A Method for Developing Ontologies from User-Generated Classication Systems

Abstract Web 2.0 applications enabled users to classify information resources using their own vocabularies. The bottom-up nature of these user-generated classification systems have turned them into interesting knowledge sources, since they provide a rich terminology generated by potentially large user communities. Previous research has shown that it is possible to elicit some emergent semantics from the aggregation of individual classifications in these systems. However the generation of ontologies from them is still an open research problem. In this thesis we address the problem of how to tap into user-generated classification systems for building domain ontologies. Our objective is to design a method to develop domain ontologies from user-generated classifications systems. To do so, we rely on ontologies in the Web of Data to formalize the semantics of the knowledge collected from the classification system. Current ontology development methodologies have recognized the importance of reusing knowledge from existing resources. Thus, our work is framed within the NeOn methodology scenario for building ontologies by reusing and reengineering non-ontological resources. The main contributions of this work are: An integrated method to develop ontologies from user-generated classification systems. With this method we extract a domain terminology from the classification system and then we formalize the semantics of this terminology by reusing ontologies in the Web of Data. Identification and adaptation of existing techniques for implementing the activities in the method so that they can fulfill the requirements of each activity. A novel study about emerging semantics in user-generated lists. Resumen La web 2.0 permitió a los usuarios clasificar recursos de información usando su propio vocabulario. Estos sistemas de clasificación generados por usuarios son recursos interesantes para la extracción de conocimiento debido principalmente a que proveen una extensa terminología generada por grandes comunidades de usuarios. Se ha demostrado en investigaciones previas que es posible obtener una semántica emergente de estos sistemas. Sin embargo la generación de ontologías a partir de ellos es todavía un problema de investigación abierto. Esta tesis trata el problema de cómo aprovechar los sistemas de clasificación generados por usuarios en la construcción de ontologías de dominio. Así el objetivo de la tesis es diseñar un método para desarrollar ontologías de dominio a partir de sistemas de clasificación generados por usuarios. El método propuesto reutiliza conceptualizaciones existentes en ontologías publicadas en la Web de Datos para formalizar la semántica del conocimiento que se extrae del sistema de clasificación. Por tanto, este trabajo está enmarcado dentro del escenario para desarrollar ontologías mediante la reutilización y reingeniería de recursos no ontológicos que se ha definido en la Metodología NeOn. Las principales contribuciones de este trabajo son: Un método integrado para desarrollar una ontología de dominio a partir de sistemas de clasificación generados por usuarios. En este método se extrae una terminología de dominio del sistema de clasificación y posteriormente se formaliza su semántica reutilizando ontologías en la Web de Datos. La identificación y adaptación de un conjunto de técnicas para implementar las actividades propuestas en el método de tal manera que puedan cumplir automáticamente los requerimientos de cada actividad. Un novedoso estudio acerca de la semántica emergente en las listas generadas por usuarios en la Web.

Map4rdf - Faceted Browser for Geospatial Datasets

Recently we have seen a large increase in the amount of geospatial data that is being published using RDF and Linked Data principles. Eorts such as the W3C Geo XG, and most recently the GeoSPARQL initiative are providing the necessary vocabularies to pub- lish this kind of information on the Web of Data. In this context it is necessary to develop applications that consume and take advantage of these geospatial datasets. In this paper we present map4rdf, a faceted browsing tool for exploring and visualizing RDF datasets enhanced with geospatial information.

