" . - - a ; - n4sch:_columnname_ "SUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "4"^^ . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:create true; - n4sch:CoreClass false; - n4sch:label "Adverse Events Sequence Number"; - n4sch:short_label "AESEQ"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "--SEQ"; - n4sch:label "Sequence Number"; - n4sch:create true . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required"; - n4sch:Order "5"^^; - n4sch:_columnname_ "AESEQ" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AEGRPID"; - n4sch:create true; - n4sch:label "Adverse Events Group ID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEGRPID"; - n4sch:Order "6"^^ . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:short_label "--GRPID"; - n4sch:label "Group ID"; - n4sch:create true . - - a n4sch:Class; - n4sch:create true; - n4sch:CoreClass false; - n4sch:label "Adverse Events Reference ID"; - n4sch:from_domains "AE"; - n4sch:short_label "AEREFID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "AEREFID"; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "7"^^ . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Reference ID"; - n4sch:from_domains "AE"; - n4sch:short_label "--REFID"; - n4sch:create true . - - a n4sch:Class; - n4sch:create true; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Sponsor-Defined Identifier"; - n4sch:short_label "AESPID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:create true; - n4sch:short_label "--SPID"; - n4sch:CoreClass false; - n4sch:label "Sponsor ID"; - n4sch:from_domains "AE" . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESPID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "8"^^; - n4sch:Core "Permissible" . - - a n4sch:Class; - n4sch:short_label "AETERM"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Reported Term for the Adverse Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:short_label "--TERM"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:label "Reported Term" . - - a ; - n4sch:_columnname_ "AETERM"; - n4sch:Order "9"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AEMODIFY"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Modified Reported Term"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Modified Reported Term"; - n4sch:short_label "--MODIFY"; - n4sch:create false . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "AEMODIFY"; - n4sch:Order "10"^^; - n4sch:_domain_ "AE" . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Lowest Level Term"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AELLT"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "--LLT"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Lowest Level Term" . - - a ; - n4sch:_columnname_ "AELLT"; - n4sch:Order "11"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Expected" . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:short_label "AELLTCD"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:label "Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:short_label "--LLTCD"; - n4sch:CoreClass false . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "AELLTCD"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "12"^^ . - - a n4sch:Class; - n4sch:short_label "AEDECOD"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Dictionary-Derived Term"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:Order "13"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "AEDECOD"; - n4sch:_domain_ "AE"; - n4sch:Core "Required" . - - a n4sch:Class; - n4sch:label "Dictionary-Derived Term"; - n4sch:short_label "--DECOD"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Preferred Term Code"; - n4sch:CoreClass false; - n4sch:short_label "AEPTCD"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:short_label "--PTCD"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code" . - - a ; - n4sch:_columnname_ "AEPTCD"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "14"^^ . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term"; - n4sch:short_label "AEHLT"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLT"; - n4sch:Order "15"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term"; - n4sch:short_label "--HLT"; - n4sch:create false . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term Code"; - n4sch:short_label "AEHLTCD"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:short_label "--HLTCD"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:label "High Level Term Code" . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLTCD"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "16"^^ . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:short_label "AEHLGT"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:create false; - n4sch:short_label "--HLGT"; - n4sch:from_domains "AE" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "17"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLGT"; - n4sch:Core "Expected" . - - - a n4sch:Class; - n4sch:short_label "AEHLGTCD"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:label "High Level Group Term Code"; - n4sch:short_label "--HLGTCD"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:from_domains "AE" . - - a ; - n4sch:_columnname_ "AEHLGTCD"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "AE"; - n4sch:Order "18"^^; - n4sch:Core "Expected" . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AECAT"; - n4sch:create false; - n4sch:label "Category for Adverse Event"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:short_label "--CAT"; - n4sch:CoreClass false; - n4sch:label "Category"; - n4sch:create false . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "19"^^; - n4sch:_columnname_ "AECAT" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:short_label "AESCAT"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Subcategory for Adverse Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:label "Subcategory"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:short_label "--SCAT"; - n4sch:CoreClass false . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESCAT"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "20"^^ . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AEPRESP"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pre-Specified Adverse Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - n4sch:TO . - - a n4sch:Class; - n4sch:short_label "--PRESP"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Pre-specified"; - n4sch:create false . - - a ; - n4sch:Order "21"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "AEPRESP"; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible" . - - - a n4sch:Class; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class"; - n4sch:short_label "AEBODSYS"; - n4sch:SUBCLASS_OF . - - - a n4sch:Relationship; - 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n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM ; - n4sch:TO . - - n4sch:MAPS_TO_CLASS - . - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM - ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - n4sch:TO - ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:FROM ; - n4sch:TO . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:TO ; - n4sch:FROM . - - - n4sch:FROM ; - n4sch:TO . - - n4sch:TO ; - n4sch:FROM . - - n4sch:FROM ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:FROM - ; - n4sch:TO . - - n4sch:TO - ; - n4sch:FROM . diff --git a/tests/test_data_providers/data/export_sdtm_v4_2domains.ttl b/tests/test_data_providers/data/export_sdtm_v4_2domains.ttl deleted file mode 100644 index bd8ed47..0000000 --- a/tests/test_data_providers/data/export_sdtm_v4_2domains.ttl +++ /dev/null @@ -1,2786 +0,0 @@ -@prefix n4sch: . - - a ; - n4sch:_filename_ "export_sdtm_2domains.ttl"; - n4sch:HAS_TABLE , ; - n4sch:_tag_ "MDR3_2" . - - a ; - n4sch:_domain_ "DM"; - n4sch:SortOrder "STUDYID,USUBJID" . - - a ; - n4sch:_domain_ "AE"; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ" . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , ; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:create true . - - a n4sch:Class; - n4sch:label "Study"; - n4sch:from_domains "AE,DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , - , , - , , - , - , - , - , , - , , - , , - , - , , - , , - , - , , - , , - , - , - , , - , , - , , - , , - , - ; - n4sch:create true; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:CLASS_RELATES_TO , , - , , - , , - , - , , - , , - , , - , , - , , - , - , - , , - , , - , , - , , - , , - , , - , , - , , - , - , , - , - , , - , - , - , , - , - , , - , - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Study"; - n4sch:label "STUDYID" . - - a n4sch:Class; - n4sch:create true; - n4sch:CoreClass false; - n4sch:label "Adverse Events Identifiers"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY , - , , - , . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "--REFID" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "--GRPID"; - n4sch:Class.label "Adverse Events Identifiers" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Identifiers"; - n4sch:label "--SPID" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Adverse Events Identifiers" . - - a n4sch:Property; - n4sch:Class.label "Subject"; - n4sch:label "USUBJID" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Reference Time Point"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Modified Reported Term"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Standard Toxicity Grade"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Relationship to Non-Study Treatment"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Adverse Event"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events Lowest Level Term"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Occurred with Overdose"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Study Day of Start of Adverse Event"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Relative to Reference Time Point"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Congenital Anomaly or Birth Defect"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Action Taken"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Primary System Organ Class Code"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Action Taken with Study Treatment"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Duration of Adverse Event"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Subcategory for Adverse Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Dictionary-Derived Term"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Results in Death"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "End Date/Time of Adverse Event"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Category for Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events Serious Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Causality"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events Preferred Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Location of Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Is Life Threatening"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Study Day of End of Adverse Event"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Reported Term for the Adverse Event"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Severity/Intensity"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:label "Adverse Events Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Medically Important Serious Event"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Outcome of Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:label "Adverse Events End Relative to Reference Period"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events Persist or Signif Disability/Incapacity"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Start Date/Time of Adverse Event"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events Epoch"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Concomitant or Additional Trtmnt Given"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pre-Specified Adverse Event"; - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Adverse Events Involves Cancer"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a - n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Primary System Organ Class"; - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a - n4sch:Property; - n4sch:Class.label "Subject Identifier for the Study"; - n4sch:label "SUBJID" . - - - a n4sch:Property; - n4sch:label "--TERM"; - n4sch:Class.label "Reported Term for the Adverse Event" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Reported Term" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Modified Reported Term"; - n4sch:label "--MODIFY" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Modified Reported Term" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events Lowest Level Term"; - n4sch:label "--LLT" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Lowest Level Term" . - - a n4sch:Class; - n4sch:label "Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - - a n4sch:Property; - n4sch:label "--LLTCD"; - n4sch:Class.label "Adverse Events Lowest Level Term Code" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Dictionary-Derived Term"; - n4sch:label "--DECOD" . - - a n4sch:Class; - n4sch:label "Dictionary-Derived Term"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code" . - - - a n4sch:Property; - n4sch:Class.label "Adverse Events Preferred Term Code"; - n4sch:label "--PTCD" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events High Level Term"; - n4sch:label "--HLT" . - - - a n4sch:Property; - n4sch:label "--HLTCD"; - n4sch:Class.label "Adverse Events High Level Term Code" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term Code" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--HLGT"; - n4sch:Class.label "Adverse Events High Level Group Term" . - - a n4sch:Class; - n4sch:label "High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE" . - - - a n4sch:Property; - n4sch:label "--HLGTCD"; - n4sch:Class.label "Adverse Events High Level Group Term Code" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Category" . - - a n4sch:Property; - n4sch:label "--CAT"; - n4sch:Class.label "Category for Adverse Event" . - 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- a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AESCAN"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "35"^^ . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESCONG"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "36"^^; - n4sch:_domain_ "AE" . - - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "37"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESDISAB" . - - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESDTH"; - n4sch:Order "38"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected" . - - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Order "39"^^; - n4sch:_columnname_ "AESHOSP"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "40"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "AESLIFE" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "AESOD"; - n4sch:_domain_ "AE"; - n4sch:Order "41"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "42"^^; - n4sch:_columnname_ "AESMIE"; - n4sch:_domain_ "AE" . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "43"^^; - n4sch:_columnname_ "AECONTRT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "AETOXGR"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE"; - n4sch:Order "44"^^ . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EPOCH"; - n4sch:Order "45"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESTDTC"; - n4sch:Order "46"^^ . - - a ; - n4sch:_columnname_ "AEENDTC"; - n4sch:Order "47"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:Order "48"^^; - n4sch:_columnname_ "AESTDY" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "49"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENDY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "AE"; - n4sch:Order "50"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEDUR" . - - n4sch:HAS_PROPERTY . - - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEENRF"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "51"^^ . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "52"^^; - n4sch:_columnname_ "AEENRTPT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENTPT"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "53"^^ . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "RFSTDTC"; - n4sch:Core "Expected"; - n4sch:Order "5"^^; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:Order "6"^^; - n4sch:_columnname_ "RFENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Order "7"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:Core "Expected" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Order "8"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "9"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Expected"; - n4sch:Order "10"^^; - n4sch:_columnname_ "RFPENDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM" . - - a ; - n4sch:Order "11"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "DTHDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "DTHFL"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "INVID"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "14"^^; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "INVNAM"; - n4sch:Order "15"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "16"^^; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY ; - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AGE" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "AGEU"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:Order "18"^^ . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "RACE"; - n4sch:Order "20"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "21"^^; - n4sch:_columnname_ "ETHNIC"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible" . - - a ; - n4sch:_columnname_ "ARMCD"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "22"^^ . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Required"; - n4sch:_columnname_ "ARM"; - n4sch:_domain_ "DM" . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARMCD"; - n4sch:_domain_ "DM"; - n4sch:Order "24"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Required" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "25"^^; - n4sch:Core "Required" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "COUNTRY"; - n4sch:Order "26"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DMDTC"; - n4sch:_domain_ "DM" . - - a ; - n4sch:Order "28"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:MAPS_TO_CLASS . - - n4sch:HAS_TABLE - , . - - n4sch:MAPS_TO_CLASS - ; - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "BRTHDTC" . - - n4sch:HAS_PROPERTY , - , , - , , - , , - , , - , ; - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "--DTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "DTHDTC" . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFENDTC" . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Class; - n4sch:label "Timing"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:HAS_PROPERTY , , - , . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "RFXENDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:label "--ENDTC"; - n4sch:Class.label "Date/Time" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "RFPENDTC" . - - a n4sch:Property; - n4sch:Class.label "Date/Time"; - n4sch:label "--STDTC" . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - n4sch:HAS_PROPERTY - ; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Study Day"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:HAS_PROPERTY , , - ; - n4sch:SUBCLASS_OF . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day" . - - a n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day" . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day" . - - n4sch:SUBCLASS_OF - ; - n4sch:HAS_PROPERTY . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - n4sch:CLASS_RELATES_TO , - . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO , - , ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Reported Term"; - n4sch:label "--TERM" . - - a n4sch:Property; - n4sch:label "--MODIFY"; - n4sch:Class.label "Modified Reported Term" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--LLT"; - n4sch:Class.label "Lowest Level Term" . - - a n4sch:Property; - n4sch:Class.label "Lowest Level Term Code"; - n4sch:label "--LLTCD" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--DECOD"; - n4sch:Class.label "Dictionary-Derived Term" . - - a n4sch:Property; - n4sch:Class.label "Preferred Term Code"; - n4sch:label "--PTCD" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--HLT"; - n4sch:Class.label "High Level Term" . - - a n4sch:Property; - n4sch:Class.label "High Level Term Code"; - n4sch:label "--HLTCD" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term"; - n4sch:label "--HLGT" . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term Code"; - n4sch:label "--HLGTCD" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "HAS_SUBCATEGORY" . - - a n4sch:Property; - n4sch:Class.label "Category"; - n4sch:label "--CAT" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SCAT"; - n4sch:Class.label "Subcategory" . - - a n4sch:Property; - n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - n4sch:HAS_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - n4sch:HAS_PROPERTY - . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--STDTC" . - - a n4sch:Property; - n4sch:label "--DTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFENDTC" . - - n4sch:Class.label "Timing"; - a n4sch:Property; - n4sch:label "RFSTDTC" . - - n4sch:HAS_PROPERTY , - , , - , , - , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:label "DTHDTC"; - n4sch:Class.label "Timing" . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY , , - , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:label "BRTHDTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--ENDTC" . - - a n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFXSTDTC" . - - n4sch:SUBCLASS_OF ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFICDTC" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "--STDY" . - - a n4sch:Property; - n4sch:Class.label "Timing"; - n4sch:label "RFPENDTC" . - - a n4sch:Property; - n4sch:label "RFXENDTC"; - n4sch:Class.label "Timing" . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:HAS_PROPERTY - . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , - , , - , - , , - , - , , - , , - , , - , , - , , - , - , , - , - , , - , - , - , , - , , - , , - , , - , , - , , - , - , , - . - - n4sch:CLASS_RELATES_TO , - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , , - , , - . - - n4sch:MAPS_TO_CLASS - . diff --git a/tests/test_data_providers/data/export_sdtm_v5_2domains.ttl b/tests/test_data_providers/data/export_sdtm_v5_2domains.ttl deleted file mode 100644 index e621a41..0000000 --- a/tests/test_data_providers/data/export_sdtm_v5_2domains.ttl +++ /dev/null @@ -1,2135 +0,0 @@ -@prefix n4sch: . - - a ; - n4sch:_filename_ "export_sdtm_2domains.ttl"; - n4sch:HAS_TABLE , ; - n4sch:_tag_ "MDR3_2" . - - a ; - n4sch:_domain_ "AE"; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ" . - - a ; - n4sch:_domain_ "DM"; - n4sch:SortOrder "STUDYID,USUBJID" . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:short_label "DM"; - n4sch:CLASS_RELATES_TO , ; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:create true . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study"; - n4sch:short_label "STUDYID"; - n4sch:from_domains "AE,DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:CLASS_RELATES_TO , , - , , - , , - , - , - , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , - , - , , - , - , , - , , - , , - , , - , , - , , - , - , , - , , - , , - , , - ; - n4sch:short_label "USUBJID"; - n4sch:create false . - - a n4sch:Class; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , - , - , - , - , , - , , - , , - , - , , - , , - , - , , - , , - , - , - ; - n4sch:short_label "AE"; - n4sch:create true; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Required" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "AE" . - - a n4sch:Class; - n4sch:label "Adverse Events Domain Abbreviation"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:short_label "DOMAIN"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE,DM"; - n4sch:short_label "DOMAIN"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Domain Abbreviation" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE" . