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1.  Collaborative Authoring of Biomedical Terminologies Using A Semantic Wiki 
To be broadly useful, biomedical terminologies need to capture the knowledge and expertise of multiple experts, research groups and end users. Consequently, the construction of such a terminology requires collaboration among multiple participants. This paper summarizes several terminology projects which employ a collaborative authoring mode in development, along with the various tools used by these projects to support collaboration, such as mailing list, issue tracking system, client-side GUI software and Wiki system. We then discuss the essential functional requirements for a collaborative authoring tool in the context of terminology development, and analyze the inherent features of Semantic Wiki that enable it to be a competent tool used in this type of effort. To demonstrate, we describe a prototype system of collaborative authoring for health care terminologies built upon the Semantic Wiki technology. Finally, we discuss the potential issues that might be associated with this open Semantic Wiki platform.
PMCID: PMC2815405  PMID: 20351856
2.  Measuring the Impact of a Moving Target: Towards a Dynamic Framework for Evaluating Collaborative Adaptive Interactive Technologies 
Background
Website evaluation is a key issue for researchers, organizations, and others responsible for designing, maintaining, endorsing, approving, and/or assessing the use and impact of interventions designed to influence health and health services. Traditionally, these evaluations have included elements such as content credibility, interface usability, and overall design aesthetics. With the emergence of collaborative, adaptive, and interactive ("Web 2.0") technologies such as wikis and other forms of social networking applications, these metrics may no longer be sufficient to adequately assess the quality, use or impact of a health website. Collaborative, adaptive, interactive applications support different ways for people to interact with health information on the Web, including the potential for increased user participation in the design, creation, and maintenance of such sites.
Objective
We propose a framework that addresses how to evaluate collaborative, adaptive, and interactive applications.
Methods
In this paper, we conducted a comprehensive review of a variety of databases using terminology related to this area.
Results
We present a review of evaluation frameworks and also propose a framework that incorporates collaborative, adaptive, and interactive technologies, grounded in evaluation theory.
Conclusion
This framework can be applied by researchers who wish to compare Web-based interventions, non-profit organizations, and clinical groups who aim to provide health information and support about a particular health concern via the Web, and decisions about funding grants by agencies interested in the role of social networks and collaborative, adaptive, and interactive technologies technologies to improve health and the health system.
doi:10.2196/jmir.1058
PMCID: PMC2762807  PMID: 19632973
Evaluation; framework; Internet; eHealth; consumer health information
3.  Collaborative authoring: a case study of the use of a wiki as a tool to keep systematic reviews up to date 
Open Medicine  2011;5(4):e201-e208.
Background
Systematic reviews are recognized as the most effective means of summarizing research evidence. However, they are limited by the time and effort required to keep them up to date. Wikis present a unique opportunity to facilitate collaboration among many authors. The purpose of this study was to examine the use of a wiki as an online collaborative tool for the updating of a type of systematic review known as a scoping review.
Methods
An existing peer-reviewed scoping review on asynchronous telehealth was previously published on an open, publicly available wiki. Log file analysis, user questionnaires and content analysis were used to collect descriptive and evaluative data on the use of the site from 9 June 2009 to 10 April 2010. Blog postings from referring sites were also analyzed.
Results
During the 10-month study period, there were a total of 1222 visits to the site, 3996 page views and 875 unique visitors from around the globe. Five unique visitors (0.6% of the total number of visitors) submitted a total of 6 contributions to the site: 3 contributions were made to the article itself, and 3 to the discussion pages. None of the contributions enhanced the evidence base of the scoping review. The commentary about the project in the blogosphere was positive, tempered with some skepticism.
Interpretations
Despite the fact that wikis provide an easy-to-use, free and powerful means to edit information, fewer than 1% of visitors contributed content to the wiki. These results may be a function of limited interest in the topic area, the review methodology itself, lack of familiarity with the wiki, and the incentive structure of academic publishing. Controversial and timely topics in addition to incentives and organizational support for Web 2.0 impact metrics might motivate greater participation in online collaborative efforts to keep scientific knowledge up to date.
