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This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type\u2019s identity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, through<jats:italic>in silico<\/jats:italic>experiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis - providing a new method for defining novel biomarkers and providing an opportunity for new biological insights.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-14-263","type":"journal-article","created":{"date-parts":[[2013,8,30]],"date-time":"2013-08-30T18:14:07Z","timestamp":1377886447000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Ontology based molecular signatures for immune cell types via gene expression analysis"],"prefix":"10.1186","volume":"14","author":[{"given":"Terrence F","family":"Meehan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole A","family":"Vasilevsky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher J","family":"Mungall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David S","family":"Dougall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa A","family":"Haendel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judith A","family":"Blake","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander D","family":"Diehl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,8,30]]},"reference":[{"key":"6056_CR1","unstructured":"Immunological Genome Project. http:\/\/www.immgen.org,"},{"issue":"6018","key":"6056_CR2","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1126\/science.1197891","volume":"331","author":"SD Kahn","year":"2011","unstructured":"Kahn SD: On the future of genomic data. 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