spec: add upset-basic specification

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New Specification: upset-basic

Related to #5250

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specification.md

upset-basic: UpSet Plot for Multi-Set Intersection Analysis

Description

An UpSet plot visualizes intersections of multiple sets using a matrix-based layout that scales far better than Venn diagrams beyond 3 sets. A horizontal bar chart shows individual set sizes, a dot-matrix indicates which sets participate in each intersection, and a vertical bar chart above shows the intersection cardinality. This is the modern standard for set intersection analysis, making complex overlaps between many sets immediately readable.

Applications

• Comparing gene sets from multiple genomic experiments to identify shared and unique biological pathways
• Analyzing feature overlap across machine learning model versions to understand model evolution
• Visualizing user segments across multiple marketing criteria to find high-value audience intersections
• Showing bug categories that overlap across software modules to prioritize cross-cutting issues

Data

• element (str) — unique item identifier
• sets (list[str]) — which sets this element belongs to (each element can belong to one or more sets)
• Size: 4–15 sets, 100–10,000 elements
• Example: genomic experiment results where each gene (element) belongs to one or more differential expression sets

Notes

• Intersections should be sorted by size (descending) by default, with degree-based sorting as an alternative
• Connected dots in the matrix show which sets form each intersection; unconnected dots indicate non-membership
• Horizontal bars on the left show individual set sizes (total members per set)
• Vertical bars on top show intersection cardinality (number of elements in each specific intersection)
• Matrix rows represent sets; columns represent unique intersections
• Lines connecting dots in the same column should be clearly visible to indicate set combinations
• Consider using color or shading to distinguish intersection degree (number of sets involved)
• Superior to Venn diagrams for more than 3 sets; complements the existing venn-basic specification

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