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

Reports 2021-2025

• Adam Craig, Carl Taswell, 2024, FAIR Metrics for Motivating Excellence in Peer Review presented September 2024 at eScience 2024 the IEEE 20th International Conference on eScience in Osaka, Japan.

  Past attempts to measure the quality of peer review have relied on either subjective ratings or tangentially related factors such as the sheer number or length of reviews. Previously, we introduced the Fair Attribution to Indexed Reports (FAIR) Metrics to quantify adherence to good citation practices via systematic semantic comparison of statements in the target document to those found in cited and uncited prior reports. In the present work, we define new FAIR Metrics for assessing the quality of peer review, extend the FAIR Metrics module of the PDP-DREAM Ontology with additional classes and properties needed to record FAIR Metrics analysis of a peer review, and demonstrate use with a simple example.

• Carl Taswell, 2024, Biomedical Informatics Needs New Nosology for Collective, Community, Social and Public Health presented July 2024 at the AIME 2024 22nd International Conference on Artificial Intelligence in Medicine (AIME) in Salt Lake City, Utah.

  Pharmacogenomic molecular imaging of neurodegenerative disorders and dementias has served as the motivating problem in precision medicine guiding software development for the past two decades in the PORTAL-DOORS Project (PDP). This work in data sciences, artificial intelligence, biomedical informatics and translational research with clinical trials at Brain Health Alliance has been pursued to support the mission of advancing theranostics with molecular imaging for disorders of the brain and nervous system. The history and published literature associated with PDP for the NPDS Cyberinfrastructure will be surveyed since its inception in 2006. This collection of published work, involving 5 dozen conference and journal papers over 18 years, has always been publicly available at www.PORTALDOORS.org. This review of PDP will highlight PDP-DREAM Software to support truth in science and integrity in research with a call for a new nosology and new metrics to evaluate and measure collective, community, social, and public health.

• Carl Taswell, 2024, Unfairness by the FAIR Principles Promoters: A Case Study on the Absence of Accountability for Integrity in Research Publishing presented with slides May 2024 at the ISRES/ARSTE International Conference on Advances in Technology, Education and Science (ICATES) in Alanya, Turkey.

  This survey reviews and analyzes the evidence from the historical record of published literature relevant to the plagiarism by the Wilkinson et al 2016 FAIR Principles of the previously published Taswell 2007 PORTAL-DOORS Principles. The analysis discusses this plagiarism by Wilkinson et al of Taswell's published research within the cultural framework of practices by both for-profit and not-for-profit publishers that should promote ethics in publishing. These publishing ethics must include the distinction between unintentional omission of citation followed by apology and correction versus intentional exclusion of citation followed by authors' idea-laundering plagiarism with authors' false claims of independent development and by editors' idea-bleaching censorship of public open scientific debate. When both plagiarizing authors and censoring editors act complicitly together in citation cartels with willful disregard of the historical record of published literature available in public online and offline libraries and data repositories, then mis-information, dis-information, anti-information, caco-information, and mal-information will continue to pollute and harm the reproducibility, validity, and integrity of medical, scientific, and engineering research.

• S. Koby Taswell, Adam Craig, 2023, Guardians 2023: Who are the Guardians of Truth and Integrity? Brainiacs Journal 2023 Volume 4 Issue 2 Edoc Y331839FB, also available via DOI 10.48085/Y331839FB.

  On October 9th, Brain Health Alliance (BHA, a US 501-c-3 nonprofit organization) hosted Guardians 2023, our 2nd annual conference entitled Who are the Guardians of Truth and Integrity? The Guardians conferences focus on the global impact of information cyberwars on citizens of planet Earth. Internationally in media of many forms, information has been warped and twisted, resulting in disease, death, and destruction around the globe. To combat the spread of lies and extremified propaganda, the Guardians conferences strive to promote better understanding and awareness about the harm caused by information wars, and to advance learning and knowledge about how to support truth and integrity through technological and sociological research and education for communications in science, engineering, and medicine.

• Carl Taswell, 2023, Reproducibility, Validity, and Integrity in Scholarly Research: What Accountability for Willful Disregard? Brainiacs Journal 2023 Volume 4 Issue 2 Edoc L3570F30F, also available via DOI 10.48085/L3570F30F.

