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Thank you very much for the excellent Reactome tools. I am preparing to use them on my data.

Upon preparation, I see that this is frequently true not only in the results from the analysis service, but also from the Pathway Analysis GUI:

Entities_ratio is often not equal to num_Entities_found/num_Entities_total
Reactions_ratio is often not equal to num_Reactions_found/num_Reactions_total

Is the ratio supposed to be calculated using num_found and num_total? Or is the ratio some other equation? If so, what is the equation?

Thank you again for the Reactome database and the tools to access the information within.

Thank you very much for your excellent tools and providing multiple ways to access the Reactome data.

SUMMARY:

I am running the POST /identifiers/for example using the UniProt example data downloaded into a local file.

The curl command "Execute" provides is:

Trying the curl command:

$ curl -X POST "https://reactome.org/AnalysisService/identifiers/form?interactors=false&pageSize=20&page=1&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL&pValue=1&includeDisease=true" -H  "accept: application/json" -H  "content-type: multipart/form-data"

Produces this Error:

{"code":400,"reason":"Bad Request","messages":["Could not parse multipart servlet request; nested exception is org.apache.commons.fileupload.FileUploadException: the request was rejected because no multipart boundary was found"]}

QUESTIONS

1. The file containing the IDs is "UniProt.txt" and is stored on my PC locally. I do not see "UniProt.txt" anywhere in the curl example. Should the filename be there? If yes, what is the format of the filename in the curl command?

2. Can you provide a curl example using a local file which runs, so I can mimic it?

Thank you again for the great tool set and for an amazing database.

DV

FYI: I am seeing a difference between the results of pathway analyses done through the GUI on the web and the results run and downloaded from the API on the same data.

This analysis was done using the UniProt data downloaded from https://reactome.org/PathwayBrowser/#TOOL=AT

The inputs for both analyses are:

• projection=true
• interactors=false

For the run with the API, includeDisease= true. I am not sure how to set that for the GUI on the web.