How orthogonal are the OBO Foundry ontologies?

<p>Abstract</p> <p>Background</p> <p>Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to establish a set of principles for ontology development with the eventual goal of creating a set of interoperable reference ontologies in the domain of biomedicine. One of the key requirements to achieve this goal is to ensure that ontology developers reuse term definitions that others have already created rather than create their own definitions, thereby making the ontologies orthogonal.</p> <p>Methods</p> <p>We used a simple lexical algorithm to analyze the extent to which the set of OBO Foundry candidate ontologies identified from September 2009 to September 2010 conforms to this vision. Specifically, we analyzed (1) the level of explicit term reuse in this set of ontologies, (2) the level of overlap, where two ontologies define similar terms independently, and (3) how the levels of reuse and overlap changed during the course of this year.</p> <p>Results</p> <p>We found that 30% of the ontologies reuse terms from other Foundry candidates and 96% of the candidate ontologies contain terms that overlap with terms from the other ontologies. We found that while term reuse increased among the ontologies between September 2009 and September 2010, the level of overlap among the ontologies remained relatively constant. Additionally, we analyzed the six ontologies announced as OBO Foundry members on March 5, 2010, and identified that the level of overlap was extremely low, but, notably, so was the level of term reuse.</p> <p>Conclusions</p> <p>We have created a prototype web application that allows OBO Foundry ontology developers to see which classes from their ontologies overlap with classes from other ontologies in the OBO Foundry (<url>http://obomap.bioontology.org</url>). From our analysis, we conclude that while the OBO Foundry has made significant progress toward orthogonality during the period of this study through increased adoption of explicit term reuse, a large amount of overlap remains among these ontologies. Furthermore, the characteristics of the identified overlap, such as the terms it comprises and its distribution among the ontologies, indicate that the achieving orthogonality will be exceptionally difficult, if not impossible.</p

Effects of various levels of organic acids and of virginiamycin on performance, blood parameters, immunoglobulins and microbial population of broiler chicks

This experiment was conducted to investigate the effects of various levels of organic acids and virginiamycin on performance, blood parameters, immunoglobulin and microbial population of broiler chickens. This trial was conducted in a completely randomized design using five treatments and four replicates. The dietary treatments included a control diet without additives, diets containing 0.05%, 0.10% and 0.15% mixtures of organic acids, and a diet containing virginiamycin as an antibiotic. Based on the results, there was no significant effect of the experimental diets on feed intake of the broilers during the starter period. However, at the end of the grower period and throughout the rearing period, feed intake was significantly improved by experimental dietary treatments. Moreover, diets including organic acids enhanced the microbial population of broiler gut. Thus, the current findings support the conclusion that organic acids improve productive traits and health status in broiler chickens.Keywords: Broiler, growth, haematology, gu

Comparison of effects of age and sex on serum protein electrophoretic pattern in one-humped camels (Camelus dromedarius) in Semnan, Iran

Abstract The aim of this study was to evaluate the influence of age and sex on the concentration of total serum protein measured by the biuret method and protein fractions determined using cellulose acetate electrophoresis in apparently healthy camels (Camelus dromedarius). Blood samples were collected from 21 camels (12 males and 9 females). The camels were further divided into two groups: 12 young camels at the age of 3 months to 2 years and 9 adult camels at the age of 3-15 years. Cellulose acetate electrophoresis of serum proteins identified five protein fractions in adult camels as young camels, these five protein fractions include albumin, α1 and α2, β and γ-globulins. In adult camels, serum levels (g/l) of total protein, albumin, α1-globulins, α2-globulins, β-globulins and γ-globulins were 80.9±3.10, 42.9±3.10, 1.3±0.22, 2.2±0.30, 11.8±0.30 and 22.6±0.20, respectively. However, in young camels, these levels (g/l) were 66.8±2.90, 40.2±2.40, 1.0±0.14, 2.6±0.30, 10.6±0.80 and 12.3±1.20, respectively. The albumin/globulin (A/G) ratio was 2.08±0.28 in adult camels and 3.77±0.53 in young ones. The mean serum concentrations of total protein and γ-globulins were significantly (P&lt;0.05) higher and the A/G ratio was significantly lower in adult camels compared to young camels. The mean concentrations of γ-globulins were significantly higher and the A/G ratio was significantly (P&lt;0.05) lower in females compared to male camels. The results of the present study indicate a significant effect of age and sex on the concentrations of some of the serum protein fractions in dromedary camels

3D Voronoi Tessellation for the Study of Mechanical Behavior of Rocks at Different Scales

Numerical investigation of crack damage development and microfracturing in brittle rocks is a widely studied topic, given the number of applications involved. In the framework of the Discrete Element Method (DEM) formulation, the grain-based distinct element model with random polygonal blocks can represent an alternative to the Bonded-Particle Model (BPM) based on particles. Recently, a new engine called Neper has been made available for generating 3D Voronoi grains. The aim of this study is to investigate the applicability of a Neper-based 3D Voronoi tessellation technique for the simulation of the mechanical macro response of rocks. Simulation of unconfined compression tests on synthetic specimens is conducted and a calibration procedure tested. The issue related to scale effects is also addressed, with an application to the case study of a deep geothermal reservoir

