CiteULike: dullhunk's library [1389 articles]

Systems biology driven software design for the research enterprise

John Boyle — 2008-06-25T23:08:38-00:00

BMC Bioinformatics, Vol. 9 (25 June 2008), 295.

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.

P Jaiswal — 2008-07-24T15:44:02-00:00

Comparative and functional genomics, Vol. 6, No. 7-8. (2005), pp. 388-397.

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.

Chemistry Su Doku: v. 1

2008-07-24T13:21:35-00:00

(09 December 2005)

Bringing Chemical Data onto the Semantic Web

KR Taylor — 2006-12-24T18:39:37-00:00

J. Chem. Inf. Model., Vol. 46, No. 3. (22 May 2006), pp. 939-952.

The importance of stupidity in scientific research

Martin Schwartz — 2008-07-16T21:24:00-00:00

J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771.

10.1242/jcs.033340

Life, logic and information

Paul Nurse — 2008-07-23T19:24:45-00:00

Nature, Vol. 454, No. 7203. (24 July 2008), pp. 424-426.

Romance among robots

Andrew Knoll — 2008-07-23T19:23:42-00:00

Nature, Vol. 454, No. 7203. (24 July 2008), pp. 407-407.

Doctorate gets a lesson in management

John Kirkland — 2008-07-23T19:23:24-00:00

Nature, Vol. 454, No. 7203. (24 July 2008), pp. 408-408.

Fewer academics are not the answer to funding woes

Philip Strange — 2008-07-23T19:21:03-00:00

Nature, Vol. 454, No. 7203. (24 July 2008), pp. 397-397.

China's challenges

2008-07-23T19:18:54-00:00

Nature, Vol. 454, No. 7203. (24 July 2008), pp. 367-368.

An Algorithm to Determine Peer-Reviewers

Marko Rodriguez — 2007-07-19T08:51:55-00:00

(24 May 2006)

The peer-review process is the most widely accepted certification mechanism for legitimizing the written results of researchers within the scientific community. An essential component of this process is the identification of competent referees to review a submitted manuscript. This paper presents an algorithm to automatically determine the most appropriate reviewers for a manuscript by way of a co-authorship network data structure and a relative-rank particle-swarm algorithm. This approach is novel in that it is not limited to a pre-selected set of referees, is computationally efficient, requires no human-intervention, and can automatically identify conflict of interest situations. The algorithm is validated using referee bid data from the 2005 Joint Conference on Digital Libraries.

Computational biology resources lack persistence and usability.

S Veretnik — 2008-07-19T16:31:34-00:00

PLoS computational biology, Vol. 4, No. 7. (July 2008)

AGRICULTURAL RESEARCH: Reinventing Rice to Feed the World

Dennis Normile — 2008-07-18T11:01:31-00:00

Science, Vol. 321, No. 5887. (18 July 2008), pp. 330-333.

10.1126/science.321.5887.330

Electronic Publication and the Narrowing of Science and Scholarship

James Evans — 2008-07-18T07:21:32-00:00

Science, Vol. 321, No. 5887. (18 July 2008), pp. 395-399.

Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print--scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse--electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles. The forced browsing of print archives may have stretched scientists and scholars to anchor findings deeply into past and present scholarship. Searching online is more efficient and following hyperlinks quickly puts researchers in touch with prevailing opinion, but this may accelerate consensus and narrow the range of findings and ideas built upon. 10.1126/science.1150473

Biology in the 1980s, plus or minus a decade.

M Robertson — 2008-07-17T14:21:36-00:00

Nature, Vol. 285, No. 5764. (5 June 1980), pp. 358-359.

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.

ME Aranguren — 2008-05-16T04:27:27-00:00

BMC bioinformatics, Vol. 9 Suppl 5 (2008)

BACKGROUND: Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training. RESULTS: Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (http://odps.sourceforge.net/). CONCLUSIONS: Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.

Perils of perversity

Walter Gratzer — 2008-07-03T06:17:57-00:00

Nature, Vol. 454, No. 7200. (02 July 2008), pp. 28-29.

