Dataset Information

BioModels linked dataset.

ABSTRACT: BioModels Database is a reference repository of mathematical models used in biology. Models are stored as SBML files on a file system and metadata is provided in a relational database. Models can be retrieved through a web interface and programmatically via web services. In addition to those more traditional ways to access information, Linked Data using Semantic Web technologies (such as the Resource Description Framework, RDF), is becoming an increasingly popular means to describe and expose biological relevant data.We present the BioModels Linked Dataset, which exposes the models’ content as a dereferencable interlinked dataset. BioModels Linked Dataset makes use of the wealth of annotations available within a large number of manually curated models to link and integrate data and models from other resources.The BioModels Linked Dataset provides users with a dataset interoperable with other semantic web resources. It supports powerful search queries, some of which were not previously available to users and allow integration of data from multiple resources. This provides a distributed platform to find similar models for comparison, processing and enrichment.

SUBMITTER: Wimalaratne SM

PROVIDER: S-EPMC4423647 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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BioModels linked dataset.

Wimalaratne Sarala M SM Grenon Pierre P Hermjakob Henning H Le Novère Nicolas N Laibe Camille C

BMC systems biology 20140815

<h4>Background</h4>BioModels Database is a reference repository of mathematical models used in biology. Models are stored as SBML files on a file system and metadata is provided in a relational database. Models can be retrieved through a web interface and programmatically via web services. In addition to those more traditional ways to access information, Linked Data using Semantic Web technologies (such as the Resource Description Framework, RDF), is becoming an increasingly popular means to des ...[more]

PMID: 25182954

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Project description:Between 2012 and 2017, N = 2814 youth between the ages of 4 and 20 were in child protective services (CPS) custody in Hamilton County, Ohio, and placed in out-of-home care. Child welfare administrative records were extracted and linked to electronic health records for all encounters at Cincinnati Children's Hospital Medical Center, with n = 2787 (99.1%) of records successfully linked prior to de-identifying the data for research purposes. Child welfare administrative data fields in the dataset include demographics, dates of entry into and exit from protective custody and out-of-home care, reasons for entry into custody, dates of placement changes, reasons for placement changes, and types of placement (e.g., foster home, kinship home, group home, residential treatment, independent living). Electronic health records (EHR) data fields include demographics, all inpatient and outpatient encounters with medications, diagnoses, screening results, laboratory test results, flowsheet data, and problem list entries. Data have been coded to capture broader categories of health needs and encounter details, medications, and other health concerns. Due to the high representation of children in CPS custody and out-of-home care who are also represented in the EHR data, this dataset provides a comprehensive view of the medical needs and health concerns for school-aged children in CPS custody in an entire county. As a result, these data can be useful for understanding the emergence of global and specific health concerns, frequency of healthcare use, and placement stability for all youth in CPS custody in this community, accounting for variation due to other health and child welfare factors. These data are likely generalizable to other mid-sized urban communities where academic medical centers provide healthcare for children in CPS custody. De-identified data may be made available to other researchers with approved data transfer agreements between academic institutions in place.

Project description:BackgroundA useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable.MethodsWe analysed 13734 models from BioModels Database and the Physiome Model Repository. For each model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database.ResultsWe observed continuous updates in the majority of models. Surprisingly, even the early models are still being modified. We furthermore detected that many updates target annotations, which improves the information one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are available from GitHub https://github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at https://hub.docker.com/r/binfalse/bives-statsgenerator/ . The website https://most.bio.informatik.uni-rostock.de/ provides interactive access to model versions and their evolutionary statistics.ConclusionThe reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a model's provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the maintainers of model repositories to offer transparent model provenance to their users.

Project description:Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification.BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database.BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License.

Dataset Information

BioModels linked dataset.

Publications

BioModels linked dataset.

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