The CEL Manual
Contents
1. Syntax and C C Example and Human Male Drunk Type concept constructor some keyword Description Existential restriction 4RN C Syntax some RN C Example some has child Male Remarks Only atomic roles are allowed in an existential restriction Type concept constructor compose keyword Description Binary role composition RN o RN2 Syntax compose RN RN2 Example compose has parent has brother Type role constructor 3 2 Knowledge Base Declarations This section introduces the commands used to build up ontologies There are two kinds of role axiom declarations and four kinds of concept axiom declarations define primitive role macro Description Syntax Arguments Example Remarks Defines a role name and its properties such as its super roles and transitivity define primitive role RN amp key transitive nil parent nil parents nil right identity nil left identity nil RN role name transitive if set to t declares that the role name is transitive parent specifies a super role or alternatively use parents with a singleton set see examples parents specifies a list of super roles sright identity specifies a right identity role for RN sleft identity specifies a left identity role for RN define primitive role has descendant transitive t define primitive role conj role parents r Tn define primitive role cont in right identity part of This macro integra2. To get started it is perhaps advisable to generate some simple ontologies using a standard text editor such as emacs The following simple ontology is provided as the file tboxes med tbox of the CEL distribution The concept name HDSNT is an abbreviation for heart desease needing treatment define primitive role cont in parent comp of implies Pericardium and Tissue some cont in Heart implies Pericarditis and Inflammation some has loc Pericardium implies Inflammation and Disease some acts on Tissue implies and Disease some has loc some comp of Heart and Heartdisease some has state NeedsTreatment define concept HDSNT and Heartdisease some has state NeedsTreatment Starting up the reasoner CEL can be started by simply calling the executable in the bin subdirectory of the distribution After the reasoner has been successfully loaded the greeting screen will appear and CEL will prompt for commands from the user Loading the ontology At the prompt write down the following command load ontology med tbox CEL searches for the specified ontology not only in the current directory but also in the directory tboxes A full path to the ontology file can also be given Classifying the Ontology After having read in and preprocessed the ontology CEL is ready to classify it The user may want to check this status by asking ontology prepared The answer will then be t i e
3. The CEL Manual Boontawee Suntisrivaraporn Institute for Theoretical Computer Science TU Dresden Germany meng tcs inf tu dresden de Abstract Description logics DLs are an important family of formalisms for reasoning about ontologies CEL is a reasoner for the description logic EL supporting as its main reasoning task the computation of the subsumption hierarchy induced by ELT ontologies The most distinguishing feature of CEL is that unlike other modern DL reasoners it implements a tractable i e polynomial time algorithm The supported description logic EL offers a selected set of expressive means that are tailored towards the formulation of medical and biological ontologies Contents 1 Introduction to CEL 1 2 An Overview of CEL Ontologies 3 3 Macros and Functions 4 3 1 Concept and Role Construction 2 2 0 0 2 00000 0004 4 3 2 Knowledge Base Declarations 2 2 0 0 000 eee eee 5 3 3 Operations on the Ontology TBox 0 8 3 4 Query Commands 0000 a 9 3 5 Other Commands sar io 4 hoe ke Pe Be Pe ea ee et 11 4 An Example Learning by Doing 12 1 Introduction to CEL The description logic E introduced in 1 is tailored towards the formulation of medical and biological ontologies A distinguishing feature of ELt compared to other description logics such as SHZQ and OWL 3 4 is that despite offering considerable expressivity reasoning in is tractable i e can
4. ainment between a role composition on the lhs and a role name on the rhs DL notatioin RN1 o RNa E RN3 CEL syntax role inclusion compose RN RN2 RN3 We note that only role inclusion and implies are sufficient to express any ELT ontologies The additional commands are included for ease of use and for compatibility with other DL reasoners 3 Macros and Functions In this section we give a detailes description of all commands offered by CEL The commands are arranged in five groups 3 1 Concept and Role Construction In CEL concept and role names can be used without prior declaration To form concept and role names we recommend the use of alphanumerical characters probably including symbols such as and Per default CEL does not distinguish capital letters from lower case ones All symbols will automatically be capitalized when processing In case of the need for case distinction symbols shall be embraced within a pair of vertical bars that is MALE is equivalent to Male but MALE is not to Malel Complex concepts and roles can be constructed using the constructors of ELT as summarized in the grammar on Page 3 In the following the syntax is described in more detail top keyword Description The predefined most general concept of any ontology the top con cept T aka logical truth Syntax top Type concept constructor and keyword Description N ary conjunction C1 M MC
5. be performed in polynomial time which stands for a polynomial time Classifier for the description logic ELt This is clearly an advantage over the EXPTIME worst case complexity of reasoning in SHIZO and OWL The ultimate goal of CEL is to provide a highly efficient reasoner for the descrip tion logic E A main emphasis of CEL is on reasoning with ontologies formulated in E L in particular on computing the subsumption hierarchy induced by such an ontology As of now CEL implements a practically useful subset of E L that we call EL More precisely E L provides for the following concept constructors e top concept T e conjunction C N D e existential restriction Jr C For building up ontologies the following means of expressivity are available e primitive concept definitions A EC D concept definitions A D general concept inclusion GCI axioms C C D concept equivalence axioms C D e transitivity assertions for roles ror C r e role hierarchy axioms r E s e right identity rules ros E r and left identity rules ros E s e role inclusion RI axioms of the form ros Ct The ontology classification algorithm implemented in CEL has been proposed in 2 This algorithm is a refinement for implementation purposes of the well known polynomial time algorithm for computing classification in E giving i
6. concept name C possibly complex concept define concept Father and Man some has child Human This macro states both the necessary and sufficient conditions for CN In CEL a concept name may have multiple definitions concept inclusion implies macro Description Asserts a general concept inclusion GCI between two concepts Syntax implies C C2 Arguments C C gt 2 possibly complex concepts Examples implies and Man some has sibling Parent Uncle Remarks The equivalent DL notation is Cy E Co equivalent macro Description Asserts an equivalence between two concepts Syntax equivalent C C2 Arguments C C gt 2 possibly complex concept Examples equivalent and Man some has sibling some has child Female and Uncle some has niece top Remarks The equivalent DL notation is Cy Co 3 3 Operations on the Ontology TBox clear ontology clear tbox macro Description Removes all axioms and initializes everything Syntax clear tbox Remarks This macro is internally called whenever a new ontology is loaded load ontology load tbox macro Description Reads in and and normalizes the input ontology Syntax load tbox tbozfile Arguments tbozfile path of the input ontology file If a filename is given without path the ontology is assumed to be either in the current directory or in the subdirectory tboxes Remarks The file specified by tbox file is a
7. en on the console screen output hierarchy macro Description Outputs a visualized representation of the computed taxonomy Syntax output hierarchy filename Arguments filename file name possibly with path to which the subsumption relationships are written If not given the output is written on the console screen Remarks This feature is available only after classification in mode 1 With large input ontologies outputs in this format might become a mess and could be very large output hasse macro Description Outputs the computed Hasse diagram by identifying the parents and children of each concept name Syntax output hasse filename Arguments filename file name possibly with path to which the subsumption relationships are written If not given the output is written on the console screen Remarks This feature is available only after classification in mode 1 4 An Example Learning by Doing In this section we illustrate the use of CEL step by step This includes e creating an ontology e starting up the reasoner e loading the ontology e classifying the ontology e querying subsumptions and e output the classification 12 Creating an Ontology CEL is a reasoning backend and as such does not provide an ontology editor to create and maintain ontologies Any ontology editor that produces KRSS syntax and supports a subset of the expressive means provided by EL can be used together with CEL
8. ion in mode 1 children macro Description Returns a list of direct subsumees of a concept name Syntax children CN Arguments CN concept name Remarks This feature is available only after classification in mode 1 ancestors super concepts macro Description Syntax Arguments Returns a list of all direct and indirect subsumers of a concept name ancestors CN CN concept name descendants sub concepts macro Description Returns a list of all direct and indirect subsumees of a concept name Syntax descendants CN Arguments CN concept name role macro Description Checks if the given name is known as a role name Syntax concept RN Arguments RN name to be tested all roles macro Description Retrieves the list of all role names occurring in the ontology Syntax all roles role subsumes macro Description Syntax Arguments Remarks Queries if one role name subsumes the other role subsumes RN RNo RN RN o role names DL equivalent notation is RN Ee RN 10 role implies macro Description Queries if one role name implies is subsumed by the other Syntax role implies RN RN Arguments RN RN role names Remarks Identical to role subsumes but with swapped arguments transitive macro Description Checks if a role name is specified as transitive Syntax transitive RN Arguments RN role name 3 5 Other Commands
