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.

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:0000284 large and small daughter nuclei output_of B FYPO:0001270 complete but unequal mitotic sister chromatid segregation
  • Meaning: If large and small daughter nuclei are formed, you can infer that complete but unequal mitotic sister chromatid segregation took place.
  • Search results: A query for FYPO:0001270 should retrieve genes annotated to FYPO:0000284 as well as genes annotated directly to FYPO:0001270.
  • 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.
  • 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.

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:0001009 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, the desired behavior is different, because a large-scale process or structure is normal only if all of its parts are normal. We therefore want to suppress the display of terms linked by has_part in the "normal phenotype" branch of FYPO (although this is not yet implemented as of this draft, 2015-03-11). See ​https://sourceforge.net/p/pombase/curation-tool/770/

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.
  • Note: As of this document draft (2015-03-11), there are asserted is_a links in FYPO that duplicate the has_part links for this and many similar terms. FYPO:0001490 is therefore not a good example for testing PomBase search or Canto display behavior at present.

• 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.

• Relation in FYPO: A FYPO:0001007 normal mitosis has_part B FYPO:0004396 normal mitotic spindle elongation
  • Meaning: If mitosis is normal, its parts, including spindle elongation, are normal.
  • Search results: A query for FYPO:0001007 should retrieve genes annotated directly to FYPO:0001007 and genes annotated to FYPO:0004396
  • Canto: At present (2015-03-11) term view for "FYPO:0001007 normal mitosis" should offer "FYPO:0004396 normal mitotic spindle elongation" as a suggestion. When SF #770 is done, this should change so that the "part" terms are not suggested on the "whole" term page.