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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
3
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 [email protected]
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The SBGN version of author tool can be accessed at http://brie8.cshl.org:8080/ReactomeTools/AuthorTool/authorToolLaunch.html
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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