[Medicago] Medicago Community Annotation Portal
medicago from net.bio.net
(by medicago from net.bio.net)
Mon May 14 08:31:16 EST 2012
The Community Annotation portal at the J. Craig Venter Institute (JCVI) is now open for business. We are actively seeking members of the Medicago and other plant communities to assist in enhancing the quality of the Medicago truncatula annotation. You can help in two areas:- annotation of gene structure and function, and curation of mutant information.
Structural and Functional Annotation
Both structural and functional annotations are generated by automated pipelines. While this process does generate good quality annotations, there is always room for improvement. There are several ways the community can participate in the community annotation of Medicago truncatula.
Structural Annotation: Improving these gene structures is the first step in improving the annotation. If you have the coding sequence (CDS) of any gene/gene family members, we can map them to the current gene set and adjust the models based on the CDS you provide. From the EuCAP website, you will be able to log in and view the structures of the genes based upon the data you submitted, as well as the previous automated prediction for reference.
Functional Annotation: Assigning gene names/functions is always a challenge. Working on a particular gene or gene family, you are often in a position to provide more accurate descriptions than those that have been assigned computationally. To change the functional annotation, you can fill out the spreadsheet found at http://medicago.jcvi.org/cgi-bin/medicago/annotation.cgi?page=community_annot that allows you to input your gene symbol, gene name and gene description. Once we have this information, we can extract the current information for these genes, and add the new and improved information. You will be able to view both old and new information, and approve or make adjustments as you like.
To suggest changes to gene structure or function, you will need to send us supporting information either in the form of FASTA sequences for gene structure or by completing the spreadsheet, described above, for gene function. We will then create an account for you that will be associated with your gene or gene family that will allow you to log in, view your evidence and suggest changes.
Mutant/phenotype/allele information and Mtg Locus association
We have adopted and databased the collection of mutant class information formerly assembled and curated by Julia Frugoli (http://www.genome.clemson.edu/affiliated_cugi/medicago/genelist.html) that has not been updated since ~ 2006. Our goal is to expand the current dataset with information on mutants isolated and characterized since that time and, where possible, to associate these mutant loci with the Mtg identifiers assigned to the annotated genes on the genome sequence. From the same login page, you will also be able to see the current list of mutant loci, edit the information associated with these loci if appropriate and add information about new mutants, their phenotypes and, if known, their Mtg locus identifiers.
To view and curate or add to mutant information, you need simply to create an account at http://medicago.jcvi.org/cgi-bin/medicago/eucap/eucap.pl. Alternatively, you can send an email to mtrucatula from jcvi.org.
All the information that you submit goes first into temporary tables where it is first inspected by a curator before being adopted and displayed as part of the pubic genome annotation. The overall goal is to improve all aspects of the Medicago truncatula genome annotation. Don't hesitate to e-mail us at mtruncatula from jcvi.org<mailto:mtruncatula from jcvi.org> if you have any questions, comments, or are interested in helping us with our efforts.
We look forward to hearing from you.
The JCVI Medicago Team
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