1. SRI International Bioinformatics Update your computers! To install a patch: Tools => Instant Patch => Download and Activate All Patches

2. Editing Pathway/Genome Databases Part I: Compounds, Reactions and Pathways Ron Caspi

3. SRI International Bioinformatics Why Curation is Important! Database curation greatly enhances the usefulness of the data “in silico” information less solid than experimental evidence

4. SRI International Bioinformatics Pathway Tools Paradigms Separate database from user interface Navigator provides one interface to the DB Editors provide an alternative interface to the DB Reuse information whenever possible! A PGDB should not describe the same biological or chemical entity more than once Compounds are the building blocks of reactions Reactions are the building blocks of pathways

5. SRI International Bioinformatics List of Editors Compound Editor Compound Structure Editor Reaction Editor Pathway Editor Synonym Editor Protein Editor Gene Editor Intron Editor (Eukaryotes only) Transcription Unit Editor Publication Editor Frame Editor Relationships Editor Ontology Editor

6. SRI International Bioinformatics Invoking the Editors Or: Right-Click on an Object Handle Use the “New” command

7. SRI International Bioinformatics Saving Changes The user must save changes explicitly with Save DB To discard changes made since last save l File => Revert Current DB

8. SRI International Bioinformatics The File Menu: DB commands List Unsaved Changes in Current DB Revert Current DB Refresh All Current DBs Checkpoint Current DB Revert to Checkpoint in Current DB Delete a DB Save Current DB Attempt to Reconnect to Oracle

9. SRI International Bioinformatics Editing rules: Support Policy Do not alter DB schema l e.g. do not add or remove classes or slots Do not modify the EcoCyc or MetaCyc datasets

10. SRI International Bioinformatics Compound Editor Create or edit a compound Invoke by: New: Compound => New Existing: Right-Click compound name, select Compound Editor Common name and synonyms links to other DBs

11. SRI International Bioinformatics More Compound Editing Compound Structure Editor Mol files Exporting to other DBs Merging

12. SRI International Bioinformatics Reaction Editor Create or edit a reaction Invoke by: New: Reaction => New Existing: Right-Click reaction name, select Reaction Editor Entering Reaction Equation Compound Resolver

13. SRI International Bioinformatics Pathway Editor Graphically create and modify pathways Two tools: l Connections Editor: to add reactions, remove reactions, alter connections l Segment Editor: to enter a linear pathway segment(s) Invoking the pathway editor: New: Pathway => New Existing: Right-Click pathway name, select Pathway Editor command

14. SRI International Bioinformatics Connections Editor Operations Two main display panes: l left: unconnected pathway reactions l right: draws connected reactions (looks like the regular Pathway Tools window) Connecting reactions: l select initial reaction (in either pane) ===> red and green reactions l select a green reaction Additional Commands: l Exit: keep changes, abort changes l 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 l 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

15. SRI International Bioinformatics Connections Editor Limitations Ambiguity in some complicated situations on ordering: l link may be ignored l dialog box for disambiguating l pathway drawn in bizarre arrangement Fix: l try removing offending link and add links in different order Pathway editor does not handle polymerization pathways In circular pathways, Pathway editor does not permit specification which compound should be at the top

16. SRI International Bioinformatics Pathway Segment Editor To enter linear sequence of reactions (arguably) faster than with the Connections Editor Reactions are specified by EC numbers or reaction substrates One segment may contain up to 7 reactions

17. SRI International Bioinformatics Creating Links with External Databases Creating links from a pathway/genome db to an external database To define a new external database: Tools => Ontology Browser View => Browse from new root / type Databases Highlight Databases Frame => Create => Instance Enter frame name, frame edit Enter Common Name, Static-Search-URL e.g. http:/gene.pharma.com/dbquery? Creating links to a pathway/genome db see http://biocyc.org/linking.shtmlhttp://biocyc.org/linking.shtml

18. SRI International Bioinformatics Make sure that… You perform all exercises on the Hb. pylori database, not on your own!!!

19. SRI International Bioinformatics Creating New Reactions Create the following five reactions: 1. ascorbate + H 2 O = 3-keto-L-gulonate 2. 3-keto-L-gulonate + ATP = 3-keto-L-gulonate-6-phosphate + ADP 3. 3-keto-L-gulonate-6-phosphate = L-xylulose-5-phosphate + CO 2 4. L-xylulose-5-phosphate = L-ribulose-5-phosphate* 5. L-ribulose-5-phosphate = xylulose-5-phosphate

20. SRI International Bioinformatics Create a New Compound

21. SRI International Bioinformatics Define a New Pathway Define the pathway L-ascorbate degradation to xylulose-5- phosphate by connecting the reactions together Assign class: (Pathways -> Degradation/Utilization/Assimilation -> Carboxylates, Other) Add a link to non-oxidative branch of the pentose phosphate pathway (Generation of precursor metabolites and energy => Pentose phosphate pathways =>) Add a reverse link from non-oxidative branch of the pentose phosphate pathway to the new pathway

22. SRI International Bioinformatics Pathway Curation Class Common Name Synonyms Evidence code Citations Comments Links Hypothetical reactions

23. SRI International Bioinformatics Evidence Codes for Pathways http://brg.ai.sri.com/ptools/evidence-ontology.html EV-AS: Author statement l NAS – non-traceable l TAS - traceable EV-COMP: Inferred from computation l AINF - Artificial inference l HINF - Human inference EV-EXP: Inferred from experiment l IDA - inferred from direct assay l IEP - inferred from expression pattern l IGI - inferred from genetic interaction l IMP- inferred from mutant phenotype l IPI - inferred from physical interaction EV-IC: Inferred by curator

24. SRI International Bioinformatics Super Pathways Create more complex metabolic networks using superpathways Example: superpathway of alanine biosynthesis composed of alanine biosynthesis I alanine biosynthesis II alanine biosynthesis III

25. SRI International Bioinformatics Pathway Export Export l Edit => Add Pathway to File Export List l File => Export => Selected Pathways to File

26. SRI International Bioinformatics Constraint Checking General rules that constrain the valid relationships among instances Constraints are checked when new facts are asserted to assure that the DB remains logically consistent Constraints on slots: l Domain violation checks to make sure the slots are in instances of the appropriate class l Range violation : u value type u value cardinality l Inverse l Cardinality l Lisp-predicate

27. SRI International Bioinformatics Consistency Checking (correctify-kb) Removes newlines from names Converts “<“ to “|” in string citations Checks isozyme sequence similarity Fixes 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 Checks reaction balancing Checks compound structures Calculates sub- and super-pathways Finds missing sub-pathways links Verifies chromosome components and positions

28. SRI International Bioinformatics Run (correctify- kb) Open the database Hb. pylori (HypCyc) Run (correctify-kb) Analyze output