Coinciding with the onset of S3DB conception we made the argument for moving beyond XML in integrative bioinformatics was detailed in a report in 2005.
Wang X, R Gorlitsky, and JS Almeida (2005) From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, Sep;23(9):1099-103 [PMID:16151403].
The motivation for developing S3DB and the introduction to the idea of separating domain of discourse from its instantiation by using rules as diadic predicates was proposed the following year:
Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071. [PMID:16964209].