MedicCyc

[Pankaj Jaiswal]

Dear Ewa,

I just saw that MedicCyc is online now. Congratulations. As you know I 
am one of the PIs on the Gramene project and also lead the development 
of the RiceCyc and rice genome annotation in Gramene database using 
various tools. We just started doing the manual annotations of the 
RiceCyc. With this reference, last time you said that MedicCyc is 
emphasizing work on secondary metabolism section of the pathways and 
would like to compare RiceCyc with it.

With this reference do you think we can collaborate with your group on 
curating the RiceCyc's portion of Secondary metabolism? Also, being a 
comparative plant database on our pathway site 
[http://www.gramene.org/pathway/] we are hosting the AraCyc and RiceCyc 
that allows the plant researchers to use both the datasets for 
comparative studies. Do you think it is okay for us to add MedicCyc 
database on Gramene's pathway database. This will help plant researchers 
in finding all the three Rice, Medicago and Arabidopsis pathways for 
comparative studies. This will be a read only copy of the MedicCyc and 
needless to mention your group will be kindly acknowledged for the 
contribution as well as the source providers of the MedicCyc. We will 
link back to the MedicCyc website [http://www.noble.org/MedicCyc/] from 
the MedicCyc version we are interested in hosting.

Best regards
Pankaj

Urbanczyk-Wochniak, Ewa wrote:
> Dear Curators,
> 
>  
> 
>  
> 
> Recently I came across the RiceCyc database at 
> http://www.gramene.org/pathway/, which I found really interesting. We 
> are working now on similar Medicago truncatula biochemical pathways 
> database. So far we have a preliminary MedicCyc (temporary name for 
> MedicagoCyc) and we are doing curation on 1.0 version. We are using 
> annotation from affy chip (about 60K of non-redundant Madicago 
> truncatula transcripts) for building first Medicago pathways. We are 
> going to publish it on our web page soon, but we would like to compare 
> MedicCyc with yours RiceCyc and AraCyc for unique datasets in plants. 
> Manuscript, describing MedicCyc and comparing the other databases is 
> under preparation now, and we assume to have it ready soon. On our web 
> and in manuscript we would like to reference the RiceCyc URL. For 
> primary metabolism we are almost exactly reproducing from AraCyc and 
> RiceCyc. Our major interest lays in secondary metabolism, since at The 
> Noble Foundation we have real experts in this field (especially in 
> isoflavonoids and triterpene saponin). When the Medicago genome is 
> released (hopefully at the beginning of next year) and better annotation 
> become available, we will continue the MediCyc curation process.
> 
>  
> 
> All the best,
> 
>  
> 
> Ewa
> 
>  
> 
> Ewa Urbanczyk-Wochniak, Ph.D. 
> 
> The Samuel Roberts Noble Foundation
> 
> 2510 Sam Noble Parkway
> 
> Ardmore, OK 73401
> 
> Tele# 580-224-6151 (office)
> 
> Tele# 580-224-6712 (lab)
> 
>  
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683