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Hi John,
I wonder how those in commercial enterprises, such as Cycorp, are viewing this patent. Given (what I believe to be) the volume of prior art, is this patent a real threat within our community, or is it merely a distraction?
Cameron. On Fri, Sep 3, 2010 at 3:57 PM, John F. Sowa <sowa@xxxxxxxxxxx> wrote:
In my previous note about the patent by Werner Ceusters, et al., I
didn't go into detail about the patent description, which has a very
lengthy description of formal ontologies and how they are used.
I received an offline note, saying that the description was very
dangerous, because the so-called inventors submitted another patent
application as a "continuation" of the previous patent. Although
the continuation has only one fairly general claim, the "inventors"
could add any claims they wish up until the time that the patent
is granted.
At the end of this note, I copied the presentation or "teaching"
from that patent, which describes how they use the formal ontology.
There is nothing new in it. All of it has been published and
implemented many times over during the past half century. But the
patent examiners didn't know that. They granted the patent, and
it's quite likely that they will approve this "continuation".
For a patent application, the US patent law allows the "inventors"
to add any new claims they please to the application up until the
date the patent is granted. Since this application has just one
claim, that indicates the "inventors" plan to stuff the application
with many more claims just before it is granted.
I suggest that readers of Ontolog Forum look at the description
quoted below with one thought in mind: "Is this similar to anything
I have done or plan to do with a formal ontology." If so, these
"inventors" (or any company they assign the patent to) could sue you.
John Sowa
________________________________________________________________________
http://www.faqs.org/patents/app/20090259459
The Formal Ontology
[0038] The formal ontology according to the current invention comprises
a plurality of concepts one part of them being independent of a specific
language, the other part being those concepts that explain the
relationships between language-independent concepts and language as a
medium of communication. By independent of language it is meant that the
concepts do not depend on a particular language to be given a definition
within the system. For example, in English, the word "dog" is a label
applied to the concept of a particular animal. In other languages the
same concept may be labeled with a different word, such as "Hund" in
German, "cane" in Italian, or "perro" in Spanish. In reality, regardless
of the label used in a particular language, the concept of the animal
remains reasonably constant. The concept is therefore said to be
independent of a specific language. Similarly, in the domain ontology
according to the current invention, the concept for this particular
animal is not dependent on a particular language. By keeping concepts
independent of a specific language, the system according to the current
invention can link concepts contained in the formal ontology to terms in
more than one language.
[0039] However, although the concepts are independent of any specific
language (such as English, French, . . . ), in the present invention
they are not represented as being independent of language as a medium of
communication. The second part of the formal ontology, the linguistic
ontology, contains concepts about how humans interpret language. For
example, the linguistic ontology according to the current invention
contains the concept labeled "dispositive doing", which as a real world
object relates to instances of an actor doing something to an actee. The
concept is independent of a specific language because the notion of
actor and actee in the context of the real world object, an action, is
common to all languages. However, the concept is not totally independent
of language in that the concept governs how the relationship between the
actor and actee is understood by human beings.
For example, in the sentence [0040] "The doctor treated the patient."
it is understood in language that the action "treated" has an actor
"doctor" and an actee "patient". That is, in the real world human beings
understand that doctors treat patients, and patients don't treat
doctors. The linguistic ontology applies this understanding to the real
world object "treatment".
[0041] Thus, the concepts that are contained in the formal ontology are
of two types generally. The first type of concept relates to real world
objects that are recognized by human beings as metaphysical instances.
These concepts comprise physical entities, procedures, ideas, etc and
are contained in the domain ontology. The second type of concept relates
to how human beings understand language and allows the identification of
real world instances. That is, how human beings understand the
interactions of real world objects represented by the concepts in the
domain ontology.
