Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive. A simple interface allows the user to query for differential gene expression either by gene names or attributes or by biological conditions, e.g. diseases, organism parts or cell types. Since our previous report we made 20 monthly releases and, as of Release 11.08 (August 2011), the database supports 19 species, which contains expression data measured for 19,014 biological conditions in 136,551 assays from 5598 independent studies.

An approach to semantic query expansion system based on Hepatitis ontology.

BACKGROUND: Ontology development, as an increasingly practical vehicle applied in various fields, plays a significant role in knowledge management. This paper, focusing on constructing and querying a hepatitis ontology, aims to provide a framework for ontology-based medical services. The paper is devoted to the algorithm of query expansion for the hepatitis ontology, including synonym expansion, hypernym/hyponym expansion and expansion of similar words. It applies semantic similarity calculation to judge the similarity of retrieval terms. RESULTS: The paper proposes a new prototype system. The accuracy of query expansion is improved in both precision@40 and AP@40, which indicates that query expansion improves the accuracy of the query after using the method proposed in this paper. CONCLUSIONS: The paper has adopted semantic similarity computing to improve retrieval performance. Experiments show that search precision of query expansion is higher based on domain concept relationship.

Clarifying Definitions for the Massage Therapy Profession: the Results of the Best Practices Symposium.

BACKGROUND: Massage therapists are at times unclear about the definition of massage therapy, which creates challenges for the profession. It is important to investigate the current definitions and to consider the field as a whole in order to move toward clarity on what constitutes the constructs within the profession. PURPOSE: To determine how a sample of experts understand and describe the field of massage therapy as a step toward clarifying definitions for massage and massage therapy, and framing the process of massage therapy practice. SETTING: A two-day symposium held in 2010 with the purpose of gathering knowledge to inform and aid in the creation of massage therapy best practice guidelines for stress and low back pain. PARTICIPANTS: Thirty-two experts in the field of massage therapy from the United States, Europe, and Canada. DESIGN: Qualitative analysis of secondary cross-sectional data using a grounded theory approach. RESULTS: Three over-arching themes were identified: 1) What is massage?; 2) The multidimensional nature of massage therapy; and 3) The influencing factors on massage therapy practice. DISCUSSION: The data offered clarifying definitions for massage and massage therapy, as well as a framework for the context for massage therapy practice. These clarifications can serve as initial steps toward the ultimate goal of creating new theory for the field of massage therapy, which can then be applied in practice, education, research, and policy. CONCLUSIONS: Foundational research into how experts in the profession understand and describe the field of massage therapy is limited. Understanding the potential differences between the terms massage and massage therapy could contribute to a transformation in the profession in the areas of education, practice, research, policy and/or regulation. Additionally, framing the context for massage therapy practice invites future discussions to further clarify practice issues.

Process for massage therapy practice and essential assessment.

BACKGROUND: Little evidence exists about processes in massage therapy practice. Investigating current frameworks is warranted. This qualitative study is a secondary data analysis using grounded theory to understand how massage therapy experts describe massage therapy practice. METHODS: 31 massage therapy experts were invited to a 2-day symposium to discuss best practices for the profession. Through qualitative analysis, memoing, and discussion, the data were summarized into themes. RESULTS: Three themes were identified around massage therapy practice: 1) client centered, 2) structure for practice, and 3) influencing factors. Each theme is clarified and expanded. DISCUSSION: Conceptual models were developed for research and clinical practice and a definition for massage therapy practice was identified. Challenges and limitations are discussed. CONCLUSION: The goal of providing these models is to give massage therapists tools to deliver the best possible care. The models need testing to see if they help advance the profession.

Human Development Domain of the Ontology of Craniofacial Development and Malformation.

In this paper we describe an ontological scheme for representing anatomical entities undergoing morphological transformation and changes in phenotype during prenatal development. This is a proposed component of the Anatomical Transformation Abstraction (ATA) of the Foundational Model of Anatomy (FMA) Ontology that was created to provide an ontological framework for capturing knowledge about human development from the zygote to postnatal life. It is designed to initially describe the structural properties of the anatomical entities that participate in human development and then enhance their description with developmental properties, such as temporal attributes and developmental processes. This approach facilitates the correlation and integration of the classical but static representation of embryology with the evolving novel concepts of developmental biology, which primarily deals with the experimental data on the mechanisms of embryogenesis and organogenesis. This is important for describing and understanding the underlying processes involved in structural malformations. In this study we focused on the development of the lips and the palate in conjunction with our work on the pathogenesis and classification of cleft lip and palate (CL/P) in the FaceBase program. Our aim here is to create the Craniofacial Human Development Ontology (CHDO) to support the Ontology of Craniofacial Development and Malformation (OCDM), which provides the infrastructure for integrating multiple and disparate craniofacial data generated by FaceBase researchers.

Towards understanding craniofacial abnormalities: the ontology of craniofacial development and malformation.

We introduce the Ontology of Craniofacial Development and Malformation (OCDM), a project of the NIH-funded FaceBase consortium, whose goal is to gather data from multiple species, at levels ranging from genes to gross anatomy, in order to understand the causes of craniofacial abnormalities. The OCDM is being developed in order to facilitate integration of these diverse forms of data in a central Hub. It currently consists of several components, including human adult and developmental anatomy, corresponding mouse structures, and malformations. Example queries show the potential of the OCDM for intelligent data annotation and querying.

