Tag Archives: edam

Term Scope for EDAM and SWO

Recently on the SWORD mailing list, there has been a discussion as to which new terms should be added to the EDAM portion of the ontology, and which belong in the scope of SWO. For the record (and posterity), here … Continue reading

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SWO-EDAM Merge: Issues Arising from Data Merge

In the longer term, Parameter and Report may be roles rather than classes within Data. For now, however, they remain in their original location within SWO. Additionally, in the near-to-medium future, the Core data class may become obsolete, and all … Continue reading

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SWO-EDAM Merge: merging data hierarchies

There are fewer classes within SWO data hierarchy compared with the SWO data format specification hierarchy, and therefore this merge step was simpler. A list of issues arising is available in a separate post. The following changes were made: Made … Continue reading

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SWO-EDAM Merge: General issues arising

This post will be updated as work on the SWO-EDAM merge progresses, and describes issues which need to be addressed but which don’t belong to any one particular hierarchy. Some of the points raised here are just my opinion, and … Continue reading

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SWO-EDAM Merge: Issues arising from Format Merge

Until the EDAM OWL files become the master versions of the ontology, it is not useful to obsolete EDAM classes and replace them with the appropriate SWO classes. Instead, a number of equivalence statements were used. Once the EDAM OWL … Continue reading

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SWO-EDAM Merge: Merging format hierarchies

Import of EDAM:Format into SWO:Data format specification The following steps have been performed and committed within the development subdirectory of the SWO subversion repository. This merging is not complete (due to the EDAM OWL file not being the master version … Continue reading

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SWO-EDAM Merge: Modifying EDAM in OWL

While on the whole the conversion process between OBO and OWL (in either direction) is relatively good these days using Protege 4.1 (which makes use of the OWLAPI underneath), there were some manual changes required. This post describes all changes … Continue reading

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SWO-EDAM Merge: Converting EDAM from OBO to OWL

The majority of the work described in this post was performed by Jon Ison. One-time changes made in the EDAM OBO file Various subsets of terms within EDAM were defined using the http://edamontology.org#subsetannotation type. The following subsets are defined (with … Continue reading

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SWO-EDAM Merge: Overview

We are currently in the process of merging the SWO and EDAM ontologies. While some of the hierarchies (e.g. SWO data format specification with EDAM Format and SWO data with EDAM Data) are relatively straightforward to merge, others (e.g. the … Continue reading

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