MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

UNSUPERVISED INDEXING OF MEDLINE ARTICLES THROUGH GRAPH-BASED RANKING

The biomedical literature is extensively catalogued and indexed in MEDLINE. MEDLINE indexing is done by trained human indexers, who identify the most important concepts in each article, and is expensive and inconsistent. Automating the indexing task is difficult: the National Library of Medicine produces the Medical Text Indexer (MTI), which suggests potential indexing terms to the indexers. MTI’s output is not good enough to work unattended. In my thesis, I propose a different way to approach the indexing task called MEDRank. MEDRank creates graphs representing the concepts in biomedical articles and their relationships within the text, and applies graph-based ranking algorithms to identify the most important concepts in each article. I evaluate the performance of several automated indexing solutions, including my own, by comparing their output to the indexing terms selected by the human indexers. MEDRank outperformed all other evaluated indexing solutions, including MTI, in general indexing performance and precision. MEDRank can be used to cluster documents, index any kind of biomedical text with standard vocabularies, or could become part of MTI itself.

Citation analysis of faculty publication: beyond Science Citation Index and Social Science Citation Index.

When evaluated for promotion or tenure, faculty members are increasingly judged more on the quality than on the quantity of their scholarly publications. As a result, they want help from librarians in locating all citations to their published works for documentation in their curriculum vitae. Citation analysis using Science Citation Index and Social Science Citation Index provides a logical starting point in measuring quality, but the limitations of these sources leave a void in coverage of citations to an author's work. This article discusses alternative and additional methods of locating citations to published works.

Text Classification and Indexing in IP Networks

Internet on elektronisen postin perusrakenne ja ollut tärkeä tiedonlähde akateemisille käyttäjille jo pitkään. Siitä on tullut merkittävä tietolähde kaupallisille yrityksille niiden pyrkiessä pitämään yhteyttä asiakkaisiinsa ja seuraamaan kilpailijoitansa. WWW:n kasvu sekä määrällisesti että sen moninaisuus on luonut kasvavan kysynnän kehittyneille tiedonhallintapalveluille. Tällaisia palveluja ovet ryhmittely ja luokittelu, tiedon löytäminen ja suodattaminen sekä lähteiden käytön personointi ja seuranta. Vaikka WWW:stä saatavan tieteellisen ja kaupallisesti arvokkaan tiedon määrä on huomattavasti kasvanut viime vuosina sen etsiminen ja löytyminen on edelleen tavanomaisen Internet hakukoneen varassa. Tietojen hakuun kohdistuvien kasvavien ja muuttuvien tarpeiden tyydyttämisestä on tullut monimutkainen tehtävä Internet hakukoneille. Luokittelu ja indeksointi ovat merkittävä osa luotettavan ja täsmällisen tiedon etsimisessä ja löytämisessä. Tämä diplomityö esittelee luokittelussa ja indeksoinnissa käytettävät yleisimmät menetelmät ja niitä käyttäviä sovelluksia ja projekteja, joissa tiedon hakuun liittyvät ongelmat on pyritty ratkaisemaan.

Multimodal semantic-associative collateral labelling and indexing of still images

A novel framework for multimodal semantic-associative collateral image labelling, aiming at associating image regions with textual keywords, is described. Both the primary image and collateral textual modalities are exploited in a cooperative and complementary fashion. The collateral content and context based knowledge is used to bias the mapping from the low-level region-based visual primitives to the high-level visual concepts defined in a visual vocabulary. We introduce the notion of collateral context, which is represented as a co-occurrence matrix, of the visual keywords, A collaborative mapping scheme is devised using statistical methods like Gaussian distribution or Euclidean distance together with collateral content and context-driven inference mechanism. Finally, we use Self Organising Maps to examine the classification and retrieval effectiveness of the proposed high-level image feature vector model which is constructed based on the image labelling results.