PMCID: PMC3345378  PMID: 22567076
4.  Conceptualizing and Advancing Research Networking Systems 
Science in general, and biomedical research in particular, is becoming more collaborative. As a result, collaboration with the right individuals, teams, and institutions is increasingly crucial for scientific progress. We propose Research Networking Systems (RNS) as a new type of system designed to help scientists identify and choose collaborators, and suggest a corresponding research agenda. The research agenda covers four areas: foundations, presentation, architecture, and evaluation. Foundations includes project-, institution- and discipline-specific motivational factors; the role of social networks; and impression formation based on information beyond expertise and interests. Presentation addresses representing expertise in a comprehensive and up-to-date manner; the role of controlled vocabularies and folksonomies; the tension between seekers’ need for comprehensive information and potential collaborators’ desire to control how they are seen by others; and the need to support serendipitous discovery of collaborative opportunities. Architecture considers aggregation and synthesis of information from multiple sources, social system interoperability, and integration with the user’s primary work context. Lastly, evaluation focuses on assessment of collaboration decisions, measurement of user-specific costs and benefits, and how the large-scale impact of RNS could be evaluated with longitudinal and naturalistic methods. We hope that this article stimulates the human-computer interaction, computer-supported cooperative work, and related communities to pursue a broad and comprehensive agenda for developing research networking systems.
doi:10.1145/2147783.2147785
PMCID: PMC3872832  PMID: 24376309
Design; Human Factors; Management; Theory; Online knowledge communities; social networks; social software; Web 2.0; Web 2.0 applications; Web collaborative software
5.  Wikis and Collaborative Writing Applications in Health Care: A Scoping Review Protocol 
JMIR Research Protocols  2012;1(1):e1.
The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. While researchers have conducted systematic reviews on a range of software-based information and communication technologies as well as other social media (eg, virtual communities of practice, virtual peer-to-peer communities, and electronic support groups), none have reviewed collaborative writing applications in the medical sector. The overarching goal of this project is to explore the depth and breadth of evidence for the use of collaborative writing applications in health care. Thus, the purposes of this scoping review will be to (1) map the literature on collaborative writing applications; (2) compare the applications’ features; (3) describe the evidence of each application’s positive and negative effects as a KT intervention in health care; (4) inventory and describe the barriers and facilitators that affect the applications’ use; and (5) produce an action plan and a research agenda. A six-stage framework for scoping reviews will be used: (1) identifying the research question; (2) identifying relevant studies within the selected databases (using the EPPI-Reviewer software to classify the studies); (3) selecting studies (an iterative process in which two reviewers search the literature, refine the search strategy, and review articles for inclusion); (4) charting the data (using EPPI-Reviewer’s data-charting form); (5) collating, summarizing, and reporting the results (performing a descriptive, numerical, and interpretive synthesis); and (6) consulting knowledge users during three planned meetings. Since this scoping review concerns the use of collaborative writing applications as KT interventions in health care, we will use the Knowledge to Action (KTA) framework to describe and compare the various studies and collaborative writing projects we find. In addition to guiding the use of collaborative writing applications in health care, this scoping review will advance the science of KT by testing tools that could be used to evaluate other social media. We also expect to identify areas that require further systematic reviews and primary research and to produce a highly relevant research agenda that explores and leverages the potential of collaborative writing software. To date, this is the first study to use the KTA framework to study the role collaborative writing applications in KT, and the first to involve three national and international institutional knowledge users as part of the research process.
doi:10.2196/resprot.1993
PMCID: PMC3626140  PMID: 23612481
6.  Facebook for Scientists: Requirements and Services for Optimizing How Scientific Collaborations Are Established 
Background
As biomedical research projects become increasingly interdisciplinary and complex, collaboration with appropriate individuals, teams, and institutions becomes ever more crucial to project success. While social networks are extremely important in determining how scientific collaborations are formed, social networking technologies have not yet been studied as a tool to help form scientific collaborations. Many currently emerging expertise locating systems include social networking technologies, but it is unclear whether they make the process of finding collaborators more efficient and effective.
Objective
This study was conducted to answer the following questions: (1) Which requirements should systems for finding collaborators in biomedical science fulfill? and (2) Which information technology services can address these requirements?
Methods
The background research phase encompassed a thorough review of the literature, affinity diagramming, contextual inquiry, and semistructured interviews. This phase yielded five themes suggestive of requirements for systems to support the formation of collaborations. In the next phase, the generative phase, we brainstormed and selected design ideas for formal concept validation with end users. Then, three related, well-validated ideas were selected for implementation and evaluation in a prototype.
