Provenance in databases tutorial outline semantic scholar. Curated databases in bioinformatics and other disciplines are the result of a great deal of manual annotation, correc tion and transfer of data from other sources. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its integrity and scienti. Most reference works that one traditionally found on the reference shelves of libraries dictionaries, encyclopedias, gazetteers etc. Riain, edward curry digital enterprise research institute deri national university of ireland, galway galway, ireland abstractprovenance is a cornerstone element in the process of enabling quality assessment for the web of data. Digitalisation of virus knowledge sib, swissprot group viral complete genomes database ontologies go human virus metadata viral diagnostic by ngs reference proteomes. Combining provenance and security policies in a webbased. Details about each type of resource are provided below. In particular, the metadata carried by our technique can use the prov data model already developed by the w3c provenance interchange working group 2. The ease with whic h one can cop y and transform data on the w eb, has made it increasingly di cult to determine the origins of a piece of data.
In acm sigmod international conference on management of data, 2006. Provenance tracking has been studied in a variety of settings, particularly database management systems. This briefing presents the need for the curation, including the semantic annotation, of the processes that filter or transform data as part of a bioinformatics analysis and the vital part this will play in data integration. The current approach to managing provenance in curated data bases is for the database designer to augment the schema with. Combining provenance and security policies in a webbased document management system brian j. A provenance model for manually curated data springerlink. Dynamic provenance for sparql updates using named graphs. In curated databases, data elements are often copied. Introduction curated databases, which consist of data extracted from original sources, printed articles, and other databases, are a valuable source of data for scientists. Provenance queries essentially query the behavior of programs, and it was a signi.
Provenance as dependency analysis mathematical structures. Proceedings of the 2008 symposium on principles of database systems pods 2008 112. This is for curated databases which are used for archival purposes. The topics of annotation, provenance, and\ud citation are central, because curated databases are heavily\ud crossreferenced with, and include data from, other databases, and much of the work of a curator is annotating existing data. We describe an approach in which we track the users actions while browsing source databases and copy ing data into a curated database, in order to record the. Most curators believe that additional record keeping is needed to record where the data comes from its provenance. Some sources unreliable and some curators too curated db db db journal abstract curators hi, everybody. Since it is now easy to publish databases on the web, there has been an explosion in the number of new curated databases used in scienti. In this paper we motivate and present a simple model of provenance for manually curated databases and discuss ongoing and future work.
Provenance management in curated databases abstract curated databases in bioinformatics and other disciplines are the result of a great deal of manual annotation, correction and transfer of data from other sources. Most reference works that one traditionally found on the reference shelves of libraries. Provenance information is used in areas like curated databases, data warehouses and escience to trace errors, es. In this paper we study the problem of tracking provenance of scientific data in. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its integrity and scienti c value. On explicit provenance management in rdfs graphs p. Data provenance support in relational databases for stored. Provenance index databases getty research institute. We describe how provenance has been used in manually curated databases.
The perm provenance management system in action boris glavic database technology research group. Also, curated databases are updated in place with local copies of source data rather than constructed as views of source databases. Curated database definition of curated database by. April 15, 2008 principles of provenance 14 curated databases created by manual effort of scientists curators copy from papers, other dbs which often copy from each other. We investigate the problem of secure and efficient provenance transmission and pr ocessing for sensor networks, and we use provenance to detect packet loss attacks staged by malicious sensor nodes. Curated databases are databases that are populated and updated with a great deal of human effort. In acm pods symposium on principles of database systems, 2007.
Available formats pdf please select a format to send. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its. Jun 27, 2006 provenance management in curated databases peter buneman university of edinburgh edinburgh, uk adriane p. Provenance management in curated databases edinburgh. On the importance of curated databases sib swiss institute of bioinformatics geneva, switzerland. There has been some examination 2, 8, 16, 22, 24 of provenance issues in data warehouses. Research into data provenance has been active for al.
