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Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance.
We implemented a semantically integrated resource named BioGateway, comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse representations. We present a detailed analysis of the obstacles that had to be overcome in creating BioGateway. We demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data.
The time is ripe for launching a community effort aimed at a wider acceptance and application of Semantic Web technologies in the life sciences. We call for the creation of a forum that strives to implement a truly semantic life science foundation for Semantic Systems Biology.
Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at http://www.semantic-systems-biology.org/biogateway webcite.
Systems Biology aims to offer a holistic view of the way in which biological systems work. Systems Biology is an integrative biology, and is already instrumental in rationalising the exploitation of the so-called "-omics" technologies. These technologies are producing massive amounts of biological data which are often stored in disparate, specialised repositories that may not always abide by common standards for data formats [1-3]. This wealth of information is difficult to exploit, since there are complexities involved in combining various data sources to answer even relatively simple questions [4].
A powerful integration of available biological data and knowledge needs an efficient information retrieval and management system. Semantic Web technologies are designed to meet this challenge, and the Semantic Web promises an infrastructure that comprises machine understandable content and therefore a World Wide Web consisting of linked data instead of documents alone. Indeed, computational systems based on a semantic integration of raw data and ontological relationships will provide a sophisticated framework to interrogate and retrieve pertinent information. Integrated knowledge resources may even allow the deployment of advanced computational reasoning approaches [5] in order to generate new hypotheses about the functionality of biological systems.
We are witnessing a growing acceptance of Semantic Web technologies for knowledge integration in the life sciences. This is illustrated by the existence of a W3C special interest group [6] (Semantic Web Health Care and Life Sciences Interest Group – HCLS IG) and many other projects and languages that exploit semantic technologies. For example, the Resource Description Framework (RDF) [7] and the Web Ontology Language (OWL) [8] can be used to represent biological information and the SPARQL query language [9] can be used for the retrieval of information. Semantic Web technologies have the potential to add a new dimension of knowledge integration to Systems Biology that is expected to be among the early adopters of these technologies [10].
To explore the potential for Systems Biology we constructed BioGateway [11], a system built on an RDF store that aggregates bio-ontologies and other biological information sources. Mathematical modelling lies at the core of Systems Biology. By integrating a systems network with a mathematical model, one can simulate the behaviour of the network, and thus predict the outcome of new experiments. Systems Biology is, however, also an integrative approach, and with BioGateway we add a semantic foundation for data integration. Semantic Knowledge Bases (KBs) offer a querying and reasoning component, through which new hypotheses about the system and its components can be obtained. We call this combination Semantic Systems Biology (SSB), a form of systems biology in which new hypotheses concerning a biological system are generated through queries and reasoning on integrated data, as opposed to being generated through a mathematical model. We believe that Semantic Systems Biology may provide a powerful complement to the mathematical model-based Systems Biology.
BioGateway data model
RDF-ing the resources
A suitable data representation is necessary to share and uniformly query the RDF integrated repository. Although different means exist to translate ontologies in the Open Biomedical Ontologies Format (OBOF) to several representations [12], there is no accepted mapping of OBO ontologies to RDF. The mapping used for BioGateway is an extended and improved version of the mapping from the ONTO-PERL suite [13]: it was devised to retain a high-fidelity conversion (i.e. no information is lost) and to facilitate querying. The ONTO-PERL suite is a Perl API that can be used to programmatically manipulate ontologies in OBO format. ONTO-PERL offers the possibility of translating an ontology in OBO format to any of the following representations: RDF, XML, OWL, DOT, GML, XGMML and SBML. Such translations are required to accommodate the different semantics of the languages in the mapping process [14], which is difficult since the semantics of OBO are not precisely defined [15].
The proposed mapping from OBO to RDF (Table 1) has undergone several refinements, not only to capture all of the OBO specification elements [16], but also to ensure a relatively natural translation, allowing users familiar with the OBOF to immediately recognise the corresponding tags. More details about the proposed format conversions can be found within the ONTO-PERL source code [17], and the entire list of RDF-ied resources that are integrated into BioGateway can be found on the project resources web page [18].
Table 1. OBOF to RDF mapping. Mapping used by the BioGateway pipeline to translate ontologies represented in OBOF (e.g. the Gene Ontology) into RDF.
BioGateway graphs
BioGateway is a system based on an RDF store that combines information from various resources [18]:
• The entire set of candidate OBO Foundry ontologies [19];
• The complete collection of annotations included in the Gene Ontology Annotation (GOA) files [20];
• A minimised version of the NCBI taxonomy [21] (including only the names, ranks, and taxonomic hierarchy);
• A subset of SWISS-PROT [22] (including only the accession numbers, synonyms, encoding genes, annotated functions and diseases); and
• The Cell Cycle Ontology (CCO) [23].
All the imported data sources, when converted to RDF graphs, share a basic URI:
http://www.semantic-systems-biology.org webcite
This means that each resource (e.g. each protein from SWISS-PROT, each taxon from the NCBI taxonomy, and each OBO term) has a URI of the form:
http://www.semantic-systems-biology.org/SSB#resource webcite
Each of the imported data sources is represented as an individual graph with a specific URI in the following form:
http://www.semantic-systems-biology.org/graph_name webcite
Additionally, the SSB graph combines all the constituent graphs of BioGateway, containing approximately 175 million triples. Intermediate graphs for the GOA files and the OBO Foundry candidate ontologies contain approximately 160 million triples and 8 million triples, respectively (Table 2).
Table 2. Resource figures within BioGateway. BioGateway integrates several public resources. It holds more than 175 million triples. Intermediate graphs for the GOA files and the OBO Foundry candidate ontologies contain approximately 160 million triples and 8 million triples, respectively. These numbers are constantly increasing, depending on the new data annotations.
Many of the RDF graphs in BioGateway contain orthogonal resources that are not connected to each other, such as SWISS-PROT and the OBO Foundry ontologies. SWISS-PROT resources are, however, linked to GO resources via GOA resources. This also interlinks the three sub-ontologies of GO. To accommodate evidence codes from GOA, a reified or n-ary node is created. For example, the following excerpt from a GOA file [24] would be converted into the RDF structure shown in Figure 1:
Figure 1. RDF model of a GOA entry. The protein O03042 (Ribulose bisphosphate carboxylase large chain) is annotated with the GO term GO:0000287 (Magnesium Ion Binding), a term in the Molecular Function subtree from GO. Therefore, O03042 has the molecular function of binding magnesium ion. This fact is supported by an evidence code named "Inferred from Electronic Annotation" (IEA), that is, this is an annotation that depends on computation or the automated transfer of annotations from a database (for instance, an annotation based on "hits" obtained using sequence similarity searches which were not reviewed by curators).
UniProtKB O03042 O03042 GO:0000287 GOA:spkw|GO_REF:0000004 IEA
BioGateway scaffold: BioMetarel and Metaonto
Two ontologies were created in order to provide a scaffold for integrating all the graphs: BioMetarel and Metaonto.
BioMetarel [25] holds the predicate or relation types used to link terms. It also links the unique identifiers of the relation types with their user-friendly names. BioMetarel also contains all the meta-information, such as transitivity and reflexivity, in regard to the biomedical relation types that are used. This relation ontology consists of a generic scaffold, the Metarel ontology [26], to which the following relations are added: all the elation types of the Relation Ontology (RO) [27], and all the relation types that are used in the OBO Foundry ontologies. Unfortunately, these relation types were not consistently named throughout the candidate ontologies (e.g. the subsumption relation was called both: is a and Is_A, and the partonomic relation both: part_of and is_part_of). A consistent list of relation types was manually created for BioMetarel. As a rule, we chose to include a verb in every relation type name, conjugated as the third person singular in the present tense. The application of this rule predominantly involved the addition of the verb is. As a consequence, we can return triples in the form of a pseudo-grammatical sentence such as: blood is located in vein. This rule also prompted us to transform names such as anatomical_relation to: is anatomically related to, and surrounding to: surrounds. In fact, the meaning of several poorly named relation types became clearer by adhering to this style.
The most straightforward use of BioMetarel is to connect the unique identifiers of the relation types with their user-friendly names. However, we observed that the inclusion of the full BioMetarel in each graph interfered with some specific queries, such as the listing of all the resources of a graph. It is more convenient for querying and exploring a graph when an RDF graph relates only to a single topic. We therefore created a lightweight subontology of BioMetarel called Biorel. This subontology contains only relation types, with no metaclasses and metarelations between relation types. This made Biorel more suitable for inclusion in every RDF graph in BioGateway. An example of a query over this scaffold is shown in Figure 2.
