Word-sense disambiguation in biomedical ontologies

With the ever increase in biomedical literature, text-mining has emerged as an important technology to support bio-curation and search. Word sense disambiguation (WSD), the correct identification of terms in text in the light of ambiguity, is an important problem in text-mining. Since the late 1940s many approaches based on supervised (decision trees, naive Bayes, neural networks, support vector machines) and unsupervised machine learning (context-clustering, word-clustering, co-occurrence graphs) have been developed. Knowledge-based methods that make use of the WordNet computational lexicon have also been developed. But only few make use of ontologies, i.e. hierarchical controlled vocabularies, to solve the problem and none exploit inference over ontologies and the use of metadata from publications. This thesis addresses the WSD problem in biomedical ontologies by suggesting different approaches for word sense disambiguation that use ontologies and metadata. The "Closest Sense" method assumes that the ontology defines multiple senses of the term; it computes the shortest path of co-occurring terms in the document to one of these senses. The "Term Cooc" method defines a log-odds ratio for co-occurring terms including inferred co-occurrences. The "MetaData" approach trains a classifier on metadata; it does not require any ontology, but requires training data, which the other methods do not. These approaches are compared to each other when applied to a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The MetaData approach performs best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The Term Cooc approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The Closest Sense approach achieves on average 80% success rate. Furthermore, the thesis showcases applications ranging from ontology design to semantic search where WSD is important

Ταξική αποστασία στους Ντιντιέ Εριμπόν και Εντουάρ Λουί, σχεδίασμα για μια προσέγγιση της διαταξικότητας.

Η παρούσα εργασία προσεγγίζει το θέμα της «ταξικής αποστασίας» ή της κατάστασης των «διαταξικών», μέσω της ανάγνωσης και της αξιοποίησης της θεωρίας των έξεων και της «αυτοκοινωνιοανάλυσης» του Πιέρ Μπουρντιέ, την μελέτη του de Gaulezac περι ταξικής νεύρωσης και τις αυτοβιογραφικές αφηγήσεις των συγγραφέων Ντιντιέ Εριμπόν και Εντουάρ Λουί, ενώ, τέλος, συμβουλεύεται την αναλυτική των σχέσεων εξουσίας και αντίστασης ή ελευθερίας στο έργο του Μισέλ ΦουκώThis paper approaches the theme of "trans-class" or the situation of the "cross-class", through the reading and utilization of Pierre Bourdieu's class theory and "auto-socioanalysis", de Gaulezac's study of class neurosis and autobiographical narratives of the writers Didier Eribon and Édouard Louis, while, finally, he consults the analysis of the relations of authority and resistance or freedom in the work of Michel Foucaul

Effect of Direct Current Electric Fields on Cone Like Retinal Photoreceptor Cells

Studies show that electric fields are used as therapy during nerve and tissue injuries along with trans-retinal stimulation. However, cellular and molecular changes induced by such treatments remain largely unknown especially in retinal photoreceptor cells.The 661W cells were stimulated with a constant dcEF of field strength 5 V/cm during 30 min or 5 h depending on the parameters studied.In response to dcEF, the cells aligned perpendicular to the field by forming a leading edge with extended membrane protrusions towards the cathode. Using immunofluorescence and live cell imaging, we show that the cell membrane depolarized at the cathodal side. The microtubules spread into the direction of migration. Also, the microtubule organization center re-oriented into this direction. Concomitantly with the microtubules, actin filaments reorganized in an asymmetrical fashion mainly at the cathodal side. The Golgi apparatus, which is involved in many steps of actin synthesis, moved to the cathodal side. In the last 2 h of the 5 h experiment, microtubules positioned themselves at the rear (anodal side), like the nucleus. The averaged displacement of the whole cells under dcEF was 155% of control for 3 V/cm and 235% for 5 V/cm. The average speed increased by 142% and 243% respectively. Inside the cells mitochondria moved to the cathodal side, where the energy consuming producing processes take place. In this line, we measured an increase in ATP production and O2 consumption. Mitochondrial calcium was found more on the anodal side, at the site of the nucleus with its calcium delivering endoplasmic reticulum. In addition, oxymetry studies reveal an increased ATP synthesis by 115.2% and oxygen consumption by 113.3% 3 h after dcEF stimulation. An analysis of differentially expressed genes by RNA sequencing revealed an upregulation of genes involved in cellular movement, cell to cell and intracellular signaling, molecular transport, assembly and organization.The mechanisms found can enhance our understanding regarding the beneficial effects of EF treatment in retinal diseases

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

<p>Abstract</p> <p>Background</p> <p>Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.</p> <p>Results</p> <p>The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate.</p> <p>Conclusion</p> <p>Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90% success given a consistently modelled ontology. Overall, the results show that well structured ontologies can play a very important role to improve disambiguation.</p> <p>Availability</p> <p>The three benchmark datasets created for the purpose of disambiguation are available in Additional file <supplr sid="S1">1</supplr>.</p> <suppl id="S1"> <title> <p>Additional file 1</p> </title> <text> <p><b>Benchmark datasets used in the experiments.</b> The three corpora (High quality/Low quantity corpus; Medium quality/Medium quantity corpus; Low quality/High quantity corpus) are given in the form of PubMed identifiers (PMID) for True/False cases for the 7 ambiguous terms examined (GO/MeSH/UMLS identifiers are also given).</p> </text> <file name="1471-2105-10-28-S1.txt"> <p>Click here for file</p> </file> </suppl