Results
Five main themes of systems requirements emerged: (1) beyond expertise, successful collaborations require compatibility with respect to personality, work style, productivity, and many other factors (compatibility); (2) finding appropriate collaborators requires the ability to effectively search in domains other than your own using information that is comprehensive and descriptive (communication); (3) social networks are important for finding potential collaborators, assessing their suitability and compatibility, and establishing contact with them (intermediation); (4) information profiles must be complete, correct, up-to-date, and comprehensive and allow fine-grained control over access to information by different audiences (information quality and access); (5) keeping online profiles up-to-date should require little or no effort and be integrated into the scientist’s existing workflow (motivation). Based on the requirements, 16 design ideas underwent formal validation with end users. Of those, three were chosen to be implemented and evaluated in a system prototype, “Digital|Vita”: maintaining, formatting, and semi-automated updating of biographical information; searching for experts; and building and maintaining the social network and managing document flow.
Conclusions
In addition to quantitative and factual information about potential collaborators, social connectedness, personal and professional compatibility, and power differentials also influence whether collaborations are formed. Current systems only partially model these requirements. Services in Digital|Vita combine an existing workflow, maintaining and formatting biographical information, with collaboration-searching functions in a novel way. Several barriers to the adoption of systems such as Digital|Vita exist, such as potential adoption asymmetries between junior and senior researchers and the tension between public and private information. Developers and researchers may consider one or more of the services described in this paper for implementation in their own expertise locating systems.
doi:10.2196/jmir.1047
PMCID: PMC2553246  PMID: 18701421
Expertise locating systems; computer supported collaborative work; information systems; collaborators; research; social networks; translational research
7.  Agile methods in biomedical software development: a multi-site experience report 
BMC Bioinformatics  2006;7:273.
Background
Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods.
Results
We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations.
Conclusion
We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods.
doi:10.1186/1471-2105-7-273
PMCID: PMC1539031  PMID: 16734914
8.  The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community 
BMC Bioinformatics  2009;10(Suppl 6):S1.
The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in.
doi:10.1186/1471-2105-10-S6-S1
PMCID: PMC2697632  PMID: 19534734
9.  Mining the Gene Wiki for functional genomic knowledge 
BMC Genomics  2011;12:603.
Background
Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology.
Results
Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses.
Conclusions
The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.
doi:10.1186/1471-2164-12-603
PMCID: PMC3271090  PMID: 22165947
10.  Automated seeding of specialised wiki knowledgebases with BioKb 
BMC Bioinformatics  2009;10:291.
Background
Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to collaborate around a specific domain, for example a biological pathway. Automatically gathered seed data could be modified by the group and enriched with domain specific information.
Results
We describe a software system, BioKb, implemented as a plugin for the TWiki engine, and designed to facilitate construction of a field-specific wiki containing collaborative and automatically generated content. Features of this system include: query of publicly available resources such as KEGG, iHOP and MeSH, to generate 'seed' content for topics; simple definition of structure for topics of different types via an administration page; and interactive incorporation of relevant PubMed references. An exemplar is shown for the use of this system, in the creation of the RAASWiki knowledgebase on the renin-angiotensin-aldosterone system (RAAS). RAASWiki has been seeded with data by use of BioKb, and will be the subject of ongoing development into an extensive knowledgebase on the RAAS.
Conclusion
The BioKb system is available from http://www.bioinf.mvm.ed.ac.uk/twiki/bin/view/TWiki/BioKbPlugin as a plugin for the TWiki engine.
doi:10.1186/1471-2105-10-291
PMCID: PMC2753848  PMID: 19758431
11.  The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches 
Journal of proteome research  2008;7(11):4848-4857.
Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies.
doi:10.1021/pr800443f
PMCID: PMC2677910  PMID: 18817429
Collaboratory; data analysis tools; structural biology; mass spectrometry
12.  Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies 
Genes & Nutrition  2010;5(3):189-203.