[0042] The concepts that are contained in the formal ontology will
depend on the knowledge area that the ontology is to be applied to, as
well as on the principles according to which human languages function
independent of the knowledge area. The domain ontology may contain
concepts comprising general knowledge about the world, or may be limited
to a specific knowledge area of interest to a user. Similarly, the
linguistic ontology may define very broad rules about how language
functions, or it may define very narrow rules to limit the relationships
that can exist between concepts in the domain ontology. In a preferred
embodiment of the system according to the current invention, the
concepts contained in the domain ontology are limited to the knowledge
area of medical concepts complemented by a linguistic ontology
containing the concepts required to understand how natural language
functions, and how humans deal with natural language. However,
ontologies built with concepts from other knowledge areas can be created
with equal success.
[0043] By allowing the concepts in the formal ontology to remain
independent of specific language, the system according to the current
invention allows documents in a variety of languages to be indexed and
searched independent of the language(s) known by the system user.
According to a preferred embodiment of the invention, the concepts in
the formal ontology are tagged with labels in English to allow easy
maintenance of the formal ontology by a user. However, the labels in
English are for ease of use in maintaining the formal ontology only and
do not contribute to the functioning of the system in indexing or
retrieval of documents. The concepts in the formal ontology can be
alternatively labeled in Dutch, German, French, Italian or any other
language desired by the user. Alternatively, the concepts may be labeled
using a coding system that is completely independent of language, such
as ICD-9 or ICD-10.
[0044] The basic architecture of the formal ontology of the current
invention is a directed graph, i.e. a hierarchical structure that allows
multiple parents. Referring to FIG. 2, an example of the hierarchical
structure is shown. In the hierarchy shown in FIG. 2, a primary node
comprises a single primary concept. In the example shown, the single
primary concept is the concept "City". The primary concept has as direct
children, narrower related concepts, such as "European City" and "North
American City". Each of the child concepts further have one or more
child concepts that further narrow the primary concept. For example, the
concept of "European City" may be narrowed to "French City", "German
City" and "Belgian City". The concept of "North American City" may be
narrowed to "Canadian City" and "US. City".
[0045] The hierarchical structure of the formal ontology, creates the
most basic relationships between concepts contained in the formal
ontology, that of parent and child in a strict formal subsumption
interpretation, and that of siblings. The formal subsumption
interpretation guarantees that all characteristics described of a
parent, apply to all of its children without any exception. Referring
again to the example, the concept of "City", which occupies the highest
level of the hierarchy is the parent concept to "European City" and
"North American City". By reciprocal relationship, the concepts of
"European City" and "North American City" are the children of the
concept "City". Further, the concept of "European City" is the parent of
the concept "German City", etc. Further, the concept of "City" is the
grandparent concept to the concept "German City", etc. Still further,
the concepts of "European City" and "North American City" have the
relationship of siblings since they share a common parent.
[0046] Regardless of the knowledge area of the concepts contained in the
formal ontology according to the current invention, a similar
hierarchical structure with parent/child and sibling relationships
exists. This is true of both the general world concepts in the domain
ontology and the linguistic concepts in the linguistic ontology. In a
preferred embodiment of the invention, the highest level of the
hierarchy is occupied by a primary concept with a label such as "Domain
Entity". According to the preferred embodiment of the invention, the
primary concept of "Domain Entity" encompasses all real things whether
they be physical entities, states, ideas, etc. The primary concept may
then preferably be sub-divided into physical entities, states, ideas,
linguistic concepts, etc. at the next lower level of the ontology.
[0047] It should be apparent that because the hierarchical structure of
the formal ontology, that all concepts in the ontology can be traced
back to a single related concept at the highest level of the ontology,
such as "Domain Entity". On the most basic level therefore, the degree
of relatedness between two concepts can be measured by how many steps in
the hierarchy must be traversed to find a common ancestor for the two
concepts. Again referring to the example, the concepts of "Brussels" and
"Antwerp" are siblings since they share a common parent, and are
therefore closely related to each other within the hierarchy. By
contrast, one must traverse the hierarchy back to the primary concept of
"City" to find a common ancestor for the concepts of "Brussels" and
"Chicago". Since the concepts of "Brussels" and "Chicago" share only a
great-grandparent concept in common, they are less closely related
within the context of the hierarchy than are the concepts "Brussels" and
"Antwerp".
