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1.  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
2.  SIDD: A Semantically Integrated Database towards a Global View of Human Disease 
PLoS ONE  2013;8(10):e75504.
Background
A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data.
Methodology
To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy.
Conclusions
A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD.
doi:10.1371/journal.pone.0075504
PMCID: PMC3795748  PMID: 24146757
3.  Design and Development of a Linked Open Data-Based Health Information Representation and Visualization System: Potentials and Preliminary Evaluation 
JMIR Medical Informatics  2014;2(2):e31.
Background
Healthcare organizations around the world are challenged by pressures to reduce cost, improve coordination and outcome, and provide more with less. This requires effective planning and evidence-based practice by generating important information from available data. Thus, flexible and user-friendly ways to represent, query, and visualize health data becomes increasingly important. International organizations such as the World Health Organization (WHO) regularly publish vital data on priority health topics that can be utilized for public health policy and health service development. However, the data in most portals is displayed in either Excel or PDF formats, which makes information discovery and reuse difficult. Linked Open Data (LOD)—a new Semantic Web set of best practice of standards to publish and link heterogeneous data—can be applied to the representation and management of public level health data to alleviate such challenges. However, the technologies behind building LOD systems and their effectiveness for health data are yet to be assessed.
Objective
The objective of this study is to evaluate whether Linked Data technologies are potential options for health information representation, visualization, and retrieval systems development and to identify the available tools and methodologies to build Linked Data-based health information systems.
Methods
We used the Resource Description Framework (RDF) for data representation, Fuseki triple store for data storage, and Sgvizler for information visualization. Additionally, we integrated SPARQL query interface for interacting with the data. We primarily use the WHO health observatory dataset to test the system. All the data were represented using RDF and interlinked with other related datasets on the Web of Data using Silk—a link discovery framework for Web of Data. A preliminary usability assessment was conducted following the System Usability Scale (SUS) method.
Results
We developed an LOD-based health information representation, querying, and visualization system by using Linked Data tools. We imported more than 20,000 HIV-related data elements on mortality, prevalence, incidence, and related variables, which are freely available from the WHO global health observatory database. Additionally, we automatically linked 5312 data elements from DBpedia, Bio2RDF, and LinkedCT using the Silk framework. The system users can retrieve and visualize health information according to their interests. For users who are not familiar with SPARQL queries, we integrated a Linked Data search engine interface to search and browse the data. We used the system to represent and store the data, facilitating flexible queries and different kinds of visualizations. The preliminary user evaluation score by public health data managers and users was 82 on the SUS usability measurement scale. The need to write queries in the interface was the main reported difficulty of LOD-based systems to the end user.
Conclusions
The system introduced in this article shows that current LOD technologies are a promising alternative to represent heterogeneous health data in a flexible and reusable manner so that they can serve intelligent queries, and ultimately support decision-making. However, the development of advanced text-based search engines is necessary to increase its usability especially for nontechnical users. Further research with large datasets is recommended in the future to unfold the potential of Linked Data and Semantic Web for future health information systems development.
doi:10.2196/medinform.3531
PMCID: PMC4288106  PMID: 25601195
Linked Open Data; Semantic Web; ontology; health information systems; HIV; WHO; public health; public health informatics; visualization
4.  P4-S The Mouse Genome Informatics Database: An Integrated Resource for Mouse Genetics and Genomics 
The Mouse Genome Informatics (MGI; http://www.informatics.jax.org/) database integrates genetic and genomic data with the primary mission of facilitating the use of the mouse as a model system for understanding human biology and disease processes. MGI is the authoritative source of official mouse genetic nomenclature, gene ontology annotations, mammalian phenotype annotations, and mouse anatomy terms. MGI staff enforce the use of standardized genetic nomenclature, ontologies, and controlled vocabularies to describe mouse sequence data, genes, strains, expression data, alleles, and phenotypes. Extensive links between gene-centric information in MGI and other informatics resources (e.g., OMIM, Ensembl, UCSC, NCBI, UniProt) are maintained and updated on a regular basis.
