TeMOwl

TeMOwl provides unified access to semantic data i.e. controlled vocabularies, terminologies, ontologies and knowledge resources.
TeMOwl provides unified access to semantic data i.e. controlled vocabularies, terminologies, ontologies and knowledge resources. It hides complexity of different semantic service providers including their various data formats. Further it aggregates (integrates, maps or alings) different information resources. Concepts, things of thought, are often defined within multiple resources, even though they refer to the same thing. The system tries to unify those. Technically the concept of semantic information is a considered a bounded-context (cf Domain-Driven-Design) within our architecture. The encapsulation of this broad and complex ecosystem is desired. TeMOwl protects other components consuming semantic information from changes and advances within the domain, and acts as an anti-corruption layer to them. TeMOwl is an API Service, that offers programmatic access to semantic information. API to retrieve and export Terminologies and their contents. Some API Calls expect and/or return a TerminologyID. This ID is configured by the System and depends on the system configuration. A list of all available Terminologies can be obtained via the API Call \terminologies. On top of this API different view components are and will be developed.

For developers
Type:
Helper tool, Software, Service
API Type:
REST under OpenAPI2 specification
Categories:
Ontology services
Applicability domain:
Ontology
Topic:
Identifier mapping, Information extraction
Targeted users:
Software Developers, Researchers
Relevant OpenRiskNet case study:
DataCure - Data curation and creation of pre-reasoned datasets and searching

Provided by:
Fraunhofer SCAI
Contact:
Dr. Marc Jacobs (Zimmermann) Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Tel.: +49 - 2241 - 14 - 2276 Fax.: +49 - 2241 - 14 - 2656 E-mail: Marc.Jacobs@scai.fraunhofer.de Internet: http://www.scai.fraunhofer.de
Login required:
Yes
Implementation status:
API documentation available (Swagger-OpenAPI v2), Containerised, Available as web service, Application programming interface available
Technology readiness level:
TRL 4 – technology validated in lab
Integration status:
Integration in progress
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Report
Case Study description - Data curation and creation of pre-reasoned datasets and searching [DataCure]
10 May 2019
Abstract:
DataCure establishes a process for data curation and annotation that makes use of APIs (eliminating the need for manual file sharing) and semantic annotations for a more systematic and reproducible data curation workflow. In this case study, users are provided with capabilities to allow access to different OpenRiskNet data sources and target specific entries in an automated fashion for the purpose of identifying data and metadata associated with a chemical or other endpoint of interest. The datasets can be curated using an OpenRiskNet services developed for this case study and re-submitted to the data source. Text mining facilities and workflows are also included for the purposes of data searching, extraction and annotation. A first step in this process was to define APIs and provide the semantic annotation for selected databases (e.g. diXa, FDA datasets, ToxCast and ChEMBL). During the preparation for these use cases, it became clear that the existing ontologies do not cover all requirements of the semantic interoperability layer. Therefore, ontology development and design of the annotation process as an online or an offline/preprocessing step form an ancillary part of this case study.
Additional materials:
Case Study report

Target audience: Risk assessors, Researchers, Data managers, Data owners, OpenRiskNet stakeholders, Data modellers, Bioinformaticians, Data providers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, UM, UoB, NTUA, Fraunhofer, IM
Report