OGI and the Ontario Institute for Cancer Research (OICR) partnered to co-host a 1 hour web conference/webinar about the Reactome Database - an open-source, manually-curated resource of core pathways and reactions in human biology, used by biologists as an online textbook of biology and by bioinformaticians to make discoveries about biological pathways.
The presentation was led by Dr. Robin Haw, Manager of Reactome Outreach, Ontario Institute for Cancer Research and provided:
- an introduction to Reactome,
- pathway visualization in Reactome,
- querying Reactome via the web interface,
- mapping Gene Expression data to Reactome pathways.
Click here to download the slide presentation
Q&A
How can we link results from Reactome to Cytoscape?
The simplest way to link between a pathway in Reactome and Cytoscape is by clicking the "Cytoscape" link at the bottom of every pathway webpage. Assuming Cytoscape is installed on your computer, click this link.
This should download the Apoptosis pathway from Reactome into Cytoscape. Alternatively, you could download the BioPAX ("BioPAX2" and "BioPAX3") file from the bottom of every Reactome pathway webpage and import it into Cytoscape. If you go to the Reactome data download webpage, you can download the BioPAX files reflecting all the pathways in Reactome.
Is there any measure of the completeness of particular pathways within Reactome? i.e. how can we measure how much is missing in Reactome, based on what's in KEGG and other resources?
One way to compare the completeness of a particular pathway in Reactome with KEGG or another pathway database would be to download the pathway participants/molecules for each of the databases for a given pathway. A good source of pathway information would be the BioPAX or SBML data files from the databases that provide this information.
How can we edit a pathway?
Unfortunately, there is no way at present to edit Reactome pathways unless you have participated in the curation of a Reactome pathway.
How can we get access to the 3032 complexes? Are they all human or are some from other species?
You can download the human protein-protein interaction data from the Reactome data download webpage and parse the file for complex data.
We have a tool called Reactome BioMart that will allow you to download the complex information and links to the pathway.
- You can then select the database (e.g. "REACTOME") and the dataset (e.g. "complex"):
- On the left-hand side of the page, a panel will appear that allows you to configure your query.
- Clicking on "Filters" takes you to a page where you can specify terms that will constrain the information that BioMart extracts from the database. These terms are essentially query terms.
- Clicking on "Attributes" allows you to specify which attributes get displayed in the list of results that BioMart returns to you. There will always be some default attributes already set, e.g. for complex, these are "Complex stable ID" and "Complex DB_ID".
- Once you have set up the filters and attributes, click on the "Results" button to run the query. The results are presented in a tabular form and by default, only the first 20 results are shown. You can display up to 200 results lines in a single page. In the panel above the results table, you can also export the entire results set in a number of different file formats e.g. text, html or xls.
Can we download in standard SMBL format to load it in other programs such as CellDesigner?
Yes, you can download the SBML file from the bottom of every Reactome pathway webpage and import it into CellDesigner. There might be a few warnings from the libSBML consistency check and you will have to set the compartment size but it should work. If you go to the Reactome data download webpage, you can download the SBML files reflecting all the pathways in Reactome.
Any plans to add Google Street View to Reactome, i.e. link to the PDB where available?
It's an interesting idea. I think we are keen to provide link outs from the new pathway layout view to external databases. We currently don't link to PDB but I think we could look into this.
What other databases link back to Reactome? Interpro?
Reactome is cross-referenced to the NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and GO.
