Plant Pathways - Reactome Curation Workshop

From Gramene Outreach
Jump to: navigation, search

October 25-29, 2010, 9:00 am - 5:00 pm

Workshop Agenda

What to Bring

You'll need a laptop computer with wireless card - Windows or Linux or Mac are all equally fine. The only hardware limitation is that if you use a Mac, try to bring an external two-button mouse. Many of the operations within the curator tool for data entry are remarkably tricky without one.

In Advance

The goal of this workshop is to provide you with enough understanding of the Reactome data model for representing biological processes at a molecular level, the software tool used to collect and organize relevant data for pathway annotation, and the web tools used to visualize and analyze these data, so that you can begin to use them effectively to annotate rice, maize, and other plant biological processes of interest to you.

The main focus of the workshop will be the software tool for data entry. To become proficient, you will need to use the tool to annotate processes yourselves, so we’ll alternate between presentations of features of the tool and the data model and sessions in which you will apply this material to actual processes.
Some candidates for annotation include:

Biosynthetic pathways:
abscisic acid synthesis and catabolism [2]
gibberellins synthesis and catabolism [2]
biotin synthesis [2]
Regulatory pathways:
Rho GTPase cycle [1]
a step in the cell cycle [1]
Gibberellic acid signaling
ABA signaling [2]
ethylene signaling [2]
COPI Mediated Transport [1]

These are only suggestions. Other processes, based on your interests or ideas you have while browsing (below) are also possible.

This PowerPoint file introduces basic concepts of pathway curation and distinctive features of their implementation in Reactome.

Here are some more detailed materials to review for background. A paper by Vastrik et al. describes the Reactome data model. A preprint of a paper to be published in the January 2011 Nucleic Acids Research database issue describes the current state of the human Reactome database and our newly redesigned web site.

Two web links are worth exploring because they will both show you more about the actual database, and because they will show you two kinds of computationally generated templates for rice processes that may be useful starting points for streamlined manual curation. We will explore both of these templates carefully in the workshop; the point now is to get a sense of what is there and how well it fits – or fails to fit! – the real biology of rice and your understanding of how to represent that biology at a molecular level.

A link to the current human Reactome database. You can browse the human version of your favorite well-conserved process, like the TCA cycle or aspects of DNA replication and cell cycle progression. A detailed users’ guide is here. A useful exercise is to re-set the default species for browsing: in the red-text-on-blue-background bar near the top of the page in the white box that says Homo sapiens by default, use the drop-down menu to choose Oryza sativa (or any other species on the list of interest to you). The effect of this is to change the displays on the home page from the comprehensive list of manually curated human processes to the subset of that list for which homologous reactions can be inferred based on orthology in the species you’ve chosen. The computational process used to make these inferences is described here. Look at your favorite process (if our program managed to infer it), and see how well the computer did compared to what you know about the real biology of the process. Suggested pathways above marked [1] are examples of rice inferences made computationally from human curated material.

A link to a draft rice Reactome database, assembled by translating RiceCyc data into Reactome format and concatenating these data (for reasons that will become clear when we start discussing the curation process) with a large amount of human data. To home in on the rice data, choose “tools” from the top menu bar; then “advanced search” from the drop-down menu. Fill out the form to restrict the search to the class “pathway” whose field name “species” has the exact value only of Oryza sativa. Choose pathways of interest to you from the resulting list and explore them. Suggested pathways tagged [2] above are imports from RiceCyc and can be found here. The current users’ guide will help you get around, and this tutorial in the form of a Word document you can download will introduce you systematically but briefly to the features of our new web site.

Venue and Transportation

The meeting will be at CSHL, Williams bldg #5

Travel information to CSHL is here. Note that the Long Island Railroad will be almost completely shut down on Sunday October 24, so the suggestion to use the Airtrain monorail and then the railroad to get from Kennedy Airport to Syosset won't work that day. (Trains are not needed to get from the airport into Manhattan, and will be running as usual the rest of the week.)


About the workshop

Workshop material

Curation Exercises

On-line curators' guide
On-line guide for making pathway layouts (entity level views)

Download and set up Curator Tool Software

This process is described in the curators' guide and in more detail in this PowerPoint file.

Annotating modified residues (co- and post-translational modifications) and replaced residues (genetic variants)

This process is described in the curators' guide and in more detail in this PowerPoint file.

Curator tool projects

These are curator tool files that you can download and open locally with your installation of the tool, that might be useful as models.

The Arabidopsis ABA metabolism and regulation pathway developed during the workshop, including its diagram is in this curator tool file.

Here are curator tool files for several pathways of human metabolism.
pyruvate metabolism and TCA cycle
nitric oxide metabolism
porphyrin metabolism
hexose transport

Contact Information


Name Email Affiliation Notes
Vindhya Amarasinghe Oregon State University Rice pathways curator
Palitha Dharmawardhana Oregon State University Gramene curator
Marcela K. Monaco Cold Spring Harbor Laboratory Gramene pathways curator
Hardeep Nahal University of Toronto Arabidopsis pathways curator
TBA Maize pathways curator
Peter D'Eustachio Peter.D' New York University Reactome Editor-in-Chief
Pankaj Jaiswal Oregon State University Gramene Co-PI
Doreen Ware CSHL/USDA Gramene Co-PI



From left to right: Palitha Dharmawardhana (OSU/Gramene), Vindhya Amarasinghe (OSU/Gramene), Marcela K. Monaco (CSHL/Gramene), Doreen Ware (CSHL/USDA, Gramene PI), Peter D’Eustachio (NYU/Reactome), and Hardeep Nahal (UT/BAR).