Monthly Archives: May 2013

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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Bug with ‘swo2’ and ‘swo’ prefix fixed

While examining the code today, I noticed that swo_core had incorrect ontology prefixes ‘swo’ and ‘swo2’ set to ‘http://www.ebi.ac.uk/swo/http://www.ebi.ac.uk/efo/swo/’. This error was only present in an obsolete term SWO_0000399 (I must have introduced a bug when I made that term … Continue reading

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SWO imports edam.owl rather than edam sub-modules

When the original merge between SWO and EDAM occurred, EDAM in OWL was stored in separate modules: edam_core, edam_data, edam_obsoletes, edam_operations, and edam_topics. These have now been superceded by a single file to import, edam.owl. As such, all module files … Continue reading

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Bug with ‘data’ prefix fixed

While examining the code today, I noticed that there were both ‘data’ and ‘data2’ prefixes in swo_core.owl and swo_data.owl. For some reason, both swo_core and swo_data had incorrect ontology prefixes ‘data’ and ‘data2’ set to “http://www.ebi.ac.uk/swo/data/http://www.ebi.ac.uk/swo/data/”, which is a weird … Continue reading

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