Altered translation of GATA1 in Diamond-Blackfan anemia

Ribosomal protein haploinsufficiency occurs in diverse human diseases including Diamond-Blackfan anemia (DBA),1,2 congenital asplenia,3 and T-cell leukemia.4 Yet how mutations in such ubiquitously expressed proteins result in cell-type and tissue specific defects remains a mystery.5 Here, we show that GATA1 mutations that reduce full-length protein levels of this critical hematopoietic transcription factor can cause DBA in rare instances. We show that ribosomal protein haploinsufficiency, the more common cause of DBA, can similarly reduce translation of GATA1 mRNA - a phenomenon that appears to result from this mRNA having a higher threshold for initiation of translation. In primary hematopoietic cells from patients with RPS19 mutations, a transcriptional signature of GATA1 target genes is globally and specifically reduced, confirming that the activity, but not the mRNA level, of GATA1 is reduced in DBA patients with ribosomal protein mutations. The defective hematopoiesis observed in DBA patients with ribosomal protein haploinsufficiency can be at least partially overcome by increasing GATA1 protein levels. Our results provide a paradigm by which selective defects in translation due to mutations in ubiquitous ribosomal proteins can result in human disease

Altered translation of GATA1 in Diamond-Blackfan anemia

Ribosomal protein haploinsufficiency occurs in diverse human diseases including Diamond-Blackfan anemia (DBA)[superscript 1, 2], congenital asplenia[superscript 3] and T cell leukemia[superscript 4]. Yet, how mutations in genes encoding ubiquitously expressed proteins such as these result in cell-type– and tissue-specific defects remains unknown[superscript 5]. Here, we identify mutations in GATA1, encoding the critical hematopoietic transcription factor GATA-binding protein-1, that reduce levels of full-length GATA1 protein and cause DBA in rare instances. We show that ribosomal protein haploinsufficiency, the more common cause of DBA, can lead to decreased GATA1 mRNA translation, possibly resulting from a higher threshold for initiation of translation of this mRNA in comparison with other mRNAs. In primary hematopoietic cells from patients with mutations in RPS19, encoding ribosomal protein S19, the amplitude of a transcriptional signature of GATA1 target genes was globally and specifically reduced, indicating that the activity, but not the mRNA level, of GATA1 is decreased in patients with DBA associated with mutations affecting ribosomal proteins. Moreover, the defective hematopoiesis observed in patients with DBA associated with ribosomal protein haploinsufficiency could be partially overcome by increasing GATA1 protein levels. Our results provide a paradigm by which selective defects in translation due to mutations affecting ubiquitous ribosomal proteins can result in human disease.National Institutes of Health (U.S.) (Grant P01 HL32262)National Institutes of Health (U.S.) (Grant U54 HG003067-09

Is it safe to withhold long-term anticoagulation therapy in patients with small pulmonary emboli diagnosed by SPECT scintigraphy?

Background: The need for anticoagulation therapy (AC) in patients with subsegmental pulmonary embolism (SSPE) diagnosed by computed tomography of the pulmonary arteries (CTPA) has been questioned, as these patients run low risk for recurrent venous thromboembolism (VTE) during 3 months of follow-up. Whether this applies also to patients with small PE diagnosed with pulmonary scintigraphy has not yet been evaluated, however. Methods: We therefore retrospectively evaluated 54 patients (mean age 62 ± 19 years, 36 [67 %] women) with small PE diagnosed by ventilation/perfusion singe photon emission computed tomography (V/P SPECT) who did not receive conventional long-term AC. Results: More than half of our patients (36[67 %]) received less than 48 h of AC, 11 (20 %) patients were treated for 2-14 days, and 7 (13 %) for 15-30 days. The majority (28 [52 %]) of our patients had a non-low simplified pulmonary emboli severity index (S-PESI), and 7 (13 %) had malignancy. D-dimer was negative in 18 (33 %), positive in 10 (19 %), and not analyzed in 28 (52 %) patients. Phlebography of the lower extremities had been performed with negative result in one patient. During 90 days of follow up no deaths or PE occurred. Seven patients were readmitted to hospital, whereof two (2/54 [4 %]) were diagnosed with deep venous thrombosis (DVT) necessitating AC therapy. Conclusion: In conclusion, withholding longterm AC therapy in patients with SSPE diagnosed by V/P SPECT resulted in 4 % risk for recurrence of VTE during 90 days of follow up, and can therefore currently not be recommended

Analysis of Term Reuse, Term Overlap and Extracted Mappings across AgroPortal Semantic Resources

International audienceOntologies in agronomy facilitate data integration, information exchange, search and query of agronomic data, and other knowledge-intensive tasks. We have developed AgroPortal, an open community-based repository of agronomy and related domains semantic resources. From a corpus of ontologies, terminologies, and thesauri taken from Agro-Portal, we have generated, extracted and analyzed more than 400,000 mappings between concepts based on: (i) reuse of the same URI between concepts in different resources-term reuse; (ii) lexical similarity of concept names and synonyms-term overlap; and (iii) declared map-pings properties between concepts-extracted mappings. We developed an interactive visualization of each mapping construct separately and combined which helps users identify most prominent ontologies, relevant thematic clusters, areas of a domain that are not well covered, and pertinent ontologies as background knowledge. By comparing the size of the semantic resources to the number of their mappings, we found that most of them have under 5% of their terms mapped. Our results show the need of an ontology alignment framework in AgroPortal where map-pings between semantic resources will be assembled, compared, analysed and automatically updated when semantic resources evolve