[Gmod-phendiver] Best Practice

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[Gmod-phendiver] Best Practice

Daniel Lang
Hi,

Dave Clements said this would be the best place to ask my questions on
phenotype annotations.

We are starting to annotate phenotypes in moss (www.cosmoss.org) and I
have read with great interest the recent paper about the ND extension of
CHADO.

In principle we want to integrate phenotypes from the literature and
link them to cosmoss genes and integrate data from large-scale
phenotyping experiments like it was recently done by Harnsomburana et al
(PMID:21702966).

Although, we're maintaining GO/PO annotations for our moss, I'm no
ontology expert and would greatly appreciate some startup advice.

In principal I want to generate EQ annotations and use an interface
like phenote (-syntax/xml) and feed it in a rich database schema where
I can either use existing interfaces or easily build web interfaces to
query data and make it available.

Am I correct to assume that CHADO is the way to go? Are there tools to
load pheno-syntax or phenoxml into Chado?  Can I load OWL that includes
annotations (i.e. instances)?

What are the best to query ontology annotations either cmdline or web
interfaces?

Questions over questions...

Best,
Daniel

--
Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     [hidden email]

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