Brain Health Alliance (BHA), a 501c3 not-for-profit organization, will host an online virtual workshop at ASIST 2022 for the library, data, and information sciences community to discuss the now tragically prevalent information cyberwars impacting global citizens of planet earth. These online information wars have resulted in real deaths with loss of life and destruction of entire cities that many believe should have been prevented, whether in the current fight to stop the spread of viral disease, in political election voting disputes and the fight to stop the spread of polarizing and extremified propaganda, and in military campaigns and the fight by freedom-loving peoples who defend their sovereign territory to stop unnecessary wars of aggression, invasion, and criminal genocide. We believe that when some choose to spread propaganda and lies for autocratic dictators, others must stand up and fight to defend truth and integrity in support of democracy and the freedom to live in safety without fear of being imprisoned or poisoned to death for speaking and writing the truth with integrity that should save lives. The BHA workshop on guardians of truth and integrity will provide tutorials with training sessions on open-source PDP-DREAM software and open-access NPDS data repositories from the PORTAL-DOORS Project with its mission to promote transparency, reproducibility, accountability, and citational justice in scholarly communications. In order to support democratic societies for all global citizens of planet earth who wish to be free and safe from unnecessary wars of criminal genocide, we must build the necessary software systems and electronic digital cyberinfrastructure to assure that all citizens of planet earth in every society and country have access to the free flow of information without censorship by any single person, organization, or government.
S. Koby Taswell, Anousha Athreya, Madhavi Akella, and Carl Taswell, 2021,
Truth in Science
Brainiacs Journal 2021 Volume 2 Issue 1 Edoc M85EC99EE,
also available via DOI 10.48085/M85EC99EE.
Truth, honesty, and integrity remain crucial to the pursuit of science as a self-correcting discipline to explore, discover, and process information about the world around us. When following the scientific method, we hypothesize, experiment, and repeatedly retest our results, investigating whether or not those results can be confirmed as reproducible and valid. Conducting this process rigorously with unbiased and objective investigations enables greater confidence in obtaining results we consider more reliable and trustworthy. Such truthful information can be used to avoid harm and prevent injury by those who may wish to apply it in their daily lives in the form of a medicine, machine, or method of some kind. However, in recent years, some scientists and lay persons have violated these tenets of truth in science to further their professional or personal agenda by spreading false information in scientific literature and on social media. This misconduct can be evaluated by assessing the authors' awareness of the document's truthfulness prior to publishing it and their willingness to correct the mistakes and false information when brought to their attention. Identifying these key characteristics about incidents of scientific misconduct enables analysis and introduction of a consistent collection of definitions and criteria for the terms mis-information, dis-information, anti-information, caco-information, and mal-information. Clarifying different categories of misconduct in this manner should enable more effective interventions to remediate and/or prevent each one appropriately. Without adequate safeguards to maintain reproducible science as a self-correcting endeavor with retractions of publications when necessary, false information will continue to pollute the published literature and threaten the core of science.
Integrating multimedia data in a meaningful way requires keeping track of the who, what, where, when, and how of many kinds of data and metadata in different formats. The PORTAL-DOORS-Project (PDP) was formed to design and build the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure for managing and distributing resource data and metadata in a manner compatible with both the established lexical web and the developing semantic web. PDP-DREAM software, archived at github.com/bhavius/pdp-dream, represents the first publicly available, open-source implementation of NPDS. It provides RESTful web services for software agents and user-friendly web applications for human agents so that individuals and organizations can create and publish their own problem-oriented and domain-specific repositories customized for their own purposes. In this report, we also introduce the NpdsQuads format with an approach to formatting the comments of N-quads files as name-value pairs for content from NPDS records which can be exported from and imported to NPDS repositories. We then describe the use of these tools in the curation of the PDP-DREAM ontology, which serves as the foundational ontology for the NPDS cyberinfrastructure. Finally, we discuss the planned use of PDP-DREAM software in a medical imaging clinical trial for multiple sclerosis.
In historical artifact conservation, archiving objects using entity metadata plays a significant role
in managing the related versions of the artifacts preserved, recorded and documented at various time points.
In this paper, we discuss five fields of study to display the importance of related versions in identifying patterns
over time through events in history, cultural heritage, biomedical research, performing arts, and fine arts.