Quality of Service (QoS) in MPLS networks

Telecommunications networks have been always expanding and thanks to it, new services have appeared. The old mechanisms for carrying packets have become obsolete due to the new service requirements, which have begun working in real time. Real time traffic requires strict service guarantees. When this traffic is sent through the network, enough resources must be given in order to avoid delays and information losses. When browsing through the Internet and requesting web pages, data must be sent from a server to the user. If during the transmission there is any packet drop, the packet is sent again. For the end user, it does not matter if the webpage loads in one or two seconds more. But if the user is maintaining a conversation with a VoIP program, such as Skype, one or two seconds of delay in the conversation may be catastrophic, and none of them can understand the other. In order to provide support for this new services, the networks have to evolve. For this purpose MPLS and QoS were developed. MPLS is a packet carrying mechanism used in high performance telecommunication networks which directs and carries data using pre-established paths. Now, packets are forwarded on the basis of labels, making this process faster than routing the packets with the IP addresses. MPLS also supports Traffic Engineering (TE). This refers to the process of selecting the best paths for data traffic in order to balance the traffic load between the different links. In a network with multiple paths, routing algorithms calculate the shortest one, and most of the times all traffic is directed through it, causing overload and packet drops, without distributing the packets in the other paths that the network offers and do not have any traffic. But this is not enough in order to provide the real time traffic the guarantees it needs. In fact, those mechanisms improve the network, but they do not make changes in how the traffic is treated. That is why Quality of Service (QoS) was developed. Quality of service is the ability to provide different priority to different applications, users, or data flows, or to guarantee a certain level of performance to a data flow. Traffic is distributed into different classes and each of them is treated differently, according to its Service Level Agreement (SLA). Traffic with the highest priority will have the preference over lower classes, but this does not mean it will monopolize all the resources. In order to achieve this goal, a set policies are defined to control and alter how the traffic flows. Possibilities are endless, and it depends in how the network must be structured. By using those mechanisms it is possible to provide the necessary guarantees to the real-time traffic, distributing it between categories inside the network and offering the best service for both real time data and non real time data. Las Redes de Telecomunicaciones siempre han estado en expansión y han propiciado la aparición de nuevos servicios. Los viejos mecanismos para transportar paquetes se han quedado obsoletos debido a las exigencias de los nuevos servicios, que han comenzado a operar en tiempo real. El tráfico en tiempo real requiere de unas estrictas garantías de servicio. Cuando este tráfico se envía a través de la red, necesita disponer de suficientes recursos para evitar retrasos y pérdidas de información. Cuando se navega por la red y se solicitan páginas web, los datos viajan desde un servidor hasta el usuario. Si durante la transmisión se pierde algún paquete, éste se vuelve a mandar de nuevo. Para el usuario final, no importa si la página tarda uno o dos segundos más en cargar. Ahora bien, si el usuario está manteniendo una conversación usando algún programa de VoIP (como por ejemplo Skype) uno o dos segundos de retardo en la conversación podrían ser catastróficos, y ninguno de los interlocutores sería capaz de entender al otro. Para poder dar soporte a estos nuevos servicios, las redes deben evolucionar. Para este propósito se han concebido MPLS y QoS MPLS es un mecanismo de transporte de paquetes que se usa en redes de telecomunicaciones de alto rendimiento que dirige y transporta los datos de acuerdo a caminos preestablecidos. Ahora los paquetes se encaminan en función de unas etiquetas, lo cual hace que sea mucho más rápido que encaminar los paquetes usando las direcciones IP. MPLS también soporta Ingeniería de Tráfico (TE). Consiste en seleccionar los mejores caminos para el tráfico de datos con el objetivo de balancear la carga entre los diferentes enlaces. En una red con múltiples caminos, los algoritmos de enrutamiento actuales calculan el camino más corto, y muchas veces el tráfico se dirige sólo por éste, saturando el canal, mientras que otras rutas se quedan completamente desocupadas. Ahora bien, esto no es suficiente para ofrecer al tráfico en tiempo real las garantías que necesita. De hecho, estos mecanismos mejoran la red, pero no realizan cambios a la hora de tratar el tráfico. Por esto es por lo que se ha desarrollado el concepto de Calidad de Servicio (QoS). La calidad de servicio es la capacidad para ofrecer diferentes prioridades a las diferentes aplicaciones, usuarios o flujos de datos, y para garantizar un cierto nivel de rendimiento en un flujo de datos. El tráfico se distribuye en diferentes clases y cada una de ellas se trata de forma diferente, de acuerdo a las especificaciones que se indiquen en su Contrato de Tráfico (SLA). EL tráfico con mayor prioridad tendrá preferencia sobre el resto, pero esto no significa que acapare la totalidad de los recursos. Para poder alcanzar estos objetivos se definen una serie de políticas para controlar y alterar el comportamiento del tráfico. Las posibilidades son inmensas dependiendo de cómo se quiera estructurar la red. Usando estos mecanismos se pueden proporcionar las garantías necesarias al tráfico en tiempo real, distribuyéndolo en categorías dentro de la red y ofreciendo el mejor servicio posible tanto a los datos en tiempo real como a los que no lo son.

