Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?

Minimum information models are reporting frameworks that describe the essential information that needs to be provided in a publication, so that the work can be repeated or compared to other work. In 2016, Minimum Information about Tolerogenic Antigen-Presenting cells (MITAP) was created to standardize the reporting on tolerogenic antigen-presenting cells, including tolerogenic dendritic cells (tolDCs). tolDCs is a generic term for dendritic cells that have the ability to (re-)establish immune tolerance; they have been developed as a cell therapy for autoimmune diseases or for the prevention of transplant rejection. Because protocols to generate these therapeutic cells vary widely, MITAP was deemed to be a pivotal reporting tool by and for the tolDC community. In this paper, we explored the impact that MITAP has had on the tolDC field. We did this by examining a subset of the available literature on tolDCs. Our analysis shows that MITAP is used in only the minority of relevant papers (14%), but where it is used the amount of metadata available is slightly increased over where it is not. From this, we conclude that MITAP has been a partial success, but that much more needs to be done if standardized reporting is to become common within the discipline.

A fully computational and reasonable representation for karyotypes

Summary

The human karyotype has been used as a mechanism for describing and detecting gross abnormalities in the genome for many decades. It is used both for routine diagnostic purposes and for research to further our understanding of the causes of disease. Despite these important applications there has been no rigorous computational representation of the karyotype; rather an informal, string-based representation is used, making it hard to check, organize and search data of this form. In this article, we describe our use of OWL, the Ontology Web Language, to generate a fully computational representation of the karyotype; the development of this ontology represents a significant advance from the traditional bioinformatics use for tagging and navigation and has necessitated the development of a new ontology development environment called Tawny-OWL.

Availability and implementation

The Karyotype Ontology and associated Tawny-OWL source code is available on GitHub at https://github.com/jaydchan/tawny-karyotype, under a LGPL License, Version 3.0.

What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations?

Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Recent studies have demonstrated that patients from genetically understudied populations, in particular those of black African heritage, are less likely to receive a diagnosis of mtDNA disease. It has been suggested that haplogroup context might influence the presentation and penetrance of mtDNA disease; thus, the spectrum of mutations that are associated with disease in different populations. However, to date there is only one well-established example of such an effect: the increased penetrance of two Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducted the most extensive investigation to date into the importance of haplogroup context on the pathogenicity of mtDNA mutations. We searched for proven human point mutations across 726 multiple sequence alignments derived from 33 non-human species absent of disease. A total of 58 pathogenic point mutations arise in the sequences of these species. We assessed the sequence context and found evidence of population variants that could modulate the phenotypic expression of these point mutations masking the pathogenic effects seen in humans. This supports the theory that sequence context is influential in the presentation of mtDNA disease and has implications for diagnostic practices. We have shown that our current understanding of the pathogenicity of mtDNA point mutations, primarily built on studies of individuals with haplogroups HVUKTJ, will not present a complete picture. This will have the effect of creating a diagnostic inequality, whereby individuals who do not belong to these lineages are less likely to receive a genetic diagnosis.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capturing data using graphs. The language provides the syntax using a free text document that is accessible to humans only. This paper describes SBOL-OWL, an ontology for a machine understandable definition of SBOL. This ontology acts as a semantic layer for genetic circuit designs. As a result, computational tools can understand the meaning of design entities in addition to parsing structured SBOL data. SBOL-OWL not only describes how genetic circuits can be constructed computationally, it also facilitates the use of several existing Semantic Web tools for synthetic biology. This paper demonstrates some of these features, for example, to validate designs and check for inconsistencies. Through the use of SBOL-OWL, queries can be simplified and become more intuitive. Moreover, existing reasoners can be used to infer information about genetic circuit designs that cannot be directly retrieved using existing querying mechanisms. This ontological representation of the SBOL standard provides a new perspective to the verification, representation, and querying of information about genetic circuits and is important to incorporate complex design information via the integration of biological ontologies.

