Omics Day5
Constructing Arabidopsis metabolome database, AtMetExpress (http://atmetexpress.riken.jp/).
Metabolite curation in AtMet metabolome data set and reconstruct pathway from the metabolite (Toshiaki Tokimatsu, Kozo Nishida)
We have a plan to publish our inhouse plant secondary pathway maps to wikipathways. We needed pathway information about flavonoid modifications in Arabidopsis, because existing pathway databases like KEGG and PlantCyc contained information on general flavonoid pathways. Here, we partially achieved the curation of flavonoid biosynthesis pathway in Arabidopsis. The curated flavonoids include ~100 different compounds from AtMetExpress, KNApSAcK (http://kanaya.naist.jp/KNApSAcK/), and PlantMetabolomics.org (http://plantmetabolomics.vrac.iastate.edu/ver2/). See http://www.wikipathways.com/index.php/Pathway:WP3411. We will continue to expand this pathway, especially flavonoid modification steps. THen our pathway information will be reviewd by curator in Wikipathways. We hope that Wikipathways will convert them into RDF format (http://rdf.wikipathways.org/).
We had tried to create cross reference table for the compounds in these maps using linkdbRDF package created by Nishida-san. Finally we got PubChem, Nikkaji, ChEBI, ChEMBL, and KNApSAcK IDs from KEGG IDs with linkdbRDF. Automatically link is not enough assign depends on several DB now malual curation is ongoing. This helped pathway curation of flavonois and glucosinolates in Arabidopsis.
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developed a webapp called PVT (Prime Visualization Tool) with shiny framework and have fixed some bugs. As an example, we constructed a toy app for correlation network based on d3Network. You will be able to check https://github.com/afukushima/PVT.
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examined SummarizedExperiment container in Bioconductor to use assay- and meta-data integratively in AtMetExpress see https://github.com/afukushima/PVT/tree/master/data/SummarizedExperiment.
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discussed possibility of use of SummarizedExperiment into RDF format. When combining ISAtab (http://www.isa-tools.org/) with SummarizedExperiment, it is partially possible to convert metadata into RDF using LinkedISA (http://isa-tools.github.io/linkedISA/ , a conversion tool from ISA-Tab to the RDF).
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integrated "pathview" (http://www.bioconductor.org/packages/release/bioc/html/pathview.html) bioconductor package with PVT. pathview can visualize metabolome profiles based on KEGG pathway-IDs. We will continue to embed pathview images to PVT. (However, we aware that the use of KEGG pathway map requires a license agreement.)
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created R package for linkdb RDF client (https://github.com/kozo2/linkdbRDF) to integrate multiple identifiers of major compound databases like PubChem CID, KEGG, and KNApSAcK. This helped our curation of metabolite information, especially plant secondary metabolites like flavonoids and glucosinolates.
- Data curation (adding/correcting more terminology)
Data format to add more reactions
- RDF standardization (following the guidelines)
Definition page for predicates
Glycomics (Aoki, Paul; Bolton, Evan; Fu, Gang; Kawashima, Shuichi; Kinjo, Akira; Kotera, Masaaki; Kushida, Tatsuya; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Shinmachi, Daisuke; Tokimatsu, Toshiaki; Yamada, Issaku)
Proteomics (Shin Kawano, Yuki Moriya, Shujiro Okuda, Tsuyoshi Tabata, Akiyasu C. Yoshizawa, interested: Shuichi Kawashima)
- listing required metadata for jPOST submission
- developing RDF schema and ontology of them
- jPOST structure
- TODO graph
- jPOST repository
- We discussed about metadata for submitting to jPOST. (SK, YM, SO, TT, ACY)
- We made a list of metadata candidates.
- ACY and TT visited Kyushu University to discuss about it with our 'wet' collaborator.
- We updated the list of metadata candidates.
