1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
|
#!/usr/bin/python3
import sys, os, re
import sqlite3
usageInfo = f"usage: {sys.argv[0]}\n"
usageInfo += "Reads DBpedia data from dbpedia/*, along with tree-of-life\n"
usageInfo += "node and name data from a sqlite database, associates nodes with\n"
usageInfo += "DBpedia IRIs, and adds alt-name and description information for\n"
usageInfo += "those nodes.\n"
if len(sys.argv) > 1:
print(usageInfo, file=sys.stderr)
sys.exit(1)
dbpediaDb = "dbpedia/dbpData.db"
namesToSkipFile = "genDescNamesToSkip.txt"
pickedLabelsFile = "dbpPickedLabels.txt"
dbFile = "data.db"
# Open dbs
dbpCon = sqlite3.connect(dbpediaDb)
dbpCur = dbpCon.cursor()
dbCon = sqlite3.connect(dbFile)
dbCur = dbCon.cursor()
# Get node names
print("Reading node names")
nodeNames = set()
for (name,) in dbCur.execute("SELECT name from nodes"):
nodeNames.add(name)
# Skipping certain names
print("Checking for names to skip")
oldSz = len(nodeNames)
if os.path.exists(namesToSkipFile):
with open(namesToSkipFile) as file:
for line in file:
nodeNames.remove(line.rstrip())
print(f"Skipping {oldSz - len(nodeNames)} nodes")
# Get disambiguation page labels
print("Reading disambiguation-page labels")
disambigLabels = set()
query = "SELECT labels.iri from labels INNER JOIN disambiguations ON labels.iri = disambiguations.iri"
for (label,) in dbpCur.execute(query):
disambigLabels.add(label)
# Try associating nodes with IRIs, accounting for disambiguation labels
print("Trying to associate nodes with labels")
nodeToLabel = {}
nameVariantRegex = re.compile(r"(.*) \(([^)]+)\)")
nameToVariants = {}
iterNum = 0
for (label,) in dbpCur.execute("SELECT label from labels"):
iterNum += 1
if iterNum % 1e5 == 0:
print(f"Processing line {iterNum}")
#
if label in disambigLabels:
continue
name = label.lower()
if name in nodeNames:
if name not in nameToVariants:
nameToVariants[name] = [label]
elif label not in nameToVariants[name]:
nameToVariants[name].append(label)
else:
match = nameVariantRegex.fullmatch(name)
if match != None:
subName = match.group(1)
if subName in nodeNames and match.group(2) != "disambiguation":
if subName not in nameToVariants:
nameToVariants[subName] = [label]
elif name not in nameToVariants[subName]:
nameToVariants[subName].append(label)
for (name, variants) in nameToVariants.items():
if len(variants) == 1:
nodeToLabel[name] = variants[0]
for name in nodeToLabel:
del nameToVariants[name]
nodeToLabel["cellular organisms"] = "organism" # Special case for root node
print(f"Number of conflicts: {len(nameToVariants)}")
# Try resolving conflicts
def resolveWithPickedLabels():
# Attempts conflict resolution using a file with lines of the form 'name1|label1',
# where label1 may be absent, indicating that no label should be associated with the name
print("Resolving conflicts using picked-labels")
with open(pickedLabelsFile) as file:
for line in file:
(name, _, label) = line.rstrip().partition("|")
if name not in nameToVariants:
print(f"WARNING: No conflict found for name \"{name}\"", file=sys.stderr)
continue
if label == "":
del nameToVariants[name]
else:
if label not in nameToVariants[name]:
print(f"INFO: Picked label \"{label}\" for name \"{name}\" outside choice set", file=sys.stderr)
nodeToLabel[name] = label
del nameToVariants[name]
print(f"Remaining number of conflicts: {len(nameToVariants)}")
def resolveWithCategoryList():
# Attempts conflict resolution using category-text in labels of the form 'name1 (category1)'
# Does a generic-category pass first (avoid stuff like Pan being classified as a horse instead of an ape)
print("Resolving conflicts using category-list")
generalCategories = {
"species", "genus",
"plant", "fungus", "animal",
"annelid", "mollusc", "arthropod", "crustacean", "insect", "bug",
"fish", "amphibian", "reptile", "bird", "mammal",
}
specificCategories = {
"protist", "alveolate", "dinoflagellates",
"orchid", "Poaceae", "fern", "moss", "alga",
"bryozoan", "hydrozoan",
"sponge", "cnidarian", "coral", "polychaete", "echinoderm",
"bivalve", "gastropod", "chiton",
"shrimp", "decapod", "crab", "barnacle", "copepod",
"arachnid", "spider", "harvestman", "mite",