An ontology-based comparative anatomy information system.

INTRODUCTION: This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback. METHODS: The anatomical structures of the species to be compared, as well as the mappings between species, are modeled on templates from the Foundational Model of Anatomy knowledge base, and compared using graph-matching techniques. A graphical user interface allows users to issue queries that retrieve information concerning similarities and differences between structures in the species being examined. Queries from diverse information sources, including domain experts, peer-reviewed articles, and reference books, have been used to test the system and to illustrate its potential use in comparative anatomy studies. RESULTS: 157 test queries were submitted to the CAIS system, and all of them were correctly answered. The interface was evaluated in terms of clarity and ease of use. This testing determined that the application works well, and is fairly intuitive to use, but users want to see more clarification of the meaning of the different types of possible queries. Some of the interface issues will naturally be resolved as we refine our conceptual model to deal with partial and complex homologies in the content. CONCLUSIONS: The CAIS system and its associated methods are expected to be useful to biologists and translational medicine researchers. Possible applications range from supporting theoretical work in clarifying and modeling ontogenetic, physiological, pathological, and evolutionary transformations, to concrete techniques for improving the analysis of genotype-phenotype relationships among various animal models in support of a wide array of clinical and scientific initiatives.

Anatomy ontologies and potential users: bridging the gap.

MOTIVATION: To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations. METHODS: Annotations from three diverse multi-species public-domain datasets provided a set of use cases for matching anatomical terms in two major anatomical ontologies (the Foundational Model of Anatomy and Uberon), using two lexical-matching applications (Zooma and Ontology Mapper). RESULTS: Approximately 1500 terms were identified; Uberon/Zooma mappings provided 286 matches, compared to the control and Ontology Mapper returned 319 matches. For the Foundational Model of Anatomy, Zooma returned 312 matches, and Ontology Mapper returned 397. CONCLUSIONS: Our results indicate that for our datasets the anatomical entities or concepts are embedded in user-generated complex terms, and while lexical mapping works, anatomy ontologies do not provide the majority of terms users supply when annotating data. Provision of searchable cross-products for compositional terms is a key requirement for using ontologies.

Steps toward massage therapy guidelines: a first report to the profession.

The massage profession has grown rapidly since the late 1980s. As with business startups that begin informally and successfully mature into larger enterprises, growth brings new organizational challenges, together with greater visibility and opportunity. The maturation of massage as a health care profession increases the need for a process to formalize the synthesis of massage therapy knowledge from clinical experience and research-to collect what we know and to make such baseline knowledge widely available to practitioners, consumers, and other health care stakeholders. In short, we need to create a process for setting guidelines.The present paper lays out the motivations and framework for creating massage therapy guidelines that are informed both by research and by clinical experience. It also acts as a report to the massage therapy profession and to other stakeholders about the work of the Best Practices Committee of the Massage Therapy Foundation since 2006. And it has the additional goal of providing a health care literature basis for future academic discussions of massage.The discussion here is based on a definition from the Institute of Medicine and on research into the nature of expertise. Guidelines are targeted for submission to the National Guideline Clearinghouse. Challenges in creating guidelines for massage therapy are discussed. Various stakeholders are considered. Current literature from the wider scope of health care is extensively reviewed. Topics addressed include guideline creation, credentialing of complementary and alternative medicine practitioners, definition of competence, and the increasing role of technology (that is, informatics) in managing training and task-necessary competencies. Finally, a process for creation of massage therapy guidelines is proposed. A central feature of the proposal is the use of a "World Café" symposium to elicit knowledge and solutions from diverse experts. The role of transparency and broad and open peer review is emphasized as essential to the usability and credibility of guidelines.

A graphical user interface for a comparative anatomy information system: design, implementation and usage scenarios.

Building on our previous design work in the development of the Structural Difference Method (SDM) for describing anatomical similarities and differences across species, we describe the design and implementation of the associated comparative anatomy information system (CAIS) interface and provide scenarios from the literature for its use by research scientists.

Of mice and men: design of a comparative anatomy information system.

In previous work, we proposed an approach called the Structural Difference Method (SDM) to correlating the anatomy of Homo sapiens with selected species, using the Foundational Model of Anatomy (FMA) as a framework and graph matching as a method, for determining similarities and differences between species. In this paper, we present the design of a comparative anatomy information system that utilizes the SDM and allows users to issue queries to determine the similarities and differences between two species. Our system will serve as a pilot project for cross-species anatomical information collection, storage, and retrieval. The underlying data structure of a mapping, and the syntax and semantics of the system's query language, are presented.

An approach to the anatomical correlation of species through the Foundational Model of Anatomy.

The increasing need for extrapolating information from one species to another has been highlighted by contemporary research in bioinformatics, genomics, proteomics, and animal models of human disease, as well as other fields. We propose an approach to correlating the anatomy of Homo sapiens with selected species, using the Foundational Model of Anatomy (FMA) as a framework, and graph matching as a method, for determining similarities and differences in the nodes and relationships (edges) defined by the attributed graph of the FMA. We illustrate our approach by comparing anatomical structures of mouse and human that present prototypical mapping problems.