PDP Site DREAM Principles

PDP: Info | NPDS | DREAM | FAIR | Design | Diristries | Entities | Privacy

PDP Reports: DREAM Principles

Reports: 2006-2010 | 2011-2015 | 2016-2020 | 2021-2025

Reports 2021-2025

• Adam Craig, Anousha Athreya, Carl Taswell, 2023, Managing Lexical-Semantic Hybrid Records of FAIR Metrics Analyses with the NPDS Cyberinfrastructure Brainiacs Journal 2023 Volume 4 Issue 2 Edoc D5B2734F2, also via DOI 10.48085/D5B2734F2.

  Current approaches to plagiarism detection often focus on finding lexical matches rather than semantic similarities in the text content that is compared. But the more important unanswered questions remain whether similar concepts expressed in related topical contexts are semantically equivalent as idea-laundering plagiarism by humans or algorithm-generated plagiarism by machines. Now publicly available and easily accessible, text-generating algorithms have automated the process of assembling a text derived from but not attributed to published content scraped from the web. The FAIR Metrics, with FAIR an acronym for Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records, measure how appropriately a document cites prior records based on whether they contain similar claims that are equivalent in meaning. We demonstrate herein a workflow with results for manual evaluation of the FAIR Metrics to quantify the extent of plagiarism in 8 articles retracted or reported for plagiarism. We also demonstrate use of the Nexus-PORTAL-DOORS-Scribe (NPDS) Cyberinfrastructure to manage semantic descriptions of the concept mappings and entity equivalence evaluations made using concepts and relationships from the PDP-DREAM Ontology.

• Adam Craig and Carl Taswell, 2023, Managing Bibliometrics with Contributor Roles and Literature Provenance for NPDS Metadata Records Brainiacs Journal 2023 Volume 4 Issue 1 Edoc X934EF46B, also via DOI 10.48085/X934EF46B.

  Tracking the provenance of information and knowledge with sources, concepts, ideas and the contributions of creators, inventors, and scholars remains essential to the reproducibility of scientific results, the reliability of engineering methods, the integrity of clinical trials, and the fair allocation of research and development resources. Since the first version, the PORTAL-DOORS Project (PDP) has provided schemas for the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure which have always supported inclusion of provenance data as part of the metadata describing the entity corresponding to an NPDS record. However, PDP has not yet provided alternative templated formats for the provenance infosubset (aka, provenance facet) of the entire infoset that documents the entity for the identified NPDS record. Therefore, this report introduces a template for the provenance facet suitable for a generic entity type, along with alternatives appropriate for various specific entity types, including a template for authored publications that enables descriptions of contributor roles compatible with the CRediT taxonomy. By extending the PDP-DREAM ontology and creating a provenance subontology for the NPDS cyberinfrastructure with semantic classes and properties for these contributor roles, semantic search in NPDS repositories can be facilitated to support more effective discovery of resources with consideration of entities as same, similar, related, or different.

• Adam Craig and Carl Taswell, 2022, Inclusion and Exclusion Criteria for Automating Adherence to Scope of Conference Calls for Papers presented September 2022 at the 4th IEEE Conference on Transdisciplinary Artificial Intelligence (TransAI) in Laguna Hills, California; also via DOI 10.1109/TransAI54797.2022.00018.

  To conduct a well-designed and reproducible study, researchers must define and adhere to clear inclusion and exclusion criteria for subjects. Similarly, a well-run journal or conference should publish easily understood inclusion and exclusion criteria that determine which submissions will receive more detailed peer review. This will empower authors to identify the conferences and journals that are the best fit for their manuscripts while allowing organizers and peer reviewers to spend more time on the submissions that are of greatest interest. To provide a more systematic way of representing these criteria, we extend the syntax for concept-validating constraints of the Nexus-PORTAL-DOORS-Scribe cyberinfrastructure, which already serve as criteria for inclusion of records in a repository, to allow description of exclusion criteria.

• Aniruddh Anand and Carl Taswell, 2022, An Information-Resilient Big-Data Workbench with PDP-DREAM Software presented October 2022 at the 85th ASIS&T Annual Meeting of the Association for Information Science and Technology in Pittsburgh, Pennsylvania.

