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https://mediadive.dsmz.de/rest/solution/6128 +mediadive.medium:C106 biolink:has_part mediadive.ingredient:286 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6128 +mediadive.medium:C106 biolink:has_part mediadive.ingredient:2363 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6128 +mediadive.medium:C108 biolink:has_part mediadive.ingredient:286 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6247 +mediadive.medium:C108 biolink:has_part mediadive.ingredient:286 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6099 +mediadive.medium:C108 biolink:has_part mediadive.ingredient:2152 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6160 +mediadive.medium:C108 biolink:has_part mediadive.ingredient:286 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6160 +mediadive.medium:C108 biolink:has_part mediadive.ingredient:286 BFO:0000051 https://mediadive.dsmz.de/rest/solution/6246 diff --git a/kg_bacdive/transform.py b/kg_bacdive/transform.py index 30dae5a..479e2e2 100644 --- a/kg_bacdive/transform.py +++ b/kg_bacdive/transform.py @@ -4,7 +4,7 @@ from typing import List, Optional from kg_bacdive.transform_utils.bacdive.bacdive import BacDiveTransform -from kg_bacdive.transform_utils.mediadive.mediadive import MediaDiveDiveTransform +from kg_bacdive.transform_utils.mediadive.mediadive import MediaDiveTransform from kg_bacdive.transform_utils.ontology.ontology_transform import ONTOLOGIES, OntologyTransform from kg_bacdive.transform_utils.traits.traits import TraitsTransform @@ -19,7 +19,7 @@ # "ProteinAtlasTransform": ProteinAtlasTransform, # "STRINGTransform": STRINGTransform, "BacDiveTransform": BacDiveTransform, - "MediaDiveDiveTransform": MediaDiveDiveTransform, + "MediaDiveTransform": MediaDiveTransform, "TraitsTransform": TraitsTransform, } diff --git a/kg_bacdive/transform_utils/constants.py b/kg_bacdive/transform_utils/constants.py index e1455f1..480ba83 100644 --- a/kg_bacdive/transform_utils/constants.py +++ b/kg_bacdive/transform_utils/constants.py @@ -68,7 +68,7 @@ CHEBI_PREFIX = "CHEBI:" CAS_RN_PREFIX = "CAS-RN:" PUBCHEM_PREFIX = "PubChem:" -MEDIADIVE_COMPOUND_PREFIX = "mediadive.ingredient:" +MEDIADIVE_INGREDIENT_PREFIX = "mediadive.ingredient:" MEDIADIVE_SOLUTION_PREFIX = "mediadive.solution:" MEDIADIVE_MEDIUM_PREFIX = "mediadive.medium:" GO_PREFIX = "GO:" diff --git a/kg_bacdive/transform_utils/mediadive/__init__.py b/kg_bacdive/transform_utils/mediadive/__init__.py index b814cbd..87d6f85 100644 --- a/kg_bacdive/transform_utils/mediadive/__init__.py +++ b/kg_bacdive/transform_utils/mediadive/__init__.py @@ -1,4 +1,4 @@ """BacDive transform.""" -from .mediadive import MediaDiveDiveTransform +from .mediadive import MediaDiveTransform -__all__ = ["MediaDiveDiveTransform"] +__all__ = ["MediaDiveTransform"] diff --git a/kg_bacdive/transform_utils/mediadive/mediadive.py b/kg_bacdive/transform_utils/mediadive/mediadive.py index c554efe..a0d174c 100644 --- a/kg_bacdive/transform_utils/mediadive/mediadive.py +++ b/kg_bacdive/transform_utils/mediadive/mediadive.py @@ -43,9 +43,9 @@ KEGG_KEY, KEGG_PREFIX, MEDIADIVE_COMPLEX_MEDIUM_COLUMN, - MEDIADIVE_COMPOUND_PREFIX, MEDIADIVE_DESC_COLUMN, MEDIADIVE_ID_COLUMN, + MEDIADIVE_INGREDIENT_PREFIX, MEDIADIVE_LINK_COLUMN, MEDIADIVE_MAX_PH_COLUMN, MEDIADIVE_MEDIUM_PREFIX, @@ -72,10 +72,10 @@ SOLUTIONS_KEY, ) from kg_bacdive.transform_utils.transform import Transform -from kg_bacdive.utils.pandas_utils import drop_duplicates +from kg_bacdive.utils.pandas_utils import drop_duplicates, establish_transitive_relationship -class MediaDiveDiveTransform(Transform): +class MediaDiveTransform(Transform): """Template for how the transform class would be designed.""" @@ -144,7 +144,7 @@ def standardize_compound_id(self, id: str): elif data[CAS_RN_KEY] is not None: return CAS_RN_PREFIX + str(data[CAS_RN_KEY]) else: - return MEDIADIVE_COMPOUND_PREFIX + id + return MEDIADIVE_INGREDIENT_PREFIX + id def download_yaml_and_get_json( self, @@ -296,4 +296,10 @@ def run(self, data_file: Union[Optional[Path], Optional[str]] = None): progress.update() drop_duplicates(self.output_node_file) - drop_duplicates(self.output_edge_file) + establish_transitive_relationship( + self.output_edge_file, + MEDIADIVE_MEDIUM_PREFIX, + MEDIADIVE_SOLUTION_PREFIX, + MEDIUM_TO_INGREDIENT_EDGE, + MEDIADIVE_INGREDIENT_PREFIX, + ) diff --git a/kg_bacdive/utils/pandas_utils.py b/kg_bacdive/utils/pandas_utils.py index 0e3b80d..0402936 100644 --- a/kg_bacdive/utils/pandas_utils.py +++ b/kg_bacdive/utils/pandas_utils.py @@ -3,6 +3,8 @@ import pandas as pd +from kg_bacdive.transform_utils.constants import OBJECT_COLUMN, PREDICATE_COLUMN, SUBJECT_COLUMN + def drop_duplicates(file_path: Path): """ @@ -14,3 +16,55 @@ def drop_duplicates(file_path: Path): df = pd.read_csv(file_path, sep="\t", low_memory=False) df = df.drop_duplicates() df.to_csv(file_path, sep="\t", index=False) + return df + + +def establish_transitive_relationship( + file_path: Path, + subject_prefix: str, + intermediate_prefix: str, + predicate: str, + object_prefix: str, +) -> pd.DataFrame: + """ + Establish transitive relationship given the predicate is the same. + + e.g.: Existent relations: + 1. A => predicate => B + 2. B => predicate => C + + This function adds the relation A => predicate => C + + + :param file_path: Filepath of the edge file. + :param subject_prefix: Subject prefix (A in the example) + :param intermediate_prefix: Intermediate prefix that connects the subject to object (B in the example). + :param predicate: The common predicate between all relations. + :param object_prefix: Object prefix (C in the example) + :return: Core dataframe with additional deduced rows. + """ + df = drop_duplicates(file_path) + df_relations = df.loc[df[PREDICATE_COLUMN] == predicate] + subject_condition = df_relations[SUBJECT_COLUMN].str.startswith(subject_prefix) + intermediate_subject_condition = df_relations[SUBJECT_COLUMN].str.startswith( + intermediate_prefix + ) + object_condition = df_relations[OBJECT_COLUMN].str.startswith(object_prefix) + intermediate_object_condition = df_relations[OBJECT_COLUMN].str.startswith(intermediate_prefix) + subject_intermediate_df = df_relations[subject_condition & intermediate_object_condition] + intermediate_object_df = df_relations[intermediate_subject_condition & object_condition] + + list_of_dfs_to_append = [] + + for row in subject_intermediate_df.iterrows(): + transitive_relations_df = intermediate_object_df.loc[ + intermediate_object_df[SUBJECT_COLUMN] == row[1].object + ] + transitive_relations_df.loc[ + transitive_relations_df[SUBJECT_COLUMN] == row[1].object, SUBJECT_COLUMN + ] = row[1].subject + list_of_dfs_to_append.append(transitive_relations_df) + + df = pd.concat([df] + list_of_dfs_to_append) + df.to_csv(file_path, sep="\t", index=False) + return df diff --git a/merged_graph_stats.yaml b/merged_graph_stats.yaml index 238045d..2b842a5 100644 --- a/merged_graph_stats.yaml +++ b/merged_graph_stats.yaml @@ -9,13 +9,13 @@ edge_stats: unknown: count: 36244 biolink:has_part: - count: 84816 + count: 102140 provided_by: unknown: - count: 84816 + count: 102140 source: unknown: - count: 84816 + count: 102140 biolink:has_phenotype: count: 19727 provided_by: @@ -124,13 +124,13 @@ edge_stats: unknown: count: 2027 biolink:ChemicalEntity-biolink:has_part-biolink:ChemicalEntity: - count: 84816 + count: 102140 provided_by: unknown: - count: 84816 + count: 102140 source: unknown: - count: 84816 + count: 102140 biolink:ChemicalEntity-biolink:has_part-biolink:ChemicalSubstance: count: 50254 provided_by: @@ -464,7 +464,7 @@ edge_stats: - unknown source: - unknown - total_edges: 1324137 + total_edges: 1341461 graph_name: kg-bacdive graph node_stats: count_by_category: diff --git a/notebook/MergedKG_exploration.ipynb b/notebook/MergedKG_exploration.ipynb new file mode 100644 index 0000000..9059360 --- /dev/null +++ b/notebook/MergedKG_exploration.ipynb @@ -0,0 +1,1293 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "6894e493-b721-48be-a996-9d3f87f79628", + "metadata": {}, + "outputs": [], + "source": [ + "%reset -f" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "50bc3eb8-4b07-4dd5-9cdd-75b74664555a", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "import tarfile\n", + "import pandas as pd" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "d574805b-de0c-40d5-b6ad-290daaccd656", + "metadata": {}, + "outputs": [], + "source": [ + "MERGED_TAR = Path.cwd().parent / \"data/merged/merged-kg.tar.gz\"" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "77bd23c9-bbbd-46db-a98b-a5f067bb3568", + "metadata": {}, + "outputs": [], + "source": [ + "tar = tarfile.open(MERGED_TAR, \"r:gz\")\n", + "# Extract the TSV file\n", + "for member in tar.getmembers():\n", + " f = tar.extractfile(member)\n", + " if '_nodes.tsv' in member.name:\n", + " # Read the TSV file into a pandas DataFrame\n", + " df_nodes = pd.read_csv(f, sep='\\t', low_memory=False)\n", + " elif '_edges.tsv' in member.name:\n", + " # Read the TSV file into a pandas DataFrame\n", + " df_edges = pd.read_csv(f, sep='\\t', low_memory=False)\n", + "\n", + "# Close the tar.gz file\n", + "tar.close()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a6badbc1-c9b3-4851-844a-5a3ce37f43db", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " id \\\n", + "1249568 urn:uuid:653df055-46ac-4a5a-b881-b8e8c4804d9b \n", + "1249573 urn:uuid:1d669c12-6bcc-49fd-989c-8436ca92721d \n", + "1249574 urn:uuid:66116aa2-411a-4ca3-be36-6b30014ed72a \n", + "1249575 urn:uuid:20396f7b-2db6-4061-9e0c-e97b236f7513 \n", + "1249577 urn:uuid:ad93aa8e-920c-474e-a114-39110088c83e \n", + "... ... \n", + "1340686 urn:uuid:013ef9c3-c5d7-4301-bb2c-cdc4374a3b73 \n", + "1340700 urn:uuid:486fe651-41c2-4fb4-bcae-6b8bf36befb3 \n", + "1340803 urn:uuid:868448b2-db0e-48c7-988b-1ba8557bf0b2 \n", + "1340809 urn:uuid:b61b5cd7-1312-43fc-8c7a-f9bec69d1904 \n", + "1340818 urn:uuid:855bd741-7061-43f4-9ab7-fcdb899b34f8 \n", + "\n", + " subject predicate object \\\n", + "1249568 mediadive.solution:1 biolink:has_part mediadive.ingredient:2 \n", + "1249573 mediadive.solution:1 biolink:has_part mediadive.ingredient:2111 \n", + "1249574 mediadive.solution:1 biolink:has_part mediadive.ingredient:724 \n", + "1249575 mediadive.solution:1 biolink:has_part mediadive.ingredient:2110 \n", + "1249577 mediadive.solution:1 biolink:has_part mediadive.ingredient:2112 \n", + "... ... ... ... \n", + "1340686 mediadive.solution:6241 biolink:has_part mediadive.ingredient:286 \n", + "1340700 mediadive.solution:6242 biolink:has_part mediadive.ingredient:286 \n", + "1340803 mediadive.solution:6247 biolink:has_part mediadive.ingredient:286 \n", + "1340809 mediadive.solution:6099 biolink:has_part mediadive.ingredient:286 \n", + "1340818 mediadive.solution:6246 biolink:has_part mediadive.ingredient:286 \n", + "\n", + " relation provided_by knowledge_source \n", + "1249568 BFO:0000051 NaN Graph \n", + "1249573 BFO:0000051 NaN Graph \n", + "1249574 BFO:0000051 NaN Graph \n", + "1249575 BFO:0000051 NaN Graph \n", + "1249577 BFO:0000051 NaN Graph \n", + "... ... ... ... \n", + "1340686 BFO:0000051 NaN Graph \n", + "1340700 BFO:0000051 NaN Graph \n", + "1340803 BFO:0000051 NaN Graph \n", + "1340809 BFO:0000051 NaN Graph \n", + "1340818 BFO:0000051 NaN Graph \n", + "\n", + "[1962 rows x 7 columns]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "solution_subject_condition = df_mediadive[\"subject\"].str.startswith(\"mediadive.solution:\")\n", + "ingredient_object_condition = df_mediadive[\"object\"].str.startswith(\"mediadive.ingredient:\")\n", + "\n", + "solution_ingredient_df = df_mediadive[solution_subject_condition & ingredient_object_condition]\n", + "solution_ingredient_df" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5976c9ed-43c5-4c9c-b00a-233836d2a9d2", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}