Digest of the Lawyers reports annotated, volumes 1-70 ... with full index to annotation.

Mode of access: Internet.

The Hebrew prophets for English readers, in the language of the Revised version of the English Bible, printed in their poetical form, with headings and brief annotation.

v. 1. Amos, Hosea, Isaiah (1-39) and Micah.-v.2. Zephaniah, Nahum, Habakkuk, and Jeremiah.-v.3. Obadiah, Ezekiel, and Isaiah (40-71)-v.4. Haggai, Zechariah, Malachi, Joel, Deutero-Zechariah, Jonah, and Daniel.

Development and evaluation of an automated annotation pipeline and cDNA annotation system

Manual curation has long been held to be the gold standard for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an uninformative filter that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Definition and spatial annotation of the dynamic secretome during early kidney development

The term secretome has been defined as a set of secreted proteins (Grimmond et al. [2003] Genome Res 13:1350-1359). The term secreted protein encompasses all proteins exported from the cell including growth factors, extracellular proteinases, morphogens, and extracellular matrix molecules. Defining the genes encoding secreted proteins that change in expression during organogenesis, the dynamic secretome, is likely to point to key drivers of morphogenesis. Such secreted proteins are involved in the reciprocal interactions between the ureteric bud (UB) and the metanephric mesenchyme (AM) that occur during organogenesis of the metanephros. Some key metanephric secreted proteins have been identified, but many remain to be determined. In this study, microarray expression profiling of E10.5, E11.5, and E13.5 kidney and consensus bioinformatic analysis were used to define a dynamic secretome of early metanephric development. In situ hybridisation was used to confirm microarray results and clarify spatial expression patterns for these genes. Forty-one secreted factors were dynamically expressed between the E10.5 and E13.5 timeframe profiled, and 25 of these factors had not previously been implicated in kidney development. A text-based anatomical ontology was used to spatially annotate the expression pattern of these genes in cultured metanephric explants.

Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs

T he international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM(2), comprised 60,770 full- length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein- coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full- length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web- based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full- length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding ( including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full- length cDNAs. The total number of distinct non- protein- coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and. nal expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.

Development of a multi-tiered speech annotation system for accented English

This paper discusses methodological issues in the development of a multitiered, phonetic annotation system, intended to capture pronunciation variation in the speech of second language learners and to serve in construction of a data base for training ASR models to recognize major pronunciation variants in the assessment of accented English.

Image annotation with Photocopain

Photo annotation is a resource-intensive task, yet is increasingly essential as image archives and personal photo collections grow in size. There is an inherent con?ict in the process of describing and archiving personal experiences, because casual users are generally unwilling to expend large amounts of e?ort on creating the annotations which are required to organise their collections so that they can make best use of them. This paper describes the Photocopain system, a semi-automatic image annotation system which combines information about the context in which a photograph was captured with information from other readily available sources in order to generate outline annotations for that photograph that the user may further extend or amend.

Une histoire du sens:la sémantique linguistique depuis Bréal

Il y a plus d'un siècle, Michel Bréal institua l'analyse du sens dans le langage. À partir de là, le développement de la sémantique repose sur des paradigmes, qui constituent de véritables métaphores de la nature générale du langage. Cet ouvrage montre que, hors des modèles logiques, la sémantique s'est historiquement développée à travers quatre paradigmes. Le sens linguistique relève de la vie mentale des individus pour le paradigme psychologiste qui réunit Bréal, Brunot, Damourette et Pichon, Guillaume et Bally. La nature incertaine de cette vie mentale porte le structuralisme de Saussure, Greimas, Rastier et Wierzbicka à envisager le sens comme dérivant de l'équilibre des oppositions internes à la langue. Les déterminismes de cette organisation sont associés aux conditions de sa mise en oeuvre pour le paradigme de l'énonciation élaboré par Benveniste, Ducrot, Anscombre, Nølke et Culioli. Ils sont pour le cognitivisme de Kleiber, de Cadiot, de Fuchs et pour la Grammaire cognitive dérivés d'un esprit au fonctionnement mécaniste. Permettant de délimiter la forme et l'évolution des paradigmes scientifiques, l'analyse des théories donne à voir l'état actuel de la discipline et les questions qu'elle sera appelée à résoudre.

Représentation, topologie et sémantique linguistique

The different aspects of language are, we know structured by systematic relationships and recent research suggests that the meaning is no exception to this rule. Languages let talking topics to return to their experience of the universe, this reference in is no less the result of the value that characterizes the signs as an integral part of a system of representation. This article contains representations which substantiates the grammatical value of words define in topological terms. This conceptual topology to realise the noun syntax and interpretation. It is therefore suggested that spatialisantes representations intervene as a condition of the Organization referential and structural language sequences.

Sémantique et diachronie du système verbal français

Le système verbal du français contemporain résulte d’une évolution séculaire et l’examen diachronique des valeurs de chacune des formes contribue à la compréhension de la sémantique verbale contemporaine. Parallèlement, l’étude diachronique du système verbal français ne peut se dispenser d’examiner la répartition des valeurs sémantiques sur les formes (avec la diversité d’interprétations contextuelles qu’elles engendrent) au cours de leur évolution. Toutefois, bien que complémentaires, sémantique et diachronie sont rarement conjointes dans la recherche. Par sa conjonction entre études sémantiques et diachroniques, ce volume présente une meilleure idée des tendances qui caractérisent l’évolution des formes verbales du français, et de l’impact que l’observation de ces tendances peut avoir sur notre compréhension de la sémantique de ces formes en synchronie.

Task-based annotation and retrieval for image information management

Continuing advances in digital image capture and storage are resulting in a proliferation of imagery and associated problems of information overload in image domains. In this work we present a framework that supports image management using an interactive approach that captures and reuses task-based contextual information. Our framework models the relationship between images and domain tasks they support by monitoring the interactive manipulation and annotation of task-relevant imagery. During image analysis, interactions are captured and a task context is dynamically constructed so that human expertise, proficiency and knowledge can be leveraged to support other users in carrying out similar domain tasks using case-based reasoning techniques. In this article we present our framework for capturing task context and describe how we have implemented the framework as two image retrieval applications in the geo-spatial and medical domains. We present an evaluation that tests the efficiency of our algorithms for retrieving image context information and the effectiveness of the framework for carrying out goal-directed image tasks. © 2010 Springer Science+Business Media, LLC.

Semantic annotation for knowledge management:requirements and a survey of the state of the art

While much of a company's knowledge can be found in text repositories, current content management systems have limited capabilities for structuring and interpreting documents. In the emerging Semantic Web, search, interpretation and aggregation can be addressed by ontology-based semantic mark-up. In this paper, we examine semantic annotation, identify a number of requirements, and review the current generation of semantic annotation systems. This analysis shows that, while there is still some way to go before semantic annotation tools will be able to address fully all the knowledge management needs, research in the area is active and making good progress.