1. Editing Pathway/Genome Databases Compounds, Reactions and Pathways Ron Caspi

2. SRI International Bioinformatics Activate Editing Mode Type (enable/disable-editors t) at the listener pane

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

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 A tool helps to prevent creation of duplicate reactions

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

6. SRI International Bioinformatics List of Editors Compound Editor Compound Structure Editors Reaction Editor Synonym Editor Publication Editor Pathway Editor and Pathway Info Editor Protein/Subunit structure/Enzymatic Reaction Editors Gene Editor Intron Editor (Eukaryotes only) Transcription Unit Editor Frame Editor Relationships Editor Ontology Editor

7. SRI International Bioinformatics Saving Changes The user must save changes explicitly l File => Save Current DB l Save DB button List Unsaved Changes in Current DB Revert Current DB Checkpoint Current DB Updates to File Restore Updates from Checkpoint File

8. SRI International Bioinformatics 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

9. SRI International Bioinformatics Invoking the Editors 2. Existing Object: Right-Click on the Object Handle 1. New Object: Use the “New” command

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

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

12. SRI International Bioinformatics 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.

13. SRI International Bioinformatics More Compound Editing Compound Structure Editors (Marvin, JME) Mol files Exporting to other DBs Merging Duplicate Frame and Edit

14. SRI International Bioinformatics Reaction Editor Enter or edit a reaction equation EC number (official?) Check for balance Compound Resolver

15. SRI International Bioinformatics Pathway Info Editor Class (variant class) Common Name Synonyms Evidence code Citations (CIT) Comments External Links Hypothetical reactions Author credits

16. SRI International Bioinformatics Pathway Editor Graphically create and modify pathways Two tools: l Connections Editor: add reactions one by one l Segment Editor: enter a linear pathway segment

17. 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 display window) Connecting reactions: l select initial reaction (in either pane) ===> red and green reactions l select a green reaction Useful Commands: l choose main compounds for reaction l disconnect all reactions In circular pathways, specify which compound should be at the top Add links to other pathways, reactions, or comments

18. SRI International Bioinformatics Pathway Segment Editor To enter linear sequence of reactions simultaneously Reactions are specified by EC numbers or reaction substrates One segment may contain up to 7 reactions

19. SRI International Bioinformatics Pathway Editor Limitations Complex situations can cause ambiguity: 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 easily.

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

21. SRI International Bioinformatics Enzyme/Protein Editors To add an enzyme to a reaction: Right click the reaction, choose Edit => Create/Add enzyme. “Choose Protein”: specify ID, or “Search by genes or create new protein” => Protein subunit structure editor Protein Editor Check the Curator Guide at http://bioinformatics.ai.sri.com/ptools/curatorsguide.pdf

22. SRI International Bioinformatics Protein Editor

23. SRI International Bioinformatics Enzymatic Reaction Editor

24. SRI International Bioinformatics Protein Subunit Editor

25. SRI International Bioinformatics Super Pathways Need to keep pathways within well-defined end points Link pathways to upstream or downstream pathways with pathway links. Create more complex metabolic networks using superpathways Example: superpathway of aromatic compound degradation (aerobic)superpathway of aromatic compound degradation (aerobic) is composed of: catechol degradation II mandelate degradation I benzoate degradation (aerobic)  -ketoadipate degradation protocatechuate degradation II shikimate degradation quinate degradation 4-hydroxymandelate degradation tryptophan degradation I

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

27. SRI International Bioinformatics Creating Links to External Databases Creating links from a PGDB to external databases 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? Enter a value for Search-Object-Class (e.g. Proteins) Creating links to a PGDB see http://biocyc.org/linking.shtmlhttp://biocyc.org/linking.shtml

28. 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

29. SRI International Bioinformatics Consistency Checking (correctify-kb) Removes newlines from names Converts “<“ to “|” in string citations Checks isozyme sequence similarity Fixes references between polypeptides and 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

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

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

32. SRI International Bioinformatics Creating New Reactions Don’t forget to include spaces between chemical names and terms such as “+” and “=“: 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 6. xylulose-5-phosphate = D-ribulose-5-phosphate

33. SRI International Bioinformatics Fill Reaction frame ID’s in your handout ReactionFrame ID ascorbate + H2O = 3-keto-L-gulonateXXX 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

34. SRI International Bioinformatics Duplicate Reaction? Frame ID of the new reaction to be created. This frame will NOT be created unless you choose “Keep” Frame ID of the existing reaction. This reaction will NOT be transferred into your database until you click “Import”! Record this BEFORE you click “Import”

35. SRI International Bioinformatics Define a New Pathway Define the pathway L-ascorbate degradation to D-ribulose-5- phosphate by connecting the reactions together Assign class: (Pathways -> Degradation/Utilization/Assimilation -> Carboxylates, Other) Add the reactions, conect them, and add a link to the pathway 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

36. SRI International Bioinformatics Run (correctify- kb) Open the database Hb. pylori (HypCyc) (so ‘hyp) Run (correctify-kb) Analyze output