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Compounds are the building blocks of reactions Reactions are the building blocks of compounds A PGDB should not describe the same biological entity more than once ¡<£Z£ZZ££ó49¨Invoking the Editors¨Y Right-Click on an Object Handle Edit Notes Show Shift-Middle-Click on an Object Handle¡6"'"'óC:¨Saving Changes¨w The user must save changes explicitly with Save KB To discard changes made since last save Special -> KB -> Revert KB¡8] Oó84¨ Naming Frames¡¨*Use names with biological meaning Recommendation: do not change names if they have been in use for more than 1 hour Conventions: hyphens as word separators name length is restricted to 40 characters instance names are written in uppercase most class names are capitalized (e.g, Compounds) - use |¡&¨¨ó95¨Naming Conventions °Compounds: mnemonics, others with prefix C Genes: use same id as genome project Polypeptides: use mnemonic plus suffix -MONOMER Protein complexes: use mnemonic plus suffix -CPLX Enzymatic reactions: use mnemonic plus suffix -ENZRXN Reactions: use mnemonic or EC number plus suffix -RXN Pathways: use mnemonic plus suffix -PWY ¡YYó,%¨Pathway Editor¡¨To graphically create and modify pathways Two tools: Connections Editor: to add reactions, remove reactions, alter connections Always invoked first Segment Editor: to enter a linear pathway segment Invoking the pathway editor: New: Special => Create Pathway or Edit New Pathway in Pathway Mode Existing: Right-Click menu for pathway, select Pathway Editor command ¡l66ªó-&¨Connections Editor Operations¡¨Two main display panes: left: unconnected pathway reactions right: draws connected reactions (looks like the regular Pathway Tools window) Connecting reactions: select initial reaction (in either pane) ===> red and green reactions select a green reaction Additional Commands: Exit: keep changes, abort changes Reaction: add reaction, add reaction(s) from history, create new reaction frame, clone a reaction frame, add connection, delete predecessor/successor link, disconnect reaction, delete reaction from pathway, choose main compounds for reaction, edit reaction frame Pathways: enter a linear pathway segment, guess pathway predecessor list, disconnect all reactions, invoke relationships editor, add subpathway by name, add subpathway by substring, add subpathway by class, delete subpathway¡ZuZZ^ZZ Zu^ ªt¥ ó.'¨Connections Editor Limitations¡¨nAmbiguity in some complicated situations on ordering: link may be ignored dialog box for disambiguating pathway drawn in bizarre arrangement Fix: try removing offending link and add links in different order Pathway editor does not handle polymerization pathways Pathway editor does not permit specification (for a circular pathway) which compound should be on top¡j6X=6X=ó/(¨Pathway Segment Editor¡¨¶To enter linear sequence of reactions faster than with the Connections Editor Reactions are specified by EC numbers or reaction substrates One segment may contain up to 7 reactionsó0)¨Reaction Editor¡¨áTo create a new reaction frame in a P/G database Contains Compound Resolver Can automatically create enzymatic-reaction and protein frames and their relationship links Invoke by: Create Reaction from Reaction Mode Entering Reaction Equation: Reaction frame id, Reaction EC number, Reaction equation, Enzymatic-Reaction frame id, Enzymatic-Reaction names, Protein Complex?, Protein Frame id, Protein names, Show rxn, Edit rnx frame, Balanced?, Done, Abort Compound Resolution Tool ¡8òÖòÖª,C Z8ó"¨Citations I ÞMay be stored in Citations slot of objects: As a single value (e.g., [SMITH95] or [85224678] (Medline UID)) May