Squashed commit of the following:

commit 502581d Merge: 37ce60f 713f527 Author: Evan Morris <[email protected]> Date: Mon Dec 9 16:09:17 2024 -0500 Merge pull request #265 from RobokopU24/add_GHaction Added a GitHub action... commit 37ce60f Merge: cd9a6c5 90c6231 Author: Evan Morris <[email protected]> Date: Mon Dec 9 16:07:41 2024 -0500 Merge pull request #242 from RobokopU24/DnlRKorn-patch-4 Fixed regex pattern issue in loadCTD.py commit cd9a6c5 Merge: fcf6611 d63d4bb Author: Evan Morris <[email protected]> Date: Mon Dec 9 16:04:50 2024 -0500 Merge pull request #240 from RobokopU24/DnlRKorn-patch-2 Dynamically load latest version of GenomeAlliance data commit fcf6611 Merge: 43874d9 2a39e3a Author: Evan Morris <[email protected]> Date: Mon Dec 9 16:00:09 2024 -0500 Merge pull request #272 from RobokopU24/drugcentral-logscale-potencies Convert activity type mapping to log-scale. commit 2a39e3a Author: Evan Morris <[email protected]> Date: Tue Dec 3 12:18:36 2024 -0500 making all instances of affinity/affinity parameter use the constants commit 43874d9 Merge: 1867684 3491e3f Author: Evan Morris <[email protected]> Date: Mon Dec 2 11:53:28 2024 -0500 Merge pull request #267 from RobokopU24/LINCS Lincs commit 3491e3f Author: Evan Morris <[email protected]> Date: Mon Dec 2 11:51:21 2024 -0500 fixing parser see commit description fixing several bugs and broken variable names - fixing source data download location - source data delimiter is comma not tab - cleaning up properties (they need to be a dictionary, but node props were unnecessary anyway) simplifying/fixing qualifier handling - using predicates like RO:0002212 includes directionality and will normalize to qualified version, old implementation didn't work anyway, so this is better commit d2bead1 Author: Evan Morris <[email protected]> Date: Mon Dec 2 11:46:07 2024 -0500 fixing missing comma, making quote usage consistent commit 46f8117 Author: Evan Morris <[email protected]> Date: Tue Nov 26 10:56:15 2024 -0500 general clean up, fixing imports, removing template comments commit bc1e533 Author: beasleyjonm <[email protected]> Date: Mon Nov 25 16:38:44 2024 -0500 Changed how activity parameters are described in log-scale. commit 896e7af Author: beasleyjonm <[email protected]> Date: Sat Nov 23 21:03:48 2024 -0500 Convert activity type mapping to log-scale. The activity and potency types on Drug Central are log-scaled, so let's add the "p" in front of the activity types to reflect that. commit 1867684 Merge: 52149ee 224d0b5 Author: beasleyjonm <[email protected]> Date: Thu Nov 21 12:19:08 2024 -0500 Merge pull request #260 from RobokopU24/Issue257 Add in all Monarch KG edge properties on ingest. commit 52149ee Merge: 6b8f389 7bbdc00 Author: beasleyjonm <[email protected]> Date: Thu Nov 21 12:14:21 2024 -0500 Merge pull request #268 from RobokopU24/collapsed_qualifiers_kg Collapsed qualifiers kg commit 7bbdc00 Author: beasleyjonm <[email protected]> Date: Thu Nov 7 12:35:08 2024 -0500 Update collapse_qualifiers.py commit 0839bcc Author: Jon-Michael Beasley <[email protected]> Date: Thu Oct 31 13:42:46 2024 -0400 Updated to fix code and add option to create collapsed qualifier Neo4j dump. commit 0abf23c Author: Jon-Michael Beasley <[email protected]> Date: Thu Oct 31 11:30:51 2024 -0400 Added script to collapse object qualifier statements to the edge predicates. commit 56e8b5b Author: James Chung <[email protected]> Date: Thu Oct 31 08:14:15 2024 -0400 return variable added commit af3037a Author: James Chung <[email protected]> Date: Wed Oct 30 23:35:18 2024 -0400 LINCS parsers first try commit b2eef57 Author: James Chung <[email protected]> Date: Wed Oct 30 23:34:52 2024 -0400 LINCS parser first try commit 713f527 Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 10:51:47 2024 -0400 setting environment variable commit 26b1073 Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 10:34:55 2024 -0400 trying again with fresh eyes commit 99fc5ee Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 10:29:49 2024 -0400 trying again with fresh eyes commit cc587c2 Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 10:18:03 