  Commentary on reproducibility, validity, and integrity in scholarly research.

• 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 available 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.

• S. Koby Taswell, Aniruddh Anand, Max Montes-Soza, Carl Taswell, 2023, BabbleNewt: A Simplified, Consistent, and Interoperable Reference Citation Format for Bibliographic Metadata Brainiacs Journal 2023 Volume 4 Issue 2 Edoc K562CB81C, also available via DOI 10.48085/K562CB81C.

  Of the diverse bibliographic metadata formats, BibTeX and BibLaTeX have been dominant across mathematics, computing, and engineering due to their use with the TeX and LaTeX typesetting compilers. Despite success in these fields as well as the publishing industry, both BibTeX and BibLaTeX have some deficiencies, notably inconsistencies in the format definitions and use of macros, pseudo-records, programs and processing methods across different software implementations and installations. These inconsistencies contribute to bibliography parsing and document typesetting errors especially problematic with difficult debugging for large bibliography files. A subproject within the PORTAL-DOORS Project (PDP), the BabbleNewt Project aims to address these concerns by designing a set of formats which iterate on the original BibTeX and BibLaTeX formats while enabling easy conversion between them and a newly designed simplified, consistent, and interoperable format called BabbleNewt. The set of related formats implemented for bibliography processors by PDP BabbleNewt includes two formats PdpBibtex and PdpBiblatex corresponding to the original BibTeX and BibLaTeX, two generalized transition formats PdpBibtexgen and PdpBiblatexgen, and the novel format PdpBabblenewt.

• Adam Craig, Anousha Athreya, Carl Taswell, 2023, Example Evaluations of Plagiarism Cases Using FAIR Metrics and the PDP-DREAM Ontology presented October 2023 at the IEEE 19th International Conference on e-Science in Limassol, Cyprus; also via DOI 10.1109/e-Science58273.2023.10254806.

  The FAIR Metrics, with acronym FAIR for Fair Acknowledgment of Information Records and Fair Attribution to Indexed Reports, measure how appropriately a document cites prior literature. We demonstrate use of a novel workflow for manual evaluation of the FAIR Metrics on five example publications, three of which were retracted for plagiarism. We recorded results of the analyses in Nexus-PORTAL-DOORS-Scribe (NPDS) records as an open access data set for continuing development of automated plagiarism detection tools.

• Anousha Athreya, Adam Craig, S. Koby Taswell, and Carl Taswell, 2023, Opening democratised portals and doors to the free flow of findable facts Research Features (ISSN 2399-1534) Issue 148 pp 54-57, also online.

  Communication barriers across different scientific communities have increased the need for interoperable information systems. Available tools and technologies for finding and accessing data across fields of study continue to face obstacles and have not yet risen to the challenge. Established in 2006, the PORTAL-DOORS Project (PDP) continues to work on developing and maintaining the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure as an open information management system founded on the principle of supporting the free flow of findable facts for democracies around the world.

• 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 available 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.

• Carl Taswell, 2022, Epistemic Injustice, Open Access, and Citational Justice Brainiacs Journal 2022 Volume 3 Issue 2 Edoc X3B678B7A, also available via DOI 10.48085/X3B678B7A.

  Commentary on epistemic injustice, open access, and citational justice.

• 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 10.48085/HA46280EF.

  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.

• Adam Craig, S. Koby Taswell, Anousha Athreya, and Carl Taswell, 2022, Guardians 2022: Who are the Guardians of Truth and Integrity? a half-day workshop hosted October 2022 online for the 85th Annual Meeting of the Association for Information Science & Technology in Pittsburgh, Pennsylvania.