Figure 2. Querying the BioGateway graph scaffold. A copy of Biorel is added to every graph, except for BioMetarel and Metaonto. These exist as separate graphs that need to be addressed specifically within the queries.
Having such a relation infrastructure implemented in BioGateway allowed us to build a consistent RDF scaffold for other resources, such as GOA associations together with the evidence codes. All that needed to be done to create the integrated graph was to consistently use appropriate identifiers for the predicates in the RDF triples. The integration of OBO Foundry ontologies with respect to the classes did not pose problems since these are given different identifiers in different ontologies, and they are orthogonal as a design principle.
A small ontology named Metaonto was created in the OBO format for the mapping between the names of the OBO ontologies and the prefixes they use in their unique identifiers. The mapping is helpful for users who want to explore the OBO Foundry with queries in BioGateway. Meta-information such as the names of the RDF graphs, what the graphs are about, and characteristics of the relation types are accessible as results of the so-called "ontological queries" (in contrast to "biological queries", see Section: Queries). In summary, the integration of data in BioGateway has been achieved based on the use of BioMetarel, the use of the same URIs for equivalent resources in the data sources (SWISS-PROT, GOA, NCBI taxonomy), and the orthogonality of OBO ontologies with respect to the classes.
Design of BioGateway
While defining the specifications of the RDF translations for each of the integrated resources, we also developed a library of queries that were used to test performance (see Section: Queries). This resulted in an RDF model that is adequately suited for querying, especially in terms of performance. During this process we have paid attention to several quality constraints:
1. Quick results: A relatively quick query answer is always a desirable feature for any system. A query builder wants to see a quick and sound answer on a small query pattern or on a small part of the data before he launches into a heavier query. Therefore, we have systematically tested the response time with a suite of queries. This quality constraint turned out to be our biggest challenge during the development of the system. The query performance is dependent on different factors, making the subject difficult to investigate. In particular, disk access and the caching of earlier results, as well as seemingly unimportant details in the query itself can have a profound impact on the query performance, resulting in differences of one to two orders of magnitude in query time. For this reason, we removed any unnecessary chains in the RDF translations to allow short queries and to avoid inhibitive bottlenecks in the performance. The idea to provide the data in both singular and composed graphs was also inspired by performance issues. Demanding queries can now be targeted to the relevant parts of the data. Due to these optimisations, most queries described in this paper return an answer within one second, and the chance of getting an answer on a more complex query within a reasonable time are also better.
2. Human readable output: As RDF works with URIs, many outputs from SPARQL queries might be difficult to comprehend. We tried to avoid such outputs as much as possible by creating labels for all the terms and all the relation types that can be used to present the results to the user.
3. Good practice: RDF is a Semantic Web standard that implies good design practices [28] as it pertains to integration with other efforts within the framework of the Semantic Web. Orthogonality was achieved for all the terms, meaning that the proteins in SWISS-PROT received the same unique identifiers as the proteins in GOA. Otherwise, combining these graphs in a single query would not be possible.
A common and unique namespace called SSB (short for Semantic Systems Biology) was defined to gather all the resources accessible as graphs from BioGateway (Figure 3): http://www.semantic-systems-biology.org webcite. This namespace serves as an umbrella for each piece of information stored within BioGateway; thus, a possible resource naming conflict is avoided.
Figure 3. The BioGateway graphs architecture. Four frameworks (A-D) are implemented within BioGateway. All of them are interlinked via a common set of relations and share the same namespace: SSB. In A, all the ontologies (Oi) are integrated into one single graph named SSB. In B, each ontology (Oi) has its own single graph named Oi. In C, all the transitive closure ontologies (Oi,tc) belong to one single graph named SSB_tc. In D, each transitive closure ontology (Oi,tc) has its own single graph named Oi,tc.
Simulating transitive closure
Transitive closure is an important feature in biomedical knowledge representation, especially when it concerns partonomy [29]. In addition, transitive closure along the is_a relation type is also desirable. Transitivity cannot, however, be expressed in RDF, and therefore had to be created explicitly by adding all the necessary triples programmatically (see Section: BioGateway architecture). That is, if resources A, B and C are related via part_of (A part_of B part_of C), a third triple A part_of C is created. This operation was done for the candidate OBO ontologies, CCO and BioMetarel, thus allowing transitivity in queries to be exploited with little impact on the performance of BioGateway.
Transitive closure provides a scaffold for being able to reach other terms from a given term (e.g. "is the term leptotene part of the term meiosis?", see Figure 4). In addition, transitive closure supports queries involving compositions of relationships such as: "if a protein P is located in L, and L is part of C and C is a D, then P is located in D".
Figure 4. A transitivity example. In the case of the term leptotene (GO:0000237), which is originally only linked to the terms cell cycle phase (GO:0022403) via an is_a relation and meiotic prophase I (GO:0007128) via a part_of relation, the following implicit relations are added: leptotene is_a biological_process (GO:0008150), leptotene is_a cellular process (GO:0009987), leptotene is_a cell cycle process (GO:0022402), leptotene is_a cell cycle phase (GO:0022403), leptotene part_of meiosis (GO:0007126), leptotene part_of meiosis I (GO:0007127), leptotene part_of meiotic prophase I (GO:0007128), leptotene part_of meiotic cell cycle (GO:0051321) and leptotene part_of M phase of meiotic cell cycle (GO:0051327).
BioGateway architecture
BioGateway serves as a gateway to distributed resources on the Web. A pipeline lies at the core of the system: such a pipeline automatically gathers, integrates and loads data into the RDF storage system (Figure 5). This pipeline is run every three months and builds the entire repository from scratch, ensuring integration of the latest available data. Before processing the resources to be integrated, they are automatically retrieved from their original locations so that the latest data is collected.
Figure 5. The BioGateway pipeline. Information resources are converted to RDF documents which are uploaded to a triple store, where they can be queried using SPARQL: First, the candidate OBO Foundry ontologies, the GOA files, the NCBI taxonomy and SWISS-PROT are integrated within the common framework defined by the in-house ontologies: BioMetarel and Metaonto. Then, for each resource, an RDF graph (and for the OBO foundry its corresponding transitive closure graph) is created and loaded into Virtuoso. This platform provides an interface (via SPARQL) to interrogate the system.
Initially, the complete set of candidate ontologies from the OBO foundry is processed by the pipeline. These ontologies are currently undergoing a coordinated redesign to facilitate information sharing and data analysis in the life sciences community. Thus, this set of ontologies is continuously being improved, and regular updates are needed for the BioGateway resource. All those ontologies are automatically retrieved and converted to RDF files that are then loaded into the common data repository.
The entire set of GOA files is also retrieved and integrated into BioGateway. The GOA provides connections between gene products and GO terms [30]. The integrated GOA set comprises 893 files that provide annotations for complete non-redundant proteomes covering many species. The BioGateway pipeline generates the corresponding RDF file for each of the 893 files [31]. Next, protein information from SWISS-PROT is added to BioGateway and finally, BioGateway holds the two ontologies developed in-house, Metaonto and BioMetarel that provide the scaffold for the integration and unification of the other ontologies and data (see above).
The pipeline additionally generates the transitive closure graphs (see Section: Simulating transitive closure) of the candidate OBO foundry ontologies, CCO and BioMetarel.
The RDF files are then uploaded into RDF graphs in Open Virtuoso [32]. Virtuoso contains an endpoint to which SPARQL queries can be submitted [33].
Handling of relations
The relations play a key role in the integration of different data sources. Many interesting queries (for instance, "which proteins are located_in the cell wall, or any part_of it?" or "what regulates DNA replication?") might exploit the information that is contained in the relations connecting the terms. The OBO Foundry has a policy of using a small set of shared relations for the different ontologies; the implementation of the policy is, however, far from complete. In order to create a self-contained ontology file, all relation types need to be included in the same file, with a name and a unique identifier. This has led to redundant sections for the relations of the 44 imported OBO candidate ontology files with several inconsistencies. Some relations with the same unique identifiers had different names (e.g. part_of and is_part_of). This complicates their usage, and in particular, the process of building queries over different resources that should ideally share the same relation. Moreover, the identifiers cannot serve to communicate with users, as some of them were not meant to be humanly readable, such as BSPO_0000095 (Spatial Ontology [34]) or DESCINHERM (Worm Anatomy Ontology [35]). We therefore decided not to load the redundant sections into the system and to use our own relation ontology Biorel (see Section: BioGateway scaffold: BioMetarel and Metaonto), which extends the relations that are used in the OBO Foundry ontologies.
We used the relations of the OBO Foundry to integrate the various data sources, including those that were not OBO-formatted. The GOA-associations essentially consist of relations between proteins in UniProt and terms in the Gene Ontology (GO). These relations were easily mapped to the OBO relation types: has function, is located in, and participates in for the GO molecular functions, GO cellular components and GO biological processes, respectively.