Capturing interactive data transformation operations using. The work discusses key software engineering aspects for provenance capture and consumption and analyzes the suitability of the framework under the deployment of a realworld scenario. Lncs 4145 a provenance model for manually curated data. Though information provenance has been recognized as a hard problem in computing science british computing society, 2004, many fundamental research issues in provenance have yet to be. Pdf metadata and provenance management bruce berriman and. Biological database curation biological databases on a number. Development of a data management architecture for the. Combining le system metadata with content analysis. Current database technology provides little assistance for managing provenance. Provenance management approach in curated databases in scienti. Since it is now easy to publish databases on the web. Provenance information concerning the creation, attribution, or version history of such data is crucial for. Curated databases in bioinformatics and other disciplines are the result of a great deal of manual annotation, correction and transfer of data from other sources.
An architecture for provenance management in databases is also described by 1. Provenance management in curated databases citeseerx. Provenance management in curated databases peter buneman university of edinburgh edinburgh, uk adriane p. Integration is a central activity in bioinformatics. References 1 peter buneman, adriane chapman, and james cheney. Curated bibliography as bib source file xg provenance wiki. Any database developed, edited or pared by one or more persons with domain expertise who add value to the final product. Data provenance in curated databases is discussed in. Curated databases present a number of challenges for database research. Provenance, from the french word provenir meaning to come from, describes the lineage of an entity. Many curated databases are constructed by scientists integrating various. Provenance management for linked data springerlink. Incorporating provenance in database systems by adriane p. Additional databases provides access to the collectors files, payments to artists, and public collections.
A lightweight secure scheme for detecting provenance. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. Curation, annotation, provenance, archiving, citation. The purpose of this paper is to describe the challenges involved in managing provenance for manually curated databases, and to summarize our. Curated database definition of curated database by medical. Recording and managing the provenance of data is of paramount importance, as it allows supporting trust mechanisms, access control and privacy policies, digital rights management, quality management and assessment, in addition to reputability, reliability and accountability of data sources.
Provenance arises in a number of contex ts, including curated databases, work. Provenance management in databases under schema evolution. For example, at the 2006 acm sigmod conference in the paper, provenance management in curated databases, peter buneman described the two types of provenance as workflow and data flow. May 14, 2016 tracking the provenance of information published on the web is of crucial importance for effectively supporting trustworthiness, accountability and repeatability in the web of data. Citeseerx provenance management in curated databases. Provenance management in curated databases proceedings of.
Capturing interactive data transformation operations using provenance work ows tope omitola1, andr e freitas 2, edward curry, s ean oriain, nicholas gibbins 1, and nigel shadbolt 1 web and internet science wais research group school of electronics and computer science university of. Provenance algebra and materialized viewbased provenance. Such manual bookkeeping is time consuming, errorprone and often incomplete. The topics of annotation, provenance, and citation are central, because curated databases are heavily crossreferenced with, and include data from, other databases, and much of the work of a curator is annotating existing data. Our approach, called psp, leverages the xml capabilities of sql. Provenance is critical information in escience to accurately interpret scientific results. W e use the term data pr ovenanc e to refer to the pro cess of tracing and. A primer on database provenance computer science illinois.
Provenance management in curated databases acm digital library. We define the provenance management problem for manually curated data. A semantic web framework for generic provenance management andre freitas, arnaud legendre, sean o. Pdf curated databases are databases that are populated and updated with a great deal of human effort. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its integrity and scientific value. Like the paper reference works they have replaced, they usually. Although provenance modeling, collection, and querying have been studied extensively for effort flow and curated databases, provenance in. They have also shown that the space overhead for doing so is acceptable. Provenance management in curated databases p buneman, a chapman, j cheney proceedings of the 2006 acm sigmod international conference on management of, 2006. However, although many candidate definitions of provenance have been proposed, the mathematical or semantic foundations of data provenance have received comparatively little attention. Provenance management in curated databases proceedings of the. Capturing interactive data transformation operations the concept of interactive data transformation is strongly related to data curation, where human intervention in the data aggregation, cleaning, and transformation is increased. A di erent type of provenance, that has been studied for relational databases and work ows, models which part of a process query, workow.
Most of the data stored in a curated database is a result of manual transfor. Introduction provenance and security are intimately related. Some basic issues p eter buneman, sanjeev khanna and w angchiew t an univ ersit yof p ennsylv ania abstract. The getty provenance index gpi provides access to archival inventories, sales catalogs, and dealer stock books. The value of curated databases lies in the organization and the quality of the data they contain. In this paper, we focus on providing data provenance management in relational databases for stored procedures. An efficient and secure method for detecting provenance.
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