Instructions for Arabidopsis Reactome Authors

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Instructions for Arabidopsis Reactome Authors
Janet Higgins November 2008 janet.higgins_at_bbsrc.ac
.uk
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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

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Workflow for authoring and curation of pathways
in Arabidopsis Reactome
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Scientific expert
Author
Data
Author tool
Reactome curator
Data
Curator tool
Revise Data
Data and revisions
Arabidopsis Reactome (development)
Review Data
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Reactome Data Model
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• 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.
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3. Types of Reaction
Binding/complex formation
Transcription
Translation
A
mRNA
A
A
B
Regulation
B
Degradation
Cytosol Nucleus
Catalyst
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Authoring a module(Please refer to slide number
in brackets)
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• 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
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Information Required
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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.
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Format your information as shown below in a word
document

• NAME OF EVENT Pathway eg Formation of CDKDCYCH
  complex by CDK-activating kinase
• GO biological process for pathways normally
• EVENT compartment nucleoplasm GO0005654
• 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
  CDKDCYCH complex
• EVENT compartment eg nucleoplasm
  GO0005654
• PubMed IDs for reactions, the
  experimental evidence
• SPECIES Arabidopsis thaliana
• INPUT 1 eg Phospho-(Ser162,Thr168)
  CDKD2 AT1G66750
• INPUT 2 eg CYCH1 AT5G26720
• CATALYST where applicable including GO
  molecular function
• OUTPUT eg Phospho-(Ser162,Thr168
  ) CDKD2 CYCH1 complex
• SUMMATION if more information will be
  helpful

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Gene and Reference list in Excel
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Example of gene list
Example of reference list
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How to use the Author Tool
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• 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_at_arabidopsisreactome.org

The SBGN version of author tool can be accessed
at http//brie8.cshl.org8080/ReactomeTools/Author
Tool/authorToolLaunch.html
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Author Tool Graphic Editor
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Produce Associate Phosphorylate Inhibit Activate I
nteract Encode
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Author Tool Property Editor
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SBGN Author Tool Graphic Editor
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Produce Associate Phosphorylate
Inhibit Activate Interact Encode
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Example of Phosphorylationhttp//n55960/cgi-bin/e
ventbrowser?DBtest_reactome_9_ath_allFOCUS_SPECI
ESArabidopsis20thalianaID47737
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EVENT
nucleoplasm GO0005654
Arabidopsis thaliana NCBI taxonomy3702
Phosphorylation of CDTa by CDKA/CYCD21
CDT1a AT2G31270
Phospho - CDT1a AT2G31270
nucleoplasm GO0005654
nucleoplasm GO0005654
Catalyst
CDKA1CYCD21 complex
PubMed Id 15316110
INPUT
OUTPUT
CYCD21 AT2G22490
CDKA1 AT2G48750
made up of

CDKA1CYCD21 complex
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Example of Complex Formationhttp//n55960/cgi-bin
/eventbrowser?DBtest_reactome_9_ath_allFOCUS_SPE
CIESArabidopsis20thalianaID47539
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EVENT
nucleoplasm GO0005654
Arabidopsis thaliana NCBI taxonomy3702
Phospho-(Ser162,Thr168) CDKD2 AT1G66750
Formation of CDKDCYCH Complex
nucleoplasm GO0005654
Phospho-(Ser162,Thr168) CDKD2 CYCH1 complex
nucleoplasm GO0005654
nucleoplasm GO0005654
PubMed Id 16856985
CYCH1 AT5G26720
INPUT
OUTPUT
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Example of Transport http//n55960/cgi-bin/eventb
rowser?DBtest_reactome_9_ath_allID47328
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EVENT
Arabidopsis thaliana NCBI taxonomy3702
Transport of CDKA into the nucleus
CDKA1 AT1G66750
CDKA1 AT1G66750
cytosol GO0005654
nucleoplasm GO0005654
Regulated by
ICK1 At2g23430
PubMed Id 16845478
INPUT
OUTPUT
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Example of Transcription
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Example in developer copy of Reactome
EVENT
nucleoplasm GO0005654
Arabidopsis thaliana NCBI taxonomy3702
PubMed Id 15767265
Transcription of PRR5 regulated by CCA1 and LHY
prr5 mRNA RefSeqNM_122355
This is a black box reaction so it requires no
input
nucleoplasm GO0005654
Positive or negative regulation
CCA1 AT2G46830
LHY AT1G01060
OUTPUT
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Example of Translation
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Example in developer copy of Reactome
EVENT
cytosol GO0005829
Arabidopsis thaliana NCBI taxonomy3702
PubMed Id 15767265
Translation of mRNA to PRR5 protein
PRR5 AT5G24470
prr5 mRNA RefSeqNM_122355
cytosol GO0005829
cytosol GO0005829
OUTPUT
INPUT