  PORTAL-DOORS Project DREAM Software, available as an open-source C#-centric codebase from a Github public repository at PDP-DREAM, implements the PDP-DREAM principles and PDP-FAIR metrics with web-enabled workbench software for distributed data repositories in the Nexus-PORTAL-DOORS-Scribe Cyberinfrastructure. PDP-DREAM Software has been developed for Microsoft platform technologies with ASP.NET Core, SQL Server, and Internet Information Server. As a web-enabled workbench, PDP-DREAM provides many features for big data management with tools and services to support information resilience in defense of truth in science and integrity in research.

• Adam Craig and Carl Taswell, 2021, PDP-DREAM Software for Integrating Multimedia Data with Interoperable Repositories Brainiacs Journal 2021 Volume 2 Issue 1 Edoc HA46280EF, also via DOI 10.48085/HA46280EF.

  Integrating multimedia data in a meaningful way requires keeping track of the who, what, where, when, and how of many kinds of data and metadata in different formats. The PORTAL-DOORS-Project (PDP) was formed to design and build the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure for managing and distributing resource data and metadata in a manner compatible with both the established lexical web and the developing semantic web. PDP-DREAM software, archived at github.com/bhavius/pdp-dream, represents the first publicly available, open-source implementation of NPDS. It provides RESTful web services for software agents and user-friendly web applications for human agents so that individuals and organizations can create and publish their own problem-oriented and domain-specific repositories customized for their own purposes. In this report, we also introduce the NpdsQuads format with an approach to formatting the comments of N-quads files as name-value pairs for content from NPDS records which can be exported from and imported to NPDS repositories. We then describe the use of these tools in the curation of the PDP-DREAM ontology, which serves as the foundational ontology for the NPDS cyberinfrastructure. Finally, we discuss the planned use of PDP-DREAM software in a medical imaging clinical trial for multiple sclerosis.

• Carl Taswell, 2021, The NPDS Cyberinfrastructure presented October 2021 with slides at the Science Gateways 2021 Conference in San Diego, California.

  The Nexus-PORTAL-DOORS-Scribe (NPDS) Cyberinfrastructure provides a ‘who what where’ diristry-registry-directory system for identifying, describing, locating and linking things on the internet, web and grid. PORTAL registries identify resources with unique labels and lexical tags in a manner compatible with the lexical web. DOORS directories specify locations and semantic descriptions for these identified resources in a manner compatible with the semantic web. PORTAL registries and DOORS directories were designed to be analogous to IRIS registries and DNS directories. This original design has been enhanced with Nexus diristries to provide integrated services combining the functions of both PORTAL registries and DOORS directories. The principles for the PORTAL-DOORS Project (PDP) were first proposed and described by Taswell in 2006 as the foundation for work on PDP and the NPDS cyberinfrastructure. This work on PDP and NPDS has been continuously available since 2007 from a publicly accessible web site at www.PORTALDOORS.org. The 2006 PDP principles were renamed the 2019 DREAM principles with the acronym DREAM for "Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata". PDP-DREAM software, available as open source software at Github, provides a comprehensive suite of software for management of the data repositories in the NPDS cyberinfrastructure. A version of PDP-DREAM software has been implemented with Microsoft platform technologies (C#, SQL Server, IIS Server), has been tested on the previews for Net 6, and will be fully validated for compatibility with Net 6 concomitant with its general availability release later in 2021.

Reports 2016-2020

• Adam Craig, Peter Hong, Shreya Choksi, Anousha Athreya, and Carl Taswell, 2020, Survey, Analysis, and Requirements for Semantic Enhancement to Support Machine Understanding of Scientific Literature Brainiacs Journal 2020 Volume 1 Issue 1 Edoc D11DABE6D, also via DOI 10.48085/D11DABE6D.

  Adoption of the proposed recommendations with standards set forth by the World Wide Web Consortium (W3C) regarding the semantic web remains a work in progress, especially with regard to their use in the published research literature. Proponents of the semantic enhancement of scholarly publishing have described it as a visionary breakthrough for the way in which both individuals and machines should be able to obtain meaningful information from data, text, and content management systems. However, the availability and prevalence of useful real-world resources remains limited. In this report, we present a survey of those scholarly research journals that focus on the semantic web and ontology engineering. We highlight noteworthy examples of publishers offering semantic enhancement and markup services in hopes of shedding light on tools that could revolutionize how both academic scholars and the lay public find and understand the published results of scientific research. We then consider the implications of these findings for the growth and development of the semantic web as a whole. We also review proposals for how the semantic web could accelerate the advancement of brain sciences and brain health. Finally, we propose a novel approach to scholarly publishing represented by our planned semantic enhancement workflow process for the Brainiacs Journal. By surveying the current use of the semantic web, we show the need for more motivated and enthusiastic adoption of semantic enhancement in scholarly publishing in order to 'stand on the shoulders of giants' and reap the benefits of published research.

