/gene/ json results need tweaking

[cmungall]

E.g. Note some of these will require further discussion

http://127.0.0.1:8282/gene/NCBIGene:388552.json

• add a JSON LD context
  • fields like 'summary' should be mapped in the context (what annotation property should we use @mellybelly ?)
• phenotype associations IDs aren't unique (Chris/Nicole)
• We have taxon and tax_xref. Should probably be unified
  • id should always be a CURIE
  • label should contain label
• diseases
  • some don't have labels
• interactions
  • ""affinity chromatography technology" etc should be mapped to a URI in our JSON LD context. @mellybelly which vocabulary?

General

• use null rather than "" for no data

[cmungall]

Note we have

    "source": {
        "id": "nlx_151671-2",
        "label": "ClinVar, via Office of Rare Diseases (9435)"
    }

And

"source": {

    "id": "nlx_151671-2",
    "label": "ClinVar, via NCBI curation"

}

The relationship between id and label is functional.

The via part should probably be modeled in the relationship between data and source (it is already?)

[mellybelly]

@cmungall I would use OBI or ERO for techniques for the interactions. We'll need these for expression and phentoyping in some cases too. We should pull in a slice of these two ontologies - assays and techniques. @mbrush can you help with this?

For summary, maybe one of these: http://purl.org/dc/terms/description http://www.w3.org/2004/02/skos/core#definition Probably prefer the former.

[mbrush]

@mellybelly the techniques in the BioGrid interaction data map to the PSI-MI 'ontology' (http://purl.obolibrary.org/obo/mi.owl), which is actually a pretty rich vocabulary. We should consider if we would use the IRIs from this ontology, or try to get terms into OBI/ERO with mappings to PSI-MI terms. As for any additional techniques needed, I can work to get them into OBI and/or ERO as needed.

BioGrid techniques are here: http://wiki.thebiogrid.org/doku.php/experimental_systems Earlier JIRA ticket about this is here: https://support.crbs.ucsd.edu/browse/NIF-11813

[kshefchek]

No longer relevant but we should create a new issue for exporting data as JSON.