Download PHI-Canto video tutorial text - PHI-base

PHI-Canto Video Tutorial Script
Slide 1
Welcome to this tutorial introducing PHI-Canto: the PHI-base Canto tool for author self-curation.
My name is Alayne Cuzick and I work at Rothamsted Research where PHI-base (the pathogen host
interactions database) has been developed and is maintained. PHI-base contains manually curated
molecular and biological information on genes proven to affect the outcome of pathogen-host
interactions.
In this tutorial I’m going to introduce you to PHI-Canto and demonstrate the curation of an example
publication using saved screen shots generated from the PHI-Canto website.
#Slide 2
Canto is a community self-curation tool originally developed for the curation of literature documenting
fission yeast mutant phenotypes into PomBase you can see their website for further information.
PHI-Canto has been adapted from Canto for PomBase to incorporate the multi-species data in PHIbase and enable authors to self-curate their data into PHI-base upon peer-reviewed publication.
I’ll run through the various data capture models for you
Canto captures data like this:
gene ID details-> gene annotation (such as a phenotype or a GO term)-> annotation extensions (for
additional details related to the annotation)
#
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 (the multi-species PHI-base) data like this:
pathogen gene -> pathogen gene annotation -> annotation extensions specifying the host data
#Slide 3
To get started with PHI-Canto curation you will need the PubMed ID of the publication to be curated
and the UniProtKB IDs of the genes to be curated.
#Slide 4
I have selected this publication as an example ‘Fusarium graminearum gene deletion mutants map1
and tri5 reveal similarities and differences in the pathogenicity requirements to cause disease on
Arabidopsis and wheat floral tissue’.
In this example we will be curating data from one pathogen species- Fusarium graminearum, two
pathogen genes TRI5 (encoding trichodiene synthase required for mycotoxin biosynthesis) and
MAP1 (encoding a MAP Kinase) and two host species Arabidopsis and Wheat. We will generate 4 PHI
phenotype annotations and 2 GO term annotations. I will also demonstrate the duplicate and edit
functions to aid in speedy curation.
#Slide 5
Let’s get started and see what PHI-Canto looks like.
# Type in the PHI-Canto web address or access it through the PHI-base website.
# So Step1 for curation is to type in the PubMed ID and # click find
#Slide 6
Check the publication details displayed are for the expected paper and # continue
#Slide 7
For Step 2 select # start curating and enter the # curator’s name and email followed by # continue
#Slide 8
Next is Step 3 where we need to add the UniProt IDs for TRI5 and MAP1 genes to create a pathogen
gene list. # And continue.
#Slide 9
Confirm the correct pathogen genes have been pulled up from the UniProt IDs. More genes can be
added if required or existing genes removed. Running through the contents for these headings from
left to right we have the entered UniProt ID under systematic identifier, next to this we have the
UniProt entry name ID which PHI-Canto uses as the gene name, then we have synonyms, gene
product information and the pathogen organism in this example Gibberella zeae is also known as
Fusarium graminearum as described in the publication. # Click continue
#Slide 10
Brought to PubMed ID summary page currently showing our entered pathogen genes on the left and
the publication details on the right. # It is possible to pause and reactivate curation when you see
this button or submit to curators once finished.
# For Step 4 we shall select a pathogen gene to curate by clicking on the # UniProt entry name, in
this case for TRI5
#Slide 11
This brings up the TRI5 gene page. For Step 5 we can choose the curation type for our first
annotation. There are 8 different curation types available.
PHI phenotype, effector gene, genetic interaction within a pathogen, physical interaction within a
pathogen, GO molecular function, GO biological process, GO cellular component and posttranslational modification. Further details are available on our help pages.
We are going to curate a # PHI phenotype annotation. The Fusarium graminearum Tri5 deletion
mutant has been inoculated onto Arabidopsis floral tissue. We shall be annotating this pathogenhost interaction outcome using one of nine upper level PHI phenotypes. Firstly, we need to provide
the # allele details for the TRI5 deletion mutant by clicking on single allele.
#Slide 12
Enter the UniProt entry name under allele name and select deletion from the drop down menu for
allele type. # Note that PHI-Canto now changes the allele name to include delta to indicate deletion.
# Select ok.
#Slide 13
A pathogen genotype has now been created for TRI5Delta. To continue click # on the add a new PHI
phenotype for this genotype link
#Slide 14
And we move onto Step5c adding an annotation term. # In this case to the curation type ‘PHI
phenotype’. # I am looking for ‘unaffected pathogenicity’ in the search box # which is one of 9 upper
level PHI phenotype outcome terms used in the preliminary annotation. Subsequent additional PHI
phenotype annotations can be made using lower level terms such as unaltered spores and so on.
#Slide 15
Definitions for our 9 high-level phenotype outcomes are available in our publication here.
#Slide 16
Back to the annotation term. # In some cases it is possible to add child terms to your annotation
term, in this case there are none available. # There is also an option to suggest new child terms if
you wish by clicking on the link. # Once ready to move on click proceed.
#Slide 17
For the next step we can choose an evidence code for our annotation term from the drop down
menu. In this example the TRI5Delta genotype resulted in unaffected pathogenicity as a PHI
Phenotype annotation term and this was tested with a functional test in the host organism
Arabidopsis.
