Changes between Version 62 and Version 63 of RelationsAndTransitivity


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Timestamp:
Mar 13, 2015, 11:55:54 AM (6 years ago)
Author:
mah79
Comment:

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  • RelationsAndTransitivity

    v62 v63  
    99Meaning: Phenotype '''A''' results from phenotype '''B'''. A mutation that causes phenotype '''A''' must also cause phenotype '''B'''.
    1010
    11 Search results: A query for '''A''' should retrieve both genes annotated directly to '''A''' and genes annotated to '''B'''.
     11Search 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'''.
    1212
    1313Canto: The term page for '''B''' should offer '''A''' among the suggested terms.
    1414
    15 === Example: ===
     15=== Examples: ===
    1616 * Relation in FYPO: '''A''' FYPO:0000284 large and small daughter nuclei ''output_of'' '''B''' FYPO:0001270 complete but unequal mitotic sister chromatid segregation
    1717  * Meaning: If large and small daughter nuclei are formed, you can infer that complete but unequal mitotic sister chromatid segregation took place.
    18   * Search results: A query for FYPO:0000284 should retrieve genes annotated directly to FYPO:0000284 and genes annotated to FYPO:0001270.
     18  * Search results: A query for FYPO:0001270 should retrieve genes annotated to FYPO:0000284 as well as genes annotated directly to FYPO:0001270.
    1919  * Canto: The term view for "FYPO:0001270 complete but unequal mitotic sister chromatid segregation" should offer "FYPO:0000284 large and small daughter nuclei" as a suggestion.
    2020
    21 
    22 === Example: ===
    23  * Relation in FYPO: '''A'''  FYPO:0002458 viable branched vegetative cell
    24   ''output_of'' '''B''' FYPO:0001972 abnormal cytokinetic cell separation resulting in septated cell
    25   * Meaning:  viable branched vegetative cell, you can infer that abnormal cytokinetic cell separation resulting in septated cell took place.
    26   * Search results: A query for FYPO:0002458 should retrieve genes annotated directly to FYPO:0001972 and genes annotated to FYPO:*****.
    27   * Canto: The term view for "FYPO:0002458 " viable branched vegetative cell should offer "FYPO:0001972  abnormal cytokinetic cell separation resulting in septated cell" as a suggestion.
     21 * Relation in FYPO: '''A''' FYPO:0002458 viable branched vegetative cell
     22 ''output_of'' '''B''' FYPO:0001972 abnormal cytokinetic cell separation resulting in septated cell
     23  * Meaning: If you see a viable branched vegetative cell, you can infer that abnormal cytokinetic cell separation resulting in septated cell took place.
     24  * Search results: A query for FYPO:000 should retrieve genes annotated to FYPO:000 as well as genes annotated directly to FYPO:000.
     25  * Canto: The term view for "FYPO:0002458 viable branched vegetative cell" should offer "FYPO:0001972 abnormal cytokinetic cell separation resulting in septated cell" as a suggestion.
    2826
    2927== has_output ==
     
    3331Meaning: Phenotype '''A''' always leads to phenotype '''B'''. A mutation that causes phenotype '''A''' therefore also causes phenotype '''B'''.
    3432
    35 Search results: A query for '''B''' should retrieve both genes annotated directly to '''B''' and genes annotated to '''A'''.
     33Search results: A query for '''A''' should retrieve both genes annotated directly to '''A''' and genes annotated to '''B'''.
    3634
    3735Canto: The term page for '''B''' should offer '''A''' among the suggested terms.
     
    3937=== Examples: ===
    4038 * Relation in FYPO: '''A''' FYPO:0002797 decreased protein degradation ''has_output'' '''B''' FYPO:0000836 increased protein level
    41   * Meaning: If protein degradation is decreased, the level of some protein will be increased.
    42   * Search results: A query for FYPO:0000836 should retrieve genes annotated directly to FYPO:0000836 and genes annotated to FYPO:0002797.
     39  * 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.
     40  * Search results: A query for FYPO:0000836 should retrieve all genes annotated directly to FYPO:0000836 and genes annotated to FYPO:0002797.
    4341  * Canto: The term view for "FYPO:0000836 increased protein level" should offer "FYPO:0002797 decreased protein degradation" as a suggestion.
    4442
    4543 * Relation in FYPO: '''A''' FYPO:0001009 abolished actomyosin contractile ring assembly ''has_output'' '''B''' FYPO:0001008 actomyosin contractile ring absent
    46   * Meaning: If contractile ring assembly is abolished, no contractile ring will be present.
     44  * 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.
    4745  * Search results: A query for FYPO:0001009 should retrieve genes annotated directly to FYPO:0001009 and genes annotated to FYPO:0001008
    4846  * Canto: The term view for "FYPO:0001008 actomyosin contractile ring absent" should offer "FYPO:0001009 abolished actomyosin contractile ring assembly" as a suggestion.
     
    5553Meaning: A mutation that causes phenotype '''A''' causes a phenotype with feature '''B'''.
    5654
    57 Search results:  A query for '''B''' should retrieve both genes annotated directly to '''B''' and genes annotated to '''A'''.
     55Search results: A query for '''B''' should retrieve both genes annotated directly to '''B''' and genes annotated to '''A'''.
    5856
    5957Canto: 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/
     
    6159'''Note:''' This should ONLY be done for FYPO; GO annotations should (continue to) not be propagated over ''has_part'' in either direction.
    6260
    63 === Examples:  ===
     61=== Examples: ===
    6462 * Relation in FYPO: '''A''' FYPO:0001490 inviable elongated vegetative cell ''has_part'' '''B''' FYPO:0000049 inviable cell
    6563  * Meaning: A vegetative cell that is inviable and elongated is elongated.