The integration of all the ontologies into the OBO Foundry allows for the detection of many engineering flaws, particularly ontologies that may be hard to find in a systematic way using other tools (see Section: OBO foundry principles checking). The periodic reassembly of BioGateway can therefore be exploited for quality control and the curation of the entire OBO Foundry. In addition, individual ontology engineers may find their uploaded ontology in the system, and launch dedicated queries designed for quality control.
OBO foundry principles checking
The OBO Foundry proposes 10 principles to which OBO bio-ontology engineers should commit [36]. That set of principles governs ontology development, and aims to ensure well-documented and redundancy-free ontologies (i.e. orthogonality), as well as syntactical correctness (e.g. OBOF specification compliance) and logical completeness (e.g. is_a completeness). Three of these principles can easily be checked by using BioGateway:
1. The ontologies include textual definitions for all terms.
2. The ontology uses relations that are unambiguously defined following the pattern of definitions laid down in the OBO RO.
3. The ontology must be orthogonal to other ontologies already lodged within OBO.
In particular, the orthogonality principle, that forbids the use of terms with the same name but likely with different meanings in disparate ontologies, might be difficult to check with any other tool. The following query looks for terms which have an identical name in the human disease ontology (DOID) and mouse pathology ontology (MPATH):
BASE <http://www.semantic-systems-biology.org/ webcite>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema# webcite>
PREFIX ssb: <http://www.semantic-systems-biology.org/SSB# webcite>
SELECT ?common_name ?term_id_1 ?term_id_2
GRAPH <human_disease> {
?term_id_1 a ssb:DOID.
?term_id_1 rdfs:label ?common_name.
GRAPH <mouse_pathology> {
?term_id_2 a ssb:MPATH.
?term_id_2 rdfs:label ?common_name.
The answer to the previous query highlights the term named "hyperplasia" as a repeated term. The two other listed principles can be checked in a similar way.
We have also created a query to find all the terms that have no outgoing is_a relationship. This can return the root terms of the ontology, but unfortunately most of the returned terms are just orphans that miss any outgoing is_a relationship. Many candidate OBO Foundry ontologies are not is_a complete. This may be due to the use of some ontology editors (e.g. OBO-Edit) that hide the terms in the hierarchy that have an outgoing relationship. In BioGateway, one can easily trace these terms.
Visualisation of query results
The visualisation of triple-based resources poses a special challenge. It is necessary to develop and deploy new interfaces to manipulate, query and visualise this knowledge in an intuitive way. An SPARQL browser (still under development) enables one to query and visually explore the results obtained using BioGateway, and can be accessed from the SSB website. With this interface, users can define SPARQL queries to be launched over the resources integrated within BioGateway. The SPARQL endpoint could also be customised (by default it points to the SSB endpoint) (Figure 6). After executing a query, a network of results are displayed (Figure 7). A tabular representation of the result is also available.
Figure 6. The SPARQL viewer in BioGateway. The queries are selected from the drop-down menu on the top right: In this case, the query "Get proteins in the nucleus" is selected. Queries can be customised, for example, by changing the parameters.
Figure 7. SPARQL execution result. The query from Figure 6 has been executed, and the results displayed. The appearance of the network can be configured.
SPARQL queries can be executed against the BioGateway triple store. Many sample queries are available at the website. For example, the following SPARQL query retrieves human proteins that are located in the nucleus. The metadata about this query are presented in the first five lines at the top (lines starting with # are not interpreted by the query engine): name, parameters that can be changed and function; the rest constitutes the query itself (note the use of transitivity).
# NAME: get_proteins_in_nucleus
# PARAMETER: GO_0005634: the nucleus
# PARAMETER: 25.H_sapiens: the GOA graph for human
# FUNCTION: returns all the human proteins that have the
# nucleus as annotated location
BASE <http://www.semantic-systems-biology.org/ webcite>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema# webcite>
PREFIX ssb: <http://www.semantic-systems-biology.org/SSB# webcite>
SELECT ?protein ?sublocation ?protein_id
GRAPH <25.H_sapiens> {
?protein_id ssb:located_in ?sublocation_id.
?protein_id rdfs:label ?protein.
GRAPH <gene_ontology_edit_tc>{
?sublocation_id rdfs:label ?sublocation.
?sublocation_id ssb:is_a ?sublocpart_id.
?sublocpart_id ssb:part_of ssb:GO_0005634.
One-click query access
BioGateway provides a library of optimised, easily customisable SPARQL queries that make the resources easily accessible to both laymen users and experts, although even SPARQL experts will not easily find their way through RDF resources with which they are not acquainted. Therefore, we tried to reflect the basic query requirements in the library. This makes BioGateway accessible with a single click, and is a building block for future applications.
The library was split into a section with biological queries and a section with ontological queries. The biological queries are designed for use by biomedical scientists, and draw on the most relevant part of the KB. Some examples of biological queries read as follows:
1. Get the proteins with a specific function/location/process for any of the annotated organisms. For example, in Section: Queries, a query that returns all the human proteins that are located in the nucleus is discussed.
2. Get the information on the function, location, process and associated disease for a given protein.
3. Get the proteins that are involved in the "psoriasis" disease.
The set of ontological queries shows how SPARQL can be used to explore BioGateway, particularly the OBO ontologies. This set of queries is intended for users who are interested in ontology engineering. Any future applications that build on the results of SPARQL queries will certainly benefit from the availability of basic navigation-type queries such as get neighbourhood, get the root of an ontology, get the hierarchy to the root, get graphs, etc. These queries explore the typical network structure of RDF models. In contrast, the ontological queries show the RDF semantics that are available in BioGateway, such as subsumption, transitivity and the composition of relations. Some examples of ontological queries read as follows:
1. Query the OBO Foundry: search on names and get their unique identifiers.
2. Get all the neighbouring terms of a given term.
3. Get all the properties, such as definition, synonyms, etc. of a given OBO term.
Both sections of the library help to make BioGateway a workbench for creating SPARQL queries. The results of a query can often be used to copy-and-paste as a parameter in other queries. We further elaborate on this idea in the Section: Combining regular RDF graphs with transitive closure graphs. All the queries in the library were provided with a name, its function and a list of parameters that can be customised in a query. By properly using prefixes, an SPARQL query can be written in such a way that a parameter only needs to be replaced in one fixed place. All the queries in the library were written in this way.
Combining regular RDF graphs with transitive closure graphs
One of the ontological queries in the library is designed to find the closest common ancestor in the hierarchy of an ontology for two given terms:
# NAME: get_common_ancestor
# PARAMETER: GO_0002617: the first query-term
# PARAMETER: GO_0034125: the second query-term
# FUNCTION: returns the closest common ancestor-term in the
# hierarchy for two given terms
BASE <http://www.semantic-systems-biology.org/ webcite>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema# webcite>
PREFIX ssb: <http://www.semantic-systems-biology.org/SSB# webcite>
PREFIX term1_id: <SSB#GO_0002617>
PREFIX term2_id: <SSB#GO_0034125>
SELECT distinct ?common_ancestor ?common_ancestor_id
GRAPH <SSB_tc> {
term1_id: ssb:is_a ?common_ancestor_id.
term2_id: ssb:is_a ?common_ancestor_id.
term1_id: ssb:is_a ?direct_child.
term2_id: ssb:is_a ?direct_child.
?direct_child ssb:is_a ?common_ancestor_id.
?common_ancestor_id rdfs:label ?common_ancestor.
For this query, we need both the regular RDF ontology and its transitive closure (SSB_tc that is generated by the pipeline, see Section: BioGateway architecture). In fact, the query might be reduced to: find all the ancestors of both terms that do not have any descendants that are ancestral to both terms. To find all the terms that are ancestors of both terms we need the transitive closure graph, as in that form all the ancestors are directly linked to their descendants. Two triples in the query are enough to retrieve their id:
GRAPH <SSB_tc> {
term1_id: ssb:is_a ?common_ancestor_id.
term2_id: ssb:is_a ?common_ancestor_id.
We find all the common ancestors with this query, while we only want the closest ones. Therefore, we check for the children of this set of ancestors. This can be best accomplished in the ontology without transitive closure:
?direct_child ssb:is_a ?common_ancestor_id.
Additionally, we check whether these children belong to the same set of common ancestors as defined before:
term1_id: ssb:is_a ?direct_child.
term2_id: ssb:is_a ?direct_child.
