wiki:RelationsAndTransitivity

Describing how annotation is propagated over relations in FYPO

Note: It isn't really correct to refer to ancestors and descendants for relations other than is_a and part_of.

output_of

Propagation: Annotations should propagate over output_of in the direction output A implies input B (A output_of B: all genes annotated to A should have annotation to B inferred).

Meaning: Phenotype A results from phenotype B. A mutation that causes phenotype A must also cause phenotype B. (B may or may not have other outcomes in addition to phenotype A. There isn't another way to get phenotype A.)

Search results: A query for B should retrieve both genes annotated directly to B and genes annotated to A. Genes annotated to A can therefore be found by searching directly for A or by searching for B. A query for A will not necessarily retrieve all genes annotated to B.

Canto: TBD (under discussion)

Examples:

  • Relation in FYPO: A FYPO:0000349 abnormal Golgi morphology output_of B FYPO:0000806 abnormal Golgi organization
    • Meaning: If Golgi morphology is abnormal, you can infer that abnormal Golgi organization took place. Golgi organization could be abnormal in ways that do or don't affect the morphology (e.g. timing), so you can't make an inference in the other direction.
    • Search results: A query for FYPO:0000806 should retrieve genes annotated to FYPO:0000349 as well as genes annotated directly to FYPO:0000806. A query for FYPO:0000349 should not retrieve genes annotated directly to FYPO:0000806.
    • Canto: TBD (under discussion)
  • Relation in FYPO: A FYPO:0002458 viable branched vegetative cell output_of B FYPO:0001972 abnormal cytokinetic cell separation resulting in septated cell
    • Meaning: If you see a viable branched vegetative cell, you can infer that abnormal cytokinetic cell separation resulting in septated cell took place.
    • Search results: A query for FYPO:0001972 should retrieve genes annotated to FYPO:0002458 as well as genes annotated directly to FYPO:0001972. A query for FYPO:0001972 should not retrieve genes annotated directly to FYPO:0002458.
    • Canto: TBD (under discussion)

has_output

Propagation: Annotations should propagate over has_output in the direction input A implies output B (A has_output B: all genes annotated to A should have annotation to B inferred).

Meaning: Phenotype A always leads to phenotype B. A mutation that causes phenotype A therefore also causes phenotype B. (There may or may not be another way to get phenotype B.)

Search results: A query for A should retrieve both genes annotated directly to A and genes annotated to B.

Canto: The term page for B should offer A among the suggested terms.

Examples:

  • Relation in FYPO: A FYPO:0002797 decreased protein degradation has_output B FYPO:0000836 increased protein level
    • Meaning: If protein degradation is decreased, the level of some protein will be increased. Genes annotated to FYPO:0002797 should have annotation to FYPO:0000836 inferred.
    • Search results: A query for FYPO:0000836 should retrieve all genes annotated directly to FYPO:0000836 and genes annotated to FYPO:0002797.
    • Canto: The term view for "FYPO:0000836 increased protein level" should offer "FYPO:0002797 decreased protein degradation" as a suggestion.
  • Relation in FYPO: A FYPO:0001009 abolished actomyosin contractile ring assembly has_output B FYPO:0001008 actomyosin contractile ring absent
    • Meaning: If contractile ring assembly is abolished, no contractile ring will be present. Genes annotated to FYPO:0001009 should have annotation to FYPO:0001008 inferred.
    • Search results: A query for FYPO:0001009 should retrieve genes annotated directly to FYPO:0001009 and genes annotated to FYPO:0001008
    • Canto: The term view for "FYPO:0001008 actomyosin contractile ring absent" should offer "FYPO:0001009 abolished actomyosin contractile ring assembly" as a suggestion.

has_part

Propagation: Annotations should propagate over has_part (A has_part B: all genes annotated to A should have annotation to B inferred).

Meaning: A mutation that causes phenotype A causes a phenotype with feature B.

Search results: A query for B should retrieve both genes annotated directly to B and genes annotated to A.

Canto: For abnormal phenotypes, the term page for B should offer A among the suggested terms. For normal phenotypes, a question arose about the desired behavior, because a large-scale process or structure is normal only if all of its parts are normal. We have removed has_part links between "normal" terms in FYPO (even though they would be biologically and ontologically correct) to get around this problem.

Note: This should ONLY be done for FYPO; GO annotations should (continue to) not be propagated over has_part in either direction.

Examples:

  • Relation in FYPO: A FYPO:0001490 inviable elongated vegetative cell has_part B FYPO:0000049 inviable cell
    • Meaning: A vegetative cell that is inviable and elongated is elongated.
    • Search results: A query for FYPO:0000049 should retrieve genes annotated directly to FYPO:0000049 (if any, but this term should not be used directly) and genes annotated to FYPO:0001490
    • Canto: The term view for "FYPO:0000049 inviable cell" should offer "FYPO:0001490 inviable elongated vegetative cell" as a suggestion.
  • Relation in FYPO: A FYPO:0004382 meroterically attached lagging mitotic chromosomes has_part B FYPO:0000228 lagging mitotic chromosomes
    • Meaning: A cell that has meroterically attached lagging mitotic chromosomes has lagging mitotic chromosomes.
    • Search results: A query for FYPO:0000228 should retrieve genes annotated directly to FYPO:0000228 and genes annotated to FYPO:0004382
    • Canto: The term view for "FYPO:0000228 lagging mitotic chromosomes" should offer "FYPO:0004382 meroterically attached lagging mitotic chromosomes" as a suggestion.
Last modified 4 years ago Last modified on Feb 22, 2017, 3:35:25 PM