Hello there,
i´m beginning to work with MapMan and tried to use a mapping for Oryza sativa transcriptomical data. So my problem is, that my dataset is annotated with TC- Numbern from the TIGR- Database (OSGI.032811;http://compbio.dfci.harvard.edu/tgi/plant.html) and some additional information about the blast-hits (like protein-name, see below for example). Is it possible to create a Mapping with a generally metabolic overview from TC-Numbern?
I have also a complete GO-term annotation but for a better overview i need MapMan.

Example:

ID: TC493978

Description: TC493978 weakly similar to UniRef100_P43293 Cluster: Probable serine/threonine-protein kinase NAK; n=2; Arabidopsis thaliana|Rep: Probable serine/threonine-protein kinase NAK - Arabidopsis thaliana (Mouse-ear cress), partial (78%) # #

Hi Martin,

i guess the simplest solution for your request would be to run an automatic annotation job using
the TC sequences as input. If you agree, i can obtain release 19 from the web site you referred
to and run the TC sequences through our automated annotation pipeline to create a mapping
file that you could then use to visualize and analyse the data in MapMan.

cheers,
Marc

Hi Marc,
if i understand it right, you want to annotate a existing Mapping to the TC- ID´s from the Rice- Database (http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=rice)?

Actually, I don´t know what the "automated annotation pipeline" could be, but if it is possible to create a mapping which uses the TC-ID´s it would be great

Hi Martin,

what i would do is use the actual TC sequences to feed them into our automated annotation
pipeline which uses sequence similarity and domain content to compute a probable MapMan
bin for each sequence (based on hand curated reference mappings - for more information
on the process have a look at http://mapman.gabipd.org/web/guest/app/mercator). The final
result of this process is a mapping file that assigns each TC sequence identifier to at least
one MapMan bin. This file can then be used in MapMan to visualize data that uses the same
identifiers.

What i would need to know from you would be exactly which release of the OS Gene Index
to use as input to make sure that the mapping file will match the IDs used in your data files.
The latest release is #19 and was published 23rd march 2011.

I hope this answers your question,
cheers,
Marc

Hi Marc,
so i´m going to use the latest release of the OS Gene Index.

But i´m a bit confused. You feed the "automated annotation pipeline" with the TC- Identifyer and I get a Template for a MapMan visualization?
Or is it necessary to load my TC-Dataset into Mercator to create a mapping?

greetz Martin

Hi Martin,

there was a little misunderstanding - the automated annotation pipeline uses the actual TC sequences
(as i wrote in the last post ;-) ) as input. Based on similarity and domain searches against several reference
data bases, the annotation pipeline assigns a MapMan bin to each input sequence and thereby produces
a mapping file.

I will feed the latest TC sequence version into the pipeline and notify you when the mapping file is ready.

best greetings,
Marc

Hi again,

the mapping is ready and can be obtained from the MapManStore
(http://mapman.gabipd.org/web/guest/mapmanstore). The name is
OSGI.release_19.mapping.m02

I hope you'll find it useful - best greetings,
Marc

Hi Marc,
thanks a lot, it works wonderful

Hello again,
i have some additional question with the same problem. I need a mapping for transcriptomical data from the OSGI- Database for Zea mais (Release 19.0
6-5-09). Could u help me?

greetz Martin

Hi Martin,

please point me to the FASTA file containing the sequences you need a mapping for
(ideally via a direct link) and I will submit that to the mercator annotation pipeline.
(and please have some patience - I've been away for a few days and received
three other requests in the meantime)

cheers,
Marc

Hi Marc,
no problem, there´s no hurry. So i have a link, but it´s a bit tricky ... on Mac i have to log in as Gast, but it´s not necessary if you use a PC.

ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Zea_mays/

Hey Marc,
did u find time for my mapping?

Hi - the mapping is done - you can obtain it from the mapman store:
http://mapman.gabipd.org/web/guest/mapmanstore

cheers,
Marc

Thanks a lot Marc