be attached to specific slot values: By putting citation in an annotation called CITATION May be placed within the text in a COMMENT slot Example text: The subunit structure of this enzyme was determined by Jones and colleages |CITS: [88345698]|. ¡,D*51o,D*51oªO ó#¨ Citations II¨}Creating Publications Frames Special => Hierarchy Viewer Frame => Find Publications Frame => Create => Instance Frame => Edit¡:a* +ó$¨&Creating Links with External Databases¨d Object Correspondence Creating links to a pathway/genome db Creating links from a pathway/genome dbó<.¨Ocelot Concurrency Control I¨ÑSimultaneous updates Optimistic concurrency control optimistic: assumes conflicts will be infrequent allows users to make changes at will checks for conflicts at times of saving Public vs. private workspaces ¡`4~4~ó=/¨Ocelot Concurrency Control II¨ãSave KB operation 1. 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No conflicts found => save to Oracle Saves to current organism KB Unsaved KB indicator (*)¡666ó>0¨Ocelot Concurrency Control III¨Revert KB operation Refresh KB operation automatically at 2:00 am if the user does not have any unsaved updates in their wokspace¡:)@)@ªyó?1¨Editing rules: Support Policy¨d Do not alter KB schema e.g. do not add or remove classes or slots Do not modify the E. coli dataset¡6+"+"óA3¨The Special Menu: KB¨iShow KB Modifications Revert KB Refresh KB Reconnect to Oracle Checkpoint KB Restore Checkpoint Delete KBó(!¨Constraint Checking¡¨cGeneral rules that constrain the valid relationships among instances Constraints are checked when new facts are asserted to assure that the KB remains logically consistent Constraints on slots: Domain violation checks to make sure they should be in instances of that class Range violation : value type value cardinality Inverse Cardinality Lisp-predicate ¡VÂa$Âa$ó' ¨Consistency Checking¡¨ãRemoves newlines from names Converts < to | in string citations Check isozyme sequence similarity Fix references from polypeptides to genes Changes compound names to ids in a variety of slots Matches physiological regulators to other regulators Cross-references compounds to reactions Checks pathways predecessors/reactions/subs Check reactions Check compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions¡ääª, 5êø+ ï `ð ÿÿÿÌ33ÌÌÌÿ²²²`ð ÿÿÿÿÿÿÿÿÿÿ`ð ÿÿÌff3333ÌÿÌf`ð ÿÿÿ333ÝÝÝMMMêêê`ð ÿÿÿÿÌfÿÌÌÀÀÀ`ð ÿÿÿÀÀÀfÿÿ`ð ÿÿÿ3ÿÿÌÌ̲²²£>ÿý?" dÿÌfþd@ÿÿïÿÿÿÿÿÿ ÿÌfþ£ÿý?lKd@ÿÿïÿÿÿÿÿÿÿÌfþpDÿÌfþ´#Àu2üÒ ddÔ»<¬ £nÿý?" dd@ÿÿïÿÿÿÿÿÿ @@``P£R ø ô Ì ¤`£p£@£@ù 0 +ð#Pðð©ð( ð ðð ð ðfù3xa¢xa¢¿¿ÀË1ÿ ?"ñ¿ððÐðÃ3 ðQ¨Stone Serif 32 Pt bold italic¢ª ðô ð ð`Pú3xa¢xa¢¿¿ÀË1ÿ ?"ñ¿ðÀððÃ3 ð>¨ìTitle in Arial Bold 24pt Points arial 24pt Sub-points 20pt and bullet 50% Additional sub point footer area 14pt arial text box to begin at 2.25 vertical 2.5 horizontal title to be .75 vertical and .75 horizontal Fourth level Fifth level¢$4u ª íð~² ð CðHAÁ0C:\pkarp\talks\ov9.tiff"ñ¿ð^´ðÚ¢ ð ³ðB`ß3
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Compounds are the building blocks of reactions Reactions are the building blocks of compounds A PGDB should not describe the same biological entity more than once ¡<£Z£ZZ££ó49¨Invoking the Editors¨Y Right-Click on an Object Handle Edit Notes Show Shift-Middle-Click on an Object Handle¡6"'"'óC:¨Saving Changes¨w The user must save changes explicitly with Save KB To discard changes made since last save Special -> KB -> Revert KB¡8] Oó84¨ Naming Frames¡¨*Use names with biological meaning Recommendation: do not change names if they have been in use for more than 1 hour Conventions: hyphens as word separators name length is restricted to 40 characters instance names are