| | An example of reasoning over gene sequences, based on a program by CM | | You can run and change this example using the Internet Business Logic system at www.reengineeringllc.com | | the reasoning done to get answers can be quite complex, but you can get step-by-step English explanations | | The tables below contain data invented for test purposes only. Version 20040920 | | >>---------> Please send questions and comments to internet.business.logic@gmail.com <---------<< INTRON the feature some-item1 is an intron (an intron is defined as the space between 2 consecutive exons) some-exon1 followed by some-exon2 separated by a symbol - = that-item1 IPART_OF that-exon1 is an inferred part of some-item2 IPART_OF that-exon2 is an inferred part of that-item2 SIZE the size of the feature that-item1 is some-length --------------------------------------------------------------------------------------------------------- the feature that-item1 is an intron of size that-length and is a part of that-item2 TRANSPOSON the feature some-item1 is a transposon (a replicating element that inserts itself in DNA) INTRON the feature some-item2 is an intron (an intron is defined as the space between 2 consecutive exons) CONTAINS the feature that-item2 contains the feature that-item1 ---------------------------------------------------------------------------------------------------------- the intron that-item2 contains the transposon that-item1 INST_OF the feature some-item1 is an instance of the type variation UPSTREAM the feature some-item2 is an upstream region CONTAINS the feature that-item2 contains the feature that-item1 IPART_OF that-item2 is an inferred part of some-item3 ---------------------------------------------------------------------- VARIATION that-item1 is a variation that is upstream of that-item3 TERMINAL some-item is of type some-type starting some-start and ending some-end ---------------------------------------------------------------------------------------------------- PFEATURE that-item has the partonomy based feature that-type starting that-start and ending that-end NONTERMINAL some-item has the feature some-type OUTER_CHILDBEG that-item has an outer child begin some-start OUTER_CHILDEND that-item has an outer child end some-end ---------------------------------------------------------------------------------------------------- PFEATURE that-item has the partonomy based feature that-type starting that-start and ending that-end IPART_OF some-item2 is an inferred part of some-item1 TERMINAL that-item2 is of type some-type starting some-start and ending some-end that-start is less than or equal that-end ------------------------------------------------------------------------ CHILDBEG that-item1 starts at that-start and has orientation 1 IPART_OF some-item2 is an inferred part of some-item1 TERMINAL that-item2 is of type some-type starting some-start and ending some-end that-start is greater than that-end --------------------------------------------------------------------------------- CHILDBEG that-item1 starts at that-start and has orientation -1 CHILDBEG this-item starts at this-start and has orientation this-orientation ============================================================================ IPART_OF some-item2 is an inferred part of some-item1 TERMINAL that-item2 is of type some-type starting some-start and ending some-end that-start is less than or equal that-end ------------------------------------------------------------------------ CHILDEND that-item1 ends at that-end and has orientation 1 IPART_OF some-item2 is an inferred part of some-item1 TERMINAL that-item2 is of type some-type starting some-start and ending some-end that-start is greater than that-end ------------------------------------------------------------------------ CHILDEND that-item1 ends at that-end and has orientation -1 CHILDEND this-item ends at this-end and has orientation this-orientation ========================================================================== IPART_OF some-item1 is an inferred part of some-item min some-start : CHILDBEG that-item starts at some-start and has orientation 1 = some-min-start --------------------------------------------------------------------------------------------- OUTER_CHILDBEG that-item has an outer child begin that-min-start IPART_OF some-item1 is an inferred part of some-item max some-start : CHILDBEG that-item starts at some-start and has orientation -1 = some-min-start --------------------------------------------------------------------------------------------- OUTER_CHILDBEG that-item has an outer child begin that-min-start IPART_OF some-item1 is an inferred part of some-item max some-end : CHILDEND that-item ends at some-end and has orientation 1 = some-min-end --------------------------------------------------------------------------------------- OUTER_CHILDEND that-item has an outer child end that-min-end IPART_OF some-item1 is an inferred part of some-item min some-end : CHILDEND that-item ends at some-end and has orientation -1 = some-min-end ---------------------------------------------------------------------------------------- OUTER_CHILDEND that-item has an outer child end that-min-end BEG the start of the feature some-item1 is at some-position1 BEG the start of the feature some-item2 is at some-position2 