Dizeez @ Future of Genetic Medicine V

Recently, we have added several new features to the Dizeez game (previously described here). In particular, the game now allows players to select a specific area of biology (for example, by disease or protein family) that best matches their expertise. Also, a “recap” functionality has been added at the end of the game, that shows supporting evidence (in Gene Wiki and PubMed GeneRIFs) for each gene-disease association played. Users can review the game log and even suggest new evidences.

To ‘live test’ the new features, we brought the game to The Future of Genomic Medicine V conference held March 1 to 2 2012  at the Scripps Institution of Oceanography in La Jolla. In two days, we had 189 games played to completion by over 60 unique individuals – 22 registered users played 143 out of 189 games. Overall, players provided 2026 guesses across 1791 unique gene-disease assertions.

Notably, almost half of our registered users provided ten or more guesses with overall accuracy higher than 30%. Perhaps not surprisingly, overall accuracy seems to correlate with the amount of time spent on each association (Ben would agree here) – so throwing random guesses at it might be not a good strategy for players. Equally importantly, this observation reveals a useful filtering metric for our downstream data mining.

As before, we mined the game logs for novel gene annotations, i.e. gene-disease links well established in the literature, but not yet mirrored as structured annotations. Among the gene-disease assertions provided most often by game players, we had 13 associations occurring 4 or more times. Since all of these associations were previously known via Gene Wiki and/or OMIM, they just provided a positive control.

After removing all gene-disease links already annotated in Gene Wiki/OMIM/PharmGKB, there were 18 assertions  that were provided by players two or more times. We quickly ranked them using the Normalized Medline Distance (NMD) as a proxy for gene and disease co-occurrence in Pubmed articles.  Results could easily be verified by a quick literature search. The top five associations are summarized here:

 

Gene Symbol Disease name Disease Ontology ID NMD PubMed support
ABCB5 acute myeloid leukemia DOID:9119 0.75 2204413819477512, 19394083
HOXB7 leukemia DOID:1059 0.83 2118393920672360
SULF1 carcinoma DOID:305 0.83 2110478521851062
ALPP retinoblastoma DOID:768 0.87 15172750
FOXM1 Melanoma DOID:1909 0.89 2228016222094256

Interestingly, almost all the publications listed above are very recent  (2010-12).

Once again, the game proved useful in identifying novel gene-disease annotations in a short period of time based on the voluntary contributions of a self-selected group of players.

 


Leave a Reply

Your email address will not be published. Required fields are marked *

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>