Research Repositories Research Articles

Efficient Conceptual Rule Mining on Text Clusters in Web Documents

Text mining is a modern and computational approach attempts to determine new, formerly unidentified information by pertaining techniques from normal language processing and data mining. Clustering, one of the conventional data mining techniques is an unsubstantiated learning pattern where clustering techniques attempt to recognize intrinsic groupings of the text documents, so that a set of clusters is formed in which clusters reveal high intra-cluster comparison and low inter-cluster similarity. Most current document clustering methods are based on the Vector Space Model (VSM), which is a widely used data representation for text classification and clustering. Moreover, weighting these features accurately also affects the result of the clustering algorithm substantially. The previous work described the conceptual text clustering to web documents, containing various mark up language formats associated with the documents (term extraction mode). In this work, we are going to present a Conceptual rule mining which is generated for the sentence meaning and related sentences in the document. Weights are appropriated for the sentences having higher contribution to the topic of the document. Conditional probability is evaluated for the sentence weights. Probability ratio is identified for the sentence similarity from which unique sentence meaning contributing to the document topic are listed. Experiments are conducted with the web documents extracted from the research repositories to evaluate the efficiency of the proposed efficient conceptual rule mining on text clusters in web documents and compared with an existing Model for Concept Based Clustering and Classification in terms of Topic related rules, Weights of the influential sentence, Topic Sensitivity..

Development and validation of an instrument to measure student knowledge gains for chemical and physical change for grades 6–8

Teachers tend to instruct topically, which requires the student to use multiple and interconnected concepts to succeed in each instructional unit. Therefore, it is beneficial to combine research on related concepts to form topic driven instruments to better assist teachers in assessing and instructing students. Chemical and physical change as a topic is often students' first introduction to chemical reactions; however, understanding the distinction is contingent upon a host of advanced ideas. As such, chemical and physical change is best evaluated with a strong emphasis on particle properties and behavior. To date, there was no instrument specifically designed for grades 6–8 (ages 11–14) that focused on the topic of chemical and physical change including its underlying conceptions such as the particulate nature of matter. By making use of well-designed and tested items from previously published research and item repositories, the chemical and physical change assessment (CPCA) was designed to translate findings from research to a practical and classroom-ready assessment. The CPCA went through two versions to result in a 19-item assessment that has generated valid and reliable data to date. Revisions to the assessment were driven by psychometric properties of the items as well as student validation interviews.

Bodies of Data: Genomic Data and Bioscience Data Sharing

The biosciences have become information sciences, in which knowledge is often produced in silica, by the manipulation and analysis of large datasets. Genomics has been at the forefront of the data explosion and is a model for bioscience as a large-scale endeavor. Large genome research datasets are frequently shared through research repositories. To protect the interests of people from whom the data were derived (data sources), human data are often shared through a controlled access mechanism, in which data repositories can, in theory, place limitations on who uses the data and for what purpose. Controlled access is an innovative governance mechanism, but it may not protect data sources the way policy makers intended. Here, I describe one controlled access process in some detail, and provide insight into how and why researchers fail to comply with data use restrictions.

Hyperbaric oxygen in the critically ill

To review aspects of hyperbaric medicine pertinent to treating critically ill patients with hyperbaric oxygen in both monoplace and multiplace chambers. Literature review of online databases, research repositories, and clinical trial registries. The search of these resources produced information regarding technical considerations, feasibility, risk, and patient management. Hyperbaric oxygen is used in treating a number of disorders that occur in critically ill patients, including acute carbon monoxide poisoning, arterial gas embolism, severe decompression sickness, clostridial gas gangrene, necrotizing fasciitis, and acute crush injury. Most chambers in the United States treat outpatients with problem nonhealing wounds, and many chambers are not hospital-based. Only a few hyperbaric medicine centers have intensive care unit-level staffing, specialized equipment, a 24/7 schedule, and experience in treating critically ill patients. Not all intensive care unit-related equipment can be subjected to hyperbaric pressurization, and some equipment may increase the risk for fire inside the chamber. Treating critically ill patients with hyperbaric oxygen requires specialized equipment and personnel with intensive care unit skills and knowledge of the physiology and risks unique to hyperbaric oxygen exposure. Like with all medical interventions, it is important to consider the risk vs. the benefit of hyperbaric oxygen for any given critical care disorder, but hyperbaric oxygen can be delivered safely to critically ill patients. Many critical care environments without present hyperbaric oxygen capability may wish to consider offering hyperbaric oxygen to patients with hyperbaric oxygen-approved indications.

