Additional file 1: Table S1. of Comparison, alignment, and synchronization of cell line information between CLO and EFO

EFO cell lines drawn from external sources. In the initial step of the EFO-CLO comparison and alignment process, there are 428 and 20 EFO cell lines which were imported from Cell Line Ontology and 20 in BRENDA Tissue and Enzyme Source Ontology respectively. These 448 EFO cell lines were excluded from the entire mapping process. File is stored in Microsoft Excel spreadsheet (xlsx) format. (XLSX 47 kb

Additional file 2: Table S2. of Comparison, alignment, and synchronization of cell line information between CLO and EFO

Final EFO-CLO alignment result. The 874 EFO-CLO mapped cell lines aligned and merged into CLO (Tab. 1 in the excel file) and 344 EFO unique immortalized permanent cell lines added to CLO (Tab. 2 in the excel file). File is stored in Microsoft Excel spreadsheet (xlsx) format. (XLSX 54 kb

Additional file 1: of Reporting phenotypes in mouse models when considering body size as a potential confounder

Supplementary Methods. (DOCX 21 kb

Summary of statistical analysis testing if GBS and GBS-related AEs occur independently of vaccine type.

<p>Note: GBS-related muscle and neurological AEs studied here included musculoskeletal pain, paraesthesia, and muscular weakness.</p

LAIV-specific adverse events. 3,707 TIV-induced AE cases were reported.

<p>LAIV-specific adverse events. 3,707 TIV-induced AE cases were reported.</p

Comparison of reporting rates of GBS cases associated with TIV and LAIV administrations.

<p>The Y-axis is the number of GBS cases per 1000 case reports for either TIV or LAIV group. The comparison starts the year when both groups have available data in VAERS.</p

Diagram of AE counts grouped by related symptoms.

<p>Behavior/neurological system contains the most adverse events distributed in two groups of vaccines (40 adverse events; 25 in TIV, 15 in LAIV) but the clusters are significantly different in processes. TIV's behavior/neurological AEs are much more closely related to those of muscle and movement disorder while LAIV's behavior/neurological AEs cluster around pain in the head. Respiratory system AEs is listed as the most significant cluster in LAIV group with 16 AEs. Full listing can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049941#pone-0049941-t001" target="_blank">Table 1</a> (TIV) and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049941#pone-0049941-t002" target="_blank">Table 2</a> (LAIV).</p

Comparison of case report distributions of GBS and GBS-related adverse events associated with TIV and LAIV based on age using the data from 2003.

<p>(A) In TIV, all but one selected AEs (paraesthesia) followed the expected age range of the populations who were more at risk of GBS (young children and the elderly). (B) In LAIV recipients, age distribution is scattered across all age ranges.</p

Workflow of the CODAE integrative AE bioinformatics analysis.

<p>A generalized version of CODAE for detection of significant AE terms for one vaccine or one group of vaccines is outlined in (A). See details in the text. An expanded CODAE solution to analyze and compare AEs associated with the two vaccination groups is shown in (B). VAERS records were retrieved based on the query criteria of 4 TIVs (Afluria, Fluarix, Fluvirin, and Fluzone) year 1990–2011 and 1 LAIV (FluMist) year 2003–2011. Parallel analyses of the Proportional Reporting Ratios and Chi-square significant test were performed on individual AEs to identify enriched and significant AEs in each group. Base level filtration of 0.2% of total number of reports was also applied to each AEs. AEs that were identified to have PRR > = 2, Chi-square > = 4, and number of reports > = 0.2% of total reports were then classified based on OAE hierarchical structure. Classification of AEs filtered out AEs that overlapped between the 2 groups.</p

Additional file 2: of Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

The list of journals mined for disease-phenotype assocations. (PDF 13 kb