Knowledge Extraction
Knowledge Extraction
Knowledge extraction is the creation of knowledge from structured (relational databases, XML) and unstructured (text, documents, images) sources. The
resulting knowledge needs to be in a machine-readable and machine-interpretable format and must represent knowledge in a manner that facilitates inferencing.
Although it is methodically similar to information extraction (NLP) and ETL (data warehouse), the main criterion is that the extraction result goes beyond the
creation of structured information or the transformation into a relational schema. It requires either the reuse of existing formal knowledge (reusing identifiers or
ontologies) or the generation of a schema based on the source data.
The RDB2RDF W3C group [1] is currently standardizing a language for extraction of resource description frameworks (RDF) from relational databases. Another
popular example for knowledge extraction is the transformation of Wikipedia into structured data and also the mapping to existing knowledge (see DBpedia and
Freebase).
Overview
After the standardization of knowledge representation languages such as RDF and OWL, much research has been conducted in the area, especially regarding
transforming relational databases into RDF, identity resolution, knowledge discovery and ontology learning. The general process uses traditional methods from
information extraction and extract, transform, and load (ETL), which transform the data from the sources into structured formats.
The following criteria can be used to categorize approaches in this topic (some of them only account for extraction from relational databases):[2]
Source Which data sources are covered: Text, Relational Databases, XML, CSV
Exposition How is the extracted knowledge made explicit (ontology file, semantic database)? How can you query it?
Is the knowledge extraction process executed once to produce a dump or is the result synchronized with the source? Static or dynamic. Are
Synchronization
changes to the result written back (bi-directional)
The tool is able to reuse existing vocabularies in the extraction. For example, the table column 'firstName' can be mapped to foaf:firstName.
Reuse of vocabularies
Some automatic approaches are not capable of mapping vocab.
Automatization The degree to which the extraction is assisted/automated. Manual, GUI, semi-automatic, automatic.
Requires a domain
A pre-existing ontology is needed to map to it. So either a mapping is created or a schema is learned from the source (ontology learning).
ontology
Examples
Entity linking
1. DBpedia Spotlight, OpenCalais, Dandelion dataTXT (http://dandelion.eu/datatxt/), the Zemanta API, Extractiv (http://www.extractiv.com/demo.
html) and PoolParty Extractor (http://poolparty.biz/products/poolparty-extractor/) analyze free text via named-entity recognition and then
disambiguates candidates via name resolution and links the found entities to the DBpedia knowledge repository[3] (Dandelion dataTXT demo
(https://dandelion.eu/products/datatxt/nex/demo/?exec=true#results) or DBpedia Spotlight web demo (http://spotlight.dbpedia.org/rest/annotat
e?text=President%20Obama%20called%20Wednesday%20on%20Congress%20to%20extend%20a%20tax%20break%20for%20students%
20included%20in%20last%20year%27s%20economic%20stimulus%20package,%20arguing%20that%20the%20policy%20provides%20mor
e%20generous%20assistance.&confidence=0.2&support=20) or PoolParty Extractor Demo (http://poolparty.biz/demozone/?url=http%3A%2
F%2Fen.wikipedia.org%2Fw%2Findex.php%3Ftitle%3DKnowledge_extraction%26printable%3Dyes&domain=ssw)).
As President Obama is linked to a DBpedia LinkedData resource, further information can be retrieved automatically and a Semantic
Reasoner can for example infer that the mentioned entity is of the type Person (http://xmlns.com/foaf/0.1/Person) (using FOAF (software))
and of type Presidents of the United States (http://dbpedia.org/class/yago/PresidentsOfTheUnitedStates) (using YAGO). Counter examples:
Methods that only recognize entities or link to Wikipedia articles and other targets that do not provide further retrieval of structured data and
formal knowledge.
