Pathway Editor Tool -- Release #2
Contents
1. 2 33 Log Window2. NADIPIH Amount Roe i j cofactor in Add to Process F et entity id entity name entity role number Special echab272 5d deltas 24 c substrate 1 basic echShefO Sd 3 phosphatid product 1 basic acd achd ds WADP cofactor in 1 basic Figure 2 11 Add Molecule Window Select EC Number for Gene Product Selectan EC number C Use anew EC numberthatis never used with this enzyme MALEC numbers in the database RE Name of Selected EC Number Use an EC numberthatis assigned to some process M Curent entered EC numbers for this enzyme Name of Selected EC Number Selected EC Number Use selected EC number Don t use any EC number for this process Figure 2 12 Adding an EC number for an enzyme a Molecule Ol Entity ld acd fachd d306 11d5 bd1 3 00b0d0794900 Entity MADP Properties Specialization basic molecules Other names NADF beta Nicotinamide adenine dinucleotide phosphate Triphosphopyridine nucleotide Nicotinamide adenine dinucleotide phosphate TPH Cross Links Processes Pathways Figure 2 13 Molecule Detail Window Molecules can also be edited in the process wizard window When the user clicks on the edit button on the control panel a popup menu asks the user whether s he wants to edit the global properties of the molecule or those properties of the molecule that are specific to this process
3. E E EC Muses Add Another EC Number Cancel Figure 2 15 Editing molecule information within a process ae 2 5 Editing Pathways Processes and Molecular Entities Pathways processes and molecular entities can be edited in different forms as shown in figures 2 17 2 18 and 2 19 When the user selects a process for editing or removal using the Pathway Browser and if there are multiple organisms associated with the process an additional context menu as shown in figure 2 20 will pop up showing a list of different organisms containing a process with the same name After selecting the organism the process associated to that organism is edited Pathway Wizard Step 1s Step 1 GENERAL PATHWAY INFORMATION iosynthesis of Ribotlayvin FM and FAC Metabolic Pathway Incomplete Last Update Date unknown Verified Verification Date Figure 9 3 1 Save and Exit Back Mest Cancel Figure 2 17 Editing a pathway Process Wizard Stepi Step 1 GENERAL PROCESS INFORMATION Mame Phosphatase Location Other ie Other l Reversible Ves E No Motes Save and Exit Mest Figure 2 18 Editing a process Molecule Pi GENERAL MOLECULE INFORMATION Default Name Fi Specialization Basic Molecule M Control Panel Add Remove hake Default Save and Exit Back ext Figure 2 19 Editing a molecule HE Genomes Pathway Browser 1 1 metabol
4. Editor k dd new process to the pathway new editori i i F m a i T a ie P NEH T b Figure 2 4 Screen shot for adding a process to a pathway Add Process Add a Process Choose from all existing processes Proceess detal id process name 81768b4 delta 7 Sterol 5 desaturase s lfeade delta 7 Sterol S desaturase 803445 delta Sterol S desaturase ascbtbl delta Sterol S desaturase Fafi de deoxy Adenylate kinase 591 aeb0 deoxy Adenylate kinaze b176180 deoxy Adenylate kinase dallaecd deoxy Sdenylate kinase 45t6tc40 phosphatase dabbe4 phosphatase 4660b3e A 20 ydrosysteroid dehydrogenase THbaz6 A 20 hydrosysteroid dehydrogenase i Orcreate new proces Cancel Figure 2 5 List of available processes is shown to the user before a new process is created As this pathway is just created there is no process in it yet If we click the Add button in the processes page of the pathway wizard we get the screen in figure 2 5 From the Add process form users can choose an existing process from the processes list or create a new process The process list has all the available processes in the database server and the processes are listed by their names and ids Clicking one process in the list we can get some detailed information for that process and this information is shown in the right pane This could help users determine whether it is the right proce
5. the transactions that are committed in that session are not rolled back The user has to manually roll back those changes In order to help the user see what changes have been made in that session a log window is displayed whenever the user wants to exit through the cancel button The log window is shown in Figure 2 33 Logs concerning the changes are also saved to a file on the hard drive for the user to check later Below are the changes that you have made in this session a pathway with name Biosyhthesis of histidine and id 52abaSed 490 48beb41 1 ebdaf 733 sAdd process with name delta 7 Sterol desaturase and id 81 68b4 d368 4152 ah Create a copy of the processidelta 7 Sterol 5 desaturase with new id and id b04c2 sReplace the global copy of this process with the newly created local copy for this pathwe tae aii deta 7 Sterol 5 desaturase with id bO4c 1c 9900 4891be35 3 10408 gt Remove cofactor out NADP with id ec65b403 5dc 1 11d7 bd23 0040459 Remove regulator Ot P450 with id ac4 facd c d306 11d5bd13 00b000 549 sAdd catalyzing molecule phosphatase with id Ga60dbe 3 2 9ct 4433 dat1 5 ch gt Update process with id bO4c271c 990 4a91be35 31d4085 1bea set name delta 7 Sterol 5desaturase gt 5et notes 8et location Nucleus f Return to the wizard to roll back the changes manually fo Exit the wizard and save this information into log file located at c PathwayEditorLog tet
