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SciGraph / golr-loader

Convert SciGraph queries into json that can be loaded by Golr
Apache License 2.0
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Add a generic object loader #6

Open cmungall opened 9 years ago

cmungall commented 9 years ago

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 https://github.com/monarch-initiative/monarch-app/issues/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):

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 commented 9 years ago

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 commented 9 years ago

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

ccondit commented 9 years ago

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 notifications@github.com wrote:

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

— Reply to this email directly or view it on GitHub https://github.com/SciGraph/golr-loader/issues/6#issuecomment-110509214.

cmungall commented 9 years ago

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