• S. Koby Taswell, Christopher Triggle, June Vayo, Shiladitya Dutta, and Carl Taswell, 2020, The Hitchhiker's Guide to Scholarly Research Integrity also via DOI 10.1002/pra2.223 presented with hyperlinked version and slides October 2020 at the 83rd ASIS&T Annual Meeting of the Association for Information Science and Technology

  The pursuit of truth in research should be both an ideal in aspiration and also a reality in practice. The PORTAL-DOORS Project (PDP) strives to promote creative authenticity, fair citation, and adherence to integrity and ethics in scholarly research publishing using the FAIR family of quantitative metrics with acronym FAIR for the phrases Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records, and the DREAM principles with acronym DREAM for the phrase Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata. This report presents formalized definitions for idea-laundering plagiarism by authors, idea-bleaching censorship by editors, and proposed assertion claims for authors, reviewers, editors, and publishers in ethical peer-reviewed publishing to support integrity in research. All of these principles have been implemented in version 2 of the PDP-DREAM ontology written in OWL 2. This PDP-DREAM ontology will serve as the model foundation for development of a software-guided workflow process intended to manage the ethical peer-reviewed publishing of web-enabled open access journals operated online with PDP software.

• Shiladitya Dutta, Kelechi Uhegbu, Sathvik Nori, Sohyb Mashkoor, S. Koby Taswell, and Carl Taswell, 2020, DREAM Principles from the PORTAL-DOORS Project and NPDS Cyberinfrastructure also via DOI 10.1109/ICSC.2020.00044 presented February 2020 at the 14th IEEE International Conference on Semantic Computing in San Diego, California.

  The PORTAL-DOORS Project (PDP) has been pursued to develop the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure as a distributed network system of data repositories to manage lexical and semantic data and metadata from and/or about online and offline resources. Designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style in a manner analogous to IRIS-DNS, the NPDS cyberinfrastructure provides distributed multilevel metadata management as an open, flexible, and extensible networked system of independent community customizable who-what-where registries, directories, and diristries for identifying, describing, locating, and linking things on the internet, web and grid. In the current work reported here, we combined our original principles from PDP, HDMM, and NPDS together with additional principles for scientific reproducibility and social engineering related to our family of quantitative metrics with acronym FAIR for Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records. We call this new consolidated collection of principles the DREAM principles with acronym DREAM for the phrase Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata. To codify these DREAM principles as a concrete artifact for the semantic web, and thus to operationalize their use, we developed an OWL 2.0 ontology that we named the PDP-DREAM ontology.

• Shiladitya Dutta, Pooja Kowshik, Adarsh Ambati, Sathvik Nori, S. Koby Taswell, and Carl Taswell, 2019, Managing Scientific Literature with Software from the PORTAL-DOORS Project also via DOI 10.1109/eScience.2019.00081 presented with slides and demo video September 2019 at the Bridging from Concepts to Data and Computation for eScience (BC2DC'19) Workshop of the IEEE 15th International Conference on eScience in San Diego, California. See also IEEE Xplore eScience conference series proceedings.

  Scholarly research associated with finding and citing scientific literature in the 21st century requires new approaches to address the continuing problems that occur with the provenance of content in the literature as well as the peer and editorial review process for publishing this literature. The PORTAL-DOORS Project (PDP) has developed software for the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure in support of identifying, describing, locating and linking things on the internet, web and grid with both lexical and semantic tools and applications. This presentation of our PDP software will highlight Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata with the DREAM principles, and the Fair Acknowledgment of Information Records also called the Fair Attribution to Indexed Reports with the FAIR metrics. This software demonstration will explain use of the network of metadata repositories for scientific literature accessible from www.portaldoors.org, and use of the open source software that powers the NPDS cyberinfrastructure, PDP websites and PDP web services. Our PDP software for the NPDS cyberinfrastructure will be released publicly at this presentation of the software where we will also discuss challenges in the peer review process that include plagiarism detection.