The last two checks go in an optional clause, since we only want the common ancestors for which these checks fail. In this way, we can filter the common ancestors for which this type of ?direct_child does not exist:
Semantic comparative analysis
Comparative bioinformatics has yielded important new hypotheses by identifying and comparing similar features (e.g. genomic sequences) in different species. Comparison of these features allows the formulation of hypotheses with respect to the functions of genes and their products, as well as the localisations of gene products and the processes in which they are involved. BioGateway enables an innovative way of exploring such similarities by taking into account the stored annotations across the different organisms under consideration. The following simple query shows how this potential use can be exploited to retrieve all the proteins that have the same function (GO_0005216: ion channel activity), are located in the same cellular compartment (GO_0005764: lysosome), and participate in the same process (GO_0006811: ion transport) in any of the organisms of the repository:
BASE <http://www.semantic-systems-biology.org/ webcite>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema# webcite>
PREFIX ssb: <http://www.semantic-systems-biology.org/SSB# webcite>
SELECT distinct ?organism ?protein ?protein_id
GRAPH <SSB_tc> {
?protein_id ssb:has_function ssb:GO_0005216.
?protein_id ssb:located_in ssb:GO_0005764.
?protein_id ssb:participates_in ssb:GO_0006811.
?protein_id rdfs:label ?protein.
?protein_id ssb:has_source ?organism_id.
?organism_id rdfs:label ?organism.
ORDER BY ?organism
The query returns 11 proteins fulfilling the conditions of same function, location and process found in four organisms (C. elegans, H. sapiens, M. musculus and R. norvegicus). Not surprisingly, some of the entries are ortholog proteins (such as KCNE1_HUMAN and KCNE1_MOUSE). Some simple modifications, such as using an OPTIONAL clause over the first triple, may find that many other proteins (such as VATM_DICDI in D. discoideum) also share the same location and process.
Discussion and perspectives
The life sciences community is becoming aware of the need for standards to communicate and store data and metadata [19,37,38]. The W3C provides standards to represent (e.g. RDF, OWL) and retrieve (e.g. SPARQL) knowledge. Although there are still limitations with respect to the representation of some types of information (e.g. spatio-temporal information) and it may prove difficult to model complex scenarios (such as expression data from microarray experiments), these standards have been shown to accommodate information that can be queried to gain further biological insights [39-41].
To demonstrate the utility of such standards, we built BioGateway, an RDF triple store that integrates different life sciences knowledge resources. We have shown that the use of the Semantic Web technologies makes data integration straightforward, and also allows for the enabling of flexible and fine-grained information retrieval from KBs. At the same time, we experienced some problems such as considerable upfront investment in the creation of content in RDF and performance issues while querying either very large triple stores and/or using complex queries. Other projects [42-46] have attempted similar integration. Such projects, compared to BioGateway, either used smaller data sets or offer limited query possibilities due to performance issues. They experienced similar problems. Compared to those other initiatives, BioGateway demonstrates that a sound design paves the way for reasoning and information exploitation (combination of transitive and non-transitive graphs). Thus, BioGateway provides an implicit implementation methodology that is materialised by a working system.
From our reflection upon our own experience and other similar initiatives, we identified the problems that remain to be solved in order for the Semantic Web to become a reality in Life Sciences:
Biological identifiers
A universal resolvable mechanism for identifying biological entities is vital for a Life Sciences Semantic Web [47]. The problem of setting up a global infrastructure for biological identifiers is largely a social, not a technical one [48] as a deep agreement by the community is required. There have been different attempts in that direction. For example, the OBO Foundry insists that the ontologies have unique identifiers that are orthogonal to identifiers in other OBO Foundry ontologies. Such identifiers are, however, not resolvable, and therefore not scalable [47]. There are mechanisms that are currently proposed for resolvable identifiers such as URIs [49], LSIDs [50], OKKAM IDs [51] and MIRIAM URIs [52]. In this respect, it is appropriate to mention that the newly established group Shared Names [53] has taken up the challenge of finding a broadly acceptable solution to this problem.
Lack of semantic content
Most biological information is either not semantically codified or it has been semantically codified with a poor axiomatisation [54]. This information should at least be semantically codified with RDF or with a rich axiomisation if using OWL. Best practices are needed to help biologists create rich semantic content in ontologies [55], so that in the future a global and distributed group of high-quality RDF/OWL encoded content will become a reality. A number of complementary approaches are being pursued to help create semantically enriched content (e.g. microformats [56], GRDDL [57], RDFa [58]).
Current technology limitations
Even though ontology editors (e.g. Protégé [59], OBO-Edit [60]), reasoners (e.g. FaCT++ [61]), APIs (e.g. OWL API [62]) and platforms supporting the data integration (e.g. OpenLink Virtuoso) for the Semantic Web have advanced over the last few years, they still fall short of constituting an established and robust technology, especially in regard to their utility and reliability. On the language side, however, OWL is evolving quickly and many new features have appeared in OWL 2 [63], increasing its utility.
Academia and industry are combining efforts to bolster the development of reliable and sound Semantic Web technologies. Although research advances are more clearly appreciated at a middleware level (e.g. reasoners), that allows for the development of concrete applications such as BioGateway, scalability and visualisation (formerly relatively neglected) are becoming key aspects while developing these technologies to support the popularisation of the Semantic Web (e.g. the LarKC project aims to overcome reasoning limitations with vast amounts of data [64]).
The aforementioned difficulties were succinctly summarised in the title of the panel discussion during the recent SWAT4LS workshop [65]: "If the Semantic Web is so good, how come most people use OBO for ontologies and PERL for data integration?" There are various reasons for the slow pace of the adoption of Semantic Web technologies, but two of them stand out: there is a paucity of applications that demonstrate the usefulness of the Semantic Web, whereas the Semantic Web is seen as an obscure technology that is difficult to use. To illustrate this, most biologists are still unaware of the importance of semantically codifying knowledge, and perceive languages such as RDF or OWL as overly complex. They appear find the OBOF language much more suitable and intuitive than OWL or RDF. Concerning the paucity of applications, BioGateway aims at providing a demonstration of the benefits of Semantic Web technologies by facilitating a resource for querying integrated resources in order to exploit RDF.
While building BioGateway, the choice of RDF, as opposed to using OWL, resided mainly on the benefits obtained while adequately combining a set of data, a given set of queries and a query engine (OpenVirtuoso in our case). Such a combination of elements impacts many aspects, such as the speed of answers, inferencing capabilities and scalability. Some projects such as Wolfram Alpha [66], that aims to provide a "computational knowledge engine", are exploring alternative representational ways that could eventually support or complement the Semantic Web vision.
The problems observed during the development of BioGateway and other RDF stores can only be addressed at the community level. Therefore, we make a public call for the creation and development of a Semantic Systems Biology community with the following aims:
1. Encourage and facilitate the creation of semantic bio-content.
2. Develop best practices that will be commonly accepted for such content creation.
3. Collect and index such content.
4. Agree upon, and encourage a mechanism for identifying biological entities.
5. Facilitate the communication between the semantic technology developers and the life scientist: the users of such technology.
This community should have objectives beyond those of the OBO Foundry: it should build upon the best of OBO (the community, the content creation guidelines, and the content) and exploit it in a standardised platform with emerging Semantic Web qualities. As a first step towards such a community, we have built the Semantic Systems Biology wiki [67]. We venture to consider the following topics to organise and structure the life sciences Semantic Web resources, and to define a set of principles to which such a community should commit:
1. Orthogonality: avoid duplications of efforts;
2. A defined set of RDF tags (e.g. definition, function, has evidence, etc.);
3. A unique identifier per resource, plus an ID resolution (e.g. purl.org);
4. Comply to an accepted top-level ontology;
5. Comply to an accepted set of common relations;
6. Identify a list of prospective resource applications (e.g. hypothesis generation);
7. Resource peer review (community evaluation);
8. Tooling (e.g. visualisation);
9. Address persistence-related issues;
10. Providing explicit semantics;
11. Rich axiomatisation (and hence, rich querying).
We strongly feel that this is the appropriate moment to establish such a community to bolster and extend the current efforts (e.g. HCLS IG, NeuroCommons [68] that also use RDF-based triple technology, but in contrast to BioGateway in which the RDF modelling has been carefully devised to provide simple query construction, NeuroCommons uses not only RDF representations but also OWL ones) and to begin building a universal, interoperable knowledge architecture [69]. Such a structured resource will further ensure that Semantic Web technologies will become one of the most crucial means for knowledge integration in the life sciences [70,71]. BioGateway is a demonstrative step towards such an end.
BioGateway is built using an automated pipeline implemented in Perl (the source code is available at the SSB website [18]). This pipeline automatically integrates publicly available resources as well as in-house resources (e.g. Metarel).