The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution in ‘omics’ technologies, it has discipline-specific requirements for analytical and bioinformatic procedures. In addition to measurements of the parameters of interest (measures of health), extensive description of the subjects of study and foods or diets consumed is central for describing the nutritional phenotype. We propose and pursue an infrastructural activity of constructing the “Nutritional Phenotype database” (dbNP). When fully developed, dbNP will be a research and collaboration tool and a publicly available data and knowledge repository. Creation and implementation of the dbNP will maximize benefits to the research community by enabling integration and interrogation of data from multiple studies, from different research groups, different countries and different—omics levels. The dbNP is designed to facilitate storage of biologically relevant, pre-processed—omics data, as well as study descriptive and study participant phenotype data. It is also important to enable the combination of this information at different levels (e.g. to facilitate linkage of data describing participant phenotype, genotype and food intake with information on study design and—omics measurements, and to combine all of this with existing knowledge). The biological information stored in the database (i.e. genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition) is tailored to nutrition research and embedded in an environment of standard procedures and protocols, annotations, modular data-basing, networking and integrated bioinformatics. The dbNP is an evolving enterprise, which is only sustainable if it is accepted and adopted by the wider nutrition and health research community as an open source, pre-competitive and publicly available resource where many partners both can contribute and profit from its developments. We introduce the Nutrigenomics Organisation (NuGO, http://www.nugo.org) as a membership association responsible for establishing and curating the dbNP. Within NuGO, all efforts related to dbNP (i.e. usage, coordination, integration, facilitation and maintenance) will be directed towards a sustainable and federated infrastructure.
doi:10.1007/s12263-010-0167-9
PMCID: PMC2935528  PMID: 21052526
Nutritional phenotype; Nutrigenomics; Database
13.  Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies 
Genes & Nutrition  2010;5(3):189-203.
The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution in ‘omics’ technologies, it has discipline-specific requirements for analytical and bioinformatic procedures. In addition to measurements of the parameters of interest (measures of health), extensive description of the subjects of study and foods or diets consumed is central for describing the nutritional phenotype. We propose and pursue an infrastructural activity of constructing the “Nutritional Phenotype database” (dbNP). When fully developed, dbNP will be a research and collaboration tool and a publicly available data and knowledge repository. Creation and implementation of the dbNP will maximize benefits to the research community by enabling integration and interrogation of data from multiple studies, from different research groups, different countries and different—omics levels. The dbNP is designed to facilitate storage of biologically relevant, pre-processed—omics data, as well as study descriptive and study participant phenotype data. It is also important to enable the combination of this information at different levels (e.g. to facilitate linkage of data describing participant phenotype, genotype and food intake with information on study design and—omics measurements, and to combine all of this with existing knowledge). The biological information stored in the database (i.e. genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition) is tailored to nutrition research and embedded in an environment of standard procedures and protocols, annotations, modular data-basing, networking and integrated bioinformatics. The dbNP is an evolving enterprise, which is only sustainable if it is accepted and adopted by the wider nutrition and health research community as an open source, pre-competitive and publicly available resource where many partners both can contribute and profit from its developments. We introduce the Nutrigenomics Organisation (NuGO, http://www.nugo.org) as a membership association responsible for establishing and curating the dbNP. Within NuGO, all efforts related to dbNP (i.e. usage, coordination, integration, facilitation and maintenance) will be directed towards a sustainable and federated infrastructure.
doi:10.1007/s12263-010-0167-9
PMCID: PMC2935528  PMID: 21052526
Nutritional phenotype; Nutrigenomics; Database
14.  TOPSAN: a collaborative annotation environment for structural genomics 
BMC Bioinformatics  2010;11:426.
Background
Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-reviewed manuscript. Because of this they are not accessible by the standard tools of literature searches, remaining underutilized by the broad biological community.
Results
To address this issue we have developed TOPSAN, The Open Protein Structure Annotation Network, a web-based platform that combines the openness of the wiki model with the quality control of scientific communication. TOPSAN enables research collaborations and scientific dialogue among globally distributed participants, the results of which are reviewed by experts and eventually validated by peer review. The immediate goal of TOPSAN is to harness the combined experience, knowledge, and data from such collaborations in order to enhance the impact of the astonishing number and diversity of structures being determined by structural genomics centers and high-throughput structural biology.