When building a RDB representation of a problem domain, the starting point is frequently an entity-relationship diagram (ERD). Typically, each entity is
represented as a database table, each attribute of the entity becomes a column in that table, and relationships between entities are indicated by foreign keys. Each
table typically defines a particular class of entity, each column one of its attributes. Each row in the table describes an entity instance, uniquely identified by a
primary key. The table rows collectively describe an entity set. In an equivalent RDF representation of the same entity set:
So, to render an equivalent view based on RDF semantics, the basic mapping algorithm would be as follows:
Early mentioning of this basic or direct mapping can be found in Tim Berners-Lee's comparison of the ER model to the RDF model.[4]
The 1:1 mapping mentioned above exposes the legacy data as RDF in a straightforward way, additional refinements can be employed to improve the usefulness of
RDF output respective the given Use Cases. Normally, information is lost during the transformation of an entity-relationship diagram (ERD) to relational tables
(Details can be found in object-relational impedance mismatch) and has to be reverse engineered. From a conceptual view, approaches for extraction can come
from two directions. The first direction tries to extract or learn an OWL schema from the given database schema. Early approaches used a fixed amount of
manually created mapping rules to refine the 1:1 mapping.[5][6][7] More elaborate methods are employing heuristics or learning algorithms to induce schematic
information (methods overlap with ontology learning). While some approaches try to extract the information from the structure inherent in the SQL schema[8]
(analysing e.g. foreign keys), others analyse the content and the values in the tables to create conceptual hierarchies[9] (e.g. a columns with few values are
candidates for becoming categories). The second direction tries to map the schema and its contents to a pre-existing domain ontology (see also: ontology
alignment). Often, however, a suitable domain ontology does not exist and has to be created first.
XML
As XML is structured as a tree, any data can be easily represented in RDF, which is structured as a graph. XML2RDF (http://rhizomik.net/html/redefer/xml2rdf/) is
one example of an approach that uses RDF blank nodes and transforms XML elements and attributes to RDF properties. The topic however is more complex as in
the case of relational databases. In a relational table the primary key is an ideal candidate for becoming the subject of the extracted triples. An XML element,
however, can be transformed - depending on the context- as a subject, a predicate or object of a triple. XSLT can be used a standard transformation language to
manually convert XML to RDF.
Req.
Data Data Mapping Vocabulary Mapping Uses
Name Data Source Domain
Exposition Synchronisation Language Reuse Automat. GUI
Ontology
CSV2RDF4LOD (http://logd.tw.
CSV ETL static RDF true manual false false
rpi.edu/technology/csv2rdf4lod)
automatic (domain-
specific, for use
CoNLL-RDF (https://github.co SPARQL/ cases in language
TSV, CoNLL static none true false false
m/acoli-repo/conll-rdf) RDF stream technology,
preserves relations
between rows)
Convert2RDF (http://www.mind
swap.org/~mhgrove/ConvertTo Delimited text file ETL static RDF/DAML true manual false true
RDF/)
DataMaster (http://protegewiki.
RDB ETL static proprietary true manual true true
stanford.edu/wiki/DataMaster)
MAPONTO (http://www.cs.toro
nto.edu/semanticweb/mapont RDB ETL static proprietary true manual true false
o/)
proprietary xml
METAmorphoses (https://meta
RDB ETL static based mapping true manual false true
morphoses.sourceforge.net/)
language
MappingMaster (https://web.ar
chive.org/web/2011072304215
CSV ETL static MappingMaster true GUI false true
5/http://protege.cim3.net/cgi-bi
n/wiki.pl?MappingMaster)
ODEMapster (https://web.archi
ve.org/web/20160304121216/ht
RDB ETL static proprietary true manual true true
tp://neon-toolkit.org/wiki/ODEM
apster)
OntoWiki CSV Importer Plug-in
- DataCube & Tabular (https://
The RDF Data
web.archive.org/web/20110724 CSV ETL static true semi-automatic false true
Cube Vocaublary
231333/http://aksw.org/Project
s/Stats2RDF)
RDBToOnto (https://web.archiv
automatic, the user
e.org/web/20160816225339/htt
furthermore has the
p://tao-project.eu/researchandd RDB ETL static none false false true
chance to fine-tune
evelopment/demosanddownloa
results
ds/RDBToOnto.html)
RDF 123 (http://ebiquity.umbc.