6. 3 4 dioxyge animals ia aah sacha adhd Aih A asin Sheta stercid deltaed dehuer animals Add to the encoding gene list Current list of the genes for this gene product Genes encoding this gene product ID GENE ORGANISM OS66371d Oeld 46ed 997d 32de6 Ascorbate 2 Cloe genase prokanva bacteria and archaeal Remove the selected gene from the list cancel _ Figure 2 22 Selecting genes that encode for an enzyme 2 6 Deleting pathways processes and molecules Using the Pathway Editor s functionality embedded in the Pathway Browser s tree view context menu a user can remove data from the database Right clicking on a pathway and then selecting Editor and then Delete from database as shown in figure 2 23 will remove a pathway from the database S Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources EE Sy Pathways H k a demo pathway H ot aa Hicsynthesis ar a H Pena Find molecular entities involved in activation and inhibition Biosynthesis ar List all reversible processes Oe Biosynthesis a Tabulate the details of molecular entities involved Oe Biosynthesis ar Molecular Entities involved in each process of this pathway i Biosynthesis ar List all related pathways Ei T Biosynthesis of List a genes involved in this pathways H Biosynthesis of a ba PA VEW the pathway graph in an external window HEE Biosynthesis of Biosynthesis
7. Figure 2 14 shows the edit menu in the process window Step 2 COMPONENTS OF THE PROCESS Control Panel entity id entity_name entity_role number ec65b270 5d 3 phosphatd product 4 ec65b272 5d deltaS24 c substrate i ITa E Add New ac4racbd d3 NADP cofactor in z Remove Save and Exit wom File View Query Web Resources Customize Help Pathways Z Serine and glycine metabolism ry Processes EL ri S 2 hydroxy acid dehydrogenase 5 L Substrate peura and Processes involving this molecular entity Synonyms of this molecular entity View the molecular structure BR glycolate E p Product paes the peneem from this process Figure 2 14 Molecule Editing Menu If the user chooses editing global properties of the molecule then the molecule wizard window is launched and through the molecule wizard which is shown in Figure 2 19 the user can edit different properties of the molecule On the other hand if the user wants to edit the molecule properties related to this process the window in Figure 2 15 is shown Through this window the user can change the role amount and if applicable EC information This window can also be launched from the Pathway Browser window by choosing the edit its role menu item in the edit menu shown in Figure 2 14 Edit Molecule Properties alanine ghyoxylate or glycineoxaloacetate transamin Amount Update i
8. ean Editor amp Edit process new editor H E Nonerntpee TSE Yi Nor enzymatic la Nor enzymatic ga Norrenzymatic Figure 2 24 Removing a process from a pathway To remove a process from the database select the Process root and find the correct process Right click on the process and then select Editor and then Delete from database To remove a molecule from the database follow the same technique as deleting a pathway or process from the database To remove a molecule from a process select a process select a molecule listed under the process right click select Editor and finally select Remove from process as shown in figure Lo Tea I Ei Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Customize Help oy Pathways PA H a a demo pathway HEE aa a Biosynthesis and degradation of ascorbate oi Processes cer Ascorbate 2 3 dioxpgenase E Substrate H Product Catalyzing Protein st Ascorbate 2 a dioxpgeras Pathways and Processes involving this molecular entity Synonyms of this molecular entity Swiss Prot page For this protein Oh Gene information with this protein L gulonolactone Hl L threonate dehy Hl Lactonase l g Mon enzymatic lt Non enzymatic fli Nor enzymatic H E Nor enzpmatic Chess Figure 2 25 Removing a molecule from a process Edit molecule new editor Editor i Change its rol
