Bioinformatics use case (expanded)

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Greetings!

An expanded use case for property graphs in bioinformatics.

The authors imported a database with 20,140 proteins and 2.2 million
interactions. There are confidence scores assigned to each interaction
between proteins.

One very common task in bioinformatics is to follow the interaction
paths (edges) between two proteins and to select the path that has the
highest confidence score. That is to say the edges in the graph are
scored and one task is to find the best scoring path between two or
more proteins.

The advantage of a property graph database is that it stores its edges
as directed pointers so traversal is much faster than the equivalent
relational database. The same holds true for a weighted graph, except
there a property graph can quickly find the weights for the various
paths and return the best path between two proteins.

A number of relationships are represented and weighted between
proteins by the String 9.1 database but the details are beyond the
scope of this use case.

Hope everyone is having a great day!

Patrick

- -- 
Patrick Durusau
patrick@durusau.net
Technical Advisory Board, OASIS (TAB)
Co-Chair, OpenDocument Format TC (OASIS)
Editor, OpenDocument Format TC, Project Editor ISO/IEC 26300
Former Chair, V1 - US TAG to JTC 1/SC 34
Convener, JTC 1/SC 34/WG 3 (Topic Maps)
Co-Editor, ISO 13250-5 (Topic Maps)

Another Word For It (blog): http://tm.durusau.net
Homepage: http://www.durusau.net
Twitter: patrickDurusau
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Received on Monday, 9 December 2013 20:20:54 UTC