[Feedback] Site Feedback: Bulk download option for PlantReactome

[feedback at gramene.org]

URL         : http://plantreactome.gramene.org/index.php?page_id=328&lang=en

Subject     : Bulk download option for PlantReactome

Name        : Tiejun Cheng

Email       : chengt2 at ncbi.nlm.nih.gov

Organization: National Center for Biotechnology Information, NIH

Comments    : Dear Sir/Madam,

Our team (PubChem at NCBI, https://pubchem.ncbi.nlm.nih.gov/search/) aims to integrate chemical information from authoritative sources, which includes those in pathways.

My first question is that what's the relationship between PlantReactome and Reactome.org. The two sites are quite similar in appearance and functionality. Is PlantReactome just a subset of Reactome.org but with a focus on plant species? It seems that PlantReactome has a different data model.

My second question is that how can I download the entire PlantReactome, e.g. in BioPAX3 format?  I've checked the Download page: http://plantreactome.gramene.org/index.php?option=com_content&view=article&id=18&Itemid=242&lang=en. But I didn't find such a option. Note that Reactome.org does has such a link on its Download page: https://reactome.org/download/current/biopax.zip. I understand that I can download each individual pathway via the PathwayBrowser, e.g. http://plantreactome.gramene.org/PathwayBrowser/#/R-BVU-8933811&DTAB=DT. But for our purpose, that will be very inefficient, i.e. too many requests to your web server. Moreover, where can I get the entire list of pathways/identifiers in PlantReactome? This ContentService seems not working: http://plantreactome.gramene.org/ContentService/#/pathways/getTopLevelPathwaysUsingGET

Best regards,

Tiejun Cheng

Staff at PubChem/NCBI/NIH

http://www.warelab.org/bugs/view.php?id=5782