Business Process Flow Diagrams in Tissue Bank Informatics System Design, and Identification and Communication of Best Practices: The Pharmaceutical Industry Experience

Pfizer, Inc.'s Tissue Bank, in conjunction with Pfizer's BioBank (biofluid repository), endeavored to create an overarching internal software package to cover all general functions of both research facilities, including sample receipt, reconciliation, processing, storage, and ordering. Business process flow diagrams were developed by the Tissue Bank and Informatics teams as a way of characterizing best practices both within the Bank and in its interactions with key internal and external stakeholders. Besides serving as a first step for the software development, such formalized process maps greatly assisted the identification and communication of best practices and the optimization of current procedures. The diagrams shared here could assist other biospecimen research repositories (both pharmaceutical and other settings) for comparative purposes or as a guide to successful informatics design. Therefore, it is recommended that biorepositories consider establishing formalized business process flow diagrams for their laboratories, to address these objectives of communication and strategy.

Experiences in Deploying Metadata Analysis Tools for Institutional Repositories

Current institutional repository software provides few tools to help metadata librarians understand and analyze their collections. In this article, we compare and contrast metadata analysis tools that were developed simultaneously, but independently, at two New Zealand institutions during a period of national investment in research repositories: the Metadata Analysis Tool (MAT) at The University of Waikato, and the Kiwi Research Information Service (KRIS) at the National Library of New Zealand. The tools have many similarities: they are convenient, online, on-demand services that harvest metadata using OAI-PMH; they were developed in response to feedback from repository administrators; and they both help pinpoint specific metadata errors as well as generating summary statistics. They also have significant differences: one is a dedicated tool wheres the other is part of a wider access tool; one gives a holistic view of the metadata whereas the other looks for specific problems; one seeks patterns in the data values whereas the other checks that those values conform to metadata standards. Both tools work in a complementary manner to existing Web-based administration tools. We have observed that discovery and correction of metadata errors can be quickly achieved by switching Web browser views from the analysis tool to the repository interface, and back. We summarize the findings from both tools’ deployment into a checklist of requirements for metadata analysis tools.

Comparing Repository Types: Challenges and Barriers for Subject-Based Repositories, Research Repositories, National Repository Systems and Institutional Repositories in Serving Scholarly Communication

After two decades of repository development, some conclusions may be drawn as to which type of repository and what kind of service best supports digital scholarly communication, and thus the production of new knowledge. Four types of publication repository may be distinguished, namely the subject-based repository, research repository, national repository system and institutional repository. Two important shifts in the role of repositories may be noted. With regard to content, a well-defined and high quality corpus is essential. This implies that repository services are likely to be most successful when constructed with the user and reader uppermost in mind. With regard to service, high value to specific scholarly communities is essential. This implies that repositories are likely to be most useful to scholars when they offer dedicated services supporting the production of new knowledge. Along these lines, challenges and barriers to repository development may be identified in three key dimensions: a) identification and deposit of content; b) access and use of services; and c) preservation of content and sustainability of service. An indicative comparison of challenges and barriers in some major world regions such as Europe, North America and East Asia plus Australia is offered in conclusion.

Facial Recognition From Volume-Rendered Magnetic Resonance Imaging Data

Three-dimensional (3-D) reconstructions of computed tomography (CT) and magnetic resonance (MR) brain imaging studies are a routine component of both clinical practice and clinical and translational research. A side effect of such reconstructions is the creation of a potentially recognizable face. The Health Insurance Portability and Accountability Act of 1996 (HIPAA) Privacy Rule requires that individually identifiable health information may not be used for research unless identifiers that may be associated with the health information including "Full face photographic images and other comparable images ..." are removed (de-identification). Thus, a key question is: Are reconstructed facial images comparable to full-face photographs for the purpose of identification? To address this question, MR images were selected from existing research repositories and subjects were asked to pair an MR reconstruction with one of 40 photographs. The chance probability that an observer could match a photograph with its 3-D MR image was 1 in 40 (0.025), and we considered 4 successes out of 40 (4/40, 0.1) to indicate that a subject could identify persons' faces from their 3-D MR images. Forty percent of the subjects were able to successfully match photographs with MR images with success rates higher than the null hypothesis success rate. The Blyth-Still-Casella 95% confidence interval for the 40% success rate was 29%-52%, and the 40% success rate was significantly higher ( P < 0.001) than our null hypothesis success rate of 1 in 10 (0.10).