  Brain Health Alliance (BHA), a US 501-c-3 nonprofit organization, will host an online virtual workshop at ASIST 2022 for the library, data, and information sciences community to discuss the now tragically prevalent information cyberwars impacting global citizens of planet earth. These online information wars have resulted in real deaths with loss of life and destruction of entire cities that many believe should have been prevented, whether in the current fight to stop the spread of viral disease, in political election voting disputes and the fight to stop the spread of polarizing and extremified propaganda, and in military campaigns and the fight by freedom-loving peoples who defend their sovereign territory to stop unnecessary wars of aggression, invasion, and criminal genocide. We believe that when some choose to spread propaganda and lies for autocratic dictators, others must stand up and fight to defend truth and integrity in support of democracy and the freedom to live in safety without fear of being imprisoned or poisoned to death for speaking and writing the truth with integrity that should save lives. The BHA workshop on guardians of truth and integrity will provide tutorials with training sessions on open-source PDP-DREAM software and open-access NPDS data repositories from the PORTAL-DOORS Project with its mission to promote transparency, reproducibility, accountability, and citational justice in scholarly communications. In order to support democratic societies for all global citizens of planet earth who wish to be free and safe from unnecessary wars of criminal genocide, we must build the necessary software systems and electronic digital cyberinfrastructure to assure that all citizens of planet earth in every society and country have access to the free flow of information without censorship by any single person, organization, or government.

• 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, Christina Lee, Nithyaa Bala, and Carl Taswell, 2022, Motivating and Maintaining Ethics, Equity, Effectiveness, Efficiency, and Expertise in Peer Review Brainiacs Journal 2022 Volume 3 Issue 1 Edoc I5B147D9D, also available via DOI 10.48085/I5B147D9D.

  Scientists who engage in science and the scientific endeavor should seek truth with conviction of morals and commitment to ethics. While the number of publications continues to increase, the number of retractions has increased at a faster rate. Journals publish fraudulent research papers despite claims of peer review and adherence to publishing ethics. Nevertheless, appropriate ethical peer review will remain a gatekeeper when selecting research manuscripts in scholarly publishing and approving research applications for grant funding. However, this peer review must become more open, fair, transparent, equitable, and just with new recommendations and guidelines for reproducible and accountable reviews that support and promote fair citation and citational justice. We should engineer this new peer-review process with modern informatics technology and information science to provide and defend better safeguards for truth and integrity, to clarify and maintain the provenance of information and ideas, and to rebuild and restore trust in scholarly research institutions. Indeed, this new approach will be necessary in the current post-truth era to counter the ease and speed with which mis-information, dis-information, anti-information, caco-information, and mal-information spread through the internet, web, news, and social media. The most important question for application of new peer-review methods to these information wars should be ‘Who does what when?’ in support of reproducible and accountable reviews. Who refers to the authors, reviewers, editors, and publishers as participants in the review process. What refers to disclosure of the participants' identities, the material content of author manuscripts and reviewer commentaries, and other communications between authors and reviewers. When refers to tracking the sequential points in time for which disclosure of whose identity, which content, and which communication at which step of the peer-review process for which audience of readers and reviewers. We believe that quality peer review, and peer review of peer review, must be motivated and maintained by elevating their status and prestige to an art and a science. Both peer review itself and peer review analyses of peer reviews should be incentivised by publishing peer reviews as citable references separately from the research report reviewed while crossreferenced and crosslinked to the report reviewed.

• Carl Taswell, 2021, Research Scholar's Oath Brainiacs Journal 2021 Volume 2 Issue 1 Edoc P3F95585B, also available via DOI 10.48085/P3F95585B.

  Commentary on truth in science and integrity in research.

• S. Koby Taswell, Anousha Athreya, Madhavi Akella, and Carl Taswell, 2021, Truth in Science Brainiacs Journal 2021 Volume 2 Issue 1 Edoc M85EC99EE, also available via DOI 10.48085/M85EC99EE.

  Truth, honesty, and integrity remain crucial to the pursuit of science as a self-correcting discipline to explore, discover, and process information about the world around us. When following the scientific method, we hypothesize, experiment, and repeatedly retest our results, investigating whether or not those results can be confirmed as reproducible and valid. Conducting this process rigorously with unbiased and objective investigations enables greater confidence in obtaining results we consider more reliable and trustworthy. Such truthful information can be used to avoid harm and prevent injury by those who may wish to apply it in their daily lives in the form of a medicine, machine, or method of some kind. However, in recent years, some scientists and lay persons have violated these tenets of truth in science to further their professional or personal agenda by spreading false information in scientific literature and on social media. This misconduct can be evaluated by assessing the authors' awareness of the document's truthfulness prior to publishing it and their willingness to correct the mistakes and false information when brought to their attention. Identifying these key characteristics about incidents of scientific misconduct enables analysis and introduction of a consistent collection of definitions and criteria for the terms mis-information, dis-information, anti-information, caco-information, and mal-information. Clarifying different categories of misconduct in this manner should enable more effective interventions to remediate and/or prevent each one appropriately. Without adequate safeguards to maintain reproducible science as a self-correcting endeavor with retractions of publications when necessary, false information will continue to pollute the published literature and threaten the core of science.