"dragonfly", "mantis", "cicada", "grasshopper", "planthopper",
"beetle", "fly", "butterfly", "moth", "wasp",
"catfish",
"frog",
"lizard",
"horse", "sheep", "cattle", "mouse",
}
namesToRemove = set()
for (name, variants) in nameToVariants.items():
found = False
for label in variants:
match = nameVariantRegex.match(label)
if match != None and match.group(2) in generalCategories:
nodeToLabel[name] = label
namesToRemove.add(name)
found = True
break
if not found:
for label in variants:
match = nameVariantRegex.match(label)
if match != None and match.group(2) in specificCategories:
nodeToLabel[name] = label
namesToRemove.add(name)
break
for name in namesToRemove:
del nameToVariants[name]
print(f"Remaining number of conflicts: {len(nameToVariants)}")
def resolveWithTypeData():
# Attempts conflict-resolution using dbpedia's instance-type data
print("Resolving conflicts using instance-type data")
taxonTypes = { # Obtained from the DBpedia ontology
"http://dbpedia.org/ontology/Species",
"http://dbpedia.org/ontology/Archaea",
"http://dbpedia.org/ontology/Bacteria",
"http://dbpedia.org/ontology/Eukaryote",
"http://dbpedia.org/ontology/Plant",
"http://dbpedia.org/ontology/ClubMoss",
"http://dbpedia.org/ontology/Conifer",
"http://dbpedia.org/ontology/CultivatedVariety",
"http://dbpedia.org/ontology/Cycad",
"http://dbpedia.org/ontology/Fern",
"http://dbpedia.org/ontology/FloweringPlant",
"http://dbpedia.org/ontology/Grape",
"http://dbpedia.org/ontology/Ginkgo",
"http://dbpedia.org/ontology/Gnetophytes",
"http://dbpedia.org/ontology/GreenAlga",
"http://dbpedia.org/ontology/Moss",
"http://dbpedia.org/ontology/Fungus",
"http://dbpedia.org/ontology/Animal",
"http://dbpedia.org/ontology/Fish",
"http://dbpedia.org/ontology/Crustacean",
"http://dbpedia.org/ontology/Mollusca",
"http://dbpedia.org/ontology/Insect",
"http://dbpedia.org/ontology/Arachnid",
"http://dbpedia.org/ontology/Amphibian",
"http://dbpedia.org/ontology/Reptile",
"http://dbpedia.org/ontology/Bird",
"http://dbpedia.org/ontology/Mammal",
"http://dbpedia.org/ontology/Cat",
"http://dbpedia.org/ontology/Dog",
"http://dbpedia.org/ontology/Horse",
}
iterNum = 0
for (label, type) in dbpCur.execute("SELECT label, type from labels INNER JOIN types on labels.iri = types.iri"):
iterNum += 1
if iterNum % 1e5 == 0:
print(f"Processing line {iterNum}")
#
if type in taxonTypes:
name = label.lower()
if name in nameToVariants:
nodeToLabel[name] = label
del nameToVariants[name]
else:
match = nameVariantRegex.fullmatch(name)
if match != None:
name = match.group(1)
if name in nameToVariants:
nodeToLabel[name] = label
del nameToVariants[name]
print(f"Remaining number of conflicts: {len(nameToVariants)}")
resolveWithPickedLabels()
# Associate nodes with IRIs
print("Getting node IRIs")
nodeToIri = {}
iterNum = 0
for (name, label) in nodeToLabel.items():
row = dbpCur.execute("SELECT iri FROM labels where label = ? COLLATE NOCASE", (label,)).fetchone()
if row == None:
print(f"ERROR: Couldn't find label {label}", file=sys.stderr)
sys.exit(1)
else:
nodeToIri[name] = row[0]
# Resolve redirects
print("Resolving redirects")
redirectingIriSet = set()
iterNum = 0
for (name, iri) in nodeToIri.items():
iterNum += 1
if iterNum % 1e4 == 0:
print(f"At iteration {iterNum}")
#
row = dbpCur.execute("SELECT target FROM redirects where iri = ?", (iri,)).fetchone()
if row != None:
nodeToIri[name] = row[0]
redirectingIriSet.add(name)
# Find descriptions, and add to db
print("Adding node description data")
dbCur.execute("CREATE TABLE descs (name TEXT PRIMARY KEY, desc TEXT, redirected INT, wiki_id INT, from_dbp INT)")
dbCur.execute("CREATE INDEX descs_id_idx ON descs(wiki_id)") # wiki_id intentionally left non-unique
iterNum = 0
for (name, iri) in nodeToIri.items():
iterNum += 1
if iterNum % 1e4 == 0:
print(f"At iteration {iterNum}")
#
query = "SELECT abstract, id FROM abstracts INNER JOIN ids ON abstracts.iri = ids.iri WHERE ids.iri = ?"
row = dbpCur.execute(query, (iri,)).fetchone()
if row != None:
dbCur.execute("INSERT INTO descs VALUES (?, ?, ?, ?, ?)",
(name, row[0], 1 if name in redirectingIriSet else 0, row[1], 1))
# Close dbs
dbCon.commit()
dbCon.close()
dbpCon.commit()
dbpCon.close()
|