Using the Web-based query interfaces for MGI, users can query for a mouse gene or genes according to diverse biological attributes of those genes, including phenotype associations, gene expression, functional annotation, and genome location. The MGI MouseBLAST server allows users to interrogate the MGI database using nucleotide and/or protein sequences. Functional and phenotypic data from MGI can be viewed in a broader genomic context using an interactive genome browser called Mouse GBrowse. The power of the MGI database as a research tool for biomedicine stems from the degree to which data from diverse sources are integrated. Integration, in turn, allows the data to be evaluated in new contexts. For example, integration makes possible such complex queries as “Find all genes from Chromosome 1 where the function is annotated as transcription factor and there is a knockout allele that results in eye dysmorphology.”
PMCID: PMC2291881
5.  Atlas – a data warehouse for integrative bioinformatics 
BMC Bioinformatics  2005;6:34.
Background
We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development.
Description
The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations.
Conclusion
The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at:
doi:10.1186/1471-2105-6-34
PMCID: PMC554782  PMID: 15723693
6.  Visualizing genomic information across chromosomes with PhenoGram 
BioData Mining  2013;6:18.
Background
With the abundance of information and analysis results being collected for genetic loci, user-friendly and flexible data visualization approaches can inform and improve the analysis and dissemination of these data. A chromosomal ideogram is an idealized graphic representation of chromosomes. Ideograms can be combined with overlaid points, lines, and/or shapes, to provide summary information from studies of various kinds, such as genome-wide association studies or phenome-wide association studies, coupled with genomic location information. To facilitate visualizing varied data in multiple ways using ideograms, we have developed a flexible software tool called PhenoGram which exists as a web-based tool and also a command-line program.
Results
With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail. We have now used PhenoGram to produce a variety of different plots, and provide these as examples herein. These plots include visualization of the genomic coverage of SNPs from a genotyping array, highlighting the chromosomal coverage of imputed SNPs, copy-number variation region coverage, as well as plots similar to the NHGRI GWA Catalog of genome-wide association results.
Conclusions
PhenoGram is a versatile, user-friendly software tool fostering the exploration and sharing of genomic information. Through visualization of data, researchers can both explore and share complex results, facilitating a greater understanding of these data.
doi:10.1186/1756-0381-6-18
PMCID: PMC4015356  PMID: 24131735
Data visualization; Bioinformatics; Genome-wide association study; GWAS; Copy-number variants; CNV; SNP; Ideogram
7.  ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining 
BMC Bioinformatics  2008;9(Suppl 9):S5.
Background
New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed.
Results
We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network.
Conclusion
The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.
doi:10.1186/1471-2105-9-S9-S5
PMCID: PMC2537576  PMID: 18793469
8.  Interpretation of Medical Imaging Data with a Mobile Application: A Mobile Digital Imaging Processing Environment 
Digital Imaging Processing (DIP) requires data extraction and output from a visualization tool to be consistent. Data handling and transmission between the server and a user is a systematic process in service interpretation. The use of integrated medical services for management and viewing of imaging data in combination with a mobile visualization tool can be greatly facilitated by data analysis and interpretation. This paper presents an integrated mobile application and DIP service, called M-DIP. The objective of the system is to (1) automate the direct data tiling, conversion, pre-tiling of brain images from Medical Imaging NetCDF (MINC), Neuroimaging Informatics Technology Initiative (NIFTI) to RAW formats; (2) speed up querying of imaging measurement; and (3) display high-level of images with three dimensions in real world coordinates. In addition, M-DIP provides the ability to work on a mobile or tablet device without any software installation using web-based protocols. M-DIP implements three levels of architecture with a relational middle-layer database, a stand-alone DIP server, and a mobile application logic middle level realizing user interpretation for direct querying and communication. This imaging software has the ability to display biological imaging data at multiple zoom levels and to increase its quality to meet users’ expectations. Interpretation of bioimaging data is facilitated by an interface analogous to online mapping services using real world coordinate browsing. This allows mobile devices to display multiple datasets simultaneously from a remote site. M-DIP can be used as a measurement repository that can be accessed by any network environment, such as a portable mobile or tablet device. In addition, this system and combination with mobile applications are establishing a virtualization tool in the neuroinformatics field to speed interpretation services.
doi:10.3389/fneur.2013.00085
PMCID: PMC3701154  PMID: 23847587
mobile digital imaging processing; mobile visualization tool; medical science; bioimaging; biomedical research; neuroinformatics
9.  Visualization of protein interaction networks: problems and solutions 
BMC Bioinformatics  2013;14(Suppl 1):S1.