• Adam Craig, Adarsh Ambati, Shiladitya Dutta, Pooja Kowshik, Sathvik Nori, S. Koby Taswell, Qiyuan Wu, and Carl Taswell, 2019, DREAM Principles and FAIR Metrics from the PORTAL-DOORS Project for the Semantic Web also via DOI 10.1109/ECAI46879.2019.9042003 presented with slides June 2019 at the 11th Annual IEEE International Conference on Electronics, Computers and Artificial Intelligence in Pitesti, Romania.

  Articles published in Scientific Data by Wilkinson et al. argued for the adoption of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles of data management without citing any of the prior work published by Taswell. However, these principles were first proposed and described by Taswell in 2006 as the foundation for work on the PORTAL-DOORS Project (PDP) and the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure, and have been published in numerous conference presentations, journal articles, and patents. This work on PDP and NPDS has been continuously available since 2007 from a publicly accessible web site at www.portaldoors.org, and discussed in person at conferences with several key authors of the Wilkinson et al. papers. Paraphrasing without citing the PDP and NPDS principles while renaming them as the FAIR principles raises questions about both the ‘FAIRness’ and the fairness of the authors of the Wilkinson et al. papers. Promoting these principles with the use of the term ‘metrics’, which are not metrics by definition of the term metric as used in most fields of science, also raises questions about their commitment to maintaining consistency of usage for basic terminology across different fields of science as should be expected for terms in ontology mapping with knowledge engineering for the semantic web. Therefore, in the present report, we clarify the origin of their FAIR principles by identifying our PDP and NPDS principles that constitute the historical precedent for their FAIR principles. Moreover, as the comprehensively summarizing phrase for all of our PDP and NPDS principles, we rename them the DREAM principles with the acronym DREAM for Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata. Finally, we define numerically valid quantitative FAIR metrics to monitor and measure the DREAM principles from the perspective of the most important principle, ie, the Fair Acknowledgment of Information Records and Fair Attribution to Indexed Reports, for maintaining fair standards of citation in scholarly research and publishing.

• Shiladitya Dutta and Carl Taswell, 2018, SPARQL-Based Search Engine and Agent for Finding Brain Literature and Converting References to NPDS Metadata Records presented December 2018 as Abstract B277 at the 11th International Conference on Brain Informatics in Arlington, Texas.

  We describe CoVaSEA (Concept-Validating Search Engine Agent): an automated web crawler/query engine that is interoperable with the Nexus-PORTAL-DOORS System. The Nexus-PORTAL-DOORS System (NPDS) is a data management system that organizes repositories of lexical metadata (in PORTAL servers) and semantic representations (in DOORS servers) of resources. Due to the purpose built hybridized nature of NPDS, it is well placed to perform a variety of data analysis tasks. However, many of these tasks require records of semantic descriptions which are labor intensive to create and maintain due to the substantial and rapidly increasing quantities of brain related literature available on the open web. To remedy this, we created CoVaSEA with the intention of providing an automated method for users to navigate and expand the semantic records of brain literature in the NPDS directories. To this end, CoVaSEA integrates multiple features which benefit NPDS including: (A) An implementation of SPARQL query based search to allow retrieval and manipulation of RDF descriptions, (B) Targeted web-crawling for relevant articles from external biomedical literature databases to broaden NPDS records, and (C) Translation of free-form text into RDF triples to derive the semantic portrayals of lexical data. CoVaSEA consists of three principal components: the web-crawler, the lexical to semantic converter, and the SPARQL query engine. The web crawler retrieves articles along with their basic metadata (title, abstract, author(s), etc.) from several of biomedical literature databases via REST API. However, in order to capture a full semantic description of the data in each article, key RDF triples which describe the abstract are constructed. First, each of the unique nouns in the passage are registered via coreference resolution and pronomial anaphora. Then the sentences are parsed into constituency tree format so that the subject(s), verb(s), and object(s) can be extracted. Once the SVO triples are extracted, they are transformed into valid RDF by assigning unique resource identifiers (URI) to each part of the triples. This is accomplished by using various databases (i.e. MeSH) for terminology and select named entities, word sense disambiguation for standard words, and literals for any other sections. These triples are stored via the Scribe API in either a DOORS directory or a localized triplestore where they can be retrieved via the SPARQL query engine. In order to create a more conducive user experience, the query engine supports the capability to construct SPARQL queries from expressions in conjunctive normal form, thus circumventing the need to know SPARQL syntax. With the distinct advantage that the system is automated, CoVaSEA presents the capability to search “externally” to furnish large numbers of brain-related literature descriptions on a regular basis and search “internally” to provide a method of retrieving those descriptions, thus laying the groundwork for a variety of future NPDS applications for which semantic metadata stores of brain literature are a functional necessity.

