Category Archives: ontology

Assorted modifications December 2014

This is a catch-all blog post outlining the final modifications I made to SWO prior to the 1.5 release. This will be the last bit of work I am doing (for the moment) on SWO as I have reached the … Continue reading

Posted in modeling, ontology | Leave a comment

Thoughts for the Future as of December 2014

I’m about to finish the current round of work on SWO, and there are a couple of issues outstanding that will need looking at by the next ontologist to work on SWO. I’ve also added these to the issue tracker. … Continue reading

Posted in modeling, ontology | Leave a comment

Definition and ID changes

I’ve recently been adding more natural language definitions. Mainly, the definitions were for higher level terms; while I am interested in adding definitions for terms such as “R”, the higher level ones are being completed first so as to provide … Continue reading

Posted in modeling, ontology | Tagged , | Leave a comment

Refactoring objective specification hierarchy

The refactoring of the objective specification hierarchy in SWO is part of a larger effort to merge the final distinct hierarchies in EDAM/SWO that can be usefully integrated. The EDAM operation hierarchy has been placed under information processing, and the … Continue reading

Posted in information processing | 1 Comment

A number of small changes to SWO

This week I did a number of small changes to SWO, and here is a summary of the changes: SBML Model (http://www.ebi.ac.uk/efo/swo/SWO_0000380) was made obsolete. This class was asserted underneath algorithm and had no annotation or axiomisation. It was used … Continue reading

Posted in ontology | Leave a comment

FACS ( fluorescence-activated cell sorter) obsoleted

FACS ( fluorescence-activated cell sorter) was a class which was a child of algorithm. This doesn’t make much sense as FACS itself is more likely to be either a machine or an experimental method, both of which are out of … Continue reading

Posted in data format specification, modeling, software | Leave a comment

Making SWO Satisfiable

Over the past few days I have been working to fix the approximately 170 unsatisfiable classes that were present in SWO. The vast majority of these were due to improper linking of software classes directly to a data format specification, … Continue reading

Posted in data format specification, modeling, ontology, software | Leave a comment

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

Posted in ontology | Tagged , , | 2 Comments

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

Posted in ontology | Tagged , , | 1 Comment

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

Posted in ontology | Tagged , | 1 Comment