that-item1 is not equal that-item2 that-position1 is less than or equal that-position2 END the end of the feature that-item2 is at some-position3 END the end of the feature that-item1 is at some-position4 that-position3 is less than or equal that-position4 --------------------------------------------------------------- CONTAINS the feature that-item1 contains the feature that-item2 LPOS the left end position of the feature some-item is some-left-position RPOS the right end position of the feature that-item is some-right-position some-point is a known start or end of a feature that-point is greater than or equal that-left-position that-point is less than or equal that-right-position ------------------------------------------------------------------------- POINT_INSIDE that-point is inside the feature that-item TERMINAL some-item is of type some-type starting some-point and ending some-end ------------------------------------------------------------------------------- that-point is a known start or end of a feature TERMINAL some-item is of type some-type starting some-start and ending some-point ------------------------------------------------------------------------------- that-point is a known start or end of a feature RANGE the range of the feature some-feature starts at some-position and ends at some-position2 -------------------------------------------------------------------------------------------------- BEG the start of the feature that-feature is at that-position RANGE the range of the feature some-feature starts at some-position1 and ends at some-position -------------------------------------------------------------------------------------------------- END the end of the feature that-feature is at that-position IPFEATURE the ipfeature some-feature is of type some-type starting at some-position1 ending at some-position2 ------------------------------------------------------------------------------------------------------------- RANGE the range of the feature that-feature starts at that-position1 and ends at that-position2 RANGE the range of the feature some-feature starts at some-position1 and ends at some-position2 that-position1 is less than that-position2 -------------------------------------------------------------------------------------------------- ORI the orientation of the feature that-feature is 1 RANGE the range of the feature some-feature starts at some-position1 and ends at some-position2 that-position1 is greater than that-position2 -------------------------------------------------------------------------------------------------- ORI the orientation of the feature that-feature is -1 RANGE the range of the feature some-feature starts at some-position and ends at that-position ------------------------------------------------------------------------------------------------- ORI the orientation of the feature that-feature is 0 ORI the orientation of the feature this-feature is this-orientation =================================================================== RANGE the range of the feature some-feature starts at some-position1 and ends at some-position2 that-position1 is less than that-position2 that-position2 - that-position1 = some-length -------------------------------------------------------------------------------------------------- SIZE the size of the feature that-feature is that-length RANGE the range of the feature some-feature starts at some-position1 and ends at some-position2 that-position1 is greater than that-position2 that-position1 - that-position2 = some-length -------------------------------------------------------------------------------------------------- SIZE the size of the feature that-feature is that-length RANGE the range of the feature some-feature starts at some-position and ends at that-position -------------------------------------------------------------------------------------------------- SIZE the size of the feature that-feature is 0 BEG the start of the feature some-feature is at some-position ORI the orientation of the feature that-feature is 1 ----------------------------------------------------------------------- LPOS the left end position of the feature that-feature is that-position END the end of the feature some-feature is at some-position ORI the orientation of the feature that-feature is -1 ----------------------------------------------------------------------- LPOS the left end position of the feature that-feature is that-position BEG the start of the feature some-feature is at some-position ORI the orientation of the feature that-feature is -1 ------------------------------------------------------------------------ RPOS the right end position of the feature that-feature is that-position END the end of the feature some-feature is at some-position ORI the orientation of the feature that-feature is 1 ------------------------------------------------------------------------ RPOS the right end position of the feature that-feature is that-position IPFEATURE the ipfeature some-feature is of type some-type starting at some-position1 ending at some-position2 ------------------------------------------------------------------------------------------------------------ FTYPE the ftype of the feature that-feature is that-type FTYPE the ftype of the feature some-feature is some-subtype in the