written in uppercase most class names are capitalized (e.g, Compounds) - use |¡&¨¨ó95¨Naming Conventions °Compounds: mnemonics, others with prefix C Genes: use same id as genome project Polypeptides: use mnemonic plus suffix -MONOMER Protein complexes: use mnemonic plus suffix -CPLX Enzymatic reactions: use mnemonic plus suffix -ENZRXN Reactions: use mnemonic or EC number plus suffix -RXN Pathways: use mnemonic plus suffix -PWY ¡YYó,%¨Pathway Editor¡¨To graphically create and modify pathways Two tools: Connections Editor: to add reactions, remove reactions, alter connections Always invoked first Segment Editor: to enter a linear pathway segment Invoking the pathway editor: New: Special => Create Pathway or Edit New Pathway in Pathway Mode Existing: Right-Click menu for pathway, select Pathway Editor command ¡l66ªó-&¨Connections Editor Operations¡¨Two main display panes: left: unconnected pathway reactions right: draws connected reactions (looks like the regular Pathway Tools window) Connecting reactions: select initial reaction (in either pane) ===> red and green reactions select a green reaction Additional Commands: Exit: keep changes, abort changes Reaction: add reaction, add reaction(s) from history, create new reaction frame, clone a reaction frame, add connection, delete predecessor/successor link, disconnect reaction, delete reaction from pathway, choose main compounds for reaction, edit reaction frame Pathways: enter a linear pathway segment, guess pathway predecessor list, disconnect all reactions, invoke relationships editor, add subpathway by name, add subpathway by substring, add subpathway by class, delete subpathway¡ZuZZ^ZZ Zu^ ªt¥ ó.'¨Connections Editor Limitations¡¨nAmbiguity in some complicated situations on ordering: link may be ignored dialog box for disambiguating pathway drawn in bizarre arrangement Fix: try removing offending link and add links in different order Pathway editor does not handle polymerization pathways Pathway editor does not permit specification (for a circular pathway) which compound should be on top¡j6X=6X=ó/(¨Pathway Segment Editor¡¨¶To enter linear sequence of reactions faster than with the Connections Editor Reactions are specified by EC numbers or reaction substrates One segment may contain up to 7 reactionsó0)¨Reaction Editor¡¨áTo create a new reaction frame in a P/G database Contains Compound Resolver Can automatically create enzymatic-reaction and protein frames and their relationship links Invoke by: Create Reaction from Reaction Mode Entering Reaction Equation: Reaction frame id, Reaction EC number, Reaction equation, Enzymatic-Reaction frame id, Enzymatic-Reaction names, Protein Complex?, Protein Frame id, Protein names, Show rxn, Edit rnx frame, Balanced?, Done, Abort Compound Resolution Tool ¡8òÖòÖª,C Z8ó"¨Citations I ÞMay be stored in Citations slot of objects: As a single value (e.g., [SMITH95] or [85224678] (Medline UID)) May be attached to specific slot values: By putting citation in an annotation called CITATION May be placed within the text in a COMMENT slot Example text: The subunit structure of this enzyme was determined by Jones and colleages |CITS: [88345698]|. ¡,D*51o,D*51oªO ó#¨ Citations II¨}Creating Publications Frames Special => Hierarchy Viewer Frame => Find Publications Frame => Create => Instance Frame => Edit¡:a* +ó$¨&Creating Links with External Databases¨d Object Correspondence Creating links to a pathway/genome db Creating links from a pathway/genome dbó<.