9. ofl View the pathway graph in a specific organism H TE Biosynthesis of E View the pathway graph in the internal window E Cholesterol biod l i Delete pathway E T Citrate cycle Set pathway organism G dati ir E a Ba gi Degradction Edit pathway new editor E oy Derivatives andi T Denvatiwes and degradation of tryptophan SS Folate pathway aie Formation and degradation of thacyighicerc Fly Processes SHGARMAQ GY OFS BHO e Figure 2 23 Deleting a pathway Collapsing a pathway node down and then opening the processes node then right clicking a selected process and then selecting Editor and then Delete process from pathway as shown in figure 2 24 will not remove the process from the database but will remove the process from the pathway S Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Customize Help ie Pathways A Se a demo pathway E aa aS Biosynthesis and degradation of ascorbate ry Processes a GE corbas 2 tedicwugerncce i ih vi cory Glucone Processes sharing activators and inhibitors with this process ne q Glucura List all genes involved in this process Glucura View the process graph in an external window fe L galact p AAP E a L gulorms view the process graph in the internal window la L threor Yi Lactone _ process organism A HEN
10. One aspect of the Molecule Wizard that differs from the other two wizards is that when creating or editing an enzyme within a process the genes which encode for the enzyme must be provided The step showing the current genes that encode for the enzyme is shown in figure 2 21 Molecule Ascorbate 7 3 dioxypenase GENE INFORMATION Contral Panel Genes encoding this gene product GENE ORGANISM D3637 1d Del Ascorbate 2 3 prokarya bac a i IET Save and Exit Back Finish Cancel Figure 2 21 Genes that encode an enzyme When the Edit Gene List button is clicked a window to add more genes is displayed as shown in figure 2 22 Select Gene Selectthe genes thatencodes this gene product Exisiting Genes Genes available inthe database IE GENE ORGANISM 138d 783 11 5 4040 a0t6 fed fe delta sterol 5 desaturase animals 24981 ct8 7a85 480c a442 2bc rf A 20 hydroxysteroid dehydroagen animals ccbb113b 339d5 4a74 9919 7ee20 1 acylglycerophosphocholine O ac animals faee4052 dbcS 4029 91 OF deSbd4 1 pyrroline 5 carbosylate dehydro animals b1 ffa456 5894 4b07 ae60 0b0d39 11beta hydrosy steroid dehydroge animals 45bc67c8 al 2d 4rcb 88fc 6fffclf3 Z Aminoadipate transaminase animals 04220185 750d 4ca0 bc9f 1a2906 Z aminomuconate semialdehyde d animals 439545a4 367d 421d 8892 3ef07 3 dehydrosphinganine reductase animals c33095a1 2378 4528 9e02 14035 3 hydroxpanthranilate
11. Version 2 0 Pathway Editor Tool Creating and Editing Biological Pathways Data User Manual Center for Computational Genomics Division of Computer Science EECS Department Case Western Reserve University Cleveland OH 44106 1 Introduction The Pathways System project which is being developed at the Center for Computational Genomics Case Western Reserve University is a set of tools for biologists to interact with pathways and processes the fundamental building blocks of biology In order to better understand the chemical interactions taking place in nature biologists need a mechanism to visualize these pathways and processes The overall goal of the project is to facilitate this discovery by providing a robust collection of biological information along with applications that provide interfaces to the data and allow visual interaction with it This report describes the pathway editor tool designed to create and edit pathways for the Pathways Database 1 1 Biological Terminology In order to understand the technical aspects of the pathway editor tool it is necessary to first explain some biological terminology employed in this paper A molecular entity is defined here to be any molecule involved in a reaction and these entities are the lowest level of abstraction that biologists analyze A process is a reaction involving a number of molecular entities Processes in general have substrates that can be considered as main inp
12. ct from a process the pathway editor makes sure that they add relevant molecules to make the process complete Pathway Editor now is an integrated component of the Pathway Browser This gives users a more consistent look and feel A screen shot of the Pathway Browser is shown in figure 1 1 In the Pathway Browser the left pane has a hierarchical tree view of existing pathways processes and molecular entities on both the database server Users can do operations like uploading pathways to or downloading pathways from database server The right pane contains a tabbed control It shows details of the pathway selected from the left pane Currently it shows the details in the form of both a hierarchical tree view and a HTML file To modify a pathway users can do simple edit operations through the tree view interface or perform some more complex operations through the forms provided by the editor component Each operation will call a stored procedure in the database server or use ad hoc query to accomplish the task The key features of Pathway Editor are e Creating new pathways processes molecular entities and storing them in the database server e Editing pathways by adding or removing processes e Editing processes by adding or removing molecular entities e Changing a molecular entity s name e Changing a molecular entity s role in a process e Adding or editing external links to local pathways processes or molecular entities e Verif