2024 -0400 trying again with fresh eyes commit 689d6e9 Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 10:02:14 2024 -0400 new script for action commit ff79e6a Author: Kathleen Carter <[email protected]> Date: Tue Oct 29 09:58:35 2024 -0400 trying again with gresh eyes commit 91d695e Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 17:23:43 2024 -0400 error tracking/loggins commit 7423a00 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 17:20:02 2024 -0400 gitHub issues error commit 24d3c91 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 17:16:19 2024 -0400 split pull requests and issues commit 736d185 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:58:49 2024 -0400 split pull requests and issues commit 55be1e5 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:50:50 2024 -0400 lets try this with github-script@v6 instead... commit 76bc6bb Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:44:57 2024 -0400 fix double/single quote issue commit 745d0c3 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:43:27 2024 -0400 fix double/single quote issue commit e887346 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:22:29 2024 -0400 fix double/single quote issue commit 979bc72 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:19:08 2024 -0400 bump commit ff0fc91 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:15:29 2024 -0400 bump commit 2ff1393 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:14:13 2024 -0400 actually invoke python... commit 3e95ae8 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:10:24 2024 -0400 update to the latest versions of checkout and setup-python commit e528db4 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:04:06 2024 -0400 bump commit 56e9918 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 15:01:21 2024 -0400 Update requirements.txt Will need PyGithub for this... commit 0d62da8 Author: Kathleen Carter <[email protected]> Date: Mon Oct 28 14:51:45 2024 -0400 Added a GitHub action to automatically add the label "Biological Context QC" to issues and PRs that mention "predicate" or "biolink:" Automatically assign this event to Kathleen commit 6b8f389 Merge: b5fcc32 f604791 Author: Evan Morris <[email protected]> Date: Thu Oct 24 15:40:23 2024 -0400 Merge pull request #263 from RobokopU24/hgnc_fix updating HGNC file location and version date for new HGNC set up commit f604791 Author: Evan Morris <[email protected]> Date: Thu Oct 24 13:23:43 2024 -0400 updating HGNC file location and version date for new HGNC set up commit b5fcc32 Merge: bc28a73 ff3099e Author: Evan Morris <[email protected]> Date: Thu Oct 24 13:06:41 2024 -0400 Merge pull request #262 from RobokopU24/dependabot/pip/mysql-connector-python-9.1.0 Bump mysql-connector-python from 8.4.0 to 9.1.0 commit ff3099e Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Oct 24 17:01:59 2024 +0000 Bump mysql-connector-python from 8.4.0 to 9.1.0 Bumps [mysql-connector-python](https://github.com/mysql/mysql-connector-python) from 8.4.0 to 9.1.0. - [Changelog](https://github.com/mysql/mysql-connector-python/blob/trunk/CHANGES.txt) - [Commits](mysql/mysql-connector-python@8.4.0...9.1.0) --- updated-dependencies: - dependency-name: mysql-connector-python dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> commit 224d0b5 Author: Daniel Korn <[email protected]> Date: Thu Sep 19 15:29:18 2024 -0400 Added all available metadata present in Monarch KG to edge properties. commit 5e9151b Author: Daniel Korn <[email protected]> Date: Thu Sep 19 13:03:18 2024 -0400 Changed Monarch KG ingest to automatically pull from the latest version. Also made process to check the metadata yaml file for the publishing date of the latest version. commit 90c6231 Author: DnlRKorn <[email protected]> Date: Thu Jul 25 13:57:52 2024 -0400 Fixed regex pattern issue in loadCTD.py Made the regex pattern a "raw" string. commit d63d4bb Author: DnlRKorn <[email protected]> Date: Thu Jul 25 11:48:15 2024 -0400 Dynamically load latest version of GenomeAlliance data Previously genome alliance data was frozen to version 5.3.0; added some code to get the latest version instead.