¨Ocelot Concurrency Control I¨ÑSimultaneous updates Optimistic concurrency control optimistic: assumes conflicts will be infrequent allows users to make changes at will checks for conflicts at times of saving Public vs. private workspaces ¡`4~4~ó=/¨Ocelot Concurrency Control II¨ãSave KB operation 1. Ocelot checks whether any changes made by user conflict with changes that may have been saved recently by others 2. No conflicts found => save to Oracle Saves to current organism KB Unsaved KB indicator (*)¡666ó>0¨Ocelot Concurrency Control III¨Revert KB operation Refresh KB operation automatically at 2:00 am if the user does not have any unsaved updates in their wokspace¡:)@)@ªyó?1¨Editing rules: Support Policy¨d Do not alter KB schema e.g. do not add or remove classes or slots Do not modify the E. coli dataset¡6+"+"óA3¨The Special Menu: KB¨iShow KB Modifications Revert KB Refresh KB Reconnect to Oracle Checkpoint KB Restore Checkpoint Delete KBó(!¨Constraint Checking¡¨cGeneral rules that constrain the valid relationships among instances Constraints are checked when new facts are asserted to assure that the KB remains logically consistent Constraints on slots: Domain violation checks to make sure they should be in instances of that class Range violation : value type value cardinality Inverse Cardinality Lisp-predicate ¡VÂa$Âa$ó' ¨Consistency Checking¡¨ãRemoves newlines from names Converts < to | in string citations Check isozyme sequence similarity Fix references from polypeptides to genes Changes compound names to ids in a variety of slots Matches physiological regulators to other regulators Cross-references compounds to reactions Checks pathways predecessors/reactions/subs Check reactions Check compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions¡ääª, 5êîï ù;b ðð´ð0ð( ðBBBC ð´ðx ð´ cð$dO¿ÿððÐðà O ð ðx ð´ cð$ðO¿ÿðÀððÃO ð ðH ð´ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ð ð¸ð0ð( ðÿÿÿÿ ð¸ðx ð¸ cð$dIO¿ÿððÐðà O ð ðx ð¸ cð$¨@O¿ÿðÀððÃO ð ðH ð¸ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ð°ð¼ð0ð( ð{D ð¼ðx ð¼ cð$L6O¿ÿððÐðà O ð ðx ð¼ cð$6O¿ÿðÀððÃO ð ðH ð¼ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ðÀðÀð0ð( ð ðÀðx ðÀ cð$Ð?O¿ÿððÐðà O ð ðx ðÀ cð$´O¿ÿðÀððÃO ð ðH ðÀ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ðÐðÄð0ð( ðÿÿÿÿ ðÄðx ðÄ cð$Ü O¿ÿððÐðà O ð ðx ðÄ cð$@:O¿ÿðÀððÃO ð ðH ðÄ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ð`ð¤ð0ð( ðÿÿÿÿ ð¤ðx ð¤ cð$O¿ÿððÐðà O ð ðx ð¤ cð$ZO¿ÿðÀððÃO ð ðH ð¤ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêîï ùÿÿÿ ðpð ð0ð( ð ð ðx ð cð$¤O¿ÿððÐðà O ð ðx ð cð$Ü´O¿ÿðÀððÃO ð ðH ð ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêr,}q' ±¯,P´¤Ä¦Ô¨äªô¬õ Yq$³Etè34é(àà Fòâ/È 0ÒÕ·DTimes New Roman ð,bð$ZÙÅí ѧ[=Qä(ÿ¶ cð$0e²0e²
¿ ô þÿÕÍÕ.+,ù®0H¨´¼ÄÌ Ô Üäìôü èäOn-screen Show -s3´ A Times New Roman Stone SerifArial Wingdings Arial NarrowMonotype Sorts Helvetica2002 07 ISMB PTools!Editing Pathway/Genome DatabasesPathway Tools ParadigmList of EditorsInvoking the EditorsSaving ChangesNaming FramesNaming ConventionsPathway EditorConnections Editor OperationsConnections Editor LimitationsPathway Segment EditorReaction Editor Citations I Citations II'Creating Links with External DatabasesOcelot Concurrency Control IOcelot Concurrency Control IIOcelot Concurrency Control IIIEditing rules: Support PolicyThe Special Menu: KBConstraint Checking
