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Editing Pathway/Genome Databases

Ron Caspi SRI International Bioinformatics

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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 SRI International Bioinformatics

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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 SRI International Bioinformatics

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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 SRI International Bioinformatics

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Activating Editing Mode

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Type (enable/disable-editors t) at the listener pane

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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 SRI International Bioinformatics

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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 SRI International Bioinformatics

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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 SRI International Bioinformatics

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Compound Editor

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

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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 SRI International Bioinformatics

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The Synonym Editor

● Lets you easily edit the synonyms and set the common name SRI International Bioinformatics

12 ● ● ● ● ● Enter or edit a reaction equation Set Conversion Type EC number (official?) Compartments (transport) Create new instances or classes

Reaction Editor

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Pathway Info Editor

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

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Evidence Codes for Pathways

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http://bioinformatics.ai.sri.com/evidence-ontology/

● Experimental evidence codes: ● ● ● ● ● ● IDA: IEP: IPI: inferred from physical interaction TAS: IGI: IMP: inferred from direct assay inferred from expression pattern traceable author statement inferred from genetic interaction inferred from mutant phenotype Full documentation for an evidence code is displayed in the Navigator (click the code icon) SRI International Bioinformatics

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Pathway Editor

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

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Connections Editor Operations

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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.

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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.

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Tutorial: Compounds, Reactions and Pathways

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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.

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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, pathway.

you MUST write down the frame ID of the identical reaction, so you could use it later when specifying the SRI International Bioinformatics

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Fill Reaction frame ID’s in your handout

Reaction

ascorbate + H2O = 3-keto-L-gulonate

Frame ID

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 SRI International Bioinformatics

Creating New Reactions

23 Don’t forget to include spaces as “+” and “=“: between chemical names and terms such 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 SRI International Bioinformatics

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Curating Enzymes

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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 SRI International Bioinformatics

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Specifying Enzyme Complexes

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Specifying Multiple Subunits

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The Enzyme Editor

General info Enzymatic Reaction(s) (1..n) Subunit(s) (0..n) SRI International Bioinformatics

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Protein Editor

For an example, open CPLX-6621 in MetaCyc SRI International Bioinformatics

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Enzymatic Reaction Editor

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Protein Subunit Editor

 Specify the copy number of each subunit  Specify UniProt ID if available, experimental MW, and any useful info that may apply 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) 32 Non PubMed citation: Enter in citation box in the form Smith06 , invoke editor by clicking out of a citation box.

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33 Tutorial: Enzymes, citations and export SRI International Bioinformatics