RobokopU24 · Dec 19, 2024 · 40bbb95 · 40bbb95
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diff --git a/.github/scripts/Bio_QC_check.py b/.github/scripts/Bio_QC_check.py
@@ -0,0 +1,46 @@
+import os
+import requests
+
+PREDICATE_KEYWORDS = ["predicate", "biolink:", "edges"]
+LABEL_NAME = "Biological Context QC"  # Label to add if keywords are found
+
+# GitHub API variables
+GITHUB_TOKEN = os.getenv("GITHUB_TOKEN")
+REPO_NAME = os.getenv("GITHUB_REPOSITORY")
+ISSUE_NUMBER = os.getenv("ISSUE_NUMBER")
+print("GITHUB_TOKEN:", GITHUB_TOKEN)
+print("REPO_NAME:", REPO_NAME)
+print("ISSUE_NUMBER:", ISSUE_NUMBER)
+
+headers = {"Authorization": f"Bearer {GITHUB_TOKEN}"}
+api_url = f"https://api.github.com/repos/{REPO_NAME}"
+
+def get_issue_details(issue_number):
+    response = requests.get(f"{api_url}/issues/{issue_number}", headers=headers)
+    response.raise_for_status()
+    return response.json()
+
+def add_label(issue_number, label_name):
+    response = requests.post(
+        f"{api_url}/issues/{issue_number}/labels",
+        headers=headers,
+        json={"labels": [label_name]}
+    )
+    response.raise_for_status()
+    print(f"Label '{label_name}' added to issue/PR #{issue_number}")
+
+def check_keywords_in_text(text, keywords):
+    return any(keyword in text for keyword in keywords)
+
+def main():
+    issue_details = get_issue_details(ISSUE_NUMBER)
+    title = issue_details["title"]
+    body = issue_details["body"]
+
+    if check_keywords_in_text(title, PREDICATE_KEYWORDS) or check_keywords_in_text(body, PREDICATE_KEYWORDS):
+        add_label(ISSUE_NUMBER, LABEL_NAME)
+    else:
+        print("No predicate keywords found.")
+
+if __name__ == "__main__":
+    main()
diff --git a/.github/workflows/label-predicate-changes.yml b/.github/workflows/label-predicate-changes.yml
@@ -0,0 +1,32 @@
+name: 'Label Predicate Changes'
+
+on:
+  pull_request:
+    types: [opened, edited, synchronize]
+  issues:
+    types: [opened, edited]
+
+jobs:
+  label_check:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install PyGithub 
+
+    - name: Run predicate check
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        ISSUE_NUMBER: ${{ github.event.pull_request.number || github.event.issue.number }}
+      run: |
+        python .github/scripts/Bio_QC_check.py
diff --git a/Common/build_manager.py b/Common/build_manager.py
@@ -18,10 +18,12 @@
 from Common.supplementation import SequenceVariantSupplementation
 from Common.meta_kg import MetaKnowledgeGraphBuilder, META_KG_FILENAME, TEST_DATA_FILENAME
 from Common.redundant_kg import generate_redundant_kg
+from Common.collapse_qualifiers import generate_collapsed_qualifiers_kg
 
 NODES_FILENAME = 'nodes.jsonl'
 EDGES_FILENAME = 'edges.jsonl'
 REDUNDANT_EDGES_FILENAME = 'redundant_edges.jsonl'
+COLLAPSED_QUALIFIERS_FILENAME = 'collapsed_qualifier_edges.jsonl'
 
 
 class GraphBuilder:
@@ -118,6 +120,51 @@ def build_graph(self, graph_id: str):
                                                 generate_test_data=needs_test_data)
 
         output_formats = graph_spec.graph_output_format.lower().split('+') if graph_spec.graph_output_format else []
+        nodes_filepath = os.path.join(graph_output_dir, NODES_FILENAME)
+        edges_filepath = os.path.join(graph_output_dir, EDGES_FILENAME)
+
+        if 'redundant_jsonl' in output_formats:
+            self.logger.info(f'Generating redundant edge KG for {graph_id}...')