Obol: integrating language and meaning in bio-ontologies

Christopher Mungall — 2005-02-07T23:39:19-00:00

Comparative and Functional Genomics, Vol. 5, No. 6-7. (August 2004), 509.

Rebels, Mavericks, and Heretics in Biology

2008-07-17T10:14:23-00:00

(19 June 2008)

This book is the first devoted to modern biology’s innovators and iconoclasts: men and women who challenged prevailing notions in their fields. Some of these scientists were Nobel Prize winners, some were considered cranks or gadflies, some were in fact wrong. The stories of these stubborn dissenters are individually fascinating. Taken together, they provide unparalleled insights into the role of dissent and controversy in science and especially the growth of biological thought over the past century. Each of the book’s nineteen specially commissioned chapters offers a detailed portrait of the intellectual rebellion of a particular scientist working in a major area of biology--genetics, evolution, embryology, ecology, biochemistry, neurobiology, and virology as well as others. An introduction by the volume’s editors and an epilogue by R. C. Lewontin draw connections among the case studies and illuminate the nonconforming scientist’s crucial function of disturbing the comfort of those in the majority. By focusing on the dynamics and impact of dissent rather than on “winners” who are credited with scientific advances, the book presents a refreshingly original perspective on the history of the life sciences. Scientists featured in this volume: Alfred Russel Wallace Hans Driesch Wilhelm Johannsen Raymond Arthur Dart C. D. Darlington Richard Goldschmidt Barbara McClintock Oswald T. Avery Roger Sperry Leon Croizat Vero Copner Wynne-Edwards Peter Mitchell Howard Temin Motoo Kimura William D. Hamilton Carl Woese Stephen Jay Gould Thelma Rowell Daniel S. Simberloff

Experience using web services for biological sequence analysis.

Heinz Stockinger — 2008-07-16T13:40:10-00:00

Briefings in bioinformatics (11 July 2008)

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

Semantic reclassification of the UMLS concepts.

Jung-Wei Fan — 2008-07-16T13:39:45-00:00

Bioinformatics (Oxford, England) (13 July 2008)

SUMMARY: Accurate semantic classification is valuable for text mining and knowledge based tasks that perform inference based on semantic classes. To benefit applications using the semantic classification of the UMLS concepts, we automatically reclassified the concepts based on their lexical and contextual features. The new classification is useful for auditing the original UMLS semantic classification and for building biomedical text mining applications. AVAILABILITY: http://www.dbmi.columbia.edu/~juf7002/reclassify_production CONTACT: fan@dbmi.columbia.edu SUPPLEMENTARY INFORMATION: at the same webpage above.

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

S Avraham — 2008-07-16T12:08:34-00:00

Nucleic acids research, Vol. 36, No. Database issue. (January 2008)

The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.

Gramene: a bird's eye view of cereal genomes.

P Jaiswal — 2008-07-16T12:08:18-00:00

Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006)

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.

Gramene: a growing plant comparative genomics resource

Chengzhi Liang — 2007-11-28T10:54:50-00:00

Nucl. Acids Res. (4 November 2007), gkm968.

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions. 10.1093/nar/gkm968

Google Still Not Indexing Hidden Web URLs

Kat Hagendorn — 2008-07-16T10:28:35-00:00

D-Lib Magazine, Vol. 14, No. 7. (July 2008)

Search engine coverage of the OAI-PMH corpus

F Mccown — 2008-07-16T10:26:31-00:00

Internet Computing, IEEE, Vol. 10, No. 2. (2006), pp. 66-73.

Having indexed much of the "surface" Web, search engines are now using various approaches to index the "deep" Web. At the same time, institutional repositories and digital libraries are adopting the open archives initiative protocol for metadata harvesting (OAI-PMH) to expose their holdings. The authors harvested nearly 10 million records from OAI-PMH repositories. From these records, they extracted 3.3 million unique resource URLs and then conducted searches on samples from this collection to determine how much of the OAI-PMH corpus the three major search engines have indexed.

Dublin Core: An obituary

J Beall — 2008-07-16T10:18:09-00:00

Library HiTech News, Vol. 21, No. 8. (2004), pp. 40-41.

The death of metadata

J Beall — 2008-07-16T10:14:43-00:00

Serials Librarian, Vol. 51, No. 2. (2006), pp. 55-74.