On patterns and re-use in bioinformatics databases

Motivation

As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that data percolates between different databases, which causes particular concerns for data correctness; if this percolation occurs, incorrect data in one database may eventually affect many others while, conversely, corrections in one database may fail to percolate to others. In this paper, we test this widely-held belief by directly looking for sentence reuse both within and between databases. Further, we investigate patterns of how sentences are reused over time. Finally, we consider the limitations of this form of analysis and the implications that this may have for bioinformatics database design.

Results

We show that reuse of annotation is common within many different databases, and that also there is a detectable level of reuse between databases. In addition, we show that there are patterns of reuse that have previously been shown to be associated with percolation errors.

Availability and implementation

Analytical software is available on request.

Minimum Information about T Regulatory Cells: A Step toward Reproducibility and Standardization

Cellular therapies with CD4+ T regulatory cells (Tregs) hold promise of efficacious treatment for the variety of autoimmune and allergic diseases as well as posttransplant complications. Nevertheless, current manufacturing of Tregs as a cellular medicinal product varies between different laboratories, which in turn hampers precise comparisons of the results between the studies performed. While the number of clinical trials testing Tregs is already substantial, it seems to be crucial to provide some standardized characteristics of Treg products in order to minimize the problem. We have previously developed reporting guidelines called minimum information about tolerogenic antigen-presenting cells, which allows the comparison between different preparations of tolerance-inducing antigen-presenting cells. Having this experience, here we describe another minimum information about Tregs (MITREG). It is important to note that MITREG does not dictate how investigators should generate or characterize Tregs, but it does require investigators to report their Treg data in a consistent and transparent manner. We hope this will, therefore, be a useful tool facilitating standardized reporting on the manufacturing of Tregs, either for research purposes or for clinical application. This way MITREG might also be an important step toward more standardized and reproducible testing of the Tregs preparations in clinical applications.

A document-centric approach for developing the tolAPC ontology

Background

There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different “formalisms” to represent and share their data – by the far most common, however, is the “office file” either in the form of a word-processor document or a spreadsheet.

Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology.

Results

We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue.

Conclusions

This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.

Mitochondrial DNA sequence context in the penetrance of mitochondrial t-RNA mutations: A study across multiple lineages with diagnostic implications

Mitochondrial DNA (mtDNA) mutations are well recognized as an important cause of inherited disease. Diseases caused by mtDNA mutations exhibit a high degree of clinical heterogeneity with a complex genotype-phenotype relationship, with many such mutations exhibiting incomplete penetrance. There is evidence that the spectrum of mutations causing mitochondrial disease might differ between different mitochondrial lineages (haplogroups) seen in different global populations. This would point to the importance of sequence context in the expression of mutations. To explore this possibility, we looked for mutations which are known to cause disease in humans, in animals of other species unaffected by mtDNA disease. The mt-tRNA genes are the location of many pathogenic mutations, with the m.3243A>G mutation on the mt-tRNA-Leu(UUR) being the most frequently seen mutation in humans. This study looked for the presence of m.3243A>G in 2784 sequences from 33 species, as well as any of the other mutations reported in association with disease located on mt-tRNA-Leu(UUR). We report a number of disease associated variations found on mt-tRNA-Leu(UUR) in other chordates, as the major population variant, with m.3243A>G being seen in 6 species. In these, we also found a number of mutations which appear compensatory and which could prevent the pathogenicity associated with this change in humans. This work has important implications for the discovery and diagnosis of mtDNA mutations in non-European populations. In addition, it might provide a partial explanation for the conflicting results in the literature that examines the role of mtDNA variants in complex traits.

Data Integration and Mining for Synthetic Biology Design

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

Minimum information about tolerogenic antigen-presenting cells (MITAP): a first step towards reproducibility and standardisation of cellular therapies

Cellular therapies with tolerogenic antigen-presenting cells (tolAPC) show great promise for the treatment of autoimmune diseases and for the prevention of destructive immune responses after transplantation. The methodologies for generating tolAPC vary greatly between different laboratories, making it difficult to compare data from different studies; thus constituting a major hurdle for the development of standardised tolAPC therapeutic products. Here we describe an initiative by members of the tolAPC field to generate a minimum information model for tolAPC (MITAP), providing a reporting framework that will make differences and similarities between tolAPC products transparent. In this way, MITAP constitutes a first but important step towards the production of standardised and reproducible tolAPC for clinical application.

The Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB

A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge; during the curation process annotations are often propagated between entries. However, this is often not made explicit. Therefore, it can be hard, potentially impossible, for a reader to identify where an annotation originated from. Within this work we attempt to identify annotation provenance and track its subsequent propagation. Specifically, we exploit annotation reuse within the UniProt Knowledgebase (UniProtKB), at the level of individual sentences. We describe a visualisation approach for the provenance and propagation of sentences in UniProtKB which enables a large-scale statistical analysis. Initially levels of sentence reuse within UniProtKB were analysed, showing that reuse is heavily prevalent, which enables the tracking of provenance and propagation. By analysing sentences throughout UniProtKB, a number of interesting propagation patterns were identified, covering over sentences. Over sentences remain in the database after they have been removed from the entries where they originally occurred. Analysing a subset of these sentences suggest that approximately are erroneous, whilst appear to be inconsistent. These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation.

Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/.

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB

Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use the UniProt Knowledgebase (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations.

Results: By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality.

Availability: Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation.

Contact:phillip.lord@newcastle.ac.uk

Bayesian integration of networks without gold standards

Motivation: Biological experiments give insight into networks of processes inside a cell, but are subject to error and uncertainty. However, due to the overlap between the large number of experiments reported in public databases it is possible to assess the chances of individual observations being correct. In order to do so, existing methods rely on high-quality ‘gold standard’ reference networks, but such reference networks are not always available.

Results: We present a novel algorithm for computing the probability of network interactions that operates without gold standard reference data. We show that our algorithm outperforms existing gold standard-based methods. Finally, we apply the new algorithm to a large collection of genetic interaction and protein–protein interaction experiments.

Availability: The integrated dataset and a reference implementation of the algorithm as a plug-in for the Ondex data integration framework are available for download at http://bio-nexus.ncl.ac.uk/projects/nogold/

Contact:darren.wilkinson@ncl.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing

Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step towards establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work.

Customizable views on semantically integrated networks for systems biology

MOTIVATION

The rise of high-throughput technologies in the post-genomic era has led to the production of large amounts of biological data. Many of these datasets are freely available on the Internet. Making optimal use of these data is a significant challenge for bioinformaticians. Various strategies for integrating data have been proposed to address this challenge. One of the most promising approaches is the development of semantically rich integrated datasets. Although well suited to computational manipulation, such integrated datasets are typically too large and complex for easy visualization and interactive exploration.

RESULTS

We have created an integrated dataset for Saccharomyces cerevisiae using the semantic data integration tool Ondex, and have developed a view-based visualization technique that allows for concise graphical representations of the integrated data. The technique was implemented in a plug-in for Cytoscape, called OndexView. We used OndexView to investigate telomere maintenance in S. cerevisiae.

AVAILABILITY

The Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible at http://bsu.ncl.ac.uk/ondexview.

An integrated dataset for in silico drug discovery

Drug development is expensive and prone to failure. It is potentially much less risky and expensive to reuse a drug developed for one condition for treating a second disease, than it is to develop an entirely new compound. Systematic approaches to drug repositioning are needed to increase throughput and find candidates more reliably. Here we address this need with an integrated systems biology dataset, developed using the Ondex data integration platform, for the in silico discovery of new drug repositioning candidates. We demonstrate that the information in this dataset allows known repositioning examples to be discovered. We also propose a means of automating the search for new treatment indications of existing compounds.

Adding a little reality to building ontologies for biology

BACKGROUND

Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics. The most widespread is for description of entities about which data have been collected, allowing integration and analysis across multiple resources. There are now over 60 ontologies in active use, increasingly developed as large, international collaborations. There are, however, many opinions on how ontologies should be authored; that is, what is appropriate for representation. Recently, a common opinion has been the "realist" approach that places restrictions upon the style of modelling considered to be appropriate.