Conclusions
TOPSAN combines features of automated annotation databases and formal, peer-reviewed scientific research literature, providing an ideal vehicle to bridge a gap between rapidly accumulating data from high-throughput technologies and a much slower pace for its analysis and integration with other, relevant research.
doi:10.1186/1471-2105-11-426
PMCID: PMC2936398  PMID: 20716366
15.  Use of a wiki as an interactive teaching tool in pathology residency education: Experience with a genomics, research, and informatics in pathology course 
Background:
The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in “Web 2.0”) in a combined informatics and genomics course could both (1) serve as an interactive, collaborative educational resource and reference and (2) actively engage trainees by requiring the creation and sharing of educational materials.
Materials and Methods:
A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP) was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software). Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki) and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics) given at our institution that did not utilize wikis.
Results:
Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12%) in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006).
Conclusions:
Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation is an effective mechanism for mastery of content. Future residents taking this course will continue to build on this wiki, keeping content current, and thereby benefit from this collaborative teaching tool.
doi:10.4103/2153-3539.100366
PMCID: PMC3445302  PMID: 23024891
Education; pathology Informatics; resident training; Wiki
16.  Collaborative research: Accomplishments & potential 
Although a substantial part of scientific research is collaborative and increasing globalization will probably lead to its increase, very few studies actually investigate the advantages, disadvantages, experiences and lessons learned from collaboration. In environmental epidemiology interdisciplinary collaboration is essential and the contrasting geographical patterns in exposure and disease make multi-location projects essential. This paper is based on a presentation given at the Annual Conference of the International Society for Environmental Epidemiology, Paris 2006, and is attempting to initiate a discussion on a framework for studying collaborative research. A review of the relevant literature showed that indeed collaborative research is rising, in some countries with impressive rates. However, there are substantial differences between countries in their outlook, need and respect for collaboration. In many situations collaborative publications receive more citations than those based on national authorship. The European Union is the most important host of collaborative research, mainly driven by the European Commission through the Framework Programmes. A critical assessment of the tools and trends of collaborative networks under FP6, showed that there was a need for a critical revision, which led to changes in FP7. In conclusion, it is useful to study the characteristics of collaborative research and set targets for the future. The added value for science and for the researchers involved may be assessed. The motivation for collaboration could be increased in the more developed countries. Particular ways to increase the efficiency and interaction in interdisciplinary and intercultural collaboration may be developed. We can work towards "the principles of collaborative research" in Environmental Epidemiology.
doi:10.1186/1476-069X-7-3
PMCID: PMC2265690  PMID: 18208596
17.  How Practice and Science Are Balanced and Blended in the NIDA Clinical Trials Network: The Bidirectional Process in the Development of the STAGE-12 Protocol as an Example 
Background
Bidirectional, collaborative partnerships between academic researchers and practitioners have been a fundamental vehicle to achieve the National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) goal of improving outcomes of community-based drug treatment. These partnerships blend clinical perspectives of practitioners and methodological expertise of researchers working together to address clinically meaningful issues through randomized clinical trials conducted in community treatment settings.
Objectives
Bidirectionality is a guiding principle of the CTN, but its operationlization at the practical level in protocol development and implementation has not been articulated. This descriptive article presents the development of one protocol as an example and model of this bidirectional, collaborative, iterative partnership between researchers and practitioners.
Methods
This article illuminates several specific issues encountered while developing STAGE-12, a behavioral intervention to facilitate 12-step mutual support group involvement, as well as the rationale for decisions taken to resolve each.
Results
The STAGE-12 protocol was successfully developed through a series of decisions taking into account both design factors and clinical practice needs and realities, thus maintaining a balance between methodological rigor and generalizability.
Conclusion
The review demonstrates the process by which research and practice have been blended in protocol development, exemplifying the underlying principle of bidirectionality, a key element in the success of the NIDA CTN.
Scientific Significance
Bidirectional partnerships as derived in the CTN, employing a hybrid model of efficacy-effectiveness research, are capable of designing and implementing protocols that are both methodologically rigorous and clinically meaningful, thus increasing likelihood of adoption and eventual improvement in public health.
doi:10.3109/00952990.2011.596970
PMCID: PMC3260794  PMID: 21854284
bidirectionality; research; clinical practice; internal validity; external validity; clinical trials network; protocol development
18.  C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training 
PLoS ONE  2008;3(2):e1621.