We describe our use of the Ashurbanipal diristry to document scholarly research on archiving tools and technologies.
We highlight the importance of the provenance infosubset in tracing metadata for cultural objects managed in NPDS repositories
and enabling interoperability with existing multimedia bibliographic formats including MARC and BIBFRAME.
In cultural object conservation, tracking provenance has served as the foundational method of managing information for historical artifacts.
To find data points, archivists identify related versions of an artifact at various time points.
In this paper, we discuss four categories with versioned examples to display the importance of data points for identifying patterns
over time through events in history, cultural heritage, performing arts, and fine arts.
We describe our use of the Ashurbanipal diristry to document scholarly research regarding library tools and technologies
for the preservation of cultural objects as well as the implementation of PORTAL-DOORS Project (PDP) utilities
for tracing provenance and distribution of cultural objects and interoperability
with bibliographic formats such as BIBFRAME and MARC from existing archival methods.
We discuss definitions of entities, equality, and equivalence as used by a transdisciplinary diversity
of research fields including mathematics, statistics, computational linguistics, computer programming, knowledge engineering, and music theory.
Declaring definitions for these concepts in the situational context of each domain specific field supports
the essential question 'Equal or equivalent entities?' about two things as same, similar, related,
or different for that field. Pattern recognition performed by artificial intelligence applications
can be described as the automated process of answering this fundamental question about the similarity or difference between two things.
With the continuing growth in use of large complex data sets for artificial intelligence applications (AIA), unbiased methods should be established for assuring the validity and reliability of both input data and output results. Advancing such standards will help to reduce problems described with the aphorism 'Garbage In, Garbage Out' (GIGO). This concern remains especially important for AIA tools that execute within the environment of interoperable systems which share, exchange, convert, and/or interchange data and metadata such as the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure and its associated Learning Intelligence aNd Knowledge System (LINKS) applications. The PORTAL-DOORS Project (PDP) has developed the NPDS cyberinfrastructure with lexical PORTAL registries, semantic DOORS directories, hybrid Nexus diristries, and Scribe registrars. As a self-referencing and self-describing system, the NPDS cyberinfrastructure has been designed to operate as a pervasive distributed network of data repositories compliant with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style. Building on the foundation of the NPDS cyberinfrastructure with its focus on data, PDP has now introduced LINKS applications with their focus on algorithms and analysis of the data. In addition, PDP has launched a pair of new websites at NPDSLINKS.net and NPDSLINKS.org which will serve respectively as the root of the NPDS cyberinfrastructure and the home for definitions and standards on quality descriptors and quantitative measures to evaluate the data contained within NPDS records. Prototypes of these descriptors and measures for use with NPDS and LINKS are introduced in this report. PDP envisions building better AIA and preventing the unwanted phenomenon of GIGO by using the combination of metrics to detect and reduce bias from data, the NPDS cyberinfrastructure for the data, and LINKS applications for the algorithms.
The PORTAL-DOORS Project (PDP) aims to develop
the Nexus-PORTAL-DOORS-Scribe (NPDS) Cyberinfrastructure
as a distributed network of data repositories that
communicate with each other using a common message exchange
standard. These data repositories include a collection of servers
with a system of registries, directories, and diristries for diverse
resources including bibliographic information records. Examples
of resource metadata representations can be viewed at PDP participating
websites. Until now, PDP has not supported convenient
import or export of bibliographic records to or from any of the
common bibliographic standards. In this report, we describe our
progress on our new PDP utilities for interoperability between
the format for NPDS records and various bibliographic formats
such as BIBFRAME, MARC, RIS, and BibLaTeX. We will detail
the import process when using a converter that transforms
bibliographic citations in other formats and stores them in an
NPDS diristry. Improved interoperability for conversion between
bibliographic records in other traditional formats with the NPDS
format will support a variety of use cases that require either
lexical and/or semantic parsing of cited references.