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ðù÷ ¿ÀÁtes One segment may contain up to 7 reactionsó0)¨Reaction Editor¡¨áTo create a new reaction frame in a P/G database Contains Compound Resolver Can automatically create enzymatic-reaction and protein frames and their relationship links Invoke by: Create Reaction from Reaction Mode Entering Reaction Equation: Reaction frame id, Reaction EC number, Reaction equation, Enzymatic-Reaction frame id, Enzymatic-Reaction names, Protein Complex?, Protein Frame id, Protein names, Show rxn, Edit rnx frame, Balanced?, Done, Abort Compound Resolution Tool ¡8òÖòÖª,C Z8ó"¨Citations I ÞMay be stored in Citations slot of objects: As a single value (e.g., [SMITH95] or [85224678] (Medline UID)) May be attached to specific slot values: By putting citation in an annotation called CITATION May be placed within the text in a COMMENT slot Example text: The subunit structure of this enzyme was determined by Jones and colleages |CITS: [88345698]|. ¡,D*51o,D*51oªO ó#¨ Citations II¨}Creating Publications Frames Special => Hierarchy Viewer Frame => Find Publications Frame => Create => Instance Frame => Edit¡:a* +ó$¨&Creating Links with External Databases¨d Object Correspondence Creating links to a pathway/genome db Creating links from a pathway/genome dbó<.¨Ocelot Concurrency Control I¨ÑSimultaneous updates Optimistic concurrency control optimistic: assumes conflicts will be infrequent allows users to make changes at will checks for conflicts at times of saving Public vs. private workspaces ¡`4~4~ó=/¨Ocelot Concurrency Control II¨ãSave KB operation 1. Ocelot checks whether any changes made by user conflict with changes that may have been saved recently by others 2. No conflicts found => save to Oracle Saves to current organism KB Unsaved KB indicator (*)¡666ó>0¨Ocelot Concurrency Control III¨Revert KB operation Refresh KB operation automatically at 2:00 am if the user does not have any unsaved updates in their wokspace¡:)@)@ªyó?1¨Editing rules: Support Policy¨d Do not alter KB schema e.g. do not add or remove classes or slots Do not modify the E. coli dataset¡6+"+"óA3¨The Special Menu: KB¨iShow KB Modifications Revert KB Refresh KB Reconnect to Oracle Checkpoint KB Restore Checkpoint Delete KBó(!¨Constraint Checking¡¨cGeneral rules that constrain the valid relationships among instances Constraints are checked when new facts are asserted to assure that the KB remains logically consistent Constraints on slots: Domain violation checks to make sure they should be in instances of that class Range violation : value type value cardinality Inverse Cardinality Lisp-predicate ¡VÂa$Âa$ó' ¨Consistency Checking¡¨ãRemoves newlines from names Converts < to | in string citations Check isozyme sequence similarity Fix references from polypeptides to genes Changes compound names to ids in a variety of slots Matches physiological regulators to other regulators Cross-references compounds to reactions Checks pathways predecessors/reactions/subs Check reactions Check compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions¡ääª, 5êÉà °ð¨ ð(ð@ð( ð ð(ð¸ ð( ð0ä· ¿Àÿ ðP ðà · ð@ *¡ ùðº ð( ð0hÿö¿Àÿ ð à ð÷ ðB *¡ øð¾ ð( ð6h¿Àÿ ð`Pðà h ð@ *¡ úðÀ ð( ð6àh¿Àÿ ð` àðÃh ðB *¡ ØðH ð( ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²îüï ù ;ã ð°ð,ð$ð( ð ð,ðr ð, SðX· ¿ÿððÐðà · ð ðr ð, Sð|B· ¿ÿðÀðð÷ ð ðH ð, ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêr|³F ·çëõ; X³£íGèÃ3é(ààRoot EntryÿÿÿÿÿÿÿÿdOÏꪹ)è ºçH|æÀPicturesÿÿÿÿÿÿÿÿCurrent Userÿÿÿÿÿÿÿÿÿÿÿÿ>SummaryInformation(ÿÿÿÿA(Uýÿÿÿ¥þÿÿÿ
¡¢£¤p¨§¹ºª«¬®¯°±²³´µýÿÿÿþÿÿÿþÿÿÿ»¼½¾¿ÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖרþÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ þÿÿÿþÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿConsistency Checking Fonts UsedDesign Template Slide Titlesö"_Àãç2 ôPeter KarpPeter KarpÂdÃÄÅÆÇÈÉÊ0uËÐÌ0íìÿÍ@TÎÏÿÿÐyÿÑ2Ò NÓPÃÔÕ'Öp×°<ÿÿØÙ'ÚpÿA¨)BCD|¾E|¾