Perfil da atividade de pesquisa publicada nos anais dos congressos brasileiros de pneumologia e tisiologia nos últimos vinte anos

Objective: To increase the knowledge base regarding pulmonology research in Brazil. Methods: A retrospective, observational study of the abstracts published in the Annals of the Brazilian Pulmonology and Phthisiology Conferences held from 1986 to 2004, quantifying the institutions of origin by geographic distribution and type, as well as categorizing the abstracts by study design and topic. Results: A total of 6467 abstracts were published. The institutions of origin were located, variously, in the Southeast (3870 abstracts), South (1309), Northeast (783), Central-West (267) and North (84). There were 94 abstracts originating from foreign institutions, especially from institutions in Portugal (56.3%) and the United States (13.8%). Most of the studies (5825) were conducted in public Brazilian institutions. There were 4234 clinical studies, 1994 case reports and 239 original research articles. A marked, progressive increase was observed in the number of clinical studies and case reports during the period evaluated. Overall, the most common themes were tuberculosis and other infections diseases (25.2%), following by oncology (11.6%), interstitial lung diseases (8.8%) and thoracic surgery (8.5%). Nevertheless, the number of abstracts on each topic varied widely from year to year. Conclusion: Public Brazilian institutions are the principal sources of pulmonology research in Brazil. Such research activity is concentrated in the southeastern part of the country. Case reports account for one-third of this activity. Although there was great variability in the subjects addressed, diseases that are highly prevalent in Brazil, such as tuberculosis and other infections diseases, were the most common topics.

DTIC retrieval and indexing terminology /

"January 1987."

Capturing and indexing rehearsals: the design and usage of a digital archive of performing arts

Preserving the cultural heritage of the performing arts raises difficult and sensitive issues, as each performance is unique by nature and the juxtaposition between the performers and the audience cannot be easily recorded. In this paper, we report on an experimental research project to preserve another aspect of the performing arts—the history of their rehearsals. We have specifically designed non-intrusive video recording and on-site documentation techniques to make this process transparent to the creative crew, and have developed a complete workflow to publish the recorded video data and their corresponding meta-data online as Open Data using state-of-the-art audio and video processing to maximize non-linear navigation and hypervideo linking. The resulting open archive is made publicly available to researchers and amateurs alike and offers a unique account of the inner workings of the worlds of theater and opera.

Capturing and indexing rehearsals: the design and usage of a digital archive of performing arts

Preserving the cultural heritage of the performing arts raises difficult and sensitive issues, as each performance is unique by nature and the juxtaposition between the performers and the audience cannot be easily recorded. In this paper, we report on an experimental research project to preserve another aspect of the performing arts—the history of their rehearsals. We have specifically designed non-intrusive video recording and on-site documentation techniques to make this process transparent to the creative crew, and have developed a complete workflow to publish the recorded video data and their corresponding meta-data online as Open Data using state-of-the-art audio and video processing to maximize non-linear navigation and hypervideo linking. The resulting open archive is made publicly available to researchers and amateurs alike and offers a unique account of the inner workings of the worlds of theater and opera.

Form, Intention, and Indexing: The Liminal and Integrated Conceptions of Work in Knowledge Organization

This paper proposes a dual conception of work in knowledge organization. The first part is a conception of work as liminal, set apart from everyday work. The second is integrated, without separation. This talk is the beginning of a larger project where we will characterize work in knowledge organization, both as it is set out in our literature (Šauperl, 2004; Hjørland 2003 Wilson, 1968), and in a philosophical argument for its fundamental importance in the activities of society (Shera, 1972; Zandonade, 2004).But in order to do this, we will co-opt the conception of liminality from the anthropology of religion (Turner, 1967), and Zen Buddhist conceptions of moral action, intention, and integration (Harvey, 2000 and cf., Harada, S., 2008).The goal for this talk is to identify the acts repeated (form) and the purpose of those acts (intention), in knowledge organization, with specific regard to thresholds (liminal points) of intention present in those acts.We can then ask the questions: Where is intention in knowledge organization liminal and where is it integrated? What are the limits of knowledge organization work when considered at a foundational level of the intention labor practices? Answering such questions, in this context, allows us to reconsider the assumptions we have about knowledge organization work and its increasingly important role in society. As a consequence, we can consider the limits of classification research if we see the foundations of knowledge organization work when we see forms and intentions. I must also say that incorporating Zen Buddhist philosophy into knowledge organization research seems like it fits well with ethics and ethical responses the practice of knowledge organization. This is because 20th Century Western interpretations of Zen are often rooted in ethical considerations. This translates easily to work.

Desarrollo de un sistema de clasificación de recursos electrónicos en el ámbito de la lógica matemática

El presente trabajo define una taxonomía para la clasificación de recursos digitales del ámbito de la lógica tradicional, y más concretamente los recursos que se podrían generar en el ámbito de la asignatura de Lógica Matemática del plan de estudios de las titulaciones de Ingeniería Técnica de Gestión y de Sistemas impartidas en la Universitat Oberta de Catalunya (UOC).