METHODOLOGY/PRINCIPAL FINDINGS

Here, we use a number of case studies for describing the results of biological experiments. We investigate the ways in which these could be represented using both realist and non-realist approaches; we consider the limitations and advantages of each of these models.

CONCLUSIONS/SIGNIFICANCE

From our analysis, we conclude that while realist principles may enable straight-forward modelling for some topics, there are crucial aspects of science and the phenomena it studies that do not fit into this approach; realism appears to be over-simplistic which, perversely, results in overly complex ontological models. We suggest that it is impossible to avoid compromise in modelling ontology; a clearer understanding of these compromises will better enable appropriate modelling, fulfilling the many needs for discrete mathematical models within computational biology.

The Seventh Annual Bio-Ontologies Meeting Moat House Hotel, Glasgow, 30 July 2004

The Annual Bio-Ontologies Meeting [1] has now reached its seventh consecutive year, running as a special interest group (SIG) of the much larger ISMB conference. This year's meeting in Glasgow had approximately 100 attendees. Since the advent of the Gene Ontology, which coincided with the first Bio-Ontologies Meeting, we have seen a year-on-year strengthening of the field; bio-ontologies has moved from being dominated by computer science to be led by biological applications; discussion is less about ‘what is an ontology?’ and more about ‘how to build an ontology which is fit for purpose?’. This strengthening of the field can be seen elsewhere. Both the main ISMB conference and this year's Pacific Symposium on Biocomputing (PSB) [2] have seen a large number of submissions to their ontologies track. For the first time a selection of the papers from the SIG is being published in this issue of Comparative and Functional Genomics. We hope that this will complement the publications of the larger conferences, bringing to a wider audience the cutting edge research that characterizes the Bio-Ontologies SIG.

Modeling biomedical experimental processes with OBI

BACKGROUND

Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval.

RESULTS

The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI.

CONCLUSION

We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components.

AVAILABILITY

OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl.

Annotation of SBML models through rule-based semantic integration

BACKGROUND

The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort.

RESULTS

Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The heterogeneous data sources are first syntactically converted into ontologies, which are then aligned to a small domain ontology by applying a rule base. We demonstrate proof-of-principle of this application of rule-based mediation using off-the-shelf semantic web technology through two use cases for SBML model annotation. Existing tools and technology provide a framework around which the system is built, reducing development time and increasing usability.

CONCLUSIONS

Integrating resources in this way accommodates multiple formats with different semantics, and provides richly-modelled biological knowledge suitable for annotation of SBML models. This initial work establishes the feasibility of rule-based mediation as part of an automated SBML model annotation system.

AVAILABILITY

Detailed information on the project files as well as further information on and comparisons with similar projects is available from the project page at http://cisban-silico.cs.ncl.ac.uk/RBM/.

Building ontologies in DAML + OIL

In this article we describe an approach to representing and building ontologies advocated by the Bioinformatics and Medical Informatics groups at the University of Manchester. The hand-crafting of ontologies offers an easy and rapid avenue to delivering ontologies. Experience has shown that such approaches are unsustainable. Description logic approaches have been shown to offer computational support for building sound, complete and logically consistent ontologies. A new knowledge representation language, DAML + OIL, offers a new standard that is able to support many styles of ontology, from hand-crafted to full logic-based descriptions with reasoning support. We describe this language, the OilEd editing tool, reasoning support and a strategy for the language’s use. We finish with a current example, in the Gene Ontology Next Generation (GONG) project, that uses DAML + OIL as the basis for moving the Gene Ontology from its current hand-crafted, form to one that uses logical descriptions of a concept’s properties to deliver a more complete version of the ontology.

High detail radiography and histology of the centrodistal tarsal joint of Icelandic horses age 6 months to 6 years

REASONS FOR PERFORMING STUDY

Osteoarthrosis (OA) in the distal tarsal joints, bone spavin, is a well known condition which is common in Icelandic horses age 6-12 years.

OBJECTIVES

To determine the nature, location and age of appearance of early radiographic and histological changes in the centrodistal tarsal joint (CD) of young Icelandic horses.