About the future of libraries

Figure 1 shows a simplified picture of the information infrastructure of my library. It is by no means something special: I suppose any university library, or at least many of them can show similar pictures. What is special is that 80% of it did not exist 10 years ago. What the library usually is identified with is this little part in the lower left side of the chart: the catalogue, representing mainly the printed collections of the library. Do not think these are outdated, now or soon. But indeed, the usage of the printed collection is changing, if not decreasing so much. And however printed books are still published as manifold as ever before, it is clear that in science the role of print is fading. So what did libraries do? They developed digital libraries in which they make available vast amounts of primary and secondary information – an average university library nowadays offers its patrons hundreds of databases and thousands of electronic journals, e-books being on their way up. Library users now have easier access to more information than ever before. Libraries have been developing, and still are developing tools to use that information in teaching and research. In Amsterdam we built a connection between the contents of the library and the virtual learning environment, to help students getting easy access to the contents they need. Today we are building a tool for e-readers, to help teachers to facilitate their students with electronic information, even if that information is not yet electronically available. Maybe you think that all content is coming available in Open Access and that you do not need a library to get it. Well, Open Access still has a long way to go, but even in an OA paradise libraries will continue to organise, to connect, to disclose information, and to facilitate and to accommodate information users. And, for the time being, to integrate electronic and not electronic sources in one information environment. Moreover and maybe even more important, libraries have become centres of production of digital information themselves. Look at the right side of the figure: you find there a long list of products in which the library is involved as a producer. If there are so many Institutional Repositories nowadays, and if they slowly begin to be successful, it is because of the libraries that have built them and that organise the workflows to deposit research outputs of their universities in their institutional research archives. Sometimes we do this with a University Press as partner. In Amsterdam we developed a production pattern for e-dissertations together with Amsterdam University Press that can deliver print versions of any dissertation on a Printing on Demand basis anywhere in the world. Together with AUP we produce dictionaries, journals, e-books. As a library we make available image databases from our special collections. As a nation wide consortium we developed DARE, the Dutch Academic research REpositories. Today we work on so-called collaboratories to support research (SHARE) and we are developing production tools for so-called enriched or enhanced publications. At many universities the library is made responsible for the registration of research outputs of the university, because they know better than anyone else how to handle metadata.

The ARROW project

PurposeTo provide an overview of the Australian Research Repositories Online to the World (ARROW) project.Design/methodology/approachAn retrospective analysis of the first three years of the ARROW project.FindingsProvides information about the decisions made by the ARROW project, and reviews how they turned out.Originality/valueThis paper provides a review of the first three years of the ARROW project (which was the original funding horizon) from the perspective of the project team.

Examining the uses of shared data

Background Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose. Materials and Methods We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with reused data. Results Studies on humans, mice, chordata, and invertebrates were equally likely to be conducted using original or shared microarray data, whereas shared data was used in a relatively high proportion of studies involving fungi (odds ratio (OR)=2.4), and a relatively low proportion involving rats, bacteria, viruses, plants, or genetically-altered or inbred animals (OR<0.05). Unsurprisingly, when we looked at Major MeSH terms to represent the primary purpose of the studies, statistical and computational methods clearly dominated. The only biomedical topics with a relatively high proportion of data reuse Major MeSH terms were Promoter Regions, Evolution, and Protein Interaction Mapping. Discussion Identifying areas of particularly successful microarray data reuse—such as Saccharomyces cerevisiae datasets and studies of promoter regions and evolution—can highlight best practices to be used when developing research agendas, tools, standards, repositories, and communities in areas which have yet to receive major benefits from shared data.

The effects of context on data quality in biomedical data reuse

AbstractIntroductionThe collection of huge stores of electronically‐formatted information and advances in information processing technologies has led to dramatic changes in the conduct of biomedical science. In biology, a paradigm shift is underway due to an unprecedented flood of data, the emergence of shared research repositories, and advances in the application of data mining algorithms. As a result, the traditional model of scientific discovery of “formulate hypothesis, conduct experiment, evaluate results” is being replaced with “collect and store data, mine for new hypotheses, confirm with data or supplemental experiment” (Han et al. 2002). In clinical medicine, similar developments have made possible a variety of secondary applications of extant clinical data, including physician decision support, outcomes assessment, document retrieval, and clinician performance evaluation. The quality, or usefulness, of existing data for secondary uses has thus far been approached with a focus on issues of technical access and the mathematical format of data. Largely ignored in these efforts are the effects on quality introduced when data captured for one purpose is reused for another. This panel brings together four researchers with on going studies in the biomedical domain focused on the effects of context on the quality of data for secondary uses. Drawing from empirical evidence the topics to be addressed include; 1) the effects of context on data reuse, 2) anticipating, identifying and accounting for these effects, and 3) the future implications of large‐scale data reuse for information professionals in the biomedical domain.