13. deaminase Q Riboflavin kinase View the pathway graph in the internal window Qf Riboflavin synthase 7 Uracil reductase Processes i Molecular Entities lt Organism unspecified Signaling Pathways Explorer Pathway Biosynthesis of Riboflavin FMIN and FAD Metabolic Pathways Figure 2 9 Graph view of the created pathway 2 4 Creating and editing molecules for processes There are two ways to add molecules to a process the molecular information step in the Process Wizard or right clicking in a process in the Pathway Browser and clicking on Add basic molecule or Add enzyme buttons Both methods are shown in figure 2 10 Process Wizard Step 2 1 Step 2 COMPONENTS OF THE PROCESS J Existing Components ofthe Process Erith Ar Rer Edit Save and Exit Back Next gt Cancel OR HE Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Customize Help El Pathways 5j Z Biosynthesis and degradation of ascorbate Fl gg Processes a rar Ascorbate 2 Cioxpgenase I Py E i gt Editor if cm og Glucorases a Glucuronate aeiae Hik Glucuronate reductase L galactonolactone oxidase Zi Lequlonolactone oxidase 2 10 Adding a molecule to a process Related Pathways Display selected molecular entities New Add enzyme to mR process If the user wants to add a component to a proce
14. e 2 7 Adding organism information to processes As organism information is provided at the process level adding it to the database is done through the process wizard form In the process wizard form there is an Organisms page It is used to display organism information for that process as shown in figure 2 26 Process Wizard Step 4 Step 4 ORGANISM INFORMATION Control Organisms computed through enzyme s Beal MAME plants yeasts Organisms associated directly withthe process Add Organism Remove Save and Exit Back Cancel Figure 2 26 Organism information for a process If a process is enzymatic organism information will be filled out automatically from the information contained in the genes of the enzyme If the process is non enzymatic organism information will have to be filled out manually as shown below Process Wizard Step 4 Step 4 ORGANISM INFORMATION Organisms computed through enzymei s MAME Organisms associated directly withthe process Add Organism Remove S Add Organism Organism Name prokarya bactena and archaeal plants yeasts animals OF Cancel Figure 2 28 Form for associating an organism to a process We can view the effect of adding organism information to processes on the pathway through the Pathway Browser After drawing the pathway graph right click the graph and then click highlight processes happen in selected organis
15. e entered now or later This feature allows users to create pathway incrementally Now let s type in the name and click the Save and Exit button then we get the screen in figure 2 3 From figure 2 3 we can see that in the right pane the pathway with the name we just entered is listed as the only child node of topmost node Pathways Expanding this node we see an empty Processes node because we have not added any processes to this pathway yet Because of the constraints in the database any operations like adding processes adding external links can only be performed after the pathway is created al Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Help Pathways Biosynthesis of histidine a Processes Processes H fe Molecular Entities M SHELIA g Figure 2 3 Screen shot after creating a new pathway with name Biosynthesis of histidine Also instead of clicking the Save and Exit button the next button can be clicked and more information can be filled out about the pathway including the process information The next section discusses creating and adding processes into a pathway 2 3 Creating and editing processes for a pathway Adding processes to existing or newly created pathway is done through the pathway wizard form There is a Processes page in the pathway form Switching to this page a list of processes 1f any that are involved in the sel