• 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 available 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.

• Anousha Athreya, S. Koby Taswell, Andrew Kang, Ishani Das, and Carl Taswell, 2021, Ashurbanipal: A Diristry to Document Multimedia Metadata Tools for Transdisciplinary Archives presented December 2021 at the International Conference on Computational Science and Computational Intelligence (CSCI) Symposium on Computational Science (CSCI-ISCS) in Las Vegas, Nevada.

  In historical artifact conservation, archiving objects using entity metadata plays a significant role in managing the related versions of the artifacts preserved, recorded and documented at various time points. In this paper, we discuss five fields of study to display the importance of related versions in identifying patterns over time through events in history, cultural heritage, biomedical research, performing arts, and fine arts. We describe our use of the Ashurbanipal diristry to document scholarly research on archiving tools and technologies. We highlight the importance of the provenance infosubset in tracing metadata for cultural objects managed in NPDS repositories and enabling interoperability with existing multimedia bibliographic formats including MARC and BIBFRAME.

• Anousha Athreya, S. Koby Taswell, and Carl Taswell, 2021, Management Software for Monitoring Related Versions of Cultural Heritage Artifacts for Libraries and Museums also available via DOI 10.1002/pra2.526 presented November 2021 at the 84th Annual Meeting of the Association for Information Science & Technology in Salt Lake City, Utah.

  In cultural object conservation, tracking provenance has served as the foundational method of managing information for historical artifacts. To find data points, archivists identify related versions of an artifact at various time points. In this paper, we discuss four categories with versioned examples to display the importance of data points for identifying patterns over time through events in history, cultural heritage, performing arts, and fine arts. We describe our use of the Ashurbanipal diristry to document scholarly research regarding library tools and technologies for the preservation of cultural objects as well as the implementation of PORTAL-DOORS Project (PDP) utilities for tracing provenance and distribution of cultural objects and interoperability with bibliographic formats such as BIBFRAME and MARC from existing archival methods.

• 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

• Anousha Athreya, S. Koby Taswell, Sohyb Mashkoor, and Carl Taswell, 2020, The Essential Enquiry 'Equal or Equivalent Entities?' About Two Things as Same, Similar, Related, or Different Brainiacs Journal 2020 Volume 1 Issue 1 Edoc PEDADC885, also available via DOI 10.48085/PEDADC885.

  We discuss definitions of entities, equality, and equivalence as used by a transdisciplinary diversity of research fields including mathematics, statistics, computational linguistics, computer programming, knowledge engineering, music theory, and genomics. Declaring definitions for these concepts in the situational context of each domain specific field supports the essential question 'Equal or equivalent entities?' about two things as same, similar, related, or different for that field. Pattern recognition performed by artificial intelligence applications whether with supervised and unsupervised learning or with deductive and inferential logic, with machine learning or logical reasoning, can be described as the automated process of answering this fundamental question about the similarity, relatedness, or difference between two things.

• Shreya Choksi and Carl Taswell, 2020, The Nexus-PORTAL-DOORS-Scribe (NPDS) Learning Intelligence aNd Knowledge System (LINKS) Brainiacs Journal 2020 Volume 1 Issue 1 Edoc B61CA3D89, also available via DOI 10.48085/B61CA3D89.