In the mid-1990s, information professionals and computer scientists began to pay much attention to the concept of metadata. The rise of the World Wide Web highlighted the need to enable discovery, or finding desired information, on the Internet. Metadata was the hot topic at library and information science conferences and in professional literature, and many librarians and others expended enormous efforts creating and implementing newmetadata schemes. One of these schemes, the Dublin Core, emerged in 1995 and quickly became the metadata standard of choice for digital objects. Although abundant resources have been put into the development and implementation of Dublin Core, the schema has largely failed. In addition, many other metadata schemes and profiles have also been developed, most of them specific to a particular community. The result is a Tower of Babel of metadata schemes, and sharing metadata among professional communities is becoming increasingly difficult. Multiple schemes also make the ideal of successful federated searching all but impossible. Full-text searching, offered as a solution by some, is also a failure for most serious information-seeking needs. On the other hand, the implementation of the MARC format in libraries has been the most successful metadata implementation in history. MARC, along with various content standards, has worked successfully for decades as a metadata schema. The library community's implementation of the MARC metadata standard should be more widely adopted or used as a model for metadata schema design. A single, proven, comprehensive metadata standard will better enable discovery and control of information than a proliferation of minor schemes ever will. © 2006 by The Haworth Press, Inc. All rights reserved.

The roles, reasons and restrictions of science blogs

John Wilkins — 2008-07-15T07:51:06-00:00

Trends in Ecology & Evolution, Vol. In Press, Corrected Proof

Over the past few years, blogging ([`]web logging') has become a major social movement, and as such includes blogs by scientists about science. Blogs are highly idiosyncratic, personal and ephemeral means of public expression, and yet they contribute to the current practice and reputation of science as much as, if not more than, any popular scientific work or visual presentation. It is important, therefore, to understand this phenomenon.

Semantic Map of Services for Structural Bioinformatics

P Tuffery — 2008-07-14T12:57:08-00:00

Scientific and Statistical Database Management, 2006. 18th International Conference on (2006), pp. 217-224.

We present a semantic map of resources for structural bioinformatics applied to proteins, i.e., various methods to predict and analyze protein structures in silico. Our map depicts resources on two levels: a logical level that provides a high-level description of the scientific concepts using a domain ontology; a physical level, that describes the actual resources implementing these connections. Scientists can use our system to express a query that captures their scientific aim, and are guided to identify the resources best meeting their needs. It is intended to provide scientists a tool to register and share knowledge about the available services in this field. Our approach addresses the problem of semantic interoperability of scientific resources publicly available on the Web

Bioinformatics Services Discovery Using Ontology Classification

H Menager — 2008-07-14T12:56:07-00:00

Services, 2007 IEEE Congress on (2007), pp. 106-113.

The number of available bioinformatics resources is overwhelming. The most critical issues met by scientists are (1) to identify the resources suitable to express their protocols, and (2) to compose them in an executable workflow. Many advanced projects offer solutions to the composition of services in a workflow, while others address the interoperability of services. We present an approach that allows the organization of bioinformatics resources in a scientifically meaningful framework that leverages existing effort on interoperability and workflow composition and execution. We present ServiceSemanticMap, a system that allows users to explore the wide availability of bioinformatics resources organized with respect to an ontology. The user interacts with the system through a graph-based interface, discovering the resources by exploring the graph. The system exploits a resource catalog where providers may register their bioinformatics tools through a Web resource entry form. We demonstrate the approach with a semantic map devoted to structural bioinformatics. Our approach is collaborative: a group of experts develop and maintain the ontology, while providers and users may register new resources. The first version of the system is demonstrated on line for structural bioinformatics at http: / /bioserv. rpbs . jussieu . fr/SBMap/'index. html.

Gene Ontology annotations: what they mean and where they come from.

DP Hill — 2008-05-11T16:21:46-00:00

BMC bioinformatics, Vol. 9 Suppl 5 (2008)

To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists.

Future of open access could be online and peer-reviewed

Massimo Sandal — 2008-07-09T19:52:43-00:00

Nature, Vol. 454, No. 7201. (10 July 2008), pp. 158-158.

