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#!/usr/bin/python3
import sys, 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"
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 row in dbCur.execute("SELECT name from nodes"):
nodeNames.add(row[0])
# 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("Processing line {}".format(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] = [name] # Intentionally ignoring case here
elif name not in nameToVariants[subName]:
nameToVariants[subName].append(name)
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("Number of conflicts: {}".format(len(nameToVariants)))
# Try conflict resolution via category-list
# 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("Number of conflicts: {}".format(len(nameToVariants)))
# Try conflict resolution via taxon-type information
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("Processing line {}".format(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("Number of conflicts: {}".format(len(nameToVariants)))
# Try conflict resolution via picked-labels
print("Resolving conflicts using picked-labels")
with open(pickedLabelsFile) as file:
for line in file:
pickedLabel = line.rstrip()
name = pickedLabel.lower()
if name in nameToVariants:
nodeToLabel[name] = pickedLabel
del nameToVariants[name]
else:
match = nameVariantRegex.match(pickedLabel)
if match == None:
print("WARNING: Picked label {} not found (1)".format(pickedLabel), file=sys.stderr)
else:
name = match.group(1)
if name not in nameToVariants:
print("WARNING: Picked label {} not found (2)".format(pickedLabel), file=sys.stderr)
else:
nodeToLabel[name] = pickedLabel
del nameToVariants[name]
print("Number of conflicts: {}".format(len(nameToVariants)))
# Associate nodes with IRIs
print("Getting nodes 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("ERROR: Couldn't find label {}".format(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("At iteration {}".format(iterNum))
#
row = dbpCur.execute("SELECT target FROM redirects where iri = ?", (iri,)).fetchone()
if row != None:
nodeToIri[name] = row[0]
redirectingIriSet.add(iri)
# Find descriptions, and add to db
print("Adding node description data")
dbCur.execute("CREATE TABLE descs (name TEXT PRIMARY KEY, desc TEXT, redirected INT)")
iterNum = 0
for (name, iri) in nodeToIri.items():
iterNum += 1
if iterNum % 1e4 == 0:
print("At iteration {}".format(iterNum))
#
row = dbpCur.execute("SELECT abstract FROM abstracts where iri = ?", (iri,)).fetchone()
if row != None:
dbCur.execute("INSERT INTO descs VALUES (?, ?, ?)", (name, row[0], 1 if name in redirectingIriSet else 0))
# Close dbs
dbCon.commit()
dbCon.close()
dbpCon.commit()
dbpCon.close()
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