Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows

Muhammad Junaid Malik and Thomas Fahringer
Institute of Computer Science, University of Innsbruck, Technikerstraße 21a, A-6020 Innsbruck, Austria {malik,tf}@dps.uibk.ac.at

Abstract. Automatic workflow composition with the help of ontologies has been addressed by numerous researchers in the past. While ontologies are very useful for automatic and semiautomatic workflow composition, ontology creation itself remains a very difficult and important task. In this paper we present a novel technique to synthesize ontologies for the Abstract Grid Workflow Language (AGWL). AGWL has been used for years to create Grid workflow applications at a high level of abstraction. In order to semi-automatically generate ontologies we use an AGWL Ontology (AGWO - an ontological description of the AGWL language), structural information of one or several input workflows of a given application domain, and semantic enrichment of the structural information with the help of the user. Experiments demonstrate ...

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Introduction

The Grid [1] has eliminated the need for dedicated computational facilities and made it possible for the scientists to leverage the computational power of resources located at geographically remote distances. The Grid workflow programming model [2] has been highly successful in the last decade in facilitating the composition of medium to large-scale applications from existing basic activities defining a sequence of tasks to manage computational science processes. A Grid workflow application represents a collection of computational tasks (activities) interconnected in a directed graph through control and data flow dependencies that are suitable for execution on the Grid. The complexity of the workflows has increased over the years with the increasing complexity of scientific applications. Domain scientists create Grid workflows with the help of Grid workflow composition tools and execute them with runtime environments such as available like [3], [9], [10], [11], [12], and [13]. Although these tools have greatly simplified the effort of a workflow designer through features such as auto-completion and design suggestions [14], [13] for workflows. Nevertheless the manual workflow creation is still a very demanding and tedious task. It not only requires comprehensive application domain knowledge but also sufficient skills of the incorporated workflow composition tool.

all data ports are associated with an AGWL data class) with the AGWL ontology (an ontological description of the AGWL language) which results in an intermediate ontology. The final ontology can then be used to automatically created workflows of the given domain. Numerous research projects tried to automatically generate workflows which include [3]. To address the above mentioned problems. Composing a Grid workflow is so demanding and complex that often the domain scientists have to jointly work with workflow composition tool experts to create a usable workflow. we found that there are two major problems when a scientist tries to create an ontology by hand. so that the execution of the activities of the workflow takes place in a certain predefined order and to satisfy all the input and output dependencies of these activities. We extract mainly information about activities and their input and output ports which we denote to as concepts in the following. Section-3 gives more details about the AGWL ontology. Such changes to the domain knowledge must be reflected in the domain ontology as well. As an example. Semi-automated ontology synthesis not only expedites the process of ontology creation but it also supports automatic updates of ontologies. this paper proposes a new method for semiautomatic ontology synthesis for Grid workflows specified with AGWL. [13]. [12]. Commonly there exist a large variety of workflows or sub-workflows for each different domain targeting specific scientific or technical experiments. consider a workflow that supports movie rendering. Successful approaches rely on the completeness of domain ontologies (a formal representation of knowledge as a set of concepts within a given application domain) which commonly must be manually created. In the first step one or several AGWL compliant input workflows of the same application domain are parsed and analyzed for the information available in the workflows. The next step associates concepts (for instance. most of the ontology structure (intermediate ontology) is created automatically. The traditional workflow design approach relies greatly on the capabilities of a human workflow composer and thus is prone to errors and very time consuming. and [19]. ii) Changes of the domain knowledge require the domain ontology to be updated as well. Based on our experience with manual ontology creation for Grid workflows used in Askalon. . Although the system is not fully automatic and requires user interaction. The workflow designer must know all of the details about these workflows and their corresponding activities. i) Manual ontology creation not only requires extensive domain knowledge and excellent ontology development skills but is also very time consuming. Our approach for ontology creation is performed in three phases. Most of these approaches are based on the analysis of the input data and functional description of the workflow activities with the help of domain ontologies [20]. the user has to provide semantic information for all concepts which is used to derive the final ontology associated with the domain of the input workflows. Thereafter. Thomas Fahringer A Grid workflow designer is responsible for creating efficient Grid workflows.2 Muhammad Junaid. A new activity could be introduced that performs the conversion of movie into a new format with supports better movie quality.