• Adam G Craig, Seung-Ho Bae, Carl Taswell, 2017, Message Exchange between Independent Implementations of Servers in the Nexus-PORTAL-DOORS System presented December 2017 at the 10th International SWAT4HCLS Conference in Rome, Italy; published as CEUR Workshop Proceedings Vol 2042 Paper 6.

  To search and summarize research on biomedical questions, reasoning agents require access to high-quality semantic markup. The Nexus-PORTAL-DOORS v1.0 API and message exchange format empower organizations to manage and share their own collections of lexical metadata and RDF descriptions of knowledge resources. In this systems demonstration, NPDS servers built on Microsoft’s .NET framework distribute records to NPDS servers built on the MEAN solution stack for caching and distribution to clients.

• Adam G Craig, Seung-Ho Bae, Carl Taswell, 2017, Bridging the Semantic and Lexical Webs: Concept-Validating and Hypothesis-Exploring Ontologies for the Nexus-PORTAL-DOORS System presented July 2017 at the Special Track on Bio- and Medical Informatics and Cybernetics: BMIC 2017 in the context of the 21st Multi-conference on Systemics, Cybernetics and Informatics: WMSCI 2017 Orlando, Florida; published as JSCI 2017 Vol 15 Num 5 pages 8-13; see also XML and RDF files for NPDS v0.9.3 schemas and ontologies.

  The Nexus-PORTAL-DOORS System (NPDS) has been designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style to provide an infrastructure system for managing both lexical and semantic metadata about both and physical entities. We describe here how compatibility between version 0.9 of the NPDS schema, the new NPDS-interfacing ontologies, and the domain-specific concept-validating hypothesis-exploring ontologies allows NPDS to bootstrap the semantic web onto the more developed lexical web. We then describe how this system will serve as the foundation of a planned platform for automated meta-analysis.

• Seung-Ho Bae, Adam G Craig, Carl Taswell, 2017, Expanding Nexus Diristries of Dementia Literature with the NPDS Concept-Validating Search Engine Agent with poster presented July 2017 at the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society in Jeju Island, South Korea; see also a video demo of CoVaSEA Software.

  Even though online databases make it easier than ever to access the biomedical and scientific literature about dementia, accelerating growth in the size of these databases has made it more difficult for humans to gather and analyze manually all articles relevant to any given topic. We document a Nexus-PORTAL-DOORS System (NPDS) Concept-Validating Search Engine Agent that can populate Nexus diristries with concept-validated metadata records for citations of journal articles found in literature databases.

• Adam Craig, Seung-Ho Bae, Teja Veeramacheneni, S Koby Taswell, Carl Taswell, 2016, Web Service APIs for Scribe Registrars, Nexus Diristries, PORTAL Registries and DOORS Directories in the NPD System presented December 2016 at the 9th International SWAT4LS Conference in Amsterdam, Netherlands.

  The Nexus-PORTAL-DOORS System (NPDS) has been designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style to provide an infrastructure system for managing both lexical and semantic metadata about both and physical entities. We describe version 0.8 of NPDS, including the separation of concerns between the original Problem-Oriented Registry of Tags And Labels (PORTAL) registries and the Domain Ontology Oriented Resource System (DOORS) directories, the combined registry and directory functionality of Nexus diristries, and the RESTful read-only web service API through which resource representation metadata records can be retrieved from these NPDS servers. We also introduce Scribe registrars with a corresponding RESTful read-write web service API for management of metadata records by both software agents accessing the web services directly and human users accessing them indirectly via web applications.

• Martin Skarzynski, Adam Craig, Carl Taswell, 2015, SOLOMON: An Ontology for Sensory-Onset, Language-Onset and Motor-Onset Dementias also via DOI 10.1109/BIBM.2015.7359814 presented November 2015 at the IEEE International Conference on Bioinformatics and Biomedicine in Washington DC.

  The PORTAL-DOORS system (PDS) has been designed as a resource metadata management system intended to support applications such as automated searches of online resources and meta-analyses of published literature. PDS comprises a network of Problem Oriented Registry of Tags and Labels (PORTAL) lexical registries and Domain Ontology Oriented Resource System (DOORS) semantic directories. Here we introduce a PDS-compliant concept-validating registry and hypothesisexploring ontology that organizes focal-onset dementias including Sensory-Onset, Language-Onset and Motor-ONset (SOLOMON) dementias with novel classifying and relating concepts. This approach facilitates semantic search of resources and exploration of hypotheses related to neurodegeneration. SOLOMON interoperates with other PDS registries and ontologies including BrainWatch, ManRay and GeneScene.