A user-centred evaluation framework for the Sealife semantic web browsers

BACKGROUND: Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. METHODS: This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. RESULTS: It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. CONCLUSION: Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues

Semantic Web Applications and Tools for Life Sciences, 2008 – Introduction

BACKGROUND: Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. METHODS: This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. RESULTS: It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. CONCLUSION: Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues

Clonal Analysis Delineates Transcriptional Programs of Osteogenic and Adipogenic Lineages of Adult Mouse Skeletal Progenitors.

Bone, cartilage, and marrow adipocytes are generated by skeletal progenitors, but the relationships between lineages and mechanisms controlling their differentiation are poorly understood. We established mouse clonal skeletal progenitors with distinct differentiation properties and analyzed their transcriptome. Unipotent osteogenic and adipogenic cells expressed specific transcriptional programs, whereas bipotent clones combined expression of those genes and did not show a unique signature. We tested potential regulators of lineage commitment and found that in the presence of interferon-γ (IFNγ) adipogenic clones can be induced to osteogenesis and that their adipogenic capacity is inhibited. Analysis of IFNγ-regulated genes showed that lineage signatures and fate commitment of skeletal progenitors were controlled by EGR1 and EGR2. Knockdown experiments revealed that EGR1 is a positive regulator of the adipogenic transcriptional program and differentiation capacity, whereas EGR2 inhibits the osteogenic program and potency. Therefore, our work revealed transcriptional signatures of osteogenic and adipogenic lineages and mechanism triggering cell fate.This study was supported by the Collaborative Research Grant SFB-655 (German Research Foundation - DFG) to K.A. The Next Generation Sequencing facility was also supported by the SFB-655. P.B. and M. Riminucci are supported by Fondazione Cenci Bolognetti, Telethon (grant GGP15198)

GoPubMed: Exploring Pubmed with Ontological Background Knowledge

With the ever increasing size of scientific literature, finding relevant documents and answering questions has become even more of a challenge. Recently, ontologies - hierarchical, controlled vocabularies - have been introduced to annotate genomic data. They can also improve the question answering and the selection of relevant documents in the literature search. Search engines such as GoPubMed.org use ontological background knowledge to give an overview over large query results and to help answering questions. We review the problems and solutions underlying these next generation intelligent search engines and give examples of the power of this new search paradigm

Neurotophin Receptor p75NTR Regulates Immune Function of Plasmacytoid Dendritic Cells

Plasmacytoid dendritic cells (pDCs) regulate innate and adaptive immunity. Neurotrophins and their receptors control the function of neuronal tissue. In addition, they have been demonstrated to be part of the immune response but little is known about the effector immune cells involved. We report, for the first time, the expression and immune-regulatory function of the low affinity neurotrophin receptor p75 neurotrophin receptor (p75NTR) by the antigen-presenting pDCs, mediated by toll-like receptor (TLR) 9 activation and differential phosphorylation of interferon regulatory factor 3 and 7. The modulation of p75NTR on pDCs significantly influences disease progression of asthma in an ovalbumin-induced mouse model mediated by the TLR9 signaling pathway. p75NTR activation of pDCs from patients with asthma increased allergen-specific T cell proliferation and cytokine secretion in nerve growth factor concentration-dependent manner. Further, p75NTR activation of pDCs delayed the onset of autoimmune diabetes in RIP-CD80GP mice and aggravated graft-versus-host disease in a xenotransplantation model. Thus, p75NTR signaling on pDCs constitutes a new and critical mechanism connecting neurotrophin signaling and immune response regulation with great therapeutic potential for a variety of immune disorders

Topic Strategies and the Internal Structure of Nominal Arguments in Greek and Italian

In this article, we argue that a set of unexpected contrasts in the interpretation of clitic-left-dislocated indefinites in Greek and Italian derive from structural variation in the nominal syntax of the two languages. Greek resists nonreferential indefinites in clitic left-dislocation, resorting to the topicalization of an often bare noun for nonreferential topics. By contrast, clitic left-dislocation is employed in Italian for topics regardless of their definite/indefinite interpretation. We argue that this contrast is directly linked to the wide availability of bare nouns in Greek, which stems from a structural difference in the nominal syntax of the two languages. In particular, we hypothesize that Greek nominal arguments lack a D layer. Rather, they are Number Phrases. We situate this analysis in the context of Chierchia’s (1998) typology of nominals. We argue that, on a par with Italian nouns, Greek nouns are [−arg, +pred]. However, they do not employ a syntactic head (D) for type-shifting to e . Rather, they resort to covert type-shifting, a hypothesis that is necessary to account for the distribution and interpretations of bare nouns in Greek, vis-à-vis other [−arg, +pred] languages like Italian and French. </jats:p