PDP/Site/Papers

PORTAL-DOORS Project NPDS Cyberinfrastructure System Papers

• 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 with slides presented 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 with slides and demo video presented 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 web sites 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 with slides presented 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 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 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.

• 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.

• Carl Taswell, 2010, A New PDS PORTAL for Clinical TeleGaming Rehabilitation and Intervention 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 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, 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, 2009, The Hierarchically Distributed Mobile Metadata (HDMM) Style of Architecture for Pervasive Metadata Networks 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 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.

• 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" 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 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 web sites 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, 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.