1. We use a real-world movie rendering algorithm workflow known as Povray [7] as an example workflow. section-2 gives the description of the terminology used in the paper. WorkConvert flow Input and Workflow Output parts of the Output workflow describe the input data and output data of the workflow respectively. The first activity takes scene data as input and initializes the process by creating multiple ini files for parallel execution of the Render activity. Apart from activities. this is consumed by the third activity Convert which combines these individual frames and creates a movie using these frames. an AGWL workflow comprises of four Render parts Workflow Header. and version of the workflow. Section-7 provides the related work targeted at ontology synthesis followed by the section-8 which provides the concluding remarks and potential future research prospective for the system. The Povray workflow is composed of three independent activities. and function attributes. followed by section-4 which provides the details of the implementation of the proposed system. The Workflow Header contains information about the domain. Render activity takes this input from first activity and generates images for individual frames of the movie. 2 Prerequisite An account of the terminology used in this paper is given below to better understand the process of the ontology creation with the proposed ontology synthesis system. Figure-2 shows the flowchart of the application. Povray movie rendercorresponding data inports and outports specify. Workflow Input. It then packs the frames into a tarball. Section-6 gives an account of the experiments performed using the proposed system and the results. Each element contains a number of attributes which exInitialize plain different properties of the workflow for example an activity contains name. Askalon uses AGWL to represent Parallel region workflows. and the Workflow Body. type. name. which is followed by section-3 describing the AGWL Ontology. the Grid workScene start data flows also have other elements as well which include control-flow. functions of the activity and its Fig. Section-5 describes the different algorithm used to perform the core of ontology synthesis operations.ing workflow . author. Workflow Output. type. data-flow and data-ports etc. A Grid workflow is a collection of computational tasks (activities) orchestrated in a predefined order to achieve the required execution goals input on the Grid.Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows 3 The paper is organized as follows. Each workflow activity contains data about the name. Workflow body contains the AGWL description of the workflow activities.

like material sciences. These basic concepts present in the AGWO are Function and Data. Each of these concepts may have one or more associated properties or subconcepts. An AGWL activity and AGWL data are represented using the concepts Function and Data respectively in the ontology. 4 Methodology . AGWL provides a rich set of constructs to created grid workflows for any type of scientific applications. These concepts are used as parent concepts for the domain specific concepts when creating a new ontology. mathematics and computer graphics. isOutputOf. and hasPart etc. Figure-2 shows the definition of these ontological concepts for AGWO. AGWO thus contains two distinct types of concepts which are extended for each new domain ontology. Whereas the concept Data has object-Properties hasRepresentation. The LDB database contains the lexicon of the semantic concepts. The Function and Data base concepts are also associated together using hasInput and hasOuput object-Properties. isPartOf. the proposed system extracts and processes a lot of information. control and data flows to specify execution flow and data flow during the execution of the workflow. Thomas Fahringer ing the input data required by the activity and output data produced by the activity.4 Muhammad Junaid. An OWL ontology is formal representation of the domain knowledge using the Web Ontology Language OWL [17]. AGWL ontology is the ontological representation of the basic AGWL constructs in the form of and OWL ontology. The object-Properties defined for the Function concept include hasInput and hasOutput. These constructs encoded as OWL concepts are inherited from the &OWL. This is also referred to as completeness of the ontology. whereas the ODB contains the workflow data and intermediate ontology structure etc created during the ontology synthesis process. isInputTo. AGWO contains two basic types of concepts that provide foundations for the extended domain concepts. meteorology. AGWO Abstract Grid Workflow Language [4] (AGWL) is the UML based workflow language used to create Grid Workflows for Askalon Grid Development environment. and by adding their parent concepts using owl:SubclassOf construct. 3 Abstract Grid Workflow Ontology. AGWL has already been put to use for creating workflows from diverse scientific domains. two databases Lexicon database LDB and the Ontology database ODB are used to store this information.Thing concept (the base concepts for all OWL ontologies). astrology. Ontology is said to be valid if it contains sufficient domain knowledge to express all the domain concepts. Further semantic information to these concepts is added by specifying owl:onProperty. AGWL provides different activity type constructs to represent computational tasks of different types. To synthesize ontologies.