The following public resources are integrated under the BioGateway umbrella:
• Candidate OBO foundry ontologies (CVS repository [72], all ontologies);
• SWISS-PROT (FTP site [73]);
• NCBI taxonomy (FTP site [74]);
• GOA files (FTP site [75], all files);
• CCO (HTTP site [76]).
Auxiliary ontologies
Metarel, Biorel and Metaonto were manually created using OBO-Edit [60]. Metarel was developed in-house to describe relations between relation types and will be described elsewhere [77]. Biorel was generated by combining RO and all the relations used in OBOF. BioMetarel was produced by adding Metarel to the relations in Biorel on their RDF translations, with SPARUL [78] – an update language for RDF graphs.
The conversion of GOA, SWISS-PROT and NCBI files to RDF was performed with the newly developed ONTO-PERL modules GoaToRdf, SwissProtToRdf and NcbiToRdf, respectively. The Ontology module from ONTO-PERL was used for converting ontologies from the OBO format to RDF. This conversion has been optimised, as compared to the originally published version of ONTO-PERL to minimise the number of blank nodes for the sake of query performance (see Section: Results). In the course of conversion, any relations present in the ontologies were omitted (to be replaced with Biorel during uploading to the triple store, see Section: RDF endpoint).
The conversion from SWISS-PROT and NCBI was partial content-wise. In the case of SWISS-PROT, the fields accession numbers, synonyms, encoding genes, annotated functions and diseases were retained. In the case of NCBI, the fields: taxon identifier, species, genus, family and relations were retained.
Transitive closures
To increase the utility of the RDF representation, transitive closures were added programmatically with the use of the Ontolome module from ONTO-PERL [79]. During the transitive closure construction, each ontology term is inspected and its transitive relations (part_of and is_a) are expanded so that explicit relations to its ancestors are added (using the depth-first search algorithm [80]). This generation only considers the subsumption relation (is_a) and the partonomic relation (part_of). This was done for all OBO ontologies, CCO and BioMetarel.
RDF endpoint
The RDF files were uploaded into the Virtuoso server using the Perl DBI module [81], the ODBC interface (DBD::ODBC [82]) and the OpenLink iODBC library [83]. All RDF files were uploaded as individual graphs. In the course of uploading, four additional integrated graphs were created: the SSB graph including all individual graphs, the SSB_tc graph containing all the transitive closures, the OBO graph comprising all the OBO candidate ontologies and the GOA graph combining all the GOA graphs. A copy of the Biorel graph was added during the upload to each of the graphs (except Biorel and BioMetarel).
Web interface
A web interface [84] for querying BioGateway with SPARQL was developed using the Joomla content management system [85] and JavaScript. This interface provides a set of pre-cooked queries showing sample query possibilities on the system, and an edit-box (form) that points to the SPARQL endpoint through simple HTML technology.
Graph visualisation
The SPARQL Browser [86], a web application for displaying query results, was developed with Flex technologies [87]. The source code is available at http://www.netthreads.co.uk webcite.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
EA was the main architect and engineer of BioGateway. WB designed and implemented Metarel and Metaonto, and he optimised the architecture for SPARQL querying. AR developed the SPARQL visualiser. ME and RS provided bio-ontologies expertise. VM provided expertise in biological data integration, and oversaw the shaping of the manuscript. BDB and MK contributed their expertise about knowledge management in systems biology and steered the project. All authors contributed to the writing of the manuscript.
This work was funded by the EU FP6 (LSHG-CT-2004-512143). EA and WB received funding from the European Science Foundation (ESF) for the activity entitled Frontiers of Functional Genomics, VM was funded by FUGE Mid-Norway, ME by University of Manchester and EPSRC. We wish to thank Nirmala Seethappan, Bjørn Lindi and Kent Overholdt for their help in setting up the system at NTNU.
This article has been published as part of BMC Bioinformatics Volume 10 Supplement 10, 2009: Semantic Web Applications and Tools for Life Sciences, 2008. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/10?issue=S10.
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Mel Karmazin, now CEO of Sirius Satellite Radio, started in the radio business at age 17 and rose to the top by being the glibbest and most persistent ad salesman. But his able patter hasn't served him as well in recent years. After leaving Viacom because he couldn't coexist with equally alpha Sumner Redstone, Karmazin had hoped to restore his reputation in the nascent but promising satellite-radio market. That market hasn't quite developed as he'd hope. His future, and the future of satellite radio, will be determined by consumer and government acceptance of the merger of the two satellite-radio companies — XM and his own Sirius. And Karmazin has turned to a Washington Times' op ed to use his legendary gladhanding skills to sell everyone on the merger's merits. Don't be fooled. Excerpts and translations, after the jump.
We built our industry by providing choice. Now we're ready to increase choice, raising it to the next level. This a la carte offering represents the first-ever in subscription media. Consumers will have two different a la carte packages to choose from, in addition to six other programming options.Please, please, please ... be too stupid to realize that this isn't a la carte. Your phone contract, with its minute tiers and additional fees for unlimited texting or web access, and your TV plan with its premium packages works exactly the same way. And, please, don't think about all those consumers lobbying the government for true a la carte cable, not tiered subscriptions. The only way the government will approve this merger is if we adopt the trendy phrase "a la carte," without really meaning it.
The new programming packages will be available through existing devices, with the exception of the a la carte packages. A la carte programming will require a new device, which will be priced in line with those currently on the market. So, after our merger, we will not only offer more choice but will make choice cheaper.Existing customers will not be offered more choice. For them, choice will be more expensive.
The audio entertainment market today is brimming with competition and will be even more competitive after our merger. MP3 players, iPods, HD radio, Internet radio, satellite radio and mobile phones are revolutionizing the listening experience. There has never been a better time to be a consumer.Satellite radio is such a weak offering that it can only compete by having a monopoly. There has never been a worse time to be in the satellite-radio business.
However, the efficiencies and cost savings we realize from the merger will allow us to compete more aggressively with terrestrial radio, the 800-pound gorilla that still dominates the industry. Terrestrial radio reaches 230 million weekly listeners who access terrestrial programming free of charge in virtually every home and vehicle in America.We are still obsessed with terrestrial radio, despite other modes revolutionizing the audio market, because we can't figure out how to make a profit from expensive subscriptions while they manage to do it by giving their broadcasts away.
As for passing the regulatory hurdle of demonstrating that the merger is in the public interest, this transaction is a slam-dunk ...I'm writing this op ed for a Washington daily precisely because I'm worried we won't be getting regulatory approval.


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Tel: +44 (0)1208 269 159
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DogCam Bullet cameras started in 2005 in sunny Cornwall as a family run business. Almost exactly a decade later, it was bought by telematics solutions designer, developer and manufacturer, Trakm8 Ltd.
Dogcam continue to specialise in helmet cameras and head camera technology. We develop and retail the finest miniature wearable camera equipment available, backed up by the very best customer service and after sales care.
We also carry a large range of covert filming equipment as supplied to Police forces, Armed forces, Special forces, film companies, and the BBC as well as for our loyal public customers.
DogCamSport are the main UK portal for GoPro 4 and RoadHawk Cameras as well as a wide range of LawMate undercover filming equipment.
Price: £89.95
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New GoPro cameras and Mounts
Dogcamsport have been retailing GoPro cameras since before they became so famous.
Our knowledgeable staff have been using GoPro cameras for a number of years and love to give help and advice on the subject.
We now carry every single GoPro camera, mount and accessory as well as a huge amount of after market parts for your GoPro cameras.
To see our huge range of GoPro 4 UK Cameras and accessories please click below.
Click to see more GoPro 4 cameras and accessories
Thankyou to everyone who came to visit us on our stand at the Autosport Trade Show
We've never spoken to so many people in such a short amount of time and best of all we sold
a record amount of High Definition in car camera kits. If you would like more info on the Autosport in car camera then
please don't hesitate to contact us for more info and check out all the videos coming in from our new found customers!
So, you might not have seen much in the way of updates on here recently but that's because we've been hard at work with this new website. We've hopefully made everything much easier to find.
Please keep your eyes peeled for new products over the next few weeks...lots of exciting things happening all at once.
We would also like to take this opportunity to say a massive thanks to our customers for giving us the BUSIEST December on record!
One thing we know for sure....there will be a lot of happy faces over the next few days when you start opening your presents!
Happy Christmas and have a safe and relaxing time from all of the DogCam team!
Looks just like a light switch but in actual fact this is a tiny high definition camera coupled with a PIR motion sensor.
It has a 5 day battery standby time and records really clear video and audio using a wide angled lens.
Best of all....i's made by Lawmate so the build quality is superb. More info on the WS10 Spy Camera Light Switch
It's been a while since GoPro have released a new camera but it has finally been announced today.