The pursuit of truth in research should be both an
ideal in aspiration and also a reality in practice. The PORTAL-DOORS
Project (PDP) strives to promote creative authenticity,
fair citation, and adherence to integrity and ethics in scholarly
research publishing using the FAIR family of quantitative metrics
with acronym FAIR for the phrases Fair Attribution to Indexed
Reports and Fair Acknowledgment of Information Records, and the
DREAM principles with acronym DREAM for the phrase Discoverable
Data with Reproducible Results for Equivalent Entities
with Accessible Attributes and Manageable Metadata. This report
presents formalized definitions for idea-laundering plagiarism
by authors, idea-bleaching censorship by editors, and proposed
assertion claims for authors, reviewers, editors, and publishers in
ethical peer-reviewed publishing to support integrity in research.
All of these principles have been implemented in version 2 of the
PDP-DREAM ontology written in OWL 2. This PDP-DREAM
ontology will serve as the model foundation for development of a
software-guided workflow process intended to manage the ethical
peer-reviewed publishing of web-enabled open access journals
operated online with PDP software.
The PORTAL-DOORS Project (PDP) has been
pursued to develop the Nexus-PORTAL-DOORS-Scribe (NPDS)
cyberinfrastructure as a distributed network system of data
repositories to manage lexical and semantic data and metadata
from and/or about online and offline resources. Designed
with the Hierarchically Distributed Mobile Metadata (HDMM)
architectural style in a manner analogous to IRIS-DNS, the
NPDS cyberinfrastructure provides distributed multilevel metadata
management as an open, flexible, and extensible networked
system of independent community customizable who-what-where
registries, directories, and diristries for identifying, describing,
locating, and linking things on the internet, web and grid.
In the current work reported here, we combined our original
principles from PDP, HDMM, and NPDS together with additional
principles for scientific reproducibility and social engineering
related to our family of quantitative metrics with acronym FAIR
for Fair Attribution to Indexed Reports and Fair Acknowledgment
of Information Records.We call this new consolidated collection of
principles the DREAM principles with acronym DREAM for the phrase
Discoverable Data with Reproducible Results for Equivalent
Entities with Accessible Attributes and Manageable Metadata
To codify these DREAM principles as a concrete artifact for the
semantic web, and thus to operationalize their use, we developed
an OWL 2.0 ontology that we named the PDP-DREAM ontology.
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.
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
and use of the open source software that powers the NPDS cyberinfrastructure, PDP websites and PDP web services.
Our PDP software for the NPDS cyberinfrastructure will be released publicly at this presentation of the software
where we will also discuss challenges in the peer review process that include plagiarism detection.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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 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.
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.
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.
The PORTAL-DOORS System has been designed as a distributed network system with hierarchical authorities
for entity registering and attribute publishing of mobile metadata. An alternate bootstrapping
design with self-referencing and self-describing features has been implemented with an integrated model
for the combined registry-directories that co-exists with the independent model for the separate registries
and directories. The concept of multilevel metadata about metadata has been implemented with the use
of entity, record, infoset, representation and message metadata. This multilevel metadata about metadata
improves the efficiency of search and analysis of the metadata content within the networked system. The
methods facilitate search of varying scope both within and across the registries, directories and registrydirectories
focused on different problem oriented domains. Maintaining the integrity of these problem
oriented domains serves to improve the efficiency of search throughout the system.
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.
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.
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.
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.
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.
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.
The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned
by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained
when a dynamic synergism can be created between people and a sufficient number of infrastructure systems
and tools for the semantic web in analogy with those for the original web. The domain name system (DNS),
web browsers, and the benefits of publishing web pages motivated many people to register domain names
and publish websites on the original web. An analogous resource label system, semantic search applications,
and the benefits of collaborative semantic networks will motivate people to register resource labels
and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System
(DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems
for resource metadata within a paradigm that can serve as a bridge between the original web and the
semantic web. The Internet Registry Information Service (IRIS) registers domain names while DNS publishes
domain addresses with mapping of names to addresses for the original web.
Analogously, PORTAL registers resource labels and tags while DOORS
publishes resource locations and descriptions with mapping of labels to locations for the semantic
web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical
A Domain Ontology Oriented Resource System (DOORS) and a Problem Oriented Registry of Tags And Labels (PORTAL) are infrastructure systems for resource metadata within a paradigm serving as a bridge between the original web and the semantic web. IRIS registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. They provide an analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks. Advertising is supported in several ways. Businesses purchase the right to display their products or services in association with searches. Also, content providers accept placement of advertising. Ads are then selected for display based on the content displayed utilizing the invention to match service providers with advertisers.
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.