After converting a workflow into canonical format the data in the resulting canonical relations can be easily analyzed and processed using standard SQL commands. name. A block-diagram of the sys. The workflow parser parses and analyzes the different parts of the workflow and extracts information to convert the workflow into canonical format. It takes one or a set of workflows belonging to a specific domain provided by the user and performs the canonicalization operation on these workflows. The first phase is the analysis and parsing of the workflow.Fig. Figure-5(a) and 5(b) shows AGWL representation of an activity and its respective canonical form. followed by creation [Domain] [Domain] of intermediate ontology structure based on the information collected in parsing phase and the semantic enrichment of the interme. The process of ontology synthesis is performed in three phases. type. For example some workflow headers only contain the name attribute and do not contain information like domain. . 3. name.Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows 5 The proposed ontology synthesis system is built as part of ASKALON [3] grid workflow development environment. category. function and I. As all the workflows elements are not structurally identical. The initial parsing of the workflow yields datasets contained in the workflow (e.1 Workflow Parsing and Canonicalization The first component of the system is the workflow parser. AGWL workflows are XML Documents comprising of the four sections as shown in the Figure-4. 2. Input AGWL Base Ontology Ontology/ Lexicon Database AGWL workflows User Input Workflow Parser Analyzer AGWL Parser Canonicalizer Ontology Structure builder AGWL Concept extractor AGWL to OWL Mapper intermediate rmedi Ontology Ontology Semantic Updater Semantic Concept builder Ontology Constructor Target Ontology Output Fig.Function and Data concepts tem is shown in Figure-3. 4. an activity and data inport datasets looks like A. source respectively). As the proposed system is used to synthesize ontologies for AGWL [4] based workflows therefore the parser is specifically designed to parse the AGWL workflows. Block diagram of the ontology synthesis system.g. and also the attributes of similar workflow elements may vary in number so these datasets need to be normalized before they can be canonicalized and stored in the database. type. AGWL ontology (AGWO) diate ontology.

the next step is to create the intermediate structure of the ontology. transforming that information into unique class concepts by representing the canonical data in OWL format. 4. 4.e.dps. or version.6 Muhammad Junaid.pov" type="agwl:file"/> <!--more data ports --> {Workflow Input} </cgwdInput> <cgwdBody> <parallelFor name="ParallelFor_1"> <activity function="" name="Render2" type="Povray:Render2"> <dataIns><dataIn category="" name="iniFile" source="PovrayWorkflow/iniFile" type="agwl:file"/></dataIns> <dataOuts><dataOut category="" name="frameTarball" saveto="" type="agwl:file"/></dataOuts> </activity> </parallelFor> <activity function="" name="Convert" type="Povray:Convert"> <dataIns><dataIn category="" name="frameTarballs" source="ParallelFor_1/frameTarballs" type="agwl:collection"/></dataIns> <dataOuts><dataOut category="" name="outFile" saveto="" type="agwl:file"/></dataOuts> </activity> {Workflow Body} </cgwdBody> <cgwdOutput> <dataOut category="" name="finalMovie" saveto="gsiftp://karwendel. activities and dataports. We have just used one activity Convert to create this intermediate ontology. where as the activity related data is store in the activity relation.uibk.at//home/kassian/pov/scherk. Similarly activities in the workflow may also have varying number of attributes.uibk. In the canonicalization process.1. Thomas Fahringer <?xml version="1.dps. This is performed by retrieving the canonical information from the Ontology database ODB.ac.0" encoding="UTF-8"?> encoding <cgwd author="Peter" domain="POVRAY" name="PovrayWorkflow" version=""> {Workflow Header} <cgwdInput> <dataIn category="" name="povFile" source="gsiftp://karwendel. Workflow data is stored in the workflow relation. The missing information is collected from existing data present in the workflow lexicon database. all the attributes of the extracted workflow structures are analyzed. Each newly created concept is assigned a parent data or function class concept in the AGWO. This canonicalized information is then stored in the ontology database ODB. When an attribute without an attribute value is found the user is asked to provide value for this attribute. The other two relations act port and wf port are used to store dataports for activities and workflows respectively. This process is performed for all the workflow components i. which results in an intermediate ontology. Database schema of the canonical relational database is shown in Figure-4. At this point the structure of the ontology is similar to as shown in Figure-6(a).ac. This process is known as canonicalization. AGWL representation of Povray workflow author.2 Structural foundations of the Ontology After a canonical relational database from the candidate workflow is created.at/~/mymovie. The four database relations in the schema are used to store the required information. After the normalization process. The process continues until all the attributes values are filled in these datasets. the next step is to add information to these attributes if it is missing.gif" source="Convert/outFile" type="agwl:file"/> <!--Data representation ommited --> {Workflow Output} </cgwdOutput> </cgwd> Fig. Normalization is the process of adding missing attributes to the workflow elements so that all the elements become identical in terms of the number and types of attributes. and if no information is found in the database then with the help of user input. .