The Role of a National Library in Supporting Research Information Infrastructure

The National Library of Australia is collaborating in a national program to improve the nation’s research information infrastructure. These activities have provided a focus for the Library in its engagement with the university community. The Library has developed integrated discovery services, actively participated in three research information infrastructure projects, and worked with partners on the problem of sustaining university repositories to support long-term access. The Library is an active partner in Project ARROW (Australian Research Repositories Online to the World), which is developing a solution for institutional repositories in collaboration with a commercial vendor, and also in the Australian Partnership for Sustainable Repositories (APSR), where the Library is helping to develop a sound approach to assessing the obsolescence risk of file formats, advising on a strategy for including preservation metadata in the repositories, and seeking to influence the future development of open source repository software to make use of preservation metadata.

Open Access Initiatives in India - an Evaluation

Developing countries have embraced open access with a view to promoting visibility of research done in these regions. Open access initiatives described in this paper are based on interviews with information professionals responsible for creation and maintenance of online research repositories in India. Open access journals, e-print archives and e-theses repositories are covered with an emphasis on the sciences including the physical sciences, mathematics and the biomedical sciences. Existing repositories were identified from the Registry of Open Access Repositories located at http://archives.eprints.org. Key contacts were facilitated by well-known local open access advocates. Participants were contacted by e-mail and sites visited wherever possible. Many universities in India are at present lacking in infrastructure for establishing institutional repositories, so most of the institutions visited were research institutes and informatics centres. Semi-structured interviews were conducted to ascertain the background of participants, institutional culture, software selection, nature of funding, submission policies and future plans of these repositories. Also covered were promotion methods, user feedback and institutional support. Barriers to setting up institutional repositories are identified in this paper. Special features are described. Based on participant feedback a list of best practices is presented. The study has definite implications for the role of Canadian librarians in the promotion of Canadian research.

Teaching intellectual property rights as part of the information literacy syllabus

PurposeTo argue that in the knowledge economy, those who are expert in understanding intellectual property issues, such as librarians and information professionals, have a special responsibility for creating policy, encouraging understanding and resolving legal disputes and conflicts unique to this aspect of the information society. One way of achieving this is through the educational impact of systematic information literacy programmes which include intellectual property issues as part of the syllabus.Design/methodology/approachAn overview of current practice and current opinion.FindingsThat the current culture, especially in higher education towards intellectual property rights, remains both confused and confusing, above all for the “information illiterate” starting out on degree‐level programmes. Attitudes and policies need to be clarified so that a coherent approach to a range of different but related intellectual property (IP) matters such as plagiarism, self‐archiving on research repositories and respect for commercially owned copyright material is uniformly developed. Debate must be differentiated from policy which in turn must be implemented via the information literacy (IL) syllabus.Research limitations/ImplicationsThis is a statement of opinion that could be tested by practical case study investigation.Practical implicationsSuggests that information literacy programmes be promoted as a way of enhancing students' understanding of intellectual property issues.Originality/valueThis paper brings together different IP issues which are not normally considered together, such as institutional research repositories, student plagiarism and commercial IP entitlements. It points out ways of unifying these in a single coherent philosophy of information society rights and ownership. This philosophy should form one of the mainstays of the information literacy syllabus.

TH‐A‐ValA‐01: The Value Proposition of the Physicist in Informatics

There exists today a vacuum in the knowledge to transform medicine with information technology (informatics). Many diagnostic physicists today get pulled into their institution's PACS implementation willingly or not and find themselves trying to provide informatics leadership. For those physicists who are interested, aiding a facility with informatics can be very rewarding. There is a strong affinity between the informatics skill set and the role of diagnostic physics in the way we bridge the worlds of science and technology with medicine. Many of the leaders of the Society of Imaging Informatics in Medicine (SIIM, formerly SCAR), are diagnostic physicists. There is an opportunity of growth for the profession to provide leadership in the changing face of medicine. A subcommittee on Imaging Informatics has been established by the AAPM to understand this opportunity. The views expressed in this talk are my own and do not necessarily reflect the opinions of the committee.We will try and present a roadmap for those physicists who are being called in to fill the informatics roles of their department or are interested in expanding their clinical tool set to include informatics. Most physicists trained today have a solid grounding in computer science. In addition to a good comprehension in computer science, an informaticist needs to know about systems management, systems integration, and project management.Systems management includes the information technology principles needed to ensure smooth operations of a large IT service such as PACS. This includes availability monitoring, change management, failure mode effects analysis, problem management, performance monitoring, disaster recovery, and continuity management to name a few. A physicist should not be a PACS administrator, but instead be the person to train the PACS administrators and provide the oversight and strategy to allow the facility take advantage of information technology. This is identical to our role in working closely and training technologists in image quality. The majority of PACS administrators are at the same educational level of imaging technologists.Systems integration is a crucial part of any IT project implemented today. The need to understand the role and value of open standards based integration such as DICOM, HL7, and IHE is critical in helping to set the vision of how the facility will interoperate with the enterprise.Project management and good communication skills are very useful in helping to coordinate large initiatives such as PACS that requires many parties to work in concert. This typically entails take the strategy view and keeping it on track at the tactical level.Also discussed will be how some basic informatics skills can help you do your job better as a physicist. There are open source tools available that can enable you to setup DICOM research repositories as well as help you automate some of the quality control role of the department to monitor image quality and dose. There is an immense amount of data that can be mined from DICOM data with some basic tools. Film printer and monitor calibration data can also be remotely monitored and aggregated with simple network management protocol (SNMP) agents.In conclusion the physicist is positioned to be a technology advocate for physicians, and extending this to include informatics can be very rewarding. There could even be some benefit to recognizing informatics in the curriculum of diagnostic physicists.Learning objectives:1. Understand the opportunity of imaging informatics for medical physicists.2. Discuss the overlap in the skill sets between informaticists and physicists.3. Discuss the pros and cons of being involved in clinical informatics projects like PACS.4. Discuss the benefits and problems of being a dual role diagnostic physicist.5. Identify additional areas a physicist should pursue to play the role of an informaticist:• Principles of Systems Management• Systems Interoperability and Data Integrity• Project Management

