Add a generic object loader

[cmungall]

The current loader is association-centric; i.e. each document is a relationship between two objects. This is useful for the majority of queries.

It would also be useful to have an object-centric loader. (TBD: define yaml in monarch repo). E.g. for monarch-initiative/monarch-app#756 (one row per variant).

Here we would have only one document per object. Relationships would be loaded into a multi-valued field named after the property. This means we have a less generic schema than oban.

Example fields (core):

• id/curie
• label
• category
• type
• type_closure
• description/definition
• synomyms

This would be extended depending on the object type. E.g. for genomic features like variants we may have chrom, start, end (for simplicitly we would flatten to a single reference; for more complexity use cypher). For variants we may have a pathogenicity score. Etc.

@cmungall will define core schema, cc @nlwashington

Note that the mechanism here could be used to load ontology classes; but may as well just use owltools loader for this (cc @hdietze @kltm)

[nlwashington]

we already have basically built this for genomic features (which includes genes and variants), and it's already loaded into a special golr schema to include faldo positional information and properties. would this suffice? should we just add to this? @ccondit can you list what we have in that schema? good idea to add description and synonyms.

[nlwashington]

for genes, they also need strand (which we haven't put in yet).

[ccondit]

schema is here:
http://geoffrey.crbs.ucsd.edu:8080/solr/feature-location/admin/file/?contentType=text/xml;charset=utf-8&file=schema.xml

i actually didn't generate it using golr - just made it by hand.

On Tue, Jun 9, 2015 at 2:30 PM Nicole Washington [email protected]
wrote:

for genes, they also need strand (which we haven't put in yet).

—
Reply to this email directly or view it on GitHub
#6 (comment).

[cmungall]

I think features can remain a special case with special code for now,