a010260c82d5dc73f51bf6e97fe81a24bccd53e2
hiram
  Sat Jul 19 15:59:50 2025 -0700
do not need to prefix bacteria with the word "bacteria"

diff --git src/hg/makeDb/doc/asmHubs/commonNames.py src/hg/makeDb/doc/asmHubs/commonNames.py
index 4e4e4b0fa79..4780209b998 100755
--- src/hg/makeDb/doc/asmHubs/commonNames.py
+++ src/hg/makeDb/doc/asmHubs/commonNames.py
@@ -53,31 +53,31 @@
             pat = re.compile(r'\?')
             orgName = pat.sub('', orgName)
             pat = re.compile(r'.*ism name:\s+')
             orgName = pat.sub('', orgName)
            
 
             pat = re.compile(r'.*ganism name:\s+', re.IGNORECASE)
             sciName = pat.sub('', line)
             pat = re.compile(r'\s+\(.*\)$')
             sciName = pat.sub('', sciName)
             pat = re.compile(r'[()\[\]+*]')
             sciName = pat.sub('', sciName)
             pat = re.compile(r'\?')
             sciName = pat.sub(' ', sciName)
 
-            pat = r'kinetoplastids|firmicutes|proteobacteria|high G|enterobacteria|agent of'
+            pat = r'bacteria|kinetoplastids|firmicutes|proteobacteria|high G|enterobacteria|agent of'
             if re.search(pat, orgName):
               orgName = sciName
             else:
               pat = r'apicomplexans|ants|bacteria|bryozoans|bugs|ciliates|crustaceans|diatoms|hydrozoans|dinoflagellates|gastropods|hemichordates|nematodes|flatworm|pelagophytes|scorpions|ascomycete|basidiomycete|budding|microsporidian|smut|fungi|eukaryotes|flies|beetles|mosquitos|bees|moths|sponges|^mites|ticks|^comb|jellies|jellyfishes|chitons|bivalves|bony fishes|birds|eudicots|snakes|bats|tunicates|tsetse fly|cellular slime molds|stony corals'
               if re.search(pat, orgName):
                 order = orgName.split()[0]
                 if re.search('budding', order):
                   order = "budding yeast"
                 elif re.search('smut', order):
                   order = "smut fungi"
                 elif re.search('bony', order):
                   order = "bony fish"
                 elif re.search('ascomycete', order):
                   order = "ascomycetes"
                 elif re.search('eudicots', order):
@@ -114,31 +114,31 @@
                   order = "flatworm"
                 elif re.search('nematodes', order):
                   order = "nematode"
                 elif re.search('basidiomycete', order):
                   order = "basidiomycetes"
                 words = sciName.split()
                 restWords = " ".join(words[1:])
                 if re.search("eukaryotes", orgName):
                   orgName = words[0][0].upper() + "." + restWords
                 elif re.search("apicomplexans", orgName):
                   orgName = "apicomplexans " + words[0][0].upper() + "." + restWords
                 elif re.search("ants", orgName):
                   orgName = "ant " + words[0][0].upper() + "." + restWords
                 elif re.search("dinoflagellates", orgName):
                   orgName = "dinoflagellates " + words[0][0].upper() + "." + restWords
-                elif re.search("bacteria", orgName):
+                elif re.search("\bbacteria\b", orgName):
                   orgName = "bacteria " + words[0][0].upper() + "." + restWords
                 elif re.search("hemichordates", orgName):
                   orgName = "hemichordates " + words[0][0].upper() + "." + restWords
                 elif re.search("bryozoans", orgName):
                   orgName = "bryozoans " + words[0][0].upper() + "." + restWords
                 elif re.search("ciliates", orgName):
                   orgName = "ciliates " + words[0][0].upper() + "." + restWords
                 elif re.search("diatoms", orgName):
                   orgName = "diatoms " + words[0][0].upper() + "." + restWords
                 elif re.search("hydrozoans", orgName):
                   orgName = "hydrozoans " + words[0][0].upper() + "." + restWords
                 elif re.search("gastropods", orgName):
                   orgName = "gastropods " + words[0][0].upper() + "." + restWords
                 elif re.search("pelagophytes", orgName):
                   orgName = "pelagophytes " + words[0][0].upper() + "." + restWords