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1.  A UML profile for the OBO relation ontology 
BMC Genomics  2012;13(Suppl 5):S3.
Background
Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain.
Results
We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO).
Conclusions
The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.
doi:10.1186/1471-2164-13-S5-S3
PMCID: PMC3477006  PMID: 23095840
2.  Developing a semantically rich ontology for the biobank-administration domain 
Background
Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases.
Results
We created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data with perfect accuracy. In addition, we began development of a mapping from the ontology to pre-existing biobank data structures commonly used in the U.S.
Conclusions
In conclusion, we created OMIABIS, an ontology of biobank administration. We found that basing its development on pre-existing resources to meet the BBMRI use cases resulted in a biobanking ontology that is re-useable in environments other than BBMRI. Our ontology retrieved all true positives and no false positives when queried according to the competency questions we derived from the BBMRI use cases. Mapping OMIABIS to a data structure used for biospecimen collections in a medical center in Little Rock, AR showed adequate coverage of our ontology.
doi:10.1186/2041-1480-4-23
PMCID: PMC4021870  PMID: 24103726
3.  Time for gender mainstreaming in editorial policies 
The HIV epidemic has been continuously growing among women, and in some parts of the world, HIV-infected women outnumber men. Women's greater vulnerability to HIV, both biologically and socially, influences their health risk and health outcome. This disparity between sexes has been established for other diseases, for example, autoimmune diseases, malignancies and cardiovascular diseases. Differences in drug effects and treatment outcomes have also been demonstrated.
Despite proven sex and gender differences, women continue to be underrepresented in clinical trials, and the absence of gender analyses in published literature is striking. There is a growing advocacy for consideration of women in research, in particular in the HIV field, and gender mainstreaming of policies is increasingly called for. However, these efforts have not translated into improved reporting of sex-disaggregated data and provision of gender analysis in published literature; science editors, as well as publishers, lag behind in this effort.
Instructions for authors issued by journals contain many guidelines for good standards of reporting, and a policy on sex-disaggregated data and gender analysis should not be amiss here. It is time for editors and publishers to demonstrate leadership in changing the paradigm in the world of scientific publication. We encourage authors, peer reviewers and fellow editors to lend their support by taking necessary measures to substantially improve reporting of gender analysis. Editors' associations could play an essential role in facilitating a transition to improved standard editorial policies.
doi:10.1186/1758-2652-14-11
PMCID: PMC3059266  PMID: 21385405
4.  Big3. Editorial 
Summary
Objectives
To provide an editorial introduction into the 2014 IMIA Yearbook of Medical Informatics with an overview of the content, the new publishing scheme, and upcoming 25th anniversary.
Methods
A brief overview of the 2014 special topic, Big Data - Smart Health Strategies, and an outline of the novel publishing model is provided in conjunction with a call for proposals to celebrate the 25th anniversary of the Yearbook.
Results
‘Big Data’ has become the latest buzzword in informatics and promise new approaches and interventions that can improve health, well-being, and quality of life. This edition of the Yearbook acknowledges the fact that we just started to explore the opportunities that ‘Big Data’ will bring. However, it will become apparent to the reader that its pervasive nature has invaded all aspects of biomedical informatics – some to a higher degree than others. It was our goal to provide a comprehensive view at the state of ‘Big Data’ today, explore its strengths and weaknesses, as well as its risks, discuss emerging trends, tools, and applications, and stimulate the development of the field through the aggregation of excellent survey papers and working group contributions to the topic.
Conclusions
For the first time in history will the IMIA Yearbook be published in an open access online format allowing a broader readership especially in resource poor countries. For the first time, thanks to the online format, will the IMIA Yearbook be published twice in the year, with two different tracks of papers. We anticipate that the important role of the IMIA yearbook will further increase with these changes just in time for its 25th anniversary in 2016.
doi:10.15265/IY-2014-0030
PMCID: PMC4287079  PMID: 24853037
Editorial; 2014 IMIA Yearbook of Medical Informatics; open access online format; Big Data; survey of biomedical informatics; IMIA and its societies
5.  The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments 
Background
The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.
Description
Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases.
