Transcript PHI-Canto video tutorial slides - PHI-base

PHI-Canto: The PHI-base
Canto tool for author
self-curation
http://curation.phi-base.org/
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PHI-Canto has been adapted from
Canto for PomBase
(https://curation.pombase.org/)
Data capture models
Canto captures data like this:
gene -> gene annotation -> annotation extensions (for additional annotation detail)
In PHI-base, we are trying to capture the data like this:
pathogen gene-> host -> pathogen-host interaction annotation
For PHI-Canto the tool has been configured to interpret (multi-species PHI-base) data like this:
pathogen gene -> pathogen gene annotation -> annotation extensions specifying the host data
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What you will need to get started
The PubMed ID of the publication to
be curated
The UniProtKB ID(s) of the gene(s) to
be curated
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Example publication for curation
One pathogen species: Fusarium graminearum
Two pathogen genes: TRI5 and MAP1
Two host species: Arabidopsis and wheat
We will annotate 4 PHI phenotype terms and 2 GO terms
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Step 1:
Use the PubMed ID to find the paper
PHI-Canto
or
www.phi-base.org
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Check the Paper details are correct
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Step 2:
Assign curator using email address
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Step 3:
Add UniProt IDs to create a pathogen
gene list
UniProt ID for TRI5
UniProt ID for MAP1
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Confirm Pathogen genes
Fusarium graminearum
The gene name is automatically displayed as the UniProtKB entry name
More genes can be added if required or existing genes removed
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PubMed ID Summary page
TRI5
Curation can be paused and reactivated as required
Step 4
Select pathogen gene to curate
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Step 5: Making an annotation
part a
Select the type of curation
Making a PHI phenotype annotation
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Step 5b:
Provide the allele details
Dropdown menu
Making a PHI phenotype annotation
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Pathogen genotype created for TRI5
deletion mutant allele (TRI5Delta)
Making a PHI phenotype annotation
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Step 5c:
Add annotation term
Curation type: PHI Phenotype term
Select one of 9 upper PHI phenotype
outcome terms for
first annotation.
Additional PHI
phenotype
annotations can be14
made later.
Making a PHI phenotype annotation
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Add or suggest child terms to the
annotation term (as required)
Making a PHI phenotype annotation
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Step 5d: Enter evidence code to support
the annotation term
In this example the TRI5Delta
genotype resulted in
unaffected pathogenicity as a
PHI Phenotype annotation
term using a functional test in
the host organism Arabidopsis.
Making a PHI phenotype annotation
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Step 5e:
Enter relevant annotation extensions
Some extensions are
entered as free text,
and others as controlled
vocabs from drop down
menus
Making a PHI phenotype annotation
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Building the annotation extensions
Making a PHI phenotype annotation
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Entered extensions visible below
Making a PHI phenotype annotation
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Building the annotation extensions
Making a PHI phenotype annotation
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Building the annotation extensions
Making a PHI phenotype annotation
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Building the annotation extensions
Making a PHI phenotype annotation
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Building the annotation extensions
Making a PHI phenotype annotation
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Completed annotation extensions
Annotation extensions
can be removed by
clicking on the red X
Making a PHI phenotype annotation
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Additional details can be added
to the annotation
Making a PHI phenotype annotation
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Summary of annotations made for this
genotype (TRI5Delta)- visual check
Click back through to
PubMed ID summary
page if ready for final
Step 6: Submit to curators
One annotation
For speedy curation
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Duplicate and edit to create a new
annotation for the TRI5Delta genotype
e.g. different host
Duplicating and editing an annotation
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Delete the host ID and strain
extensions using the red X
Duplicating and editing an annotation
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Enter the new host details into the
annotation extensions
Wheat
Add in another extension
The disease caused by
Fusarium graminearum
on wheat ears is called
ear blight
Duplicating and editing an annotation
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Check extensions added so far
Duplicating and editing an annotation
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Enter new PHI Phenotype
annotation term name
Duplicating and editing an annotation
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Check edited annotation
Duplicating and editing an annotation
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Summary of 2 annotations now made
for this genotype (TRI5Delta)
1st Annotation
2nd Annotation
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Genotype summary for publication
2 annotations have now been made to the
TRI5Delta pathogen genotype for this Publication
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PubMed ID summary page
TRI5
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Adding GO term annotation for TRI5
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Making a GO biological process annotation
Adding an annotation for
‘GO biological process’
Making a GO biological process annotation
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Child term options
Making a GO biological process annotation
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Choose the evidence code
for the GO annotation
Select from drop down menus
Making a GO biological process annotation
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Add annotation extensions or additional
comments for the GO annotation
Additional comments
Making a GO biological process annotation
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New GO annotation to the gene TRI5
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PubMed ID summary page
MAP1
Annotating another pathogen gene
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MAP1 curation
MAP1
I have created a map1delta mutant single allele genotype
Annotated 2 PHI phenotypes with evidence codes and relevant extensions
I have added a GO molecular function annotation term with evidence code to the MAP1 gene
Annotating another pathogen gene
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Summary of annotations made to the
MAP1 Gene
Annotating another pathogen gene
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Step 6: Check PubMed ID summary
page and submit to curators
2 genes
4 PHI phenotype
annotations
Submit
to
curators
2 GO
annotations
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Add any further comments for the
curation team
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Post submission (or a pause) – the
author is brought back to this page
Recent sessions visible
here for quick access
Key point 1 :
Can only have ONE assigned curator per PubMed ID to prevent duplications
Key point 2:
Each author can have several papers under curation at the same time
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Helping the author during curation
Key point 3:
Each author has various ways to obtain help
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Our vision
Typical Paper:
Curation of a single gene deletion in a pathogen tested on two hosts
and some in vitro characterisation - Take 15 mins
Start with a Pubmed ID
use the duplication function
manual checking as the annotation extension is built
More complex paper:
Curation of a single and double gene deletion in a pathogen
tested on two or more hosts
Detailed microscopy with reporter strains
Detailed in vitro characterisation of each strain - Take 30 - 45 mins
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Thank you for watching this tutorial on PHI-Canto
We welcome PHI-Canto feed-back by email to
[email protected]
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