Hindawi Publishing Corporation Autism Research and Treatment Volume 2011, Article ID 307152, 8 pages doi:10.1155/2011/307152 Research Article Developing a Deeper Understanding of Autism: Connecting Knowledge through Literature Mining Marta Macedoni-Luksˇicˇ,1 Ingrid Petricˇ,2 Bojan Cestnik,3 and Tanja Urbancˇicˇ2, 3 1 Department of Child Neurology, University Pediatric Hospital Ljubljana, Bohoriˇceva 20, 1000 Ljubljana, Slovenia 2 Centre for Systems and Information Technologies, University of Nova Gorica, Vipavska 13, 5000 Nova Gorica, Slovenia 3 Department of Knowledge Technologies, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia Correspondence should be addressed to Marta Macedoni-Luksˇicˇ, mmacedoni@gmail.com Received 9 February 2011; Accepted 13 April 2011 Academic Editor: Mohammad Ghaziuddin Copyright © 2011 Marta Macedoni-Luksˇicˇ et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In the ﬁeld of autism, an enormous increase in available information makes it very diﬃcult to connect fragments of knowledge into a more coherent picture. We present a literature mining method, RaJoLink, to search for matched themes in unrelated literature that may contribute to a better understanding of complex pathological conditions, such as autism. 214 full text articles on autism, published in PubMed, served as a source of data. Using ontology construction, we identiﬁed the main concepts of what is already known about autism. Then, the RaJoLink method, based on Swanson’s ABC model, was used to reveal potentially interesting, but not yet investigated, connections between diﬀerent concepts in research. Among the more interesting concepts identiﬁed with RaJoLink in our study were calcineurin and NF-kappaB. Both terms can be linked to neuro-immune abnormalities in the brain of patients with autism. Further research is needed to provide stronger evidence about calcineurin and NF-kappaB involvement in autism. However, the analysis presented conﬁrms that this method could support experts on their way towards discovering hidden relationships and towards a better understanding of the disorder. 1. Introduction Autism spectrum disorders (ASDs) are currently one of the leading causes of developmental disability with approxi- mately 1% children aﬀected [1]. Etiologically, many diﬀerent factors are involved. Among known genetic conditions that are associated with ASD in higher percentage compared with general population are fragile X syndrome (FXS), tuberous sclerosis, fragile premutation, phenylketonuria, 15q11-13 duplication, 16p11.2 duplication, and mutations in NGLN3, 4, phosphatase and tensin homolog (PTEN), and SHANK3, to name some of them. Better knowledge about the neurobiological basis of these disorders has led to many commonalities across them regarding underpinnings mechanisms and, most importantly, to potential targeted treatments [2–4]. One of recently most intensively studied area of gene- environmental interaction possibly involved in development of ASD is suspected immunological factors and processes. These factors include prenatal, genetic, and postnatal ﬁnd- ings, as well as the discovery of a dysfunctional chronic proinﬂammatory state in brain tissue and cerebrospinal ﬂuid in subsets of autistic patients [5]. Some genes, such as the tyrosine kinase receptor 7q31 metastasis receptor site (MET) gene, an immune-related gene aﬀecting tyrosine kinase that can be involved in innate immune dysfunction, can double the risk of autism [6]. Other immune abnormalities pos- sibly linked to autism are familial autoimmunity, maternal transfer of autoantibodies from the mother to child during pregnancy, production of antibodies against brain tissue in autistic patients, lower levels of normal immunoglobulins, and elevation of some cytokines [5]. Besides immune dys- functions there are other epigenetic mechanisms potentially linked to autism such as increased level of oxidative stress, mitochondrial dysfunction, and excitotoxicity [2, 3]. Despite these very exciting new discoveries in the ﬁeld of ASD, there are still a number of unique challenges including the heterogeneity of the disorder, the large number