Conclusions
In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.
doi:10.1186/2041-1480-4-20
PMCID: PMC3852282  PMID: 24093723
Gene ontology; Cellular component ontology; Subcellular anatomy ontology; Neuroscience; Annotation; Ontology language; Ontology integration; Neuroscience information framework
6.  A Network-Theoretic Approach for Decompositional Translation across Open Biological Ontologies 
Journal of biomedical informatics  2010;43(4):608-612.
Biological ontologies are now being widely used for annotation, sharing and retrieval of the biological data. Many of these ontologies are hosted under the umbrella of the Open Biological Ontologies Foundry. In order to support interterminology mapping, composite terms in these ontologies need to be translated into atomic or primitive terms in other, orthogonal ontologies, for example, gluconeogenesis (biological process term) to glucose (chemical ontology term). Identifying such decompositional ontology translations is a challenging problem. In this paper, we propose a network-theoretic approach based on the structure of the integrated OBO relationship graph. We use a network-theoretic measure, called the clustering coefficient, to find relevant atomic terms in the neighborhood of a composite term. By eliminating the existing GO to ChEBI Ontology mappings from OBO, we evaluate whether the proposed approach can re-identify the corresponding relationships. The results indicate that the network structure provides strong cues for decompositional ontology translation and the existing relationships can be used to identify new translations.
doi:10.1016/j.jbi.2010.01.007
PMCID: PMC3444745  PMID: 20144734
network theory; biomedical ontologies; ontology translation; open biomedical ontologies
7.  On the Ontology Based Representation of Cell Lines 
PLoS ONE  2012;7(11):e48584.
Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT) integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.
doi:10.1371/journal.pone.0048584
PMCID: PMC3492450  PMID: 23144907
8.  Obol: Integrating Language and Meaning in Bio-Ontologies 
Comparative and Functional Genomics  2004;5(6-7):509-520.
Ontologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language.With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non-trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.
The software is available under an open-source license from: http://www.fruitfly. org/~cjm/obol. Supplementary material for this article can be found at: http://www. interscience.wiley.com/jpages/1531-6912/suppmat.
doi:10.1002/cfg.435
PMCID: PMC2447432  PMID: 18629143
9.  The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web 
PLoS ONE  2011;6(10):e25513.
Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).
doi:10.1371/journal.pone.0025513
PMCID: PMC3184996  PMID: 21991315
10.  DeMO: An Ontology for Discrete-event Modeling and Simulation 
Simulation  2011;87(9):747-773.
Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community.
doi:10.1177/0037549710386843
PMCID: PMC3423901  PMID: 22919114
Discrete systems; simulation environments; standards; Web-based environments
11.  Ontology Alignment Architecture for Semantic Sensor Web Integration 
Sensors (Basel, Switzerland)  2013;13(9):12581-12604.
Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.
doi:10.3390/s130912581
PMCID: PMC3821309  PMID: 24051523
semantic sensor web; ontology alignment; fuzzy logic
12.  Automatic Background Knowledge Selection for Matching Biomedical Ontologies 
PLoS ONE  2014;9(11):e111226.
Ontology matching is a growing field of research that is of critical importance for the semantic web initiative. The use of background knowledge for ontology matching is often a key factor for success, particularly in complex and lexically rich domains such as the life sciences. However, in most ontology matching systems, the background knowledge sources are either predefined by the system or have to be provided by the user. In this paper, we present a novel methodology for automatically selecting background knowledge sources for any given ontologies to match. This methodology measures the usefulness of each background knowledge source by assessing the fraction of classes mapped through it over those mapped directly, which we call the mapping gain. We implemented this methodology in the AgreementMakerLight ontology matching framework, and evaluate it using the benchmark biomedical ontology matching tasks from the Ontology Alignment Evaluation Initiative (OAEI) 2013. In each matching problem, our methodology consistently identified the sources of background knowledge that led to the highest improvements over the baseline alignment (i.e., without background knowledge). Furthermore, our proposed mapping gain parameter is strongly correlated with the F-measure of the produced alignments, thus making it a good estimator for ontology matching techniques based on background knowledge.
doi:10.1371/journal.pone.0111226
PMCID: PMC4224389  PMID: 25379899
13.  Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature 
PLoS Biology  2004;2(11):e309.
We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org.
With the increasing availability of full-text scientific papers online, new tools, such as Textpresso, will help to extract information and knowledge from research literature
doi:10.1371/journal.pbio.0020309
PMCID: PMC517822  PMID: 15383839
14.  OLS Dialog: An open-source front end to the Ontology Lookup Service 
BMC Bioinformatics  2010;11:34.
Background
With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.
Results
In order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.
Conclusions
As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.
doi:10.1186/1471-2105-11-34
PMCID: PMC2823706  PMID: 20078892
15.  PHENOGO: ASSIGNING PHENOTYPIC CONTEXT TO GENE ONTOLOGY ANNOTATIONS WITH NATURAL LANGUAGE PROCESSING 
Natural language processing (NLP) is a high throughput technology because it can process vast quantities of text within a reasonable time period. It has the potential to substantially facilitate biomedical research by extracting, linking, and organizing massive amounts of information that occur in biomedical journal articles as well as in textual fields of biological databases. Until recently, much of the work in biological NLP and text mining has revolved around recognizing the occurrence of biomolecular entities in articles, and in extracting particular relationships among the entities. Now, researchers have recognized a need to link the extracted information to ontologies or knowledge bases, which is a more difficult task. One such knowledge base is Gene Ontology annotations (GOA), which significantly increases semantic computations over the function, cellular components and processes of genes. For multicellular organisms, these annotations can be refined with phenotypic context, such as the cell type, tissue, and organ because establishing phenotypic contexts in which a gene is expressed is a crucial step for understanding the development and the molecular underpinning of the pathophysiology of diseases. In this paper, we propose a system, PhenoGO, which automatically augments annotations in GOA with additional context. PhenoGO utilizes an existing NLP system, called BioMedLEE, an existing knowledge-based phenotype organizer system (PhenOS) in conjunction with MeSH indexing and established biomedical ontologies. More specifically, PhenoGO adds phenotypic contextual information to existing associations between gene products and GO terms as specified in GOA. The system also maps the context to identifiers that are associated with different biomedical ontologies, including the UMLS, Cell Ontology, Mouse Anatomy, NCBI taxonomy, GO, and Mammalian Phenotype Ontology. In addition, PhenoGO was evaluated for coding of anatomical and cellular information and assigning the coded phenotypes to the correct GOA; results obtained show that PhenoGO has a precision of 91% and recall of 92%, demonstrating that the PhenoGO NLP system can accurately encode a large number of anatomical and cellular ontologies to GO annotations. The PhenoGO Database may be accessed at the following URL: http://www.phenoGO.org
PMCID: PMC2906243  PMID: 17094228
16.  Automatic, context-specific generation of Gene Ontology slims 
BMC Bioinformatics  2010;11:498.
Background
The use of ontologies to control vocabulary and structure annotation has added value to genome-scale data, and contributed to the capture and re-use of knowledge across research domains. Gene Ontology (GO) is widely used to capture detailed expert knowledge in genomic-scale datasets and as a consequence has grown to contain many terms, making it unwieldy for many applications. To increase its ease of manipulation and efficiency of use, subsets called GO slims are often created by collapsing terms upward into more general, high-level terms relevant to a particular context. Creation of a GO slim currently requires manipulation and editing of GO by an expert (or community) familiar with both the ontology and the biological context. Decisions about which terms to include are necessarily subjective, and the creation process itself and subsequent curation are time-consuming and largely manual.
Results
Here we present an objective framework for generating customised ontology slims for specific annotated datasets, exploiting information latent in the structure of the ontology graph and in the annotation data. This framework combines ontology engineering approaches, and a data-driven algorithm that draws on graph and information theory. We illustrate this method by application to GO, generating GO slims at different information thresholds, characterising their depth of semantics and demonstrating the resulting gains in statistical power.
Conclusions
Our GO slim creation pipeline is available for use in conjunction with any GO-annotated dataset, and creates dataset-specific, objectively defined slims. This method is fast and scalable for application to other biomedical ontologies.
doi:10.1186/1471-2105-11-498
PMCID: PMC3098080  PMID: 20929524
17.  A semantic proteomics dashboard (SemPoD) for data management in translational research 
BMC Systems Biology  2012;6(Suppl 3):S20.