|¾S"ñ¿@ñ÷ð8óDóEÐdúgþý4RdRdT¥z[ 0¦ÿÿÿ^ÿÿÿpûppû@ÿ úgþý4(d(dT¥z[ 00úÿÿ ÿÿÿpû@pûp<ý4dddd¥ß 0¼¦X,¼º°öÊ;ÇÊ;<ý4!d!d¥|- 0l¥<ý4dddd¥|- 0l¥r0º___PPT10 ÀÀ2º___PPT9/È 0Ò?Ù Ú%OÙ Ú=ð©'ó*#¨ Editing Pathway/Genome Databasesó1*¨Pathway Tools Paradigm¨F Separate database from user interface Navigator provides one view of the DB Editors provide an alternative view of the DB Reuse information whenever possible! Compounds are the building blocks of reactions Reactions are the building blocks of compounds A PGDB should not describe the same biological entity more than once ¡<£Z£ZZ££óG;¨List of Editors¨Gene Editor Transcription Unit Editor Protein Editor Reaction Editor Chemical Compound Editor Pathway Editor Publication Editor Metabolic Overview Editoró49¨Invoking the Editors¨, Right-Click on an Object Handle Edit Show ¡&""óC:¨Saving Changes¨w The user must save changes explicitly with Save KB To discard changes made since last save Special -> KB -> Revert KB¡8] Oó84¨ Naming Frames¡¨*Use names with biological meaning Recommendation: do not change names if they have been in use for more than 1 hour Conventions: hyphens as word separators name length is restricted to 40 characters instance names are written in uppercase most class names are capitalized (e.g, Compounds) - use |¡&¨¨ó95¨Naming Conventions °Compounds: mnemonics, others with prefix C Genes: use same id as genome project Polypeptides: use mnemonic plus suffix -MONOMER Protein complexes: use mnemonic plus suffix -CPLX Enzymatic reactions: use mnemonic plus suffix -ENZRXN Reactions: use mnemonic or EC number plus suffix -RXN Pathways: use mnemonic plus suffix -PWY ¡YYó,%¨Pathway Editor¡¨To graphically create and modify pathways Two tools: Connections Editor: to add reactions, remove reactions, alter connections Always invoked first Segment Editor: to enter a linear pathway segment Invoking the pathway editor: New: Special => Create Pathway or Edit New Pathway in Pathway Mode Existing: Right-Click menu for pathway, select Pathway Editor command ¡l66ó-&¨Connections Editor Operations¡¨Two main display panes: left: unconnected pathway reactions right: draws connected reactions (looks like the regular Pathway Tools window) Connecting reactions: select initial reaction (in either pane) ===> red and green reactions select a green reaction Additional Commands: Exit: keep changes, abort changes Reaction: add reaction, add reaction(s) from history, create new reaction frame, clone a reaction frame, add connection, delete predecessor/successor link, disconnect reaction, delete reaction from pathway, choose main compounds for reaction, edit reaction frame Pathways: enter a linear pathway segment, guess pathway predecessor list, disconnect all reactions, invoke relationships editor, add subpathway by name, add subpathway by substring, add subpathway by class, delete subpathway¡ZuZZ^ZZ Zu^ ªPÄ ó.'¨Connections Editor Limitations¡¨nAmbiguity in some complicated situations on ordering: link may be ignored dialog box for disambiguating pathway drawn in bizarre arrangement Fix: try removing offending link and add links in different order Pathway editor does not handle polymerization pathways Pathway editor does not permit specification (for a circular pathway) which compound should be on top¡j6X=6X=ó/(¨Pathway Segment Editor¡¨¶To enter linear sequence of reactions faster than with the Connections Editor Reactions are specified by EC numbers or reaction substrates One segment may contain up to 7 reactionsó0)¨Reaction Editor¡¨áTo create a new reaction frame in a P/G database Contains Compound Resolver Can automatically create enzymatic-reaction and protein frames and their relationship links Invoke by: Create Reaction from Reaction Mode Entering Reaction Equation: Reaction frame id, Reaction EC number, Reaction equation, Enzymatic-Reaction frame id, Enzymatic-Reaction names, Protein