Reports 2011-2015

• S Koby Taswell, Adam Craig, Diana Leung, Stephan Loh, Martin Skarzynski, Sara Gharabaghi, Bohan Zhou, Carl Taswell, 2015, Hypothesis-Exploring Methods for Automated Meta-Analyses of Brain Imaging Literature presented October 2015 at the Annual Meeting of the Western Region Society of Nuclear Medicine in Monterey, California.

  The PORTAL-DOORS system (PDS) has been designed as a resource metadata management system intended to support applications such as automated searches of online resources and meta-analyses of published literature. We present a methodological approach with a PDS-compliant concept-validating registry and hypothesis-exploring ontology that organizes focal-onset dementias including Sensory-Onset, Language-Onset and Motor-ONset(SOLOMON) dementias with novel classifying and relating concepts. This approach facilitates semantic search of resources and exploration of hypotheses related to neurodegeneration. SOLOMON interoperates with other PDS registries and ontologies including BrainWatch, ManRayand GeneScene.

• Daniel Lockery, James Peters, Carl Taswell, 2011, CTGaming: A Problem-Oriented Registry for Clinical TeleGaming Rehabilitation and Intervention published in February 2011 Journal of Emerging Technologies in Web Intelligence 3(1):28-37.

  A clinical telegaming registry, called CTGaming, has been added as a new Problem-Oriented Registry of Tags And Labels (PORTAL) to the collection of prototype PORTAL registries for ongoing development of the PORTAL-DOORS System (PDS). As a distributed system of interacting PORTAL registries and DOORS directories, PDS provides metadata management services for who-what-where metadata about both online and offline resources. For the CTGaming PORTAL, the scope of the problem-oriented specialty domain for the registry encompasses gaming in physiotherapy, rehabilitation and intervention via telecare, and in general, diagnostic and therapeutic telegaming. This new PORTAL registry has also been incorporated into the design of an existing clinical telegaming system (CTGS). Operating as an adaptive gaming application for telerehabilitation, the CTGS functions either locally in a clinical care setting or remotely in a telecare setting in patients' homes. Operating in concert with the CTGS, the CTGaming PORTAL has been established as a host for metadata representations of resources in the field of clinical telegaming with metadata representations for resources relevant to the CTGS served upon request. These resources may include external resources from the public web as well as internal resources such as telegaming session data from the private medical records associated with the CTGS.

Reports 2006-2010

• Carl Taswell, 2010, A New PDS PORTAL for Clinical TeleGaming Rehabilitation and Intervention also via DOI 10.1109/BIBMW.2010.5703953 presented December 2010 at the IEEE BIBM Conference, Hong Kong, China.

  A registry for resources relevant to Clinical TeleGaming, called CTGaming, has been added as a new Problem Oriented Registry of Tags And Labels (PORTAL) to the collection of prototype PORTAL registries for ongoing development of the PORTAL-DOORS System (PDS). As a distributed system of interacting PORTAL registries and DOORS directories, PDS provides management services for who-what-where metadata about both online and offline resources. For the CTGaming PORTAL, the scope of the problem-oriented specialty domain for the registry encompasses gaming in physiotherapy, rehabilitation and intervention via telecare, and in general, diagnostic and therapeutic telegaming.

• Carl Taswell, 2010, Concept Validating Methods for Maintaining the Integrity of Problem Oriented Domains in the PORTAL-DOORS System presented November 2010 at the AMIA IDAMAP Conference, Washington DC.

  As a distributed system of interacting PORTAL registries and DOORS directories, the PORTAL-DOORS System (PDS) provides management services for who-what-where metadata about both online and offline resources. PDS has been designed to facilitate search of varying scope both within and across registries and directories focused on different problem oriented domains. Maintaining the integrity of these problem oriented domains remains an essential requirement for maintaining the efficiency of search throughout the system. This report describes the new methods used in PDS to distinguish different specialty domains and demonstrates the approach for several registries including GeneScene and ManRay with concepts such as genes and radiopharmaceuticals. Metadata records are now tested by concept validating methods for the presence of any concepts required for each problem oriented domain. Invalid records are moved to a more appropriate registry or else deleted.