16. ected pathway is shown Using the buttons on this page add edit or delete process operations are allowed as shown in the first image in figure 2 4 The second image in figure 2 4 shows an alternative way of adding a process to a pathway In the Pathway Browser open a pathway and then right click on Processes and then select Editor and finally New Process This will open the Process Wizard to create a new process Pathway Wizard Step 2 i Step 2 PROCESSES in the PATHWAY Control Panel Existing Processes in this Pathwar process_id process name Add New Process Remove Save and Exit Back Ment Cancel Ha Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Customize Help Pathways a a demo pathway z aa a Biosynthesis and degradation of ascorbate z Biosynthesis and degradation of Biotin A Biosynthesis and degradation of catechola 4 A Biosynthesis and degradation of histidine Biosynthesis and degradation of thyroid ho Z Biosynthesis of aromatic amino acids and c g Y Biosynthesis of glycerophospholipids Biosynthesis of Pantothenate Coenzyme i Biosynthesis of Riboflavin FMM and FAD Biosynthesis of thiamin in E coli z Cholesterol biosynthesis ot Citrate cycle ag gue Se Conve Display selected processes Te Degrac et Derivat St Deriva fet Folate pathway Display all processes
17. er deletes a process from the pathway form the process is only removed from that pathway and it is still in the database thus this operation does not affect the other pathways that use the process After users have added several processes to a pathway they may want to see what the pathway looks like They can right click the Pathway node in the right pane and in the pop up menu choose Show graph This will lead users to the graph view of the created pathway as shown in figure 2 9 S Genomes Pathway Browser 1 1 metabolic pathways PE File view Query Web Resources Ci Help E E Pathways Biosynthesis of Riboflavin FMN and F Bi Processes F 6 7 Dimethyl 8 rbityllumazine syntl amp Substrate E Find molecular entities involved in activation and inhibition List all reversible processes Tabulate the details of molecular entities involved ESE L EE Molecular Entities involved in each process of this pathway 5 amino 6 tibitylamino 2 4 List all related pathways g Piaduct List all genes involved in this pathway Pi View the pathway graph in an external window 6 7 dimethyl 8 ribityllumaz view the pathway graph in a specific organism ge Catalyzing Protein 6 7 dimethyl S ribityllumazi 2E 6 7 dimethyl 3 ribityllumazi 7 ry FMN adenylyltransterase Set pathway organism p f GTP cyclohydrolase II Editor gt i Non enzymatic Q Phosphatase F Pyrimidine
18. ic pathways File View Query Web Resources Customize Help Qe Pathways 4 Biosynthesis and degradation of ascorbate Related Pathways 3 Processes Ep fw Ascorbate 2 3 dioxygenase 7 Glucono Mactonase PathwayName Connected Entity Name Qi Glucuronate reductase i Glucuronate reductase i L galactonolactone oxidase ar L qgulonolactone oxidase es er L threonate dehydrogenase F Lactonase Qi Non enzymatic Qe Non enzymatic Qi Non enzymatic i Non enzymatic QF Non enzymatic 2 eR 1 3ba3dd4b dbf1 4cdf abOf a17fd22e2306 Ascorbate 2 3 dioxygenase in prokarya bacteria and archaea O0b0c4d66 3af0 40b8 9830 c5ae66885436 Ascorbate 2 3 dioxyqenase in animals _ b9e21c7 90dd 4292 96e2 0229fa79da72 2 Aminomuconate semialdeehyde dehydrogenase in prokarya bact 730be0ee 1699 4e56 9dd9 4 15a 724f9ab 7 2 Aminomuconate eklesie dehydrogenase in animals Figure 2 20 Selecting an organism The forms shown in figure 2 17 2 18 2 19 have a consistent look and feel design Because of the hierarchies existing between pathways processes and molecules when editing a molecule or process the process checks the occurrence of that molecule or process in other processes or pathways If there are multiple occurrences the program will alert the users that their operations will affect all of them It gives users the choice to see those processes or pathways before making those changes
19. m in the pop up menu Figure 2 29 shows a list of organisms related to the processes in that pathway After selecting one of the organisms we get the screen in figure 2 30 In Figure 2 30 all the processes of this pathway which exist in plants and yeasts are highlighted S Genomes Pathway Browser 1 1 metabolic pathways Sales File view Query Web Resources Customize Help Qe Pathways t Biosynthesis of m DE R E7 IESTI ETT EDE Find molecular entities involved in activation and inhibition W Q amp SQ BHO g iiniscudes Eniti List all reversible processes Tabulate the details of molecular entities involved Molecular Entities involved in each process of this pathway List all related pathways List all genes involved in this pathway View the pathway graph in an external window View the pathway graph in a specific organism View the pathway graph in the internal window plants yeasts prokarya bacteria and archaea y unspecified Set pathway organism Editor Metabolic Pathways Signaling Pathways Explorer Pathway Biosynthesis of Riboflavin FMN and FAD Organism unspecified Figure 2 29 Highlighting processes for a specified organism HE Genomes Pathway Browser 1 1 v03 Pathways from Biochemical Pathways BAR File View Query Web Resources Customize Help Qe Pathways SA Biosynthesis and degradation of ascorbate 129 results S Biosynthe
