Lincs

Common/data_sources.py

@@ -19,6 +19,7 @@
 HMDB = 'HMDB'
 HUMAN_GOA = 'HumanGOA'
 INTACT = 'IntAct'
+LINCS = 'LINCS'
 LITCOIN = 'LitCoin'
 LITCOIN_SAPBERT = 'LitCoinSapBERT'
 LITCOIN_ENTITY_EXTRACTOR = 'LitCoinEntityExtractor'
@@ -67,6 +68,7 @@
     HUMAN_GOA: ("parsers.GOA.src.loadGOA", "HumanGOALoader"),
     HUMAN_STRING: ("parsers.STRING.src.loadSTRINGDB", "HumanSTRINGDBLoader"),
     INTACT: ("parsers.IntAct.src.loadIA", "IALoader"),
+    LINCS: ("parsers.LINCS.src.loadLINCS", "LINCSLoader"),
     LITCOIN: ("parsers.LitCoin.src.loadLitCoin", "LitCoinLoader"),
     LITCOIN_ENTITY_EXTRACTOR: ("parsers.LitCoin.src.loadLitCoin", "LitCoinEntityExtractorLoader"),
     LITCOIN_SAPBERT: ("parsers.LitCoin.src.loadLitCoin", "LitCoinSapBERTLoader"),

parsers/LINCS/src/loadLINCS.py

@@ -0,0 +1,95 @@
+import os
+import enum
+
+from Common.extractor import Extractor
+from Common.loader_interface import SourceDataLoader
+from Common.biolink_constants import *
+from Common.prefixes import PUBCHEM_COMPOUND
+from Common.utils import GetData
+
+
+class GENERICDATACOLS(enum.IntEnum):
+    SOURCE_ID = 2
+    SOURCE_LABEL = 3
+    TARGET_ID = 5
+    TARGET_LABEL = 6
+    PREDICATE = 7
+
+
+PREDICATE_MAPPING = {
+    "in_similarity_relationship_with": "biolink:chemically_similar_to",
+    "negatively_regulates": "RO:0002212",
+    "positively_regulates": "RO:0002213"
+}
+
+
+##############
+# Class: LINCS loader
+#
+# By: James Chung
+# Date: 10/30/2024
+# Desc: Class that loads/parses the data in Library of Integrated Network-Based Cellular Signatures.
+# 
+##############
+class LINCSLoader(SourceDataLoader):
+
+    source_id: str = 'LINCS'
+    provenance_id: str = 'infores:lincs'
+    parsing_version: str = '1.0'
+
+    def __init__(self, test_mode: bool = False, source_data_dir: str = None):
+        """
+        :param test_mode - sets the run into test mode
+        :param source_data_dir - the specific storage directory to save files in
+        """
+        super().__init__(test_mode=test_mode, source_data_dir=source_data_dir)
+
+        self.data_url = 'https://stars.renci.org/var/data_services/LINCS/'
+        self.edge_file = "LINCS.lookup.edges.csv"
+        self.data_files = [self.edge_file]
+
+    def get_latest_source_version(self) -> str:
+        # The KG was generated from Data Distillery KG. There was no version defined.
+        latest_version = 'v1.0'
+        return latest_version
+
+    def get_data(self) -> bool:
+        source_data_url = f'{self.data_url}{self.edge_file}'
+        data_puller = GetData()
+        data_puller.pull_via_http(source_data_url, self.data_path)
+        return True
+
+    def parse_data(self) -> dict:
+        """
+        Parses the data file for graph nodes/edges
+
+        :return: ret_val: load_metadata
+        """
+        extractor = Extractor(file_writer=self.output_file_writer)
+        lincs_file: str = os.path.join(self.data_path, self.edge_file)
+        with open(lincs_file, 'rt') as fp:
+            extractor.csv_extract(fp,
+                                  lambda line: self.resolve_id(line[GENERICDATACOLS.SOURCE_ID.value]),  # source id
+                                  lambda line: self.resolve_id(line[GENERICDATACOLS.TARGET_ID.value]),  # target id
+                                  lambda line: PREDICATE_MAPPING[line[GENERICDATACOLS.PREDICATE.value]],  # predicate extractor
+                                  lambda line: {},  # subject properties
+                                  lambda line: {},  # object properties
+                                  lambda line: self.get_edge_properties(),  # edge properties
+                                  comment_character='#',
+                                  delim=',',
+                                  has_header_row=True)
+        return extractor.load_metadata
+
+    @staticmethod
+    def resolve_id(idstring: str):
+        if idstring.startswith("PUBCHEM"):
+            return idstring.replace("PUBCHEM", PUBCHEM_COMPOUND)
+        return idstring
+
+    def get_edge_properties(self):
+        properties = {
+            PRIMARY_KNOWLEDGE_SOURCE: self.provenance_id,
+            KNOWLEDGE_LEVEL: KNOWLEDGE_ASSERTION,
+            AGENT_TYPE: DATA_PIPELINE
+        }
+        return properties