Background
Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization.
Methods
In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases.
Results
Currently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central.
Conclusion
A current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point of view, open-source, free and extensible tools, like Cytoscape, guarantee a long term sustainability due to the largeness of the developers and users communities, and provide a great flexibility since new functions are continuously added by the developer community through new plug-ins, but the emerging parallel, often closed-source tools like NAViGaTOR, can offer near real-time response time also in the analysis of very huge PINs.
doi:10.1186/1471-2105-14-S1-S1
PMCID: PMC3548679  PMID: 23368786
10.  iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks 
BMC Bioinformatics  2011;12:380.
Background
The speed at which biological datasets are being accumulated stands in contrast to our ability to integrate them meaningfully. Large-scale biological databases containing datasets of genes, proteins, cells, organs, and diseases are being created but they are not connected. Integration of these vast but heterogeneous sources of information will allow the systematic and comprehensive analysis of molecular and clinical datasets, spanning hundreds of dimensions and thousands of individuals. This integration is essential to capitalize on the value of current and future molecular- and cellular-level data on humans to gain novel insights about health and disease.
Results
We describe a new open-source Cytoscape plugin named iCTNet (integrated Complex Traits Networks). iCTNet integrates several data sources to allow automated and systematic creation of networks with up to five layers of omics information: phenotype-SNP association, protein-protein interaction, disease-tissue, tissue-gene, and drug-gene relationships. It facilitates the generation of general or specific network views with diverse options for more than 200 diseases. Built-in tools are provided to prioritize candidate genes and create modules of specific phenotypes.
Conclusions
iCTNet provides a user-friendly interface to search, integrate, visualize, and analyze genome-scale biological networks for human complex traits. We argue this tool is a key instrument that facilitates systematic integration of disparate large-scale data through network visualization, ultimately allowing the identification of disease similarities and the design of novel therapeutic approaches.
The online database and Cytoscape plugin are freely available for academic use at: http://www.cs.queensu.ca/ictnet
doi:10.1186/1471-2105-12-380
PMCID: PMC3190406  PMID: 21943367
11.  DAVID: Database for Annotation, Visualization, and Integrated Discovery 
Genome Biology  2003;4(5):P3.
Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. Database for Annotation, Visualization, and Integrated Discovery (DAVID) provides querybased access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information.
Background
Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information.
Results
Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains.
Conclusions
Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.
doi:10.1186/gb-2003-4-5-p3
PMCID: PMC3720094  PMID: 12734009
12.  Managing and querying gene expression data using Curray 
BMC Proceedings  2011;5(Suppl 2):S10.
Background
In principle, gene expression data can be viewed as providing just the three-valued expression profiles of target biological elements relative to an experiment at hand. Although complicated, gathering expression profiles does not pose much of a challenge from a query language standpoint. What is interesting is how these expression profiles are used to tease out information from the vast array of information repositories that ascribe meaning to the expression profiles. Since such annotations are inherently experiment specific functions, much the same way as queries in databases, developing a querying system for gene expression data appears to be pointless. Instead, developing tools and techniques to support individual assignment has been considered prudent in contemporary research.
Results
We propose a gene expression data management and querying system that is able to support pre-expression, expression and post-expression level analysis and reduce impedance mismatch between analysis systems. To this end, we propose a new, platform-independent and general purpose query language called Curray, for Custom Microarray query language, to support online expression data analysis using distributed resources. It includes features to design expression analysis pipelines using language constructs at the conceptual level. The ability to include user defined functions as a first-class language feature facilitates unlimited analysis support and removes language limitations. We show that Curray’s declarative and extensible features nimbly allow flexible modeling and room for customization.