[0048] It should further be recognized that a single concept can have
more than one direct parent. For example, in addition to the child
concepts shown in FIG. 2, the concept "City" may have a child concept
"Capital City". In this case "Paris", "Berlin" and "Brussels" would be
children of the concept "Capital City" in addition to being children of
"French City", "German City" and "Belgian City" respectively. By
allowing a concept to have multiple parent concepts, the degree of
relatedness between two concepts within the hierarchy may vary based on
the context of the relationship. As can be seen from the examples,
"Paris", "Berlin" and "Brussels" are more closely related in the context
of "Capital City" than in the context of "European City". The only
limitation on the structure of the hierarchy is that a concept cannot
have itself as an ancestor, which would lead to a circular reference of
a concept to itself.
[0049] As stated above, the most basic relationship between concepts in
the formal ontology according to the current invention is the link
created by the parent/child relationship. However, the relationships
that can exist between two concepts in the formal ontology according to
the present invention is not limited to that of parent and child. By
allowing other relationships to exist, the richness of the knowledge
contained in the formal ontology is greatly enhanced, while limiting the
overall size of the ontology. For example, in reality the medical
concepts of "brain", "inflammation" and "meningitis" are quite closely
related. However, the concept "brain" refers to a body part, whereas
"inflammation" is a symptom and "meningitis" is a disease. If a formal
ontology were limited to parent/child relationships as a measure of the
relatedness of concepts it is likely that the degree of relatedness
between these three concepts within the ontology would potentially be
very low. This is because a large number of parent/child relationships
would likely have to be traversed before a common ancestor was found for
all three concepts. This would of course lead to an inaccurate
reflection of reality. A potential solution to this problem would be to
construct a formal ontology with sufficient detail to narrow the gap
between these concepts in the hierarchy. For example, the concepts of
the body part "brain" and the symptom "inflammation" could be made
children of the concept of the disease "meningitis". However, in order
to provide an accurate reflection of reality it would be necessary to
construct similar relationships between "brain" and "inflammation" and
every other concept that they are related to. Since the concepts of
"brain" and "inflammation" would most likely be attached to a large
number of concepts, this would result in a large number of such
parent/child relationships. Further, similar parent child relationships
would have to be built for every concept in the ontology. This would
result in an unmanageably large ontology. In addition, such a solution
would violate the formal subsumption nature of the parent/child
relationships exploited in this invention.
[0050] The current system solves this problem by providing a large
number of link types for linking concepts within the formal ontology.
The link types within the formal ontology according to the current
invention are used to define relationships between concepts. For
example, in reality the concept of "brain" is linked to the concept
"meningitis" in that the brain is the location for the disease
meningitis. Using the link types available in the formal ontology, a
user can create a link between the concepts "brain" and "meningitis" in
the formal ontology so that this conceptual link is also recognized by
the system. A user may further create a link between the concept
"inflammation" and the concept "meningitis" in the formal ontology to
indicate that inflammation is a symptom of meningitis. Again, this
allows the system to recognize a conceptual link that exists in reality.
Furthermore, by linking the concepts "brain" and "inflammation" to the
concept "meningitis", a conceptual link between the brain and
inflammation is created. That is, the link through the concept
"meningitis" shortens the distance between "brain" and "inflammation"
within the ontology. By shortening the distance between these two
concepts, the conceptual linkage between the two concepts in the
ontology is increased.
[0051] An advantage of this type of linking of concepts is that it
allows for more accurate indexing of documents because the deep meaning
of the text can be pulled out. For example, a text that contains a
discussion of meningitis may contain very few instances of the exact
term "meningitis". However, the document may contain a significant
number of references to inflammation in the brain. A standard indexing
technique that looks only for the specific concept "meningitis" may rank
such a document of very low relevance, while in reality it may have a
very high relevance to the subject. In contrast, the system according to
the current invention will recognize the linkage between the concepts of
"brain", "inflammation", "meningitis" and as a result rank the document
with a more accurate relevance to the subject.