(b) Structure of the target ontology . Database schema for the canonicalized information (a) Structure of intermediate ontology Fig. 6.avi" type="agwl:file"> <dataRepresentation> <storageType>FileSystem</storageType> <contentType>File</contentType> <archiveType>tgz</archiveType> <cardinality>single</cardinality> </dataRepresentation> </dataOut> </dataOuts> </activity> 7 Activity ID 1 Sid xxxxxxxx wf-id 1 Name Convert Type Activity Function Conversion Act_Port Wf-id 1 1 sid xxxxxxxx xxxxxxxx a-id 1 2 Parent 1 1 Element DataIn DataOut Name MovieYuv MovieAvi Category GenericData GenericData Type agwl:file agwl:file Source gsiftp:// NULL Saveto NULL gsiftp:// Act_Port_Data_representation storge FileSystem FileSystem content File File archive None tgz cardinality Single Single (a) Activity data sid id name domain version (b) Canonical form of the activity in database author a_id sid Element parent-id * wfid sid saveto wf_port Element parent-id archive cardinality saveto source category name act_port archive cardinality content storage workflow 1 1 1 activity * source category type Function name content storage * sid id name wf-id Fig.Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows <activity function=“ “ name=“Convert" type=“ "> <dataIns> <dataIn category="GenericData" name=“MovieYuv“ source=“gsiftp://" type=“"> <dataRepresentation> <storageType>FileSystem</storageType> <contentType>File</contentType> <archiveType>none</archiveType> <cardinality>single</cardinality> </dataRepresentation> </dataIn> </dataIns> <dataOuts> <dataOut category=“" name=“MovieAvi“ saveto=“Movie. 5.

i. Figure-6(b) shows a simple ontology with semantically enriched Povray activity type Convert information. so the user specifies appropriate meanings representing exactly what an element is.3 Semantic Association and Meaning Specification The next step in the process is semantic enrichment of the intermediate ontology. During this interactive process all the information given by the user is stored in the lexicon database. AGWO is AGWL Ontology whereas AGWL[] is a set of input AGWL workflows or AGWL activities. The procedure uses two databases LDB and ODB for information storage and produces the Ontology. Thomas Fahringer 4. User can also create additional concepts if a concept cannot be associated to any of the existing parent concepts. similarly an element from a workflow can be data or an activity. data meanings and in case of an activity a meaningful name is given to the activity which describes the function performed by this activity. As discussed earlier there are two basic type of concepts. Two subprocedures normalize() and canonicalize() are invoked by the main program appearing on line 20 and 21 of the algorithm.4 Formation and Merger of Semantic / Structural Constructs Upon completion of this semantic association the intermediate and semantic representation of the ontology is combined to form the target ontology which describes the domain knowledge as represented by the workflow or activities used for creation of the ontology. 4. Both the former steps (parsing and structure creation) are carried out automatically except for the canonicalization process which may request user input if the lexicon database does not contain a matching record. In this step semantic information is acquired from the user to semantically enrich the existing concepts in the intermediate ontology. The process of merging the structure and semantic concepts is performed partially with the help of user for atomic activities and nested activities and other complex activity types. In case of data a name is given to the data element which specifies the contents of the element. This step requires much more user interaction in comparison to the steps mentioned earlier. i. In this phase every concept from the intermediate ontology is presented to user and the user is asked to classify the concept by giving the meaningful concept name and by associating it with the appropriate parent. whereas merging of structure and semantic concepts for data elements is performed automatically. the objective of these functions calls are . So for further workflow components if a user has to specify meanings for an activity he can choose from among the existing meanings from the lexicon. 5 Algorithm The algorithm1 provides the pseudo-code representation of the ontology synthesis process. Data and Functions.e. The procedure synthesizeOntology() takes two parameters AGWO and AGWL[].8 Muhammad Junaid.e.