ontology, that-subtype is a subclass of some-type --------------------------------------------------------------------- INST_OF the feature that-feature is an instance of the type that-type FTYPE the ftype of the feature some-feature is some-upstream-item upstream followed by some-item separated by a symbol - = that-upstream-item in the ontology, upstream is a subclass of some-type --------------------------------------------------------------------- INST_OF the feature that-feature is an instance of the type that-type INST_OF the feature some-item is an instance of the type upstream -------------------------------------------------------------------- UPSTREAM the feature that-item is an upstream region some-item1 is an immediate part of some-item2 --------------------------------------------- IPART_OF that-item1 is an inferred part of that-item2 some-item1 is a part of some-item2 with rank some-rank ----------------------------------------------------- IPART_OF that-item1 is an inferred part of that-item2 some-exon1 followed by some-exon2 separated by a symbol - = some-intron that-exon1 is a part of some-transcript with rank some-rank ------------------------------------------------------------------------ IPART_OF that-intron is an inferred part of that-transcript upstream followed by that-item separated by a symbol - = some-upstream-ID -------------------------------------------------------------------------- IPART_OF that-upstream-ID is an inferred part of that-item INST_OF the feature some-item is an instance of the type intron -------------------------------------------------------------------------------------------------------- INTRON the feature that-item is an intron (an intron is defined as the space between 2 consecutive exons) INST_OF the feature some-item is an instance of the type upstream --------------------------------------------------------------------------------------- UPSTREAM the feature that-item is an upstream (an upstream region is left of a feature) IFEATURE the ifeature some-feature is of type some-type starting at some-position1 ending at some-position2 ----------------------------------------------------------------------------------------------------------- IPFEATURE the ipfeature that-feature is of type that-type starting at that-position1 ending at that-position2 PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 -------------------------------------------------------------------------------------------------------------- IPFEATURE the ipfeature that-item is of type that-type starting at that-position1 ending at that-position2 EXON the feature some-exon1 is an exon (a transcribed part of a transcript) EXON the feature some-exon2 is an exon (a transcribed part of a transcript) that-exon1 and that-exon2 are consecutive siblings END the end of the feature that-exon1 is at some-position1 BEG the start of the feature that-exon2 is at some-position2 that-exon1 followed by that-exon2 separated by a symbol - = some-exon1-exon2 ----------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-exon1-exon2 is of type intron starting at that-position1 ending at that-position2 PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 INST_OF the feature that-item is an instance of the type variation SIZE the size of the feature that-item is 1 ----------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type snp starting at that-position1 ending at that-position2 PFEATURE some-item has the partonomy based feature upstream starting some-feature-end and ending some-end ORI the orientation of the feature that-item is some-orientation 1000 * that-orientation = some-1000*orientation that-feature-end - that-1000*orientation = some-begin upstream followed by that-item separated by a symbol - = some-upstream-ID ------------------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type that-upstream-ID starting at that-begin ending at that-feature-end PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 INST_OF the feature that-item is an instance of the type gene some-transcript is an immediate part of that-item INST_OF the feature that-transcript is an instance of the type mRNA ----------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type pcgene starting at that-position1 ending at that-position2 | Adrian added the following rule. Is it correct ? If so, should the above rule be dropped ? PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 INST_OF the feature that-item is an instance of the type gene that-item is a part of some-transcript with rank some-rank INST_OF the feature that-transcript is an instance of the type mRNA ----------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type pcgene starting at that-position1 ending at that-position2 PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 INST_OF the feature that-item is an instance of the type mRNA some-translation1 is an immediate part of that-item INST_OF the feature that-translation1 is an instance of the type translation some-translation2 is an immediate part of that-item INST_OF the feature that-translation2 is an instance of the type translation that-translation1 is not equal that-translation2 ----------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type dicistronic_mRNA starting at that-position1 ending at that-position2 PFEATURE