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Instructions for Arabidopsis Reactome Authors

Instructions for Arabidopsis Reactome Authors. Janet Higgins November 2008 janet.higgins@bbsrc.ac.uk. Contents. Workflow in Arabidopsis Reactome Reactome Data Model Types of Reaction Authoring a module Information required Formatting of the information in Word document

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Instructions for Arabidopsis Reactome Authors

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  1. Instructions for Arabidopsis Reactome Authors Janet Higgins November 2008 janet.higgins@bbsrc.ac.uk

  2. Contents • Workflow in Arabidopsis Reactome • Reactome Data Model • Types of Reaction • Authoring a module • Information required • Formatting of the information in Word document • Gene and reference list in Excel • How to use Author Tool • Author Tool – Graphic editor • Author Tool – Property editor • SBGN Author Tool – Graphic editor • Example of Phosphorylation reaction in Reactome • Example of Complex formation in Reactome • Example of Transport in Reactome • Example of Transcription in Reactome • Example of Translation in Reactome

  3. Peer Review Arabidopsis Reactome (web) 1 Workflow for authoring and curation of pathways in Arabidopsis Reactome Scientific expert Author Data Author tool Reactome curator Data Curator tool Revise Data Data and revisions Arabidopsis Reactome (development) Review Data

  4. Input 1 Reaction Output Input 2 2 Reactome Data Model Life on the cellular level is a network of molecular interactions. Molecules are synthesized and degraded, transported from one location to another, and form complexes with other molecules. Reactome represents all of this complexity as reactions in which input physical entities are converted to output entities as shown below Reactions are linked together by shared physical entities: a product from one reaction may be a substrate in another reaction and may catalyze another. Reactions are grouped into pathways (sets of interlinked reactions), pathways are grouped into larger pathways forming a hierarchical structure.

  5. Transport Phosphorylation Dephosphorylation A A A A P A 3 3. Types of Reaction Binding/complex formation Transcription Translation A mRNA A A B Regulation B Degradation Cytosol Nucleus Catalyst

  6. 4 Authoring a module(Please refer to slide number in brackets) • Make a list of genes in the pathway (7) and group them into separate mini-pathways. • Collate the information (5 and 6) in a word document. • Optional - Input your pathway using Author Tool (8-10). The Reactome Curator can use the information in a word document to input the pathway directly into Curator Tool. • Make a list of references (7) used as experimental evidence for reactions and pathways. Slides 12 to 16 shows examples of different types of reaction showing the information required for each reaction. Please click on the links to see the reaction in Reactome

  7. Information Required 5 1. The entities involved and what state they are in (ie dimer, phosphorylated etc) and their compartment 2. If applicable, the catalyst - composed of the actual entity with a GO molecular function ID assigned to it if available. 3. The compartment where this event takes place - we do allow adjacent compartments eg an entity in the cytosol binds to an entity in the plasma membrane 4. A PUBMED literature reference which defines the event, experimentally, in Arabidopsis. 5. IDs – AGI for proteins, ChEBI/KEGG IDs for small molecules, GO compartment IDs for compartments and GO molecular function IDs for mol function. Also, GO Biological Process terms for Pathways. 6. The organism - obviously we are working on Arabidopsis but if an event is described experimentally in another organism (and there are many examples of that), we create the event in that organism and link it to our Arabidopsis event, showing the homologs in Arabidopsis. 7. Summations – these are free text summaries we can add to pathways and reactions to give extra meaning to what is happening in that particular event. For pathways, we would expect a fairly substantial explanation of the pathway, for reactions we expect a short description of that reaction may be helpful.

  8. 6 Format your information as shown below in a word document • NAME OF EVENT: Pathway eg Formation of CDKD:CYCH complex by CDK-activating kinase • GO biological process: for pathways normally • EVENT compartment: nucleoplasm GO:0005654 • PubMed IDs: for pathways, reviews • SPECIES:Arabidopsis thaliana • SUMMATION: eg The CDK-activating kinase pathway involving CDKF and CDKD associated with CYCH is required for full activation of the CDKA/CYCD complex. • 1.1 NAME OF EVENT: Reaction eg Formation of CDKD:CYCH complex • EVENT compartment: egnucleoplasm GO:0005654 • PubMed IDs: for reactions, the experimental evidence • SPECIES:Arabidopsis thaliana • INPUT 1: eg Phospho-(Ser162,Thr168) CDKD;2 AT1G66750 • INPUT 2: eg CYCH;1 AT5G26720 • CATALYST: where applicable including GO molecular function • OUTPUT: eg Phospho-(Ser162,Thr168) CDKD;2 :CYCH;1 complex • SUMMATION: if more information will be helpful

  9. 7 Gene and Reference list in Excel Example of gene list Example of reference list

  10. 8 How to use the Author Tool • Start Author Tool version 3.0 in Java Web Start from http://n55960/download/index.html • Add Objects by clicking on them in the Palette. • Join the objects together using the various options available. • Add detail in Property editor. • A user guide will be available later this year, if you have any questions email help@arabidopsisreactome.org The SBGN version of author tool can be accessed at http://brie8.cshl.org:8080/ReactomeTools/AuthorTool/authorToolLaunch.html

  11. 9 Author Tool – Graphic Editor Produce Associate Phosphorylate Inhibit Activate Interact Encode

  12. 10 Author Tool – Property Editor

  13. 11 SBGN Author Tool – Graphic Editor Produce Associate Phosphorylate Inhibit Activate Interact Encode

  14. 12 Example of Phosphorylationhttp://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47737& EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 Phosphorylation of CDTa by CDKA/CYCD2;1 CDT1a AT2G31270 Phospho - CDT1a AT2G31270 nucleoplasm GO:0005654 nucleoplasm GO:0005654 Catalyst CDKA;1:CYCD2;1 complex PubMed Id 15316110 INPUT OUTPUT CDKA;1 AT2G48750 CYCD2;1 AT2G22490 made up of + CDKA;1:CYCD2;1 complex

  15. 13 Example of Complex Formationhttp://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47539& EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 Phospho-(Ser162,Thr168) CDKD;2 AT1G66750 Formation of CDKD:CYCH Complex nucleoplasm GO:0005654 Phospho-(Ser162,Thr168) CDKD;2 :CYCH;1 complex nucleoplasm GO:0005654 nucleoplasm GO:0005654 PubMed Id 16856985 CYCH;1 AT5G26720 INPUT OUTPUT

  16. 14 Example of Transport http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&ID=47328& EVENT Arabidopsis thaliana NCBI taxonomy:3702 Transport of CDKA into the nucleus CDKA;1 AT1G66750 CDKA;1 AT1G66750 cytosol GO:0005654 nucleoplasm GO:0005654 Regulated by ICK1 At2g23430 PubMed Id 16845478 INPUT OUTPUT

  17. 15 Example of Transcription Example in developer copy of Reactome EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 PubMed Id 15767265 Transcription of PRR5 regulated by CCA1 and LHY prr5 mRNA RefSeq:NM_122355 This is a black box reaction so it requires no input nucleoplasm GO:0005654 Positive or negative regulation CCA1 AT2G46830 LHY AT1G01060 OUTPUT

  18. 16 Example of Translation Example in developer copy of Reactome EVENT cytosol GO:0005829 Arabidopsis thaliana NCBI taxonomy:3702 PubMed Id 15767265 Translation of mRNA to PRR5 protein PRR5 AT5G24470 prr5 mRNA RefSeq:NM_122355 cytosol GO:0005829 cytosol GO:0005829 INPUT OUTPUT

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