Author Archives: Allyson Lister

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

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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

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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

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Minimal annotation requested for all SWO classes

All SWO classes should have a minimum level of annotation. Some older classes do not yet have all required annotation, as the updating of these classes to the minimum requirements is ongoing. Requirements ID and label: These are basic requirements. … Continue reading

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Natural Language Definitions

External classes and SWO classes both have natural language definitions, but are handled slightly differently. Examples of usage of any class, whether internal or external, should not go in the definition itself, but placed in an example of usage annotation … Continue reading

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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

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maturity, purchase cost, license

Jon Ison recently requested four types of updates and new classes within SWO. Some parts of his requests are already in SWO, but all could do with a little look at again, to make sure we’ve got what he needs. … Continue reading

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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 ( was made obsolete. This class was asserted underneath algorithm and had no annotation or axiomisation. It was used … Continue reading

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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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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

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