Repositories: What is the Target? An Arrow Perspective

The key observation about institutional research repositories is that they are under used. This paper looks at why take-up has been slow, and what might encourage researchers to use these facilities. This paper surveys the evolution of practice and rationale for the institutional research repository, looks at existing use studies and opinion surveys of users, and examines ways in which university libraries, the main proponents, have changed their approaches in response to their experience. The experience of Swinburne University of Technology, a partner in the Australian ARROW project, is drawn upon.

Cyberbanks and Other Virtual Research Repositories

Few things seem more a part of the material world than biological specimens. Yet the processes by which collections of specimens are assembled, translated into information, combined with more information, and distributed are taking research repositories into the virtual realm.The term “virtual” has a number of meanings, and so a research repository can qualify as virtual in a variety of ways. The term would seem to apply, for example, to (1) constructing a repository by forming a network among institutions; (2) using the Internet or the World Wide Web to solicit specimens and information; (3) integrating web-based technology into the operation of the bank; (4) using the Internet or web-based technology to manage relationships with donors or collection sites and recipients; and (5) digitizing specimens. The all-digital repository would seem the most virtual of all possible repositories, a true cyberbank.

Expanding the Ethical Analysis of Biobanks

Biobanks are repositories of human biological materials collected for biomedical research. There are over 300 million stored specimens in the United States, and the number grows by 20 million per year. In the post-genome world of high throughput gene sequencing and computational biology, biobanks hold the promise of facilitating large-scale research studies. New organizational and operational models of research repositories also raise complex issues of big science, big business, and big ethical concerns.

LOINC, a universal standard for identifying laboratory observations: a 5-year update.

The Logical Observation Identifier Names and Codes (LOINC) database provides a universal code system for reporting laboratory and other clinical observations. Its purpose is to identify observations in electronic messages such as Health Level Seven (HL7) observation messages, so that when hospitals, health maintenance organizations, pharmaceutical manufacturers, researchers, and public health departments receive such messages from multiple sources, they can automatically file the results in the right slots of their medical records, research, and/or public health systems. For each observation, the database includes a code (of which 25 000 are laboratory test observations), a long formal name, a "short" 30-character name, and synonyms. The database comes with a mapping program called Regenstrief LOINC Mapping Assistant (RELMA(TM)) to assist the mapping of local test codes to LOINC codes and to facilitate browsing of the LOINC results. Both LOINC and RELMA are available at no cost from http://www.regenstrief.org/loinc/. The LOINC medical database carries records for >30 000 different observations. LOINC codes are being used by large reference laboratories and federal agencies, e.g., the CDC and the Department of Veterans Affairs, and are part of the Health Insurance Portability and Accountability Act (HIPAA) attachment proposal. Internationally, they have been adopted in Switzerland, Hong Kong, Australia, and Canada, and by the German national standards organization, the Deutsches Instituts für Normung. Laboratories should include LOINC codes in their outbound HL7 messages so that clinical and research clients can easily integrate these results into their clinical and research repositories. Laboratories should also encourage instrument vendors to deliver LOINC codes in their instrument outputs and demand LOINC codes in HL7 messages they get from reference laboratories to avoid the need to lump so many referral tests under the "send out lab" code.