Understanding the function of every protein is one major objective of bioinformatics. Currently, a large amount of information (e.g., sequence, structure and dynamics) is being produced by experiments and predictions that are associated with protein function. Integrating these diverse data about protein sequence, structure, dynamics and other protein features allows further exploration and establishment of the relationships between protein sequence, structure, dynamics and function, and thereby controlling the function of target proteins. However, information integration in protein data resources faces challenges at technology level for interfacing heterogeneous data formats and standards and at application level for semantic interpretation of dissimilar data and queries.
In this research, a semantic web services infrastructure, called Web Services for Protein data resources (WSP), for flexible and user-oriented integration of protein data resources, is proposed. This infrastructure includes a method for modeling protein web services, a service publication algorithm, an efficient service discovery (matching) algorithm, and an optimal service chaining algorithm. Rather than relying on syntactic matching, the matching algorithm discovers services based on their similarity to the requested service. Therefore, users can locate services that semantically match their data requirements even if they are syntactically distinctive. Furthermore, WSP supports a workflow-based approach for service integration. The chaining algorithm is used to select and chain services, based on the criteria of service accuracy and data interoperability. The algorithm generates a web services workflow which automatically integrates the results from individual services.
A number of experiments are conducted to evaluate the performance of the matching algorithm. The results reveal that the algorithm can discover services with reasonable performance. Also, a composite service, which integrates protein dynamics and conservation, is experimented using the WSP infrastructure.
| Identifer | oai:union.ndltd.org:PITT/oai:PITTETD:etd-11082006-011004 |
| Date | 30 January 2007 |
| Creators | Liu, Xiong |
| Contributors | John Vries, Vladimir Zadorozhny, Hassan Karimi, Ivet Bahar, Michael Lewis |
| Publisher | University of Pittsburgh |
| Source Sets | University of Pittsburgh |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.library.pitt.edu/ETD/available/etd-11082006-011004/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to University of Pittsburgh or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
Page generated in 0.0128 seconds