The makeConcept() function requests user input and converts the OWL structures into meaningful ontological concepts for the domain. The OBO framework load concepts from existing ontologies only which can act as potential parents for the newly discovered concepts. This makes the target ontology to be applicable in a broader perspective rather than sticking to defined set of pre-known concepts. concept extraction and semantic enrichment of these concepts. This reduces the . getWFoutports() etc. As a acknowledgement to their importance and widely acclaimed reputation. are the information extraction functions. 6 7 Experiments Related work Use of ontologies to leverage knowledge in the field of semantic web is well known. Use of ontologies in the context of automatic workflow composition has driven the scientists in this domain towards the development of automatic ontology synthesis techniques. Once the intermediate Ontology is created each one of the OWL structures is enriched with semantic information using makeConcept() function calls. The functions OWL Structure() perform the task of creating OWL structure without any semantic information. creating definitions for these terms using online information source and then creating relationship between the selected terms. which now represent the ontology concepts. in contrast to the approach of predicting a relationship. getActivities(). A similar approach has been used to generate ontologies in the [22] OBO Edit tool. Several ontology synthesis approaches have been adopted to automate the process of ontology synthesis. These three steps are extracting the terms or keywords for ontologies from the source text. our system automatically establishes relations based on the occurrences of such concepts in the reference ontology AGWO. Ontologies have widely been used in many scientific domains and have given promising results. In addition to this. we extend this functionality by providing the user a chance to create new concepts on-the-fly if no suitable parent concepts have been found in the database. In our approach. The resulting conceptual representation of these OWL structures is then combined together and added to the target ontology O using the add Concept function call. Our approach of ontology synthesis is based on a three step process of AGWL parsing and analysis.Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows 9 pretty straight forward and have already been explained in the section-4. The other functions like getWFInports(). The process of ontology creation in OBO DOG4DAG plugin also uses a three step process for ontology creation. besides the use of lexicon database for searching existing concepts. automatic ontology synthesis has become a focus of many researchers. The function createIntermediateOntology() creates the intermediate Ontology representation using these OWL structures as placeholders for actual concepts.1. The OWL encoded structures are used as placeholders in the intermediate ontology. and their functionality is mentioned in the comment line appearing next to function call.

