Sequence Coordinates

• CURIE: gmeow:SequenceCoordinates
• IRI: https://blackcatinformatics.ca/gmeow/SequenceCoordinates
• Category: class
• Defined by: gmeow:slices/places
• Box roles: TBox role (What is this?)

Frame-relative coordinates on a biological sequence: a start position, an end position, and a strand orientation, all expressed relative to an explicit reference assembly (Principle 11).

Structure

Subclass of: gmeow:Entity, gufo:Object

Practical Pattern

Use gmeow:SequenceCoordinates as a specialized kind of gmeow:Entity, gufo:Object. Add statement metadata or a standpoint when the assertion needs provenance, confidence, or vantage.

Common Companion Terms

gmeow:Entity

External Equivalences

Equivalent or closely aligned targets: faldo

Linkages

Generated from the canonical mapping DSL. SSSOM files are the generated public interchange form for term equivalences.

Term Equivalences

Usage Advice

Use when

• Use for frame-relative coordinates on a biological sequence — start, end, and strand in an explicit reference assembly (FALDO alignment).

Avoid when

• Avoid coordinates without gmeow:inReferenceAssembly (the frame gate requires it) and avoid asserting liftover results as triples — that is solver-layer (Principle 12).

How to use

• Mint SequenceCoordinates, set gmeow:sequenceStart / gmeow:sequenceEnd / gmeow:sequenceStrand, and declare gmeow:inReferenceAssembly.

Examples

• ex:brca1Coords a gmeow:SequenceCoordinates; gmeow:sequenceStart 43044295; gmeow:sequenceEnd 43125483; gmeow:inReferenceAssembly gmeow:referenceFrameGRCh38.