Complex?, Protein Frame id, Protein names, Show rxn, Edit rnx frame, Balanced?, Done, Abort Compound Resolution Tool ¡8òÖòÖª,C[9ó"¨Citations I ÞMay be stored in Citations slot of objects: As a single value (e.g., [SMITH95] or [85224678] (Medline UID)) May be attached to specific slot values: By putting citation in an annotation called CITATION May be placed within the text in a COMMENT slot Example text: The subunit structure of this enzyme was determined by Jones and colleages |CITS: [88345698]|. ¡,D*51o,D*51oªP ó#¨ Citations II¨}Creating Publications Frames Special => Hierarchy Viewer Frame => Find Publications Frame => Create => Instance Frame => Edit¡:a* +ó$¨&Creating Links with External Databases¨d Object Correspondence Creating links to a pathway/genome db Creating links from a pathway/genome dbó<.¨Ocelot Concurrency Control I¨²Simultaneous updates Optimistic concurrency control optimistic: assumes conflicts will be infrequent allows users to make changes at will checks for conflicts at times of saving ¡84~4~ó=/¨Ocelot Concurrency Control II¨ãSave KB operation 1. Ocelot checks whether any changes made by user conflict with changes that may have been saved recently by others 2. No conflicts found => save to Oracle Saves to current organism KB Unsaved KB indicator (*)¡666ó>0¨Ocelot Concurrency Control III¨Revert KB operation Refresh KB operation automatically at 2:00 am if the user does not have any unsaved updates in their wokspace¡:)@)@ªyó?1¨Editing rules: Support Policy¨p Do not alter KB schema e.g. do not add or remove classes or slots Do not modify the E. coli or MetaCyc datasets¡6+.+.ª` óA3¨The Special Menu: KB¨iShow KB Modifications Revert KB Refresh KB Reconnect to Oracle Checkpoint KB Restore Checkpoint Delete KBó(!¨Constraint Checking¡¨cGeneral rules that constrain the valid relationships among instances Constraints are checked when new facts are asserted to assure that the KB remains logically consistent Constraints on slots: Domain violation checks to make sure they should be in instances of that class Range violation : value type value cardinality Inverse Cardinality Lisp-predicate ¡VÂa$Âa$ó' ¨Consistency Checking¡¨ãRemoves newlines from names Converts < to | in string citations Check isozyme sequence similarity Fix references from polypeptides to genes Changes compound names to ids in a variety of slots Matches physiological regulators to other regulators Cross-references compounds to reactions Checks pathways predecessors/reactions/subs Check reactions Check compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions¡ääª,6êî
ï ¬ð¤ ðð<ð( ðp¥sdÈsÐAsä q ðð~ ð sð*¤ ¼¿ÿððÐðà ¼ ð ð~ ð sð*x ¼¿ÿðÀððü ð ðH ð ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²yº___PPT10Y+Dñ='ñ ¦ÿÿÿÿ=ñ @Bñ +îï ù K0 ððð0ð( ðdàdh ððx ð cð$ÔÓ¿ÿððÐðà ¼ ð ðx ð cð$Xý¿ÿðÀððà ð ðH ð ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²îï ù K0 ððð0ð( ðÿÿÿÿ ððx ð cð$ü¿ÿððÐðà ¼ ð ðx ð cð$Xļ¿ÿðÀððü ð ðH ð ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²î
ï ¬ð¤0ðÜð<ð( ð ðÜð~ ðÜ sð*×¼¿ÿððÐðà ¼ ð ð~ ðÜ sð*Ø×¼¿ÿðÀððü ð ðH ðÜ ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²yº___PPT10Y+Dñ='ñ ¦ÿÿÿÿ=ñ @Bñ +î
ï ¬ð¤àðèð<ð( ð++++........++++ ðèð~ ðè sð* ÿððÐðà ¼ ð ð~ ðè sð*t_ÿðÀððü ð ðH ðè ð0Þ½h¿ÿ ?ð ÿÿÿÌ33ÌÌÌÿ²²²yº___PPT10Y+Dñ='ñ ¦ÿÿÿÿ=ñ @Bñ +îï ùK0 ð`ð¤ð0ð( ðÿÿÿÿ ð¤ðx ð¤ cð$û¼¿ÿððÐðà ¼ ð ðx ð¤ cð$Tü¼¿ÿðÀððü ð ðH ð¤ ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêyº___PPT10Y+Dñ='ñ ¦ÿÿÿÿ=ñ @Bñ +îï ùK0 ðpð ð0ð( ð ð ðx ð cð$ò¿ÿððÐðà ò ð ðx ð cð$$ ò¿ÿðÀððÃò ð ðH ð ð0Þ½h¿ÿ ?ð ÿÿÿÿÿÿúýaýÎÎÎü(ôêyº___PPT10Y+Dñ='ñ ¦ÿÿÿÿ=ñ @Bñ +r8ãí" ;$K&' 0u-4®!<[(?è*õ1? ¿í§2G
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