feat: add reactome_searcher

Author: ChenZiHong-Gavin

examples/input_examples/search_reactome_demo.jsonl

@@ -0,0 +1,4 @@
+{"content": "R-HSA-69278", "type": "reactome_id"}
+{"content": "apoptosis", "type": "keyword"}
+{"content": "TP53", "type": "gene_symbol"}
+{"content": "MAPK1\nERK2\nPTEN", "type": "gene_list"}

examples/search/search_reactome/search_reactome_config.yaml

@@ -0,0 +1,29 @@
+global_params:
+  working_dir: cache
+  kv_backend: rocksdb # key-value store backend, support: rocksdb, json_kv
+  graph_backend: kuzu # graph database backend, support: kuzu, networkx
+
+nodes:
+  - id: read_step
+    op_name: read
+    type: source
+    dependencies: []
+    params:
+      input_path:
+        - examples/input_examples/search_reactome_demo.jsonl # input file path, support json, jsonl, txt, pdf. See examples/input_examples for examples
+
+  - id: search_step
+    op_name: search
+    type: map_batch
+    dependencies:
+      - read_step # search_step depends on read_step
+    execution_params:
+      replicas: 1
+      batch_size: 10
+    save_output: true
+    params:
+      data_source: reactome # data source for searcher, support: uniprot, ncbi, rnacentral, reactome
+      reactome_params:
+        species: "Homo sapiens" # species name, support: Homo sapiens, Mus musculus, Rattus norvegicus, etc.
+        timeout: 30 # request timeout in seconds
+        max_retries: 3 # maximum number of retries for failed requests

graphgen/models/__init__.py

@@ -43,6 +43,7 @@
     )
     from .rephraser import StyleControlledRephraser
     from .searcher.db.ncbi_searcher import NCBISearch
+    from .searcher.db.reactome_searcher import ReactomeSearcher
     from .searcher.db.rnacentral_searcher import RNACentralSearch
     from .searcher.db.uniprot_searcher import UniProtSearch
     from .searcher.kg.wiki_search import WikiSearch
@@ -97,6 +98,7 @@
     # Searcher
     "NCBISearch": ".searcher.db.ncbi_searcher",
     "RNACentralSearch": ".searcher.db.rnacentral_searcher",
+    "ReactomeSearcher": ".searcher.db.reactome_searcher",
     "UniProtSearch": ".searcher.db.uniprot_searcher",
     "WikiSearch": ".searcher.kg.wiki_search",
     "BingSearch": ".searcher.web.bing_search",