Nanoinformatics approaches for information extraction and text mining in nanomedical research texts

La nanotecnología es un área de investigación de reciente creación que trata con la manipulación y el control de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. A escala nanométrica, los materiales exhiben fenómenos físicos, químicos y biológicos singulares, muy distintos a los que manifiestan a escala convencional. En medicina, los compuestos miniaturizados a nanoescala y los materiales nanoestructurados ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, así como una mejora en la focalización del medicamento hacia la diana terapéutica, revelando así nuevas propiedades diagnósticas y terapéuticas. A su vez, la complejidad de la información a nivel nano es mucho mayor que en los niveles biológicos convencionales (desde el nivel de población hasta el nivel de célula) y, por tanto, cualquier flujo de trabajo en nanomedicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Desafortunadamente, la informática biomédica todavía no ha proporcionado el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, ni ha adaptado sus métodos y herramientas a este nuevo campo de investigación. En este contexto, la nueva área de la nanoinformática pretende detectar y establecer los vínculos existentes entre la medicina, la nanotecnología y la informática, fomentando así la aplicación de métodos computacionales para resolver las cuestiones y problemas que surgen con la información en la amplia intersección entre la biomedicina y la nanotecnología. Las observaciones expuestas previamente determinan el contexto de esta tesis doctoral, la cual se centra en analizar el dominio de la nanomedicina en profundidad, así como en el desarrollo de estrategias y herramientas para establecer correspondencias entre las distintas disciplinas, fuentes de datos, recursos computacionales y técnicas orientadas a la extracción de información y la minería de textos, con el objetivo final de hacer uso de los datos nanomédicos disponibles. El autor analiza, a través de casos reales, alguna de las tareas de investigación en nanomedicina que requieren o que pueden beneficiarse del uso de métodos y herramientas nanoinformáticas, ilustrando de esta forma los inconvenientes y limitaciones actuales de los enfoques de informática biomédica a la hora de tratar con datos pertenecientes al dominio nanomédico. Se discuten tres escenarios diferentes como ejemplos de actividades que los investigadores realizan mientras llevan a cabo su investigación, comparando los contextos biomédico y nanomédico: i) búsqueda en la Web de fuentes de datos y recursos computacionales que den soporte a su investigación; ii) búsqueda en la literatura científica de resultados experimentales y publicaciones relacionadas con su investigación; iii) búsqueda en registros de ensayos clínicos de resultados clínicos relacionados con su investigación. El desarrollo de estas actividades requiere el uso de herramientas y servicios informáticos, como exploradores Web, bases de datos de referencias bibliográficas indexando la literatura biomédica y registros online de ensayos clínicos, respectivamente. Para cada escenario, este documento proporciona un análisis detallado de los posibles obstáculos que pueden dificultar el desarrollo y el resultado de las diferentes tareas de investigación en cada uno de los dos campos citados (biomedicina y nanomedicina), poniendo especial énfasis en los retos existentes en la investigación nanomédica, campo en el que se han detectado las mayores dificultades. El autor ilustra cómo la aplicación de metodologías provenientes de la informática biomédica a estos escenarios resulta efectiva en el dominio biomédico, mientras que dichas metodologías presentan serias limitaciones cuando son aplicadas al contexto nanomédico. Para abordar dichas limitaciones, el autor propone un enfoque nanoinformático, original, diseñado específicamente para tratar con las características especiales que la información presenta a nivel nano. El enfoque consiste en un análisis en profundidad de la literatura científica y de los registros de ensayos clínicos disponibles para extraer información relevante sobre experimentos y resultados en nanomedicina —patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.—, seguido del desarrollo de mecanismos para estructurar y analizar dicha información automáticamente. Este análisis concluye con la generación de un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento y de test anotados manualmente—, el cual ha sido aplicado a la clasificación de registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nanodrogas y nanodispositivos de aquellos enfocados a testear productos farmacéuticos tradicionales. El presente trabajo pretende proporcionar los métodos necesarios para organizar, depurar, filtrar y validar parte de los datos nanomédicos existentes en la actualidad a una escala adecuada para la toma de decisiones. Análisis similares para otras tareas de investigación en nanomedicina ayudarían a detectar qué recursos nanoinformáticos se requieren para cumplir los objetivos actuales en el área, así como a generar conjunto de datos de referencia, estructurados y densos en información, a partir de literatura y otros fuentes no estructuradas para poder aplicar nuevos algoritmos e inferir nueva información de valor para la investigación en nanomedicina. ABSTRACT Nanotechnology is a research area of recent development that deals with the manipulation and control of matter with dimensions ranging from 1 to 100 nanometers. At the nanoscale, materials exhibit singular physical, chemical and biological phenomena, very different from those manifested at the conventional scale. In medicine, nanosized compounds and nanostructured materials offer improved drug targeting and efficacy with respect to traditional formulations, and reveal novel diagnostic and therapeutic properties. Nevertheless, the complexity of information at the nano level is much higher than the complexity at the conventional biological levels (from populations to the cell). Thus, any nanomedical research workflow inherently demands advanced information management. Unfortunately, Biomedical Informatics (BMI) has not yet provided the necessary framework to deal with such information challenges, nor adapted its methods and tools to the new research field. In this context, the novel area of nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods to solve informational issues at the wide intersection between biomedicine and nanotechnology. The above observations determine the context of this doctoral dissertation, which is focused on analyzing the nanomedical domain in-depth, and developing nanoinformatics strategies and tools to map across disciplines, data sources, computational resources, and information extraction and text mining techniques, for leveraging available nanomedical data. The author analyzes, through real-life case studies, some research tasks in nanomedicine that would require or could benefit from the use of nanoinformatics methods and tools, illustrating present drawbacks and limitations of BMI approaches to deal with data belonging to the nanomedical domain. Three different scenarios, comparing both the biomedical and nanomedical contexts, are discussed as examples of activities that researchers would perform while conducting their research: i) searching over the Web for data sources and computational resources supporting their research; ii) searching the literature for experimental results and publications related to their research, and iii) searching clinical trial registries for clinical results related to their research. The development of these activities will depend on the use of informatics tools and services, such as web browsers, databases of citations and abstracts indexing the biomedical literature, and web-based clinical trial registries, respectively. For each scenario, this document provides a detailed analysis of the potential information barriers that could hamper the successful development of the different research tasks in both fields (biomedicine and nanomedicine), emphasizing the existing challenges for nanomedical research —where the major barriers have been found. The author illustrates how the application of BMI methodologies to these scenarios can be proven successful in the biomedical domain, whilst these methodologies present severe limitations when applied to the nanomedical context. To address such limitations, the author proposes an original nanoinformatics approach specifically designed to deal with the special characteristics of information at the nano level. This approach consists of an in-depth analysis of the scientific literature and available clinical trial registries to extract relevant information about experiments and results in nanomedicine —textual patterns, common vocabulary, experiment descriptors, characterization parameters, etc.—, followed by the development of mechanisms to automatically structure and analyze this information. This analysis resulted in the generation of a gold standard —a manually annotated training or reference set—, which was applied to the automatic classification of clinical trial summaries, distinguishing studies focused on nanodrugs and nanodevices from those aimed at testing traditional pharmaceuticals. The present work aims to provide the necessary methods for organizing, curating and validating existing nanomedical data on a scale suitable for decision-making. Similar analysis for different nanomedical research tasks would help to detect which nanoinformatics resources are required to meet current goals in the field, as well as to generate densely populated and machine-interpretable reference datasets from the literature and other unstructured sources for further testing novel algorithms and inferring new valuable information for nanomedicine.

