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DifferencesWithOldRO
The original relations ontology (ID space "OBO_REL") was a direct translation of the 2005 RO paper into OBO format. It suffered a number of problems, such as lack of clarity in the semantics of class level relations.
Here we use "RO" to refer to the obo/owl version of the current ontology, and "OBO_REL" to refer to the original 2005 version.
Note that many of the differences described here were originally announced on the RO and BFO lists
OBO_REL used identifiers of the form "OBO_REL:part_of", which were translated to URIs of the form http://obofoundry.org/ro#part_of
RO follows the obofoundry ID policy and uses numeric identifiers with corresponding IRIs of the form http://purl.obolibrary.org/obo/RO_nnnnnnn
See Identifiers for more details
We have ceded some core relations to BFO, where they are generic and are required to define BFO classes.
Examples:
http://purl.obolibrary.org/obo/BFO_0000050 is part of (replaces OBO_REL:part_of)
These relations were intended to be part of BFO1.2 -- however, this version of BFO was never formally released, and BFO2 instead used temporalized relations. Relations such as BFO:0000050 are now managed within RO, rather than BFO, despite the ID.
See ROAndBFO for more information.
The original OBO_REL followed the Genome Biology paper in defining relations as class-level. However, these class-level relations caused a lot of confusion and are not really required - in OWL (and in OBO-Format, which is a subset of OWL) we have instance level relationships that are quantified (e.g. finger SubClassOf part_of some hand).
RO makes a clean break with OBO_REL, and abandons class level relations.
For a discussion of how RO aligns with OBO_REL in terms of temporal quantification, see ROAndTime.
An exception is made for a small number of "macro" relations such as RO_0002161 (never in taxon), which is modeled as an annotation property and expanded to a more complex OWL statement using an OWL macro expansion engine. See the OWL macros section of the obo format spec for more details
For OBO_REL, the source was obo-format, and OWL was derived from this. There was an experiment to use Common Logic Interchange Format as the source, but this was abandoned.
The source version of RO is in OWL, and a subset of this is translated to generate ro.obo
OBO_REL followed the Genome Biology paper in declaring relations "instance_of" and "is_a". These have been eliminated in RO, because they are redundant with existing OWL predicates (class assertion and subClassOf, respectively). All relations in RO now correspond to OWL properties.
There has been some discussion of bringing back these builtins in a special-purpose edition of the .obo file, see this ticket for more details.