[0052] The number of link types that can be provided for an ontology is
only limited by the number of such relationships that can exist in
reality. According to a preferred embodiment of the invention, a user
can use the available concepts and link types to build criteria and
concept criteria. A criteria according to this embodiment is comprised
of a concept with an associated link type. For example, the link type
HAS-LOCATION can be associated with the concept BRAIN to produce the
criteria [HAS-LOCATION] [BRAIN]. This criteria can further be used to
define a property of another concept as part of a concept criteria. For
example [MENINGITIS] [HAS-LOCATION BRAIN]. The association of the
criteria [HAS_LOCATION] [BRAIN] to the concept MENINGITIS provides a
partial definition of the concept meningitis.
[0053] In a preferred embodiment of the invention, each link type from a
first concept to a second concept has a complimentary reciprocal or
contra link type that can be established from the second concept to the
first concept. For example in reality, when two objects "A" and "B" are
close to each other, we say that "A" is close to "B" and "B" is close to
"A". In such case where a relation operates bi-directionally, the
ontology is constructed by placing the same link type twice, from "A" to
"B" and from "B" to "A". E.g.: A IS-NEAR-OF B, B IS-NEAR-OF A.
[0054] A second case of paired link types according to this embodiment
is used to describe an inverse relationship. For example, where concept
"A" performs some action on "B", "A" is defined as acting on "B" whereas
"B" is defined as being acted on by "A". E.g.: A HAS-ACTOR B<-> B
IS-ACTOR-OF A; or A IS-SPATIAL-PART-OF B<-> B HAS-SPATIAL-PART A. The
link types can be declared each other's inverse by use of either CONTRA
or AUTOCONTRA attributes that can be assigned to them.
[0055] he operation of link types and reciprocation will now be
explained by means of example. Prior to the explanation, it is necessary
to define what is meant herein by the term "instance". As used herein,
the term "instance" refers to an individual manifestation or embodiment
of a concept in the real world (i.e. metaphysical instances). By
example, for the concept of the disease meningitis, an individual
diagnosed case of meningitis contracted by a specific person would be an
occurrence or "instance" of the disease.
[0056] Now if we declare in the formal ontology "MENINGITIS" IS-CAUSE-OF
"INFLAMMATION IN THE BRAIN", then it means that all metaphysical
instances of meningitis cause inflammation in the brain. However, this
does not provide any reciprocal information about metaphysical instances
of inflammation in the brain.
[0057] By contrast, if we declared "INFLAMMATION IN THE BRAIN" HAS-CAUSE
"MENINGITIS", then it means that all metaphysical instances of
inflammation in the brain are caused by meningitis. Here again however,
we are provided with no information about metaphysical instances of
meningitis.
[0058] By declaring a CONTRA, such as "MENINGITIS" IS-CAUSE-OF CONTRA
HAS-CAUSE "INFLAMMATION IN THE BRAIN", the system according to the
current invention provides information about all instances of
meningitis: all instances of meningitis cause inflammation in the brain.
By declaring a CONTRA, the system also provides information about some
instances of inflammation in the brain: some instances of inflammation
in the brain are caused by meningitis.
[0059] By declaring an AUTOCONTRA, such as "MENINGITIS" IS-CAUSE-OF
AUTOCONTRA HAS-CAUSE "INFLAMMATION IN THE BRAIN", the system according
to the current invention provides information about all instances of
meningitis and all instances of inflammation in the brain: all instances
of meningitis cause inflammation in the brain AND all instances of
inflammation in the brain are caused by meningitis.
[0060] By using the various link types, and CONTRA and AUTOCONTRA
declarations to link concepts within the ontology, a user can build
definitions of the concepts in the ontology, while giving it a precise
semantics as to how these declarations are to be applied by interpreting
events in the world, this however without the computational burdens
related to full first order logic.
[0061] As stated above, creating a link between two concepts defines a
relationship between the two concepts. It also defines something about
at least one of the concepts itself, such as "brain" is the location of
"meningitis", or "inflammation" is a symptom of "meningitis". By
creating these two links, a user enriches the knowledge contained on the
ontology by providing a definition for the concept "meningitis" based on
its interactions with other concepts in the ontology. In a preferred
embodiment of the invention, a full definition can be created for each
concept in the formal ontology. The full definition as it is used here
means the set of necessary and sufficient links that a concept has to
identify occurrences in the real world as instances of the concept. In
other words: the set of all links of a given concept in the ontology
defines what is true for all occurrences in the real world that are
instances of the concept. The full definitions assigned to a concept in
the ontology allow occurrences in the real world to be recognized as
instances of the particular concept.
