Repository guide

Marta Costa edited this page Oct 26, 2015 · 4 revisions

The repository top level looks like this:

external_tools/ # same as fbbtdv/tools

fbcv_tools/ # fbcv specific scripts

src/

releases/

The structure below src and releases is essentially identical to that for the Drosophila anatomy and development repo (fbbtdv), so the guide for this repository is mostly applicable here.

The fbcv release process is rather more involved, as it requires knitting together elements in OBO and OWL. Currently src/trunk/ontologies contains:

catalog-v001.xml             # used to guide merge of imports to lethal_phase-edit.owl
fbcv-edit.obo                # The rest of fbcv - in OBO foemat
lethal_phase-edit.owl        # OWL file of lethal phase terms*
imports/
    FBdv_life_stage_export_filter.xml   # OE filter for generating slice of FBdv
    FBdv_life_stages.obo    #  OBO file generated by filter.
    FBdv_life_stages_with_reciprocal_timing_rel.obo # After scripted addn reciprocal timing rel
    timing_relations_occurrent_only.owl             # File of 
    FBdv_life_stages_with_reciprocal_timing_rel.owl # For import

* this structure is likely to change soon. The most sustainable balance is likely to involve maintenance of the dpo entirely in OWL, with the rest of fbcv remaining in OBO. The major drawback of this is that the auto-def system depends on parsing formal definitions in OBO, but that should probably be switched to a system specifying variable substitution in textual defs.

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