Open PHACTS Lenses

Hi All,

You can find a demo of the use of lenses in the Open PHACTS project at
http://openphacts.cs.man.ac.uk:9092/QueryExpander/mapURI

The lenses allow you to change the operational equivalence that is applied between database records.

The default lens equates chemicals that claim to be the same chemical entity or share the same InChI, while genes and proteins are deemed as equivalent*. (This meets the main requirements of the Open PHACTS project.)

The Chemistry Parent/Child Relationships equate chemical compounds, e.g. a salt or charged compound, with their unsalted or unchanged counterpart. This will return a larger set of equivalent identifiers. Again genes and proteins are deemed as equivalent.

As a concrete example, you may want to try the ChemSpider identifier for fluvastatin
http://www.chemspider.com/Chemical-Structure.393587.html<http://www.chemspider.com/Chemical-Structure.393587>

Under the default lens you will get alternative forms of the URL in 6 datasets, but these are all the same (by InChI representation) chemical.
http://openphacts.cs.man.ac.uk:9092/QueryExpander/mapUri?Uri=http%3A%2F%2Fwww.chemspider.com%2FChemical-Structure.393587.html&lensUri=http%3A%2F%2Fno%2FBaseURI%2FSet%2F%2FLens%2FDefault&Pattern+Filter=&graph=&format=text%2Fhtml<http://openphacts.cs.man.ac.uk:9092/QueryExpander/mapUri?Uri=http://www.chemspider.com/Chemical-Structure.393587.html&lensUri=http://no/BaseURI/Set//Lens/Default&Pattern+Filter=&graph=&format=text/html>

Under the parent child lens you see that there are two chemical compounds returned, fluvastatin and its non-sterochemistry counterpart.
http://openphacts.cs.man.ac.uk:9092/QueryExpander/mapUri?Uri=http%3A%2F%2Fwww.chemspider.com%2FChemical-Structure.393587.html&lensUri=http%3A%2F%2Fno%2FBaseURI%2FSet%2F%2FLens%2FChemistryParentChild&Pattern+Filter=&graph=&format=text%2Fhtml<http://openphacts.cs.man.ac.uk:9092/QueryExpander/mapUri?Uri=http://www.chemspider.com/Chemical-Structure.393587.html&lensUri=http://no/BaseURI/Set//Lens/ChemistryParentChild&Pattern+Filter=&graph=&format=text/html>

[1] is a paper outlining the vision of lenses. In [2,3] we outline the query performance and rules for controlling the co-reference computation.

Feel free to ask if you have any questions

Alasdair

*We plan to add a lens where you can keep genes and proteins distinct.

[1] http://ceur-ws.org/Vol-951/paper5.pdf
[2] http://ceur-ws.org/Vol-1034/BrenninkmeijerEtAl_COLD2013.pdf
[3] https://www.researchgate.net/publication/259243588_Computing_Identity_Co-Reference_Across_Drug_Discovery_Datasets

Alasdair J G Gray
Lecturer in Computer Science, Heriot-Watt University, UK.
Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Telephone: +44 131 451 3429
Twitter: @gray_alasdair
Arrange a Meeting: http://doodle.com/agray

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