Background
One of the primary challenges in translational research data management is breaking down the barriers between the multiple data silos and the integration of 'omics data with clinical information to complete the cycle from the bench to the bedside. The role of contextual metadata, also called provenance information, is a key factor ineffective data integration, reproducibility of results, correct attribution of original source, and answering research queries involving "What", "Where", "When", "Which", "Who", "How", and "Why" (also known as the W7 model). But, at present there is limited or no effective approach to managing and leveraging provenance information for integrating data across studies or projects. Hence, there is an urgent need for a paradigm shift in creating a "provenance-aware" informatics platform to address this challenge. We introduce an ontology-driven, intuitive Semantic Proteomics Dashboard (SemPoD) that uses provenance together with domain information (semantic provenance) to enable researchers to query, compare, and correlate different types of data across multiple projects, and allow integration with legacy data to support their ongoing research.
Results
The SemPoD platform, currently in use at the Case Center for Proteomics and Bioinformatics (CPB), consists of three components: (a) Ontology-driven Visual Query Composer, (b) Result Explorer, and (c) Query Manager. Currently, SemPoD allows provenance-aware querying of 1153 mass-spectrometry experiments from 20 different projects. SemPod uses the systems molecular biology provenance ontology (SysPro) to support a dynamic query composition interface, which automatically updates the components of the query interface based on previous user selections and efficientlyprunes the result set usinga "smart filtering" approach. The SysPro ontology re-uses terms from the PROV-ontology (PROV-O) being developed by the World Wide Web Consortium (W3C) provenance working group, the minimum information required for reporting a molecular interaction experiment (MIMIx), and the minimum information about a proteomics experiment (MIAPE) guidelines. The SemPoD was evaluated both in terms of user feedback and as scalability of the system.
Conclusions
SemPoD is an intuitive and powerful provenance ontology-driven data access and query platform that uses the MIAPE and MIMIx metadata guideline to create an integrated view over large-scale systems molecular biology datasets. SemPoD leverages the SysPro ontology to create an intuitive dashboard for biologists to compose queries, explore the results, and use a query manager for storing queries for later use. SemPoD can be deployed over many existing database applications storing 'omics data, including, as illustrated here, the LabKey data-management system. The initial user feedback evaluating the usability and functionality of SemPoD has been very positive and it is being considered for wider deployment beyond the proteomics domain, and in other 'omics' centers.
doi:10.1186/1752-0509-6-S3-S20
PMCID: PMC3524316  PMID: 23282161
18.  Definition of an Ontology Matching Algorithm for Context Integration in Smart Cities 
Sensors (Basel, Switzerland)  2014;14(12):23581-23619.
In this paper we describe a novel proposal in the field of smart cities: using an ontology matching algorithm to guarantee the automatic information exchange between the agents and the smart city. A smart city is composed by different types of agents that behave as producers and/or consumers of the information in the smart city. In our proposal, the data from the context is obtained by sensor and device agents while users interact with the smart city by means of user or system agents. The knowledge of each agent, as well as the smart city's knowledge, is semantically represented using different ontologies. To have an open city, that is fully accessible to any agent and therefore to provide enhanced services to the users, there is the need to ensure a seamless communication between agents and the city, regardless of their inner knowledge representations, i.e., ontologies. To meet this goal we use ontology matching techniques, specifically we have defined a new ontology matching algorithm called OntoPhil to be deployed within a smart city, which has never been done before. OntoPhil was tested on the benchmarks provided by the well known evaluation initiative, Ontology Alignment Evaluation Initiative, and also compared to other matching algorithms, although these algorithms were not specifically designed for smart cities. Additionally, specific tests involving a smart city's ontology and different types of agents were conducted to validate the usefulness of OntoPhil in the smart city environment.
doi:10.3390/s141223581
PMCID: PMC4299078  PMID: 25494353
information fusion; ambient intelligence; context-awareness; smart city; ontology; ontology matching; multi-agent system
19.  Bringing Ontology to the Gene Ontology 
We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinformatics applications requires explicating in machine-processible form the implicit background information that enables human users to interpret the meaning of the vocabulary terms. In the case of GO, this process would involve rendering the meanings of GO into a formal (logical) language with the help of domain experts, and adding additional information required to support the chosen formalization. A controlled vocabulary augmented in these ways is commonly called an ontology. In this paper, we make a modest exploration to determine the ontological requirements for this extended version of GO. Using the terms within the three GO hierarchies (molecular function, biological process and cellular component), we investigate the facility with which GO concepts can be ontologized, using available tools from the philosophical and ontological engineering literature.
doi:10.1002/cfg.253
PMCID: PMC2447385  PMID: 18629099
20.  A relation based measure of semantic similarity for Gene Ontology annotations 
BMC Bioinformatics  2008;9:468.