[0062] A further feature of the formal ontology provided according to
the invention is the subsumption of child concepts within parent
concepts, which results in full inheritability of links from parent to
child concepts. That is, a child concept will automatically be linked to
all concepts that its parent is linked to. For example, the concept
"meningitis" may have the child concepts of "viral meningitis" and
"bacterial meningitis", both of which are more specific concepts
subsumed within the concept "meningitis". Thus the link established
between the concept of "meningitis" and "brain" will automatically be
established between the concept of "viral meningitis" and "brain", and
"bacterial meningitis" and "brain". Therefore, "viral meningitis" and
"bacterial meningitis" will inherit the definition of the parent concept
"meningitis", but will be further defined based on the further links
that each has to other concepts. In this way, the system according to
the current invention can recognize each instance of either "viral
meningitis" or "bacterial meningitis" as an instance of "meningitis",
but will not necessarily recognize each instance of "meningitis" as
"viral meningitis" or "bacterial meningitis". This feature provides the
advantage of allowing a user to propagate a link to the progeny of a
concept by establishing a single link.
[0063] As stated above, the link types provided as part of the formal
ontology can be used by a user to define relationships between two
concepts. At the same time the link types can provide full definitions
of the concepts in the formal ontology. However, it is recognized in
reality that, some relationships between concepts do not make sense. For
example, it is recognized in reality that the disease "meningitis"
cannot not have "inflammation" as a location. In computerized systems
however, such nonsensical relationships are not automatically recognized
unless you make the system work under a "close world assumption" (i.e.
what is not known, is not allowed), or if it is specified explicitly
what is not allowed. It is necessary to teach a natural language
understanding system what are and are not appropriate relationships
between concepts.
[0064] The system according to the current invention solves this problem
by providing the linguistic ontology as part of the formal ontology. The
linguistic ontology contains the rules about how language works as well
as the principles that the human mind adheres to when representing
reality at the conscious level of a human being.
[0065] In the linguistic ontology provided according to the current
invention, rules are established regarding what relationships can exist
between concepts on the basis of how these relations are expressed in
language in general (though independent of a specific language). For
example, a rule may be established that the concept "disease" in the
formal ontology cannot be linked to the concept "symptom" in the formal
ontology as a location. Because "meningitis" and "inflammation" are
children of "disease" and "symptom" respectively in the hierarchy, the
rule prohibiting this link would be inherited by them. As a result, the
definition of inflammation as a location for meningitis could not exist
in the formal ontology.
[0066] In one embodiment, the linguistic ontology may be set up so that
there is an absolute prohibition against using certain link types to
link certain concepts. In the example above, a user would not be able to
create a link indicating the concept "inflammation" as a location for
the concept "meningitis". Alternatively, the linguistic ontology could
be set up such that a verification by the user will be required when a
prohibited link is proposed. In this embodiment, the user still has the
option to create the link.
[0067] The rules established in the linguistic ontology may be as broad
or restricting as required for a given application or knowledge area.
[0068] A second application of the linguistic ontology is that it
restricts the possible representations of reality to those that are
closest to the way reality is talked about by means of language. For
example, in a shooting event, there are a number of participants such as
the shooter, the deer, the bullet, the gun, etc. There is only that one
specific event that happened (the shooting) in a precise way (the deer
hit by the bullet shot from the gun by the shooter), but there are
different ways to represent it formally: it can be represented from the
viewpoint of the deer, the bullet, the shooter, etc. The present
invention exploits the way humans usually talk about such an event,
giving a central place to those aspects that are put central by the
story teller.
[0069] A third application follows from the second in that sometimes
single events are described as distinguishable entities by means of
natural language. An example is the notion of baby brought on earth,
wherein the view of "birth" (the baby's viewpoint) is equally preferred
in medical language usage as that of "parturition" (the mother's point
of view) or "delivery" (the physician's point of view).
