[Obo-format] OBO Format questions

[Dilvan M. <di...@st...>]

   Hi,

   I would like to clarify some OBO 1.0 format questions, they are
also applicable to the OBO format 1.2:

1- There is a tag to represent the is_a hierarchy (is_a:), but also
one can also create a relation is_a, using the relationship: tag. This
syntax is confusing. But my actual question is what should happen if
someone declares a is_a relationship (using the relationship: tag) and
them, in its [Typedef] stanza, declares this relationship to be
is_cyclic: true or is_transitive: false?

2- What happens when, for a Term, the same synonym is declared twice?
Shouldn't this be interpreted as a parser error?

3- Can a relation be declared obsolete (the syntax allows it)? If so,
how to interpret it?

4- Two Dbxref like: DiffAvg:"572.74" and DiffAvg: "572.74" (from the
psi-mod.obo) are flagged by obo-diff as different (the second has an
extra space after :). Is that the intended behavior?

5- The fly_development.obo ontology has a term with a develops_from
relation with an obsolete term (FBdv:00005317). Shouldn't it be
flagged by the OBO edit during parsing? Is it a bug?

6- There are lot of relations (specially in the OBO 1.2 format) that
do not declare defaults (for the case when the tag doesn't appear for
a term). Such as is_cyclic: is_transitive: is_symmetric: . What should
be the default assumption for each of them (including the OBO 1.2
format ones)?

   If this information is available or should be discussed elsewhere,
please point me to the appropriate resource. Thanks in advance for any
help.
-- 
Dilvan de Abreu Moreira, Ph.D.     di...@st...
SMI-Stanford Phone: 650-725 6236     http://java.icmc.usp.br
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