Conclusions
The developments proposed in this article allow users to view their expression data from a conceptual standpoint - experiments, probes, expressions, mapping, etc. at multiple levels of representation and independent of the underlying chip technologies. It also allows transparent roll-up and drill-down along representation hierarchies from raw data to standards such as MIAME and MAGE-ML using linguistic constructs. Curray also allows seamless integration with distributed web resources through its LifeDB system of which it is a part.
doi:10.1186/1753-6561-5-S2-S10
PMCID: PMC3090758  PMID: 21554758
13.  Design and utilization of the colorectal and pancreatic neoplasm virtual biorepository: An early detection research network initiative 
Background:
The Early Detection Research Network (EDRN) colorectal and pancreatic neoplasm virtual biorepository is a bioinformatics-driven system that provides high-quality clinicopathology-rich information for clinical biospecimens. This NCI-sponsored EDRN resource supports translational cancer research. The information model of this biorepository is based on three components: (a) development of common data elements (CDE), (b) a robust data entry tool and (c) comprehensive data query tools.
Methods:
The aim of the EDRN initiative is to develop and sustain a virtual biorepository for support of translational research. High-quality biospecimens were accrued and annotated with pertinent clinical, epidemiologic, molecular and genomic information. A user-friendly annotation tool and query tool was developed for this purpose. The various components of this annotation tool include: CDEs are developed from the College of American Pathologists (CAP) Cancer Checklists and North American Association of Central Cancer Registries (NAACR) standards. The CDEs provides semantic and syntactic interoperability of the data sets by describing them in the form of metadata or data descriptor. The data entry tool is a portable and flexible Oracle-based data entry application, which is an easily mastered, web-based tool. The data query tool facilitates investigators to search deidentified information within the warehouse through a “point and click” interface thus enabling only the selected data elements to be essentially copied into a data mart using a dimensional-modeled structure from the warehouse’s relational structure.
Results:
The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository database contains multimodal datasets that are available to investigators via a web-based query tool. At present, the database holds 2,405 cases and 2,068 tumor accessions. The data disclosure is strictly regulated by user’s authorization. The high-quality and well-characterized biospecimens have been used in different translational science research projects as well as to further various epidemiologic and genomics studies.
Conclusions:
The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository with a tangible translational biomedical informatics infrastructure facilitates translational research. The data query tool acts as a central source and provides a mechanism for researchers to efficiently query clinically annotated datasets and biospecimens that are pertinent to their research areas. The tool ensures patient health information protection by disclosing only deidentified data with Institutional Review Board and Health Insurance Portability and Accountability Act protocols.
doi:10.4103/2153-3539.70831
PMCID: PMC2956178  PMID: 21031013
Colorectal and pancreatic neoplasm; tissue banking informatics
14.  A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research 
Plant Methods  2008;4:11.
Background
For omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment.
Results
The database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e.g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute.
Conclusion
The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research.
doi:10.1186/1746-4811-4-11
PMCID: PMC2409336  PMID: 18495032
15.  Exploring and linking biomedical resources through multidimensional semantic spaces 
BMC Bioinformatics  2012;13(Suppl 1):S6.
Background
The semantic integration of biomedical resources is still a challenging issue which is required for effective information processing and data analysis. The availability of comprehensive knowledge resources such as biomedical ontologies and integrated thesauri greatly facilitates this integration effort by means of semantic annotation, which allows disparate data formats and contents to be expressed under a common semantic space. In this paper, we propose a multidimensional representation for such a semantic space, where dimensions regard the different perspectives in biomedical research (e.g., population, disease, anatomy and protein/genes).
Results
This paper presents a novel method for building multidimensional semantic spaces from semantically annotated biomedical data collections. This method consists of two main processes: knowledge and data normalization. The former one arranges the concepts provided by a reference knowledge resource (e.g., biomedical ontologies and thesauri) into a set of hierarchical dimensions for analysis purposes. The latter one reduces the annotation set associated to each collection item into a set of points of the multidimensional space. Additionally, we have developed a visual tool, called 3D-Browser, which implements OLAP-like operators over the generated multidimensional space. The method and the tool have been tested and evaluated in the context of the Health-e-Child (HeC) project. Automatic semantic annotation was applied to tag three collections of abstracts taken from PubMed, one for each target disease of the project, the Uniprot database, and the HeC patient record database. We adopted the UMLS Meta-thesaurus 2010AA as the reference knowledge resource.