[0070] The domain and linguistic ontologies have thus far been spoken of
as being separate entities within the formal ontology. However, in the
current invention they are connected within the formal ontology in that
a concept may have both a domain and a linguistic concept as a direct
parent. For example, the linguistic concept of "dispositive doing" may
have as a child the concept of a "treatment", wherein a "treatment" as
an action has a physician as actor and a patient or disease as actee. At
the same time, "treatment" may descend from the parent concept
"healthcare procedure" in the domain ontology. Within the domain
ontology, the concept of a "treatment" is defined as a real world
object, but this definition cannot be used to relate the object to other
real world objects. The linguistic ontology defines how the real world
object actively relates to other concepts and relates other concepts in
language.
[0071} As indicated above, the formal ontology according to the current
system is independent of any specific language, although not independent
of language altogether. However, free text documents are written in
specific languages. In order to be useful for indexing free text
documents it is necessary to relate the language independent concepts to
specific languages.
[0072] The system according to the current invention accomplishes this
by providing a lexicon of terms that are linked to the formal ontology.
The terms contained in the lexicon may comprise single words or
multi-word units that correspond to concepts, criteria and concept
criteria in the formal ontology. Further, each term in the lexicon may
be linked to more than one concept, criteria or concept criteria in the
formal ontology, which allows for the existence of homonyms. Likewise,
each concept, criteria and concept criteria may be linked to more than
one term in the lexicon, such as when terms in two or more languages are
contained in the lexicon.
[0073] When indexing a free text document or interpreting a query to
retrieve an indexed document, the system according to the current
invention uses the lexicon of terms to segment the free text and to
relate the free text to the concepts, criteria and concept criteria
contained in the formal ontology. Thus, the current system makes use of
both terms and independent concepts in the analysis of free text.
Managing the System, System Architecture
[0074] An additional feature of the present invention provides a
management system for managing the formal ontology. As discussed, the
formal ontology according to the current invention can be constructed
using any available relational database system, such as ORACLE®, SYBASE®
and SQLSERVER®. The ontology itself is abstracted away from the
relational database system by wrapping access to the database into a
management tool that exposes functionality to the user. The database
functions as a physical storage medium for the ontology. According to
the current invention a management tool is provided for giving a user
access to the ontology for the purpose of adding to or manipulating the
ontology. The tool allows the user to view the formal ontology using a
variety of different criteria that together give a complete picture of
the structure of the formal ontology. In a preferred embodiment of the
invention a user can view several different views of the ontology at
once as a layout, allowing the ontology to be viewed from several
perspectives at once.
[0075]The management system for maintaining the formal ontology will be
explained with reference to FIG. 3, which shows the architecture of the
ontology management system according to the current invention. The
formal ontology and lexicon of terms are stored on a database 20, which
is in communication with a server 22, which houses the server based
component of the ontology management tool 26. The server based component
of the ontology management system comprises a relational database which
controls access to the formal ontology, and contains the components for
building the formal ontology, such as the hierarchical structure, link
types, setting rules in the linguistic ontology, linking terms to
concepts, etc, along with the tools for creating multiple views of the
ontology. The ontology management system further comprises a client
based component(s) 24 that allows a user to access and maintain the
ontology via the server based component 22. The system can be
implemented on a number of platforms, including but not limited to
WINDOWS®, SOLARIS®, UNIX® and LINUX®. Preferably, the management tool 26
is a set of business objects. A low layer is a thin wrapper on top of
the database structure that implements the base functions to access a
particular relational database. A middle layer also exposes a set of
functions that manage multi-user access to any type of supported
database, such as a relational database. As such the middle layer allows
the creation of customized versions of the management tool within
certain limited parameters. A top layer implements the high level
interface. This interface surfaces functionality from a logical point of
view to outside users (e.g. "getConceptTree" is a high level layer
function that makes use of the underlying middle and low level layer
functions to populate a tree object with information about the place of
a concept in the formal ontology). Functionality implemented by the low
and middle layers includes but is not limited to the linking of external
databases, database manipulation and navigation, and text searching.