METHODS

Slab sections from the CD of young Icelandic horses were examined by high detail radiography (age 6 months to 6 years, n = 111) and histology (age 6 months to 4 years, n = 82) to detect and describe the early changes indicative of OA. Horses younger than 5 years were unridden.

RESULTS

Chondronecrotic lesions histologically similar to those described in the early pathogenesis of OA were seen in 33% of the joints, located both medially and laterally. Radiographic sclerosis of the subchondral bone was recorded in 60% of the specimens, most often medially. Medial location was not associated with chondronecrosis, but was strongly related to age. Sclerosis was an infrequent finding on the lateral side, and was probably secondary to chondronecrosis in the corresponding part of the joint. Small defects in the subchondral bone were considered to be the most specific radiographic sign of OA as they were strongly associated with chondronecrosis.

CONCLUSIONS

The high prevalence of chondronecrosis in the young horses indicates an early onset and slow progression of the disease. The early appearance also shows that the initiation of the disease is unrelated to the use of horses for riding. As clinical manifestation of OA in the distal tarsal joints is most often described in mature or old horses, the first stages of the disease are not likely to result in clinical signs. Subchondral bone sclerosis did not appear to be a primary factor in the development of OA in the CD but was considered to reflect an uneven distribution of biomechanical forces within the joint.

POTENTIAL RELEVANCE

The development of OA in the CD of young Icelandic horses seems to be due to poor conformation or joint architecture rather than trauma or overloading. These aetiological factors are likely to be of importance for OA in the distal tarsal joints in other breeds as well. The influence of hindlimb conformation and the architecture of the distal tarsal joints on the biomechanics of joints need to be investigated, preferably by locomotion analysis in young horses.

Relationship between scintigraphic and radiographic evaluations of spinous processes in the thoracolumbar spine in riding horses without clinical signs of back problems

REASONS FOR PERFORMING STUDY

Radiography and scintigraphy are used to aid diagnosis of the cause of back pain, but a large variation in appearance and radiopharmaceutical uptake in fully functioning horses make diagnosis difficult.

OBJECTIVES

To describe the range of and compare scintigraphic and radiographic findings in the spinous processes of horses without clinical signs of back problems.

METHODS

Thirty-three apparently normal riding horses underwent scintigraphic and radiographic examinations of the spinous processes in the thoracolumbar spine. Scintigraphic images were evaluated in a continuous blue, green and red colour scale, and the level of radiopharmaceutical uptake in the spinous processes from T10-L2 was graded into none, mild, moderate or severe increased radiopharmaceutical uptake. Structural changes along the borders of the spinous processes and the width of the interspinous spaces from T10-L2 were recorded.

RESULTS

Only 7 horses had no scintigraphic or radiographic findings. Nine horses had no increased radiopharmaceutical uptake, 17 had no sclerosis, 21 had no radiolucencies and 11 had normal spacing of the spinous processes (>4 mm wide). The majority of findings in 26 horses were located from T13-18 and were mild.

CONCLUSIONS

The findings of a wide spectrum of scintigraphic and radiographic changes leads to the conclusion that changes within this range found in affected horses cannot be interpreted as clinically significant.

POTENTIAL RELEVANCE

To determine whether scintigraphy and/or radiography can be used to separate horses with back pain from horses without clinical signs, the results from this study should be compared to the scintigraphic and radiographic findings in horses with clinical signs.

Reader performance in radiographic diagnosis of signs of mitral regurgitation in cavalier King Charles spaniels

OBJECTIVES

To measure accuracy and variability of diagnosis by radiography of heart enlargement (HE) and heart failure (HF) in mitral regurgitation (MR).

METHODS

Sixteen readers representing four levels of experience evaluated 50 sets of radiographs with varying severity of MR for presence or absence of HE, left atrial enlargement (LAE) and HF. The performance of the readers was compared with a reference standard, using area under the curve (AUC) of receiver operating characteristic (ROC) curves. The interreader agreement value kappa (K) was calculated. A subset of difficult cases of HF was analysed before and after removing an outlying reader from each group.