• Carl Taswell, 2010, A Distributed Infrastructure for Metadata about Metadata: The HDMM Architectural Style and PORTAL-DOORS System also via DOI 10.3390/fi2020156 submitted 30 December 2009, published online 1 June 2010 Future Internet 2(2):156-189.

  Both the IRIS-DNS System and the PORTAL-DOORS System share a common architectural style for pervasive metadata networks that operate as distributed metadata management systems with hierarchical authorities for entity registering and attribute publishing. Hierarchical control of metadata redistribution throughout the registry-directory networks constitutes an essential characteristic of this architectural style called Hierarchically Distributed Mobile Metadata (HDMM) with its focus on moving the metadata for who what where as fast as possible from servers in response to requests from clients. The novel concept of multilevel metadata about metadata has also been defined for the PORTAL-DOORS System with the use of entity, record, infoset, representation and message metadata. Other new features implemented include the use of aliases, priorities and metaresources.

• Carl Taswell, 2010, Use of NLM Medical Subject Headings with the MeSH2010 Thesaurus in the PORTAL-DOORS System presented June 2010 at the IMIA 8th HealthGrid Conference, Paris, France.

  The NLM MeSH Thesaurus has been incorporated for use in the PORTAL-DOORS System (PDS) for resource metadata management on the semantic web. All 25588 descriptor records from the NLM 2010 MeSH Thesaurus have been exposed as web accessible resources by the PDS MeSH2010 Thesaurus implemented as a PDS PORTAL Registry operating as a RESTful web service. Examples of records from the PDS MeSH2010 PORTAL are demonstrated along with their use by records in other PDS PORTAL Registries that reference the concepts from the MeSH2010 Thesaurus. Use of this important biomedical terminology will greatly enhance the quality of metadata content of other PDS records thus improving cross-domain searches between different problem oriented domains and amongst different clinical specialty fields.

• Carl Taswell, 2010, Management of Multilevel Metadata in the PORTAL-DOORS System with Bootstrapping published in USPTO provisional application filed 25 May 2010, application filed 19 May 2011, patent issued 11 Nov 2014, with USPTO patent number US 8,886,628 B1.

  The PORTAL-DOORS System has been designed as a distributed network system with hierarchical authorities for entity registering and attribute publishing of mobile metadata. An alternate bootstrapping design with self-referencing and self-describing features has been implemented with an integrated model for the combined registry-directories that co-exists with the independent model for the separate registries and directories. The concept of multilevel metadata about metadata has been implemented with the use of entity, record, infoset, representation and message metadata. This multilevel metadata about metadata improves the efficiency of search and analysis of the metadata content within the networked system. The methods facilitate search of varying scope both within and across the registries, directories and registrydirectories focused on different problem oriented domains. Maintaining the integrity of these problem oriented domains serves to improve the efficiency of search throughout the system.

• Carl Taswell, 2010, Use of the MeSH Thesaurus in the PORTAL-DOORS System presented March 2010 at the AMIA Summit on Clinical Research Informatics, San Francisco.

  The NLM MeSH Thesaurus has been incorporated for use in the PORTAL-DOORS System (PDS) for resource metadata management on the semantic web. Use of this important biomedical terminology will greatly enhance the quality of metadata content of the PDS records thus improving cross-registry searches between different clinical specialty fields.

• Carl Taswell, 2010, Provenance and Reproducibility IEEE Computer 2010 Volume 43 Number 12 Page 8.

  Commentary on provenance and reproducibility for computational sciences and engineering.

• Carl Taswell, 2009, The Hierarchically Distributed Mobile Metadata (HDMM) Style of Architecture for Pervasive Metadata Networks also via DOI 10.1109/I-SPAN.2009.73 presented December 2009 at the IEEE 10th International Symposium on Pervasive Systems, Algorithms and Networks (ISPAN), Kiaosiung, Taiwan.

  The Internet Registry Information Service (IRIS) registers domain names while the Domain Name System (DNS) publishes domain addresses with mapping of names to addresses for the original web. Analogously, the Problem Oriented Registry of Tags And Labels (PORTAL) registers resource labels and tags while the Domain Ontology Oriented Resource System (DOORS) publishes resource locations and descriptions with mapping of labels to locations for the semantic web. Both the IRIS-DNS System and the PORTAL-DOORS System share a common architectural style for pervasive metadata networks that operate as distributed metadata management systems with hierarchical authorities for entity registering and attribute publishing. Hierarchical control of metadata redistribution throughout the registry-directory networks constitutes an essential characteristic of this architectural style called Hierarchically Distributed Mobile Metadata (HDMM) with its focus on moving the metadata for who what where as fast as possible from servers in response to requests from clients.

