Publishing Orthology and Diseases Information in the Linked Open Data Cloud

The Linked Data initiative offers a straight method to publish structured data in the World Wide Web and link it to other data, resulting in a world wide network of semantically codified data known as the Linked Open Data cloud. The size of the Linked Open Data cloud, i.e. the amount of data published using Linked Data principles, is growing exponentially, including life sciences data. However, key information for biological research is still missing in the Linked Open Data cloud. For example, the relation between orthologs genes and genetic diseases is absent, even though such information can be used for hypothesis generation regarding human diseases. The OGOLOD system, an extension of the OGO Knowledge Base, publishes orthologs/diseases information using Linked Data. This gives the scientists the ability to query the structured information in connection with other Linked Data and to discover new information related to orthologs and human diseases in the cloud.

Towards extracting non-strict independent and-parallelism using sharing and freeness information

Logic programming systems which exploit and-parallelism among non-deterministic goals rely on notions of independence among those goals in order to ensure certain efficiency properties. "Non-strict" independence (NSI) is a more relaxed notion than the traditional notion of "strict" independence (SI) which still ensures the relevant efficiency properties and can allow considerable more parallelism than SI. However, all compilation technology developed to date has been based on SI, presumably because of the intrinsic complexity of exploiting NSI. This is related to the fact that NSI cannot be determined "a priori" as SI. This paper fills this gap by developing a technique for compile-time detection and annotation of NSI. It also proposes algorithms for combined compile- time/run-time detection, presenting novel run-time checks for this type of parallelism. Also, a transformation procedure to eliminate shared variables among parallel goals is presented, attempting to perform as much work as possible at compiletime. The approach is based on the knowledge of certain properties about run-time instantiations of program variables —sharing and freeness— for which compile-time technology is available, with new approaches being currently proposed.

Concurrent library abstraction without information hiding

The commonly accepted approach to specifying libraries of concurrent algorithms is a library abstraction. Its idea is to relate a library to another one that abstracts away from details of its implementation and is simpler to reason about. A library abstraction relation has to validate the Abstraction Theorem: while proving a property of the client of the concurrent library, the library can be soundly replaced with its abstract implementation. Typically a library abstraction relation, such as linearizability, assumes a complete information hiding between a library and its client, which disallows them to communicate by means of shared memory. However, such way of communication may be used in a program, and correctness of interactions on a shared memory depends on the implicit contract between the library and the client. In this work we approach library abstraction without any assumptions about information hiding. To be able to formulate the contract between components of the program, we augment machine states of the program with two abstract states, views, of the client and the library. It enables formalising the contract with the internal safety, which requires components to preserve each other's views whenever their command is executed. We define the library a a correspondence between possible uses of a concrete and an abstract library. For our library abstraction relation and traces of a program, components of which follow their contract, we prove an Abstraction Theorem. RESUMEN. La técnica más aceptada actualmente para la especificación de librerías de algoritmos concurrentes es la abstracción de librerías (library abstraction). La idea subyacente es relacionar la librería original con otra que abstrae los detalles de implementación y conóon que describa dicha abstracción de librerías debe validar el Teorema de Abstracción: durante la prueba de la validez de una propiedad del cliente de la librería concurrente, el reemplazo de esta última por su implementación abstracta es lógicamente correcto. Usualmente, una relación de abstracción de librerías como la linearizabilidad (linearizability), tiene como premisa el ocultamiento de información entre el cliente y la librería (information hiding), es decir, que no se les permite comunicarse mediante la memoria compartida. Sin embargo, dicha comunicación ocurre en la práctica y la correctitud de estas interacciones en una memoria compartida depende de un contrato implícito entre la librería y el cliente. En este trabajo, se propone un nueva definición del concepto de abtracción de librerías que no presupone un ocultamiento de información entre la librería y el cliente. Con el fin de establecer un contrato entre diferentes componentes de un programa, extendemos la máquina de estados subyacente con dos estados abstractos que representan las vistas del cliente y la librería. Esto permite la formalización de la propiedad de seguridad interna (internal safety), que requiere que cada componente preserva la vista del otro durante la ejecuci on de un comando. Consecuentemente, se define la relación de abstracción de librerías mediante una correspondencia entre los usos posibles de una librería abstracta y una concreta. Finalmente, se prueba el Teorema de Abstracción para la relación de abstracción de librerías propuesta, para cualquier traza de un programa y cualquier componente que satisface los contratos apropiados.

