Taxon constraints on developmental stages in composite

[fbastian]

The composite does not include the "in_taxon" relations of species-specific developmental stages. They are correctly present in the bridge ontologies from the google code repository.

[cmungall]

Can you give an example? I seem them here, e.g.

[Term]
id: HsapDv:0000003
name: Carnegie stage 01 (human)
namespace: human_developmental_stage
def: "Embryonic stage defined by a fertilized oocyte and presence of pronuclei." [http://embryology.med.unsw.edu.au/embryology/index.php?title=Carnegie_stage_table]
comment: Starts at day 1 post-fertilization, beginning of the first week.
synonym: "CS01" EXACT [EHDAA2:CS01]
xref: EHDAA2:CS01
xref: XUO:0000130
is_a: CS:0 ! Carnegie stage
is_a: UBERON:0000067 ! embryo stage part
is_a: UBERON:0000105 ! life cycle stage
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens
relationship: part_of HsapDv:0000002 ! embryonic human stage (human)
relationship: part_of UBERON:0000068 ! embryo stage
property_value: start_dpf "0.0" xsd:float
property_value: start_dpf "0.0" xsd:float

[fbastian]

Example:

[Term]
id: OanaDv:0000006
name: aged stage (platypus)
namespace: platypus_developmental_stage
def: "Mature stage that refers to a adult platypus which is over 10 years." [Bgee:curator]
comment: There is little information on the longevity of platypuses. They can live up to 12 years in the wild (see http://www.mspca.org/programs/wildlife-resources/species-information/about-platypuss.html) and one captive specimen was at least 22.6 years old when it died (see http://genomics.senescence.info/species/entry.php?species=Ornithorhynchus_anatinus). Over 10 years old is usually no more a breeding age.
is_a: UBERON:0000105 ! life cycle stage
relationship: immediately_preceded_by UBERON:0018241 ! prime adult stage
relationship: part_of UBERON:0000113 ! post-juvenile adult stage
property_value: start_mph "120.0" xsd:float

[cmungall]

ah, they were being added... but then stripped out as they were dangling. Made them non-dangling by ensuring all referenced taxa are in the ncbitaxon import

[fbastian]

If it helps, you can find all taxa used in Bgee, or in our homology annotations, along with their ancestors, at: http://svn.code.sf.net/p/bgee/code/trunk/external/uberon/taxon_ids_for_constraints.txt

[fbastian]

OK, so now, there are taxon constraints, but none of the species-specific stages are merged anymore. Their EquivalentClass axioms are correct, but I think they should be completely gone from the merged composite ontology, shouldn't they?
(This is similar to the bug described in issue #521 )

[cmungall]

You mean ones like this?

[Term]
id: RnorDv:0000000
intersection_of: UBERON:0000105 ! life cycle stage
intersection_of: part_of NCBITaxon:10116 ! Rattus norvegicus
relationship: only_in_taxon NCBITaxon:10116 ! Rattus norvegicus

Ultimately the whole xref based linking strategy is a hack and we're paying the price. This should all be fixed by a proper imports + linking by logical axioms approach as outlined in #529

[fbastian]

You just need to provide us with one proper example, we would handle the other ontologies.

[cmungall]

OK, to make each ssDv into a composite ssDv do something like this

owltools rnordv/rnordv.obo rnordv/rnordv-bridge-to-uberon.obo --merge-support-ontologies --reasoner elk --merge-species-ontology -s rat -t  NCBITaxon:10116 -q RO:0002087 -o -f obo rnordv/composite-rnordv

The resulting ontology can be combined with the main composite ontology as part of the build process.

The resulting ontology should look like the source ontology for the ss terms, and the generic terms should end up like this:

[Term]
id: UBERON:0000109
relationship: immediately_preceded_by RnorDv:0000004 {gci_filler="NCBITaxon:10116", gci_relation="part_of"} ! cleavage and blastula stage (rat)

[Term]
id: UBERON:0000110
relationship: immediately_preceded_by RnorDv:0000006 {gci_filler="NCBITaxon:10116", gci_relation="part_of"} ! primitive streak stage (rat)

This only needs done for non-MOD/human.

[gouttegd]

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