add support for PCL (#174)

Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>
hubmapconsortium · Aug 19, 2022 · 340d2b8 · 340d2b8
1 parent 389a5f4
commit 340d2b8
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Showing 6 changed files with 38 additions and 18 deletions.
diff --git a/graphs/ccf_Brain_graph.pdf b/graphs/ccf_Brain_graph.pdf
diff --git a/graphs/ccf_Brain_graph.png b/graphs/ccf_Brain_graph.png
diff --git a/src/ccf_tools.py b/src/ccf_tools.py
@@ -34,13 +34,13 @@ def parse_asctb(path):
     where each pair of adjacent columns => a subject-object pair for testing"""
 
     def is_valid_id(content):
-        if re.match("(CL|UBERON)\:[0-9]+", content['id']):
+        if re.match("(CL|UBERON|PCL)\:[0-9]+", content['id']):
             return content
         else:
             logger.warning(f"No valid ID provided for '{content['id']}', label: {content['name']}, user_label: {content['rdfs_label']}")
             return False
     def check_id(id):
-      return re.match("(CL|UBERON)\:[0-9]+", id)
+      return re.match("(CL|UBERON|PCL)\:[0-9]+", id)
 
     asct_b_tab = json.load(open(path))
     as_invalid_terms = set()

diff --git a/src/template_generation_tools.py b/src/template_generation_tools.py
@@ -94,7 +94,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
   del_index = []
   for t in no_valid_class:
-    logger.warning(f"Unrecognised UBERON/CL entity '{t}'")
+    logger.warning(f"Unrecognised UBERON/CL/PCL entity '{t}'")
     del_index.extend(ccf_tools_df[(ccf_tools_df['s'] == t) | (ccf_tools_df['o'] == t)].index)
 
   # Drop rows with unrecognized UBERON/CL terms 
@@ -116,7 +116,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
     if 'CL' in r['o']:
       records_cl_sub.append({'ID': r['o'], 'present_in_taxon': 'NCBITaxon:9606', 'in_subset': 'human_reference_atlas'})
 
-    if 'CL' in r['s'] and 'UBERON' in r['o']:
+    if ('CL' in r['s'] or 'PCL' in r['s']) and 'UBERON' in r['o']:
       terms_ct_as.add(f"({r['s']} {r['o']})")
       all_ct.add(r['s'])
       all_as.add(r['o'])
@@ -125,7 +125,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
       terms_pairs.add(f"({r['s']} {r['o']})")
       all_as.add(r['s'])
       all_as.add(r['o'])
-    elif 'CL' in r['s'] and 'CL' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and ('CL' in r['o'] or 'PCL' in r['o']):
       relation_ct.add(f"({r['s']} {r['o']})")
       terms_pairs.add(f"({r['s']} {r['o']})")
       all_ct.add(r['s'])
@@ -192,7 +192,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
 
@@ -210,7 +210,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
   for _, r in rows_nvso.iterrows():
     if 'UBERON' in r['s'] and 'UBERON' in r['o']:
       indirect_as.add((r['s'], r['o']))
-    elif 'CL' in r['s'] and 'CL' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and ('CL' in r['o'] or 'PCL' in r['o']):
       indirect_ct.add((r['s'], r['o']))
 
   terms_pairs = terms_pairs - terms_valid_subclass
@@ -241,7 +241,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
   # INDIRECT PART OF CHECK
@@ -263,7 +263,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
   for _, r in rows_nvponr.iterrows():
     if 'UBERON' in r['s'] and 'UBERON' in r['o']:
       indirect_as.add((r['s'], r['o']))
-    elif 'CL' in r['s'] and 'CL' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and ('CL' in r['o'] or 'PCL' in r['o']):
       indirect_ct.add((r['s'], r['o']))
 
   terms_pairs = terms_pairs - terms_valid_po
@@ -296,7 +296,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
   # INDIRECT OVERLAPS CHECK
@@ -313,7 +313,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
   for _, r in rows_nvonr.iterrows():
     if 'UBERON' in r['s'] and 'UBERON' in r['o']:
       indirect_as.add((r['s'], r['o']))
-    elif 'CL' in r['s'] and 'CL' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and ('CL' in r['o'] or 'PCL' in r['o']):
       indirect_ct.add((r['s'], r['o']))
 
   terms_pairs = terms_pairs - transform_to_str(valid_overlaps)
@@ -338,7 +338,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
   terms_ct_as = terms_ct_as - transform_to_str(valid_ct_as_locatedin)
@@ -368,7 +368,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
   terms_pairs = terms_pairs - transform_to_str(valid_conn_to)
@@ -399,7 +399,7 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
 
     if 'UBERON' in s and 'UBERON' in o:
       valid_as.add((s,o))
-    elif 'CL' in s and 'CL' in o:
+    elif ('CL' in s or 'PCL' in s) and ('CL' in o or 'PCL' in o):
       valid_ct.add((s,o))
 