A Semantic Approach to Problem-Based Learning with Conceptual Models

El aprendizaje basado en problemas se lleva aplicando con éxito durante las últimas tres décadas en un amplio rango de entornos de aprendizaje. Este enfoque educacional consiste en proponer problemas a los estudiantes de forma que puedan aprender sobre un dominio particular mediante el desarrollo de soluciones a dichos problemas. Si esto se aplica al modelado de conocimiento, y en particular al basado en Razonamiento Cualitativo, las soluciones a los problemas pasan a ser modelos que representan el compotamiento del sistema dinámico propuesto. Por lo tanto, la tarea del estudiante en este caso es acercar su modelo inicial (su primer intento de representar el sistema) a los modelos objetivo que proporcionan soluciones al problema, a la vez que adquieren conocimiento sobre el dominio durante el proceso. En esta tesis proponemos KaiSem, un método que usa tecnologías y recursos semánticos para guiar a los estudiantes durante el proceso de modelado, ayudándoles a adquirir tanto conocimiento como sea posible sin la directa supervisión de un profesor. Dado que tanto estudiantes como profesores crean sus modelos de forma independiente, estos tendrán diferentes terminologías y estructuras, dando lugar a un conjunto de modelos altamente heterogéneo. Para lidiar con tal heterogeneidad, proporcionamos una técnica de anclaje semántico para determinar, de forma automática, enlaces entre la terminología libre usada por los estudiantes y algunos vocabularios disponibles en la Web de Datos, facilitando con ello la interoperabilidad y posterior alineación de modelos. Por último, proporcionamos una técnica de feedback semántico para comparar los modelos ya alineados y generar feedback basado en las posibles discrepancias entre ellos. Este feedback es comunicado en forma de sugerencias individualizadas que el estudiante puede utilizar para acercar su modelo a los modelos objetivos en cuanto a su terminología y estructura se refiere. ABSTRACT Problem-based learning has been successfully applied over the last three decades to a diverse range of learning environments. This educational approach consists of posing problems to learners, so they can learn about a particular domain by developing solutions to them. When applied to conceptual modeling, and particularly to Qualitative Reasoning, the solutions to problems are models that represent the behavior of a dynamic system. Therefore, the learner's task is to move from their initial model, as their first attempt to represent the system, to the target models that provide solutions to that problem while acquiring domain knowledge in the process. In this thesis we propose KaiSem, a method for using semantic technologies and resources to scaffold the modeling process, helping the learners to acquire as much domain knowledge as possible without direct supervision from the teacher. Since learners and experts create their models independently, these will have different terminologies and structure, giving rise to a pool of models highly heterogeneous. To deal with such heterogeneity, we provide a semantic grounding technique to automatically determine links between the unrestricted terminology used by learners and some online vocabularies of the Web of Data, thus facilitating the interoperability and later alignment of the models. Lastly, we provide a semantic-based feedback technique to compare the aligned models and generate feedback based on the possible discrepancies. This feedback is communicated in the form of individualized suggestions, which can be used by the learner to bring their model closer in terminology and structure to the target models.

