=====Checking all inverse links==== [Checking inverses under class Evidence] [Checking inverses under class EC-BOOKKEEPING] [Checking inverses under class Compound-Mixtures] [Checking inverses under class CCO] [Checking inverses under class Paralogous-Gene-Groups] [Checking inverses under class Publications] [Checking inverses under class Organisms] [Checking inverses under class KB-DESCRIPTOR] [Checking inverses under class Gene-Ontology-Terms] [Checking inverses under class Regulation] [Checking inverses under class Generalized-Reactions] Removing bad reference to non-existent frame CPD-12424 in slot LEFT in frame RXN-11451 Removing bad reference to non-existent frame CPD-12425 in slot RIGHT in frame RXN-11451 [Checking inverses under class People] [Checking inverses under class Organizations] [Checking inverses under class Polymer-Segments] [Checking inverses under class Enzymatic-Reactions] [Checking inverses under class Notes] [Checking inverses under class Protein-Features] [Checking inverses under class Chemicals] [Checking inverses under class Databases] ===== Checking and removing any values from PATHWAY-LINKS that point to nonexistent frames ==== ===== Checking modified protein links to eliminate nonexistent frames ==== ===== Cross-referencing compounds and reactions ==== ==== Calculating sub and super pathways ==== ===== Finding missing sub pathway links ==== ==== Checking for missing sub pathway links ==== Warning:PWY-5173 is completely contained within PYRUVDEHYD-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-6535 is completely contained within GLUDEG-I-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-6537 is completely contained within PWY3O-210 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6554 is completely contained within PWY-4562 but is not listed in the SUB-PATHWAYS slot Warning:PWY4FS-5 is completely contained within PHOSLIPSYN2-PWY but is not listed in the SUB-PATHWAYS slot Warning:THRESYN-PWY is completely contained within PWY-3001 but is not listed in the SUB-PATHWAYS slot Warning:GLUTATHIONESYN-PWY is completely contained within PWYQT-4470 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6040 is completely contained within PWY-361 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6040 is completely contained within PWY-6039 but is not listed in the SUB-PATHWAYS slot Warning:METHIONINE-DEG1-PWY is completely contained within PWY-5041 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6164 is completely contained within ARO-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-5486 is completely contained within PWY-6333 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-823 is completely contained within PWY-6305 but is not listed in the SUB-PATHWAYS slot Warning:PWY1F-467 is completely contained within PWY-1121 but is not listed in the SUB-PATHWAYS slot ==Done checking all the links== ==== Checking pathways for duplicate reactions in REACTION-LIST slot ==== == Done checking pathways for duplicate reactions == ===== Validating Gene Ontology (GO) Terms ===== Replacing obsolete term GO:0016481 - negative regulation of transcription with GO:0045892 - negative regulation of transcription, DNA-dependent and reassigning instances. Replacing obsolete term GO:0045941 - positive regulation of transcription with GO:0045893 - positive regulation of transcription, DNA-dependent and reassigning instances. Replacing obsolete term GO:0045449 - regulation of transcription with GO:0006355 - regulation of transcription, DNA-dependent and reassigning instances. Replacing obsolete term GO:0006350 - transcription with GO:0006351 - transcription, DNA-dependent and reassigning instances. [GO:0045892 parents become (GO:0006355 GO:0010629 GO:0051253 GO:2000113)] [GO:0006351 parents become (GO:0032774 GO:0034645)] [GO:0043647 parents become (GO:0019637)] == Done validating GO terms == ===== Changing compound name strings to frame IDs in a variety of slots ===== [Checking class Enzymatic-Reactions] [Checking class Reactions] [Checking class Pathways] [Checking class Enzymatic-Reactions] == Done changing compound name strings to compound frame IDs == ===== Checking pathway predecessors/reactions/subs ==== ===== Removing newlines from names ==== (|GO:0000155| "two-component system sensor activity ") ===== Clearing read-only computed slot values ==== == Done running all the Misc automatic checks == ===== Checking compound structures for redundancy ===== Checking Compound structures for redundant bonds == Done checking compound structure redundancies == ====Recomputing statistics for database maizecyc==== Recomputed statistics are as follows: (PSEUDOGENE-NUMBER 0 ENZYMATIC-REACTION-NUMBER 2109 CITATION-COUNT 515 GENOME-LENGTH 2066432718 MAPPED-GENE-NUMBER 39655 UN-MAPPED-GENE-NUMBER 1 PROTEIN-GENE-NUMBER 39656 RNA-GENE-NUMBER 0 ORF-GENE-NUMBER 28135 REACTION-NUMBER 2214 NO-EC-REACTION-NUMBER 526 ORGANISM-REACTION-NUMBER 2214 TRANSPORT-REACTION-NUMBER 68 POLYPEPTIDE-NUMBER 39656 COMPLEX-NUMBER 4 ENZYME-NUMBER 8894 TRANSPORTER-NUMBER 291 CPD-NUMBER 1467 TOTAL-GENE-NUMBER 39656 OPERON-NUMBER 0 TRNA-NUMBER 6 LAST-TIME-STAMP 21-May-2012 14:33:27) == Done recomputing statistics for database maizecyc == The report from this consistency checker run can be found at C:\Documents and Settings\jaiswalp\Application Data\ptools-15-data\ptools-local\pgdbs\user\maizecyc\2.0\reports\consistency-checker-report-2012-05-21_14-32-03.txt