Transcript PubMed IDs - Arabidopsis Reactome

Instructions for Arabidopsis
Reactome Authors
Janet Higgins
November 2008
[email protected]
Contents
1.
2.
3.
4.
5.
6.
7.
8.
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15.
16.
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
Workflow for authoring and curation of
pathways in Arabidopsis Reactome
Author
1
Scientific expert
Data
Author tool
Data
Revise Data
Curator tool
Data and
revisions
Review Data
Reactome curator
Peer Review
Arabidopsis Reactome
(development)
Arabidopsis Reactome
(web)
Reactome Data Model
2
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
Input 1
Reaction
Output
Input 2
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.
3
3. Types of
Reaction
Binding/complex
formation
A
B
Transcription
Translation
A
mRNA
A
B
Regulation
Degradation
Phosphorylation
Dephosphorylation
Transport
A
A
A
P
A
Cytosol
Catalyst
A
Nucleus
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
4
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 entit
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 extr
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.
Format your information as shown below in a word document
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
6
7
Gene and Reference list in Excel
Example of gene list
Gene name
Example of reference list
AGI code
author
date
subject
PubMed
PHYA
AT1G09570
1
McClung
2006
History
PHYB
AT2G18790
2
Gardner
2006
review
16761955
PHYC
AT5G35840
3
Locke
2005
BIOMD55
16729048
PHYD
AT4G16250
4
Locke
2006
BIOMD89
17102804
PHYE
AT4G18130
5
Zeilinger
2006
PRR7/9
17102803
CRY1
AT4G08920
6
Dodd
2005
growth
16040710
CRY2
AT1G04400
7
Covington
2007
auxin
17683202
8
Ding
2007
TIC
17496120
9
McWatters
2007
ELF4
17384164
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 [email protected]
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
9
Author Tool – Property Editor
10
SBGN Author Tool – Graphic Editor
Produce
Associate
Phosphorylate
Inhibit
Activate
Interact
Encode
11
Example of Phosphorylation
12
http://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
CDKA;1:CYCD2;1 complex
made up of
AT2G48750
+
CYCD2;1
AT2G22490
Example of Complex Formation
13
http://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
nucleoplasm
GO:0005654
Formation of CDKD:CYCH
Complex
Phospho-(Ser162,Thr168)
CDKD;2 :CYCH;1 complex
nucleoplasm
GO:0005654
CYCH;1
nucleoplasm
GO:0005654
PubMed Id
16856985
AT5G26720
INPUT
OUTPUT
Example of Transport
http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&ID=47328&
EVENT
Arabidopsis thaliana NCBI taxonomy:3702
CDKA;1
AT1G66750
Transport of CDKA into
the nucleus
cytosol
GO:0005654
AT1G66750
nucleoplasm
GO:0005654
Regulated by
ICK1
At2g23430
PubMed Id
16845478
CDKA;1
INPUT
OUTPUT
14
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
This is a black box reaction
so it requires no input
prr5 mRNA
RefSeq:NM_122355
nucleoplasm
GO:0005654
Positive or negative regulation
CCA1
LHY
AT2G46830
AT1G01060
OUTPUT
Example of Translation
Example in developer copy of Reactome
EVENT
cytosol GO:0005829
Arabidopsis thaliana NCBI taxonomy:3702
PubMed Id
Translation of mRNA to
PRR5 protein
15767265
prr5 mRNA
PRR5
RefSeq:NM_122355
AT5G24470
cytosol
GO:0005829
cytosol
GO:0005829
INPUT
OUTPUT
16