20. olyamine metabolism Precursors in E coli and Metabolism of Pyride Proline and Hydroxyproline Metabolism 2 Reactions of pyruvate and phosphoenolpyruv 2 Serine and glycine metabolism B Serine lsocitrate Lyase Pathway B Sulfur Metabolism X Synthesis of purine ribonucleotide Ge Synthesis of pyrimidine ribonucleotides 2 Synthesis of serine from glycine B test pathway 1218 Processes Molecular Entities Pomoc Sane sane eee See ee Se Se ee Se Se ee SS Se Se SE Se Se Se SS E E E E Se SS E lt Metabolic Pathways Signaling Pathways Explorer Pathway Citrate cycle Organism unspecified Figure 1 1 Screen shot of the main interface of Pathway Browser 2 Working with Pathways Pathway Editor has a wizard style interface similar to an installation program Via the main wizard forms and various pop up dialog forms users can browse edit and create pathways processes and molecules This section describes the Pathway Editor the main user interface that is used to create view and manage pathway data in the database Many of the tasks in this section are described using screen shots to illustrate various functions Topics in this section include e Launching Pathway Editor e Creating new pathways processes and molecular entities e Editing pathways processes and molecular entities 2 1 Launching Pathway Editor Pathway Editor is an integrated component of the Pathways Database System It is in
21. or has the following features Familiar user interface As Pathway Editor is a component of the pathway database system it has a user interface similar to other components like Pathway Browser which has Windows explorer s look and feel design model Consistent UI reduces the study curve for end users Minimum effort to create and edit pathway data Both data gathering and editing can be time consuming and error prone Pathway Editor is designed to ease the workload by utilizing existing data e Extensible and flexible Pathway Editor interacts with pathway database As new needs arise more information should be included and additional tools should be integrated This may lead to changes in the database schema As a client side tool Pathway Editor is extensible and flexible enough for changes Hide internal logic behind the interface Users interact with the data through the user interface of Pathway Editor browse and edit data by simply clicking the mouse button The interaction between the pathway database server and Pathway Editor whether through stored procedures or ad hoc queries is transparent to users e Integrity enforcement As users perform various operations such as inserting a process into a pathway the integrity is checked and enforced For instance if the inserted process already exists in that pathway then the new copy will be redundant Also when the users delete the last remaining substrate or produ
22. oxyproline Metabolism Reactions of pyruvate and phosphoenolpy E Serine and glycine metabolism E Sulfur Metabolism 2 Synthesis of purine ribonucleotide 2 Synthesis of pyrimidine ribonucleotides E i i i E E E i i E i E GEE G4 TreeView ill f Da Figure 2 30 Highlighted processes for a specified organism 2 8 Maintaining Cross Links to External Databases Pathways database maintains records for linking local entries to external databases In table external_database_links each row records a local entry s id the external database s id and the entry s id in that database Local entries can be pathways processes or molecules Pathway Editor captures this link information and displays it to the users through a data grid Through the interface users can add delete or edit links as shown in figure 2 31 and 2 32 Pathway Wizard Step 3 i Step 3 CROSSLINK INFORMATION Control Panel Existing Crosslink Information database name externalid Add Mew Crosslink Remove Save and Exit Back Finish Cancel Figure 2 31 External link window in pathway wizard HR AddLink Database Name BRENDA BRENDA CAS genbank gene ontology genecard IUB ME IUPAC Figure 2 32 Adding an external link to a local pathway If the user wants to exit a wizard window by clicking on the cancel button