#Slide 18
Next to add in additional details about the annotation using the available extension options. In this
case for ‘TRI5Delta’ ‘functional test in host organism’ with an annotated PHI phenotype of
‘unaffected pathogenicity’ we will add in information about the # Pathogen strain NCBI taxonomy ID,
# the pathogen strain name, # the host tissue infected, # the host NCBI taxon ID and the # host
strain name. Some extensions are entered as free text and some from a dropdown menu.
#Slide 19
By clicking on the link for pathogen strain NCBI taxonomy ID …the details can be added to build the
annotation extensions
#Slide 20
As the extensions are added the information appears below
#Slide 21
Next adding in the Fusarium graminearum pathogen strain name which is PH-1
#Slide 22
And the host tissue infected the inflorescence
#Slide 23
Followed by the host NCBI taxonomy details
#Slide24
and host name and strain Arabidopsis thaliana strain Landsberg erecta
#Slide 25
Once we have entered all our annotation extensions it looks like this with the blue arrow. These
extensions can be edited by removing and re-entering as required. # proceed
#Slide 26
There is an option to record any additional information that you feel may have not been captured in
the annotation. # proceed
#Slide 27
Here is a summary for the annotations made for the # Tri5Delta genotype. # There is one annotation
under PHI phenotype. A Visual check can be made here and annotations # can be edited, deleted or
duplicated using the options on the right. # At this point the author may only be making one
annotation and may wish to proceed to the final Step6 and submit to the curators by clicking back
through the blue buttons to the PubMed ID summary page. However, we are going to make a new
annotation # using the speedy duplicate and edit options.
#Slide 28
Duplicate the annotation and select the edit option to create a new PHI phenotype annotation for
the TRI5Delta genotype. #By clicking on the annotation extension edit button we are going to
change the experimental details to include a different host plant.
#Slide 29
Under edit extensions we shall click the red cross on the experimental host ID and experimental host
strain to delete the existing extensions.
#Slide 30
The # new host NCBI taxonomy Id and host strain name can be added as before. In this case we are
changing from Arabidopsis to the wheat host Triticum aestivum strain Bobwhite. # In addition we
can now enter another extension as Fusarium graminearum infection of wheat ears causes the
disease ‘ear blight’.
#Slide 31
Next we check the extensions added so far and # click ok to continue
#Slide 32
We need to enter new the PHI Phenotype annotation term name, in this case ‘reduced virulence’
was seen when TRI5Delta was inoculated onto wheat ears.
#Slide 33
Here we can check through the edited annotation. In this case the genotype stays the same, we have
a new PHI phenotype annotation term, no change in the evidence code, and the annotation
extensions have been amended to change the host details and we have added in details on the
disease caused. # select ok to continue
#Slide 34
Now we see a summary of the 2 PHI-phenotype annotations made for this genotype (TRI5Delta)
The second annotation includes the new reduced virulence annotation term and host details
# Click Back to genotypes
#Slide 35
This Shows that 2 annotations have now been made to the TRI5Delta pathogen genotype for this
Publication. # Click back to summary
#Slide 36
Back at the PubMed ID summary page we can select the # TRI5 gene again to make a further
annotation under a different curation type. We know from the publication that TRI5 encodes for a
trichodiene synthase involved in mycotoxin biosynthesis
#Slide 37
Under curation type we shall select # GO biological process to make a new annotation
#Slide 38
Search for the correct annotation term mycotoxin biosynthetic process
#Slide39
Select child terms if required not in this case and # proceed
#Slide 40
Selecting an evidence code for this GO annotation ‘inferred from mutant phenotype’ and # proceed
#Slide41
Add in extensions none in this case # # or additional comments and proceed
#Slide42
Check the new GO annotation to the gene TRI5 looks correct # and back to the PubMed ID summary
page
#Slide43
#There is another gene, MAP1, in this publication to annotate. By clicking on it
#Slide 44
The steps can be followed through again. Without showing all the steps I have created a map1delta
mutant single allele genotype and annotated 2 PHI phenotypes with evidence codes and relevant
extensions. I have also added a GO molecular function annotation term with evidence code.
#Slide45
These annotations can be seen here in the MAP1 gene summary page
#Slide 46
Moving onto the final Step6 for the curation of this publication all the annotations can be checked
on the PubMed ID summary page. We have # 2 genes, #4 PHI phenotype annotations and #2 GO
term annotations. # This can then be submitted to the curators.
#Slide 47
Once the curation is finished there is an option to add any further comments regarding the curation
of the publication to the PHI-Canto team. # # finally a summary appears acknowledging the curation
of 2 genes for this publication.
#Slide 48
Post-submission or a pause in curation brings the author back to this page where recent sessions are
visible for quick access.
It is important to note that PHI-Canto can only have 1 assigned curator per PubMed ID to prevent
duplication however each author can several papers under curation at the same time.
#Slide 49
The author can find help by # emailing the PHI-Canto curator team or looking through the # help
documentation.
#Slide 50
Our vision is that a simple paper will take about 15 minutes to curate and a # more complex paper
could take 30-45 minutes.
#Slide 51
Thank you for your interest in PHI-Canto. I hope this has been a useful introduction for you. If you
have any queries, please feel free to contact us by email at [email protected]