Canto v912
community curation

for PHI-base

Questions? Contact curators ...
PHI-base Canto Documentation

This text document has been adapted from Canto at PomBase to Canto at PHI-base.

PHI-Canto tutorial video

Getting started

To enter a paper into Canto, you will need the PubMed ID. When you first follow a link to a curation session in Canto, you will see a message with a few basic details about the paper and how to proceed:

session welcome page

If you want to delegate curation to someone else (e.g. the first author or another current lab member), click "Reassign paper", and fill in the name and email address of the intended recipient on the next page. Note: you can also begin curation and then reassign a session later; there is a "Reassign" button at the upper right of the page.

Otherwise, click "Start curating", confirm your name and email address on the next page, and carry on.

To start curating a paper, you will first be asked to supply the UniProtKB IDs for the genes from your publication.

(PomBase-Canto uses gene names instead of UniProt IDs required for the multi-s:pecies PHI-Canto tool.)

gene list box

And then to confirm the resulting gene list:

uploaded gene list

When you have entered genes, you can then annotate your genes with any of the data types listed in the next section.

Complete the session by clicking "Continue" and then "Finish"; further comment is optional.

Once you have begun curating, the information will be preserved at a stable URL, so you do not need to complete the curation in one session. Most pages have at least one '?' icon, which link to help documentation (mouse over to see a brief description). You can use the 'Contact curators' link at any point if you get stuck, or have any questions.

Please note that you should only curate information supported by experiments supported in the paper you are curating. If you want to capture other information not directly shown in a particular paper, please contact the curators to discuss how to proceed.

Curating specific data types

You can curate any of these types of data for any gene you have put on the list for the paper:

  • PHI phenotype: Annotate the interaction phenotype of a pathogen-host interaction. This is the change in phenotype that occurs between a pathogen gene mutant and the experimental control of the pathogen gene.
  • Effector gene: Describe different aspects of the effector, including the type of effector, location in host, and the effector target.
  • Genetic interaction within pathogen: Examples: synthetic lethality, dosage suppression, phenotype enhancement.
  • Physical interaction within pathogen: Examples: co-purification, two-hybrid, affinity capture
  • GO molecular function: A molecular function is a catalytic (e.g. protein serine/threonine kinase activity, pyruvate carboxylase activity) or binding activity, or any other activity that occurs at the molecular level.
  • GO biological process: A biological process is series of events accomplished by one or more ordered assemblies of molecular functions, such as cell cycle, transport, or signal transduction.
  • GO cellular component: Cellular components include subcellular structures and macromolecular complexes, such as nucleus, nuclear inner membrane, nuclear pore, and proteasome complex.
  • post-tranlational modification: A protein modification is a covalent modification or other change that alters the measured molecular mass of a peptide or protein amino acid residue

Please note: The PHI-Canto prototype tool has a minor bug regarding adding annotation extensions to the first PHI phenotype annotation. The annotation term ‘unaffected pathogenicity’ must be selected to enable the option of adding annotation extensions. Once the annotation has been completed the author can then go back into the annotation using the edit button and modify the PHI phenotype annotation to that required for example ‘reduced virulence’.

Further information on how to use the Canto phenotype curation interface is available from Canto at PomBase.

Finishing and submitting

When you have finished entering data from your paper, click 'Submit to curators':

curation summary page

You will see a box in which you can put any comments or questions for the curators (this is optional):

submission page