CSV ETL static false false manual false true
edu/project/html/id/82/RDF123)
RDOTE (https://sourceforge.ne
RDB ETL static SQL true manual true true
t/projects/rdote/)
Relational.OWL (https://source
forge.net/projects/relational-ow RDB ETL static none false automatic false false
l/)
T2LD (http://ebiquity.umbc.ed
u/paper/html/id/480/T2LD-An-a
utomatic-framework-for-extracti CSV ETL static false false automatic false false
ng-interpreting-and-representin
g-tables-as-Linked-Data)
The RDF Data Cube
Vocabulary (https://web.archiv
Multidimensional
e.org/web/20110630083409/htt Data Cube
statistical data in true manual false
p://publishing-statistical-data.g Vocabulary
spreadsheets
ooglecode.com/svn/trunk/spec
s/src/main/html/cube.html)
TopBraid Composer (https://we
b.archive.org/web/2011071707
4012/http://www.topquadrant.c CSV ETL static SKOS false semi-automatic false true
om/products/TB_Composer.ht
ml)
Triplify (http://triplify.org) RDB LinkedData dynamic SQL true manual false false
Ultrawrap (https://capsenta.co
RDB SPARQL/ETL dynamic R2RML true semi-automatic false true
m/#section-ultrawrap)
Virtuoso RDF Views (http://virt Meta Schema
RDB SPARQL dynamic true semi-automatic false true
uoso.openlinksw.com) Language
structured and
Virtuoso Sponger (http://virtuos Virtuoso PL &
semi-structured SPARQL dynamic true semi-automatic false false
o.openlinksw.com) XSLT
data sources
VisAVis (https://web.archive.or
g/web/20130514044520/http://
RDB RDQL dynamic SQL true manual true true
www.cn.ntua.gr/~nkons/essays
_en.html#t)
XLWrap: Spreadsheet to RDF
(https://xlwrap.sourceforge.ne CSV ETL static TriG Syntax true manual false false
t/)
As a preprocessing step to knowledge extraction, it can be necessary to perform linguistic annotation by one or multiple NLP tools. Individual modules in an NLP
workflow normally build on tool-specific formats for input and output, but in the context of knowledge extraction, structured formats for representing linguistic
annotations have been applied.
In NLP, such data is typically represented in TSV formats (CSV formats with TAB as separators), often referred to as CoNLL formats. For knowledge extraction
workflows, RDF views on such data have been created in accordance with the following community standards:
Traditional information extraction[20] is a technology of natural language processing, which extracts information from typically natural language texts and
structures these in a suitable manner. The kinds of information to be identified must be specified in a model before beginning the process, which is why the whole
process of traditional Information Extraction is domain dependent. The IE is split in the following five subtasks.
Named entity recognition (NER)
Coreference resolution (CO)
Template element construction (TE)
Template relation construction (TR)
Template scenario production (ST)
The task of named entity recognition is to recognize and to categorize all named entities contained in a text (assignment of a named entity to a predefined
category). This works by application of grammar based methods or statistical models.
Coreference resolution identifies equivalent entities, which were recognized by NER, within a text. There are two relevant kinds of equivalence relationship. The
first one relates to the relationship between two different represented entities (e.g. IBM Europe and IBM) and the second one to the relationship between an entity
and their anaphoric references (e.g. it and IBM). Both kinds can be recognized by coreference resolution.
During template element construction the IE system identifies descriptive properties of entities, recognized by NER and CO. These properties correspond to
ordinary qualities like red or big.
Template relation construction identifies relations, which exist between the template elements. These relations can be of several kinds, such as works-for or
located-in, with the restriction, that both domain and range correspond to entities.
In the template scenario production events, which are described in the text, will be identified and structured with respect to the entities, recognized by NER and
CO and relations, identified by TR.
Ontology-based information extraction [10] is a subfield of information extraction, with which at least one ontology is used to guide the process of information
extraction from natural language text. The OBIE system uses methods of traditional information extraction to identify concepts, instances and relations of the used
ontologies in the text, which will be structured to an ontology after the process. Thus, the input ontologies constitute the model of information to be extracted.[21]
Ontology learning is the automatic or semi-automatic creation of ontologies, including extracting the corresponding domain's terms from natural language text. As
building ontologies manually is extremely labor-intensive and time consuming, there is great motivation to automate the process.
During semantic annotation,[22] natural language text is augmented with metadata (often represented in RDFa), which should make the semantics of contained
terms machine-understandable. At this process, which is generally semi-automatic, knowledge is extracted in the sense, that a link between lexical terms and for
example concepts from ontologies is established. Thus, knowledge is gained, which meaning of a term in the processed context was intended and therefore the
meaning of the text is grounded in machine-readable data with the ability to draw inferences. Semantic annotation is typically split into the following two subtasks.
1. Terminology extraction
2. Entity linking
At the terminology extraction level, lexical terms from the text are extracted. For this purpose a tokenizer determines at first the word boundaries and solves
abbreviations. Afterwards terms from the text, which correspond to a concept, are extracted with the help of a domain-specific lexicon to link these at entity
linking.