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM" . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:short_label "AEACNOTH"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Action Taken"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Lowest Level Term"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AELLT"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Results in Death"; - n4sch:create false; - n4sch:short_label "AESDTH"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Body System or Organ Class"; - n4sch:short_label "AEBODSYS"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:short_label "AECONTRT"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Concomitant or Additional Trtmnt Given"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:short_label "AEENRTPT"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Relative to Reference Time Point" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Adverse Events Occurred with Overdose"; - n4sch:create false; - n4sch:short_label "AESOD"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Involves Cancer"; - n4sch:short_label "AESCAN"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Study Day of End of Adverse Event"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:short_label "AEENDY" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Sequence Number"; - n4sch:short_label "AESEQ"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:short_label "AEBDSYCD"; - n4sch:create false; - n4sch:label "Adverse Events Body System or Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:short_label "AEGRPID"; - n4sch:label "Adverse Events Group ID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:short_label "AESHOSP"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term"; - n4sch:short_label "AEHLT"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Duration of Adverse Event"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AEDUR"; - n4sch:create false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:short_label "AESCAT"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Subcategory for Adverse Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:short_label "AERELNST"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Relationship to Non-Study Treatment"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Study Day of Start of Adverse Event"; - n4sch:short_label "AESTDY"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:short_label "AETERM"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Reported Term for the Adverse Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:short_label "AEHLGTCD"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events High Level Group Term"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:short_label "AEHLGT"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:short_label "AESEV"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Severity/Intensity"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Reference ID"; - n4sch:from_domains "AE"; - n4sch:short_label "AEREFID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:short_label "AEACN"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Action Taken with Study Treatment"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Other Medically Important Serious Event"; - n4sch:short_label "AESMIE"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Adverse Event"; - n4sch:create false; - n4sch:short_label "AEPATT"; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:short_label "AELOC"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Location of Event"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events End Relative to Reference Period"; - n4sch:CoreClass false; - n4sch:short_label "AEENRF"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:short_label "AELLTCD"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Is Life Threatening"; - n4sch:CoreClass false; - n4sch:short_label "AESLIFE"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:short_label "AEENDTC"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:label "End Date/Time of Adverse Event"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Standard Toxicity Grade"; - n4sch:short_label "AETOXGR"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Adverse Events Preferred Term Code"; - n4sch:CoreClass false; - n4sch:short_label "AEPTCD"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a - n4sch:Class; - n4sch:short_label "AESOC"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Adverse Events Primary System Organ Class"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:create false; - n4sch:short_label "SUBJID"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:label "Adverse Events Serious Event"; - n4sch:short_label "AESER"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AEPRESP"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pre-Specified Adverse Event"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:label "Adverse Events Epoch"; - n4sch:create false; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:short_label "EPOCH" . - - a n4sch:Class; - n4sch:label "Adverse Events High Level Term Code"; - n4sch:short_label "AEHLTCD"; - n4sch:from_domains "AE"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Sponsor-Defined Identifier"; - n4sch:create false; - n4sch:short_label "AESPID"; - n4sch:SUBCLASS_OF . - - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:short_label "AESOCCD"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Primary System Organ Class Code"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events End Reference Time Point"; - n4sch:CoreClass false; - n4sch:short_label "AEENTPT"; - n4sch:create false . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:short_label "AESDISAB"; - n4sch:from_domains "AE"; - n4sch:label "Adverse Events Persist or Signif Disability/Incapacity"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:CoreClass false; - n4sch:label "Start Date/Time of Adverse Event"; - n4sch:short_label "AESTDTC"; - n4sch:from_domains "AE" . - - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AESCONG"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Congenital Anomaly or Birth Defect"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Causality"; - n4sch:from_domains "AE"; - n4sch:short_label "AEREL"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:short_label "AEDECOD"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Adverse Events Dictionary-Derived Term"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "AEMODIFY"; - n4sch:CoreClass false; - n4sch:label "Adverse Events Modified Reported Term"; - n4sch:from_domains "AE"; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AEOUT"; - n4sch:label "Outcome of Adverse Event"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:short_label "AECAT"; - n4sch:create false; - n4sch:label "Category for Adverse Event"; - n4sch:SUBCLASS_OF . - - a ; - n4sch:_columnname_ "SUBJID"; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Permissible"; - 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n4sch:label "Investigator Name"; - n4sch:from_domains "DM"; - n4sch:create false . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "INVNAM"; - n4sch:Order "15"^^; - n4sch:Core "Permissible" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:short_label "BRTHDTC"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "16"^^; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:short_label "AGE"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:label "Age" . - - a ; - n4sch:Order "17"^^; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AGE" . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:short_label "AGEU"; - n4sch:create false; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "AGEU"; - n4sch:Core "Expected"; - n4sch:Order "18"^^ . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:short_label "SEX"; - n4sch:create false; - n4sch:label "Sex" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race"; - n4sch:create false; - n4sch:short_label "RACE" . - - a ; - n4sch:_columnname_ "RACE"; - n4sch:Order "20"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity"; - n4sch:create false; - n4sch:short_label "ETHNIC" . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "ETHNIC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_CLASS ; - n4sch:Core "Permissible" . - - a n4sch:Class; - n4sch:short_label "ARMCD"; - n4sch:label "Planned Arm Code"; - n4sch:create false; - n4sch:CoreClass false; - n4sch:from_domains "DM" . - - a ; - n4sch:_columnname_ "ARMCD"; - n4sch:MAPS_TO_CLASS ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "22"^^ . - - a n4sch:Class; - n4sch:short_label "ARM"; - n4sch:create false; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm" . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "ARM"; - n4sch:_domain_ "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:short_label "ACTARMCD"; - n4sch:label "Actual Arm Code" . - - a ; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "ACTARMCD"; - n4sch:_domain_ "DM"; - n4sch:Order "24"^^; - n4sch:Core "Required" . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:short_label "ACTARM"; - n4sch:create false; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:_domain_ "DM"; - n4sch:Order "25"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:short_label "COUNTRY"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:create false . - - a ; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "COUNTRY"; - n4sch:Order "26"^^; - n4sch:Core "Required" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Demographics Date/Time of Collection"; - n4sch:short_label "DMDTC"; - n4sch:CoreClass false; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_CLASS ; - n4sch:_columnname_ "DMDTC"; - n4sch:_domain_ "DM" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:from_domains "DM"; - n4sch:short_label "--DTC"; - n4sch:create false; - n4sch:SUBCLASS_OF . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "DMDY"; - n4sch:label "Study Day of Collection"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:SUBCLASS_OF . - - a ; - n4sch:Order "28"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_CLASS . - - a n4sch:Class; - n4sch:create false; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:short_label "--DY"; - n4sch:label "Study Day of Visit/Collection/Exam"; - n4sch:SUBCLASS_OF . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:MAPS_TO_CLASS . - - n4sch:HAS_TABLE - , . - - n4sch:MAPS_TO_CLASS - ; - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - n4sch:MAPS_TO_CLASS - . - - a n4sch:Class; - n4sch:create false; - n4sch:label "Timing"; - n4sch:CoreClass false; - n4sch:short_label "T"; - n4sch:from_domains "AE,DM" . - - a n4sch:Class; - n4sch:create false; - n4sch:short_label "DY"; - n4sch:label "Study Day"; - n4sch:CoreClass false; - n4sch:from_domains "AE,DM"; - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO , - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO , - , . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "IS_A" . - - n4sch:CLASS_RELATES_TO - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:CLASS_RELATES_TO . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "HAS_SUBCATEGORY" . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:CLASS_RELATES_TO - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:CLASS_RELATES_TO - . - -<< n4sch:CLASS_RELATES_TO >> - n4sch:relationship_type "QUALIFIES" . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF - . - - n4sch:SUBCLASS_OF - . - - - n4sch:SUBCLASS_OF . - - - n4sch:SUBCLASS_OF . - - n4sch:SUBCLASS_OF . diff --git a/tests/test_data_providers/data/mydata.csv b/tests/test_data_providers/data/mydata.csv deleted file mode 100644 index 0682f75..0000000 --- a/tests/test_data_providers/data/mydata.csv +++ /dev/null @@ -1,11 +0,0 @@ -STUDYID,USUBJID,AGE,SITEID,RFSTDTC,SEX -MEA117106,85,69,108,,M -MEA117106,86,49,103,,F -MEA117106,87,52,60,2014-07-21T10:30, -MEA117106,88,46,15,2015-04-09T09:37,M -MEA117106,89,75,59,,M -MEA117106,90,58,76,,F -MEA117106,91,74,73,2015-05-28T11:10,M -MEA117106,92,58,31,2014-07-27T10:10,M -MEA117106,93,59,31,2015-05-02T11:00,M -MEA117106,94,65,59,,F diff --git a/tests/test_data_providers/data/test_get_data_generic_rename_rdfs_01.json b/tests/test_data_providers/data/test_get_data_generic_rename_rdfs_01.json deleted file mode 100644 index d28f02d..0000000 --- a/tests/test_data_providers/data/test_get_data_generic_rename_rdfs_01.json +++ /dev/null @@ -1,188 +0,0 @@ -{ - "style": { - "node-color": "#ffffff", - "border-width": 4, - "border-color": "#000000", - "radius": 50, - "node-padding": 5, - "node-margin": 2, - "outside-position": "auto", - "node-icon-image": "", - "node-background-image": "", - "icon-position": "inside", - "icon-size": 64, - "caption-position": "inside", - "caption-max-width": 200, - "caption-color": "#000000", - "caption-font-size": 50, - "caption-font-weight": "normal", - "label-position": "inside", - "label-display": "pill", - "label-color": "#000000", - "label-background-color": "#ffffff", - "label-border-color": "#000000", - "label-border-width": 4, - "label-font-size": 40, - "label-padding": 5, - "label-margin": 4, - "directionality": "directed", - "detail-position": "inline", - "detail-orientation": "parallel", - "arrow-width": 5, - "arrow-color": "#000000", - "margin-start": 5, - "margin-end": 5, - "margin-peer": 20, - "attachment-start": "normal", - "attachment-end": "normal", - "relationship-icon-image": "", - "type-color": "#000000", - "type-background-color": "#ffffff", - "type-border-color": "#000000", - "type-border-width": 0, - "type-font-size": 16, - "type-padding": 5, - "property-position": "outside", - "property-alignment": "colon", - "property-color": "#000000", - "property-font-size": 16, - "property-font-weight": "normal" - }, - "nodes": [ - { - "id": "n3", - "position": { - "x": 120.35528190568664, - "y": -254.21522558167555 - }, - "caption": "", - "style": {}, - "labels": [ - "Class" - ], - "properties": { - "label": "Subject", - "short_label": "USUBJID" - } - }, - { - "id": "n4", - "position": { - "x": 533.5406670324633, - "y": -254.21522558167555 - }, - "caption": "", - "style": {}, - "labels": [ - "Class" - ], - "properties": { - "label": "Planned Treatment Period 1", - "short_label": "TRT01P" - } - }, - { - "id": "n5", - "position": { - "x": 120.35528190568664, - "y": 86.38578454510116 - }, - "caption": "", - "style": {}, - "labels": [ - "Property" - ], - "properties": { - "label": "rdfs:label" - } - }, - { - "id": "n6", - "position": { - "x": 533.5406670324633, - "y": 86.38578454510116 - }, - "caption": "", - "style": {}, - "labels": [ - "Property" - ], - "properties": { - "label": "rdfs:label" - } - }, - { - "id": "n7", - "position": { - "x": 533.5406670324633, - "y": -445.84319253078854 - }, - "caption": "", - "style": {}, - "labels": [ - "Class" - ], - "properties": { - "label": "Sex", - "short_label": "SEX" - } - }, - { - "id": "n8", - "position": { - "x": 884.2220750403233, - "y": -445.84319253078854 - }, - "caption": "", - "style": {}, - "labels": [ - "Property" - ], - "properties": { - "label": "rdfs:label" - } - } - ], - "relationships": [ - { - "id": "n0", - "type": "CLASS_RELATES_TO", - "style": {}, - "properties": {}, - "fromId": "n3", - "toId": "n4" - }, - { - "id": "n1", - "type": "HAS_PROPERTY", - "style": {}, - "properties": {}, - "fromId": "n3", - "toId": "n5" - }, - { - "id": "n2", - "type": "HAS_PROPERTY", - "style": {}, - "properties": {}, - "fromId": "n4", - "toId": "n6" - }, - { - "id": "n3", - "type": "CLASS_RELATES_TO", - "style": {}, - "properties": {}, - "fromId": "n3", - "toId": "n7" - }, - { - "id": "n4", - "type": "HAS_PROPERTY", - "style": {}, - "properties": {}, - "fromId": "n7", - "toId": "n8" - } - ] -} \ No newline at end of file diff --git a/tests/test_data_providers/data/testdata.xls b/tests/test_data_providers/data/testdata.xls deleted file mode 100644 index 5a28143..0000000 Binary files a/tests/test_data_providers/data/testdata.xls and /dev/null differ diff --git a/tests/tests_model_applier/test_refactor_selected.py b/tests/tests_model_applier/test_refactor_selected.py index f209023..623b978 100644 --- a/tests/tests_model_applier/test_refactor_selected.py +++ b/tests/tests_model_applier/test_refactor_selected.py @@ -13,20 +13,20 @@ def prep_data(db): # Set up the metadata # first create the nodes q1 = """ - UNWIND [{_id:19220, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:4, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19221, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:29, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19222, properties:{AEDECOD:"Nasopharyngitis", _folder_:"data/dummy_study", AESTDY:43, AEBODSYS:"Infections and infestations", USUBJID:999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19223, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:85, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19224, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:113, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19225, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:141, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19226, properties:{AEDECOD:"Nasopharyngitis", _folder_:"data/dummy_study", AESTDY:162, AEBODSYS:"Infections and infestations", USUBJID:999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19227, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:169, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19228, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:197, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19229, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:225, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19230, properties:{AEDECOD:"symptom", _folder_:"data/dummy_study", AESTDY:97, AEBODSYS:"Infections and infestations", USUBJID:9999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19231, properties:{AEDECOD:"symptom2", _folder_:"data/dummy_study", AESTDY:118, AEBODSYS:"Infections and infestations", _domain_:"AE", USUBJID:9999, STUDYID:"dummy_study0", _filename_:"gsk_mae.xlsx"}}, - {_id:19239, properties:{_folder_:"data/dummy_study", SEX:"F", _domain_:"DM", USUBJID:999, SITEID:99, ARM:"100 mg- PARALLEL", STUDYID:"dummy_study0", AGE:109, _filename_:"gsk_mdm.xlsx"}}, - {_id:19240, properties:{_folder_:"data/dummy_study", SEX:"F", _domain_:"DM", USUBJID:9999, SITEID:99, ARM:"Placebo - PARALLEL", STUDYID:"dummy_study0", AGE:66, _filename_:"gsk_mdm.xlsx"}}] AS row + UNWIND [{_id:19220, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:4, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19221, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:29, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19222, properties:{AEDECOD:"Nasopharyngitis", _folder_:"data/dummy_study", AESTDY:43, AEBODSYS:"Infections and infestations", USUBJID:999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19223, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:85, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19224, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:113, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19225, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:141, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19226, properties:{AEDECOD:"Nasopharyngitis", _folder_:"data/dummy_study", AESTDY:162, AEBODSYS:"Infections and infestations", USUBJID:999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19227, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:169, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19228, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:197, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19229, properties:{AEDECOD:"Injection site reaction", _folder_:"data/dummy_study", AESTDY:225, AEBODSYS:"General disorders and administration site conditions", _domain_:"AE", USUBJID:999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19230, properties:{AEDECOD:"symptom", _folder_:"data/dummy_study", AESTDY:97, AEBODSYS:"Infections and infestations", USUBJID:9999, _domain_:"AE", STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19231, properties:{AEDECOD:"symptom2", _folder_:"data/dummy_study", AESTDY:118, AEBODSYS:"Infections and infestations", _domain_:"AE", USUBJID:9999, STUDYID:"dummy_study0", _filename_:"mae.xlsx"}}, + {_id:19239, properties:{_folder_:"data/dummy_study", SEX:"F", _domain_:"DM", USUBJID:999, SITEID:99, ARM:"100 mg- PARALLEL", STUDYID:"dummy_study0", AGE:109, _filename_:"mdm.xlsx"}}, + {_id:19240, properties:{_folder_:"data/dummy_study", SEX:"F", _domain_:"DM", USUBJID:9999, SITEID:99, ARM:"Placebo - PARALLEL", STUDYID:"dummy_study0", AGE:66, _filename_:"mdm.xlsx"}}] AS row CREATE (n:`UIL`{`UIID`: row._id}) SET n += row.properties SET n:`Source Data Row`; """ db.query(q1) @@ -72,8 +72,8 @@ def prep_data(db): db.query(q4) q5 = """ - UNWIND [{_id:19233, properties:{_folder_:"data/dummy_study", SortOrder:"USUBJID,STUDYID", _domain_:"AE", uri:"neo4j://graph.schema#Source%20Data%20Table/AE", _filename_:"gsk_mae.xlsx"}}, - {_id:19241, properties:{_folder_:"data/dummy_study", SortOrder:"STUDYID,USUBJID", _domain_:"DM", uri:"neo4j://graph.schema#Source%20Data%20Table/DM", _filename_:"gsk_mdm.xlsx"}}] AS row + UNWIND [{_id:19233, properties:{_folder_:"data/dummy_study", SortOrder:"USUBJID,STUDYID", _domain_:"AE", uri:"neo4j://graph.schema#Source%20Data%20Table/AE", _filename_:"mae.xlsx"}}, + {_id:19241, properties:{_folder_:"data/dummy_study", SortOrder:"STUDYID,USUBJID", _domain_:"DM", uri:"neo4j://graph.schema#Source%20Data%20Table/DM", _filename_:"mdm.xlsx"}}] AS row CREATE (n:`UIL`{`UIID`: row._id}) SET n += row.properties SET n:`Source Data Table`; """ db.query(q5) @@ -249,14 +249,14 @@ def test_refactor_selected(db): # Verify nodes haven't been created for AE domain, other than for Subject class cypher = """MATCH p=(n:`Source Data Table`)-[r1:HAS_DATA]-(n2:`Source Data Row`)<-[r2:FROM_DATA]-(n3) - WHERE n._filename_ = 'gsk_mae.xlsx' + WHERE n._filename_ = 'mae.xlsx' RETURN DISTINCT n3""" result = db.query(cypher) assert len(result) == 2 # only 2 data nodes should exist for Subject (refactored above) # Verify nodes have been created for DM domain cypher = """MATCH p=(n:`Source Data Table`)-[r1:HAS_DATA]-(n2:`Source Data Row`)<-[r2:FROM_DATA]-(n3) - WHERE n._filename_ = 'gsk_mdm.xlsx' + WHERE n._filename_ = 'mdm.xlsx' RETURN DISTINCT n3""" result = db.query(cypher) assert len(result) == 11 # all 11 data nodes should now exist for DM @@ -266,17 +266,17 @@ def test_refactor_selected(db): # Verify missing nodes have now been created for AE domain cypher = """MATCH p=(n:`Source Data Table`)-[r1:HAS_DATA]-(n2:`Source Data Row`)<-[r2:FROM_DATA]-(n3) - WHERE n._filename_ = 'gsk_mae.xlsx' + WHERE n._filename_ = 'mae.xlsx' RETURN DISTINCT n3""" result = db.query(cypher) assert len(result) == 23 # all 23 data nodes should now exist for AE # Finally verify all expected relationships were created - cypher = """MATCH(n)-[r]-(n1) WHERE n._filename_ = 'gsk_mae.xlsx' RETURN DISTINCT r""" + cypher = """MATCH(n)-[r]-(n1) WHERE n._filename_ = 'mae.xlsx' RETURN DISTINCT r""" result = db.query(cypher) assert len(result) == 90 - cypher = """MATCH(n)-[r]-(n1) WHERE n._filename_ = 'gsk_mdm.xlsx' RETURN DISTINCT r""" + cypher = """MATCH(n)-[r]-(n1) WHERE n._filename_ = 'mdm.xlsx' RETURN DISTINCT r""" result = db.query(cypher) assert len(result) == 23 @@ -321,7 +321,7 @@ def test_refactor_selected_2classes_domains(db): q3 = """ MATCH p=(n:`Source Data Table`)-[r1:HAS_DATA]-(n2:`Source Data Row`) - WHERE n._filename_ = 'gsk_mae.xlsx' + WHERE n._filename_ = 'mae.xlsx' OPTIONAL MATCH (n2)<-[r2:FROM_DATA]-(n3) RETURN count(n2) as rows, count(r2) as rels """ diff --git a/tests/tests_model_manager/_archive_test_model_manager.py b/tests/tests_model_manager/_archive_test_model_manager.py deleted file mode 100644 index e153526..0000000 --- a/tests/tests_model_manager/_archive_test_model_manager.py +++ /dev/null @@ -1,325 +0,0 @@ -import pytest -from model_managers import model_manager -from utils.utils import compare_unordered_lists, compare_recordsets -import pandas as pd - - -# Provide ModelManager object that can be used by the various tests that need it -# (inside, it includes a database connection) -@pytest.fixture(scope="module") -def mm(): - mm = model_manager.ModelManager(apoc=True) - yield mm - - - -def test_create_class(mm): - mm.clean_slate() - - mm.create_class("My First Class") - result = mm.get_nodes() - assert result == [{'label': 'My First Class'}] - - mm.create_class(["A", "B"]) - result = mm.get_nodes() - assert compare_recordsets(result, [{'label': 'My First Class'}, {'label': 'A'}, {'label': 'B'}]) - - mm.create_class("A") # Merge is True by default; so, nothing gets created since class "A" already exists - result = mm.get_nodes() - assert compare_recordsets(result, [{'label': 'My First Class'}, {'label': 'A'}, {'label': 'B'}]) - - mm.create_class("A", merge=False) # A 2nd class named "A" will get created - result = mm.get_nodes() - assert compare_recordsets(result, [{'label': 'My First Class'}, {'label': 'A'}, {'label': 'A'}, {'label': 'B'}]) - - mm.create_class(["B", "X"], merge=True) # Only class "X" gets created, because "B" already exists - result = mm.get_nodes() - assert compare_recordsets(result, [{'label': 'My First Class'}, {'label': 'A'}, {'label': 'A'}, {'label': 'B'}, {'label': 'X'}]) - - - -def test_create_custom_rels_from_list(mm): - mm.clean_slate() - - mm.create_class(["Study", "Site", "Subject"]) # Note that "Race" is missing - - rels = [ - ["Study", "Site"], - ["Study", "Subject"], - ["Subject", "Race"], - ["Subject", None] - ] - - mm.create_custom_rels_from_list(rels, create_if_absent = False) - q = ''' - MATCH (:Class {label:$l1})-[r:CLASS_RELATES_TO]-(:Class {label:$l2}) - RETURN count(r) AS cnt - ''' - - result = mm.query(q, {"l1": "Study", "l2": "Site"}) - assert result[0]["cnt"] == 1 - - result = mm.query(q, {"l1": "Study", "l2": "Subject"}) - assert result[0]["cnt"] == 1 - - result = mm.query(q, {"l1": "Subject", "l2": "Race"}) - assert result[0]["cnt"] == 0 # Race was not included, because no "Race" Class was present - - mm.create_custom_rels_from_list(rels, create_if_absent = True) - result = mm.query(q, {"l1": "Study", "l2": "Site"}) - assert result[0]["cnt"] == 1 - - result = mm.query(q, {"l1": "Study", "l2": "Subject"}) - assert result[0]["cnt"] == 1 - - result = mm.query(q, {"l1": "Subject", "l2": "Race"}) - assert result[0]["cnt"] == 1 # This time it gets created - - - -def test_get_all_classes(mm): - mm.clean_slate() - - class_list = ["G", "S", "K"] - mm.create_class(class_list) - - sorted = mm.get_all_classes(sort=True) - assert sorted == [{'Class': 'G'}, {'Class': 'K'}, {'Class': 'S'}] - - unsorted = mm.get_all_classes(sort=False) - assert compare_recordsets(unsorted, [{'Class': 'G'}, {'Class': 'K'}, {'Class': 'S'}]) - - long = mm.get_all_classes(include_id=True, sort=True) - for entry in long: - assert type(entry["_id_Class"]) == int - assert entry["Class"] in class_list - - - -def test_rename_classes_by_ids(mm): - mm.clean_slate() - - # Create 3 classes - mm.create_class(["A", "B", "C"]) - q = ''' - MATCH(n) - RETURN id(n) AS node_id, n.label AS node_label - ''' - result_list = mm.query(q) - # EXAMPLE: [{'node_id': 311, 'node_label': 'A'}, {'node_id': 312, 'node_label': 'B'}, {'node_id': 313, 'node_label': 'C'}] - - # Rename the 3 classes just created - mapping = [[d['node_id'], d['node_label'] + " new"] - for d in result_list] - # EXAMPLE: [[341, 'A new'], [342, 'B new'], [343, 'C new']] - - info = mm.rename_classes_by_ids(mapping) - assert compare_recordsets(info, [{'mod': 'Class: A=>A new'}, {'mod': 'Class: B=>B new'}, {'mod': 'Class: C=>C new'}]) - - for n in mapping: - # Verify that there's exactly 1 node with the given Neo4j ID's and the new names in the "label" attribute - (node_id, new_name) = n - q = ''' - MATCH(n :Class {label: $name}) WHERE id(n) = $node_id - RETURN count(n) as number_of_nodes - ''' - params = {"name": new_name, "node_id": node_id} - result = mm.query(q, params) - assert result == [{'number_of_nodes': 1}] - - - -def test_get_label_by_id(mm): - mm.clean_slate() - - result = mm.create_class("A") - A_id = result[0][0]['neo4j_id'] - assert mm.get_label_by_id(A_id) == "A" - - assert mm.get_label_by_id("Not an int") == "NA" - assert mm.get_label_by_id(None) == "NA" - - -def test_create_property(mm): - mm.clean_slate() - - mm.create_property("C", "P", merge=True) - - q = ''' - MATCH (n:Class {label:"C"})-[r:HAS_PROPERTY]->(p:Property {label:"P"}) - RETURN COUNT(r) AS rel_count - ''' - result = mm.query(q) - assert result[0]["rel_count"] == 1 - - - -def test_delete_rels(mm): - mm.clean_slate() - - result = mm.create_class(["A", "B", "C"]) - A_id = result[0][0]['neo4j_id'] - B_id = result[1][0]['neo4j_id'] - C_id = result[2][0]['neo4j_id'] - - rels = [ - ["A", "B"], - ["A", "C"], - ["B", "C"] - ] - mm.create_custom_rels_from_list(rels, create_if_absent = False) - - q = "MATCH (:Class)-[r:CLASS_RELATES_TO]->(:Class) RETURN COUNT(r) AS num_rel" - - result = mm.query(q) - assert result[0]["num_rel"] == 3 # 3 "CLASS_RELATES_TO" relationships found - - - data = [{'_id_Class1': A_id, '_id_Class2': B_id}, - {'_id_Class1': A_id, '_id_Class2': C_id}, - {'_id_Class1': B_id, '_id_Class2': C_id}] - - mm.delete_rels(data) - - result = mm.query(q) - assert result[0]["num_rel"] == 0 # The relationships are now gone - - - -def test_get_related_classes(mm): - mm.create_class(["A", "B", "C", "Lone Wolf"]) - mm.create_class_relationship("A", "B") - mm.create_class_relationship("B", "C") - mm.create_class_relationship("A", "C") - # Note: nothing connects to Class "Lone Wolf" - - df_result = mm.get_related_classes() - print(df_result) - - q = ''' - MATCH (a {label:"A"}), (b {label:"B"}), (c {label:"C"}) - RETURN [id(a), id(b), id(c)] AS id_triplet - ''' - query_result = mm.query(q) - id_A, id_B, id_C = query_result[0]["id_triplet"] - #print(id_A, id_B, id_C) - - df_expected = pd.DataFrame( - [ [id_A,"A", id_B,"B"] , - [id_A,"A", id_C,"C"] , - [id_B,"B", id_C,"C"] - ] , - columns=["_id_Class1","Class1", "_id_Class2","Class2"]) - #print(df_expected) - - # Compare the dataframes regardless of row order, - # since get_related_classes() guarantees column order but not row order - df_result_sorted = df_result.sort_values(by=df_result.columns.tolist()).reset_index(drop=True) - df_expected_sorted = df_expected.sort_values(by=df_result.columns.tolist()).reset_index(drop=True) - #print(df_result_sorted) - assert df_expected_sorted.equals(df_result_sorted) - - - -def test_get_class_properties(mm): - - # Start by requesting a non-existent `Class` node - result = mm.get_class_properties("I_dont_exist_sorry") - assert result == {} - - # Test on one `Class` node NOT attached to any `Property` nodes - q = """ - CREATE (:Class {label: "car"}) - """ - mm.query(q) - result = mm.get_class_properties("car") - assert result == {} - - # Attach a `Property` node to the `Class` node - q = """ - MATCH (n:Class {label: "car"}) MERGE (n)-[:HAS_PROPERTY]->(p:Property {label: "color"}) - """ - mm.query(q) - - result = mm.get_class_properties("car") - assert result == {'car': ['color']} - - # Attach a 2nd `Property` node to the `Class` node - q = """ - MATCH (n:Class {label: "car"}) MERGE (n)-[:HAS_PROPERTY]->(p:Property {label: "make"}) - """ - mm.query(q) - - result = mm.get_class_properties("car") - assert result == {'car': ['color', 'make']} - - # Attach a 3rd `Property` node to the `Class` node - q = """ - MATCH (n:Class {label: "car"}) MERGE (n)-[:HAS_PROPERTY]->(p:Property {label: "year"}) - """ - mm.query(q) - - result = mm.get_class_properties("car") - assert result == {'car': ['color', 'make', 'year']} - - # Now also request a 2nd, non-existing, `Class` node - result = mm.get_class_properties(["car", "i_dont_exist"]) - assert result == {'car': ['color', 'make', 'year']} - - # Create a different `Class` node, NOT attached to any `Property` nodes - q = """ - CREATE (:Class {label: "boat"}) - """ - mm.query(q) - result = mm.get_class_properties(["car", "boat"]) - print(result) - assert result == {'car': ['color', 'make', 'year']} - # TODO: is the above result what we really want??? Or should it be: {'car': ['color', 'make', 'year'], 'boat': []} - - # Attach a `Property` node to the new ("boat") `Class` node - q = """ - MATCH (n:Class {label: "boat"}) MERGE (n)-[:HAS_PROPERTY]->(p:Property {label: "number_masts"}) - """ - mm.query(q) - - result = mm.get_class_properties(["car", "boat"]) - assert result == {'car': ['color', 'make', 'year'], 'boat': ['number_masts']} - - # Attach another `Property` node to the new ("boat") `Class` node - q = """ - MATCH (n:Class {label: "boat"}) MERGE (n)-[:HAS_PROPERTY]->(p:Property {label: "draft"}) - """ - mm.query(q) - - result = mm.get_class_properties(["car", "boat"]) - assert result == {'car': ['color', 'make', 'year'], 'boat': ['number_masts', 'draft']} - - # TODO: test the scenario of a `Property` node linked to - # by multiple distinct `Class` nodes. Alexey said: "I think it can be a valid scenario in the future" - - -def test_load_mappings_from_df_1(mm): - test_df = pd.DataFrame([ - {'Class':'ZZZ', 'Property':None}, - {'Class':'ZZZ', 'Property':'abc'}, - {'Class':'ZZZ', 'Property':'zyx', 'Source Data Table':'adsl', 'Source Data Column':'country'}, - {'Class':'ZZZ', 'Property':'new_property_no_mapping', 'Source Data Table':None, 'Source Data Column':'country'} - ]) - mm.clean_slate() - mm.query(""" - CREATE (adsl:`Source Data Table`{_domain_:'adsl'})-[:HAS_COLUMN]->(:`Source Data Column`{_columnname_:'country'}) - CREATE (adsl)-[:HAS_COLUMN]->(:`Source Data Column`{_columnname_:'dummy'}) - """) - mm.load_mappings_from_df(test_df) - result = mm.query( - """ - MATCH (adsl:`Source Data Table`{_domain_:'adsl'})-[:HAS_COLUMN]->(country:`Source Data Column`{_columnname_:'country'}), - (adsl)-[:HAS_COLUMN]->(:`Source Data Column`{_columnname_:'dummy'}), - (country)-[:MAPS_TO_PROPERTY]->(zyx:Property{label:'zyx'}), - (zyx)<-[:HAS_PROPERTY]-(class:Class{label:'ZZZ'}), - (class)-[:HAS_PROPERTY]->(:Property{label:'abc'}), - (class)-[:HAS_PROPERTY]->(:Property{label:'new_property_no_mapping'}) - RETURN * - """ - ) - assert len(result) == 1, "Check test database that the expected mapping was created" \ No newline at end of file diff --git a/tests/tests_query_builders/_archive_test_query_builder_general.py b/tests/tests_query_builders/_archive_test_query_builder_general.py deleted file mode 100644 index de4db32..0000000 --- a/tests/tests_query_builders/_archive_test_query_builder_general.py +++ /dev/null @@ -1,207 +0,0 @@ -import pytest -import re -from query_builders.query_builder import QueryBuilder - - -# Provide QueryBuilder object that can be used by the various tests that need it -# (inside, it includes a database connection) -@pytest.fixture(scope="module") -def qbr(): - qbr = QueryBuilder() - #qbr.clean_slate() #nothing is written/read to/from the database in these tests - yield qbr - - -def test_list_data_labels(qbr): - test_classes = ['Class 1', '$$$'] - generated_list = qbr.list_data_labels(classes=test_classes) - assert generated_list == ['(`class 1`:`Class 1`)', '(`$$$`:`$$$`)'] - - -def test_list_where_conditions_per_dict(qbr): - test_map = { - 'CAR': { - 'year': 2021 - }, - 'BOAT': { - 'make': 'Jeanneau' - } - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ["`car`.`year` = $par_1", "`boat`.`make` = $par_2"] - assert data_binding_dict == {"par_1": 2021, "par_2": 'Jeanneau'} - # Notice that 2021 is an integer, not a string - - - test_map = { - 'SUBJECT': { - 'USUBJID': '01-001', - 'SUBJID': '001' - }, - 'SEX': { - 'ASEX': 'Male' - } - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ["`subject`.`USUBJID` = $par_1", "`subject`.`SUBJID` = $par_2", "`sex`.`ASEX` = $par_3"] - assert data_binding_dict == {"par_1": '01-001', "par_2": '001', "par_3": 'Male'} - - # test negation - test_map = {"Sex": {"SEX": "M"}, "!Race": {"RACE": "WHITE"}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ['`sex`.`SEX` = $par_1', 'NOT (`race`.`RACE` = $par_2)'] - assert data_binding_dict == {'par_1': 'M', 'par_2': 'WHITE'} - - # Test list inclusion - test_map = { - 'CAR': { - 'year': 2021 - }, - 'BOAT': { - 'make': ['Jeanneau', 'C&C'] # value is a list - } - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ["`car`.`year` = $par_1", "`boat`.`make` in $par_2"] - assert data_binding_dict == {"par_1": 2021, "par_2": ['Jeanneau', 'C&C']} - - - # Now some pathological cases - test_map = { - 'EMPTY': { - } - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == [] - assert data_binding_dict == {} - - - test_map = { - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == [] - assert data_binding_dict == {} - - - test_map = { - 'POTENTIAL TROUBLE': { - 'My value has a single quote': "It's tricky" - }, - } - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ["`potential trouble`.`My value has a single quote` = $par_1"] - assert data_binding_dict == {"par_1" : "It's tricky"} - - -def test_where_conditions_ranges(qbr): - - #all True - test_map = {"Age": {"AGE": {"min": 18, "max": 65, "max_include": True, "min_include": True, "incl_null": True}}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - expected = ['(`age`.`AGE` IS NULL OR ($par_1 <= `age`.`AGE` <= $par_2))'] - # print(Cypher_list) - # print(expected) - assert Cypher_list == expected - assert data_binding_dict == {'par_1': 18, 'par_2': 65} - - #one False, incl_null == None - test_map = {"Age": {"AGE": {"min": 18, "max": 65, "max_include": False, "min_include": True}}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ['($par_1 <= `age`.`AGE` < $par_2)'] - assert data_binding_dict == {'par_1': 18, 'par_2': 65} - - #borders False, incl_null == None - test_map = {"Age": {"AGE": {"min": 18, "max": 65, "max_include": False, "min_include": False}}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ['($par_1 < `age`.`AGE` < $par_2)'] - assert data_binding_dict == {'par_1': 18, 'par_2': 65} - - #all False - test_map = {"Age": {"AGE": {"min": 18, "max": 65, "max_include": False, "min_include": False, "incl_null": False}}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ['(`age`.`AGE` IS NOT NULL AND ($par_1 < `age`.`AGE` < $par_2))'] - assert data_binding_dict == {'par_1': 18, 'par_2': 65} - - #incl_null == False alone - test_map = {"Age": {"AGE": {"incl_null": False}}} - - (Cypher_list, data_binding_dict) = qbr.list_where_conditions_per_dict(mp=test_map) - assert Cypher_list == ['`age`.`AGE` IS NOT NULL'] - assert data_binding_dict == {'par_1': None, 'par_2': None} - - -def test_generate_return(qbr): - # Note: the return_properties argument to qb_generate_return() is not implemented - - generated_string, data_dict = qbr.generate_return(['Single_class']) - #assert generated_string == "RETURN apoc.map.mergeList([`single_class`{.*}]) as all" - assert generated_string == "RETURN apoc.map.mergeList([CASE WHEN `single_class`{.*} IS NULL THEN {} ELSE `single_class`{.*} END]) as all" - - generated_string, data_dict = qbr.generate_return(['Study', 'Site', 'Subject', 'Parameter Category', 'Parameter']) - #assert generated_string == "RETURN apoc.map.mergeList([`study`{.*}, `site`{.*}, `subject`{.*}, `parameter category`{.*}, `parameter`{.*}]) as all" - assert generated_string.replace("\n","") == "RETURN apoc.map.mergeList([CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END, CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END, CASE WHEN `subject`{.*} IS NULL THEN {} ELSE `subject`{.*} END, CASE WHEN `parameter category`{.*} IS NULL THEN {} ELSE `parameter category`{.*} END, CASE WHEN `parameter`{.*} IS NULL THEN {} ELSE `parameter`{.*} END]) as all" - - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], - return_nodeid = True) - #assert generated_string == "RETURN apoc.map.mergeList([{`Study`:id(`study`)}, `study`{.*}, {`Site`:id(`site`)}, `site`{.*}]) as all" - assert generated_string.replace("\n","") == "RETURN apoc.map.mergeList([{`Study`:id(`study`)}, CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END, {`Site`:id(`site`)}, CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END]) as all" - - - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], - return_disjoint = True) - #assert generated_string == "RETURN collect(distinct apoc.map.mergeList([`study`{.*}])) as `Study`, collect(distinct apoc.map.mergeList([`site`{.*}])) as `Site`" - assert generated_string.replace("\n","") == "RETURN collect(distinct apoc.map.mergeList([CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END])) as `Study`, collect(distinct apoc.map.mergeList([CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END])) as `Site`" - - # testing renaming to rdfs:label (when qbr.mode = 'schema_CLASS') - qbr.mode = 'schema_CLASS' - generated_string, data_dict = qbr.generate_return(['Study', 'Site']) - crop_generate_string = re.sub(r'\s+', ' ', generated_string.replace("\n", "")) - expected = "RETURN apoc.map.mergeList([ apoc.map.fromPairs([key in keys(CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END) | [ CASE WHEN key = 'rdfs:label' THEN $rename_keys['Study'] ELSE key END, CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END[key]]]) , apoc.map.fromPairs([key in keys(CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END) | [ CASE WHEN key = 'rdfs:label' THEN $rename_keys['Site'] ELSE key END, CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END[key]]]) ]) as all" - assert crop_generate_string == expected - - # testing renaming to rdfs:label (when qbr.mode = 'schema_CLASS') - qbr.mode = 'schema_CLASS' - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], prefix_keys_with_label=True) - crop_generate_string = re.sub(r'\s+', ' ', generated_string.replace("\n", "")) - expected = "RETURN apoc.map.mergeList([ apoc.map.fromPairs([key in keys(CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END) | [ CASE WHEN key = 'rdfs:label' THEN $rename_keys['Study'] ELSE key END, CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END[key]]]) , apoc.map.fromPairs([key in keys(CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END) | [ CASE WHEN key = 'rdfs:label' THEN $rename_keys['Site'] ELSE key END, CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END[key]]]) ]) as all" - print(crop_generate_string) - print(expected) - #assert crop_generate_string == expected - qbr.mode = 'schema_PROPERTY' # returning back to 'schema_PROPERTY' mode - - # Verify that an exception is raised when given an empty list of classes - with pytest.raises(Exception): - assert qbr.generate_return([]) # an empty list is expected to raise an exception - assert qbr.generate_return('where is the list??') - assert qbr.generate_return(666) - assert qbr.generate_return((1, 2)) - assert qbr.generate_return({}) - - -def test_generate_return_return_properties(qbr): - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], - return_disjoint = True, return_nodeid = True) - #assert generated_string == "RETURN collect(distinct apoc.map.mergeList([{`Study`:id(`study`)}, `study`{.*}])) as `Study`, collect(distinct apoc.map.mergeList([{`Site`:id(`site`)}, `site`{.*}])) as `Site`" - assert generated_string.replace("\n","") == "RETURN collect(distinct apoc.map.mergeList([{`Study`:id(`study`)}, CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END])) as `Study`, collect(distinct apoc.map.mergeList([{`Site`:id(`site`)}, CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END])) as `Site`" - - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], - return_disjoint = True, return_properties=["STUDYID", "SITEID"]) - assert generated_string.replace("\n","") == "RETURN collect(distinct apoc.map.mergeList([apoc.map.clean(apoc.map.submap(" \ - "CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END, " \ - "['STUDYID', 'SITEID'], NULL, False),[],[NULL])])) as `Study`, " \ - "collect(distinct apoc.map.mergeList([apoc.map.clean(apoc.map.submap(" \ - "CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END, " \ - "['STUDYID', 'SITEID'], NULL, False),[],[NULL])])) as `Site`" - - generated_string, data_dict = qbr.generate_return(['Study', 'Site'], - return_disjoint=False, return_properties=["STUDYID", "SITEID"]) - assert generated_string.replace("\n","") == "RETURN apoc.map.mergeList([" \ - "apoc.map.clean(apoc.map.submap(CASE WHEN `study`{.*} IS NULL THEN {} ELSE `study`{.*} END, " \ - "['STUDYID', 'SITEID'], NULL, False),[],[NULL]), " \ - "apoc.map.clean(apoc.map.submap(CASE WHEN `site`{.*} IS NULL THEN {} ELSE `site`{.*} END, " \ - "['STUDYID', 'SITEID'], NULL, False),[],[NULL])]) as all" \ No newline at end of file diff --git a/tests/tests_query_builders/_archive_test_query_builder_mode_noschema.py b/tests/tests_query_builders/_archive_test_query_builder_mode_noschema.py deleted file mode 100644 index 925da83..0000000 --- a/tests/tests_query_builders/_archive_test_query_builder_mode_noschema.py +++ /dev/null @@ -1,50 +0,0 @@ -import pytest -from query_builders.query_builder import QueryBuilder - - -# Provide QueryBuilder object that can be used by the various tests that need it -# (inside, it includes a database connection) -@pytest.fixture(scope="module") -def qbr(): - qbr = QueryBuilder(mode='noschema') - qbr.clean_slate() - yield qbr - - -def test_qbns_get_label_relationships_df(qbr): - qbr.clean_slate() - my_classes = ['Apple', 'Orange', 'Fruit'] - qbr.query("CREATE (a:Apple)-[:IS_A]->(f:Fruit), (o:Orange)-[:IS_A]->(f)") - result = qbr.qbns_get_label_relationships_df(classes=my_classes).to_dict(orient='records') - expected_result = [{'souce_lbl': 'Apple', 'rel': 'IS_A', 'target_lbl': 'Fruit'}, - {'souce_lbl': 'Orange', 'rel': 'IS_A', 'target_lbl': 'Fruit'}] - assert result == expected_result - -def test_qbns_get_label_relationships_df2(qbr): - qbr.clean_slate() - ia = qbr.create_node_by_label_and_dict('Apple', {'type':1}) - io = qbr.create_node_by_label_and_dict('Orange', {'type': 3}) - if_ = qbr.create_node_by_label_and_dict('Fruit', {'n_types':9999}) - iarel = qbr.create_node_by_label_and_dict('AdditioanlInfo', {'desc': 'blah-blah'}) - qbr.link_nodes_by_ids(ia,if_,'IS_A') - qbr.link_nodes_by_ids(io, if_, 'IS_A') - qbr.link_nodes_by_ids(ia, iarel, 'IS_A') - result = qbr.qbns_get_label_relationships_df(['Apple', 'Orange', 'Fruit', 'AdditioanlInfo']).to_dict(orient='records') - expected_result = [{'souce_lbl': 'Apple', 'rel': 'IS_A', 'target_lbl': 'AdditioanlInfo'}, - {'souce_lbl': 'Apple', 'rel': 'IS_A', 'target_lbl': 'Fruit'}, - {'souce_lbl': 'Orange', 'rel': 'IS_A', 'target_lbl': 'Fruit'}] - assert result == expected_result - - -def test_qbns_generate_query_body(qbr): - qbr.clean_slate() - my_classes = ['Apple', 'Orange', 'Fruit'] - qbr.query("CREATE (a:Apple)-[:IS_A]->(f:Fruit), (o:Orange)-[:IS_A]->(f)") - cypher, cypher_dict = qbr.qbns_generate_query_body(classes=my_classes) - expected_cypher = "MATCH (`apple`:`Apple`),(`orange`:`Orange`),(`fruit`:`Fruit`),(`apple`:`Apple`)-[:`IS_A`]->(`fruit`:`Fruit`),(`orange`:`Orange`)-[:`IS_A`]->(`fruit`:`Fruit`)" - assert cypher.replace("\n", "").strip() == expected_cypher - assert cypher_dict == {} - - cypher2, cypher_dict2 = qbr.qbns_generate_query_body(classes = my_classes, - where_map = {'Apple': {'label': 'NON-EXISTING VALUE'}}) - assert cypher_dict2 == {'par_1': 'NON-EXISTING VALUE'} diff --git a/tests/tests_query_builders/_archive_test_query_builder_mode_schema.py b/tests/tests_query_builders/_archive_test_query_builder_mode_schema.py deleted file mode 100644 index b8bab08..0000000 --- a/tests/tests_query_builders/_archive_test_query_builder_mode_schema.py +++ /dev/null @@ -1,187 +0,0 @@ -import pytest -from query_builders import query_builder - - -# Provide QueryBuilder object that can be used by the various tests that need it -# (inside, it includes a database connection) -@pytest.fixture(scope="module") -def qbr(): - qbr = query_builder.QueryBuilder(mode='schema_PROPERTY') - qbr.clean_slate() - yield qbr - - -def test_qb_generate_query_body(qbr): - # Test out some pathological cases for starters (non-existent `Class` nodes) - (q, data_dict) = qbr.qb_generate_query_body([""]) - assert q.strip() == "MATCH (``:``)" - assert data_dict == {} - - (q, data_dict) = qbr.qb_generate_query_body(["cl"]) - assert q.strip() == "MATCH (`cl`:`cl`)" - assert data_dict == {} - - (q, data_dict) = qbr.qb_generate_query_body(["cl1", "cl2"]) - assert q.replace("\n", "").strip() == "MATCH (`cl1`:`cl1`),(`cl2`:`cl2`)" - assert data_dict == {} - - # A simple but non-trivial run, with 2 `Class` nodes and a "CLASS_RELATES_TO" relationship between them - qbr.clean_slate() - my_classes = qbr.mm.create_related_classes_from_list([['Study', 'Site']]) - (q, data_dict) = qbr.qb_generate_query_body(my_classes, allow_unrelated_subgraphs=True) - crop_q = q.replace("\n", "").strip() - expected_q = "MATCH (`site`:`Site`),(`study`:`Study`),(`study`)-[:`HAS_SITE`]->(`site`)" - assert crop_q == expected_q - assert data_dict == {} - - # Now, prepare the data as was done in the 1st example in testqb_list_data_relationships_per_schema() - qbr.clean_slate() - my_classes = ['Study', 'Site', 'Subject', 'Parameter Category', 'Parameter'] - qbr.query( - "UNWIND $classes as class CREATE (c1:Class{label:class})", - {'classes': my_classes} - ) - qbr.mm.create_custom_rels_from_list([['Study', 'Site'], - ['Study', 'Subject'], - ['Site', 'Subject'], - ['Parameter Category', 'Parameter']]) - (q, data_dict) = qbr.qb_generate_query_body(my_classes, allow_unrelated_subgraphs=True) - """ - Note: the internal variable match_node_list will be: - ['(`study`:`Study`)', '(`site`:`Site`)', '(`subject`:`Subject`)', '(`parameter category`:`Parameter Category`)', '(`parameter`:`Parameter`)'] - and match_relationships_per_schema will be: - ['(`parameter`)', - '(`parameter category`)-[:`HAS_PARAMETER`]->(`parameter`)', - '(`parameter category`)', - '(`site`)-[:`HAS_SUBJECT`]->(`subject`)', - '(`site`)', - '(`study`)-[:`HAS_SITE`]->(`site`)', - '(`study`)-[:`HAS_SUBJECT`]->(`subject`)', - '(`study`)', - '(`subject`)'] - """ - crop_q = q.replace("\n", "").strip() - expected_q = "MATCH (`study`:`Study`),(`site`:`Site`),(`subject`:`Subject`)," \ - "(`parameter category`:`Parameter Category`),(`parameter`:`Parameter`)," \ - "(`parameter category`)-[:`HAS_PARAMETER`]->(`parameter`)," \ - "(`site`)-[:`HAS_SUBJECT`]->(`subject`),(`study`)-[:`HAS_SITE`]->(`site`),(`study`)-[:`HAS_SUBJECT`]->(`subject`)" - # print(crop_q) - # print(expected_q) - assert crop_q == expected_q - assert data_dict == {} - - # Repeat the last run, but this time with a mapping for the Cypher clause - where_map = { - 'SITE': { - 'location': 'Miami' - }, - 'SUBJECT': { - 'user_id': 123 - } - } - - (q, data_dict) = qbr.qb_generate_query_body(my_classes, where_map=where_map, allow_unrelated_subgraphs=True) - - expected_q += " WHERE `site`.