23. sis and degradation of Biotin Process name gt Pathway name Pathway Biosynthesis and degradation of catechola reversible figure E Biosynthesis and degradation of histidine R 20 Metabolism of Di IM hwdravwetarnid Biosynthesis and degradation of thyroid ho M se j amp EN IR m Q tir My En g a Ez H g gt a A oy Process Seperate rr Molecule name DRE Biosynthesis of aromatic amino acids and c 2 Biosynthesis of glycerophospholipids Biosynthesis of Pantothenate Coenzyme Biosynthesis of Riboflavin FMN and FAD Biosynthesis of thiamin in E coli E Cholesterol biosynthesis Citrate cycle Conversions and degradation of cysteine E Degradation of glycerophospholipids Biosynthesis and degradation of ascorbate Derivatives and degradation of phenylalan S Derivatives and degradation of tryptophan f E Folate pathway E Formation and degradation of triacylglpcerc Glutathione Metabolism E Homocysteine pathway 2 Interconversions and degradation of purine y Interconversions and degradation of pyrimi Lysine Threonine Methionine and Cystein Metabolism of Choline Betaine and Sarco Metabolism of ether lipids 2 Metabolism of glucocorticoids and mineral Metabolism of Sphingophospholipids 2 Metabolism of the branched chain amino a Phenylpropanoid compounds in plants E Polyamine metabolism 2 Precursors in E coli and Metabolism of P 2 Proline and Hydr
24. ss from process wizard window then the add molecule window shown in Figure 2 11 is displayed In this window user is presented a list of available molecules in the database The molecule list is updated according to the selected radio button at the top which defines the type of the molecules to be listed in the list box below The user can select a molecule from the list assign its role from the drop down role list and adjust the amount of the molecule from the related field Having done this when the add to process button is clicked the molecule is added to the process Alternatively the user can create a new molecule 1f the molecule to be added is not in the database New molecule wizard is launched either when the user clicks on the Create New button on this window or the user types in a name in the molecule name field which is not in the current list Molecule wizard is shown in Figure 2 19 While adding a new enzyme to a process an EC number for that enzyme should be entered This window pops up automatically after adding an enzyme It is shown in figure 2 12 Users can also see the details of any molecule in the molecule list in add molecule window by firstly selecting a molecule in the list and then clicking on the show details button Molecule detail window is shown in Figure 2 13 Add molecule gt Molecule Type Basic Molecule Protein RNA Create New M1 acety spermine MEA cetyl L Lysine MAD PF
25. ss they are looking for Now let s just select one of the processes and then click the OK button Pathway Wizard Step 2 i Step 2 PROCESSES in the PATHWAY Existing Processes in this Pathway Control Panel Process id process name d ascbhthl 9 bbea tef9 856a 233bF deta 7 Sterol 5 desaturase 7 Add New Process Remove Save and Exit Back Next Cancel Figure 2 6 Screen shot after adding a process to a pathway Adding a process to a pathway is done in one transaction If the transaction is successfully committed we get the screen in figure 2 6 Figure 2 6 shows the Process page after adding a process to the newly created pathway Users can choose to create a new process by selecting the Create new process radio button and clicking the OK button on the form shown in figure 2 5 Figure 2 7 shows the Process Wizard form that allows users to enter the new process s information After the users enter all the required information the process will be added to the pathway automatically Process Wizard Stepi Step 1 GENERAL PROCESS INFORMATION Mame j Location JUnkonwn a Other Reversible hes E No Motes Save and Exit Back Figure 2 7 Screen shot after selecting create new process option in the add process dialog figure 2 5 When the user edits a process from the pathway form the program will first check whe
26. ther the selected process is used also by other pathways If this is the case it will alert the users and ask the users whether they want to keep the changes to the process in that pathway or expose the changes to all pathways as figure 2 8 shows ShowPathways This process delta Sterol 5 desaturase is shared by the following pathways Pathways Details id name a Cholesteral bi fedad0ae dd9 Testing for Us Please choose an action Create an extra copy of the process so that other pathways will not be affected I Modify this process so all the pathways containing this process will be affected OE Cancel Figure 2 8 Alert window that appears before editing a process that is involved in multiple pathways If the user selects Create an extra copy then a transaction will be started to make a copy of the selected process to replace the original one used in that pathway and all the following editing operations will be on that local copy and thus will not affect the original copy If the user chooses Modify this process then any change will affect all the pathways that use the process A process can be deleted from the database by right clicking on a process in the Pathway Browser and then selecting Editor and then Delete Process A process can also be deleted from a pathway in the Pathway Wizard by selecting the process and then clicking the Delete button When a us