Semantic Annotation of RESTful and WFS OGC services

Actualmente, la Web provee un inmenso conjunto de servicios (WS-*, RESTful, OGC WFS), los cuales están normalmente expuestos a través de diferentes estándares que permiten localizar e invocar a estos servicios. Estos servicios están, generalmente, descritos utilizando información textual, sin una descripción formal, es decir, la descripción de los servicios es únicamente sintáctica. Para facilitar el uso y entendimiento de estos servicios, es necesario anotarlos de manera formal a través de la descripción de los metadatos. El objetivo de esta tesis es proponer un enfoque para la anotación semántica de servicios Web en el dominio geoespacial. Este enfoque permite automatizar algunas de las etapas del proceso de anotación, mediante el uso combinado de recursos ontológicos y servicios externos. Este proceso ha sido evaluado satisfactoriamente con un conjunto de servicios en el dominio geoespacial. La contribución principal de este trabajo es la automatización parcial del proceso de anotación semántica de los servicios RESTful y WFS, lo cual mejora el estado del arte en esta área. Una lista detallada de las contribuciones son: • Un modelo para representar servicios Web desde el punto de vista sintáctico y semántico, teniendo en cuenta el esquema y las instancias. • Un método para anotar servicios Web utilizando ontologías y recursos externos. • Un sistema que implementa el proceso de anotación propuesto. • Un banco de pruebas para la anotación semántica de servicios RESTful y OGC WFS. Abstract The Web contains an immense collection of Web services (WS-*, RESTful, OGC WFS), normally exposed through standards that tell us how to locate and invocate them. These services are usually described using mostly textual information and without proper formal descriptions, that is, existing service descriptions mostly stay on a syntactic level. If we want to make such services potentially easier to understand and use, we may want to annotate them formally, by means of descriptive metadata. The objective of this thesis is to propose an approach for the semantic annotation of services in the geospatial domain. Our approach automates some stages of the annotation process, by using a combination of thirdparty resources and services. It has been successfully evaluated with a set of geospatial services. The main contribution of this work is the partial automation of the process of RESTful and WFS semantic annotation services, what improves the current state of the art in this area. The more detailed list of contributions are: • A model for representing Web services. • A method for annotating Web services using ontological and external resources. • A system that implements the proposed annotation process. • A gold standard for the semantic annotation of RESTful and OGC WFS services, and algorithms for evaluating the annotations.

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems

The amount of genomic and proteomic data that is entered each day into databases and the experimental literature is outstripping the ability of experimental scientists to keep pace. While generic databases derived from automated curation efforts are useful, most biological scientists tend to focus on a class or family of molecules and their biological impact. Consequently, there is a need for molecular class-specific or other specialized databases. Such databases collect and organize data around a single topic or class of molecules. If curated well, such systems are extremely useful as they allow experimental scientists to obtain a large portion of the available data most relevant to their needs from a single source. We are involved in the development of two such databases with substantial pharmacological relevance. These are the GPCRDB and NucleaRDB information systems, which collect and disseminate data related to G protein-coupled receptors and intra-nuclear hormone receptors, respectively. The GPCRDB was a pilot project aimed at building a generic molecular class-specific database capable of dealing with highly heterogeneous data. A first version of the GPCRDB project has been completed and it is routinely used by thousands of scientists. The NucleaRDB was started recently as an application of the concept for the generalization of this technology. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm/ and the NucleaRDB at http://www.receptors.org/NR/.

Customizing for clients: developing a library liaison program from need to plan*

Building on the experiences of librarian representatives to curriculum committees in the colleges of dentistry, medicine, and nursing, the Health Science Center Libraries (HSCL) Strategic Plan recommended the formation of a Library Liaison Work Group to create a formal Library Liaison Program to serve the six Health Science Center (HSC) colleges and several affiliated centers and institutes. The work group's charge was to define the purpose and scope of the program, identify models of best practice, and recommend activities for liaisons. The work group gathered background information, performed an environmental scan, and developed a philosophy statement, a program of liaison activities focusing on seven |primary areas, and a forum for liaison communication. Hallmarks of the plan included intensive subject specialization (beyond collection development), extensive communication with users, and personal information services. Specialization was expected to promote competence, communication, confidence, comfort, and customization. Development of the program required close coordination with other strategic plan implementation teams, including teams for collection development, education, and marketing. This paper discusses the HSCL's planning process and the resulting Library Liaison Program. Although focusing on an academic health center, the planning process and liaison model may be applied to any library serving diverse, subject-specific user populations.

Public library consumer health information pilot project: results of a National Library of Medicine evaluation

In October 1998, the National Library of Medicine (NLM) launched a pilot project to learn about the role of public libraries in providing health information to the public and to generate information that would assist NLM and the National Network of Libraries of Medicine (NN/LM) in learning how best to work with public libraries in the future. Three regional medical libraries (RMLs), eight resource libraries, and forty-one public libraries or library systems from nine states and the District of Columbia were selected for participation. The pilot project included an evaluation component that was carried out in parallel with project implementation. The evaluation ran through September 1999. The results of the evaluation indicated that participating public librarians were enthusiastic about the training and information materials provided as part of the project and that many public libraries used the materials and conducted their own outreach to local communities and groups. Most libraries applied the modest funds to purchase additional Internet-accessible computers and/or upgrade their health-reference materials. However, few of the participating public libraries had health information centers (although health information was perceived as a top-ten or top-five topic of interest to patrons). Also, the project generated only minimal usage of NLM's consumer health database, known as MEDLINEplus, from the premises of the monitored libraries (patron usage from home or office locations was not tracked). The evaluation results suggested a balanced follow-up by NLM and the NN/LM, with a few carefully selected national activities, complemented by a package of targeted activities that, as of January 2000, are being planned, developed, or implemented. The results also highlighted the importance of building an evaluation component into projects like this one from the outset, to assure that objectives were met and that evaluative information was available on a timely basis, as was the case here.

Miscellaneous library and book notes, undated

This folder contains three notes written in Latin.

Athapaskan clothing and related objects in the collections of Field Museum of Natural History / James W. VanStone, Curator, North American Archaeology and Ethnology, Dept. of Anthropology, Field Museum of Natural History.

n.s. no.4(1981)

Photosynthesis and related processes, by Eugene I. Rabinowitch ...

1

Photosynthesis and related processes, by Eugene I. Rabinowitch ...

2, pt.2