  With the continuing growth in use of large complex data sets for artificial intelligence applications (AIA), unbiased methods should be established for assuring the validity and reliability of both input data and output results. Advancing such standards will help to reduce problems described with the aphorism 'Garbage In, Garbage Out' (GIGO). This concern remains especially important for AIA tools that execute within the environment of interoperable systems which share, exchange, convert, and/or interchange data and metadata such as the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure and its associated Learning Intelligence aNd Knowledge System (LINKS) applications. The PORTAL-DOORS Project (PDP) has developed the NPDS cyberinfrastructure with lexical PORTAL registries, semantic DOORS directories, hybrid Nexus diristries, and Scribe registrars. As a self-referencing and self-describing system, the NPDS cyberinfrastructure has been designed to operate as a pervasive distributed network of data repositories compliant with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style. Building on the foundation of the NPDS cyberinfrastructure with its focus on data, PDP has now introduced LINKS applications with their focus on algorithms and analysis of the data. In addition, PDP has launched a pair of new websites at NPDSLINKS.net and NPDSLINKS.org which will serve respectively as the root of the NPDS cyberinfrastructure and the home for definitions and standards on quality descriptors and quantitative measures to evaluate the data contained within NPDS records. Prototypes of these descriptors and measures for use with NPDS and LINKS are described in this report. PDP envisions building better AIA and preventing the unwanted phenomenon of GIGO by using the combination of metrics to detect and reduce bias from data, the NPDS cyberinfrastructure for the data, and LINKS applications for the algorithms.

• 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 available 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.

• Anousha Athreya, S Koby Taswell, Sohyb Mashkoor, and Carl Taswell, 2020, Essential Question: 'Equal or Equivalent Entities?' About Two Things as Same, Similar, or Different also available via DOI 10.1109/TransAI49837.2020.00028 presented September 2020 at the 2nd International Conference on Transdisciplinary Artificial Intelligence (TransAI)

  We discuss definitions of entities, equality, and equivalence as used by a transdisciplinary diversity of research fields including mathematics, statistics, computational linguistics, computer programming, knowledge engineering, and music theory. Declaring definitions for these concepts in the situational context of each domain specific field supports the essential question 'Equal or equivalent entities?' about two things as same, similar, related, or different for that field. Pattern recognition performed by artificial intelligence applications can be described as the automated process of answering this fundamental question about the similarity or difference between two things.

• Shreya Choksi, Peter Hong, Sohyb Mashkoor, and Carl Taswell, 2020, NPDSLINKS: Nexus-PORTAL-DOORS-Scribe Learning Intelligence aNd Knowledge System also available via DOI 10.1109/TransAI49837.2020.00027 presented September 2020 at the 2nd International Conference on Transdisciplinary Artificial Intelligence (TransAI)

  With the continuing growth in use of large complex data sets for artificial intelligence applications (AIA), unbiased methods should be established for assuring the validity and reliability of both input data and output results. Advancing such standards will help to reduce problems described with the aphorism 'Garbage In, Garbage Out' (GIGO). This concern remains especially important for AIA tools that execute within the environment of interoperable systems which share, exchange, convert, and/or interchange data and metadata such as the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure and its associated Learning Intelligence aNd Knowledge System (LINKS) applications. The PORTAL-DOORS Project (PDP) has developed the NPDS cyberinfrastructure with lexical PORTAL registries, semantic DOORS directories, hybrid Nexus diristries, and Scribe registrars. As a self-referencing and self-describing system, the NPDS cyberinfrastructure has been designed to operate as a pervasive distributed network of data repositories compliant with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style. Building on the foundation of the NPDS cyberinfrastructure with its focus on data, PDP has now introduced LINKS applications with their focus on algorithms and analysis of the data. In addition, PDP has launched a pair of new websites at NPDSLINKS.net and NPDSLINKS.org which will serve respectively as the root of the NPDS cyberinfrastructure and the home for definitions and standards on quality descriptors and quantitative measures to evaluate the data contained within NPDS records. Prototypes of these descriptors and measures for use with NPDS and LINKS are introduced in this report. PDP envisions building better AIA and preventing the unwanted phenomenon of GIGO by using the combination of metrics to detect and reduce bias from data, the NPDS cyberinfrastructure for the data, and LINKS applications for the algorithms.

• S. Koby Taswell, Kelechi Uhegbu, Sohyb Mashkoor, Shiladitya Dutta, and Carl Taswell, 2020, Storing Bibliographic Data in Multiple Formats with the NPDS Cyberinfrastructure also available via DOI 10.1002/pra2.428 presented with poster October 2020 at the 83rd ASIS&T Annual Meeting of the Association for Information Science and Technology