RESULTS

AUC for HE was 0.89, for LAE it was 0.93 and for HF it was 0.92. Experience increased certainty of diagnosis but not accuracy. K ranges were HE, 0.53 to 0.67; LAE, 0.61 to 0.69 and HF, 0.49 to 0.58. When only difficult cases of HF were read, accuracy decreased and experienced readers performed better than inexperienced. When outlying readers were excluded, the differences between experienced and inexperienced readers increased.

CLINICAL SIGNIFICANCE

LAE, not HE, should be used to evaluate the heart size and indirectly the severity of MR on radiographs. For HF, agreement among individual readers was only moderate. Studies of reader accuracy should consider the effects of interreader variability.

Semantic similarity in biomedical ontologies

In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies.Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists.

The minimum information about a genome sequence (MIGS) specification

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology

This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).

Protein classification using ontology classification

MOTIVATION

The classification of proteins expressed by an organism is an important step in understanding the molecular biology of that organism. Traditionally, this classification has been performed by human experts. Human knowledge can recognise the functional properties that are sufficient to place an individual gene product into a particular protein family group. Automation of this task usually fails to meet the 'gold standard' of the human annotator because of the difficult recognition stage. The growing number of genomes, the rapid changes in knowledge and the central role of classification in the annotation process, however, motivates the need to automate this process.

RESULTS

We capture human understanding of how to recognise members of the protein phosphatases family by domain architecture as an ontology. By describing protein instances in terms of the domains they contain, it is possible to use description logic reasoners and our ontology to assign those proteins to a protein family class. We have tested our system on classifying the protein phosphatases of the human and Aspergillus fumigatus genomes and found that our knowledge-based, automatic classification matches, and sometimes surpasses, that of the human annotators. We have made the classification process fast and reproducible and, where appropriate knowledge is available, the method can potentially be generalised for use with any protein family.

AVAILABILITY

All components described in this paper are freely available. OWL ontology http://www.bioinf.man.ac.uk/phosphabase myGrid http://www.mygrid.org.uk Instance Store http://instancestore.man.ac.uk.

Agents in bioinformatics, computational and systems biology

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.

Culling rate of Icelandic horses due to bone spavin

A survival analysis was used to compare the culling rate of Icelandic horses due to the presence of radiographic and clinical signs of bone spavin. A follow-up study of 508 horses from a survey five years earlier was performed. In the original survey 46% of the horses had radiographic signs of bone spavin (RS) and/or lameness after flexion test of the tarsus. The horse owners were interviewed by telephone. The owners were asked if the horses were still used for riding and if not, they were regarded as culled. The owners were then asked when and why the horses were culled. During the 5 years, 98 horses had been culled, 151 had been withdrawn (sold or selected for breeding) and 259 were still used for riding. Hind limb lameness (HLL) was the most common reason for culling (n = 42). The rate of culling was low up to the age of II years, when it rose to 0.05 for horses with RS. The risk ratio for culling was twice as high for horses with RS compared with horses without RS and 5.5 times higher for culling because of HLL. The risk of culling (prognostic value) was highest for the combination of RS with lameness after flexion test, next highest for RS and lowest for lameness after flexion test as the only finding. It was concluded that bone spavin affects the duration of use of Icelandic horses and is the most common cause of culling due to disease of riding horses in the age range of 7-17 years.

