The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

BACKGROUND: The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models. FINDINGS: We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described. CONCLUSIONS: RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The Systems Biology Graphical Notation

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. © 2009 Nature America, Inc

The health care and life sciences community profile for dataset descriptions

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets

The BioPAX community standard for pathway data sharing

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved

Robust texture based biomass estimation of small fronded floating aquatic plants using j-values

This paper proposes a new method of estimation of the wet biomass of three floating aquatic plants, Spirodela polyrhiza, Lemna minor and Azolla pinnata. The method uses a homogeneity measure known as the J-value to detect the texture of the fronds of the plants from the uniform water surface. The proposed method is called J-value thresholding (JVT) and is highly accurate compared to the alternative green layer extraction (GLE). The average accuracy under normal illumination for the proposed method is 91.59% for Spirodela polyrhiza, 80.11% for Lemna minor and 77.4% for Azolla pinnata. Furthermore, it is robust to different illumination levels with the Pearson correlation coefficient of the estimates of different illumination levels being above 95%. When used to obtain the growth rate of each plant specie through linear regression, the result from the proposed method is highly consistent with the ground truth of the image

Consumption of human rabies immunoglobulin (HRIG) for major animal bites in government hospitals of Sri Lanka.

AbstractIntroduction:Rabies still remains as a significant public health problem in Sri Lanka. Published data related to the usage of human rabies immunoglobulins (HRIG) which is an expensive biological used for post exposure prophylaxis and the types of animal bites are limited. This study was designed to analyze the consumption of HRIG for major animal bites in government hospitals of Sri Lanka. Methods: A audit was carried out at the rabies unit in the Medical Research Institute (MRI) on the use of HRIG from 1st of January to 31st of December 2012 . Data was extracted from scrutinizing the forms sent to the Rabies Unit following the administration of HRIG by the government hospitals which administer HRIG. Results:1896, 2160, 2186 patients have received HRIG during 2010, 2011and 2012 respectively. The number of patients treated without adhering to the rabies treatment protocol issued by the ministry of health also has inreased over the same period of time. Each year around 60% of total HRIG has been used for stray dog and cat bites, 24% for domestic animal and 17% for wild animal bites.  Conclusions and recommendations:Annual consumption as well as the misuse of HRIG has increased from 2010 to 2012. Effective methods to control stray dogs and cats and the concept of responsible pet ownership should be encouraged. Medical officers in rabies treatment units should be trained on adherence to government protocol for anti rabies post exposure therapy.  </p