Co ) end foreach ( Ca t in ODB ) /* get AT Canonical data from DB */ do atOW L ← OW L structure(Cat ) /* OWL code for AT */ aiOW L ← OW L structure(Ci ) /* OWL code for Inport */ /* OWL code for Outport */ aoOW L ← OW L structure(Co ) storeInDB(atOW L . aoOW L ) /* Create intermediate Ontology */ foreach (W Fport in ODB) /* get WF ports from the DB */ do W FOW L ← OW L structure(W Fport ) IO ← addT oIO(W FOW L ) end /* add semantic meanings to the concepts with the help of concept vocabulary from LDB and by the input from the user */ C atOW L ← make Concept(IO atOW L ) ← user C aiOW L ← make Concept(IO aiOW L ) ← user C aoOW L ← make Concept(IO aoOW L ) ← user C wfOW L ← make Concept(IO W FOW L ) ← user LDB ← C atOW L . C W FOW L O ← CreateOntologyF ile(Domain. Na . Ni . C aiOW L . Ci . C wfOW L ) /* add concepts to ontology */ return OntologyF ileO end 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 . C aoOW L . /* Database for information Storage */ LDB /* Lexicon Database */ Result: O /* target Ontology for the Given AGWL workflows/ activities */ begin if (isSetof W F (AGW L[ ])) /* Input is a set of workflow */ then foreach (agwl in AGW L[ ] ) do W Fin [ ] ← getW F Inports(agwl) /* Workflow inports */ AT [ ] ← getActivities(agwl) /* get activity types */ W Fout [ ] ← getW F Outports(agwl) /* Workflow outports */ ODB ← W Fin /* put inPorts in the database */ ODB ← W Fout /* put outPorts in the database */ end end else AT [ ] ← AGW L[ ] /* Input is a set of activities */ end DomainW F ← user foreach ( at in AT [ ] ) /* process all activity types */ do Aa [ ] ← getAttr(at) /* get activity attributes */ Ai [ ] ← getActIP (at) /* get activity Inports */ Ao [ ] ← getActOP (at) /* get activity Outports */ Na . Ao ) ← user. Ai . Ci . Co ← Canonicalize(at. LDB /* Canonicalize adds missing information */ storeInDB(Ca . Aa .AGWL[]) Input: AGW O. Thomas Fahringer Algorithm 1: Ontology Synthesizer synthesizeOntology(AGWO.10 Muhammad Junaid. /* Abstract Grid Workflow Ontology */ AGW L[ ] /* AGWL based workflows or workflow activities */ Data: ODB. C aiOW L .owl) /* Create ontology */ O ← add Concept(C atOW L . aoOW L /* store OWL Concepts */ end IO ← CreateIntermediateOntology(aiOW L . LDB /* Normalize adds missing attributes */ Ca . Ni . aiOW L . atOW L . C aoOW L . No ) ← user. No ← N ormalize(at.

2003. This approach introduces two additional steps of validation and evolution. The limitation of the approach is the absence of relation building between different types of concepts. [27] and [21]. The quality of alignment / matching based approach becomes limited and dependent upon the availability and richness of the existing ontologies which is not the case in our where an ontology can be generated from scratch without the help of any existing domain ontologies. For example [23] a comprehensive study of the classification of concepts and matching and alignment techniques is presented. Blueprint for a New Computing Infrastructure. There are numerous other attempts on the process of ontology synthesis like [26]. but these researchers have addressed one or the other aspects of the whole ontology synthesis scenario. References 1. 2. To improve the automation process and to move the burden from the user side to the system side annotation are to be introduced which will be added to the workflow design making it more semantically enriched. The ontologies synthesized using the system has been put to test and domain workflows have successfully been created using the ontologies. The three major steps which actually create the ontology are much similar to the three steps proposed in our approach towards ontology synthesis.Semi-Automatic Composition of Ontologies for ASKANCE Grid Workflows 11 chance of having wrong relations between two concepts because the AGWO is proven to be correctly defined for all AGWL related concepts. At this point the user has to provide a fairly large amount of semantic information. Moreover in [24] a tutorial is presented which helps understanding the ontology learning process from raw text input. In [21] we see a detailed analysis of the ontology alignment techniques. But the internal functionality of the analysis and generation phases of this system relies on existing ontologies. analysis and generation. it matches/ align the newly found concepts to existing concepts in the reference ontologies and makes the decision about the use of these concept classes. edition. This approach is expected to help the system extracting the semantic information automatically by requesting much lesser user interaction. The Grid. C. a. and Kesselman. I.: Blueprint for a New Computing Infrastructure (Elsevier Series in Grid Computing). resulting in a lot of user interaction. it is based on the idea of mapping XSD file entities to OWL concepts and classes. Another attempt on automatic ontology synthesis presented by [18] performs the ontology synthesis operation using the existing ontologies for similar input information. One interesting approach much similar to our approach is XML to OWL transformation [25]. Morgan Kaufmann. 8 Conclusion and Future Work The paper proposed a semi-automated mechanism for synthesizing domain ontologies for Grid workflows created using AGWL. . Again the process of synthesis is based on three steps of concepts extraction. Foster. [23].

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