27. uts to the reaction and products which are the main outputs of the reaction In addition there are cofactors which either assist in the reaction cofactors in or are released as byproducts of the reaction cofactors out To control the rate of the reaction there are inhibitors and activators A pathway is a group of processes that join together for instance the products of one process might be substrates of another process to produce an overall effect or metabolism There are three general classes of biological pathways 1 metabolic and biochemical 2 transcription regulation and protein synthesis and 3 signal transduction Metabolic pathways are responsible for carrying out the chemical reactions that provide basic biological functions such as DNA RNA and protein synthesis and degradation energy metabolism fatty acid synthesis and many others Transcription and protein synthesis are responsible for converting genetic information into proteins gene products Signal transduction pathways are responsible for coordinating metabolic processes with transcription and protein synthesis Each of these three kinds of pathways has distinct attributes to be kept and managed in the pathways database 1 2 Overview The pathway editing tool provides a user interface for the end users to access and edit data residing in the database This section gives an overview of the design implementation and features of Pathway Editor Pathway Edit
28. voked through the context menu from the main interface For example to create a new pathway we right click on the Pathways node in the left panel of the Pathway Browser and choose Editor then New pathway from the popup menu as shown in figure 2 1 Figure 2 2 shows the wizard form for creating a new pathway Similarly you can right click on the Processes or Molecular Entities nodes to create new processes or molecules a Genomes Pathway Browser 1 1 metabolic pathways File View Query Web Resources Help Pathways _ ee Process Display selected pathways Molecul Display all pathways j Set pathways organism b Editor E New pathway Figure 2 1 Launching the Pathway Editor from the Pathway Browser interface Pathway Wizard Step 1s Step 1 GENERAL PATHWAY INFORMATION Metabolic Pathway 7 C verified Verification Date Figure 2 2 Pathway Wizard form for creating a new pathway 2 2 Creating New Pathways Using Pathway Editor to create a new pathway is quite easy As shown in Figure 2 1 we can create a new pathway by right clicking the Pathways node and choosing Editor and then New pathway in the popup context menu The screen shot of pathway wizard is shown in figure 2 2 Figure 2 2 shows the main form for creating a new pathway The only information that users need to enter at this time is the pathway s name Other information can b
29. ying pathways e Deleting pathways processes and molecules S Genomes Pathway Browser 1 1 metabolic pathways fe File View Query Web Resources Customize Help Pathways G aatestm 2 aaa test 3 Biosynthesis and degradation of ascorbate Biosynthesis and degradation of Biotin Biosynthesis and degradation of catecholamin Biosynthesis and degradation of histidine gt Biosynthesis and degradation of thyroid hormo 4 Biosynthesis of aromatic amino acids and of qu EX Biosynthesis of glycerophospholipids amp Biosynthesis of Pantothenate Coenzyme A an G Biosynthesis of Riboflavin FMN and FAD S Biosynthesis of thiamin in E coli Cholesterol biosynthesis m Citrate cycle 2 Conversions and degradation of cysteine Degradation of glycerophospholipids Derivatives and degradation of phenylalanine amp Derivatives and degradation of tryptophan nam gure Folate pathway M SH SQ RMAQ GS 6H NEHA Formation and degradation of triacylglycerols Glutathione Metabolism Homocysteine pathway Interconversions and degradation of purine de nterconversions and degradation of pyrimidine 2 Lysine Threonine Methionine and Cysteine M Metabolism of Choline Betaine and Sarcosine Metabolism of ether lipids Ge Metabolism of glucocorticoids and mineral cort Metabolism of Sphingophospholipids 2 Metabolism of the branched chain amino acid Be my pathway Phenylpropanoid compounds in plants Z P
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