Editorial

Readers may have noted that a short but very important announcement was made in the last issue of CLAE, at the top of the contents page. CLAE has been accepted by Thomson Reuters for abstracting and indexing in its SciSearch, Journal Citation Reports, and Current Contents services. This will ensure a greater visibility to the international research community. In addition, in June 2012 CLAE will receive its very first official Impact Factor – a measure of journal influence of importance to authors and readers alike. The impact factor value has not yet been decided but internal estimates by Elsevier estimate it will be around 1, and it will be applied to all CLAE issue back to January 2009 (volume 32). I would guess readers at this stage would have one of two responses – either ‘that's good news’ or perhaps ‘what's an impact factor?’ If you are in the latter camp then allow me to try and explain. Basically the impact factor or citation index of a journal is based on how many times in the previous year papers published in that journal in the previous two years were cited by authors publishing in other journals. So the 2012 impact factor for CLAE is calculated on how many times in 2011 papers that were published in CLAE in 2010 and 2009 were cited in other journals in 2011, divided by the number of papers published in CLAE 2010 and 2009. Essentially authors will try and get their work published in journals with a higher impact factor as it is thought that the paper will be cited more by other authors or the paper will have higher visibility in the arena. For universities having its published output in higher journals is one of the markers used to judge esteem. For individual authors publishing in journals with a higher impact factor or the number of times one of their papers is published is something that they are likely to add to their CVs or demonstrate the importance of their work. Journals with higher impact factors tend to be more review journals or journals with a wider spectrum so for a relatively small journal with a specialised field like CLAE it is great to be listed with a citation index. The awarding of a citation index crowns many changes that CLAE has undergone since the current Editor took the reins in 2005. CLAE has increased from four issues (in 2004) to six issues per year with at least one review article per issue and one article with continuing education per issue. The rejection rate has gone up significantly meaning that only best papers are published (currently it stands at 37%). CLAE has been Medline/Pubmed indexed for a few years now which is also a very important factor in improving visibility of the journal. The submission and reviewing process for CLAE in now entirely online and finally the editorial board has changed from being merely a list of keynote people to being an active group of keynote people who are enthusiastically involved with the journal. From the editorial board one person is appointed as a Reviews Editor plus we have two additional editors who work as Regional Editors. As ever, on behalf of CLAE I would like to thank the BCLA Council for their continued support (especially Vivien Freeman) and Elsevier for their continuing guidance (in particular Andrew Miller and Rosie Davey) and the excellent Editorial Board (Christopher Snyder, Pauline Cho, Eric Papas, Jan Bergmanson, Roger Buckley, Patrick Caroline, Dwight Cavanagh, Robin Chalmers, Michael Doughty, Nathan Efron, Michel Guillon, Nizar Hirji, Meng Lin, Florence Malet, Philip Morgan, Deborah Sweeney, Brian Tighe, Eef van Der Worp, Barry Weissman, Mark Willcox, James Wolffsohn and Craig Woods). And finally, a big thanks to the authors and reviewers who work tirelessly putting manuscripts together for publication in CLAE. Copyright © 2012 Published by Elsevier Ltd.

Knowledge Representation and Orthophemism: A Reflection Aiming to a Concept

Characteristics of speech, especially figures of speech, are used by specific communities or domains, and, in this way, reflect their identities through their choice of vocabulary. This topic should be an object of study in the context of knowledge representation once it deals with different contexts of production of documents. This study aims to explore the dimensions of the concepts of euphemism, dysphemism, and orthophemism, focusing on the latter with the goal of extracting a concept which can be included in discussions about subject analysis and indexing. Euphemism is used as an alternative to a non-preferred expression or as an alternative to an offensive attribution-to avoid potential offense taken by the listener or by other persons, for instance, pass away. Dysphemism, on the other hand, is used by speakers to talk about people and things that frustrate and annoy them-their choice of language indicates disapproval and the topic is therefore denigrated, humiliated, or degraded, for instance, kick the bucket. While euphemism tries to make something sound better, dysphemism tries to make something sound worse. Orthophemism (Allan and Burridge 2006) is also used as an alternative to expressions, but it is a preferred, formal, and direct language of expression when representing an object or a situation, for instance, die. This paper suggests that the comprehension and use of such concepts could support the following issues: possible contributions from linguistics and terminology to subject analysis as demonstrated by Talamo et al. (1992); decrease of polysemy and ambiguity of terms used to represent certain topics of documents; and construction and evaluation of indexing languages. The concept of orthophemism can also serves to support associative relationships in the context of subject analysis, indexing, and even information retrieval related to more specific requests.