addressing issue #140

Main.py

@@ -69,6 +69,7 @@ def main():
     start = time.time()
     combined_edges = dict(ent.data_files, **ont.data_files)
     # master_edges = CreatesEdgeList(data_files=combined_edges, source_file='resources/resource_info.txt')
+    # master_edges.runs_creates_knowledge_graph_edges(source_file='resources/resource_info.txt', data_files=combined_edges, cpus=cpus)
     master_edges = CreatesEdgeList(data_files=combined_edges, source_file=args.res)
     master_edges.runs_creates_knowledge_graph_edges(source_file=args.res, data_files=combined_edges, cpus=cpus)
     end = time.time(); timestamp = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")

README.rst

@@ -308,22 +308,7 @@ This project is licensed under Apache License 2.0 - see the `LICENSE.md`_ file f
 Citing this Work
 =================
 
-**ISMB Conference Pre-print:**  
-
-Callahan TJ, Tripodi IJ, Hunter LE, Baumgartner WA. `A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs <https://www.biorxiv.org/content/10.1101/2020.04.30.071407v1.abstract>`_. bioRxiv. 2020 Jan 1.
-
-
-**Zenodo**
-
-.. code:: bash
-
-   @misc{callahan_tj_2019_3401437,
-     author       = {Callahan, TJ},  
-     title        = {PheKnowLator},  
-     year         = 2019,      
-     doi          = {10.5281/zenodo.3401437},  
-     url          = {https://doi.org/10.5281/zenodo.3401437}}
-
+Please see our preprint: https://arxiv.org/abs/2307.05727
 
 .. |logo| image:: https://user-images.githubusercontent.com/8030363/195494933-d0faba60-5643-4cc6-8a48-41b4a94a7afe.png
    :target: https://github.com/callahantiff/PheKnowLator

main.ipynb

@@ -84,19 +84,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# import needed libraries\n",
     "import glob\n",
     "import json\n",
     "import pandas\n",
+    "import psutil\n",
     "import ray\n",
     "import time\n",
     "\n",
     "# import module\n",
-    "from pkt_kg import downloads, edge_list, knowledge_graph"
+    "from pkt_kg.downloads import OntData, LinkedData\n",
+    "from pkt_kg.edge_list import CreatesEdgeList\n",
+    "from pkt_kg.knowledge_graph import FullBuild, PartialBuild, PostClosureBuild"
    ]
   },
   {
@@ -143,9 +146,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ont = pkt.OntData('resources/ontology_source_list.txt', 'resources/resource_info.txt')\n",
-    "ont.downloads_data_from_url()\n",
-    "ont.writes_source_metadata_locally()"
+    "ont = OntData('resources/ontology_source_list.txt', 'resources/resource_info.txt')\n",
+    "ont.downloads_data_from_url()"
    ]
   },
   {
@@ -164,9 +166,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "edges = pkt.LinkedData('resources/edge_source_list.txt', 'resources/resource_info.txt')\n",
-    "edges.downloads_data_from_url()\n",
-    "edges.writes_source_metadata_locally()"
+    "edges = LinkedData('resources/edge_source_list.txt', 'resources/resource_info.txt')\n",
+    "edges.downloads_data_from_url()"
    ]
   },
   {
@@ -229,6 +230,15 @@
     "ray.init()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined_edges"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -259,18 +269,17 @@
    "outputs": [],
    "source": [
     "# # read in master edge dictionary\n",
-    "# master_edges = json.load(open('resources/Master_Edge_List_Dict.json', 'r'))\n",
+    "master_edges = json.load(open('resources/Master_Edge_List_Dict.json', 'r'))\n",
     "\n",
     "# read in relation data\n",
     "relation_data = open('./resources/relations_data/RELATIONS_LABELS.txt').readlines()\n",
     "relation_dict = {x.split('\\t')[0]: x.split('\\t')[1].strip('\\n') for x in relation_data}\n",
     "\n",
     "# print basic stats on each resource\n",
-    "edge_data = [[key,\n",
-    "              relation_dict[master_edges.source_info[key]['edge_relation']],\n",
-    "              ', '.join(master_edges.source_info[key]['edge_list'][0]),\n",
-    "              len(master_edges.source_info[key]['edge_list'])]\n",
-    "             for key in master_edges.source_info.keys()]\n",
+    "edge_data = [[key, master_edges[key]['edge_relation'],\n",
+    "              ', '.join(master_edges[key]['edge_list'][0]),\n",
+    "              len(master_edges[key]['edge_list'])]\n",
+    "             for key in master_edges.keys()]\n",
     "\n",
     "# convert dict to pandas df for nice printing\n",
     "df = pandas.DataFrame(edge_data, columns = ['Edge Type', 'Relation', 'Example Edge', 'Unique Edges']) \n",
@@ -357,9 +366,9 @@
    "source": [
     "# specify input arguments\n",
     "build = 'full'\n",
-    "construction_approach = 'subclass'\n",
-    "add_node_data_to_kg = 'yes'\n",
-    "add_inverse_relations_to_kg = 'yes'\n",
+    "construction_approach = 'instance'\n",
+    "add_node_data_to_kg = 'no'\n",
+    "add_inverse_relations_to_kg = 'no'\n",
     "decode_owl_semantics = 'yes'\n",
     "kg_directory_location = './resources/knowledge_graphs'\n"
    ]
@@ -397,6 +406,15 @@
     "ray.shutdown()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "kg.ontologies"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

