Hello all,
I'm experimenting with the SKG features available through json.facet API in
solr 8.11 to discover semantic relations between medical text pre-annotated
with NER algorithms.
I store the NER annotations, annotation id, span ecc in separate solr fields,
to keep text clean.
The first results looks promising but I found a behaviour that surprises me.
To give a bit of context I'm looking for covid-related papers with a standard
query (q parameter)
Then I set my foreground query to be a set of keywords in OR related to the
mithochondria, and the background query is set to *.
Then the json.facet parameters are like
"json.facet": {
"gene":{
"type": "terms",
"field": "abstracts_gene_pubtator_annotation_ids",
"sort": { "r1": "desc" },
"limit": 3,
"facet": {
"r1" : "relatedness($fore,$back)"
}
}
}
This should give gene stored in abstracts_gene_pubtator_annotation_ids that are
more likely to occur in mitochondrial papers.
Running a test query gives me this surprising result
...
"gene": {
"buckets": [
{
"val": "3091",
"count": 1,
"rtitles1": {
"relatedness": 0.55649,
"foreground_popularity": 0,
"background_popularity": 0.00018
}
},
...
or for a similar query even bigger relatedness values
...
"buckets": [
{
"val": "MESH:D028361",
"count": 1,
"rabstract_conclusions0": {
"relatedness": 0.91506,
"foreground_popularity": 5e-05,
"background_popularity": 5e-05
},
...
But If I recall the z-score formula
countFG("3091") - totalFG * probBG
------------------------------------------------
sqrt( totalFG * (1-probBG)*probBG )
and set countFG("3091") to 1 this means that the relatedness should be negative
(or at most 0) if totalFG * probBG >=1, while here I find a quite positive
relatedness.
Maybe this can be controlled with min_popularity, but I don't understand how to
use it in conjunction with type=terms and
field=abstracts_gene_pubtator_annotation_ids
Can you please tell me the correct syntax, and if my reasoning is correct?
Thank you
Danilo
Danilo Tomasoni
Fondazione The Microsoft Research - University of Trento Centre for
Computational and Systems Biology (COSBI)
Piazza Manifattura 1, 38068 Rovereto (TN), Italy
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