+            redundant_filepath = edges_filepath.replace(EDGES_FILENAME, REDUNDANT_EDGES_FILENAME)
+            generate_redundant_kg(edges_filepath, redundant_filepath)
+
+        if 'redundant_neo4j' in output_formats:
+            self.logger.info(f'Generating redundant edge KG for {graph_id}...')
+            redundant_filepath = edges_filepath.replace(EDGES_FILENAME, REDUNDANT_EDGES_FILENAME)
+            generate_redundant_kg(edges_filepath, redundant_filepath)
+            self.logger.info(f'Starting Neo4j dump pipeline for redundant {graph_id}...')
+            dump_success = create_neo4j_dump(nodes_filepath=nodes_filepath,
+                                             edges_filepath=redundant_filepath,
+                                             output_directory=graph_output_dir,
+                                             graph_id=graph_id,
+                                             graph_version=graph_version,
+                                             logger=self.logger)
+
+            if dump_success:
+                graph_output_url = self.get_graph_output_URL(graph_id, graph_version)
+                graph_metadata.set_dump_url(f'{graph_output_url}graph_{graph_version}_redundant.db.dump')
+
+        if 'collapsed_qualifiers_jsonl' in output_formats:
+            self.logger.info(f'Generating collapsed qualifier predicates KG for {graph_id}...')
+            collapsed_qualifiers_filepath = edges_filepath.replace(EDGES_FILENAME, COLLAPSED_QUALIFIERS_FILENAME)
+            generate_collapsed_qualifiers_kg(edges_filepath, collapsed_qualifiers_filepath)
+
+        if 'collapsed_qualifiers_neo4j' in output_formats:
+            self.logger.info(f'Generating collapsed qualifier predicates KG for {graph_id}...')
+            collapsed_qualifiers_filepath = edges_filepath.replace(EDGES_FILENAME, COLLAPSED_QUALIFIERS_FILENAME)
+            generate_collapsed_qualifiers_kg(edges_filepath, collapsed_qualifiers_filepath)
+            self.logger.info(f'Starting Neo4j dump pipeline for {graph_id} with collapsed qualifiers...')
+            dump_success = create_neo4j_dump(nodes_filepath=nodes_filepath,
+                                             edges_filepath=collapsed_qualifiers_filepath,
+                                             output_directory=graph_output_dir,
+                                             graph_id=graph_id,
+                                             graph_version=graph_version,
+                                             logger=self.logger)
+
+            if dump_success:
+                graph_output_url = self.get_graph_output_URL(graph_id, graph_version)
+                graph_metadata.set_dump_url(f'{graph_output_url}graph_{graph_version}_collapsed_qualifiers.db.dump')
+
         if 'neo4j' in output_formats:
             self.logger.info(f'Starting Neo4j dump pipeline for {graph_id}...')
             dump_success = create_neo4j_dump(nodes_filepath=nodes_filepath,
@@ -131,11 +178,6 @@ def build_graph(self, graph_id: str):
                 graph_output_url = self.get_graph_output_URL(graph_id, graph_version)
                 graph_metadata.set_dump_url(f'{graph_output_url}graph_{graph_version}.db.dump')
 
-        if 'redundant_jsonl' in output_formats:
-            self.logger.info(f'Generating redundant edge KG for {graph_id}...')
