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Re: [ontolog-forum] Patent application for using a formal ontology inNLP

To: ontolog-forum@xxxxxxxxxxxxxxxx
From: "John F. Sowa" <sowa@xxxxxxxxxxx>
Date: Fri, 03 Sep 2010 15:57:48 -0400
Message-id: <4C81533C.2080000@xxxxxxxxxxx>
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.    (01)

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.    (02)

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".    (03)

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.    (04)

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.    (05)

John Sowa 
________________________________________________________________________    (06)

http://www.faqs.org/patents/app/20090259459    (07)

The Formal Ontology    (08)

[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.    (09)

[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.    (010)

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".    (011)

[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.    (012)


[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.    (013)

[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.    (014)

[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".    (015)

[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.    (016)

[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.    (017)

[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".    (018)

[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.    (019)

[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.    (020)

[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.    (021)

[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.    (022)

[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.    (023)

[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.    (024)

[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.    (025)

[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.    (026)

[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.    (027)

[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.    (028)

[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.    (029)

[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.    (030)

[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.    (031)

[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.    (032)

[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.    (033)

[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.    (034)

[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.    (035)

[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.    (036)

[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.    (037)

[0067] The rules established in the linguistic ontology may be as broad 
or restricting as required for a given application or knowledge area.    (038)

[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.    (039)

[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).    (040)

[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.    (041)

[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.    (042)

[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.    (043)

[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.    (044)

Managing the System, System Architecture    (045)

[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.    (046)

[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.    (047)

Linking External Databases    (048)

[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.    (049)

[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.    (050)

[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.    (051)

[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.    (052)

Coding Using Independent Coding Systems    (053)

[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.    (054)

[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.    (055)

[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.    (056)


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