Scintigraphic evaluation of the thoracic spine in the asymptomatic riding horse

Scintigraphic evaluation of the spinous processes of the equine spine has been done by subjective evaluation of radiotracer uptake in clinically abnormal horses. To determine the range of variation in asymptomatic riding horses, 33 normal horses were examined. Two 60 degrees oblique views of the thoracic and lumbar spine were evaluated subjectively, and a semi quantitative method based on standardized regions of interest in each spinous process in T10-L3 was also applied. A ratio between each spinous process and a reference area (Rib 15 or 16) was calculated. The effects of two different color displays and a smoothing filter were assessed. The results of the subjective evaluation was compared to the calculated ratios, and the associations between age, gender, weight, height, use and increased radiotracer uptake, and ratios were analyzed. No significant association was found between age, gender, weight, height, use and increased radiotracer uptake, or ratio. One or more areas of increased radiotracer uptake between T13 and T18 were common in the asymptomatic riding horse, which may have implications for the interpretation of clinical patients. The blue, green and red color display had a higher sensitivity for detecting increased radiotracer uptake compared to the continuous grayscale. The smoothing filter used in this study had no effect on the detection of areas with increased radiotracer uptake. The association between the results of the subjective evaluation and the semi quantitative method was apparent when analyzed in T13-17. To evaluate if the semi quantitative method can replace the subjective evaluation, studies on clinically affected horses are necessary.

Day-to-day variability in glomerular filtration rate in normal dogs by scintigraphic technique

The sources of variability in variability of scintigraphic measurements of glomerular filtration rate (GFR) have not been determined. The day to day variability of GFR was studied in 18 healthy beagle dogs. The renal uptake of 99mTc-diethylenetriaminepentaacetic acid (DTPA) of each dog was measured using a scintigraphic technique three times at intervals of 5-26 days. GFR was calculated from a regression equation relating uptake to plasma clearance, derived in our laboratory. The mean GFR was 3.97 +/- 0.72 (SD) ml/min/kg with values from 2.66 to 5.67 ml/min/kg. Analysis of variance (ANOVA) using a linear mixed model showed that most variability is a result of the dogs, less because of day to day variability and very little to the measurement variability. The repeatability coefficients for the day to day variability and measurement variability were 1.06 and 0.21 ml/min/kg respectively. The day to day variability can be caused by physiological homeostatic adjustments by the kidneys needed because of fluctuations in food and fluid intake, each dog's individual capacity to adjust, and to intrinsic errors in the measurement method. These results should be considered when using the scintigraphic method for clinical evaluation and research.

ISMB 2003 Bio-ontologies SIG and Sixth Annual Bio-ontologies Meeting Report

The Annual Bio-Ontologies meeting (http://www.cs.man.ac.uk/˜stevens/meeting03/) has now been running for 6 consecutive years, as a special interest group (SIG) of the much larger ISMB conference. It met in Brisbane, Australia, this summer, the first time it was held outside North America or Europe. The bio-ontologies meeting is 1 day long and normally has around 100 attendees. This year there were many fewer, no doubt a result of the distance, global politics and SARS. The meeting consisted of a series of 30 min talks with no formal peer review or publication. Talks ranged in style from fairly formal and complete pieces of work, through works in progress, to the very informal and discursive. Each year's meeting has a theme and this year it was ‘ontologies, and text processing’. There is a tendency for those submitting talks to ignore the theme completely, but this year's theme obviously struck a chord, as half the programme was about ontologies and text analysis (http://www.cs.man.ac.uk/˜stevensr/meeting03/programme.html). Despite the smaller size of the meeting, the programme was particularly strong this year, meaning that the tension between allowing time for the many excellent talks, discussion and questions from the floor was particular keenly felt. A happy problem to have!

Differential gene expression in rats following subacute exposure to the anticonvulsant sodium valproate

Sodium valproate (VPA) is clinically employed as an anticonvulsant and, to a lesser extent, as a mood stabilizer. While the incidence of toxicity associated with the clinical use of valproate is low, serious hepatotoxicity makes up a significant percentage of these rare adverse effects, with fatalities occurring mainly in children receiving polypharmacy. Previous studies have highlighted the different pharmacological effects of acute valproate exposure, a combination of which are likely to underpin its observed broad-spectrum anticonvulsant efficacy. However, limited studies have been undertaken to investigate the subacute effects of this compound and how genomic effects may underlie the observed hepatotoxic effects. Investigation into the mild hepatoxicity observed in rats exposed to high doses of VPA may provide important information on the human situation. Male Sprague-Dawley rats were dosed with 500 mg/kg/day sodium valproate: after necropsy, mRNA was subjected to suppression PCR subtractive hybridization, identifying 8 up-regulated and 14 down-regulated mRNA species. The down-regulation of several mRNA species coding for enzymes involved in cellular energetics (e.g., succinate dehydrogenase, aldolase B) was of particular interest, as mitochondrial dysfunction is a key feature of valproate hepatotoxicity. In vitro studies were then undertaken to examine the dose and time dependence of these changes and also their effect on the overall energy levels within the cell. We demonstrate that, both in vivo and in vitro, valproate exposure in rats results in a significant decrease in pathways involved in cellular energy homeostasis. These changes may provide insight into the rare human hepatoxicity associated with this compound.