GoPro announced the new GoPro HD 2 camera today and should be available to buy in the next few days. We should be amongst the
first with GoPro HD 2 availability in the UK. The new version of the GoPro HD camera will have better low light abilities, an easier to
use menu and LCD screen. The GoPro HD2 will remain compatible with all the existing GoPro mounts.
Please click for more info and to Pre-Order the GoPro HD HERO2
Video from our sponsored rider Cameron Ross from Scotland doing his thing with one of our Bullet HD WIDE Cameras
The DC-1 is the single forward facing in car camera from RoadHawk. It has been fitted to numerous large fleets around the world
including UPS, Tarmac, LaFarge and many others. It's also very popular with members of the public looking to protect themselves
by providing evidence in the event of an accident. The feedback we get about how effective these cameras are is compelling!
RoadHawk are giving away a FREE RoadHawk DC-1 on the 1st of December.
All you need to do to enter is visit the RoadHawk Facebook Page and LIKE and SHARE
We have just had the floating back door for the GoPro cameras come in to stock ready to go.
If you're planning on taking your GoPro camera in to the water and you don't want it sinking to the bottom of the sea or river then we highly recommend this accessory from GoPro for their HD range of cameras. In fact....we carry ALL GOPRO cameras and accessories in stock ready for next day delivery and you can find everything GoPro related on one GoPro page.
We've been selling quite a few POV.HD camera systems lately for use as professional swim cameras kits.
We decided to put a kit together with a pole and all the mounts required to make a fully working underwater HD camera package.
After taking it along to a local pool we got some excellent results and the Swim Club purchased the camera there and then!
More info on the POV.HD Swim camera. The perfect tool for any underwater sports training.
As well as a lot of these cameras being used now by the likes of BBC production teams and some rather special
Hollywood film crews, the POV.HD is within the realms of us home users too. Here is a video compilation showing what this
awesome video kit can do in the snow and on the streets.
Here we have a nice bit of footage curtesy of MR A Pullen of Barford showing off his
RC flying skills by mounting a Bullet HD WIDE helmet camera to his model aircraft.
Looking for an in car camera system? We have the best in car camera systems currently on the market.
If your budget is between £99 and £1000 then check out our motorsports in car cameras
Please visit our page and leave a comment. We're getting some fantastic feedback!
Scan the QR code below for a chance to win a camera!
Well..almost! 110,000ft is pretty close. We have our friends Ed Oates and Marcus Lewer to thank for this awesome video.
They strapped a HDMax Extreme camera to their high altitude balloon and sent it up filming. These are some of the most incredible pictures we've seen from our cameras and you can watch the video here (watch it in HD) : DogCam in Space...
Check out our latest range of motorcycle camera kits. We've put a collection of bullet cameras together starting at £109.95 for our 720p HD Bullet going up to £500 for the latest POV.HD 1080p high definition top of the range camera system.
To celebrate the greatness of this year's high definition bike cameras, we've sponsored Team VSpead with HDS720 cameras so they can film each one of their races from both riders. We'll be putting updates on their progress up on our Bike Cameras Page.
To get you in the mood....here's some video from the 2011 Australian Superbike championships
Filmed with the HDS720p Bullet Camera
Click for the latest Bike Bullet Camera Packages
The new ER13 high definition bullet camera for the Lawmate PV500 evolution has just been released.
It creates law enforcement grade high definition video with full date/time stamping.
The solid state design is rugged and the camera and be head mounted or shoulder mounted.
Click here for more info on the PV500 HD Bullet camera system
Just wanted to have a quick chat about the POV.HD. We've never experienced such a high demand for a new product.
Naturally...everyone wants the camera that gives the best video quality and so the demand is MUCH higher than the current supply. This is something VIO are working on. We're expecting the second batch of POV.HD cameras in the next few days. We're hoping to fill ALL back orders by the middle of March and hopefully have some free stock available although we don't expect them to hang around here for very long.
If you would prefer to wait until free stock is available then please send a quick email to: firstname.lastname@example.com
We will email you on a first come, first served basis.
We will be on Stand K44 this year at the Broadcast Video Expo at Earls Court from the 15th to the 17th of Feb 2011.
We will have the latest range of High Definition helmet cameras and will be showcasing the POV.HD camera system and demonstrating its broadcast quality video; sharper and clearer than any other camera currently available on the market. We'll also have the HDMax Extreme camera, the HDS720p and the Bullet HD cameras with us. Come and have a chat and see if you can't squeeze a show special bargain out of us.
Click the video above to see them in action!
Right then....we all know the BBC don't mess around and when it comes to video equipment they pretty much choose the best available. That's why Graham Bell has fitted himself out with a HDMax Extreme helmet camera and a HDS720 camera on his Ski tip.
All the feedback and reviews we're seeing on these new CamSports cameras are extremely positive and we're happy to report the lowest faulty return rate from any camera we've ever sold!
Check out this year's Snow Packs here...sleek, low profile helmet cameras, you don't want to be seen with anything less on your head!
GoPro Have released their LCD screen for the GoPro HD Cameras. We expect to see stock some time in Feb.
The screen simply clips on to the back of the GoPro HD camera (not the HD960 model) and you can line your shot up or playback the video you have already recorded. The LCD BacPac is supplied with 4 replacement back doors for your existing poly carbonate housing.
Check out the latest BBC Ski Sunday Video Blog with Graham Bell and Ed Leigh.
Graham has fitted himself out with the very best snow cameras available on the market for his downhill commentary this season.
Please watch their video blog and see what they're saying about our new HD cameras!
As always, we'll be at the NEC this year showing off all the latest HD camera systems.
If you're coming along....please drop by and say hello and possibly pick up a show special bargain!
The NEW HDMax extreme helmet cameras are flying out the door and it's not hard to see why......
Imagine a 1080p high definition helmet camera about the same size as a Contour HD.
Then add a 2" Colour TFT Screen, a wired remote controller, instant playback, HD output by HDMI with cable supplied, external microphone input and a whole host of mounting options all in the box; The HDMax Extreme is here!
Video sample from Lotus Elise
New HDS-720p Camera here NOW!
We really love this little camera! It's not much bigger than your average bullet camera but squeezed in there are the same electronics used in the GoPro and Contour HD cameras. This one shoots at 720p and is waterproof down to 10m of water. The video and audio quality is really nice and we've not seen anything like this in a cameras so small. One button operation and laser level alignment.
Don't just take our word for it.....check out the under water video below and also the demo video on this page: HDS-720p
VIO POV.HD Coming Soon!
The new POV.HD from VIO takes the video quality crown from the popular GoPro cameras! This ultra high end bullet camera from V.I.O is not only perfect for filming POV for just about any sport but because of its super crisp 1080p processed video it is also the perfect companion for television production companies. If you have a requirement for THE best video quality from a wearable camera system then you should check out the new POV.HD
06/10/2010 We Have Moved.....
As from Monday 8th of November 2010 if everything has gone to plan we will be working and answering the phone from our new office in Bodmin, Cornwall. Our new office has plenty of space to welcome new members of staff as we happily expand and move forward.
Even though our address and phone number are changing the one thing that will NEVER change is the level of support and customer service you will get from us here at DCS Systems Ltd. We'll be dispatching all goods from a distribution depot close by which means we'll be able to provide next day delivery on most items right up to about 5pm.
Once again, we'd like to whole heartedly thank our fantastic customers old and new as we venture on towards an excellent end to the year and an exciting beginning to 2011.
Whilst we're here having a quick chat.....please keep an eye on our websites over the next few weeks. We have a new line-up of high definition helmet cameras and wearable camera systems coming on-line ready for the festive season starting at £95 going up to high end £500 systems. Exciting times for all of us!
02/10/2010 Possible "Crash for Cash" video caught on RoadHawk Camera!
This amazing video as featured on Sky News and Channel 5 news shows a potential "Crash for Cash" scenario being played out. The two cars in front of the lorry driver alledgedly create a staged accident by braking hard causing the lorry driver to rear end shunt the Mercedes.
This morning, police went in and arrested what they believe to be the leader of a crash for cash insurance fraud ring. It's thought this group have been involved in over 120 staged accidents in the last year!
Read more and see the crash for cash caught on video here.
01/10/2010 All PV1000 UPGRADE!
As from this date all Lawmate PV1000 digital video recorders will be fitted with 120gb hard disks giving twice the storage capacity as before. This is great news but even better than that is the price remains unchanged!
You can find the PV1000 digital video recorder here.
26/10/2010 GoPro helmet front mount in stock.