-            redundant_filepath = edges_filepath.replace(EDGES_FILENAME, REDUNDANT_EDGES_FILENAME)
-            generate_redundant_kg(edges_filepath, redundant_filepath)
-
     def build_dependencies(self, graph_spec: GraphSpec):
         for subgraph_source in graph_spec.subgraphs:
             subgraph_id = subgraph_source.id

diff --git a/Common/collapse_qualifiers.py b/Common/collapse_qualifiers.py
@@ -0,0 +1,171 @@
+try:
+    from tqdm import tqdm
+    TQDM_AVAILABLE = True
+except ImportError:
+    TQDM_AVAILABLE = False
+
+from Common.biolink_constants import PREDICATE, QUALIFIED_PREDICATE, SUBJECT_DERIVATIVE_QUALIFIER, SUBJECT_FORM_OR_VARIANT_QUALIFIER, SUBJECT_PART_QUALIFIER, \
+    SUBJECT_DIRECTION_QUALIFIER, SUBJECT_ASPECT_QUALIFIER, OBJECT_DERIVATIVE_QUALIFIER, OBJECT_FORM_OR_VARIANT_QUALIFIER, \
+    OBJECT_PART_QUALIFIER, OBJECT_DIRECTION_QUALIFIER, OBJECT_ASPECT_QUALIFIER, CAUSAL_MECHANISM_QUALIFIER, \
+    ANATOMICAL_CONTEXT_QUALIFIER, SPECIES_CONTEXT_QUALIFIER
+from Common.biolink_utils import get_biolink_model_toolkit
+from Common.utils import quick_jsonl_file_iterator
+from Common.kgx_file_writer import KGXFileWriter
+
+### The goal of this script is to collapse the qualifiers, which are in edge properties, into a single statement, then replace the
+### existing predicate label with the collapsed qualifier statement.
+
+### Call the biolink model toolkit to get the list of all qualifiers. This may change, but the way qualifiers are handled is currently hard-coded in this script.
+bmt = get_biolink_model_toolkit()
+
+def write_edge_no_q(edge, predicate, qualifiers):
+    tmp_edge = edge.copy()
+    tmp_edge[PREDICATE] = f"{predicate}"
+    for qualifier in qualifiers.keys():
+        tmp_edge.pop(qualifier, None)
+    return tmp_edge
+
+def aspect_qualifier_semantic_adjustment(aspect_qualifier):
+    # TODO check if other aspect qualifiers besides molecular interaction need to be treated differently.
+    if aspect_qualifier.split('_')[-1] == 'interaction':
+        aspect_conversion = aspect_qualifier + "_with"
+    else:
+        aspect_conversion = aspect_qualifier + "_of"
+    return aspect_conversion
+
+def form_or_variant_qualifier_semantic_adjustment(form_or_variant_qualifier):
+    # TODO check if other form_or_variant_qualifier qualifiers besides molecular interaction need to be treated differently.
+    form_or_variant_conversion = form_or_variant_qualifier + "_of"
+    return form_or_variant_conversion
+
+def causal_mechanism_qualifier_semantic_adjustment(causal_mechanism_qualifier):
+    # TODO check if other causal_mechanism qualifiers besides molecular interaction need to be treated differently.
+    causal_mechanism_qualifier = "via_"+ causal_mechanism_qualifier
+    return causal_mechanism_qualifier
+
+def species_context_qualifier_semantic_adjustment(species_context_qualifier):
+    species_context_qualifier = "in_"+ species_context_qualifier
+    return species_context_qualifier
+
+def anatomical_context_qualifier_semantic_adjustment(anatomical_context_qualifier, species_context_qualifier=False):
+    if species_context_qualifier == False:
+        anatomical_context_qualifier = "in_"+ anatomical_context_qualifier
+    return anatomical_context_qualifier
+
+def generate_collapsed_qualifiers_kg(infile, edges_file_path):
+
+    with KGXFileWriter(edges_output_file_path=edges_file_path) as kgx_file_writer:
+        for edge in tqdm(quick_jsonl_file_iterator(infile)) if TQDM_AVAILABLE else quick_jsonl_file_iterator(infile):
+
+            try:
+                edge_predicate = edge['predicate']
+            except KeyError:
+                print(f"Collapsed Qualifiers Graph Failed - missing predicate on edge: {edge}")
+                break
+
+            qualifiers = {key:value for key, value in edge.items() if bmt.is_qualifier(key)}
+            # Count the number of qualifiers and print a warning if number of qualifiers we handle in the next section doesn't match number of qualifiers detected.