Conclusions
Current knowledge resources and semantic-aware technology make possible the integration of biomedical resources. Such an integration is performed through semantic annotation of the intended biomedical data resources. This paper shows how these annotations can be exploited for integration, exploration, and analysis tasks. Results over a real scenario demonstrate the viability and usefulness of the approach, as well as the quality of the generated multidimensional semantic spaces.
doi:10.1186/1471-2105-13-S1-S6
PMCID: PMC3471347  PMID: 22373409
16.  ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms 
BMC Genomics  2011;12:83.
Background
Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN) method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by creating a user-friendly interface that identifies and provides quality scores for all potential ZFN target sites in the complete genomes of several model organisms.
Description
ZFNGenome is a GBrowse-based tool for identifying and visualizing potential target sites for OPEN-generated ZFNs. ZFNGenome currently includes a total of more than 11.6 million potential ZFN target sites, mapped within the fully sequenced genomes of seven model organisms; S. cerevisiae, C. reinhardtii, A. thaliana, D. melanogaster, D. rerio, C. elegans, and H. sapiens and can be visualized within the flexible GBrowse environment. Additional model organisms will be included in future updates. ZFNGenome provides information about each potential ZFN target site, including its chromosomal location and position relative to transcription initiation site(s). Users can query ZFNGenome using several different criteria (e.g., gene ID, transcript ID, target site sequence). Tracks in ZFNGenome also provide "uniqueness" and ZiFOpT (Zinc Finger OPEN Targeter) "confidence" scores that estimate the likelihood that a chosen ZFN target site will function in vivo. ZFNGenome is dynamically linked to ZiFDB, allowing users access to all available information about zinc finger reagents, such as the effectiveness of a given ZFN in creating double-stranded breaks.
Conclusions
ZFNGenome provides a user-friendly interface that allows researchers to access resources and information regarding genomic target sites for engineered ZFNs in seven model organisms. This genome-wide database of potential ZFN target sites should greatly facilitate the utilization of ZFNs in both basic and clinical research.
ZFNGenome is freely available at: http://bindr.gdcb.iastate.edu/ZFNGenome or at the Zinc Finger Consortium website: http://www.zincfingers.org/.
doi:10.1186/1471-2164-12-83
PMCID: PMC3042413  PMID: 21276248
17.  WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations 
BMC Genomics  2007;8:275.
Background
Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results.
Results
This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions.
Conclusion
WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at .
doi:10.1186/1471-2164-8-275
PMCID: PMC1976135  PMID: 17697334
18.  BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks 
Gene and protein networks offer a powerful approach for integration of the disparate yet complimentary types of data that result from high-throughput analyses. Although many tools and databases are currently available for accessing such data, they are left unutilized by bench scientists as they generally lack features for effective analysis and integration of both public and private datasets and do not offer an intuitive interface for use by scientists with limited computational expertise. We describe BioNetwork Bench, an open source, user-friendly suite of database and software tools for constructing, querying, and analyzing gene and protein network models. It enables biologists to analyze public as well as private gene expression; interactively query gene expression datasets; integrate data from multiple networks; store and selectively share the data and results. Finally, we describe an application of BioNetwork Bench to the assembly and iterative expansion of a gene network that controls the differentiation of retinal progenitor cells into rod photoreceptors. The tool is available from http://bionetworkbench.sourceforge.net/
Background
The emergence of high-throughput technologies has allowed many biological investigators to collect a great deal of information about the behavior of genes and gene products over time or during a particular disease state. Gene and protein networks offer a powerful approach for integration of the disparate yet complimentary types of data that result from such high-throughput analyses. There are a growing number of public databases, as well as tools for visualization and analysis of networks. However, such databases and tools have yet to be widely utilized by bench scientists, as they generally lack features for effective analysis and integration of both public and private datasets and do not offer an intuitive interface for use by biological scientists with limited computational expertise.
Results
We describe BioNetwork Bench, an open source, user-friendly suite of database and software tools for constructing, querying, and analyzing gene and protein network models. BioNetwork Bench currently supports a broad class of gene and protein network models (eg, weighted and un-weighted, undirected graphs, multi-graphs). It enables biologists to analyze public as well as private gene expression, macromolecular interaction and annotation data; interactively query gene expression datasets; integrate data from multiple networks; query multiple networks for interactions of interest; store and selectively share the data as well as results of analyses. BioNetwork Bench is implemented as a plug-in for, and hence is fully interoperable with, Cytoscape, a popular open-source software suite for visualizing macromolecular interaction networks. Finally, we describe an application of BioNetwork Bench to the problem of assembly and iterative expansion of a gene network that controls the differentiation of retinal progenitor cells into rod photoreceptors.