Bioimage Informatics: A New Area of Engineering Biology.

Hanchuan Peng — 2008-07-09T19:50:49-00:00

Bioinformatics (Oxford, England) (4 July 2008)

In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database, and visualization techniques to extract, compare, search, and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called "bioimage informatics". This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools, and other resources.

A Gene Wiki for Community Annotation of Gene Function

Jon Huss — 2008-07-08T15:23:32-00:00

PLoS Biology, Vol. 6, No. 7. (1 July 2008), e175.

A reference ontology for biomedical informatics: the foundational model of anatomy

Cornelius Rosse — 2007-08-10T12:53:31-00:00

J. of Biomedical Informatics, Vol. 36, No. 6. (December 2003), pp. 478-500.

Ontologizer 2.0 - A Multifunctional Tool for GO Term Enrichment Analysis and Data Exploration.

Sebastian Bauer — 2008-07-04T23:46:09-00:00

Bioinformatics (Oxford, England) (29 May 2008)

SUMMARY: The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene-Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent-child method (Grossmann et al., 2007), as well as topologybased algorithms (Alexa el al., 2006). A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms. AVAILABILITY: The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided:http://compbio.charite.de/ontologizer. Requirements: Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool. CONTACT: sebastian.bauer@charite.de, peter.robinson@charite.de.

Watermarking sexually reproducing diploid organisms.

Dominik Heider — 2008-07-06T11:42:29-00:00

Bioinformatics (Oxford, England) (3 July 2008)

SUMMARY: DNA watermarks are used for hiding messages or for authenticating genetically modified organisms. Recently we presented an algorithm called DNA-Crypt for generating DNA based watermarks that can be integrated into the genome by using the characteristics of the degenerative genetic code. DNA-Crypt generates the watermark by replacing single bases and thus creating synonymous codons that encrypt the hidden information. Mutations within the integrated DNA sequence can be corrected using several mutation correction codes, to keep the hidden information intact. This method has successfully been tested in asexually replicating organisms like bacteria or yeast, where the watermark is duplicated with every cell division. It has been shown that DNA watermarks produced by DNA-Crypt do not influence the transcription or translation of a protein. In sexually reproducing diploid organisms, additional problems can occur, e.g. recombination events can destroy hidden information. Using population predictions as well as statistical analyses we identified a coupled Y-chromosomal/mitochondrial DNA watermarking procedure as the most appropriate for diploid organisms. We developed a mitochondria adapted version of DNA-Crypt, which is called Project Mito that can be used in combination with the original progam. AVAILABILITY: http://www.uni-muenster.de/Biologie.NeuroVer/Tumorbiologie/DNA-Crypt/index.html CONTACT: barneko@uni-muenster.de Password: WWUTB Requirements: Java 5.0 or higher.

Schema driven assignment and implementation of life science identifiers (LSIDs).

Sapna Bafna — 2008-07-06T11:41:34-00:00

Journal of biomedical informatics (13 June 2008)

Life science identifier (LSID) is a global unique identifier standard intended to help rationalize the unique archival requirements of biological data. We describe LSID implementation architecture such that data managed by a relational database management system may be integrated with the LSID protocol as an add-on layer. The approach requires a database administrator (DBA) to specify an export schema detailing the content and structure of the archived data, and a mapping of the existing database to that schema. This specification can be expressed using SQL view syntax. In effect, we define a SQL-like language for implementing LSIDs. We describe the mapping of the view definition to an implementation as a set of databases triggers and a fixed runtime library. Thus a compiler for a domain-specific language could be written that would reduce the implementation of LSIDs to the task of writing SQL view-like definitions.

Painful Publishing

Martin Raff — 2008-07-04T10:16:14-00:00

Science, Vol. 321, No. 5885. (4 July 2008), 36a.

10.1126/science.321.5885.36a

Sharing detailed research data is associated with increased citation rate.