The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members.
doi:10.1371/journal.pone.0001621
PMCID: PMC2229842  PMID: 18286178
19.  Adopting Best Practices from Team Science in a Healthcare Improvement Research Network: The Impact on Dissemination and Implementation 
Nursing Research and Practice  2013;2013:814360.
Healthcare is a complex adaptive system, and efforts to improve through the implementation of best practice are well served by various interacting disciplines within the system. As a transdisciplinary model is new to clinicians, an infrastructure that creates academic-practice partnerships and builds capacity for scientific collaboration is necessary to test, spread, and implement improvement strategies. This paper describes the adoption of best practices from the science of team science in a healthcare improvement research network and the impact on conducting a large-scale network study. Key components of the research network infrastructure were mapped to a team science framework and evaluated in terms of their effectiveness and impact on a national study of nursing operations. Results from this study revealed an effective integration of the team science principles which facilitated the rapid collection of a large dataset. Implications of this study support a collaborative model for improvement research and stress a need for future research and funding to further evaluate the impact on dissemination and implementation.
doi:10.1155/2013/814360
PMCID: PMC3613075  PMID: 23577246
20.  WhatisKT wiki: a case study of a platform for knowledge translation terms and definitions — descriptive analysis 
Background
More than a hundred terms, often with unclear definitions and varying emphases, are used by health research and practice communities across the world who are interested in getting the best possible evidence applied (e.g., knowledge translation, implementation science, diffusion of innovations, and technology transfer). This makes finding published evidence difficult and can result in reduced, misinterpreted, or challenging interactions among professionals. Open dialogue and interaction among various professionals is needed to achieve consolidation of vocabulary. We use case report methods to describe how we sought to build an online tool to present the range of terms and facilitate the dialogue process across groups and disciplines interested in harnessing research evidence for healthcare.
Methods
We used a wiki platform from Wikispaces to present the problem of terminology and make a case and opportunity for collaboration on usage. Wikis are web sites where communities of users can collaborate online to build content and discuss progress. We gathered terms related to getting research into practice, sought published definitions, and posted these on the wiki (WhatisKT http://whatiskt.wikispaces.com/). We built the wiki in mid-2008 and promoted it through various groups and publications. This report describes the content of the site, our promotion efforts, use of the site, and how the site was used for collaboration up to the end of 2011.
Results
The WhatisKT wiki site now includes more than 120 pages. Traffic to the site has increased substantially from an average of 200 monthly visits in 2008 to 1700 in 2011. Visitors from 143 countries viewed the wiki in 2011, compared with 12 countries in 2008. However, most use has been limited to short term accesses of about 40 seconds per visit, and discussion of consolidation and solidifying terminology is conspicuously absent.
Conclusions
Although considerable interest exists in the terms and definitions related to getting research into practice based on increasing numbers of accesses, use of the WhatisKT wiki site for anything beyond quick lookups was minimal. Additional efforts must be directed towards increasing the level of interaction among the members of the site to encourage collaboration on term use.
doi:10.1186/1748-5908-8-13
PMCID: PMC3564745  PMID: 23347357
Diffusion of innovations; Research; Knowledge translation; Implementation science
21.  WikiBuild: A New Application to Support Patient and Health Care Professional Involvement in the Development of Patient Support Tools 
Active patient and public involvement as partners in their own health care and in the development of health services is key to achieving a health care system that is responsive to patients’ needs and values. It promotes better use of the health care system, and improves health outcomes, quality of life and patient satisfaction. By involving patients and health care professionals as partners in the creation and updating of patient health support tools, wikis—highly accessible, interactive vehicles of communication—have the potential to empower users to implement these support tools in daily life. Acknowledging the potential of wikis, and recognizing that they capitalize on the free and open access to information, scientists, opinion leaders and patient advocates have suggested that wikis could help decision-making constituencies improve the delivery of health care. They might also decrease its cost and improve access to knowledge within developing countries. However, little is known about the efficacy of wikis in helping to attain these goals. There is also a need to know more about the intention of patients and health care workers to use wikis, in what circumstances and what factors will influence their use of wikis. In this issue of the Journal of Medical Internet Research, Gupta et al describe how they developed and tested a new wiki-inspired application to improve asthma care. The researchers involved patients with asthma, primary care physicians, pulmonologists and certified asthma educators in the construction of an asthma action plan. Their paper—entitled “WikiBuild: a new online collaboration process for multistakeholder tool development and consensus building”—is the first description of a wiki-inspired technology built to involve patients and health care professionals in the development of a patient support tool. This innovative study has made important contributions toward how wikis could be generalized to involve multiple stakeholders in the development of other knowledge translation tools such as clinical practice guidelines or decision aids. More specifically, Gupta et al have uncovered potential action mechanisms toward increasing usage of these tools by patients and health care professionals. These are decreasing hierarchical influences, increasing usability and adapting a tool to local context. More research is now needed to determine if the use of the resulting wiki-developed plan will actually be higher than a plan developed using other methods. Furthermore, there is also a need to assess the intention of participants to continue using wiki-based processes on an ongoing basis. It is in this dynamic and continuous retroaction loop that the support tool users—both patients and health care professionals—can adapt and improve the product after its real-life shortcomings are revealed and as new evidence becomes available. As such, a wiki would be more than a simple patient support development tool, but could also become a dynamic and interactive repository and delivery tool that would facilitate ongoing and sustainable patient and professional engagement.