  The PORTAL-DOORS Project (PDP) aims to develop the Nexus-PORTAL-DOORS-Scribe (NPDS) Cyberinfrastructure as a distributed network of data repositories that communicate with each other using a common message exchange standard. These data repositories include a collection of servers with a system of registries, directories, and diristries for diverse resources including bibliographic information records. Examples of resource metadata representations can be viewed at PDP participating websites. Until now, PDP has not supported convenient import or export of bibliographic records to or from any of the common bibliographic standards. In this report, we describe our progress on our new PDP utilities for interoperability between the format for NPDS records and various bibliographic formats such as BIBFRAME, MARC, RIS, and BibLaTeX. We will detail the import process when using a converter that transforms bibliographic citations in other formats and stores them in an NPDS diristry. Improved interoperability for conversion between bibliographic records in other traditional formats with the NPDS format will support a variety of use cases that require either lexical and/or semantic parsing of cited references.

• S. Koby Taswell, Christopher Triggle, June Vayo, Shiladitya Dutta, and Carl Taswell, 2020, The Hitchhiker's Guide to Scholarly Research Integrity also available 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 available 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.

• Adam Craig, Adarsh Ambati, Shiladitya Dutta, Arush Mehrotra, S. Koby Taswell, and Carl Taswell, 2019, Definitions, Formulas, and Simulated Examples for Plagiarism Detection with FAIR Metrics also available via DOI 10.1002/pra2.6 presented with slides October 2019 at the 82nd Annual Meeting of the Association for Information Science & Technology in Melbourne, Australia.

  In prior work, we proposed a family of metrics as a tool to quantify adherence to or deviation from good citation practices in scholarly research and publishing. We called this family of metrics FAIR as an acronym for Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records, and introduced definitions for these metrics with counts of instances of correct or incorrect attribution or nonattribution in primary research articles with citations for previously published references. In the present work, we extend our FAIR family of metrics by introducing a collection of ratio-based metrics to accompany the count-based metrics described previously. We illustrate the mathematical properties of the ratio-based metrics with various simulated examples in order to assess their suitability as a means of identifying papers under peer review as more or less likely to be suspicious for plagiarism. These FAIR metrics would alert peer reviewers to prioritize low-scoring manuscripts for closer scrutiny. Finally, we outline our planned strategy for future validation of the FAIR metrics with an approach using both expert human analysts and automated algorithms for computerized analysis.

• 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 available 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 available 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 Craig and Carl Taswell, 2018, Formulation of FAIR Metrics for Primary Research Articles also available via DOI 10.1109/BIBM.2018.8621399 presented December 2018 at the SEPDA Workshop held at the IEEE 2018 BIBM Conference in Madrid, Spain.

  Measuring the merits of a scholarly article only by how often other articles or social media posts cite it creates a perverse incentive for authors to avoid citing potential rivals. To uphold established standards of scholarship, institutions should also consider one or more metrics of how appropriately an article cites relevant prior work. This paper describes the general characteristics of the FAIR Attribution to Indexed Reports (FAIR) family of metrics, which we have designed for this purpose. We formulate five FAIR metrics suitable for use with primary research articles. Two measure adherence to best practices: number of correctly attributed background statements and number of genuinely original claims. Three measure specific deviations from best practices: number of misattributed background statements, number of background statements with missing references, and number of claims falsely indicated as original. We conclude with a discussion of plans to implement a web application for calculating metric values of scholarly works described by records in Nexus-PORTAL-DOORS System (NPDS) servers.

• Adam Craig and Carl Taswell, 2018, The FAIR Metrics of Adherence to Citation Best Practices with poster presented November 2018 at the SIGMET Workshop Metrics 2018 held at the 2018 ASIS&T Annual Meeting of the Association for Information Science & Technology in Vancouver, British Columbia.

  Measuring the merits of scholarly research articles only by citation counts and how often other research articles or social media messages cite a particular publication creates a perverse incentive for some authors to refrain from citing potential rivals. This dilemma has developed despite the historical publishing standard expected in peer review for citing and discussing related prior work. To encourage and support a countervailing incentive, research organizations should also consider metrics for how well and appropriately a scholarly article cites relevant prior work in the spirit of the classic phrase and metaphor standing on the shoulders of giants. We present a proposal for a family of such article-level metrics called the FAIR metrics and described as the FAIR Attribution to Indexed Reports or the FAIR Acknowledgment of Information Records.