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

Aplicación de tecnologías de procesamiento de lenguaje natural y tecnología semántica en Brand Rain y Anpro21

Este artículo presenta la aplicación y resultados obtenidos de la investigación en técnicas de procesamiento de lenguaje natural y tecnología semántica en Brand Rain y Anpro21. Se exponen todos los proyectos relacionados con las temáticas antes mencionadas y se presenta la aplicación y ventajas de la transferencia de la investigación y nuevas tecnologías desarrolladas a la herramienta de monitorización y cálculo de reputación Brand Rain.

Milankovitch frequency peaks of ODP Site 113-693 (Table 3)

The first well logs collected below the Antarctic circle were obtained during Leg 113 at Site 693 on the Dronning Maud Land Margin (Antarctica) in the Weddell Sea. Gamma-ray, resistivity, and sonic logs were collected between 108.0 and 439.0 mbsf. The downhole logs show good agreement with the data collected from cores and provide a continuous measurement of the sedimentary record. These continuous log records show that the rather uniform Tertiary lithology seen in cores is characterized by high-frequency variability in the log data. Several thin hard streaks are identified, the largest of which coincides with a major Miocene hiatus. Associated with this hiatus is a change to lower illite content (and correspondingly lower gamma-ray counts) and to a significant increase in diatom content. Spectral analysis of the logs was performed on the lower Pliocene through upper Oligocene interval (108.0-343.0 mbsf). Between 108.0 and 245.0 mbsf, average sedimentation rates (50 and 26 m/m.y.) are high enough to show that variance is present in the orbital eccentricity (~95 k.y.) and obliquity (~41 k.y.) bands. Between 253.0 and 343.0 mbsf, the sedimentation rate (8 m/m.y.) is too low to resolve high frequency variations. The Milankovitch frequencies are best developed in the resistivity logs. Resistivity is responding to changes in porosity, which in these sediments is controlled by the abundance of biosiliceous sediments, particularly diatoms. The orbital forcing suggested by the Milankovitch frequencies may be influencing diatom productivity by inducing oscillations in upwelling, ice coverage, pack ice, and/or polynya. Although variations in diatom abundance were observed in the cores, they were not attributed to a Milankovitch signal, and therefore in this environment, downhole logs are an important contribution to the detection and understanding of orbitally influenced changes in sedimentation.

(Table 1) Consolidation test for sediments of ODP Leg 130 sites

Consolidation tests were performed on 19 samples of calcareous ooze from the Ontong Java Plateau, obtained during Ocean Drilling Program Leg 130. Rebound curves from consolidation tests on Ontong Java Plateau samples yield porosity rebounds of 1%-4% for these sediments at equivalent depths up to 1200 mbsf. The exception is a radiolarian-rich sample that has 6% rebound. A rebound correction derived from the porosity rebound vs. depth data has been combined with a correction for pore-water expansion to correct the shipboard laboratory porosity data to in-situ values. Comparison of the laboratory porosity data corrected in this manner with the downhole log data shows good agreement.

