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The paper demonstrates the potential of semantic web and its enabling technologies in biological pathway data reasoning and integration.
Lollipops were constructed using the R package 'lollipops' (github.com/pbnjay/lollipops), with pathway data obtained from Cytoscape 3.2.1 (cytoscape.org) (Lopes et al. 2010).
BioPAX offers a standard, well defined representation of biological pathway data using OWL and it has been widely used in biological data integration [15, 31].
Currently, the tool uses only SignaLink pathway data.
The pathway data were adopted from the KEGG database (www.genome.ad.jp/kegg) with a few modifications.
Aβ42Arc and Aβ42art peptides were also detected in the secretory pathway (data not shown).
Our experiments also demonstrated that odorrananlectin had no effect on the lectin-activated complement pathway (data not shown).
Currently, signalog predictions for other genomes are limited mainly by the absence of proper signaling pathway data sources.
Since KEGG pathway data for modern human samples were available [23], we compared them to our ancient data.
FMS and AGCM analyzed metabolic pathway data.
The pathway data is from MetNetDB database.
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