LHDL developed and deployed the resource-sharing infrastructure required by the LHP community and by many other groups involved with biomedical research and practice. In particular, the project realised:
- PhysiomeSpace, the first professional data management & sharing service dedicated to biomedical data (now running in beta version).
- PSLoader, an application that runs on your PC and let you import virtually any biomedical dataset, organise your collection of data in space and time, and then upload it to the data management service (sign on the PhysiomeSpace service, download it for free).
- LhpBuilder, an application with a long list of specialised functions for processing and modelling neuro-musculoskeletal system data. The software will be soon commercially distributed by SCS srl.
- LhpSimul, a powerful architecture of execution web services for the distributed execution of data-intensive algorithms; once stored on PhysiomeSpace your data can processed in batch.
- LhpSWS, semantic web services with full semantic brokering capable of combining storage and execution services in complex data processing flows; currently hidden, it will provide the necessary scalability as the execution web services and the collection of data increase.
- LHDL ontologies, a collection of specialised ontologies to annotate the data and service resources available through PhysiomeSpace. All ontologies are freely downloadable in various formats.
- LHP Data Collection, the largest collection of experimental and modelling data on the descriptive and functional anatomy, and the multiscale biomechanics of the musculoskeletal system; this large collection is progressively being uploaded on PhysiomeSpace, from where it will be freely downloadable.
The client application: PSLoader
PSLoader is a desktop application that, after authentication, allows you to import biomedical data stored in a long list of digital formats (such as
DICOM3, STL, JPG, TIFF, ANSYS, and many more), and organise them in space using a hierarchical tree where the pose of one dataset is defined with respect to the parent one. The program provides also long list of interactive views, designed to visualise whatever combination of data you can have. Each dataset is annotated with a long list of metadata that are generated automatically. Additional metadata are available for you to be annotated, so as to provide a coherent set of concepts for the data stored in the digital library and the information framework for resources searching and retrieving.
The Service: PhysiomeSpace
Once you have created the data collection in PSLoader, with a single click the entire collection can be uploaded to the PhysiomeSpace servers, where it is stored in your private space. You can then access it from a simple web interface, with which you can add, remove, annotate data resources, and assign to each resource a different set of access permissions. By default all uploaded data are open only to the data owner, but at any time you can choose with whom to share each dataset.
Alternatively, other PhysiomeSpace users can search every dataset. If the data you need is available, but its owner did not share it with you, you can send a message requesting access. This gives the data owner the possibility to talk directly to anyone willing to download the data, before granting access.
PhysiomeSpace data resources can be searched and browsed in various ways relying on the fact that each data resource is annotated by a set of metadata defined according to the LHDL Master Ontology. In addition, depending on the type of data, you can choose additional sub-ontologies to add to the data special concepts that are specific to a certain data generation modality, and that are related to a chosen way to describe what the dataset "represents". While PSLoader automatically annotates a good part of the master ontology, the user is still requested to do some manual curation. Each data resource stored on PhysiomeSpace has a quality index that scores the resources in terms of how extensive is the annotation.
Once a dataset is shared with you, you can place it in your "basket", ready to be downloaded from PSLoader next time you connect to it. The dataset can then be exported in whatever format, and used with other specialised applications.
Usage terms and conditions, data reuse and privacy policy
During the beta testing phase, the service will be open as a totally free service. The data will be uploaded under complete responsibility of the users, and no guarantee will be provided whatsoever for the continuity of the service, for the storage, the integrity, and the preservation of the data stored. The confidentiality of the data will be protected only through the access limitations of the service, and in principle system administrations are in the condition to access all uploaded data.
For further information, please visit:
http://www.livinghuman.org
Related articles:
- FP6 Projects: LHDL
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