Linking External Databases
[0076] As described thus far, the formal ontology according to the
current invention is constructed manually by a user by creating
hierarchical levels, slots within those hierarchical levels and further
filling those slots with concepts, thereby creating the basic hierarchy
with its parent/child relationships between concepts. The user further
enriches the knowledge base by using the link types provided to define
relationships between the concepts entered into the hierarchy. In
addition to being able to manually construct the formal ontology, an
alternative embodiment of the system according to the current invention
provides the ability to map data from an independent database onto the
formal ontology.
[0077] In a number of knowledge areas, large databases of information
are already in existence. In order to avoid the laborious work of
manually re-entering this information into the formal ontology, the
system according to the current invention provides the capability to
link the formal ontology to an external independent database. Although
the external data never becomes a physical part of the ontology, this
feature allows a user to access and use data contained on an independent
database as if it were part of the formal ontology.
[0078] Data in an external database is linked to the ontology by
creating a parent/child relationship between at least one concept in the
formal ontology and at least one item of data in the database. In the
case of an external database in tabular format, such as an ACCESS®
database, a user can link an entire column of data in the external
database to one or more concepts in the formal ontology by creating a
parent/child link between at least one concept in the ontology to the
header for the column in the table. Normally, when data is provided in
tabular format, each column of the table is given a header with a
descriptive title for the data contained in that column. In creating the
parent/child relationship between the concept in the ontology and the
column of data, the system analyzes the title and associates it with
appropriate concepts in the ontology. Alternatively, the system may
provide the user with a list of potential concepts that the data can be
mapped to. The system may make use of the terms contained in the lexicon
when performing this function. In an alternative embodiment of the
invention, a user can manually map an item or column of data to the
desired concept.
[0079]Referring to FIG. 4, an example of how an external independent
database may be mapped to the formal ontology is shown. The relational
database 30, server 32 and client based component 34 are as described in
FIG. 3. Databases 36 and 38 are external independent databases, such as
ACCESS® databases containing data to be mapped onto the formal ontology.
Database servers 40 and 42 associated with each database 36 and 38 allow
access to their respective databases so that queries can be run. A
database directory service 44, assigns keywords to the separate
databases 36 and 38. According to the current system, the same keyword
may be assigned to two or more databases containing similar data that
can be accessed at the same time. The database directory service
provides the location of all of the available databases to an ontology
proxy module 46. The ontology proxy module 46 receives queries from a
user via the client based component 34. The ontology proxy module then
directs the queries to the server 32 and to a database-ontology mediator
module 48. The database-ontology mediator module comprises an
ontology-to-database translator 50 and a database-to-ontology translator
52. The ontology-to-database translator 50 serves the function of
translating the ontology concept based queries to database queries that
can be used to search the databases 36 and 38 for data that is mapped to
the particular concept or concepts embodied in the query. The
database-to-ontology translator 52 serves the function of translating
the information returned from the database to a form that can be viewed
by the user via the client based component 34.
Coding Using Independent Coding Systems
[0080] In a preferred embodiment of the system according to the current
invention, the formal ontology is comprised of a knowledge base of
medical concepts. A preferred use for the system is in the indexing of
medical documents. A further preferred application of the system
according to the current invention is the coding of medical documents
using a standard medical coding system. Standard medical coding systems
that can be used in conjunction with the current invention include, but
are not limited to ICD-9, ICD-10, MedDRA and SNOMED.
[0081] To accomplish this, the medical concepts contained in the formal
ontology of the system can be mapped to the appropriate codes contained
in the appropriate independent database (i.e. ICD-9, etc).
Alternatively, the appropriate coding system may be included in the
formal ontology as a separate and parallel hierarchy to the hierarchy of
medical concepts. In this alternative embodiment, each medical concept
is linked to the appropriate code via a "has code" link type. For
example, the concept "meningitis" would be linked to the ICD-9 code
322.9 or the MedDRA code 10027252.
[0082] By linking the concepts in the ontology to the appropriate codes,
the system is able to annotate free text documents with these codes as
the documents are being indexed.
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