(Table 1) Summary of basalt unit thickness, vesicularity, number of flow units, and average porosity at ODP Site 135-839

An inflatable drill-string packer was used at Site 839 to measure the bulk in-situ permeability within basalts cored in Hole 839B. The packer was inflated at two depths, 398.2 and 326.9 mbsf; all on-board information indicated that the packer mechanically closed off the borehole, although apparently the packer hydraulically sealed the borehole only at 398.2 mbsf. Two pulse tests were run at each depth, two constant-rate injection tests were run at the first set, and four were run at the second. Of these, only the constant-rate injection tests at the first set yielded a permeability, calculated as ranging from 1 to 5 * 10**-12 m**2. Pulse tests and constant-rate injection tests for the second set did not yield valid data. The measured permeability is an upper limit; if the packer leaked during the experiments, the basalt would be less permeable. In comparison, permeabilities measured at other Deep Sea Drilling Project and Ocean Drilling Program sites in pillow basalts and flows similar to those measured in Hole 839B are mainly about 10**-13 to 10**-14 m**2. Thus, if our results are valid, the basalts at Site 839 are more permeable than ocean-floor basalts investigated elsewhere. Based on other supporting evidence, we consider these results to be a valid measure of the permeability of the basalts. Temperature data and the geochemical and geotechnical properties of the drilled sediments all indicate that the site is strongly affected by fluid flow. The heat flow is very much less than expected in young oceanic basalts, probably a result of rapid fluid circulation through the crust. The geochemistry of pore fluids is similar to that of seawater, indicating seawater flow through the sediments, and sediments are uniformly underconsolidated for their burial depth, again indicating probable fluid flow. The basalts are highly vesicular. However, the vesicularity can only account for part of the average porosity measured on the neutron porosity well log; the remainder of the measured porosity is likely present as voids and fractures within and between thin-bedded basalts. Core samples, together with porosity, density, and resistivity well-log data show locations where the basalt section is thin bedded and probably has from 15% to 35% void and fracture porosity. Thus, the measured permeability seems reasonable with respect to the high measured porosity. Much of the fluid flow at Site 839 could be directed through highly porous and permeable zones within and between the basalt flows and in the sediment layer just above the basalt. Thus, the permeability measurements give an indication of where and how fluid flow may occur within the oceanic crust of the Lau Basin.

Geochemistry of ODP Hole 128-798B

The capability of determining elemental concentrations through geochemical logging has recently been established. However, the quality of these data obtained in some environments has yet to be quantified. We assess the quality of geochemical logs compared with XRF results from a suite of core samples from Hole 798B. The resulting core/log correlations are only fair, because the tool has been adversely affected by the very high porosity of the formation. The results, however, do fall within the statistical uncertainties predicted by the processing. The recent application of a modified boron sleeve to the Ocean Drilling Program's geochemical logging tool is shown to reduce interference of borehole chlorine on the resultant chemistry.

Biotelemetry: a mechanistic approach to ecology

Remote measurement of the physiology, behaviour and energetic status of free-living animals is made possible by a variety of techniques that we refer to collectively as 'biotelemetry'. This set of tools ranges from transmitters that send their signals to receivers up to a few kilometers away to those that send data to orbiting satellites and, more frequently, to devices that log data. They enable researchers to document, for long uninterrupted periods, how undisturbed organisms interact with each other and their environment in real time. In spite of advances enabling the monitoring of many physiological and behavioural variables across a range of taxa of various sizes, these devices have yet to be embraced widely by the ecological community. Our review suggests that this technology has immense potential for research in basic and applied animal ecology. Efforts to incorporate biotelemetry into broader ecological research programs should yield novel information that has been challenging to collect historically from free-ranging animals in their natural environments. Examples of research that would benefit from biotelemetry include the assessment of animal responses to different anthropogenic perturbations and the development of life-time energy budgets.

Automated mapping of environmental variables from a SEIS or SISE perspective

The INTAMAP FP6 project has developed an interoperable framework for real-time automatic mapping of critical environmental variables by extending spatial statistical methods and employing open, web-based, data exchange protocols and visualisation tools. This paper will give an overview of the underlying problem, of the project, and discuss which problems it has solved and which open problems seem to be most relevant to deal with next. The interpolation problem that INTAMAP solves is the generic problem of spatial interpolation of environmental variables without user interaction, based on measurements of e.g. PM10, rainfall or gamma dose rate, at arbitrary locations or over a regular grid covering the area of interest. It deals with problems of varying spatial resolution of measurements, the interpolation of averages over larger areas, and with providing information on the interpolation error to the end-user. In addition, monitoring network optimisation is addressed in a non-automatic context.