In entity linking [23] a link between the extracted lexical terms from the source text and the concepts from an ontology or knowledge base such as DBpedia is
established. For this, candidate-concepts are detected appropriately to the several meanings of a term with the help of a lexicon. Finally, the context of the terms is
analyzed to determine the most appropriate disambiguation and to assign the term to the correct concept.
Note that "semantic annotation" in the context of knowledge extraction is not to be confused with semantic parsing as understood in natural language processing
(also referred to as "semantic annotation"): Semantic parsing aims a complete, machine-readable representation of natural language, whereas semantic annotation
in the sense of knowledge extraction tackles only a very elementary aspect of that.
Tools
The following criteria can be used to categorize tools, which extract knowledge from natural language text.
Source Which input formats can be processed by the tool (e.g. plain text, HTML or PDF)?
Access Paradigm Can the tool query the data source or requires a whole dump for the extraction process?
Data Synchronization Is the result of the extraction process synchronized with the source?
Uses Output Ontology Does the tool link the result with an ontology?
Mapping Automation How automated is the extraction process (manual, semi-automatic or automatic)?
Requires Ontology Does the tool need an ontology for the extraction?
Uses GUI Does the tool offer a graphical user interface?
Extracted Entities Which types of entities (e.g. named entities, concepts or relationships) can be extracted by the tool?
Applied Techniques Which techniques are applied (e.g. NLP, statistical methods, clustering or machine learning)?
Output Model Which model is used to represent the result of the tool (e. g. RDF or OWL)?
Supported Domains Which domains are supported (e.g. economy or biology)?
Supported Languages Which languages can be processed (e.g. English or German)?
The following table characterizes some tools for Knowledge Extraction from natural language sources.
Uses
Access Data Mapping Requires Uses Extracted Applied Output S
Name Source Output Approach
Paradigm Synchronization Automation Ontology GUI Entities Techniques Model
Ontology
AlchemyAPI (http
s://web.archive.or
g/web/201605131 plain text,
automatic yes SA
14853/http://www. HTML
alchemyapi.com/
api) [25]
ANNIE (http://gat
e.ac.uk/sale/tao/s finite state
plain text dump yes yes IE
plitch6.html#cha algorithms
p:annie) [26]
ASIUM (http://ww
w-ai.ijs.si/~ilpnet concepts,
semi- NLP,
2/systems/asium. plain text dump yes OL concept
automatic clustering
hierarchy
html) [27]
Attensity
Exhaustive
Extraction (http
s://web.archive.or
g/web/201207112 named
32021/http://www. entities,
automatic IE NLP
attensity.com/pro relationships,
ducts/technology/ events
semantic-server/e
xhaustive-extracti
on/) [28]
DBpedia Spotlight
annotation to NLP,
(https://web.archi
each word, statistical
ve.org/web/20120 plain text, dump, d
yes yes automatic no yes SA annotation to methods, RDFa
712015122/http:// HTML SPARQL in
non- machine
dbpedia.org/spotli
stopwords learning
ght) [29]
annotation to
EntityClassifier.eu each word,
plain text, IE, OL, rule-based d
(http://entityclassi dump yes yes automatic no yes annotation to XML
HTML SA grammar in
fier.eu) non-
stopwords
(multi-)word
NIF or
EarMark
annotation,
predicates,
instances,
compositional
IE, OL, semantics,
SA, concept NLP,
FRED (http://wit.i ontology taxonomies, machine
stc.cnr.it/stlab-too dump, d
plain text yes yes automatic no yes design frames, learning, RDF/OWL
REST API in
ls/fred/) [30] patterns, semantic heuristic
frame roles, rules
semantics periphrastic
relations,
events,
modality,
tense, entity
linking, event
linking,
sentiment
plain text,
XML,
NetOwl Extractor HTML, named
JSON,
(http://www.netow XML, entities, m
dump No Yes Automatic yes Yes IE NLP RDF-
SGML, relationships, d
l.com/) [32] OWL,
PDF, MS events
others
Office
OntoLearn
Reloaded (http://w
concepts,
wwusers.di.uniro NLP,
plain text, concept d
ma1.it/~navigli/pu dump no yes automatic yes no OL statistical proprietary
HTML hierarchy, in
bs/IJCAI_2011_N methods
instances
avigli_Velardi_Far
alli.pdf)
OntoSyphon (htt
p://turing.cs.wash dump,
concepts, NLP,
ington.edu/paper HTML, search d
no yes automatic yes no OBIE relations, statistical RDF
s/iswc2006McDo PDF, DOC engine in
instances methods
queries
well-final.pdf) [35]
named
PoolParty entities,
NLP,
Extractor (http://w plain text, concepts,
machine
ww.semantic-web. HTML, relations, RDF, d
