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Expand entity support: complexes & families #130
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Entity typeWhen it comes to integrating with factoid model, it's important to assign some sort of 'type' to a Famplex entity. To attempt this, will we use the Famplex provided
A first attempt is to follow a simple heuristic: A Example below for "AMPK": |
Turning this into an itemized issue, to stage the changes and reduce risk (in particular, changes in factoid):
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Summary
Goal: Extend grounding support for complexes & families.
Why: Second largest class of Biofactoid entity grounding errors. Ubiquitous in the literature (protein gene - 56%; Family/complex - 17.7%). Been tabled for years.
How: Re-use FamPlex, a curated resource for disambiguation of (human) complexes and families.
Background
It is common for researchers to refer to complexes and members of a family. These authors may not be concerned or possibly even aware of the precise individual component(s) of a complex or member(s) of a family to which they refer, but rather wish to convey information about a general class of function or structure. The result is that authors name entities using these broader terms, with the implicit assumption that there are individual components/members.
Example: NF-κB
There are five proteins in the mammalian NF-κB family
Various NF-κB complexes
In Biofactoid
Complexes and families represent the second largest class of errors in entity grounding. See PathwayCommons/factoid#1003 (comment).
Example
NF-κB-p62-NRF2 survival signaling is associated with high ROR1 expression in chronic lymphocytic leukemia. Sanchez-Lopez et al. Cell Death Differ. 2020 Jul;27(7):2206-2216
Phosphorylated RB Promotes Cancer Immunity by Inhibiting NF-κB Activation and PD-L1 Expression. Mol Cell
. 2019 Jan 3;73(1):22-35.e6.
Implementation
FamPlex is a resource that helps improve named entity recognition, grounding, and relationship resolution. The repository provides several comma-separated files that can be used to populate our grounding resource (Table I).
Table I. Relationship between FamPlex data and ground-search fields
Top entities referenced
Caveats
References
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