`location` = $par_1 AND `subject`.`user_id` = $par_2" # Same as before, but with an extra part - assert q.replace("\n", "").strip() == expected_q - assert data_dict == {'par_1': 'Miami', 'par_2': 123} - - -def test_generate_query_body_optional_match(qbr): - qbr_o = query_builder.QueryBuilder(allow_optional_classes=True) - qbr_o.clean_slate() - qbr_o.mm.create_related_classes_from_list([ - ['Study', 'Site'], - ['Site', 'Subject'], - ['Study', 'Subject'], - ['Site', 'SiteName'] - ]) - my_classes = ['Study', 'Site', 'SiteName**', 'Subject**'] - (q, data_dict) = qbr_o.generate_query_body(my_classes) - q_crop = q.replace("\n", "").strip().replace(chr(10), '') - - q_expected = " ".join([ - "MATCH (`study`:`Study`),(`site`:`Site`),(`study`)-[:`HAS_SITE`]->(`site`)", - "OPTIONAL MATCH (`sitename`:`SiteName`),(`site`)-[:`HAS_SITENAME`]->(`sitename`)", - "OPTIONAL MATCH (`subject`:`Subject`),(`site`)-[:`HAS_SUBJECT`]->(`subject`),(`study`)-[:`HAS_SUBJECT`]->(`subject`)" - ]) - print(q_crop) - print(q_expected) - - assert q_crop == q_expected - assert data_dict == {} - -def test_qb_list_data_relationships_per_schema(qbr): - # Preparing data : create some `Class` nodes, and some "CLASS_RELATES_TO" relationships between them - qbr.clean_slate() - my_classes = qbr.mm.create_related_classes_from_list([['Study', 'Site'], - ['Study', 'Subject'], - ['Site', 'Subject'], - ['Parameter Category', 'Parameter']]) - extra_classes = qbr.mm.create_related_classes_from_list([['Some Other Class 1', 'Some Other Class 2']]) - - #allow_unrelated_subgraphs=True - generated_list = qbr.qb_list_data_relationships_per_schema(my_classes, allow_unrelated_subgraphs=True) - expected_list = ['(`parameter category`)-[:`HAS_PARAMETER`]->(`parameter`)', - '(`site`)-[:`HAS_SUBJECT`]->(`subject`)', - '(`study`)-[:`HAS_SITE`]->(`site`)', - '(`study`)-[:`HAS_SUBJECT`]->(`subject`)', - ] - # print(generated_list) - # print(expected_list) - assert generated_list == expected_list - - #allow_unrelated_subgraphs = False - generated_list2 = [] - try: - generated_list2 = qbr.qb_list_data_relationships_per_schema(my_classes, allow_unrelated_subgraphs=False) - except Exception as e: - expected_exception = "Provided classes are not all related: ['Parameter', 'Parameter Category', 'Site', 'Study', 'Subject']" - assert str(e) == expected_exception - assert len(generated_list2) == 0 - - #subclass and custom relationship type - qbr.query(""" - MATCH (c:Class{label:'Parameter'})<-[r:CLASS_RELATES_TO]->(:Class) - SET r.relationship_type = "INCLUDES" - MERGE (c)<-[:SUBCLASS_OF]-(c2:Class{label:'Lab Parameter'}) - """) - generated_list3 = qbr.qb_list_data_relationships_per_schema( - ['Lab Parameter', 'Parameter Category', 'Site', 'Study', 'Subject'], - allow_unrelated_subgraphs=True - ) - expected_list3 = ['(`parameter category`)-[:`INCLUDES`]->(`lab parameter`)', - '(`site`)-[:`HAS_SUBJECT`]->(`subject`)', - '(`study`)-[:`HAS_SITE`]->(`site`)', - '(`study`)-[:`HAS_SUBJECT`]->(`subject`)', - ] - assert generated_list3 == expected_list3 - - - # Try out an empty list - generated_list = qbr.qb_list_data_relationships_per_schema([], allow_unrelated_subgraphs = True) - assert generated_list == [] - - # A simple case with just 1 class, and no "CLASS_RELATES_TO" relationships - my_classes = ['color'] - qbr.clean_slate() - qbr.query( - "UNWIND $classes as class CREATE (c1:Class{label:class})", - {'classes': my_classes} - ) - generated_list = qbr.qb_list_data_relationships_per_schema(my_classes, allow_unrelated_subgraphs = True) - expected_list = [] # this case the nodes with label 'color' will be matched with qb.list_data_labels - here an empty list is expected - assert generated_list == expected_list - - # A slightly more complex case, with 2 class, and a "CLASS_RELATES_TO" relationship between them - my_classes = ['car', 'vehicle'] - qbr.clean_slate() - qbr.query( - "UNWIND $classes as class CREATE (c1:Class{label:class})", - {'classes': my_classes} - ) - - qbr.mm.create_custom_rels_from_list([['car', 'vehicle']]) - generated_list = qbr.qb_list_data_relationships_per_schema(my_classes, allow_unrelated_subgraphs = True) - expected_list = ['(`car`)-[:`HAS_VEHICLE`]->(`vehicle`)'] - assert generated_list == expected_list diff --git a/tests/tests_query_builders/test_qb2.py b/tests/tests_query_builders/test_qb2.py index 69b8374..86187a3 100644 --- a/tests/tests_query_builders/test_qb2.py +++ b/tests/tests_query_builders/test_qb2.py @@ -1,4 +1,3 @@ -import re import pytest from query_builders.query_builder import QueryBuilder diff --git a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_2domains_117106.ttl b/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_2domains_117106.ttl deleted file mode 100644 index 12e5c8d..0000000 --- a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_2domains_117106.ttl +++ /dev/null @@ -1,1538 +0,0 @@ -@prefix n4sch: . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Class; - n4sch:label "Adverse Events"; - n4sch:HAS_PROPERTY , , - , , - , , - ; - n4sch:from_domains "AE"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a n4sch:Property; - n4sch:label "--REFID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "DOMAIN" . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE", "DM"; - n4sch:CLASS_RELATES_TO , , - . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Study Day of End of Observation"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Occurred with Overdose"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Action Taken with Study Treatment"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Relative to Reference Time Point"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Outcome of Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Primary System Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Epoch"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Relationship to Non-Study Treatment"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Severity"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Modified Reported Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Location of Event"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Body System or Organ Class"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Other Medically Important Serious Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Pre-specified"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Congenital Anomaly or Birth Defect"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Other Action Taken"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Toxicity Grade"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Lowest Level Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Serious Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "End Date/Time of Observation"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Start Date/Time of Observation"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study"; - n4sch:from_domains "AE", "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Category"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Dictionary-Derived Term"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO , , - ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Causality"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Is Life Threatening"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:from_domains "DM", "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term Code"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Relative to Reference Period"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Primary System Organ Class"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Persist or Signif Disability/Incapacity"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Body System or Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Results in Death"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subcategory"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Day of Start of Observation"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Involves Cancer"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Duration"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Reported Term"; - n4sch:CLASS_RELATES_TO , ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Concomitant or Additional Trtmnt Given"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Reference Time Point"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "AE" . - - a ; - n4sch:Order "37"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESDISAB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ"; - n4sch:_domain_ "AE" . - - a ; - n4sch:Order "15"^^; - n4sch:_columnname_ "AEHLT"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "20"^^; - n4sch:_columnname_ "AESCAT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESTDTC"; - n4sch:Order "46"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "24"^^; - n4sch:_columnname_ "AESOC"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESOCCD"; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "25"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "38"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESDTH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEPRESP"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AECAT"; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:Order "19"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AETOXGR"; - n4sch:Core "Permissible"; - n4sch:Order "44"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLGTCD"; - n4sch:Order "18"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "42"^^; - n4sch:_columnname_ "AESMIE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "53"^^; - n4sch:_columnname_ "AEENTPT"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AETERM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "12"^^; - n4sch:_columnname_ "AELLTCD"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:_columnname_ "AEHLGT"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "45"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "EPOCH"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "31"^^; - n4sch:_columnname_ "AEREL"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "5"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESEQ"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "41"^^; - n4sch:_columnname_ "AESOD"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEBDSYCD"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "23"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "40"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESLIFE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESPID"; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:Order "8"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESER"; - n4sch:Order "28"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEGRPID"; - n4sch:Order "6"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESEV"; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AECONTRT"; - n4sch:Order "43"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "33"^^; - n4sch:_columnname_ "AEPATT"; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "51"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENRF"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "10"^^; - n4sch:_columnname_ "AEMODIFY"; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "7"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEREFID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "4"^^; - n4sch:_columnname_ "SUBJID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "36"^^; - n4sch:_columnname_ "AESCONG"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEENDY"; - n4sch:_domain_ "AE"; - n4sch:Order "49"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "30"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEACNOTH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "35"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESCAN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "47"^^; - n4sch:_columnname_ "AEENDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "3"^^; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_columnname_ "AEPTCD"; - n4sch:Order "14"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESHOSP"; - n4sch:Order "39"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEACN"; - n4sch:Order "29"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "50"^^; - n4sch:_columnname_ "AEDUR"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "32"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AERELNST"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "52"^^; - n4sch:_columnname_ "AEENRTPT"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "11"^^; - n4sch:_columnname_ "AELLT"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "16"^^; - n4sch:_columnname_ "AEHLTCD"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESTDY"; - n4sch:Order "48"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "34"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEOUT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "26"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AELOC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AEBODSYS"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "13"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEDECOD"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Study"; - n4sch:label "STUDYID" . - - a n4sch:Property; - n4sch:Class.label "Subject"; - n4sch:label "USUBJID" . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:label "Demographics"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY , . - - a - n4sch:Property; - n4sch:Class.label "Subject Identifier for the Study"; - n4sch:label "SUBJID" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "4"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "SUBJID"; - n4sch:_domain_ "DM" . - - a n4sch:Property; - n4sch:Class.label "Reported Term"; - n4sch:label "--TERM" . - - a n4sch:Property; - n4sch:label "--MODIFY"; - n4sch:Class.label "Modified Reported Term" . - - a n4sch:Property; - n4sch:label "--LLT"; - n4sch:Class.label "Lowest Level Term" . - - a n4sch:Property; - n4sch:Class.label "Lowest Level Term Code"; - n4sch:label "--LLTCD" . - - a n4sch:Property; - n4sch:label "--DECOD"; - n4sch:Class.label "Dictionary-Derived Term" . - - a n4sch:Property; - n4sch:Class.label "Preferred Term Code"; - n4sch:label "--PTCD" . - - a n4sch:Property; - n4sch:label "--HLT"; - n4sch:Class.label "High Level Term" . - - a n4sch:Property; - n4sch:Class.label "High Level Term Code"; - n4sch:label "--HLTCD" . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term"; - n4sch:label "--HLGT" . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term Code"; - n4sch:label "--HLGTCD" . - - a n4sch:Property; - n4sch:Class.label "Category"; - n4sch:label "--CAT" . - - a n4sch:Property; - n4sch:label "--SCAT"; - n4sch:Class.label "Subcategory" . - - a n4sch:Property; - n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Investigator Name"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Actual Arm Code" . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Age" . - - a n4sch:Class; - n4sch:label "Date/Time of Informed Consent"; - n4sch:CoreClass false; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of End of Participation"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Study Site Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Sex" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of First Study Treatment" . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Reference Start Date/Time"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:label "Date/Time of Death"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Subject Reference End Date/Time"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Study Day of Visit/Collection/Exam" . - - a n4sch:Class; - n4sch:label "Planned Arm Code"; - n4sch:CoreClass false; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Investigator Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Last Study Treatment"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Death Flag"; - n4sch:from_domains "DM" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Demographics" . - - n4sch:label "DOMAIN"; - a n4sch:Property; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Demographics" . - - n4sch:HAS_PROPERTY , - , ; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:SortOrder "STUDYID,USUBJID"; - n4sch:_domain_ "DM"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:Order "23"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ARM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AGE"; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFENDTC"; - n4sch:Order "6"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AGEU"; - n4sch:Order "18"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:_columnname_ "DTHFL"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "13"^^; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible"; - n4sch:Order "28"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "11"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "DTHDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "15"^^; - n4sch:_columnname_ "INVNAM"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:_domain_ "DM"; - n4sch:Order "7"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "14"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "INVID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ACTARMCD"; - n4sch:Core "Required"; - n4sch:Order "24"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "21"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "ETHNIC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:Order "16"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFPENDTC"; - n4sch:Order "10"^^; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:Order "5"^^; - n4sch:_columnname_ "RFSTDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:Core "Required"; - n4sch:Order "25"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "20"^^; - n4sch:_columnname_ "RACE"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Core "Expected"; - n4sch:Order "8"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DMDTC"; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "26"^^; - n4sch:_columnname_ "COUNTRY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ARMCD"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - a - n4sch:Property; - n4sch:Class.label "Subject Reference Start Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "RFENDTC"; - n4sch:Class.label "Subject Reference End Date/Time" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time of First Study Treatment" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Last Study Treatment"; - n4sch:label "RFXENDTC" . - - n4sch:HAS_PROPERTY - . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time of Informed Consent" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "RFPENDTC"; - n4sch:Class.label "Date/Time of End of Participation" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Death"; - n4sch:label "DTHDTC" . - - a n4sch:Property; - n4sch:label "DTHFL"; - n4sch:Class.label "Subject Death Flag" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "SITEID"; - n4sch:Class.label "Study Site Identifier" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Investigator Identifier"; - n4sch:label "INVID" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Investigator Name"; - n4sch:label "INVNAM" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Birth"; - n4sch:label "BRTHDTC" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "AGE"; - n4sch:Class.label "Age" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "AGEU"; - n4sch:Class.label "Age Units" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "SEX"; - n4sch:Class.label "Sex" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Race"; - n4sch:label "RACE" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Ethnicity"; - n4sch:label "ETHNIC" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Planned Arm Code"; - n4sch:label "ARMCD" . - - a n4sch:Property; - n4sch:label "ARM"; - n4sch:Class.label "Description of Planned Arm" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Actual Arm Code"; - n4sch:label "ACTARMCD" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "ACTARM"; - n4sch:Class.label "Description of Actual Arm" . - - a n4sch:Property; - n4sch:label "COUNTRY"; - n4sch:Class.label "Country" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . diff --git a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_5domains_117106.ttl b/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_5domains_117106.ttl deleted file mode 100644 index 8940a3e..0000000 --- a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_5domains_117106.ttl +++ /dev/null @@ -1,2584 +0,0 @@ -@prefix n4sch: . - - a n4sch:Class; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY , , - , , - , , - ; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a n4sch:Property; - n4sch:label "--REFID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "EX", "AE", "DM", "VS", "DS"; - n4sch:CLASS_RELATES_TO , . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE", "DS"; - n4sch:label "Reported Term"; - n4sch:CLASS_RELATES_TO , ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Reference Time Point"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:from_domains "VS", "AE", "EX", "DS"; - n4sch:label "Epoch"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Action Taken with Study Treatment"; - n4sch:from_domains "AE"; - 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n4sch:from_domains "VS" . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - a ; - n4sch:Order "26"^^; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS" . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "10"^^; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EPOCH"; - n4sch:_domain_ "EX"; - n4sch:Order "16"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - a ; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_columnname_ "EXSTDTC"; - n4sch:_domain_ "EX" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "11"^^; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "DSSTDTC"; - n4sch:Core "Expected" . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "18"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:_columnname_ "EXENDTC" . - - n4sch:HAS_COLUMN , - , , - , , - , . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - , , - , . - - n4sch:CLASS_RELATES_TO , - , , - , , - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - , . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_columnname_ "EXSTDY"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "EX"; - n4sch:Order "19"^^ . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DSSTDY"; - n4sch:Order "13"^^ . - - n4sch:MAPS_TO_PROPERTY . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXENDY"; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "20"^^ . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Investigator Name"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Death Flag"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Reference Start Date/Time"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Site Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Investigator Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , , - , , - , , - , , - , , . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Last Study Treatment"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Actual Arm Code"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Reference End Date/Time"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Planned Arm Code"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Date/Time of Death"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:from_domains "DM", "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "VS", "DS", "DM"; - n4sch:CoreClass false; - n4sch:label "Study Day of Visit/Collection/Exam"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Age"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of First Study Treatment"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of End of Participation"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Sex"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Date/Time of Informed Consent"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Demographics" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - a ; - n4sch:_columnname_ "RFPENDTC"; - n4sch:Order "10"^^; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:SortOrder "STUDYID,USUBJID"; - n4sch:_domain_ "DM"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:_columnname_ "DMDTC"; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ARM"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "21"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "ETHNIC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Core "Expected"; - n4sch:Order "8"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AGE"; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "14"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "INVID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFENDTC"; - n4sch:Order "6"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:_columnname_ "DTHFL"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "20"^^; - n4sch:_columnname_ "RACE"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ACTARMCD"; - n4sch:Core "Required"; - n4sch:Order "24"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "15"^^; - n4sch:_columnname_ "INVNAM"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "ARMCD"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:Order "16"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "26"^^; - n4sch:_columnname_ "COUNTRY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible"; - n4sch:Order "28"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "11"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "DTHDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AGEU"; - n4sch:Order "18"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:_domain_ "DM"; - n4sch:Order "7"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:Order "5"^^; - n4sch:_columnname_ "RFSTDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "13"^^; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:Core "Required"; - n4sch:Order "25"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a - n4sch:Property; - n4sch:Class.label "Subject Reference Start Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "RFENDTC"; - n4sch:Class.label "Subject Reference End Date/Time" . - - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time of First Study Treatment" . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Last Study Treatment"; - n4sch:label "RFXENDTC" . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time of Informed Consent" . - - - a n4sch:Property; - n4sch:label "RFPENDTC"; - n4sch:Class.label "Date/Time of End of Participation" . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Death"; - n4sch:label "DTHDTC" . - - a n4sch:Property; - n4sch:label "DTHFL"; - n4sch:Class.label "Subject Death Flag" . - - a n4sch:Property; - n4sch:label "SITEID"; - n4sch:Class.label "Study Site Identifier" . - - a n4sch:Property; - n4sch:Class.label "Investigator Identifier"; - n4sch:label "INVID" . - - a n4sch:Property; - n4sch:Class.label "Investigator Name"; - n4sch:label "INVNAM" . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Birth"; - n4sch:label "BRTHDTC" . - - a n4sch:Property; - n4sch:label "AGE"; - n4sch:Class.label "Age" . - - a n4sch:Property; - n4sch:label "AGEU"; - n4sch:Class.label "Age Units" . - - a n4sch:Property; - n4sch:label "SEX"; - n4sch:Class.label "Sex" . - - a n4sch:Property; - n4sch:Class.label "Race"; - n4sch:label "RACE" . - - a n4sch:Property; - n4sch:Class.label "Ethnicity"; - n4sch:label "ETHNIC" . - - a n4sch:Property; - n4sch:Class.label "Planned Arm Code"; - n4sch:label "ARMCD" . - - a n4sch:Property; - n4sch:label "ARM"; - n4sch:Class.label "Description of Planned Arm" . - - a n4sch:Property; - n4sch:Class.label "Actual Arm Code"; - n4sch:label "ACTARMCD" . - - a n4sch:Property; - n4sch:label "ACTARM"; - n4sch:Class.label "Description of Actual Arm" . - - a n4sch:Property; - n4sch:label "COUNTRY"; - n4sch:Class.label "Country" . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - a ; - n4sch:Order "27"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_columnname_ "VSDTC" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - - a ; - n4sch:Order "12"^^; - n4sch:_columnname_ "DSDY"; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "28"^^; - n4sch:_columnname_ "VSDY" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Disposition" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "STUDYID" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "USUBJID" . - - a ; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "DS"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:Order "1"^^ . - - a ; - n4sch:_domain_ "DS"; - n4sch:SortOrder "USUBJID,STUDYID,DSCAT,DSSCAT,DSTERM,DSSTDTC,DSSEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - . - - a ; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "USUBJID"; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_domain_ "DS"; - n4sch:Core "Required"; - n4sch:_columnname_ "DSSEQ"; - n4sch:Order "5"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:_domain_ "DS"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:CoreClass false; - n4sch:label "Dose Form"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX", "VS"; - n4sch:label "Planned Time Point Name"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Route of Administration"; - n4sch:CoreClass false; - n4sch:from_domains "EX"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX", "VS"; - n4sch:CoreClass false; - n4sch:label "Time Point Reference"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Visit Number"; - n4sch:from_domains "VS", "EX"; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "EX", "VS"; - n4sch:CoreClass false; - n4sch:label "Planned Elapsed Time from Time Point Ref"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX"; - n4sch:label "Dose"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Dosing Frequency per Interval"; - n4sch:from_domains "EX"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX", "VS"; - n4sch:label "Visit Name"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Planned Time Point Number"; - n4sch:from_domains "VS", "EX"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:label "Dose Units"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--LNKID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "--REFID" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "DOMAIN" . - - a ; - n4sch:Core "Required"; - n4sch:Order "1"^^; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "EXTPTNUM"; - n4sch:Core "Permissible"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:SortOrder "USUBJID,STUDYID,EXTRT,EXREFID,EXSTDTC,EXSEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:_columnname_ "EXDOSFRQ"; - n4sch:Order "12"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:Order "14"^^; - n4sch:_columnname_ "VISITNUM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:_columnname_ "EXDOSU"; - n4sch:Order "10"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "5"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Required"; - n4sch:_columnname_ "EXSEQ"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:Order "8"^^; - n4sch:_columnname_ "EXTRT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXREFID"; - n4sch:_domain_ "EX"; - n4sch:Order "6"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXTPT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "15"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VISIT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:Order "13"^^; - n4sch:_columnname_ "EXROUTE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXELTM"; - n4sch:_domain_ "EX"; - n4sch:Order "23"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:_columnname_ "EXDOSE"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:Order "7"^^; - n4sch:_columnname_ "EXLNKID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXTPTREF"; - n4sch:Core "Permissible"; - n4sch:Order "24"^^; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Order "11"^^; - n4sch:_columnname_ "EXDOSFRM"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - a n4sch:Property; - n4sch:label "--TRT"; - n4sch:Class.label "Name of Treatment" . - - a n4sch:Property; - n4sch:Class.label "Dose"; - n4sch:label "--DOSE" . - - a n4sch:Property; - n4sch:label "--DOSU"; - n4sch:Class.label "Dose Units" . - - a n4sch:Property; - n4sch:label "--DOSFRM"; - n4sch:Class.label "Dose Form" . - - a n4sch:Property; - n4sch:label "--DOSFRQ"; - n4sch:Class.label "Dosing Frequency per Interval" . - - a n4sch:Property; - n4sch:Class.label "Route of Administration"; - n4sch:label "--ROUTE" . - - a n4sch:Property; - n4sch:Class.label "Visit Number"; - n4sch:label "VISITNUM" . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Expected"; - n4sch:Order "24"^^; - n4sch:_columnname_ "VISITNUM"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Visit Name"; - n4sch:label "VISIT" . - - a ; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VISIT"; - n4sch:Core "Expected"; - n4sch:Order "25"^^ . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Planned Time Point Name"; - n4sch:label "--TPT" . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSTPT"; - n4sch:Order "29"^^; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--TPTNUM"; - n4sch:Class.label "Planned Time Point Number" . - - a ; - n4sch:_columnname_ "VSTPTNUM"; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "30"^^ . - - - a n4sch:Property; - n4sch:Class.label "Planned Elapsed Time from Time Point Ref"; - n4sch:label "--ELTM" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "31"^^; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSELTM"; - n4sch:Core "Permissible" . - - a n4sch:Property; - n4sch:Class.label "Time Point Reference"; - n4sch:label "--TPTREF" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSTPTREF"; - n4sch:Order "32"^^; - n4sch:_domain_ "VS" . - - a n4sch:Class; - n4sch:from_domains "VS"; - n4sch:label "Original Units"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Result or Finding in Original Units" . - - a n4sch:Class; - n4sch:label "Derived Flag"; - n4sch:CoreClass false; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:label "Standard Units"; - n4sch:CoreClass false; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:label "Date/Time of Reference Time Point"; - n4sch:CoreClass false; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:label "Position of Subject During Observation"; - n4sch:from_domains "VS"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Reason Not Done" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Baseline Flag" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Laterality"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - , , - , . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Short Name of Measurement, Test or Examination"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Numeric Result/Finding in Standard Units"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "VS"; - n4sch:label "Completion Status"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Vital Signs" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_domain_ "VS" . - - a ; - n4sch:SortOrder "USUBJID,VSTPTNUM,VSDTC,STUDYID,VSCAT,VSSCAT,VSTESTCD,VSLOC,VSLAT,VISITNUM,VSTPTREF,VSSEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:_domain_ "VS" . - - a ; - n4sch:_columnname_ "VSRFTDTC"; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:Order "33"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "15"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "VSSTRESC"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSDRVFL"; - n4sch:_domain_ "VS"; - n4sch:Order "23"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:Order "8"^^; - n4sch:_columnname_ "VSTESTCD"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSORRESU"; - n4sch:Core "Expected"; - n4sch:Order "14"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "VSORRES"; - n4sch:_domain_ "VS"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSSPID"; - n4sch:Order "7"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:Order "12"^^; - n4sch:_columnname_ "VSPOS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "16"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Expected"; - n4sch:_columnname_ "VSSTRESN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:Order "21"^^; - n4sch:_columnname_ "VSLAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Order "6"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSGRPID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSSTRESU"; - n4sch:Core "Expected"; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSREASND"; - n4sch:_domain_ "VS"; - n4sch:Order "19"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_columnname_ "VSTEST"; - n4sch:_domain_ "VS"; - n4sch:Order "9"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSBLFL"; - n4sch:Core "Expected"; - n4sch:Order "22"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "18"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSSTAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Order "5"^^; - n4sch:_columnname_ "VSSEQ"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO - , - , , , - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--TESTCD"; - n4sch:Class.label "Short Name of Measurement, Test or Examination" . - - - a n4sch:Property; - n4sch:Class.label "Name of Measurement, Test or Examination"; - n4sch:label "--TEST" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:label "--POS"; - n4sch:Class.label "Position of Subject During Observation" . - - n4sch:HAS_PROPERTY - . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Result or Finding in Original Units"; - n4sch:label "--ORRES" . - - a n4sch:Property; - n4sch:Class.label "Original Units"; - n4sch:label "--ORRESU" . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - - a n4sch:Property; - n4sch:Class.label "Result or Finding in Standard Format"; - n4sch:label "--STRESC" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--STRESN"; - n4sch:Class.label "Numeric Result/Finding in Standard Units" . - - a n4sch:Property; - n4sch:Class.label "Standard Units"; - n4sch:label "--STRESU" . - - a n4sch:Property; - n4sch:Class.label "Completion Status"; - n4sch:label "--STAT" . - - a n4sch:Property; - n4sch:Class.label "Reason Not Done"; - n4sch:label "--REASND" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Laterality"; - n4sch:label "--LAT" . - - a n4sch:Property; - n4sch:Class.label "Baseline Flag"; - n4sch:label "--BLFL" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Derived Flag"; - n4sch:label "--DRVFL" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Reference Time Point"; - n4sch:label "--RFTDTC" . - - n4sch:HAS_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , , - , , - , , , - , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . diff --git a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_7domains_117106.ttl b/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_7domains_117106.ttl deleted file mode 100644 index 4c9ac09..0000000 --- a/utils/sdtm_mdr_to_gmodel/Map Columns to Properties_example_7domains_117106.ttl +++ /dev/null @@ -1,3881 +0,0 @@ -@prefix n4sch: . - - a n4sch:Class; - n4sch:HAS_PROPERTY , , - , , - , , - ; - n4sch:label "Adverse Events"; - n4sch:from_domains "AE"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "--REFID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--GRPID" . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "LB", "EX", "AE", "DM", "VS", "EG", "DS"; - n4sch:CLASS_RELATES_TO , . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Pre-specified"; - n4sch:CLASS_RELATES_TO , ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Serious Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Reference Time Point"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:from_domains "DS", "VS", "EG", "LB", "DM", "EX", "AE"; - n4sch:label "Subject Identifier for the Study"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Occurred with Overdose"; - n4sch:from_domains "AE"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DS", "EG", "AE", "LB", "VS"; - n4sch:CoreClass false; - n4sch:label "Category"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Relative to Reference Time Point"; - n4sch:from_domains "AE" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Involves Cancer"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Outcome of Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Other Medically Important Serious Event" . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Results in Death"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Is Life Threatening"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Severity"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Primary System Organ Class"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - 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n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "EX"; - n4sch:Order "19"^^ . - - n4sch:MAPS_TO_PROPERTY . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "48"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "LBENDY" . - - a ; - n4sch:_columnname_ "EXENDY"; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "20"^^ . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - 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n4sch:Order "16"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGSTRESC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGBLFL"; - n4sch:Core "Expected"; - n4sch:_domain_ "EG"; - n4sch:Order "25"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGSTRESU"; - n4sch:Order "18"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "19"^^; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGSTAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGEVALID"; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:Order "28"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "37"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGTPTREF"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGXFN"; - n4sch:Order "21"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "36"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGELTM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGSTRESN"; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:Order "17"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Core "Required"; - n4sch:Order "10"^^; - n4sch:_columnname_ "EGTEST"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGORRESU"; - n4sch:Core "Permissible"; - n4sch:Order "15"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Core "Expected"; - n4sch:_columnname_ "VISIT"; - n4sch:Order "30"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGPOS"; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "7"^^; - n4sch:_columnname_ "EGREFID"; - n4sch:_domain_ "EG"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Order "14"^^; - n4sch:_columnname_ "EGORRES"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "USUBJID"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , - . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "27"^^; - n4sch:_columnname_ "EGEVAL"; - n4sch:_domain_ "EG"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:Order "23"^^; - n4sch:_columnname_ "EGLEAD"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "EG"; - n4sch:Order "29"^^; - n4sch:_columnname_ "VISITNUM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EG"; - n4sch:Order "8"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGSPID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "38"^^; - n4sch:_columnname_ "EGRFTDTC"; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY , - . - - n4sch:HAS_PROPERTY , - , , - , , - ; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Class; - n4sch:label "LOINC Code"; - n4sch:CoreClass false; - n4sch:from_domains "LB"; - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO - , - , , , - , ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , - , , - , , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , - , , - , , - , . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--TESTCD"; - n4sch:Class.label "Short Name of Measurement, Test or Examination" . - - a ; - n4sch:Order "10"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "LBTESTCD"; - n4sch:Core "Required" . - - a ; - n4sch:Core "Required"; - n4sch:Order "8"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VSTESTCD"; - n4sch:_domain_ "VS" . - - - a n4sch:Property; - n4sch:Class.label "Name of Measurement, Test or Examination"; - n4sch:label "--TEST" . - - a ; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VSTEST"; - n4sch:_domain_ "VS"; - n4sch:Order "9"^^ . - - a ; - n4sch:_domain_ "LB"; - n4sch:Order "11"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "LBTEST" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:label "--POS"; - n4sch:Class.label "Position of Subject During Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:Order "12"^^; - n4sch:_columnname_ "VSPOS" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "LB"; - n4sch:CLASS_RELATES_TO ; - n4sch:label "Normal Range Upper Limit-Original Units" . - - a n4sch:Class; - 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n4sch:_columnname_ "LBORRESU"; - n4sch:Core "Expected"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Lower Limit of Quantitation"; - n4sch:CLASS_RELATES_TO , - ; - n4sch:from_domains "LB" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO , - ; - n4sch:from_domains "LB"; - n4sch:label "Normal Range Lower Limit-Standard Units" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO , - ; - n4sch:label "Normal Range Upper Limit-Standard Units"; - n4sch:from_domains "LB" . - - a n4sch:Class; - n4sch:CLASS_RELATES_TO , - ; - n4sch:label "Normal Range for Character Results"; - n4sch:from_domains "LB"; - n4sch:CoreClass false . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Result or Finding in Standard Format"; - n4sch:label "--STRESC" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Order "15"^^; - n4sch:MAPS_TO_PROPERTY ; - 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n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX"; - n4sch:label "Dose"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "--REFID" . - - a n4sch:Property; - n4sch:label "--LNKID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "DOMAIN" . - - a ; - n4sch:Core "Required"; - n4sch:Order "1"^^; - n4sch:_columnname_ "STUDYID"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Order "11"^^; - n4sch:_columnname_ "EXDOSFRM"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:SortOrder "USUBJID,STUDYID,EXTRT,EXREFID,EXSTDTC,EXSEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:_columnname_ "EXDOSU"; - n4sch:Order "10"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:_columnname_ "EXDOSE"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:Order "13"^^; - n4sch:_columnname_ "EXROUTE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:Order "8"^^; - n4sch:_columnname_ "EXTRT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "5"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Required"; - n4sch:_columnname_ "EXSEQ"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXDOSFRQ"; - n4sch:Order "12"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXREFID"; - n4sch:_domain_ "EX"; - n4sch:Order "6"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:Order "7"^^; - n4sch:_columnname_ "EXLNKID"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - a n4sch:Property; - n4sch:label "--TRT"; - n4sch:Class.label "Name of Treatment" . - - a n4sch:Property; - n4sch:Class.label "Dose"; - n4sch:label "--DOSE" . - - a n4sch:Property; - n4sch:label "--DOSU"; - n4sch:Class.label "Dose Units" . - - a n4sch:Property; - n4sch:label "--DOSFRM"; - n4sch:Class.label "Dose Form" . - - a n4sch:Property; - n4sch:label "--DOSFRQ"; - n4sch:Class.label "Dosing Frequency per Interval" . - - a n4sch:Property; - n4sch:Class.label "Route of Administration"; - n4sch:label "--ROUTE" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Laboratory Test Results"; - n4sch:label "--SPID" . - - a n4sch:Property; - n4sch:label "--REFID"; - n4sch:Class.label "Laboratory Test Results" . - - a n4sch:Property; - n4sch:Class.label "Laboratory Test Results"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Laboratory Test Results" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Laboratory Test Results" . - - a n4sch:Property; - n4sch:Class.label "Laboratory Test Results"; - n4sch:label "STUDYID" . - - a n4sch:Property; - n4sch:Class.label "Laboratory Test Results"; - n4sch:label "--GRPID" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "LB"; - n4sch:label "Measurement, Test or Examination Detail" . - 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n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "SPDEVID"; - n4sch:Order "5"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "LB"; - n4sch:Core "Permissible"; - n4sch:Order "9"^^; - n4sch:_columnname_ "LBSPID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "LBULOQ"; - n4sch:Order "41"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "25"^^; - n4sch:_columnname_ "LBNRIND"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "24"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "LBSTNRC"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "22"^^; - n4sch:_columnname_ "LBSTNRLO"; - n4sch:_domain_ "LB"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "LBORNRHI"; - n4sch:Order "18"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "LBLOINC"; - n4sch:Core "Permissible"; - n4sch:Order "29"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:Core "Required"; - n4sch:Order "2"^^; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "LBREFID"; - n4sch:Order "8"^^; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "LBORNRLO"; - n4sch:Order "17"^^; - n4sch:_domain_ "LB"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "LB"; - n4sch:_columnname_ "LBFAST"; - n4sch:Core "Permissible"; - n4sch:Order "36"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:_domain_ "LB"; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_PROPERTY , - . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "LBLLOQ"; - n4sch:_domain_ "LB"; - n4sch:Order "40"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "LB"; - n4sch:Core "Permissible"; - n4sch:Order "30"^^; - n4sch:_columnname_ "LBSPEC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "12"^^; - n4sch:_domain_ "LB"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "LBTSTDTL"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "SPDEVID"; - n4sch:Class.label "Sponsor Device Identifier" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Measurement, Test or Examination Detail"; - n4sch:label "LBTSTDTL" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Lower Limit-Original Units"; - n4sch:label "--ORNRLO" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Upper Limit-Original Units"; - n4sch:label "--ORNRHI" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Lower Limit-Standard Units"; - n4sch:label "--STNRLO" . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--STNRHI"; - n4sch:Class.label "Normal Range Upper Limit-Standard Units" . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--STNRC"; - n4sch:Class.label "Normal Range for Character Results" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Normal/Reference Range Indicator"; - n4sch:label "--NRIND" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "LOINC Code"; - n4sch:label "--LOINC" . - - a n4sch:Property; - n4sch:Class.label "Specimen Material Type"; - n4sch:label "--SPEC" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SPCCND"; - n4sch:Class.label "Specimen Condition" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "LBANMETH"; - n4sch:Class.label "Analysis Method" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--FAST"; - n4sch:Class.label "Fasting Status" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Toxicity"; - n4sch:label "--TOX" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Lower Limit of Quantitation"; - n4sch:label "--LLOQ" . - - a n4sch:Property; - n4sch:label "LBULOQ"; - n4sch:Class.label "Upper Limit of Quantitation" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , , - , , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - , , - , . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Laterality"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Vital Signs" . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_domain_ "VS" . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:SortOrder "USUBJID,VSTPTNUM,VSDTC,STUDYID,VSCAT,VSSCAT,VSTESTCD,VSLOC,VSLAT,VISITNUM,VSTPTREF,VSSEQ"; - n4sch:HAS_COLUMN , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:_domain_ "VS" . - - a ; - n4sch:Order "6"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSGRPID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSSPID"; - n4sch:Order "7"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Order "5"^^; - n4sch:_columnname_ "VSSEQ"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:Order "21"^^; - n4sch:_columnname_ "VSLAT"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Laterality"; - n4sch:label "--LAT" . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY . diff --git a/utils/sdtm_mdr_to_gmodel/export_sdtm_2domains.ttl b/utils/sdtm_mdr_to_gmodel/export_sdtm_2domains.ttl deleted file mode 100644 index 587fcbe..0000000 --- a/utils/sdtm_mdr_to_gmodel/export_sdtm_2domains.ttl +++ /dev/null @@ -1,1546 +0,0 @@ -@prefix n4sch: . - - a ; - n4sch:_filename_ "export_sdtm_2domains.ttl"; - n4sch:HAS_TABLE , ; - n4sch:_tag_ "MDR3_2" . - - a ; - n4sch:_domain_ "AE"; - n4sch:SortOrder "USUBJID,STUDYID,AECAT,AESCAT,AETERM,AELOC,AEREFID,AESTDTC,AESEQ"; - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:_domain_ "DM"; - n4sch:SortOrder "STUDYID,USUBJID" . - - a n4sch:Class; - n4sch:label "Adverse Events"; - n4sch:HAS_PROPERTY , , - , , - , , - ; - n4sch:from_domains "AE"; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "--REFID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Adverse Events" . - - a n4sch:Property; - n4sch:Class.label "Adverse Events"; - n4sch:label "DOMAIN" . - - a n4sch:Class; - n4sch:label "Subject"; - n4sch:CoreClass false; - n4sch:from_domains "AE", "DM"; - n4sch:CLASS_RELATES_TO , , - . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Epoch"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Results in Death"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Body System or Organ Class"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Requires or Prolongs Hospitalization"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Severity"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Involves Cancer"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Persist or Signif Disability/Incapacity"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subcategory"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Other Medically Important Serious Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Relationship to Non-Study Treatment"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Lowest Level Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Category"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Location of Event"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Concomitant or Additional Trtmnt Given"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Relative to Reference Time Point"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Body System or Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Other Action Taken"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Modified Reported Term"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Duration"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Lowest Level Term Code"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Reference Time Point"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Is Life Threatening"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Day of Start of Observation"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Congenital Anomaly or Birth Defect"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Causality"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "End Date/Time of Observation"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Study Day of End of Observation"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Identifier for the Study"; - n4sch:from_domains "DM", "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Primary System Organ Class"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Occurred with Overdose"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Pattern of Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Serious Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Outcome of Event"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study"; - n4sch:from_domains "AE", "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Pre-specified"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Toxicity Grade"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Primary System Organ Class Code"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "End Relative to Reference Period"; - n4sch:from_domains "AE"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "High Level Group Term"; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "Reported Term"; - n4sch:CLASS_RELATES_TO , ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Dictionary-Derived Term"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO , , - ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:label "High Level Term Code"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "High Level Group Term Code"; - n4sch:CoreClass false; - n4sch:from_domains "AE"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Action Taken with Study Treatment"; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:CoreClass false; - n4sch:label "Preferred Term Code"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "AE"; - n4sch:label "Start Date/Time of Observation"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a ; - n4sch:Order "1"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "STUDYID"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_domain_ "AE" . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "26"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AELOC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEREFID"; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "7"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEMODIFY"; - n4sch:Order "10"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESDTH"; - n4sch:Order "38"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:Order "48"^^; - n4sch:_columnname_ "AESTDY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENTPT"; - n4sch:Order "53"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "32"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AERELNST"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "22"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEBODSYS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESPID"; - n4sch:Order "8"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AELLT"; - n4sch:Order "11"^^; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESTDTC"; - n4sch:Order "46"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEENRF"; - n4sch:Order "51"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "27"^^; - n4sch:_columnname_ "AESEV"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "34"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEOUT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AELLTCD"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "12"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "52"^^; - n4sch:_columnname_ "AEENRTPT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "30"^^; - n4sch:_columnname_ "AEACNOTH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "SUBJID"; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "4"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLTCD"; - n4sch:Order "16"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "25"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESOCCD"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "42"^^; - n4sch:_columnname_ "AESMIE"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEREL"; - n4sch:Core "Expected"; - n4sch:Order "31"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:Order "37"^^; - n4sch:_columnname_ "AESDISAB"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEHLGTCD"; - n4sch:_domain_ "AE"; - n4sch:Order "18"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AESCAN"; - n4sch:_domain_ "AE"; - n4sch:Order "35"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEACN"; - n4sch:_domain_ "AE"; - n4sch:Order "29"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "50"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEDUR"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLT"; - n4sch:Order "15"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESCONG"; - n4sch:Order "36"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AEBDSYCD"; - n4sch:Order "23"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AESOD"; - n4sch:_domain_ "AE"; - n4sch:Order "41"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "28"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "AESER"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Required"; - n4sch:Order "5"^^; - n4sch:_columnname_ "AESEQ"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "49"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEENDY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEPATT"; - n4sch:Core "Permissible"; - n4sch:Order "33"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Order "43"^^; - n4sch:_columnname_ "AECONTRT"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "19"^^; - n4sch:_columnname_ "AECAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "40"^^; - n4sch:_columnname_ "AESLIFE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESOC"; - n4sch:Order "24"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AETERM"; - n4sch:Order "9"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "13"^^; - n4sch:_columnname_ "AEDECOD"; - n4sch:_domain_ "AE"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "AEGRPID"; - n4sch:Order "6"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AETOXGR"; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:Order "44"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEPTCD"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:Order "14"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EPOCH"; - n4sch:Order "45"^^; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "AEENDTC"; - n4sch:Order "47"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AEHLGT"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "39"^^; - n4sch:_columnname_ "AESHOSP"; - n4sch:_domain_ "AE"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:_domain_ "AE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "AEPRESP"; - n4sch:_domain_ "AE"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "AE"; - n4sch:_columnname_ "AESCAT"; - n4sch:Order "20"^^; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Study"; - n4sch:label "STUDYID" . - - a n4sch:Property; - n4sch:Class.label "Subject"; - n4sch:label "USUBJID" . - - a n4sch:Class; - n4sch:CoreClass true; - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - ; - n4sch:label "Demographics"; - n4sch:from_domains "DM" . - - a - n4sch:Property; - n4sch:Class.label "Subject Identifier for the Study"; - n4sch:label "SUBJID" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "SUBJID"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "4"^^; - n4sch:Core "Required" . - - a n4sch:Property; - n4sch:Class.label "Reported Term"; - n4sch:label "--TERM" . - - a n4sch:Property; - n4sch:label "--MODIFY"; - n4sch:Class.label "Modified Reported Term" . - - a n4sch:Property; - n4sch:label "--LLT"; - n4sch:Class.label "Lowest Level Term" . - - a n4sch:Property; - n4sch:Class.label "Lowest Level Term Code"; - n4sch:label "--LLTCD" . - - a n4sch:Property; - n4sch:label "--DECOD"; - n4sch:Class.label "Dictionary-Derived Term" . - - a n4sch:Property; - n4sch:Class.label "Preferred Term Code"; - n4sch:label "--PTCD" . - - a n4sch:Property; - n4sch:label "--HLT"; - n4sch:Class.label "High Level Term" . - - a n4sch:Property; - n4sch:Class.label "High Level Term Code"; - n4sch:label "--HLTCD" . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term"; - n4sch:label "--HLGT" . - - a n4sch:Property; - n4sch:Class.label "High Level Group Term Code"; - n4sch:label "--HLGTCD" . - - a n4sch:Property; - n4sch:Class.label "Category"; - n4sch:label "--CAT" . - - a n4sch:Property; - n4sch:label "--SCAT"; - n4sch:Class.label "Subcategory" . - - a n4sch:Property; - n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Actual Arm Code" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Last Study Treatment"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Death Flag"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of End of Participation"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Planned Arm Code"; - n4sch:CoreClass false; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Study Day of Visit/Collection/Exam" . - - a n4sch:Class; - n4sch:label "Date/Time of Death"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Age" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of First Study Treatment" . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Investigator Name"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity" . - - a n4sch:Class; - n4sch:label "Subject Reference End Date/Time"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Study Site Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Date/Time of Informed Consent"; - n4sch:CoreClass false; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:label "Investigator Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Sex" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Reference Start Date/Time"; - n4sch:from_domains "DM" . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:from_domains "DM"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , , - , , - , , - , ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Demographics" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:Core "Required" . - - a ; - n4sch:_columnname_ "DTHFL"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "INVNAM"; - n4sch:Order "15"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Order "8"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFSTDTC"; - n4sch:Core "Expected"; - n4sch:Order "5"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "COUNTRY"; - n4sch:Order "26"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ARMCD"; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "7"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "6"^^; - n4sch:_columnname_ "RFENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "ETHNIC"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "11"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "DTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "INVID"; - n4sch:Core "Permissible"; - n4sch:Order "14"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "ARM"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "10"^^; - n4sch:_columnname_ "RFPENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "28"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RACE"; - n4sch:Order "20"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARMCD"; - n4sch:_domain_ "DM"; - n4sch:Order "24"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "AGEU"; - n4sch:Core "Expected"; - n4sch:Order "18"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AGE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Core "Required"; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_TABLE - . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:_domain_ "DM"; - n4sch:Order "25"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "16"^^; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY - . - - a - n4sch:Property; - n4sch:Class.label "Subject Reference Start Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "RFENDTC"; - n4sch:Class.label "Subject Reference End Date/Time" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time of First Study Treatment" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Last Study Treatment"; - n4sch:label "RFXENDTC" . - - n4sch:HAS_PROPERTY - . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time of Informed Consent" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "RFPENDTC"; - n4sch:Class.label "Date/Time of End of Participation" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Death"; - n4sch:label "DTHDTC" . - - a n4sch:Property; - n4sch:label "DTHFL"; - n4sch:Class.label "Subject Death Flag" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "SITEID"; - n4sch:Class.label "Study Site Identifier" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Investigator Identifier"; - n4sch:label "INVID" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Investigator Name"; - n4sch:label "INVNAM" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Birth"; - n4sch:label "BRTHDTC" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "AGE"; - n4sch:Class.label "Age" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "AGEU"; - n4sch:Class.label "Age Units" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "SEX"; - n4sch:Class.label "Sex" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Race"; - n4sch:label "RACE" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Ethnicity"; - n4sch:label "ETHNIC" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Planned Arm Code"; - n4sch:label "ARMCD" . - - a n4sch:Property; - n4sch:label "ARM"; - n4sch:Class.label "Description of Planned Arm" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Actual Arm Code"; - n4sch:label "ACTARMCD" . - - n4sch:HAS_PROPERTY . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "ACTARM"; - n4sch:Class.label "Description of Actual Arm" . - - a n4sch:Property; - n4sch:label "COUNTRY"; - n4sch:Class.label "Country" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . diff --git a/utils/sdtm_mdr_to_gmodel/export_sdtm_5domains.ttl b/utils/sdtm_mdr_to_gmodel/export_sdtm_5domains.ttl deleted file mode 100644 index e7336f3..0000000 --- a/utils/sdtm_mdr_to_gmodel/export_sdtm_5domains.ttl +++ /dev/null @@ -1,2639 +0,0 @@ -@prefix n4sch: . - 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n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - a ; - n4sch:_columnname_ "VSLOC"; - n4sch:Order "20"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Result or Finding in Standard Format"; - n4sch:from_domains "VS" . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - a ; - n4sch:Order "16"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "26"^^ . - - a ; - n4sch:Order "10"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_columnname_ "DSSTDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_domain_ "DS"; - n4sch:Order "11"^^ . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:Order "17"^^; - n4sch:_columnname_ "EXSTDTC"; - n4sch:Core "Expected"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY , , - , , - , . - - n4sch:CLASS_RELATES_TO , - , , - , , - , . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Order "18"^^; - n4sch:_columnname_ "EXENDTC"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , , - , ; - n4sch:HAS_PROPERTY , , - , . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DSSTDY" . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:_columnname_ "EXSTDY"; - n4sch:Order "19"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible" . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "20"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXENDY"; - n4sch:_domain_ "EX" . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Age"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Death Flag"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Last Study Treatment"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Sex"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Date/Time of Death"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of End of Participation"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Reference Start Date/Time"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Site Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of First Study Treatment"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Investigator Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Actual Arm Code"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Reference End Date/Time"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:from_domains "DM", "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Date/Time of Informed Consent"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Planned Arm Code"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "VS", "DS", "DM"; - n4sch:CoreClass false; - n4sch:label "Study Day of Visit/Collection/Exam"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Investigator Name"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , , - , , - , , - , , - , , . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Demographics" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:Core "Required" . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "AGEU"; - n4sch:Core "Expected"; - n4sch:Order "18"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "ETHNIC"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "INVID"; - n4sch:Core "Permissible"; - n4sch:Order "14"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RACE"; - n4sch:Order "20"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AGE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_columnname_ "DTHFL"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:_domain_ "DM"; - n4sch:Order "25"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "28"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFSTDTC"; - n4sch:Core "Expected"; - n4sch:Order "5"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ARMCD"; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Order "8"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "INVNAM"; - n4sch:Order "15"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "10"^^; - n4sch:_columnname_ "RFPENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "7"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "6"^^; - n4sch:_columnname_ "RFENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARMCD"; - n4sch:_domain_ "DM"; - n4sch:Order "24"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "ARM"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "11"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "DTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_TABLE - , , - . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "16"^^; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "COUNTRY"; - n4sch:Order "26"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a - n4sch:Property; - n4sch:Class.label "Subject Reference Start Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "RFENDTC"; - n4sch:Class.label "Subject Reference End Date/Time" . - - - a n4sch:Property; - n4sch:label "RFXSTDTC"; - n4sch:Class.label "Date/Time of First Study Treatment" . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Last Study Treatment"; - n4sch:label "RFXENDTC" . - - a n4sch:Property; - n4sch:label "RFICDTC"; - n4sch:Class.label "Date/Time of Informed Consent" . - - - a n4sch:Property; - n4sch:label "RFPENDTC"; - n4sch:Class.label "Date/Time of End of Participation" . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Death"; - n4sch:label "DTHDTC" . - - a n4sch:Property; - n4sch:label "DTHFL"; - n4sch:Class.label "Subject Death Flag" . - - a n4sch:Property; - n4sch:label "SITEID"; - n4sch:Class.label "Study Site Identifier" . - - a n4sch:Property; - n4sch:Class.label "Investigator Identifier"; - n4sch:label "INVID" . - - a n4sch:Property; - n4sch:Class.label "Investigator Name"; - n4sch:label "INVNAM" . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Birth"; - n4sch:label "BRTHDTC" . - - a n4sch:Property; - n4sch:label "AGE"; - n4sch:Class.label "Age" . - - a n4sch:Property; - n4sch:label "AGEU"; - n4sch:Class.label "Age Units" . - - a n4sch:Property; - n4sch:label "SEX"; - n4sch:Class.label "Sex" . - - a n4sch:Property; - n4sch:Class.label "Race"; - n4sch:label "RACE" . - - a n4sch:Property; - n4sch:Class.label "Ethnicity"; - n4sch:label "ETHNIC" . - - a n4sch:Property; - n4sch:Class.label "Planned Arm Code"; - n4sch:label "ARMCD" . - - a n4sch:Property; - n4sch:label "ARM"; - n4sch:Class.label "Description of Planned Arm" . - - a n4sch:Property; - n4sch:Class.label "Actual Arm Code"; - n4sch:label "ACTARMCD" . - - a n4sch:Property; - n4sch:label "ACTARM"; - n4sch:Class.label "Description of Actual Arm" . - - a n4sch:Property; - n4sch:label "COUNTRY"; - n4sch:Class.label "Country" . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , , - , , - , , - , , - . - - a n4sch:Property; - n4sch:Class.label "Date/Time of Collection"; - n4sch:label "--DTC" . - - a ; - n4sch:Core "Expected"; - n4sch:Order "27"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VSDTC" . - - a n4sch:Property; - n4sch:label "--DY"; - n4sch:Class.label "Study Day of Visit/Collection/Exam" . - - a ; - n4sch:Order "12"^^; - n4sch:_domain_ "DS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DSDY"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "28"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VSDY"; - n4sch:Core "Permissible" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "USUBJID" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "STUDYID" . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Disposition" . - - a n4sch:Property; - n4sch:Class.label "Disposition"; - n4sch:label "--SEQ" . - - a ; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:Order "1"^^; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "STUDYID" . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DS"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DS"; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Core "Required"; - n4sch:_domain_ "DS"; - n4sch:Order "5"^^; - n4sch:_columnname_ "DSSEQ"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Class; - n4sch:label "Route of Administration"; - n4sch:CoreClass false; - n4sch:from_domains "EX"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX", "VS"; - n4sch:label "Planned Time Point Name"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX"; - n4sch:label "Dose"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Visit Number"; - n4sch:from_domains "VS", "EX"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX", "VS"; - n4sch:CoreClass false; - n4sch:label "Time Point Reference"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:label "Dose Units"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Dosing Frequency per Interval"; - n4sch:from_domains "EX"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Planned Time Point Number"; - n4sch:from_domains "VS", "EX"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "EX", "VS"; - n4sch:label "Visit Name"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EX"; - n4sch:CoreClass false; - n4sch:label "Dose Form"; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:from_domains "EX", "VS"; - n4sch:CoreClass false; - n4sch:label "Planned Elapsed Time from Time Point Ref"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:label "--SEQ"; - n4sch:Class.label "Exposure" . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:Class.label "Exposure"; - n4sch:label "--REFID" . - - a n4sch:Property; - n4sch:label "--LNKID"; - n4sch:Class.label "Exposure" . - - a ; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_columnname_ "STUDYID"; - n4sch:Core "Required"; - n4sch:_domain_ "EX"; - n4sch:Order "1"^^ . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXELTM"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "6"^^; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "EXREFID"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VISITNUM"; - n4sch:Order "14"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXDOSU"; - n4sch:Order "10"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "EX"; - n4sch:Order "15"^^; - n4sch:_columnname_ "VISIT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "EX"; - n4sch:Order "7"^^; - n4sch:_columnname_ "EXLNKID"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "5"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Required"; - n4sch:_columnname_ "EXSEQ"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "EXTPT"; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXTPTREF"; - n4sch:Order "24"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:Order "2"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "EX"; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Order "8"^^; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "EXTRT"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXROUTE"; - n4sch:Order "13"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "22"^^; - n4sch:_columnname_ "EXTPTNUM"; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "12"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXDOSFRQ"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EXDOSFRM"; - n4sch:Order "11"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:_columnname_ "EXDOSE"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO . - - a n4sch:Property; - n4sch:label "--TRT"; - n4sch:Class.label "Name of Treatment" . - - a n4sch:Property; - n4sch:Class.label "Dose"; - n4sch:label "--DOSE" . - - a n4sch:Property; - n4sch:label "--DOSU"; - n4sch:Class.label "Dose Units" . - - a n4sch:Property; - n4sch:label "--DOSFRM"; - n4sch:Class.label "Dose Form" . - - a n4sch:Property; - n4sch:label "--DOSFRQ"; - n4sch:Class.label "Dosing Frequency per Interval" . - - a n4sch:Property; - n4sch:Class.label "Route of Administration"; - n4sch:label "--ROUTE" . - - a n4sch:Property; - n4sch:Class.label "Visit Number"; - n4sch:label "VISITNUM" . - - a ; - n4sch:Order "24"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "VISITNUM"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Visit Name"; - n4sch:label "VISIT" . - - a ; - n4sch:_columnname_ "VISIT"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "VS"; - n4sch:Order "25"^^ . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Planned Time Point Name"; - n4sch:label "--TPT" . - - a ; - n4sch:_columnname_ "VSTPT"; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:Order "29"^^; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--TPTNUM"; - n4sch:Class.label "Planned Time Point Number" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "VSTPTNUM"; - n4sch:Core "Permissible"; - n4sch:Order "30"^^; - n4sch:_domain_ "VS" . - - - a n4sch:Property; - n4sch:Class.label "Planned Elapsed Time from Time Point Ref"; - n4sch:label "--ELTM" . - - a ; - n4sch:_columnname_ "VSELTM"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:Order "31"^^; - n4sch:_domain_ "VS" . - - a n4sch:Property; - n4sch:Class.label "Time Point Reference"; - n4sch:label "--TPTREF" . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSTPTREF"; - n4sch:Order "32"^^; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Laterality"; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Result or Finding in Original Units" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Numeric Result/Finding in Standard Units"; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:label "Position of Subject During Observation"; - n4sch:from_domains "VS"; - n4sch:CoreClass false . - - a n4sch:Class; - n4sch:label "Date/Time of Reference Time Point"; - n4sch:CoreClass false; - n4sch:from_domains "VS" . - - a n4sch:Class; - n4sch:from_domains "VS"; - n4sch:label "Completion Status"; - n4sch:CoreClass false . - - n4sch:CLASS_RELATES_TO , - , , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY , , - , , - , . - - a n4sch:Class; - n4sch:from_domains "VS"; - n4sch:label "Original Units"; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Reason Not Done"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Standard Units"; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:CLASS_RELATES_TO , - ; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Derived Flag"; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Short Name of Measurement, Test or Examination"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "VS"; - n4sch:label "Baseline Flag"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--SEQ" . - - a ; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - a ; - n4sch:_domain_ "VS"; - n4sch:Order "22"^^; - n4sch:_columnname_ "VSBLFL"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:Core "Required"; - n4sch:Order "9"^^; - n4sch:_columnname_ "VSTEST"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "12"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSPOS"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSGRPID"; - n4sch:Order "6"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "13"^^; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSORRES"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSRFTDTC"; - n4sch:Order "33"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSLAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSSPID"; - n4sch:_domain_ "VS"; - n4sch:Order "7"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Order "16"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "VSSTRESN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSORRESU"; - n4sch:Order "14"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSDRVFL"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "8"^^; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSTESTCD"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSREASND"; - n4sch:Core "Permissible"; - n4sch:Order "19"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_columnname_ "VSSEQ"; - n4sch:_domain_ "VS"; - n4sch:Order "5"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSSTRESC"; - n4sch:Core "Expected"; - n4sch:Order "15"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:_domain_ "VS"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_TABLE - . - - a ; - n4sch:_columnname_ "VSSTRESU"; - n4sch:_domain_ "VS"; - n4sch:Order "17"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "18"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSSTAT"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO - , - , , , - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--TESTCD"; - n4sch:Class.label "Short Name of Measurement, Test or Examination" . - - - a n4sch:Property; - n4sch:Class.label "Name of Measurement, Test or Examination"; - n4sch:label "--TEST" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--POS"; - n4sch:Class.label "Position of Subject During Observation" . - - n4sch:HAS_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Result or Finding in Original Units"; - n4sch:label "--ORRES" . - - a n4sch:Property; - n4sch:Class.label "Original Units"; - n4sch:label "--ORRESU" . - - n4sch:CLASS_RELATES_TO . - - - a n4sch:Property; - n4sch:Class.label "Result or Finding in Standard Format"; - n4sch:label "--STRESC" . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--STRESN"; - n4sch:Class.label "Numeric Result/Finding in Standard Units" . - - n4sch:HAS_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Standard Units"; - n4sch:label "--STRESU" . - - a n4sch:Property; - n4sch:Class.label "Completion Status"; - n4sch:label "--STAT" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Reason Not Done"; - n4sch:label "--REASND" . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Laterality"; - n4sch:label "--LAT" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Baseline Flag"; - n4sch:label "--BLFL" . - - a n4sch:Property; - n4sch:Class.label "Derived Flag"; - n4sch:label "--DRVFL" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Date/Time of Reference Time Point"; - n4sch:label "--RFTDTC" . - - n4sch:HAS_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . diff --git a/utils/sdtm_mdr_to_gmodel/export_sdtm_7domains.ttl b/utils/sdtm_mdr_to_gmodel/export_sdtm_7domains.ttl deleted file mode 100644 index 08a80f7..0000000 --- a/utils/sdtm_mdr_to_gmodel/export_sdtm_7domains.ttl +++ /dev/null @@ -1,4021 +0,0 @@ -@prefix n4sch: . - 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n4sch:Order "13"^^ . - - a ; - n4sch:Core "Expected"; - n4sch:_columnname_ "DSCAT"; - n4sch:_domain_ "DS"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "8"^^ . - - a ; - n4sch:_columnname_ "VSCAT"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "10"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible" . - - a ; - n4sch:_columnname_ "EGCAT"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "11"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible" . - - a n4sch:Property; - n4sch:label "--SCAT"; - n4sch:Class.label "Subcategory" . - - a ; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "VSSCAT"; - n4sch:Order "11"^^ . - - a ; - n4sch:_columnname_ "LBSCAT"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Permissible"; - n4sch:Order "14"^^ . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGSCAT"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "12"^^; - n4sch:_domain_ "EG" . - - a ; - n4sch:Order "9"^^; - n4sch:_domain_ "DS"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DSSCAT" . - - a n4sch:Property; - n4sch:Class.label "Pre-specified"; - n4sch:label "--PRESP" . - - a n4sch:Property; - n4sch:Class.label "Body System or Organ Class"; - n4sch:label "--BODSYS" . - - - a n4sch:Property; - n4sch:label "--BDSYCD"; - n4sch:Class.label "Body System or Organ Class Code" . - - a n4sch:Property; - n4sch:label "--SOC"; - n4sch:Class.label "Primary System Organ Class" . - - a - n4sch:Property; - n4sch:label "--SOCCD"; - n4sch:Class.label "Primary System Organ Class Code" . - - a n4sch:Property; - n4sch:label "--LOC"; - n4sch:Class.label "Location of Event" . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "32"^^; - n4sch:_columnname_ "LBLOC" . - - a ; - n4sch:_columnname_ "VSLOC"; - n4sch:Order "20"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--SEV"; - n4sch:Class.label "Severity" . - - a n4sch:Property; - n4sch:label "--SER"; - n4sch:Class.label "Serious Event" . - - a - n4sch:Property; - n4sch:Class.label "Action Taken with Study Treatment"; - n4sch:label "--ACN" . - - a n4sch:Property; - n4sch:label "--ACNOTH"; - n4sch:Class.label "Other Action Taken" . - - a n4sch:Property; - n4sch:Class.label "Causality"; - n4sch:label "--REL" . - - - a n4sch:Property; - n4sch:label "--RELNST"; - n4sch:Class.label "Relationship to Non-Study Treatment" . - - a n4sch:Property; - n4sch:label "--PATT"; - n4sch:Class.label "Pattern of Event" . - - a n4sch:Property; - n4sch:label "--OUT"; - n4sch:Class.label "Outcome of Event" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Involves Cancer"; - n4sch:label "--SCAN" . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--SCONG"; - n4sch:Class.label "Congenital Anomaly or Birth Defect" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--SDISAB"; - n4sch:Class.label "Persist or Signif Disability/Incapacity" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Results in Death"; - n4sch:label "--SDTH" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--SHOSP"; - n4sch:Class.label "Requires or Prolongs Hospitalization" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Is Life Threatening"; - n4sch:label "--SLIFE" . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "--SOD"; - n4sch:Class.label "Occurred with Overdose" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Other Medically Important Serious Event"; - n4sch:label "--SMIE" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:label "--CONTRT"; - n4sch:Class.label "Concomitant or Additional Trtmnt Given" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:CLASS_RELATES_TO ; - n4sch:label "Toxicity"; - n4sch:from_domains "LB" . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "LB", "EG", "VS"; - n4sch:label "Result or Finding in Standard Format" . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - . - - a n4sch:Property; - n4sch:label "--TOXGR"; - n4sch:Class.label "Toxicity Grade" . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:_columnname_ "LBTOXGR"; - n4sch:Order "39"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "LB"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , ; - n4sch:HAS_PROPERTY , , - , , - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , , - , ; - n4sch:HAS_PROPERTY , , - , . - - n4sch:CLASS_RELATES_TO , - , , - , . - - n4sch:CLASS_RELATES_TO , - , . - - a n4sch:Property; - n4sch:Class.label "Epoch"; - n4sch:label "EPOCH" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "EG"; - n4sch:Order "31"^^; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EPOCH"; - n4sch:Order "44"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "LB" . - - a ; - n4sch:Order "16"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "EX"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "26"^^ . - - a ; - n4sch:Order "10"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:_columnname_ "EPOCH"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:label "--STDTC"; - n4sch:Class.label "Start Date/Time of Observation" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:_columnname_ "DSSTDTC"; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Core "Expected"; - n4sch:_domain_ "DS"; - n4sch:Order "11"^^ . - - a ; - n4sch:Order "17"^^; - n4sch:_columnname_ "EXSTDTC"; - n4sch:Core "Expected"; - n4sch:_domain_ "EX"; - n4sch:MAPS_TO_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "End Date/Time of Observation"; - n4sch:label "--ENDTC" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:Order "46"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "LB"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "LBENDTC" . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:Order "18"^^; - n4sch:_columnname_ "EXENDTC"; - n4sch:_domain_ "EX"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - - a n4sch:Property; - n4sch:label "--STDY"; - n4sch:Class.label "Study Day of Start of Observation" . - - n4sch:HAS_PROPERTY - . - - a ; - n4sch:_columnname_ "EXSTDY"; - n4sch:Order "19"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_domain_ "EX"; - n4sch:Core "Permissible" . - - a ; - n4sch:Core "Permissible"; - n4sch:_domain_ "DS"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "DSSTDY" . - - n4sch:MAPS_TO_PROPERTY - . - - a - n4sch:Property; - n4sch:label "--ENDY"; - n4sch:Class.label "Study Day of End of Observation" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "48"^^; - n4sch:MAPS_TO_PROPERTY ; - n4sch:_columnname_ "LBENDY"; - n4sch:_domain_ "LB" . - - a ; - n4sch:MAPS_TO_PROPERTY ; - n4sch:Order "20"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EXENDY"; - n4sch:_domain_ "EX" . - - a n4sch:Property; - n4sch:Class.label "Duration"; - n4sch:label "--DUR" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a - n4sch:Property; - n4sch:label "--ENRF"; - n4sch:Class.label "End Relative to Reference Period" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "End Relative to Reference Time Point"; - n4sch:label "--ENRTPT" . - - n4sch:HAS_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "--ENTPT"; - n4sch:Class.label "End Reference Time Point" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , , - , , - , , - , , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - . - - a n4sch:Class; - n4sch:label "Date/Time of Informed Consent"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Investigator Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Sex"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Death Flag"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Birth"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Ethnicity"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Race"; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , , - , , , - , , - , , - , , - , . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of Last Study Treatment"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Description of Actual Arm"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Study Site Identifier"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Subject Reference End Date/Time"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Age Units"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Age"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EG", "LB", "DM", "VS"; - n4sch:CoreClass false; - n4sch:label "Date/Time of Collection"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Subject Reference Start Date/Time"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of First Study Treatment"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "EG", "VS", "DS", "DM", "LB"; - n4sch:CoreClass false; - n4sch:label "Study Day of Visit/Collection/Exam"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Actual Arm Code"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Planned Arm Code"; - n4sch:CoreClass false; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Investigator Name"; - n4sch:from_domains "DM"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Date/Time of Death"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:label "Country"; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:CoreClass false; - n4sch:label "Description of Planned Arm"; - n4sch:HAS_PROPERTY . - - a n4sch:Class; - n4sch:from_domains "DM"; - n4sch:label "Date/Time of End of Participation"; - n4sch:CoreClass false; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "DOMAIN"; - n4sch:Class.label "Demographics" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Demographics" . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:Core "Required" . - - a ; - n4sch:_columnname_ "INVID"; - n4sch:Core "Permissible"; - n4sch:Order "14"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - . - - a ; - n4sch:Core "Expected"; - n4sch:Order "6"^^; - n4sch:_columnname_ "RFENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "7"^^; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXSTDTC"; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Required"; - n4sch:_columnname_ "SITEID"; - n4sch:_domain_ "DM"; - n4sch:Order "13"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "INVNAM"; - n4sch:Order "15"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "17"^^; - n4sch:_domain_ "DM"; - n4sch:Core "Expected"; - n4sch:_columnname_ "AGE"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Expected"; - n4sch:Order "10"^^; - n4sch:_columnname_ "RFPENDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RFSTDTC"; - n4sch:Core "Expected"; - n4sch:Order "5"^^; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "AGEU"; - n4sch:Core "Expected"; - n4sch:Order "18"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:Order "27"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARM"; - n4sch:_domain_ "DM"; - n4sch:Order "25"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ACTARMCD"; - n4sch:_domain_ "DM"; - n4sch:Order "24"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_columnname_ "ETHNIC"; - n4sch:_domain_ "DM"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "23"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "ARM"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DTHFL"; - n4sch:_domain_ "DM"; - n4sch:Order "12"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Order "2"^^; - n4sch:_columnname_ "DOMAIN"; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "COUNTRY"; - n4sch:Order "26"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "11"^^; - n4sch:Core "Expected"; - n4sch:_columnname_ "DTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "19"^^; - n4sch:_columnname_ "SEX"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "RACE"; - n4sch:Order "20"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFXENDTC"; - n4sch:Order "8"^^; - n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "28"^^; - n4sch:Core "Permissible"; - n4sch:_columnname_ "DMDY"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_TABLE - , . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "16"^^; - n4sch:_columnname_ "BRTHDTC"; - n4sch:_domain_ "DM"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "9"^^; - n4sch:Core "Expected"; - n4sch:_domain_ "DM"; - n4sch:_columnname_ "RFICDTC"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "ARMCD"; - n4sch:_domain_ "DM"; - n4sch:Core "Required"; - n4sch:Order "22"^^; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a - n4sch:Property; - n4sch:Class.label "Subject Reference Start Date/Time"; - n4sch:label "RFSTDTC" . - - a n4sch:Property; - n4sch:label "RFENDTC"; - n4sch:Class.label "Subject Reference End Date/Time" . - 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n4sch:_domain_ "EG"; - n4sch:Order "14"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "19"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGSTAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "EGNAM"; - n4sch:Order "22"^^; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:Order "17"^^; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGSTRESN"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "USUBJID"; - n4sch:MAPS_TO_PROPERTY , - . - - a ; - n4sch:_domain_ "EG"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGDRVFL"; - n4sch:Order "26"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "13"^^; - n4sch:Core "Permissible"; - n4sch:_domain_ "EG"; - n4sch:_columnname_ "EGPOS"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Core "Permissible"; - n4sch:_columnname_ "EGRFTDTC"; - n4sch:_domain_ "EG"; - 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n4sch:Core "Expected"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:HAS_TABLE - , . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "SPDEVID"; - n4sch:Class.label "Sponsor Device Identifier" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:HAS_PROPERTY - . - - - a n4sch:Property; - n4sch:Class.label "Measurement, Test or Examination Detail"; - n4sch:label "LBTSTDTL" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Lower Limit-Original Units"; - n4sch:label "--ORNRLO" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Upper Limit-Original Units"; - n4sch:label "--ORNRHI" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:Class.label "Normal Range Lower Limit-Standard Units"; - n4sch:label "--STNRLO" . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--STNRHI"; - n4sch:Class.label "Normal Range Upper Limit-Standard Units" . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - - a n4sch:Property; - n4sch:label "--STNRC"; - n4sch:Class.label "Normal Range for Character Results" . - - n4sch:CLASS_RELATES_TO - ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Normal/Reference Range Indicator"; - n4sch:label "--NRIND" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "LOINC Code"; - n4sch:label "--LOINC" . - - a n4sch:Property; - n4sch:Class.label "Specimen Material Type"; - n4sch:label "--SPEC" . - - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "--SPCCND"; - n4sch:Class.label "Specimen Condition" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "LBANMETH"; - n4sch:Class.label "Analysis Method" . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:label "--FAST"; - n4sch:Class.label "Fasting Status" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Toxicity"; - n4sch:label "--TOX" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO - , ; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:Class.label "Lower Limit of Quantitation"; - n4sch:label "--LLOQ" . - - a n4sch:Property; - n4sch:label "LBULOQ"; - n4sch:Class.label "Upper Limit of Quantitation" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , , - , , - , , , - , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY . - - n4sch:CLASS_RELATES_TO , - , , - , , - , , - , , - , , - , - , , , - , , - , , - , , - , , - , , - , , - ; - n4sch:HAS_PROPERTY , , - , , - , . - - a n4sch:Class; - n4sch:CoreClass false; - n4sch:label "Laterality"; - n4sch:from_domains "VS"; - n4sch:HAS_PROPERTY . - - a n4sch:Property; - n4sch:label "USUBJID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--GRPID" . - - a n4sch:Property; - n4sch:label "STUDYID"; - n4sch:Class.label "Vital Signs" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "--SEQ" . - - a n4sch:Property; - n4sch:Class.label "Vital Signs"; - n4sch:label "DOMAIN" . - - a n4sch:Property; - n4sch:label "--SPID"; - n4sch:Class.label "Vital Signs" . - - a ; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY , ; - n4sch:_domain_ "VS"; - n4sch:_columnname_ "STUDYID"; - n4sch:Order "1"^^ . - - n4sch:HAS_COLUMN , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , , - , . - - a ; - n4sch:Order "3"^^; - n4sch:Core "Required"; - n4sch:_columnname_ "USUBJID"; - n4sch:_domain_ "VS"; - n4sch:MAPS_TO_PROPERTY , . - - a ; - n4sch:_columnname_ "VSSEQ"; - n4sch:_domain_ "VS"; - n4sch:Order "5"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSGRPID"; - n4sch:Order "6"^^; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "VSSPID"; - n4sch:_domain_ "VS"; - n4sch:Order "7"^^; - n4sch:Core "Permissible"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:Order "21"^^; - n4sch:_domain_ "VS"; - n4sch:Core "Permissible"; - n4sch:_columnname_ "VSLAT"; - n4sch:MAPS_TO_PROPERTY . - - a ; - n4sch:_columnname_ "DOMAIN"; - n4sch:_domain_ "VS"; - n4sch:Order "2"^^; - n4sch:Core "Required"; - n4sch:MAPS_TO_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - a n4sch:Property; - n4sch:Class.label "Laterality"; - n4sch:label "--LAT" . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:CLASS_RELATES_TO . - - n4sch:HAS_PROPERTY . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . - - n4sch:MAPS_TO_PROPERTY - . diff --git a/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl.py b/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl.py deleted file mode 100644 index 323caf7..0000000 --- a/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl.py +++ /dev/null @@ -1,244 +0,0 @@ -""" -The script utilizes MDR graph at bolt://10.40.225.48:12002 (generated from -\\uk1salx00175.corpnet2.com\RD\gmp\data\MDR\StandardMDRSpec_3_2.xlsx) -and extended with some data from SDTM ontology https://github.com/phuse-org/rdf.cdisc.org -using the following script: -https://mygithub.gsk.com/gsk-tech/cldsdtmnb/blob/main/data_prep.py -""" -import pandas as pd -from neointerface import NeoInterface -from model_managers import ModelManager - -# connecting to MDR graph -mm = ModelManager(rdf=True) -mdr_neo = NeoInterface(host="bolt://10.40.225.48:12002", - rdf_host='http://10.40.225.48:11002/rdf/', - credentials=('neo4j', 'mdr')) - -def write_meta_to_graph(for_export=False, datasets = ['DM','DS','EX','AE','LB','VS','EG'], filename=None): - """ - :param for_export: True if metadata for export is being generated (prefix in uri added and additional node (:`Data Extraction Standard`) - :param datasets: domains for which mappings are to be created - :param filename: filename to add on 'Data Extraction Standard' as metadata - :return: None - """ - mm.clean_slate() - - #getting metadata from Variables nodes of MDR to create Class and Property to map to - q = f""" - //Mapping to DataElements if exist, otherwise mapping to column label/name - MATCH (v:Variables)<-[:HAS_VARIABLE]-(ds:Datasets) - WHERE v.Dataset in $datasets - OPTIONAL MATCH (da:DataElement) - WHERE da.dataElementName = v.dataElementName - OPTIONAL MATCH (da)-[:dataElementRole]->(dar:DataElementRole) - RETURN - v.Dataset as _domain_, - ds.`Sort Order` as `SortOrder`, //TODO: can keep property name with space when NeoInterface updated to account for prop names with spaces in RDF - v.Variable as _columnname_, - v.Order as Order, - //CASE WHEN dar.label = 'Identifier Variable' AND NOT v.Dataset = 'DM' THEN - CASE WHEN dar.label = 'Identifier Variable' THEN - ds.Description - ELSE - CASE WHEN v.dataElementLabel IS NULL THEN v.Label ELSE v.dataElementLabel END - END as class, - CASE WHEN v.dataElementName IS NULL THEN v.Variable ELSE v.dataElementName END as property, - //CASE WHEN dar.label = 'Identifier Variable' AND NOT v.Dataset = 'DM' THEN True ELSE False END as CoreClass, - CASE WHEN dar.label = 'Identifier Variable' THEN True ELSE False END as CoreClass, - v.Core as CoreVar - ORDER BY _domain_, Order, _columnname_, class, property - """ - params = {'datasets': datasets} - data = mdr_neo.query(q, params) - for dataset in params['datasets']: - for key, item in {#'DOMAIN': 'Domain', - 'USUBJID': 'Subject', - 'STUDYID': 'Study', - }.items(): - data.append({'_domain_':dataset, '_columnname_':key, 'class':item, 'property':key, 'CoreClass': False, 'CoreVar': 'Required'}) - df = pd.DataFrame(data) - - #query to generate metadata nodes on NEO4J_HOST database - q_for_export1, q_for_export2 = "", "" - if for_export: - q_for_export1 = f"MERGE (f:`Data Extraction Standard`{{_tag_:'MDR3_2', _filename_:$filename}}) WITH *" - q_for_export2 = f"<-[:HAS_TABLE]-(f)" - q2 = f""" - {q_for_export1} - UNWIND $data as row - MERGE (c:Class{{label:row['class']}}) - SET c.from_domains = CASE WHEN row['_domain_'] in c.from_domains THEN c.from_domains - ELSE CASE WHEN c.from_domains IS NULL THEN [row['_domain_']] - ELSE c.from_domains + row['_domain_'] END - END - SET c.CoreClass = row['CoreClass'] - MERGE (c)-[:HAS_PROPERTY]->(p:Property{{label:row['property'], `Class.label`:row['class']}}) - MERGE (t:`Source Data Table`{{_domain_:row['_domain_']}}){q_for_export2} - SET t.`SortOrder` = CASE WHEN row['SortOrder'] is NULL THEN t['SortOrder'] ELSE row['SortOrder'] END - WITH * - MERGE (t)-[:HAS_COLUMN]->(col:`Source Data Column`{{_domain_: row['_domain_'], _columnname_:row['_columnname_']}}) - SET col.Core = row['CoreVar'] - SET col.Order = CASE WHEN row['Order'] is NULL THEN col['Order'] ELSE row['Order'] END - WITH * - MERGE (col)-[:MAPS_TO_PROPERTY]->(p) - """ - mm.query(q2, {'data': data, 'filename': filename}) - - # ------------------ LINKING----------------------- - #(0) - #-------- linking Core to all classes in domain-------- - q = """ - MATCH (core:Class), (c:Class) - WHERE (core.CoreClass = True OR core.label = 'Subject') AND core<>c AND c.label <> 'Subject' AND core.from_domains[0] in c.from_domains - MERGE (core)-[:CLASS_RELATES_TO]->(c) - """ - mm.query(q) - #-------- linking Subject to all CoreClass classes of other domains -------- - q = """ - MATCH (subj:Class), (core:Class) - WHERE subj.label = 'Subject' AND core.CoreClass AND subj<>core - MERGE (subj)-[:CLASS_RELATES_TO]->(core) - """ - mm.query(q) - # -------- linking 'Demographics' to 'Date/Time of Collection' and 'Study Day of Visit/Collection/Exam' ------- - q = """ - MATCH (demo:Class), (collection:Class) - WHERE demo.label = 'Demographics' AND collection.label in ['Date/Time of Collection', 'Study Day of Visit/Collection/Exam'] - MERGE (demo)-[:CLASS_RELATES_TO]->(collection) - """ - mm.query(q) - - - #(1) - #-------- getting 'qualifies' link -------- - q4 = """ - MATCH (x:DataElement)-[:qualifies]->(y) - RETURN x.dataElementLabel as left, y.dataElementLabel as right - """ - data = mdr_neo.query(q4) - data.append({'left': 'Body System or Organ Class', 'right': 'Dictionary-Derived Term'}) - - #-------- creating 'qualifies' CLASS_RELATES_TO metadata (to support ModelApplier.refactor_all) -------- - q5 = """ - UNWIND $data as row - MATCH (left_c:Class), (right_c:Class) - WHERE left_c.label = row['left'] and right_c.label = row['right'] - MERGE (left_c)-[:CLASS_RELATES_TO{relationship_type:'QUALIFIES'}]->(right_c) - """ - mm.query(q5, {'data': data}) - - - #(2) - #-------- getting topics ------- - q6 = """ - MATCH (de:DataElement)-[:dataElementRole]->(der:DataElementRole) - WHERE der.label = 'Topic Variable' - RETURN de.dataElementLabel as topic_class - """ - _topics = mdr_neo.query(q6) - #extending and updating topics: - df_topics = pd.DataFrame( - _topics + [{"topic_class": "Dictionary-Derived Term"}] - ) - #we rather use the long name as topic than the short name - df_topics['topic_class'] = df_topics['topic_class'].replace({ - 'Short Name of Measurement, Test or Examination':'Name of Measurement, Test or Examination'}) - topics = list(df_topics['topic_class']) - - # ------- getting Result Qualifiers and fingings topics ------- - q8_2 = """ - MATCH (de:DataElement)-[:dataElementRole]->(der:DataElementRole), - (de2:DataElement)-[:context]->(ctx:VariableGrouping) - WHERE - der.label = 'Result Qualifier' - AND de2.dataElementLabel in $topics - AND ctx.contextLabel = 'Findings Observation Class Variables' - RETURN de.dataElementLabel as rq_class, de2.dataElementLabel as topic - """ - df_resqs = pd.DataFrame(mdr_neo.query(q8_2, {'topics':topics})) - results = list(set(df_resqs['rq_class'])) - - #------- linking Result Qualifiers to topics (Findings) ------- - q8_3 = """ - UNWIND $data as row - MATCH (c:Class), (c_topic:Class) - WHERE c.label = row['rq_class'] AND c_topic.label = row['topic'] - MERGE (c_topic)-[r:CLASS_RELATES_TO]->(c) - set r.relationship_type = 'HAS_RESULT' - """ - mm.query(q8_3,{'data': df_resqs.to_dict(orient='records')}) - - #(3) - #linking grouping classes to topics - q9_1 = """ - MATCH (de:DataElement)-[:dataElementRole]->(der:DataElementRole) - WHERE der.label = 'Grouping Qualifier' - RETURN DISTINCT de.dataElementLabel as groupping_class - """ - grouppings = [res['groupping_class'] for res in mdr_neo.query(q9_1)] - - q9_2 = """ - MATCH (topic:Class), (gr:Class) - WHERE topic.label in $topics and gr.label in $grouppings - MERGE (topic)-[:CLASS_RELATES_TO{relationship_type:'IS_A'}]->(gr) - """ - mm.query(q9_2, {'topics':topics, 'grouppings':grouppings}) - - #(4) - # category to subcategory - mm.query(""" - MATCH (cat:Class), (scat:Class) - WHERE cat.label = 'Category' and scat.label = 'Subcategory' - MERGE (cat)-[:CLASS_RELATES_TO{relationship_type:'HAS_SUBCATEGORY'}]->(scat) - """) - -# --------------------------- Saving ttl ---------------------------------- -def export_ttl(filename='refactoring.ttl', add_prefixes=[]): - """ - function to export ttl file from metadata on NEO4J_HOST database - :param filename: file to store metadata (should be same as the one used for write_meta_to_graph) - :param add_prefixes: prefixes to add to uri (currently we use ['Metadata', 'mdr3_2'] prefixes for metadata for export - :return: None - """ - uri_map1 = { - "Data Extraction Standard": {"properties": "_tag_"}, - "Source Data Folder": {"properties": "_folder_"}, - "Source Data Table": {"properties": "_domain_"}, - "Source Data Column": {"properties": ["_domain_", "_columnname_"]} - } - uri_map2 = { - "Class": {"properties": "label"}, - "Property": {"properties": ["Class.label", "label"]}, - } - mm.rdf_generate_uri(uri_map1, add_prefixes=add_prefixes) - mm.rdf_generate_uri(uri_map2) - rdf = mm.rdf_get_subgraph('MATCH p=()-[]-() RETURN p') - with open(filename, "w", encoding='utf-8') as f: - f.write(rdf) - f.close() - - -write_meta_to_graph(for_export=False, datasets = ['DM','AE']) -export_ttl(filename="Map Columns to Properties_example_2domains_117106.ttl") - -filename = 'export_sdtm_2domains.ttl' -write_meta_to_graph(for_export=True, datasets=['DM','AE'], filename=filename) -export_ttl(filename=filename, add_prefixes=['Metadata', 'mdr3_2']) - -write_meta_to_graph(for_export=False, datasets = ['DM','DS','EX','AE','VS']) -export_ttl(filename="Map Columns to Properties_example_5domains_117106.ttl") - -filename = 'export_sdtm_5domains.ttl' -write_meta_to_graph(for_export=True, datasets = ['DM','DS','EX','AE','VS'], filename=filename) -export_ttl(filename=filename, add_prefixes=['Metadata', 'mdr3_2']) - -write_meta_to_graph(for_export=False, datasets = ['DM','DS','EX','AE','LB','VS','EG']) -export_ttl(filename="Map Columns to Properties_example_7domains_117106.ttl") - -filename = 'export_sdtm_7domains.ttl' -write_meta_to_graph(for_export=True, datasets = ['DM','DS','EX','AE','LB','VS','EG'], filename=filename) -export_ttl(filename=filename, add_prefixes=['Metadata', 'mdr3_2']) - - -#TODO: custom links (e.g. Subject -> Body System, Derived term and other) \ No newline at end of file diff --git a/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl_issue.py b/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl_issue.py deleted file mode 100644 index b0456b4..0000000 --- a/utils/sdtm_mdr_to_gmodel/prep_refactoring_ttl_issue.py +++ /dev/null @@ -1,46 +0,0 @@ -from data_providers.data_provider import DataProvider - -dp = DataProvider(debug = True, - mode = 'noschema') - -classes = [ - "Start Date/Time of Observation", - "Study", - "Study Identifier", - "Date/Time of First Study Treatment", - "Age", - "Race", - "Date/Time of Birth", - "Country", - "Investigator Name", - "Date/Time of Last Study Treatment", - "Subject Death Flag", - # "Study Day of Visit/Collection/Exam", - "Investigator Identifier", - "Unique Subject Identifier", - "Subject", - "Actual Arm Code", - "Date/Time of Death", - "Ethnicity", - "Sex", - "Study Site Identifier", - "Description of Actual Arm", - # "Subject Identifier for the Study", - "Description of Planned Arm", - "Date/Time of Informed Consent", - "Age Units", - "Domain", - "Domain Abbreviation", - "End Date/Time of Observation", - # "Date/Time of Collection", - "Planned Arm Code", - "Date/Time of End of Participation" -] -data = dp.get_data(classes=classes, limit=None) -print(data) -print(data.columns) -#q = dp.qb.generate_query_body(classes) -#print(q) - -p_classes = ["Study Day of Visit/Collection/Exam", "Subject Identifier for the Study", "Date/Time of Collection"] - diff --git a/utils/utils.py b/utils/utils.py index f6a547a..1e317cc 100644 --- a/utils/utils.py +++ b/utils/utils.py @@ -28,51 +28,6 @@ def compare_recordsets(jsonable1, jsonable2) -> bool: r2 = [json.loads(i) for i in sorted([json.dumps(i) for i in jsonable2])] return r1 == r2 -def compare_recordsets_old(rs1: [{}], rs2: [{}]) -> bool: - """ - We define "recordsets" as "lists of dictionaries". Each element of the lists is regarded as a "record". - - EXAMPLE of recordset: [{'Field_A': 1}, - {'Field_A': 1}, - {'Field_A': 99, 'Field_B': 'hello'}] - - Compare 2 recordsets WITHOUT REGARD to the position of the dictionaries within the lists, - and also WITHOUT REGARD to the position of the key:value pairs within the dictionaries. - Duplicates records, if present, are treated as completely separate. - - Return True if the given recordsets match, as defined above; False, otherwise. - - WARNING: this function is meant for comparing SMALL datasets, because it's Order n square! - - :param rs1: A (possibly empty) list of dictionaries - :param rs2: A (possibly empty) list of dictionaries - - :return: True if there's a match, or False otherwise - """ - - # Verify the type of the arguments - assert isinstance(rs1, list), "compare_recordsets() : The 1st argument is not a list! Value = " + str(rs1) - assert isinstance(rs2, list), "compare_recordsets() : The 2nd argument is not a list! Value = " + str(rs2) - - if len(rs1) != len(rs2): - return False # Datasets of different sizes will never match - - # Consider each element (i.e. a dictionary) in turn in the first list: - # attempt to remove it from the other list; if the removal fails, then it means - # that we have an element in the 1st list that is not present in the 2nd one (hence a mismatch) - for rec1 in rs1: - # Note: since Python 3.7 dictionaries are order-preserving, but - # built-in Python functions such as "remove" - # do not distinguish dictionaries based on order: - # {'a': 1, 'b': 2} will match {'b': 2, 'a': 1} - - try: - rs2.remove(rec1) # Remove (the first instance of) the element rec1 from the list rs2 - except Exception: - return False # The remove failed - i.e. the first list contains an element not in the 2nd one - - return True - def summarize_dataframe(df, caption="") -> None: """