dump no yes automatic yes yes OBIE learning,
at/de/poolparty-ex DOC, concepts that OWL in
statistical
ODT categorize
tractor) [37] the text,
methods
enrichments
named entity
extraction,
entity
resolution,
plain text, relationship
HTML, extraction, XML,
NLP,
Rosoka (http://ww XML, attributes, JSON, m
dump Yes Yes Automatic no Yes IE machine
w.rosoka.com/) SGML, concepts, POJO, d
learning
PDF, MS multi-vector RDF
Office sentiment
analysis,
geotagging,
language
identification
SemTag (http://w
ww2003.org/cdro
m/papers/referee machine database d
HTML dump no yes automatic yes no SA
d/p831/p831-dill.h learning record in
tml) [38][39]
concepts,
NLP,
concept
Text2Onto (http statistical
hierarchy,
s://code.google.c plain text, methods,
semi- non- d
om/p/text2onto/) HTML, dump yes no yes yes OL machine OWL
automatic taxonomic in
[40] PDF learning,
relations,
rule-based
instances,
methods
axioms
concepts,
concept
hierarchy,
non-
taxonomic NLP,
Text-To-Onto (http plain text, relations, machine
s://texttoonto.sou HTML, semi- lexical learning,
dump yes yes OL
PDF, automatic entities clustering,
rceforge.net/) [41] PostScript referring to statistical
concepts, methods
lexical
entities
referring to
relations
ThingFinder (http
s://web.archive.or
named
g/web/201206290
entities,
52702/http://inxig IE
relationships,
htfedsys.com/pro
events
ducts/sdks/tf/)
[43]
Knowledge discovery
Knowledge discovery describes the process of automatically searching large volumes of data for patterns that can be considered knowledge about the data.[44] It is
often described as deriving knowledge from the input data. Knowledge discovery developed out of the data mining domain, and is closely related to it both in
terms of methodology and terminology.[45]
The most well-known branch of data mining is knowledge discovery, also known as knowledge discovery in databases (KDD). Just as many other forms of
knowledge discovery it creates abstractions of the input data. The knowledge obtained through the process may become additional data that can be used for further
usage and discovery. Often the outcomes from knowledge discovery are not actionable, actionable knowledge discovery, also known as domain driven data
mining,[46] aims to discover and deliver actionable knowledge and insights.
Another promising application of knowledge discovery is in the area of software modernization, weakness discovery and compliance which involves
understanding existing software artifacts. This process is related to a concept of reverse engineering. Usually the knowledge obtained from existing software is
presented in the form of models to which specific queries can be made when necessary. An entity relationship is a frequent format of representing knowledge
obtained from existing software. Object Management Group (OMG) developed the specification Knowledge Discovery Metamodel (KDM) which defines an
ontology for the software assets and their relationships for the purpose of performing knowledge discovery in existing code. Knowledge discovery from existing
software systems, also known as software mining is closely related to data mining, since existing software artifacts contain enormous value for risk management
and business value, key for the evaluation and evolution of software systems. Instead of mining individual data sets, software mining focuses on metadata, such as
process flows (e.g. data flows, control flows, & call maps), architecture, database schemas, and business rules/terms/process.
Input data
Databases
Relational data
Database
Document warehouse
Data warehouse
Software
Source code
Configuration files
Build scripts
Text
Concept mining
Graphs
Molecule mining
Sequences
Data stream mining
Learning from time-varying data streams under concept drift
Web
Output formats
Data model
Metadata
Metamodels
Ontology
Knowledge representation
Knowledge tags
Business rule
Knowledge Discovery Metamodel (KDM)
Business Process Modeling Notation (BPMN)
Intermediate representation
Resource Description Framework (RDF)
Software metrics
See also
Cluster analysis
Data archaeology
Further reading
Chicco, D; Masseroli, M (2016). "Ontology-based prediction and prioritization of gene functional annotations" (https://doi.org/10.1109/TCBB.2
015.2459694). IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13 (2): 248–260. doi:10.1109/TCBB.2015.2459694 (htt
ps://doi.org/10.1109%2FTCBB.2015.2459694). PMID 27045825 (https://pubmed.ncbi.nlm.nih.gov/27045825). S2CID 2795344 (https://api.se
manticscholar.org/CorpusID:2795344).
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