+            # This will help warn us if new qualifiers are added in the future while giving us the option to still run the script as is.
+            qualifier_count = len(qualifiers.keys())
+            counted_qualifiers = 0
+
+            # The following section crafts a new collapsed qualifier statement to replace the edge predicate, but needs to do some semantic adjustment.
+            # This is where to edit if the biolink model ever changes and handles qualifiers differently.
+            # Take guidance from: https://biolink.github.io/biolink-model/reading-a-qualifier-based-statement/
+            # Example jsonl edge used here: {"subject":"UNII:7PK6VC94OU","predicate":"biolink:affects","object":"NCBIGene:6531","primary_knowledge_source":"infores:ctd","description":"decreases activity of","NCBITaxon":"9606","publications":["PMID:30776375"],"knowledge_level":"knowledge_assertion","agent_type":"manual_agent","subject_direction_qualifier":"increased","subject_aspect_qualifier":"abundance","subject_form_or_variant_qualifier":"mutant_form","subject_derivative_qualifier":"transcript","subject_part_qualifier":"polyA_tail","object_aspect_qualifier":"activity","object_direction_qualifier":"upregulated","object_form_or_variant_qualifier":"wildtype_form","object_derivative_qualifier":"protein","object_part_qualifier":"catalytic_site","causal_mechanism_qualifier":"phosyphorylation","species_context_qualifier":"human","anatomical_context_qualifier":"liver","qualified_predicate":"biolink:causes"}
+
+            qualifier_statement = ""
+
+            # Add on subject direction and aspect qualifiers first. eg. "increased_abundance_of_"
+            if SUBJECT_DIRECTION_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= qualifiers[SUBJECT_DIRECTION_QUALIFIER]
+                qualifier_statement+= "_"
+            if SUBJECT_ASPECT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= aspect_qualifier_semantic_adjustment(qualifiers[SUBJECT_ASPECT_QUALIFIER])
+                qualifier_statement+= "_"
+            # Add on subject form_or_variant qualifiers. eg. "increased_abundance_of_mutant_form_of_<subject_node>"
+            if SUBJECT_FORM_OR_VARIANT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= form_or_variant_qualifier_semantic_adjustment(qualifiers[SUBJECT_FORM_OR_VARIANT_QUALIFIER])
+                qualifier_statement+= "_"
+            # Add placeholder slot for subject node. eg. "increased_abundance_of_mutant_form_of_<subject_node>"
+            qualifier_statement+= "<subject_node>_"
+            # Add on subject derivative and part qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail"
+            if SUBJECT_DERIVATIVE_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= qualifiers[SUBJECT_DERIVATIVE_QUALIFIER]
+                qualifier_statement+= "_"
+            if SUBJECT_PART_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= qualifiers[SUBJECT_PART_QUALIFIER]
+                qualifier_statement+= "_"
+
+            # Add the qualified predicate. eg. "increased_abundance_of_mutant_form_of_<subject_node>_transcript_poly_A_tail_causes"
+            if QUALIFIED_PREDICATE in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= qualifiers[QUALIFIED_PREDICATE].replace("biolink:","")
+                qualifier_statement+= "_"
+
+            # Add on object direction and aspect qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of"
+            if OBJECT_DIRECTION_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= qualifiers[OBJECT_DIRECTION_QUALIFIER]
+                qualifier_statement+= "_"
+            if OBJECT_ASPECT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= aspect_qualifier_semantic_adjustment(qualifiers[OBJECT_ASPECT_QUALIFIER])
+                qualifier_statement+= "_"
+            # Add on object form_or_variant qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of"
+            if OBJECT_FORM_OR_VARIANT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= form_or_variant_qualifier_semantic_adjustment(qualifiers[OBJECT_FORM_OR_VARIANT_QUALIFIER])
+                qualifier_statement+= "_"
+            # Add placeholder slot for object node. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>"
+            qualifier_statement+= "<object_node>"
+
+            # Add on object derivative and part qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site"
+            # Need to start putting "_" before each qualifier as any given one could be the last in the statement.
