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 scope of SWO. To fix this, I looked at where it was used, which was only in one location: within the prada software axiom list. To fix this situation, a number of classes were touched.
- FACS data was given a definition and associated annotations.
- There was one leftover reference within swo_data.owl to edamontology.org#comment. This was removed and replaced with what the rest of the ontology uses, which is rdf:comment.
- FACS ( fluorescence-activated cell sorter) is only used for the prada software class, and there it is used incorrectly. FACS is an experimental method, not an algorithm. This class (http://www.ebi.ac.uk/efo/swo/SWO_0000139) has therefore been obsoleted in favor of using the data and data format specification changes described here.
- A new pair of classes, Data File Standard for Flow Cytometry and its child FCS3.0 were created with appropriate annotations. These were created as children of ASCII format. As part of this creation:
- references to has version (http://www.ebi.ac.uk/swo/SWO_0004000) and the class version name or number (http://purl.obolibrary.org/obo/IAO_0000129) were added.
- An individual of name FCS Data Standard Version 3.0 was created.
- FCS (http://www.ebi.ac.uk/efo/swo/SWO_0000144) was obsoleted as it was a generic term where there was no way of knowing for sure which format it was – or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class.
- The new axiom for prada (to replace the incorrect reference to algorithm and to expand upon already existing links to data) are:
'has specified data input' some ('FACS data' and ('has format specification' some FCS3.0) and ('has format specification' only FCS3.0)),