some-item has the partonomy based feature some-type starting some-position1 and ending some-position2 INST_OF the feature that-item is an instance of the type gene some-transcript is an immediate part of that-item INST_OF the feature that-transcript is an instance of the type dicistronic_mRNA --------------------------------------------------------------------------------------------------------------- IFEATURE the ifeature that-item is of type dicistronic_gene starting at that-position1 ending at that-position2 INST_OF the feature some-item is an instance of the type dicistronic_gene ------------------------------------------------------------------------- dicistronic_gene the feature that-item is of type dicistronic_gene INST_OF the feature some-item is an instance of the type dicistronic_mRNA ------------------------------------------------------------------------------------------------------------------ dicistronic_mRNA the feature that-item is of type dicistronic_mRNA (a transcript that codes for >1 proteins) INST_OF the feature some-item is an instance of the type pcgene ------------------------------------------------------------------------------------------------------------------ PCGENE the feature that-item is a pcgene (a protein coding gene is a gene where at least one of the parts is mRNA) IFEATURE the ifeature this-feature is of type this-type starting at this-position1 ending at this-position2 =============================================================================================================== NONTERMINAL this-item has the feature this-type =============================================== 1 gene 1a mRNA 1b mRNA 4 gene 4a mRNA 5 gene 5a noncodingRNA 6 gene 6a mRNA 8 gene 8a mRNA 9 gene 9a mRNA TERMINAL this-item is of type this-type starting this-start and ending this-end =============================================================================== 1p1 translation 800 4400 1:1 exon 500 1000 1:2 exon 2000 4500 1:3 exon 2000 5000 2 transposon 1200 1300 3 variation 250 251 4p1 translation 21700 51020 4:1 exon 21700 22140 4:2 exon 48900 51020 5:1 exon 51020 48900 5:2 exon 22140 21700 6p1 translation 83500 84100 6:1 exon 83400 84171 7 predicted_gene 60000 63000 8:1 exon 90000 910000 8p1 translation 90100 90400 8p2 translation 90500 90800 9:1 exon 94000 96000 9:2 exon 97000 98000 9p1 translation 94100 95000 some-item1 is an immediate part of some-upper-item some-item2 is an immediate part of that-upper-item that-item1 comes before that-item2 in a lexical ordering -------------------------------------------------------- that-item1 and that-item2 are siblings some-item1 is less than some-item2 -------------------------------------------------------- that-item1 comes before that-item2 in a lexical ordering some-item1 is a part of some-item with rank some-rank1 some-item2 is a part of that-item with rank some-rank2 that-rank2 - that-rank1 = 1 ------------------------------------------------------- that-item1 and that-item2 are consecutive siblings INST_OF the feature some-feature is an instance of the type exon ---------------------------------------------------------------------------- EXON the feature that-feature is an exon (a transcribed part of a transcript) INST_OF the feature some-feature is an instance of the type transposon ------------------------------------------------------------------------------------------------------ TRANSPOSON the feature that-feature is a transposon (a replicating element that inserts itself in DNA) this-lower-item is an immediate part of this-upper-item ======================================================== 1a 1 1b 1 1p1 1a 1p1 1b 4a 4 5a 5 6a 6 6p1 6a 8a 8 8p1 8a 8p2 8a 9a 9 this-lower-item is a part of this-upper-item with rank this-rank ================================================================ 1:1 1a 1 1:1 1b 1 1:2 1b 2 1:3 1a 2 4:1 4a 1 4:2 4a 2 5:1 5a 1 5:2 5a 2 6:1 6a 1 8:1 8a 1 9:1 9a 1 9:2 9a 2 in the ontology, this-subclass is a subclass of this-class ( this-comment ) ====================================================================================== RNA transcript no comment mRNA RNA no comment noncodingRNA RNA no comment pcgene gene protein-coding gene ncgene gene non protein-coding gene exon gene Adrian added this for testing intron gene Adrian added this for testing ??? variation Adrian added this for testing upstream ??? Adrian added this for testing transposon ??? Adrian added this for testing in the ontology, some-subclass is a subclass of some-class ( some-comment ) --------------------------------------------------------------------------- in the ontology, that-subclass is a subclass of that-class some-class is in the ontology ------------------------------------------------------- in the ontology, that-class is a subclass of that-class in the ontology, some-class1 is a subclass of some-class2 in the ontology, that-class2 is a subclass of some-class3 -------------------------------------------------------------- in the ontology, that-class1 is a subclass of that-class3 in the ontology, some-subclass is a subclass of some-class ---------------------------------------------------------- that-subclass is in the ontology in the ontology, some-subclass is a subclass of some-class ---------------------------------------------------------- that-class is in the ontology