Category Archives: modeling

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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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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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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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

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Links between data formats

This modification to SWO came out of a problem very similar to the one recently described for linking two pieces of software together. Rather than linking two pieces of software, here we would like to relate different data format specification … Continue reading

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Links between software

Until now, SWO had only one way of linking software to each other: via the defined class Software Suite, which has as its equivalent class has_part some software. This has the benefits of being straightforward and also quite useful for … Continue reading

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