9. iption of the syntax along with helpful examples is given in Section 3 1 We now give an overview of the axioms that are available for building up ontologies Such axioms can be devided into concept axioms and role axioms Primitive concept definitions state the necessary condition of a concept name DL notation CN LC CEL syntax define primitive concept CN C Concept definitions state the definition both necessary and sufficient conditions of a concept name DL notation CN C CEL syntax define concept CN C General concept inclusions state the subsumption or containment between two concept descriptions DL notation Cy E Co CEL syntax implies C1 C2 Concept equivalence axioms state the equivalence between two concept descrip tions DL notation Cy C gt CEL syntax equivalence C1 C2 Role transitivity axioms assert the transitivity of a role name DL notation RN o RN C RN CEL syntax define primitive role RN transitive t Role hierarchies assert the relationship between a role name and its super role name DL notatioin RN E RN CEL syntax define primitive role RN parent RN2 Right identity left identity rules specifies a right left identity of another role DL notatioin RN1 o RNoC RN CEL syntax define primitive role RN right identity RN and DL notatioin RN o RNa E RN CEL syntax define primitive role RN left identity RN 1 Role inclusions state the subsumption or cont
10. n 1 Currently CEL accepts inputs in a slight extension of the KRSS Knowledge Representation System Specification syntax 5 The following system requirements are assumed e Linux operating system e Physical memory at least 128MB CEL is available as a precompiled binary package which can be run on Linux platforms The package can be obtained from http lat inf tu dresden de systems cel Considerably more memory may be needed for larger ontologies The package consists of the CEL executable this user manual the related papers 1 2 and some example EL ontologies This manual details how to get CEL up and running how to create an ontology and how to classify it In Section 2 an overview of the concept and ontology language of CEL is given In Section 3 all commands offered by CEL will be described in detail including syntax and helpful examples Finally Section 4 gives a step by step introduction to CEL at work 2 An Overview of CEL Ontologies Concepts and roles are built up from sets of concept and role names which can be freely choosen by the user using the concept and role constructors provided by EL The following syntax rules describe the formation of concepts and roles in CEL C gt CN top and C Cn some RN C R RN compose RN RN2 where CN C RN and R all possibly with subscripts range over concept names concepts role names and roles respectively A more detailed descr
11. n Section 3 5 References 1 F Baader S Brandt and C Lutz Pushing the E envelope In IJCAI 05 Edin burgh UK 2005 Morgan Kaufmann Publishers 2 Franz Baader Carsten Lutz and Boontawee Suntisrivaraporn Is tractable reason ing in extensions of the description logic EL useful in practice In Proceedings of the 2005 International Workshop on Methods for Modalities M4M 05 2005 3 I Horrocks P F Patel Schneider and F van Harmelen From SHIQ and RDF to OWL The making of a web ontology language Journal of Web Semantics 1 1 7 26 2003 4 D L McGuinness and F van Harmelen OWL web ontology language overview See http www w3 org TR owl features 2004 5 P Patel Schneider and B Swartout Description logic knowledge representation sys tem specification from the krss group of the arpa knowledge sharing effort Technical report DARPA Knowledge Representation System Specification KRSS Group of the Knowledge Sharing Initiative 1993 14
12. oncept subsumes subsumes macro Description Syntax Arguments Remarks Queries if one concept name subsumes the other concept subsumes CN CNoe CN CN concept names This macro only performs a lookup in the preclassified concept hierarchy it cannot be called before the test tbox classified is positive DL equivalent notation is CNg me CN In the current version of CEL it is not possible to query the subsumption of complex concepts w r t the classified ontology To perform such a subsumption query introduce two new names for the complex concepts in the subsumption query using define concept re classify the augmented ontology and then use concept subsumes to check subsumption between the newly introduced concept names concept implies implies macro Description Syntax Arguments Remarks Queries if one concept name implies is subsumed by the other concept implies CN CN2 CN CN concept names Identical to concept subsumes but with swapped arguments concept equivalent equivalent macro Description Syntax Arguments Queries if two concept names are equivalent i e subsume each other concept equivalent CN CNo CN CN concept names parents macro Description Returns a list of direct subsumers of a concept name Syntax parents CN Arguments CN concept name Remarks This feature is available only after classificat
