Instructions for Arabidopsis Reactome Authors

Janet Higgins

November 2008

janet.higgins@bbsrc.ac.uk

Contents

1. Workflow in Arabidopsis Reactome2. Reactome Data Model3. Types of Reaction4. Authoring a module5. Information required6. Formatting of the information in Word document7. Gene and reference list in Excel8. How to use Author Tool9. Author Tool – Graphic editor10. Author Tool – Property editor11. SBGN Author Tool – Graphic editor12. Example of Phosphorylation reaction in Reactome13. Example of Complex formation in Reactome14. Example of Transport in Reactome15. Example of Transcription in Reactome16. Example of Translation in Reactome

Workflow for authoring and curation of pathways in Arabidopsis Reactome

Author

Arabidopsis Reactome(development)

Author tool

Curator tool

Review Data

Revise Data

Data

Data

Data and revisions

Scientific expert

Reactome curator

Peer Review

Arabidopsis Reactome(web)

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Reactome Data ModelLife 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

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Input 1

Input 2

OutputReaction

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.

Binding/complex formation

Degradation

Cytosol Nucleus

AA

B

Transport

A A

Phosphorylation Dephosphorylation

PAA A

Catalyst

mRNA A

B

3. Types of Reaction

Transcription Translation

Regulation

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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.

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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

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.

Information Required 5

1. 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: eg nucleoplasm 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

Format your information as shown below in a word document 6

Gene and Reference list in Excel

Gene name AGI code

PHYA AT1G09570

PHYB AT2G18790

PHYC AT5G35840

PHYD AT4G16250

PHYE AT4G18130

CRY1 AT4G08920

CRY2 AT1G04400

Example of gene list Example of reference list

  author date subject PubMed

1 McClung 2006 History  

2 Gardner 2006 review 16761955

3 Locke 2005 BIOMD55 16729048

4 Locke 2006 BIOMD89 17102804

5 Zeilinger 2006 PRR7/9 17102803

6 Dodd 2005 growth 16040710

7 Covington 2007 auxin 17683202

8 Ding 2007 TIC 17496120

9 McWatters 2007 ELF4 17384164

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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

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The SBGN version of author tool can be accessed at http://brie8.cshl.org:8080/ReactomeTools/AuthorTool/authorToolLaunch.html

Author Tool – Graphic Editor

Produce

Associate

Phosphorylate

Inhibit

Activate

Interact

Encode

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Author Tool – Property Editor 10

Produce

Associate

Phosphorylate

Inhibit

Activate

Interact

Encode

SBGN Author Tool – Graphic Editor 11

Example of Phosphorylationhttp://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47737&

nucleoplasm GO:0005654

PubMed Id

15316110

EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702

INPUT OUTPUT

Phosphorylation of CDTa by CDKA/CYCD2;1CDT1a

AT2G31270

nucleoplasm GO:0005654

Phospho - CDT1a

AT2G31270

CDKA;1:CYCD2;1 complex

Catalyst

CDKA;1:CYCD2;1 complex made up of CYCD2;1

AT2G22490+

CDKA;1

AT2G48750

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Example of Complex Formationhttp://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47539&

nucleoplasm GO:0005654

PubMed Id

16856985

Phospho-(Ser162,Thr168) CDKD;2

AT1G66750

EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702

INPUT OUTPUT

nucleoplasm GO:0005654

Formation of CDKD:CYCH Complex

CYCH;1

AT5G26720

nucleoplasm GO:0005654

Phospho-(Ser162,Thr168) CDKD;2 :CYCH;1 complex

13

Example of Transport http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&ID=47328&

cytosol GO:0005654

PubMed Id

16845478

CDKA;1

AT1G66750

EVENT Arabidopsis thaliana NCBI taxonomy:3702

INPUT OUTPUT

Transport of CDKA into the nucleus

nucleoplasm GO:0005654

CDKA;1

AT1G66750

Regulated by

ICK1 At2g23430

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Example of TranscriptionExample in developer copy of Reactome

PubMed Id

15767265

EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702

OUTPUT

Transcription of PRR5 regulated by CCA1 and LHY

nucleoplasm GO:0005654

prr5 mRNA

RefSeq:NM_122355

Positive or negative regulation

CCA1

AT2G46830

This is a black box reaction so it requires no input

LHY

AT1G01060

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Example of Translation

PubMed Id

15767265

EVENT cytosol GO:0005829 Arabidopsis thaliana NCBI taxonomy:3702

OUTPUT

Translation of mRNA to PRR5 protein

cytosol GO:0005829

prr5 mRNA

RefSeq:NM_122355

PRR5

AT5G24470

INPUT

cytosol GO:0005829

Example in developer copy of Reactome

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