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Output link predictions as SSSOM

Open caufieldjh opened this issue 3 years ago • 1 comments

The existing output for predicted links looks like this:

source_node	destination_node	score
ENSP00000451575	ENSP00000435370	0.9370759965425138
ENSP00000451575	ENSP00000435370	0.9370759965425138
ENSP00000451575	ENSP00000361636	0.9361207132288921
ENSP00000451575	ENSP00000361636	0.9361207132288921
ENSP00000451575	ENSP00000357879	0.9361171909487621

The corresponding columns in SSSOM are subject_id, object_id, and confidence. We can change the column heading and already be compliant.

It would be best to include some provenance as well, though - a string can go in additional columns, mapping_tool and mapping_tool_version. We have a few different things to keep track of here:

  • neat-ml version
  • grape version
  • contents of specific neat config So this may not capture the entirety of the mapping, but it can be a frame of reference.

caufieldjh avatar Jun 24 '22 17:06 caufieldjh

Could represent neat config full text as hash, then include in SSSOM output (don't forget docs on where to find the hash function)

caufieldjh avatar Sep 28 '22 16:09 caufieldjh