HA Piwowar — 2007-11-26T05:13:21-00:00

PLoS ONE, Vol. 2, No. 3. (2007)

BACKGROUND: Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available. PRINCIPAL FINDINGS: We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression. SIGNIFICANCE: This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

Life Sciences and the web: a new era for collaboration

Jonathan Sagotsky — 2008-07-03T09:46:41-00:00

Mol Syst Biol, Vol. 4 (1 July 2008)

Biological data integration using Semantic Web technologies.

C Pasquier — 2008-03-29T09:55:48-00:00

Biochimie (21 February 2008)

Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of disseminated biological data. However, due to some specificities of biological data, the application of these technologies to life science constitutes a real challenge. Through a use case of biological data integration, we show in this paper that current Semantic Web technologies start to become mature and can be applied for the development of large applications. However, in order to get the best from these technologies, improvements are needed both at the level of tool performance and knowledge modeling.

In rude health

2008-07-03T14:05:19-00:00

Nature, Vol. 454, No. 7200. (3 July 2008), pp. 1-2.

Three options for citation tracking: Google Scholar, Scopus and Web of Science

Nisa Bakkalbasi — 2006-06-29T21:13:39-00:00

Biomedical Digital Libraries, Vol. 3 (29 June 2006), 7.

Google Scholar revisited

Peter Jacso — 2008-07-02T15:07:48-00:00

Online Information Review, Vol. 32, No. 1. (2008), pp. 102-114.

Purpose - The purpose of this paper is to revisit Google Scholar. Design/methodology/approach - This paper discusses the strengths and weaknesses of Google Scholar. Findings - The Google Books project has given a massive and valuable boost to the already rich and diverse content of Google Scholar. The dark side of the growth is that significant gaps remain for top ranking journals and serials, and the number of duplicate, triplicate and quadruplicate records for the same source documents (which Google Scholar cannot detect reliably) has increased. Originality/value - This paper discusses the strengths and weaknesses of Google Scholar.

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

Matthew E Falagas — 2007-09-24T06:31:23-00:00

FASEB J (20 September 2007)

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.-Falagas, M. E., Pitsouni, E I., Malietzis, G. A., and Pappas, G. Comparison of Pub Med, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

Google Scholar and academic libraries: An update

KA Hartman — 2008-07-02T15:05:54-00:00

New Library World, Vol. 109, No. 5-6. (2008), pp. 211-222.

Purpose - This paper aims to update the authors' original 2005 study of Google Scholar's integration into ARL libraries' web sites. Have more ARL libraries added Google Scholar? Design/methodology/approach - The library homepages of the 113 ARL academic institutions were examined for paths or links to Google Scholar. The coding scheme focused on noting whether Google Scholar appeared on the library homepage, in the OPAC, and on various database lists and subject guides. Findings - The 2007 data indicate continued acceptance of Google Scholar and integration of this resource on the web pages of ARL libraries. The mean number of paths to Google Scholar more than doubled from 2005 to 2007. Partnering institutions were more likely to include paths to Google Scholar and the number of partnering institutions increased dramatically. Practical implications - This study is useful for those making decisions about integration of Google Scholar into library collections and services, particularly the web site. Originality/value - This paper illustrates future directions for integrating new categories of resources into the academic library web site.

Combining Semantic Web technologies with Multi-Agent Systems for integrated access to biological resources.

Francisco García-Sánchez — 2008-07-01T14:14:57-00:00

Journal of biomedical informatics (23 May 2008)

The increasing volume and diversity of information in biomedical research is demanding new approaches for data integration in this domain. Semantic Web technologies and applications can leverage the potential of biomedical information integration and discovery, facing the problem of semantic heterogeneity of biomedical information sources. In such an environment, agent technology can assist users in discovering and invoking the services available on the Internet. In this paper we present SEMMAS, an ontology-based, domain-independent framework for seamlessly integrating Intelligent Agents and Semantic Web Services. Our approach is backed with a proof-of-concept implementation where the breakthrough and efficiency of integrating disparate biomedical information sources have been tested.

Citation Statistics: the use and misuse of citation data in the assessment of scientific research

Robert Adler — 2008-07-01T10:53:17-00:00

(June 2008)

A report from the International Mathematical Union (IMU) in cooperation with the International Council of Industrial and Applied Mathematics (ICIAM) and the Institute of Mathematical Statistics (IMS)