obographs

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Implement ID/CURIE<->URI expansion and contraction

5

We want to be able to expand and contract URIs using either a simple yaml curie map or a JSON-LD file. The latter provides certain advantages such as being a...

cmungall

Property node missed for http://xmlns.com/foaf/0.1/depicts

1

This OWL file has the property: " http://xmlns.com/foaf/0.1/depicts" http://purl.obolibrary.org/obo/fbbt/vfb/vfb_ext.owl But it appears to be missing from the JSON rolled by owltools: complete node set: ~~~~~~.py {'id': 'http://purl.obolibrary.org/obo/OBI_0000312', 'lbl': 'is_specified_output_of', 'type':...

dosumis

ncbitaxon_import.owl missing some classes

1

The following classes are missing from ncbitaxon_import.owl: NCBITaxon_147554 NCBITaxon_27896 NCBITaxon_28009 NCBITaxon_3312 NCBITaxon_3378 NCBITaxon_4895 NCBITaxon_4896 NCBITaxon_4930 NCBITaxon_4932 NCBITaxon_6237 NCBITaxon_8782 They appear to be classes that are referenced *only* in never_in_taxon constraints....

tonysawfordebi

From #22

cmungall

References associated with taxon constraints are missing from go-plus.json

3

References that are associated with taxon constraints, and which are visible in go-plus.obo, are not finding their way into go-plus.json A couple of examples from go-plus.obo: [Term] id: GO:0045271 name:...

tonysawfordebi

Add some way to distinguish object properties from annotation properties

3

There is no obvious way to distinguish between OPs and APs in the current version of OBO graphs. ```js {'id': 'http://purl.obolibrary.org/obo/fbbt#IUPAC_NAME', 'lbl': 'IUPAC NAME', 'type': 'PROPERTY'}, {'id': 'http://purl.obolibrary.org/obo/RO_0002004', 'lbl': 'tracheates',...

dosumis

obographs 2 OWL conversion

4

Conversion from obo-graph to OWL would be very useful e.g. for a pure Python implementation of DOS-DPs (limited to suitable simple design patterns), or a simple, OWL-API independent OWL writer...

dosumis

GCIs in obographs

1

Any suggestions for how one might encode simple GCIs (e.g. R1 some C1 SubClassOf C2; R1 some C1 SubClassOf R2 some C2) in OBOgraphs? Or is this a step too...

dosumis

Define behavior when punning is used

2

Current spec assumes no punning. E.g. the type field of a node is one of INDIVIDUAL, CLASS, ... Should we explicitly forbid punning or explicitly say behavior is undefined?

cmungall

Support for individuals

6

Is it legal in obographs to include individuals in the 'existential graph'? Could just have edge translation to OWL depend on owl entity type of object and subject: C:C SubClassOf...

dosumis