   # AS-CT HAS PART
@@ -508,13 +508,13 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame):
       no_v_rec['ID'] = r['s']
       no_v_rec['ccf_part_of'] = r['o']
       no_valid_records.append(no_v_rec)
-    elif 'CL' in r['s'] and 'CL' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and ('CL' in r['o'] or 'PCL' in r['o']):
       invalid_ct.add((r['s'], r['o']))
       no_v_rec = dict()
       no_v_rec['ID'] = r['s']
       no_v_rec['ccf_part_of'] = r['o']
       no_valid_records.append(no_v_rec)
-    elif 'CL' in r['s'] and 'UBERON' in r['o']:
+    elif ('CL' in r['s'] or 'PCL' in r['s']) and 'UBERON' in r['o']:
       invalid_ct_as.add((r['s'], r['o']))
       no_v_rec = dict()
       no_v_rec['ID'] = r['s']

diff --git a/src/uberongraph_tools.py b/src/uberongraph_tools.py
@@ -8,6 +8,7 @@ def __init__(self):
           PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
           FROM <http://reasoner.renci.org/redundant>
@@ -23,6 +24,7 @@ def __init__(self):
           PREFIX overlaps: <http://purl.obolibrary.org/obo/RO_0002131> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
           FROM <http://reasoner.renci.org/redundant>
@@ -37,6 +39,7 @@ def __init__(self):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology/closure>
           { 
@@ -51,6 +54,7 @@ def __init__(self):
           PREFIX owl: <http://www.w3.org/2002/07/owl#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject
           FROM <http://reasoner.renci.org/ontology>
           { 
@@ -64,6 +68,7 @@ def __init__(self):
           PREFIX connected_to: <http://purl.obolibrary.org/obo/RO_0002170> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
           FROM <http://reasoner.renci.org/redundant> 
@@ -79,6 +84,7 @@ def __init__(self):
           PREFIX owl: <http://www.w3.org/2002/07/owl#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object 
           {
             VALUES ?subject {
@@ -93,6 +99,7 @@ def __init__(self):
           PREFIX owl: <http://www.w3.org/2002/07/owl#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object 
           FROM <http://reasoner.renci.org/redundant> 
           {
@@ -107,6 +114,7 @@ def __init__(self):
           PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/nonredundant>
           { 
@@ -121,6 +129,7 @@ def __init__(self):
           PREFIX overlaps: <http://purl.obolibrary.org/obo/RO_0002131> 
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/nonredundant>
           { 
@@ -135,6 +144,7 @@ def __init__(self):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
           { 
@@ -150,6 +160,7 @@ def __init__(self):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
@@ -167,6 +178,7 @@ def __init__(self):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           PREFIX has_part: <http://purl.obolibrary.org/obo/BFO_0000051>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
@@ -183,6 +195,7 @@ def __init__(self):
           PREFIX foaf: <http://xmlns.com/foaf/0.1/>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           { 
             VALUES ?subject {
@@ -196,6 +209,7 @@ def __init__(self):
           PREFIX owl: <http://www.w3.org/2002/07/owl#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/uberon/uberon-base.owl>
           PREFIX CL: <http://purl.obolibrary.org/obo/cl/cl-base.owl>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           SELECT ?subject ?object
           WHERE {
             VALUES ?subject { UBERON: CL: }
@@ -207,6 +221,7 @@ def __init__(self):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           PREFIX located_in: <http://purl.obolibrary.org/obo/RO_0001025>
           SELECT ?subject ?object
           FROM <http://reasoner.renci.org/ontology>
@@ -262,6 +277,7 @@ def construct_relation(self, subject, objects, property):
           PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
           PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
           PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+          PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
           PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> 
           PREFIX connected_to: <http://purl.obolibrary.org/obo/RO_0002170>
           PREFIX develops_from: <http://purl.obolibrary.org/obo/RO_0002202>
@@ -297,6 +313,7 @@ def construct_annotation(self, terms):
               PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
               PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
               PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+              PREFIX PCL: <http://purl.obolibrary.org/obo/PCL_>
               CONSTRUCT 
               {{
                 ?term rdf:type owl:Class; ?APT ?APVT .
@@ -335,12 +352,12 @@ def extract_results(self, list):
       return results
 
     def add_prefix(self, term):
-      return term.replace("http://purl.obolibrary.org/obo/UBERON_", "UBERON:").replace("http://purl.obolibrary.org/obo/CL_", "CL:")
+      return term.replace("http://purl.obolibrary.org/obo/UBERON_", "UBERON:").replace("http://purl.obolibrary.org/obo/CL_", "CL:").replace("http://purl.obolibrary.org/obo/PCL_", "PCL:")
 
     def add_prefix_ont(self, list_ontology):
       results = []
       for ont, version in list_ontology:
-        ont = ont.replace("http://purl.obolibrary.org/obo/uberon/uberon-base.owl", "UBERON").replace("http://purl.obolibrary.org/obo/cl/cl-base.owl", "CL")
+        ont = ont.replace("http://purl.obolibrary.org/obo/uberon/uberon-base.owl", "UBERON").replace("http://purl.obolibrary.org/obo/cl/cl-base.owl", "CL").replace("http://purl.obolibrary.org/obo/PCL_", "PCL:")
         results.extend([ont, version])
       return results
 

diff --git a/style/ubergraph-style.json b/style/ubergraph-style.json
@@ -36,6 +36,9 @@
         "http://purl.obolibrary.org/obo/CL_": {
           "fillcolor": "cyan"
         },
+        "http://purl.obolibrary.org/obo/PCL_": {
+          "fillcolor": "cyan"
+        },
         "http://purl.obolibrary.org/obo/NCBITaxon_9606": {
           "fillcolor": "white"
         }