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phenoscape / KB-DataFest-2017

Promoting Phenoscape KB Data Access and Interoperability Codefest, 2017
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Plant version of Phenoscape? #10

Open annikalsmith opened 6 years ago

annikalsmith commented 6 years ago

I'm also interested in seeing if others attending the workshop would be interested in working together to build a plant version of Phenoscape? Eg. connecting plant evolutionary phenotype information (from floras, monographs, etc) with model plant databases such as Arabidopsis (TAIR)?

Of course, this would extend far beyond the scope of this hackathon, but we could start a conversation between those who are interested.

cp-weiland commented 6 years ago

Together with some developers and plant data providers (Kew, APM, Naturalis, Senckenberg) I'm developing (with never enough time) an ontology for Floras, called FLOPO (http://aber-owl.net/ontology/FLOPO/#/), which might be integrated in sth like that. We provide a SPARQL endpoint (still very very alpha) to get annotated data from Kew's, Meise's etc annotated Floras, which we used to build the FLOPO (semantics.senckenberg.de/sparql -> but no documentation so far ;-)). Aim of the FLOPO was to cover wild type data = the whole spectrum of phenotypes and to enable e.g. search for traits of underutilized plants. Even for the plant model organisms, there might be a lack of interlinking of phenotype data to the genomics (e.g. from embl-ebi) or proteonomics data (e.g. in uniprot). A quick solution is of course using remote SPARQL queries ("WHERE { SERVICE http://sparql.uniprot.org/sparql ..."), but a dedicated service might be a much more performant solution.