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
to be 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 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
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
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.
CTGaming: A Problem-Oriented Registry for Clinical TeleGaming Rehabilitation and Intervention
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.
A New PDS PORTAL for Clinical TeleGaming Rehabilitation and Intervention
BIBM, 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.
Concept Validating Methods for Maintaining the Integrity of Problem Oriented Domains in the PORTAL-DOORS
2010 AMIA IDAMAP, 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.
The ManRay Project in Biomedical Informatics for Nuclear Medicine and PharmacoGenomic Molecular
2010 WRSNM Conference, Garden Grove CA.
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.
A Distributed Infrastructure for Metadata about Metadata: The HDMM Architectural Style and PORTAL-DOORS System
Use of NLM Medical Subject Headings with the MeSH2010 Thesaurus in the PORTAL-DOORS System
2010 HealthGrid Conference, Paris.
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.
Use of the MeSH Thesaurus in the PORTAL-DOORS System
2010 AMIA Summit Clinical Research
Informatics, San Francisco.
The Hierarchically Distributed Mobile Metadata (HDMM) Style of Architecture for Pervasive Metadata
ISPAN 2009 Intl Symposium on Pervasive Systems, Algorithms and Networks, Kiaosiung,
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.
Knowledge Engineering for PharmacoGenomic Molecular Imaging of the Brain
Intl Conference Semantics Knowledge Grid, 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.
Biomedical Informatics for Brain Imaging and Gene-Brain-Behavior Relationships
W3C HCLS F2F Meeting, Cambridge.
Alternative Bootstrapping Design for the PORTAL-DOORS Cyberinfrastructure with Self-Referencing
and Self-Describing Features
2009 book chapter in Semantic Web , IN-TECH
Application of the PORTAL-DOORS System for Use by Clinical Trials Registries
AMIA Summit Translational Bioinformatics, San Francisco.
Implementation of Prototype Biomedical Registries for PORTAL-DOORS
2009 AMIA Summit
Translational Bioinformatics, San Francisco.
Corrections to "DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing"
2008 IEEE TITB 12(3):411.
DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing
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. 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
PORTAL-DOORS Infrastructure System for Translational Biomedical Informatics on the Semantic Web
2008 AMIA Summit Translational Bioinformatics, San Francisco.
The ManRay Project: Initial Development of a Web-Enabled Ontology for Nuclear Medicine
2006 Annual Meeting Society Nuclear Medicine, San Diego.