1. SRI International Bioinformatics 1 Editing Pathway/Genome Databases Ron Caspi

2. SRI International Bioinformatics 2 Pathway Tools in Editing Mode ●The database is separate from the user interface ●The Navigator provides one interface to the DB ●Editors provide an alternative interface to the DB

3. SRI International Bioinformatics 3 Things to remember ●The editors are there for editing your own PGDB. Do not modify the EcoCyc or MetaCyc datasets ●Try to not alter the DB schema. Such changes may be overwritten when updating to a new version ●e.g. do not add or remove classes or slots ●Avoid Duplication! Reuse information whenever possible ●A PGDB should not describe the same biological or chemical entity more than once ●Some tools help preventing inadvertent creation of duplicate reactions/compounds

4. SRI International Bioinformatics 4 List of Editors ●Compound Editor/Compound Structure Editors ●Reaction Editor ●Pathway Editor and Pathway Info Editor ●Protein/Subunit structure/Enzymatic Reaction Editors ●Synonym Editor ●Publication Editor ●Author/Organization Editor ●Gene Editor ●Intron Editor (Eukaryotes only) ●Transcription Unit Editor ●External database Editor ●Frame Editor ●Ontology Editor

5. SRI International Bioinformatics 5 Activating Editing Mode ●Type (enable/disable-editors t) at the listener pane

6. SRI International Bioinformatics 6 Saving Changes ●The user must save changes explicitly ●File => Save Current DB ●Save DB button ●Revert Current DB The following commands are only available for databases stored in MySQL or Oracle: ●List Unsaved Changes in Current DB ●Checkpoint Current DB Updates to File ●Restore Updates from Checkpoint File

7. SRI International Bioinformatics 7 Other DB commands under the File menu ●Summarize databases ●Summarize current organism ●Refresh DB list ●Refresh All Current DBs ●Delete a DB ●Attempt to Reconnect to Database Server

8. SRI International Bioinformatics 8 Invoking the Editors New Object: Use the “New” command under top menus, or the “Create” command under the File menu (new feature) Existing Object: Right-Click on the Object Handle, select Edit, then the appropriate editor

9. SRI International Bioinformatics 9 Compound Editor ●Create or edit a compound ●Specify Class ●Common Name and Synonyms ●Comments, citations ●Links to other DBs

10. SRI International Bioinformatics 10 More Compound Editing ●Compound Structure Editors (Marvin, JME) http://www.chemaxon.com/marvin/index.html ●Export/Import to Mol files ●Exporting to other DBs ●Merging ●Duplicate Frame and Edit

11. SRI International Bioinformatics 11 The Synonym Editor ●Lets you easily edit the synonyms and set the common name

12. SRI International Bioinformatics 12 Reaction Editor ●Enter or edit a reaction equation ●Set Conversion Type ●EC number (official?) ●Compartments (transport) ●Create new instances or classes

13. SRI International Bioinformatics 13 Pathway Info Editor Class (variant class) Common Name Synonyms Evidence Codes Citations (CIT) Summary External Links Hypothetical reactions Enzymes not in use Author credits

14. SRI International Bioinformatics 14 Evidence Codes for Pathways ●http://bioinformatics.ai.sri.com/evidence-ontology/http://bioinformatics.ai.sri.com/evidence-ontology/ ●Experimental evidence codes: ●IDA: inferred from direct assay ●IEP: inferred from expression pattern ●IPI: inferred from physical interaction ●TAS: traceable author statement ●IGI: inferred from genetic interaction ●IMP: inferred from mutant phenotype Full documentation for an evidence code is displayed in the Navigator (click the code icon)

15. SRI International Bioinformatics 15 Pathway Editor ●Graphically create and modify pathways ●Reaction Menu: add reactions one by one ●Pathway Menu: enter a linear pathway segment, add subpathways

16. SRI International Bioinformatics 16 Connections Editor Operations

17. SRI International Bioinformatics 17 Pathway Editor Limitations ●Complex situations can cause ambiguity: ●link may be ignored ●dialog box for disambiguating ●pathway drawn in bizarre arrangement ●Fix: ●try removing offending link and add links in different order ●The Pathway Editor does not handle polymerization pathways easily.