• 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 virtual 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 virtual 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 available 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 available 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, The ManRay Project in Biomedical Informatics for Nuclear Medicine and PharmacoGenomic Molecular Imaging presented October 2010 at the WRSNM Conference, Garden Grove, California.

  The ManRay Ontology for Nuclear Medicine has been updated for OWL 2 and incorporated with the ManRay Registry in the PORTAL-DOORS System (PDS) for management of resource metadata on the semantic web. Use of this ontology and registry will facilitate exchange of data for basic research or clinical trials involving nuclear medicine and pharmacogenomic molecular imaging for personalized medicine.

• Carl Taswell, 2010, A Distributed Infrastructure for Metadata about Metadata: The HDMM Architectural Style and PORTAL-DOORS System also available 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 available 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, Knowledge Engineering for PharmacoGenomic Molecular Imaging of the Brain also available via DOI 10.1109/SKG.2009.101 presented October 2009 at the IEEE 5th International Conference on Semantics Knowledge Grid (SKG), Zhuhai, China.

  Schizophrenia, Alzheimer's disease, Parkinson's disease, and other neuropsychiatric degenerative disorders and dementias impose an enormous economic and psychosocial burden on society, communities, and families. In order to gain a better understanding of gene-brain-behavior relationships, improve treatment, and find cures for these diseases, translational research must be conducted with clinical trials of new drugs and other interventions followed by genotyping and imaging biomarkers for patients with these neuropyschiatric degenerative disorders. This research, involving pharmacogenomic molecular imaging of the brain, will be extremely costly in many ways. Therefore, knowledge engineering with effective software tools and applications built upon a semantic-enabled informatics infrastructure remains a necessary prerequisite to facilitate a reduction of those research costs by maximizing the benefit obtained from existing data and minimizing the cost of generating new data. A knowledge engineering framework that serves this goal must operate in a cross-disciplinary manner that integrates data from diverse biomedical fields while at the same time incorporating the relevant computational mathematics, statistics, and informatics analyses for productive data mining.

• 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 available 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 available 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.

• Carl Taswell, 2006, The ManRay Project: Initial Development of a Web-Enabled Ontology for Nuclear Medicine with poster presented June 2006 at the SNMMI 2006 Annual Meeting, San Diego, California.

  Objectives: The semantic web extends the original web with technologies that provide syntactic structure (XML) and semantic meaning (RDF) permitting the development of taxonomies and inference rules (Berners-Lee et al, 2001). These technologies together with the Web Ontology Language (OWL) enable the compilation of knowledge representations or collections of information known as ontologies. Biomedical ontologies have benefited from significant development in the bioinformatics and clinical informatics communities (Pinciroli et al, 2005). In contrast, there appears to be a relative dearth of progress in the specialty fields of nuclear medicine and radiopharmaceutics. With the exception of some work on a radiopharmaceutical information database (Blaine et al, 1999) which did not involve any semantic web technologies nor any internet technologies, extensive literature searches have not found any other nuclear medicine informatics projects. The ManRay project attempts to fill this gap. Methods: Ontologies for the ManRay project are constructed adhering to (1) the specifications for XML, RDF, and OWL recommended by the World Wide Web Consortium (www.w3.org), (2) the usage paradigm advocated by Lacy (see diagram on page 144 of his 2005 book on OWL), and (3) general software engineering principles of hierarchical modularity, flexibility, and extensibility. Development is guided by the “ontology steward” paradigm in which the steward hosts and manages the ontology standard but does not necessarily provide a database distributing data compliant with the standard. Thus, the steward’s web server publishes the ontology as a *.owl file while other publishers distribute their data as compliant *.rdf files that reference the ontology steward’s *.owl file. Results: The ManRay project implements an ontology for nuclear medicine, radiopharmaceutics, and molecular imaging structured as a hierarchy of *.owl files with manray.owl as the top level and separate *.owl files for imaging protocols, pharmaceuticals, and radionuclides as the lower levels. The website www.nucmedlib.org hosts the ManRay project and its ontology. Conclusions: Development and promotion of a nuclear medicine ontology as an open standard for the exchange of data constitutes the most important goal of the ManRay project. Establishment of this ontology will enable the subsequent development of informatics applications capable of performing inference, such as automated metaanalyses, on data published according to the standard. Individuals and/or organizations interested in contributing to the ManRay project are encouraged to contact the authors.

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