Background
Various measures of semantic similarity of terms in bio-ontologies such as the Gene Ontology (GO) have been used to compare gene products. Such measures of similarity have been used to annotate uncharacterized gene products and group gene products into functional groups. There are various ways to measure semantic similarity, either using the topological structure of the ontology, the instances (gene products) associated with terms or a mixture of both. We focus on an instance level definition of semantic similarity while using the information contained in the ontology, both in the graphical structure of the ontology and the semantics of relations between terms, to provide constraints on our instance level description.
Semantic similarity of terms is extended to annotations by various approaches, either though aggregation operations such as min, max and average or through an extrapolative method. These approaches introduce assumptions about how semantic similarity of terms relates to the semantic similarity of annotations that do not necessarily reflect how terms relate to each other.
Results
We exploit the semantics of relations in the GO to construct an algorithm called SSA that provides the basis of a framework that naturally extends instance based methods of semantic similarity of terms, such as Resnik's measure, to describing annotations and not just terms. Our measure attempts to correctly interpret how terms combine via their relationships in the ontological hierarchy. SSA uses these relationships to identify the most specific common ancestors between terms. We outline the set of cases in which terms can combine and associate partial order constraints with each case that order the specificity of terms. These cases form the basis for the SSA algorithm. The set of associated constraints also provide a set of principles that any improvement on our method should seek to satisfy.
Conclusion
We derive a measure of semantic similarity between annotations that exploits all available information without introducing assumptions about the nature of the ontology or data. We preserve the principles underlying instance based methods of semantic similarity of terms at the annotation level. As a result our measure better describes the information contained in annotations associated with gene products and as a result is better suited to characterizing and classifying gene products through their annotations.
doi:10.1186/1471-2105-9-468
PMCID: PMC2655092  PMID: 18983678
21.  An ontology-based nurse call management system (oNCS) with probabilistic priority assessment 
Background
The current, place-oriented nurse call systems are very static. A patient can only make calls with a button which is fixed to a wall of a room. Moreover, the system does not take into account various factors specific to a situation. In the future, there will be an evolution to a mobile button for each patient so that they can walk around freely and still make calls. The system would become person-oriented and the available context information should be taken into account to assign the correct nurse to a call.
The aim of this research is (1) the design of a software platform that supports the transition to mobile and wireless nurse call buttons in hospitals and residential care and (2) the design of a sophisticated nurse call algorithm. This algorithm dynamically adapts to the situation at hand by taking the profile information of staff members and patients into account. Additionally, the priority of a call probabilistically depends on the risk factors, assigned to a patient.
Methods
The ontology-based Nurse Call System (oNCS) was developed as an extension of a Context-Aware Service Platform. An ontology is used to manage the profile information. Rules implement the novel nurse call algorithm that takes all this information into account. Probabilistic reasoning algorithms are designed to determine the priority of a call based on the risk factors of the patient.
Results
The oNCS system is evaluated through a prototype implementation and simulations, based on a detailed dataset obtained from Ghent University Hospital. The arrival times of nurses at the location of a call, the workload distribution of calls amongst nurses and the assignment of priorities to calls are compared for the oNCS system and the current, place-oriented nurse call system. Additionally, the performance of the system is discussed.
Conclusions
The execution time of the nurse call algorithm is on average 50.333 ms. Moreover, the oNCS system significantly improves the assignment of nurses to calls. Calls generally have a nurse present faster and the workload-distribution amongst the nurses improves.
doi:10.1186/1472-6963-11-26
PMCID: PMC3045288  PMID: 21294860
22.  KA-SB: from data integration to large scale reasoning 
BMC Bioinformatics  2009;10(Suppl 10):S5.
Background
The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data.
Methods
KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning).
Results
In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts.
Conclusion
These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool , which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.
doi:10.1186/1471-2105-10-S10-S5
PMCID: PMC2755826  PMID: 19796402
23.  Editorial Comment: Symposium: Tscherne Festschrift: Editorial Comment 
doi:10.1007/s11999-013-3173-6
PMCID: PMC3734392  PMID: 23888324
25.  A new editorial board for a new editorial period 
doi:10.1186/1475-2859-3-3
PMCID: PMC406411  PMID: 15107134

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