18. SRI International Bioinformatics 18 Overview of Creating a Pathway ●Identify all the metabolites. Define any missing ones. ●Find the individual reactions in the PGDB/MetaCyc, and create new reactions if necessary. ●Compose the pathway from the individual reactions using the pathway editor ●Assign a class for the pathway ●Add a summary, citations, and evidence code ●Assign the appropriate enzymes, create complexes when appropriate. ●Curate information about enzymes and genes, including evidence codes for all enzymes.

19. SRI International Bioinformatics 19 Tutorial: Compounds, Reactions and Pathways

20. SRI International Bioinformatics 20 Import MetaCyc reactions instead of creating duplicates! If the reaction is already present in MetaCyc, you will see a window like this one You should choose the option “Import”. However, you MUST write down the frame ID of the identical reaction, so you could use it later when specifying the pathway.

21. SRI International Bioinformatics 21 Reuse existing reactions instead of creating duplicates! If the reaction is already present in your PGDB, you will see a window like this one You should choose the option “Delete”. However, you MUST write down the frame ID of the identical reaction, so you could use it later when specifying the pathway.

22. SRI International Bioinformatics 22 Fill Reaction frame ID’s in your handout ReactionFrame ID ascorbate + H2O = 3-keto-L-gulonate RXN0-707 3-keto-L-gulonate + ATP = 3-keto-L-gulonate 6-phosphate + ADP 3-keto-L-gulonate 6-phosphate = L-xylulose-5-phosphate + CO2 L-xylulose-5-phosphate = L-ribulose-5-phosphate L-ribulose-5-phosphate = xylulose-5-phosphate xylulose-5-phosphate = D-ribulose-5-phosphate

23. SRI International Bioinformatics 23 Creating New Reactions Don’t forget to include spaces between chemical names and terms such as “+” and “=“:  ascorbate + H 2 O = 3-keto-L-gulonate  3-keto-L-gulonate + ATP = 3-keto-L-gulonate-6-phosphate + ADP  3-keto-L-gulonate-6-phosphate = L-xylulose-5-phosphate + CO 2  L-xylulose-5-phosphate = L-ribulose-5-phosphate  L-ribulose-5-phosphate = xylulose-5-phosphate  xylulose-5-phosphate = D-ribulose-5-phosphate

24. SRI International Bioinformatics 24 Curating Enzymes

25. SRI International Bioinformatics 25 Adding an Enzyme to a Reaction ●To add an enzyme to a reaction: ● Right click the reaction, choose Edit → Create/Add enzyme. ●If the enzyme exists, specify its ID. If not, click “Search by genes or create new protein” ●The Protein Subunit Structure Editor pops up

26. SRI International Bioinformatics 26 Specifying Enzyme Complexes

27. SRI International Bioinformatics 27 Specifying Multiple Subunits

28. SRI International Bioinformatics 28 The Enzyme Editor General info Enzymatic Reaction(s) (1..n) Subunit(s) (0..n)

29. SRI International Bioinformatics 29 Protein Editor For an example, open CPLX-6621 in MetaCyc

30. SRI International Bioinformatics 30 Enzymatic Reaction Editor

31. SRI International Bioinformatics 31 Protein Subunit Editor Specify the copy number of each subunit Specify UniProt ID if available, experimental MW, and any useful info that may apply

32. SRI International Bioinformatics 32 Citations ●Citation boxes ●The CITS field ●File =>Import Citations from PubMed ●Publication editor (invoke by right clicking on a citation at bottom) Non PubMed citation: Enter in citation box in the form Smith06, invoke editor by clicking out of a citation box.

33. SRI International Bioinformatics 33 Tutorial: Enzymes, citations and export