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Overview
A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using Protégé.
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The guides and instructions in the pages below will help you understand the ontology structure, configure Protégé, edit the ontology, and add annotations to drive the user interfaces.
Public Releases
- Starting with version 1.10.2.1, new releases of the eagle-i Integrated Semantic Framework modules are available here: https://www.eagle-i.net/ero/
- Historical releases have been archived here: https://open.med.harvard.
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- edu/svn/ero/
- The full VIVO-ISF Ontology is available on GitHub: https://github.com/vivo-isf/vivo-isf-ontology
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Term Tracker
Ontology term requests are kept in the VIVO-ISF Ontology term tracker on GitHub: https://github.com/vivo-isf/vivo-isf-ontology/issues.
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| Term request | Example |
|---|---|
| A name/label for the proposed term | Four-terminal resistance sensor |
| A textual definition (with source) for the proposed term | "Four-terminal resistance sensors are electrical impedance measuring instruments that use separate pairs of current-carrying and voltage-sensing electrodes to make accurate measurements that can be used to compute a material's electrical resistance." Taken from: http://en.wikipedia.org/wiki/Four-terminal_sensing |
| An example of usage for the proposed term | Measuring the inherent (per square) resistance of doped silicon. |
| The desired asserted SuperClass in the ERO hierarchy or Reference Branch | Instrument, Biological process, Disease, Human studies, Instrument, Organism, Reagent, Software, Technique, Organization or any sub-classes. Consult the Ontology Browser for a list of possible SuperClasses. |
| Any additional info, synonyms, etc. | AKA - 4T sensors, 4-wire sensor, or 4-point probe |
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Documentation
A guide for editing the ISF-based eagle-i ontology is being drafted as a Google doc at https://docs.google.com/a/essaid.com/document/d/1Radat4PqKJuWktxJ3RgxWp_osfW07RZ6-EBVLG8YAsw/edit?usp=sharing
This documentation is still undergoing final review and will be transferred to this site soon.
Publications
Torniai C, Brush M, Vasilevsky N, Segerdell E, Haendel M, Shaffer C, Johnson T, Corday K. Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned , International Conference of Biomedical Ontologies (ICBO) 2011. Download the paper Download the presentation
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Overview
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