• Carl Taswell, 2009, Biomedical Informatics for Brain Imaging and Gene-Brain-Behavior Relationships presented April 2009 at the W3C HCLS F2F Meeting, Cambridge, Massachusetts.

  Slides from a talk with Q&A discussion on the PORTAL-DOORS Project for the semantic web and grid with brain imaging informatics as the motivating context and application.

• Carl Taswell, 2009, Alternative Bootstrapping Design for the PORTAL-DOORS Cyberinfrastructure with Self-Referencing and Self-Describing Features published in 2009 as a book chapter in Semantic Web, IN-TECH Publishing, Vienna, Austria.

  A new bootstrapping combined design for PDS, together with the original separate design for PDS, has been implemented for NEXUS registrars, PORTAL registries, and DOORS directories and demonstrated with the problem-oriented domains declared for the GeneScene, ManRay, BioPORT, and BrainWatch prototype registries. The combined design has many important advantages during early stages of PDS adoption and use. However, the separate design will become useful when concerns about performance, efficiency, and scalability become more significant.

• Carl Taswell, 2009, Application of the PORTAL-DOORS System for Use by Clinical Trials Registries presented March 2009 at the AMIA 2009 Summit on Translational Bioinformatics, San Francisco, California.

  Slides from a talk with Q&A discussion on the PORTAL-DOORS Project for the semantic web and grid with application to clinical trial registries and brain imaging informatics.

• Carl Taswell, 2009, Implementation of Prototype Biomedical Registries for PORTAL-DOORS presented March 2009 at the AMIA 2009 Summit on Translational Bioinformatics, San Francisco, California.

  Software implementation of the architectural design for the PORTAL-DOORS cyberinfrastructure system for resource metadata management on the semantic web has resulted in code for prototype registries in various problem-oriented domains: the GeneScene registry for genetics, ManRay for nuclear medicine, BrainWatch for brain imaging and neuropsychiatry, and BioPORT for biomedical computing. These registries facilitate translational bioinformatics by assuring globally unique identification of resources while promoting interoperability and enabling cross registry searches between different specialty fields.

• Carl Taswell, 2008, PORTAL-DOORS Infrastructure System for Translational Biomedical Informatics on the Semantic Web and Grid presented March 2008 at the AMIA 2008 Summit on Translational Bioinformatics, San Francisco, California.

  The PORTAL-DOORS infrastructure system of networked registries and directories has been designed for the semantic web and grid as an extended analogue of the IRIS-DNS system for the original web. Within the PORTAL-DOORS system, BioPORT and ManRay have been developed as prototype registries specific for the problem domains of biomedical computing and nuclear medicine. Potential applications in translational biomedical research are described with examples of study designs involving pharmacogenomics and molecular imaging.

• Carl Taswell, 2008, Corrections to "DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing" also via DOI 10.1109/TITB.2008.923764 published in 2008 IEEE TITB 12(3):411.

  Errata for the paper entitled "DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing" that was published in 2008 IEEE TITB 12(2):191-204.

• Carl Taswell, 2008, DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing also via DOI 10.1109/TITB.2007.905861 submitted 31 October 2006, published online 3 August 2007, published in print 2008 IEEE Transactions on Information Technology in Biomedicine 12(2):191-204.

  The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish websites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. The Internet Registry Information Service (IRIS) registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

• Carl Taswell, 2007, PORTALS and DOORS for the Semantic Web and Grid published in USPTO provisional application filed 17 Jun 2007, application filed 21 Sep 2007, patent issued 7 Sep 2010, with USPTO patent number US 7,792,836 B2.

  A Domain Ontology Oriented Resource System (DOORS) and a Problem Oriented Registry of Tags And Labels (PORTAL) are infrastructure systems for resource metadata within a paradigm serving as a bridge between the original web and the semantic web. IRIS registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. They provide an analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks. Advertising is supported in several ways. Businesses purchase the right to display their products or services in association with searches. Also, content providers accept placement of advertising. Ads are then selected for display based on the content displayed utilizing the invention to match service providers with advertisers.

Reports: 2006-2010 | 2011-2015 | 2016-2020 | 2021-2025