PDP/Site/Papers
PORTAL-DOORS Project NPDS Cyberinfrastructure System Papers
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.