Building an allergens ontology and maintaining it using machine learning techniques.

Alexandros G Valarakos; Vangelis Karkaletsis; Dimitra Alexopoulou; Elsa Papadimitriou; Constantine D Spyropoulos; George Vouros

doi:10.1016/j.compbiomed.2005.09.007

PubMed · 16253221

Building an allergens ontology and maintaining it using machine learning techniques.

Alexandros G Valarakos·Vangelis Karkaletsis·Dimitra Alexopoulou·Elsa Papadimitriou·Constantine D Spyropoulos·George Vouros

View original source ↗Export metadata ↓

Abstract

Ontologies are widely used for formalizing and organizing the knowledge of a particular domain of interest. This facilitates knowledge sharing and re-use by both people and systems. Ontologies are becoming increasingly important in the biomedical domain since they enable knowledge sharing in a formal, homogeneous and unambiguous way. Knowledge in a rapidly growing field such as biomedicine is usually evolving and therefore an ontology maintenance process is required to keep ontological knowledge up-to-date. This work presents our methodology for building a formally defined ontology, maintaining it exploiting machine learning techniques and domain specific corpora, and evaluating it using a well-defined experimental setting. The application of this methodology in the allergen domain is then discussed in detail presenting the ontology built, the specific techniques used and the evaluation settings.

Explore related subjects

Allergens Artificial Intelligence Databases as Topic Humans Information Management Knowledge Bases PubMed Software Terminology as Topic Journal Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Alexandros G Valarakos, Vangelis Karkaletsis, Dimitra Alexopoulou, Elsa Papadimitriou, Constantine D Spyropoulos, George Vouros. 2005-10-25. Building an allergens ontology and maintaining it using machine learning techniques.. https://doi.org/10.1016/j.compbiomed.2005.09.007

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Towards abolition of immunogenic structures in insect cells: characterization of a honey-bee (Apis mellifera) multi-gene family reveals both an allergy-related core alpha1,3-fucosyltransferase and the first insect Lewis-histo-blood-group-related antigen-synthesizing enzyme.

Glycoproteins from honey-bee (Apis mellifera), such as phospholipase A2 and hyaluronidase, are well-known major bee-venom allergens. They carry N-linked oligosaccharide structures with two types of alpha1,3-fucosylation: the modification by alpha1,3-fucose of the innermost core GlcNAc, which constitutes an epitope recognized by IgE from some bee-venom-allergic patients, and an antennal Lewis-like GalNAcbeta1,4(Fucalpha1,3)GlcNAc moiety. We now report the cloning and expression of two cDNAs encoding the relevant active alpha1,3-FucTs (alpha1,3-fucosyltransferases). The first sequence, closest to that of fruitfly (Drosophila melanogaster) FucTA, was found to be a core alpha1,3-FucT (EC 2.4.1.214), as judged by several enzyme and biochemical assays. The second cDNA encoded an enzyme, most related to Drosophila FucTC, that was shown to be capable of generating the Le(x) [Galbeta1-4(Fucalpha1-3)GlcNAc] epitope in vitro and is the first Lewis-type alpha1,3-FucT (EC 2.4.1.152) to be described in insects. The transcription levels of these two genes in various tissues were examined: FucTA was found to be predominantly expressed in the brain tissue and venom glands, whereas FucTC transcripts were detected at highest levels in venom and hypopharyngeal glands. Very low expression of a third homologue of unknown function, FucTB, was also observed in various tissues. The characterization of these honey-bee gene products not only accounts for the observed alpha1,3-fucosylation of bee-venom glycoproteins, but is expected to aid the identification and subsequent down-regulation of the FucTs in insect cell lines of biotechnological importance.

Allergens↗

PubMed2007

Transglutaminase polymerization of peanut proteins.

Transglutaminase promotes protein cross-linking reactions through an acyl transferase mechanism involving protein-bound glutaminyl residues and primary amines including the epsilon-amino group of lysine residues in soy, myosin, gluten, oat globulin, casein, and whey. Herein, we present a first report of exogenous transglutaminase catalysis of several peanut protein fractions, including purified Ara h 1. In most cases, SDS-PAGE banding patterns revealed the formation of high molecular weight polymers while catalysis of Ara h 1 resulted in distinct dimer formation. Cross-linking effects were accomplished in the presence and absence of the reducing reagent, dithiothreitol. Ortho-phthaldialdehyde assays, used to quantify the degree of polymerization, indicated approximately 21% and approximately 30% coupling over a similar time interval, using either cold hexane extracted peanut protein fractions or lightly roasted flour dispersions, respectively. Rheological measurements established that transglutaminase-modified peanut extracts exhibited lowered viscosity readings compared to nontreated dispersions. Peanut protein polymers and glycoprotein conjugates, created by covalent linkage between protein substrates and monosaccharide amino sugars, exhibited similar IgE binding activity, compared to control solutions. These results suggested that potential allergic responses were not enhanced after enzymatic modification. Ultimately, these approaches may provide novel peanut-based food ingredients with unique functional characteristics for expanded applications within the world marketplace.

Allergens↗

PubMed2007

A group-1 grass pollen allergen influences the outcome of pollen competition in maize.

Worldwide, 400 million people suffer from hay fever and seasonal asthma. The major causative agents of these allergies are pollen specific proteins called the group-1 grass pollen allergens. Although details of their antigenicity have been studied for 40 years with an eye towards immunotherapy, their function in the plant has drawn scant attention. Zea m 1 constitutes a class of abundant grass pollen allergens coded for by several genes that loosen the walls of grass cells, including the maize stigma and style. We have examined the impact of a transposon insertion into one of these genes (EXPB1, the most abundant isoform of Zea m 1) on the production of Zea m 1 protein, pollen viability, and pollen tube growth, both in vitro and in vivo. We also examined the effect of the insertional mutation on the competitive ability of the pollen by experimentally varying the sizes of the pollen load deposited onto stigmas using pollen from heterozygous plants and then screening the progeny for the presence of the transposon using PCR. We found that the insertional mutation reduced the levels of Zea m 1 in maize pollen, but had no effect on pollen viability, in vitro pollen tube growth or the proportion of progeny sired when small pollen loads are deposited onto stigmas. However, when large pollen loads are deposited onto the stigmas, the transposon mutation is vastly underrepresented in the progeny, indicating that this major pollen allergen has a large effect on pollen tube growth rates in vivo, and plays an important role in determining the outcome of the pollen-pollen competition for access to the ovules. We propose that the extraordinary abundance (4% of the extractable protein in maize pollen) of this major pollen allergen is the result of selection for a trait that functions primarily in providing differential access to ovules.

Allergens↗