pkt_kg/__version__.py

@@ -1,2 +1,2 @@
 """Current version of package pkt_kg"""
-__version__ = "3.1.1"
+__version__ = "3.1.2"

pkt_kg/knowledge_graph.py

@@ -384,7 +384,7 @@ def construct_knowledge_graph(self) -> None:
             self.graph = Graph().parse(self.merged_ont_kg, format='xml')
         else:
             log_str = '*** Merging Ontology Data ***'; print(log_str); logger.info(log_str)
-            merges_ontologies(self.ontologies, self.merged_ont_kg.split('/')[-1], self.owl_tools)
+            merges_ontologies(self.ontologies, self.write_location + '/', self.merged_ont_kg.split('/')[-1], self.owl_tools)
             self.graph.parse(self.merged_ont_kg, format='xml')
         stats = 'Merged Ontologies {}'.format(derives_graph_statistics(self.graph)); print(stats); logger.info(stats)
 
@@ -561,7 +561,7 @@ def construct_knowledge_graph(self) -> None:
             self.graph = Graph().parse(self.merged_ont_kg, format='xml')
         else:
             log_str = '*** Merging Ontology Data ***'; print(log_str); logger.info(log_str)
-            merges_ontologies(self.ontologies, self.merged_ont_kg.split('/')[-1], self.owl_tools)
+            merges_ontologies(self.ontologies, self.write_location + '/', self.merged_ont_kg.split('/')[-1], self.owl_tools)
             self.graph.parse(self.merged_ont_kg, format='xml')
         stats = 'Merged Ontologies {}'.format(derives_graph_statistics(self.graph)); print(stats); logger.info(stats)
 

pkt_kg/utils/data_utils.py

@@ -471,10 +471,13 @@ def sublist_creator(actors: Union[Dict, List], chunk_size: int) -> List:
 
     # update list to return string identifier associated with each list length
     if isinstance(actors, Dict):
-        updated_lists = []; used_ids = set()
+        updated_lists = []
         for sub in lists:
-            sub_list = [[k for k, v in actors.items() if v == x and k not in used_ids][0] for x in sub]
-            updated_lists += [sub_list]; used_ids |= set(x for y in sub_list for x in y)
+            sub_list = []
+            for x in sub:
+                temp_list = [k for k, v in actors.items() if v == x][0]
+                sub_list.append(temp_list); del actors[temp_list]
+            updated_lists += [sub_list]
     else: updated_lists = lists
 
     return updated_lists

pkt_kg/utils/kg_utils.py

@@ -239,7 +239,7 @@ def merges_ontologies(onts: List[str], loc: str, merged: str,
         None.
     """
 
-    if not onts: return None
+    if not onts or len(onts) == 0: return None
     else:
         if loc + merged in glob.glob(loc + '/*.owl'): o1, o2 = onts.pop(), loc + merged
         else: o1, o2 = onts.pop(), onts.pop()