GoPro release their new helmet front mount. This little critter is designed to hold your GoPro camera to the front of just about any helmet and you can then face the camera back on yourself. Doing this makes a very unique looking shot. If you look below you will see some video we shot over 2 years ago using this camera angle accept we didn't use a GoPro HD for this as they weren't invented back then but you get the idea! Check out this new GoPro Accessory on our GoPro HD Camera page.
15/10/2010 NEW Mini DVR 3 Bullet Camera System Available.
Everyone's been waiting for the latest update in the Mini DVR series. The New Mini DVR 3 is the 3rd generation update to the h720 unit. It uses the latest Zorro 9 chipset for encoding AVI video files at up to 13mb/s at 720x576 resolution. It still uses the smallest bullet camera on the market now with upgraded IR filters for much better colour reproduction.
Numbers of the MiniDVR3 will be limited until after Christmas so don't miss out, you won't find them anywhere else!
Read more about the fantastic new MiniDVR 3 bullet camera system.
06/10/2010 GoPro HD Wrist housing now in stock!
We are now carrying plenty of stock of the new GoPro HD wrist housing. We know you're been waiting for these so come and get 'em! Wear your GoPro HD Camera on your wrist for a completly unique filming angle.
We also have invidual flat adhesive mounts and curved adhesive mounts available so you can now buy as many or as few as you need.
Please see...... GoPro HD cameras and accessories.
17/09/2010 Sample video from the new Lawmate PV500 Evolution HD Spy Camera.
This video was shot using the Lawmate PV500 Evo HD digital video recorder and the new high definition digital button camera. It is the only HD button camera kit with touch screen controls in the world. Already being used by the UK's premier test shopping companies, undercover journalists and Sky News!
Click for more info on the PV500 Evolution HD Sky Camera Kit
14/09/2010 New Firmware available for the GoPro HD cameras.
The latest version of of the GoPro HD cameras gives you some nice new features not least being 25fps and 50fps filming modes making it a much more suitable camera for filming in the UK for TV purposes. It also adds upside down mode functionality allowing you to hang the camera upside down and it will flip the image for you automatically. Download the new GoPro HD Camera firmware here.
12/08/2010 New Lawmate equipment and website LIVE!
Lawmate have released their latest range of digital video recorders that can record in high definition along with their NEW high definition button camera and upcoming high definition bullet camera.
The PV500 Evolution and the HD Button camera can be found here: PV500 EVO with CMD-BU13
DCS Systems ltd have become the UK's authorised distributor for all new Lawmate products. Why not check out our new website which is in the process of being populated with the enitire Lawmate range. Check out the new Lawmate UK site here.
28/07/2010 GoPro HD Silicone Covers In Stock.
We're carrying stock of the silincone covers for the GoPro HD cameras.
If you want to protect your camera, keep it warm and make it look cool then grab yourself one of these new silicone covers!
Now available on the GoPro HD page.
01/07/2010 RoadHawk will be at Truckfest!
We've been invited to attend Truckfest South West this weekend 3rd and 4th of July at the Royal Bath showground. We're attending in RoadHawk mode with live displays of the RH-1 and RH-2. The Roadhawk RH-1 has been the top selling item on this website for the last two months running. This will be out first outdoor show and we'll be camping in tents so let's hope for some more sunshine this weekend.
If you're around, come and see us and grab a show special bargain!
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Summer lovin', had me some jams!
I recommend all these tunes because apparently I can't stop playing 'em: here's a quick alphabetical assessments of what's been hummin' in my iPod on Metro the past few weeks!
The Blank Tapes, "Coast To Coast" from the album Vacation
A little Zombies-meets-Badfinger surf hippie flower power pop from this (not surprising) SoCal band. The Blank Tapes is Matt Adams, an eight-track addict who piles on the tasty garage riffs atop lyrics about throwing the gear in the van and leaving baby behind, and not necessarily paranoid conspiracy theory podcasts. (Although there is a line about "Waking up the ghosts ....") Breathy a-has, peeling oranges, the radio is playing, as Matt and his pals hit your town. Sample lyric: "Malibu/touching you." Currently touring everywhere from Huntington Beach to Santa Cruz. I imagine they always will be, happily.
Cali Giraffes, "All My Life" b/w "Lazy Days" single
Evan Dando had something to do with the origins of this band, which I find confusing and yet somehow understandable (still a damned shame about Ray). But the deep adoration comes for Fastbacks' legendary bass goddess Kim Warnick's vocals on the A-side here, a jumping, joyful, but gentle lyrical variation on the meaning of Blondie's "One Way Or Another." And co-creator Mikey Davis takes the mic on the just-as-great pining and slacker days-celebrating B-side "lazy Days." Both are chockful of chiming, grinding hedonistic thrills, in the sunshine, by the fire, wherever life-loving major chord happiness can be found. A perfect match!
Daughn Gibson, "The Sound Of Law" from the album Me Moan
This sounds like a dust-kicking American Gothic soundtrack to a big 70s car racing movie, with celebrity-stars like Burt Reynolds but also some sinister dude like Jack Nicholson in an inimal subplot sabotaging the prize, or maybe in-between in some oil-saturated slice of life like Two Lane Blacktop. Anyways, next track on the Sub Pop elpee is "Phantom Rider" which is just as good, and the whole thing is certainly worth owning. Rumor has it this Pennsylvania truck driver's sound is a new thing, and it certainly drawls well and peels out of the parking lot slow. Neat neat neat nocrturnal automobile-soul rock. I give it two bong-loads and a box of Pine Tree air fresheners.
Future Bible Heroes, "Living, Loving, Partygoing" from the album Partygoing
Like a much more friendly (and queer and cool-weird and not at all violent) take on Spring Breakers, all tinsely keys and Top 40 melodies, floating from scenes like "John Waters' soiree" and "Mink Stoles' birthday," deejaying, taking "god knows what and danced till dawn," getting into clown's shoes and waking up with two friends in the same bed after sleeping for half a week. This is probably the happiest thing Stephen Merritt ever wrote, and it's gloriously transgressive while being awesomely frisky. Really gorgeous and fun and would be blasting out of every passing car stereo if a true tastemaker like John Waters himself ran the country.
Love's Not Impossible: My Top Ten Songs of 2012
We had to have some good tunes to get us through a year of watching a psychopathic plutocrat trying to pitch us back into the black and white world of fifties-era paranoia and imperialism. That victory against vileness confirmed, going back over the songs that made us swoon for the past few months is very pleasurable, as great music can transcend the tough times it was made to get through.
Below are the most repeated recent songs in my playlist, save for the tracks from bands I did publicity for. (I will say that I only do PR for bands I truly love, which is why the Big Freak roster is so small. I'm a picky and fussy little bear. But this is not the place to hype my own wares.) Also, I will note that I will not have a list of albums this year; I think there are still great full-lengths out there, but not enough for me to make a list of. You can blame that on the limited amount of albums I have access to; but I do buy and acquire enough that that's not quite the case.
It could very well be that there's too many great records coming out to keep track of 'em, and to get anything done in terms of keeping up the format of ten or twelve tracks released by one artist or group is increasingly becoming an arbitrary time-lump of expression. Yeah, it's the obvious technological changes (songs trumping long-players, even with the re-rise of vinyl), but also the fact that much more product and much less discriminating gatekeepers are flash-flooding over the trickle of sweet stuff. It's out there, but we're going to need new ways to hook in. This is making places like KEXP or NPR or WFMU, your extinction-threatened informed record store clerk, what you hear at your favorite DJ night, the journalist with an actual story, the in-touch blogger with deep tastes, even labels who don't sign every band (and publicists who don't take on every client, ahem), and of course beloved community-amping affairs like Three Imaginary Girls, that much more necessary.
Believe it or leave it.
Now to the tuneage, in order of honest amounts of plays (assuming my devices aren't fibbing):
1.) Dum Dum Girls, "Trees And Flowers"
It may be ludicrous to most big boy and bought off rock crits to say, but Dum Dum Girls is arguably the best rock band going today. Tapping into the sixties, seventies and eighties without being a straight hippie-power pop-new wave Freakbeat homage, and crystallizing a powerful dual voice in vibrant vocals and velvety music, they hypnotize as they freeze-dry your tears. Every song on this End of Daze EP is a too-sweet tease for a Dee Dee 2013.
2.) THEE Satisfaction, "Queens"
"Whatever you do, don't funk with my groove." The apex-high point on possibly the best Seattle album of the year, awE NaturalE, it is a perfect song about sleek and confident boundary setting. Catherine Harris-White and Stasia Irons are truly among the best in modern art-soul, following up the heat from their dangerous live shows with a contagious meditation on Being and Blissfulness with a little help from mentor Ish (Shabazz Palaces). There are other great songs on the Sub Pop debut full-length, but this is first pick for my own mix-tape.