13. ssumed to contain a list of com mands as shown in Subsection 3 2 After having successfully loaded the ontology it is ready to be classified see the next command classify ontology classify tbox macro Description Classifies the loaded and normalized ontology Syntax classify tbox amp key mode 2 Remarks Classify the current ontology depending on the mode of classifica tion which is defaulted to 2 In the classification mode 1 CEL additionally computes the Hasse diagram i e a directed acyclic graph DAG of the terminological hierarchy As a consequence classification in mode 1 usually takes longer time on the same on tology but it also provides users with additional features thereafter ontology prepared tbox prepared macro Description Checks if the ontology is prepared for classification Syntax tbox prepared Remarks This is a fundamental requirement for classify tbox ontology classified tbox classified macro Description Checks if the ontology is successfully classified Syntax tbox classified Remarks This test must be positive before any subsumption queries can be carried out 3 4 Query Commands concept macro Description Checks if the given name is known as a concept name Syntax concept CN Arguments CN name to be tested all concepts macro Description Retrieves the list of all concept names occurring in the ontology Syntax all concepts c
14. start function Description Loads preprocesses and classifies the ontology all in one com mand Syntax start tborfile amp key mode 2 verbosity 2 Arguments tbozfile path string pointing to the input ontology file mode mode of classification when set to 1 CEL additionally com putes the Hasse diagram verbosity the level of verbosity CEL talks to its interactive users 0 or nil for none 1 for crutial messages 2 for normal messages t for everything Remarks See load ontology and classify ontology output subsumption macro Description Syntax Arguments Outputs all computed subsumption relationships pair by pair output subsumption filename filename file name possibly with path to which the subsumption relationships are written If not given the output is written on the console screen output imp sets macro Description Syntax Arguments Outputs all computed subsumption relationships in the form of implication sets output imp sets filename filename file name possibly with path to which the subsumption relationships are written If not given the output is written on the console screen 11 output synonyms macro Description Outputs sets of told synonyms and their representative Syntax output synonyms filename Arguments filename file name possibly with path to which the subsumption relationships are written If not given the output is writt
15. tes several DL role axioms As an example we would need two DL role axioms for the first example above one for the transitivity hasDescendant ohasDescendant E hasDescendant and one for the role inclusion hasDescendant E hasChild The ar guments left identity and right identity are not part of the KRSS standard role inclusion macro Description Syntax Arguments Example Remarks Asserts an inclusion between a possibly composite role and a role name role inclusion R RN R role name or binary role composite RN role name role inclusion has daughter has child role inclusion compose has father has sister has aunt This is a generalization of define primitive role Role hier archy transitivity and right identity can be expressed in a more elegant way by using define primitive role This macro is not part of the KRSS standard define primitive concept macro Description Syntax Arguments Examples Remarks Asserts a subsumption relation between a concept name and a com plex concept define primitive concept CN C CN concept name C possibly complex concept define primitive concept Father Man define primitive concept GrandMother and Mother Female This macro states the necessary conditions for CN define concept macro Description Syntax Arguments Examples Remarks Defines a concept name define concept CN C CN
16. yes At this point the classification can be started by calling the command 13 classify ontology This may take some time depending on the size and complexity of the ontology To load and classify an ontology in one step the start function can be used Querying Subsumption When the ontology has successfully been classified to check this call ontology classified subsumption between two concept names w r t the classified ontology can be queried In the example ontology above the user might want to know if Pericarditis is in fact a heart disease needing treatment This can be checked by querying concept subsumes HDSNT Pericarditis The set of all subsumers and subsumees of a concept name can also be obtained by using ancestors and descendants respectively Output the Classification After the classification the concept hierarchy can be archived in a file or displayed on screen by using the functions output subsumption and output imp sets depending on the format and brevity needed If the classifica tion has been carried out in mode 1 it is additionally possible with output hasse to output the most compact representation of a taxonomy i e Hasse diagram By using output hierarchy a visualization of the terminological hierarchy can be displayed Moreover maximal sets of pairwise subsuming concept names called synonyms can be displayed by the function output synonyms Please refer to the more detailed ex planation i
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