Conclusions
BioNetwork Bench provides a suite of open source software for construction, querying, and selective sharing of gene and protein networks. Although initially aimed at a community of biologists interested in retinal development, the tool can be adapted easily to work with other biological systems simply by populating the associated database with the relevant datasets.
doi:10.4137/BBI.S9728
PMCID: PMC3498971
network analysis; software; network contruction; network integration
19.  SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access 
BMC Bioinformatics  2008;9:428.
Background
In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics.
Results
We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 × 109 genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested.
Conclusion
In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.
doi:10.1186/1471-2105-9-428
PMCID: PMC2576268  PMID: 18847484
20.  solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database 
BMC Bioinformatics  2010;11:525.
Background
A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases.
Description
The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application.
Conclusions
solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes underlying phenotypic variation and markers more closely linked to QTLs. solQTL is freely available on SGN and can be used in private or public mode.
doi:10.1186/1471-2105-11-525
PMCID: PMC2984588  PMID: 20964836
21.  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
22.  A natural language interface plug-in for cooperative query answering in biological databases 
BMC Genomics  2012;13(Suppl 3):S4.
Background
One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed using sophisticated tools. In such highly interpretive environments, rigidly structured databases do not always perform well. In this paper, our goal is to propose a semantic correspondence plug-in to aid natural language query processing over arbitrary biological database schema with an aim to providing cooperative responses to queries tailored to users' interpretations.
Results
Natural language interfaces for databases are generally effective when they are tuned to the underlying database schema and its semantics. Therefore, changes in database schema become impossible to support, or a substantial reorganization cost must be absorbed to reflect any change. We leverage developments in natural language parsing, rule languages and ontologies, and data integration technologies to assemble a prototype query processor that is able to transform a natural language query into a semantically equivalent structured query over the database. We allow knowledge rules and their frequent modifications as part of the underlying database schema. The approach we adopt in our plug-in overcomes some of the serious limitations of many contemporary natural language interfaces, including support for schema modifications and independence from underlying database schema.
Conclusions
The plug-in introduced in this paper is generic and facilitates connecting user selected natural language interfaces to arbitrary databases using a semantic description of the intended application. We demonstrate the feasibility of our approach with a practical example.
doi:10.1186/1471-2164-13-S3-S4
PMCID: PMC3323828  PMID: 22759613
23.  Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface 
Objective
UK primary care databases, which contain diagnostic, demographic and prescribing information for millions of patients geographically representative of the UK, represent a significant resource for health services and clinical research. They can be used to identify patients with a specified disease or condition (phenotyping) and to investigate patterns of diagnosis and symptoms. Currently, extracting such information manually is time-consuming and requires considerable expertise. In order to exploit more fully the potential of these large and complex databases, our interdisciplinary team developed generic methods allowing access to different types of user.
Materials and methods
Using the Clinical Practice Research Datalink database, we have developed an online user-focused system (TrialViz), which enables users interactively to select suitable medical general practices based on two criteria: suitability of the patient base for the intended study (phenotyping) and measures of data quality.
Results
An end-to-end system, underpinned by an innovative search algorithm, allows the user to extract information in near real-time via an intuitive query interface and to explore this information using interactive visualization tools. A usability evaluation of this system produced positive results.
Discussion
We present the challenges and results in the development of TrialViz and our plans for its extension for wider applications of clinical research.
Conclusions
Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases.
doi:10.1136/amiajnl-2013-001847
PMCID: PMC3932457  PMID: 24272162
Electronic Health records; Data visualisation; Data quality; Primary Care
24.  TreeGenes: A Forest Tree Genome Database 
The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.
doi:10.1155/2008/412875
PMCID: PMC2517852  PMID: 18725987
25.  VisANT: an online visualization and analysis tool for biological interaction data 
BMC Bioinformatics  2004;5:17.
Background
New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems.
Results
We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology.
Conclusion
VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at .
doi:10.1186/1471-2105-5-17
PMCID: PMC368431  PMID: 15028117

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