A Framework for Querying Pedigree Data

Elliott, Brendan; Akgul, S.F.; Özsoyoğlu, Z. Meral; Manilich, Elena

doi:10.1109/ssdbm.2006.8

Cited by 4 publications

(8 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A Pedigree Query Language (PQL) and evaluation of pedigree queries using NodeCodes is presented in [1]. However, this earlier work only described how NodeCodes can be used to evaluate some basic query predicates.…”

Section: Previous Workmentioning

confidence: 99%

“…We use a pedigree graph labeling system, NodeCodes, to expedite queries requiring graph traversal. NodeCodes is a graph encoding scheme originally proposed for encoding single source directed graphs [16,17], which was later adapted to encode pedigree graphs [1]. Using NodeCodes, each node of a graph is assigned labels which are sequences of integers and delimiters.…”

Section: Article In Pressmentioning

confidence: 99%

“…For a given node v, finding ancestors of v requires considering all the NodeCodes in NC(v), while any NodeCode from NC(v) is sufficient to find the descendants of v [1]. More specifically, let n v ¼ a 1 Ãa 2 Ãya mÀ1 Ãa m Ã be a NodeCode of a node v, where 2pm.…”

Section: Query Evaluationmentioning

confidence: 99%

“…Thus, there is a need for scalable data management techniques for storing and querying pedigree data due to both increasing volume of available pedigree data, and increasing use of pedigree data analysis in medical genetics for hereditary diseases. We have recently introduced a pedigree data model and a pedigree query language (PQL) having an XPath-like syntax for querying pedigree data [1]. PQL uses a compact and easy to understand syntax and enables the expression of complicated queries that traverse the pedigree structure.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Efficiently calculating inbreeding on large pedigrees databases

Elliott¹,

Cheng²,

Mayes³

et al. 2009

Information Systems

View full text Add to dashboard Cite

Section: Previous Workmentioning

confidence: 99%

Section: Article In Pressmentioning

confidence: 99%

Section: Query Evaluationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Efficiently calculating inbreeding on large pedigrees databases

Elliott¹,

Cheng²,

Mayes³

et al. 2009

Information Systems

View full text Add to dashboard Cite

“…NodeCodes is a graph encoding scheme originally proposed for encoding single source directed graphs 2,16 , which was later adapted to encode pedigree data 5 .…”

Section: Nodecodesmentioning

confidence: 99%

Scalable Computation of Kinship and Identity Coefficients on Large Pedigrees

Cheng

Elliott

Özsoyoğlu³

2008

Computational Systems Bioinformatics

View full text Add to dashboard Cite

With the rapidly expanding field of medical genetics and genetic counseling, genealogy information is becoming increasingly abundant. An important computation on pedigree data is the calculation of identity coefficients, which provide a complete description of the degree of relatedness of a pair of individuals. The areas of application of identity coefficients are numerous and diverse, from genetic counseling to disease tracking, and thus, the computation of identity coefficients merits special attention. However, the computation of identity coefficients is not done directly, but rather as the final step after computing a set of generalized kinship coefficients. In this paper, we first propose a novel Path-Counting Formula for calculating generalized kinship coefficients, which is motivated by Wright's path-counting method for computing the inbreeding coefficient for an individual. We then present an efficient and scalable scheme for calculating generalized kinship coefficients on large pedigrees using NodeCodes, a special encoding scheme for expediting the evaluation of queries on pedigree graph structures. We also perform experiments for evaluating the efficiency of our method, and compare it with the performance of the traditional recursive algorithm for three individuals. Experimental results demonstrate that the resulting scheme is more scalable and efficient than the traditional recursive methods for computing generalized kinship coefficients.

show abstract