3.) Constant Lovers, "Open Toe Heels"
Constant Lovers is a slow drag of a drug-dipped cigarette after feral sex. A stagger home after too many drinks with someone who lights all your fireworks. It's toxic-bad for you, but no mere basement-boy sludge-punk or anything like an AmRep rip off (cough cough). Don't trust the locals who pass on these guys, they're tourists in our town. This is the real Seattle sleaze and squeeze. This pole-dancing clear-heeled 3:31 freak-out is just going to shiv your liver and rot your gut but you won't smell a thing as she plows under. This is a particularly ballsy blast of hot spicy cocktail sauce at the center of their True Romance full-length (get it!!), a hard rock hassle truly good for these times. With Ben Verellen (Helms Alee) now on drums (!!!), maybe the feudal lords with labels will start buying in what's primo and already available in their own hoods and stop exporting cash and stash to GQ-core wanna-bes elsewhere.
Latest comment by: selena: "tea cozies sound so much like old pgmg. "
Recommended Show + Ticket Giveaway! Win tix to Magnetic Fields at the Neptune {3/19 & 3/20}
Huzzah! The Magnetic Fields are coming to Seattle (!!!) and we've got a pair of tickets for you to win! One of the Imaginary Girls' favorite melancholy indie-pop bands will be gracing the stage at The Neptune for two nights: Monday, 3/19 and Tuesday 3/20. Their newest album, Love at the Bottom of the Sea, was released 3/6 on Merge records. (You can take a listen to the single "Andrew in Drag" in the video above.)
But look, I don't need to explain to y'all how great they are, YOU ALREADY KNOW IT. On to the deets! Shoot an email over to tig {at} threeimaginarygirls {dot} com sometime between now and the end of the day Tuesday {3/13}, with the subject line "69 Love Songs". We'll pick a winner and notify you on Wednesday, 3/14 that you're on the list +1 -- just don't forget to let us know which night you want to attend! ♥
The Magnetic Fields — Love At The Bottom Of The Sea
The usual is all here for The Magnetic Fields fans: Stephin Merritt with Claudia Gonson, Sam Davol, John Woo, Shirley Simms, Johny Blood, and Daniel Handler making Spanish influenza-catchy, basement speakeasy lo-fi itchy, top shelf bourbon-breathed novelty hate snog orgies out of lyrical cliches, turned around and spanked sweetly.
However, there are some obvious twists on Love At The Bottom Of The Sea -- starting with the fact that they're back on Merge Records, the label that launched them as DIY synth-pop demigods in the 90s. And for the occasion TMF bring back the keyboards with all the squeaking, squonking, squealing, and the beep-beep-beeps beneath. The sweet fragrance of infatuations crooned and bleated on alt-boom classics like Get Lost and The Charm of the Highway Strip lingers here, but richly infused with the robust LP-learnin' Merritt and friends have been bringing in from late 60s/early 70s pop-folk-AM cabaret on their albums since the immense, ever-expanding 69 Love Songs.
Latest comment by: George: "Great album. We really enjoyed listening to it and writing down the lyrics. Check them out at the link bellow. http://www.dvdlyrics.com/albums-t-the_magnetic_fields-love_at_the_bottom_of_the_sea.html"
Wild Flag — Wild Flag
Wild Flag is a quartet love affair smooshing Portland and D.C.-based warrior women together, combining the velvety and violent vocals/guitars of Carrie Brownstein (Sleater-Kinney), Mary Timony (Helium), and Rebecca Cole (The Minders) with the superb shuffle and stomp of mighty drummer Janet Weiss (S-K, Quasi, etc.).
Wild Flag is a rock album that needs to be in everyone's playlist this year, as it constantly excites and snuggles up to the listener with openly emotional attempts at romantic music-fandom bonding ("Romance"), twists and turns about feeling hot and cold with mysterious scratches ("Something Came Over Me"), whilst a whole lot of skittery guitars tweak and even psyche-chug above Weiss's skin-rattling fury. It's boss.
Sounding as fresh as a debut by a Go-Go's era femme-powered new wave band made up of grown-up punks, all of those great garage gal voices bringing to mind glories recent (e.g. The Woods, by S-K) throughout, but also the brutal, passionate art-pop rants of Lene Lovich ("Boom"), and even early 70s feminist rock ("Glass Tamourine"). Dub bass notes dangle with Elastica-sharp guitar tones ("Short Version"), and all out expansive American Patti Smith-esque rock anthems spill towards the end of the ten track full-lenth ("Race Horse," "Black Tiles").
A summer "Romance" that has nothing to do with Grease: preview Wild Flag's new single
Sleater-Kinney are kind of like capers: you either really like them, or you really don't. Perhaps the most polarizing quality about them was the sound of Corin Tucker's voice -- that aside, the musicianship was almost always razor sharp and drum tight, and their breakup was a mixed bag of sadness. The reunion of drummer Janet Weiss (previously of the delectably square-jawed Stephen Malkmus and the Jicks) and guitarist Carrie Brownstein is therefore both wonderful, because they are excellent musicians, and -- despite the fact this may be Riot Grrrl sacrilege -- free of the histrionics of Tucker's vocals. Joined by Mary Timony (Helium), and Rebecca Cole (The Minders), the four come together like a Pacific Northwest rock-and-roll Voltron to create Wild Flag. Commenting on likelihood of the union, Merge Records stated on their website that "if someone drew a visual representation illustrating the ways in which all indie bands are interconnected, Brownstein, Cole, Timony, and Weiss would be in the same tiny sphere, so playing together felt almost inevitable." Amen.
Teenage Fanclub, Superchunk, and Telekinesis at Showbox at the Market October 14th
Welcome to Mergefest, Northwest edition. We're so unbelievably giddy about this show, we can hardly contain our little imaginary selves. From the moment this show was announced, we've been ticking off the days on our imaginary calendars, waiting and waiting for the magic that will occur the night of October 14th at Showbox at the Market, when the reverby swoonful magic of Teenage Fanclub will meet the crunchy and masterful indie rock of Superchunk, supported by our own hometown indie pop hereos Telekinesis. It's gonna be amazing.
On top of that amazement, all 3 bands will be touring new material! Teenage Fanclub just came out with the fabulous Shadows, which our own Chris Estey adored, stating of the track "The Fall" "Like with many great Teenage Fanclub songs, it creeps in the background till you remember what poured the Scotch into the Scotch-taped remnants of your own multi-shattered heart." Superchunk have the ever anticipated Majesty Shredding coming out in September, and Telekinesis are working on a new record right now. I'm sure we'll hear the hits we all want to hear, but we'll also be treated to some new stuff as well.
And, to celebrate, here's a video from each band:
Latest comment by: Steve: "all those three in one night. how can one contain themselves. i'll get to see two in one night and then enjoy TFC on the saturday...gotta try and savour each set..."
Summer's almost gone, time to get your Superchunk on
On Sunday, September 12th at Neptune Coffee, the Imaginary Crafty Listening Party will commence (Kelly's showing everyone how to make fabric flowers, woot!), and it will feature an original crafting soundtrack from Superchunk and the Thermals' new albums.
We have a full review of The Thermals coming up (it's a power pop romantic masterpiece), but we thought it would be good to specifically plug the seminal work of 90s punk pop royalty Superchunk. Especially since the new LP Majesty Shedding arrives along with must-have generational-rousing reissues of the band's second and third releases, No Pocky For Kitty and On The Mouth (1991 and 1993, respectively).
First of all, Majesty Shedding is the band's full-on reunion after many years and comes after Superchunk rubbed fan's tummies with their toys in the attic EP Leaves In The Gutter.
Imaginary Crafty Listening Party with brand new albums by The Thermals and Superchunk
{Thermals photo: Westin Glass / Superchunk photo: Jason Arthurs}
Last month's Imaginary Crafty Listening Party was bumpin with Lo & Behold Shrie teaching us all how to embroider {and armed us with TIG birdies to practice on} while we blissed out to the new Darren Hanlon and Menomena albums.
Latest comment by: Anonymous: ""the fabu fabric flower tutorial" Any tips on the how-to for those of us too preoccupied with real flowers?"
Teenage Fanclub — Shadows
(Teenage Fanclub play with Superchunk on October 14, 2010 at the Showbox in the Market.)
It's been a half decade since the last Teenage Fanclub record Man-Made, but their influence has never gone away, even if melancholy power pop bands have come along within that span of time which don't know how much they owe to the Scottish kings. Of course, on early 90s brightly shined gems like Bandwagonesque the band was itself unafraid to remind underground pop-lovers of Big Star or Badfinger or the brimming years of indie bands like Orange Juice and Josef K. from their own region less than ten years before.