doi:10.2196/jmir.1961
PMCID: PMC3278100  PMID: 22155746
Medical informatics; patient-centered care; wikis; collaborative writing applications; knowledge translation; patient and public involvement
22.  International Stem Cell Collaboration: How Disparate Policies between the United States and the United Kingdom Impact Research 
PLoS ONE  2011;6(3):e17684.
As the scientific community globalizes, it is increasingly important to understand the effects of international collaboration on the quality and quantity of research produced. While it is generally assumed that international collaboration enhances the quality of research, this phenomenon is not well examined. Stem cell research is unique in that it is both politically charged and a research area that often generates international collaborations, making it an ideal case through which to examine international collaborations. Furthermore, with promising medical applications, the research area is dynamic and responsive to a globalizing science environment. Thus, studying international collaborations in stem cell research elucidates the role of existing international networks in promoting quality research, as well as the effects that disparate national policies might have on research. This study examined the impact of collaboration on publication significance in the United States and the United Kingdom, world leaders in stem cell research with disparate policies. We reviewed publications by US and UK authors from 2008, along with their citation rates and the political factors that may have contributed to the number of international collaborations. The data demonstrated that international collaborations significantly increased an article's impact for UK and US investigators. While this applied to UK authors whether they were corresponding or secondary, this effect was most significant for US authors who were corresponding authors. While the UK exhibited a higher proportion of international publications than the US, this difference was consistent with overall trends in international scientific collaboration. The findings suggested that national stem cell policy differences and regulatory mechanisms driving international stem cell research in the US and UK did not affect the frequency of international collaborations, or even the countries with which the US and UK most often collaborated. Geographical and traditional collaborative relationships were the predominate considerations in establishing international collaborations.
doi:10.1371/journal.pone.0017684
PMCID: PMC3050923  PMID: 21408134
23.  The Gene Wiki: community intelligence applied to human gene annotation 
Nucleic Acids Research  2009;38(Database issue):D633-D639.
Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki ‘stubs’ for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a critical mass of users and editors. Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene_Wiki.
doi:10.1093/nar/gkp760
PMCID: PMC2808918  PMID: 19755503
24.  Making your database available through Wikipedia: the pros and cons 
Nucleic Acids Research  2011;40(D1):D9-D12.
Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.
doi:10.1093/nar/gkr1195
PMCID: PMC3245093  PMID: 22144683
25.  Research Electronic Data Capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support 
Journal of biomedical informatics  2008;42(2):377-381.
REDCap is a novel workflow methodology and software solution designed for rapid development and deployment of electronic data capture tools to support clinical and translational research. We present: 1) a brief description of the REDCap metadata-driven software toolset; 2) detail concerning the capture and use of study-related metadata from scientific research teams; 3) measures of impact for REDCap; 4) details concerning a consortium network of domestic and international institutions collaborating on the project; and 5) strengths and limitations of the REDCap system. REDCap is currently supporting 286 translational research projects in a growing collaborative network including 27 active partner institutions.
doi:10.1016/j.jbi.2008.08.010
PMCID: PMC2700030  PMID: 18929686
Medical Informatics; Electronic Data Capture; Clinical Research; Translational Research

Results 1-25 (856467)