+            if OBJECT_DERIVATIVE_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= "_"
+                qualifier_statement+= qualifiers[OBJECT_DERIVATIVE_QUALIFIER]
+            if OBJECT_PART_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= "_"
+                qualifier_statement+= qualifiers[OBJECT_PART_QUALIFIER]
+
+            # Add on mechanism qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation"
+            if CAUSAL_MECHANISM_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= "_"
+                qualifier_statement+= causal_mechanism_qualifier_semantic_adjustment(qualifiers[CAUSAL_MECHANISM_QUALIFIER])
+
+            # Add on species qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation_in_human"
+            if SPECIES_CONTEXT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= "_"
+                qualifier_statement+= species_context_qualifier_semantic_adjustment(qualifiers[SPECIES_CONTEXT_QUALIFIER])
+
+            # Add on anatomical context qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation_in_human_liver"
+            if ANATOMICAL_CONTEXT_QUALIFIER in qualifiers.keys():
+                counted_qualifiers+= 1
+                qualifier_statement+= "_"
+                if SPECIES_CONTEXT_QUALIFIER in qualifiers.keys():
+                    species_qualifier = True
+                else:
+                    species_qualifier = False
+                qualifier_statement+= anatomical_context_qualifier_semantic_adjustment(qualifiers[ANATOMICAL_CONTEXT_QUALIFIER], species_qualifier)
+
+            if counted_qualifiers < qualifier_count:
+                print(f"Qualifiers on edge: {edge} are not all being handled correctly. Please revise collapse_qualifiers.py to handle all qualifiers.")
+
+            # Either rewrite the original edge if no qualifier collapsing happened, or rewrite with new predicate from qualifier_statement.
+            edges_to_write = []
+            if qualifier_statement != "":
+                edges_to_write.append(write_edge_no_q(edge, qualifier_statement, qualifiers))
+            else: 
+                edges_to_write.append(edge)
+
+            kgx_file_writer.write_normalized_edges(edges_to_write)
diff --git a/Common/data_sources.py b/Common/data_sources.py
@@ -19,6 +19,7 @@
 HMDB = 'HMDB'
 HUMAN_GOA = 'HumanGOA'
 INTACT = 'IntAct'
+LINCS = 'LINCS'
 LITCOIN = 'LitCoin'
 LITCOIN_W_BAGEL_SERVICE = 'LitCoinBagelService'
 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_W_BAGEL_SERVICE: ("parsers.LitCoin.src.loadLitCoin", "LitCoinBagelServiceLoader"),
     # LITCOIN_ENTITY_EXTRACTOR: ("parsers.LitCoin.src.loadLitCoin", "LitCoinEntityExtractorLoader"),

diff --git a/parsers/BINDING/src/loadBINDINGDB.py b/parsers/BINDING/src/loadBINDINGDB.py
@@ -11,7 +11,8 @@
 from Common.utils import GetData, GetDataPullError
 from Common.loader_interface import SourceDataLoader
 from Common.extractor import Extractor
-from Common.biolink_constants import PUBLICATIONS, AFFINITY, AFFINITY_PARAMETER, KNOWLEDGE_LEVEL, AGENT_TYPE, KNOWLEDGE_ASSERTION, MANUAL_AGENT
+from Common.biolink_constants import PUBLICATIONS, AFFINITY, AFFINITY_PARAMETER, KNOWLEDGE_LEVEL, AGENT_TYPE, \
+    KNOWLEDGE_ASSERTION, MANUAL_AGENT
 
 # Full Binding Data.
 

diff --git a/parsers/CTD/src/loadCTD.py b/parsers/CTD/src/loadCTD.py
@@ -533,7 +533,7 @@ def convert_predicates(predicate):
         :return:
         """
         # the capture regex
-        regex = '\/|\ |\^'
+        regex = r'\/|\ |\^'
 
         # clean up the predicate
         cleaned_predicate = re.sub(regex, '_', predicate)