Interstitial lung disease in patients with rheumatoid arthritis: a comparison with cryptogenic fibrosing alveolitis

OBJECTIVES

There is a lack of information on the natural history of patients with rheumatoid arthritis (RA) and associated interstitial lung disease (ILD). However, cryptogenic fibrosing alveolitis (CFA) is known to have a poor long-term prognosis. As part of a longitudinal prospective study, we compared baseline characteristics in 18 patients with RA-ILD and 18 patients with CFA matched for age, sex and symptoms. We wished to establish whether there were significant baseline differences in clinical, physiological or radiological parameters.

METHODS

A diagnosis of ILD was confirmed by high-resolution computed tomography (HRCT) and supported by clinical and physiological findings in all patients. A number of clinical, immunological, physiological and radiological parameters were compared between the two groups. The median age in each group was 77 yr and 10 patients in each group were male.

RESULTS

Twelve of the RA patients had smoked in excess of 10 pack yr as compared with nine patients with CFA (not significant). Clubbing was found in five patients with RA-ILD and in 14 with CFA (P=0.008). Pulmonary function tests showed no significant differences between the groups in forced expiratory volume in 1s, vital capacity or gas transfer factor. HRCT showed more ground glass shadowing and peripheral disease in RA patients, but more established basal disease in those with CFA. Additionally, HRCT evidence of honeycombing was associated with an absence of rheumatoid factor and a low gas transfer factor.

CONCLUSIONS

Clubbing is more common in patients with CFA, while RA-ILD patients have a higher prevalence of rheumatoid factor. Together with the differences in baseline HRCT, these variables in two groups of patients with similar physiological impairment at baseline may be important predictors of outcome in the longer term.

Effects of a digital filter on detectability of a phantom lesion in a scintigram of the equine tarsus

The aim of this study was to examine the effects of a digital filter on the detectability of a phantom lesion in a scintigram of the equine tarsus. Lateral images containing 50, 100, 150, 500, or 1000 kcounts were acquired. A created phantom lesion of 0 (normal), 10, 15, 20, or 30% increased intensity relative to local background was placed in the centrodistal tarsal joint area in the images of different count levels. Duplicate images were filtered with a Metz filter. The complete set of filtered and unfiltered images totaling 180 images was projected as slides to a group of 9 observers. The sensitivity in 50 and 100 kcount images was improved by applying the filter. Digital filtering increased the false positive fraction at all count levels but this effect was most pronounced in 500 and 1000 kcount images. Based on receiver operating characteristic analysis, filtering of a 50 kcount image improved image quality to that of a 150 kcount image.

Semi-quantitative assessment of tibial blood flow and distribution in response to surgical intervention using first pass radionuclide angiography and intravascular vital dye

The acute vascular response in bone to surgical trauma was investigated utilizing a sheep model. Blood flow and distribution were determined using two methods; perfusion of the vasculature with an intravascular vital dye (Disulphine blue) prior to euthanasia and by radionuclide angiography (RNA) before and after each surgical intervention. The pattern of Disulphine blue distribution provided a good indication of local perfusion and response to surgical trauma (drilling holes). Radionuclide angiography provided a dynamic image of the vascular response to surgical trauma. The generation of time activity curves of the first pass of radionuclide bolus enabled calculation of the relative blood flow through selected regions. For both techniques areas of ischaemia were apparent which were directly related to the location of screw holes. We conclude that factors other than bone plate contact influence the ischaemia that develops in bone subsequent to the application of bone plates.