Can I use my own wheat affymetrix probe annotation in MapMan? If yes, could you please advise.

Dear dimah habash,

yes, in principle you can do that. But you need to structure your custom annotation in a format that can be
read by MapMan. Please read the MapMan user manual section 3.1 for the details. In addition to a custom
annotation (mapping) file you will also need to create customized pathways to display your data. Section 3.2
describes how this can be accomplished. If you have further questions, problems or comments do not
hesitate to ask us.

best greetings,
Marc

Hi
maybe I wasn't clear, I need to use my own wheat sequence annotation.
Dimah

Hi Dimah,

just to be sure we understand each other correctly: What exactly do you mean by annotation -
Do you refer to a functional classification of some kind that you made yourself for each of the
probe sets or does it refer to a descriptive text that you attached to each probe set and
that you want displayed in a pop up window in the MapMan application when "mousing over" the
pathway visualization?

cheers,
Marc

Hi

I have discussed this with our bioinformaticians- and we did correspond with you on this problem in the last two years and we were told you are writing a programm to address a problem similar to ours. We wonder if that has been achieved.

Their reply is: the problem isn't the format of MapMan annotations, it's the semantics.
We have our own annotations to Enzyme Commission (EC) terms and Gene
Ontology (GO) terms. Basically, MapMan need to provided a file which says
which EC terms and GO terms are equivalent to the MAPMAN ontology terms.
Without this we are faced with having to build a cross mapping of
equivalence between the dictionaries ourselves.

Does this answer your question, hope you can help so that we can import our own annotation into MapMan,

Regards

Dimah

Hi Dimah,

OK now i understand better what you need. We do have files that match GO terms and EC codes
to MapMan bins - albeit these are not complete since in the case of GO terms, we could not find
exactly matching terms for all MapMan bins. The EC code to MapMan translation is also not complete
since it is a work in progress. Nevertheless i am happy to provide both files to you and you they'll be
useful.

bests,
Marc

Dear Marc

Thanks, we will try them, could you please email them for me to Dimah.habash@bbsrc.ac.uk.

Regards

Dimah

Hi
We cannot save or open the files you attached, please email them to my address ASAP.
Thanks
Dimah

Thanks for these cross-ontology mappings. These files have made MAPMAN an incredibly useful piece of software for us!

Many Thanks,
Matthew Hindle
Rothamsted Research

Dear All,

we have currently the problem that part of the probes on the affymetrix chip hybridize with fungal sequences. Does anyone have made a list with which probes to exclude as they stem from a fungal contamination?

Best

Dorothea