Continue renaming from Bioentities to Famplex

README.md

@@ -6,6 +6,10 @@ developed by manual curation for use by natural language processing and
 biological modeling teams in the [DARPA Big
 Mechanism](http://www.darpa.mil/program/big-mechanism) and [Communicating with
 Computers](http://www.darpa.mil/program/communicating-with-computers) programs.
+
+Note: FamPlex used to be called Bioentities, and was renamed to better reflect
+the focus of the resource.
+
 The repository contains the following files:
 
 * ```relations.csv```. Defines membership of specific genes/proteins in
@@ -49,15 +53,15 @@ relationships, including sub-families (families within families) and complexes
 consisting of families of related subunits (e.g., PI3K, NF-kB).
 
 The ```relations.csv``` file consists of five columns: (1) the namespace for
-the subject (e.g., ```HGNC``` for gene names, ```UP``` for Uniprot, or ```BE```
-for the FamPlex namespace), (2) the identifier for the subject, (3) the
-relationship (```isa``` or ```partof```), (4) the namespace for the object, and
-(5) the identifier for the object.
+the subject (e.g., ```HGNC``` for gene names, ```UP``` for Uniprot, or
+```FPLX``` for the FamPlex namespace), (2) the identifier for the subject,
+(3) the relationship (```isa``` or ```partof```), (4) the namespace for the
+object, and (5) the identifier for the object.
 
 The ```equivalences.csv``` file consists of three columns (1) the namespace of
 an outsite entity (e.g. ```BEL```, ```PFAM```),
 (2) the identifier of the outside entity in the namespace given in the
-first column, and (3) the equivalent entity in the ```BE``` namespace.
+first column, and (3) the equivalent entity in the ```FPLX``` namespace.
 
 ## Grounding Map
 

check_references.py

@@ -137,12 +137,12 @@ def pubchem_and_chebi(db_refs):
 
     print()
     print("-- Checking for undeclared FamPlex IDs in grounding map --")
-    # Look through grounding map and find all instances with an FP' db
+    # Look through grounding map and find all instances with an FPLX db key
     entities_missing_gm = []
     for text, db_refs in gm.items():
         if db_refs is not None:
             for db_key, db_id in db_refs.items():
-                if db_key == 'FP' and db_id not in entities:
+                if db_key == 'FPLX' and db_id not in entities:
                     entities_missing_gm.append(db_id)
                     print("ERROR: ID %s referenced in grounding map "
                           "is not in entities list." % db_id)
@@ -171,7 +171,7 @@ def pubchem_and_chebi(db_refs):
         for term in (subj, obj):
             term_ns = term[0]
             term_id = term[1]
-            if term_ns == 'FP' and term_id not in entities:
+            if term_ns == 'FPLX' and term_id not in entities:
                 entities_missing_rel.append(term_id)
                 print("ERROR: ID %s referenced in relations "
                       "is not in entities list." % term_id)
@@ -181,7 +181,7 @@ def pubchem_and_chebi(db_refs):
     for ix, (subj, rel, obj) in enumerate(relationships):
         for term in (subj, obj):
             term_ns = term[0]
-            if term_ns not in ('FP', 'HGNC', 'UP'):
+            if term_ns not in ('FPLX', 'HGNC', 'UP'):
                 print("ERROR: row %d: Invalid namespace in relations.csv: %s" %
                       (ix+1, term_ns))
                 signal_error = True
@@ -256,10 +256,10 @@ def pubchem_and_chebi(db_refs):
             subj_id = subj[1]
             obj_ns = obj[0]
             obj_id = obj[1]
-            if subj_ns == 'FP' and subj_id == ent:
+            if subj_ns == 'FPLX' and subj_id == ent:
                 found = True
                 break
-            if obj_ns == 'FP' and obj_id == ent:
+            if obj_ns == 'FPLX' and obj_id == ent:
                 found = True
                 break
         if not found: