Glycogroup

Topics for Glycogroup

Glycoprotein ontology

• Hiro, Matthew, Rene and Jerven
• Done

GlycanBuilder installation in Eclipse

• Matthew, Kiyoko, Issaku, Shujiro and Masaaki
• Kiyoko got unicarb-db installed using [https://code.google.com/p/unicarb-db/wiki/UbuntuStartGuide] and can compile using ant
• Matthew looking into Vaadin upgrade to version 7
• Issaku will write documentation in Japanese, and Kiyoko will translate to English

GlycoEpitope

• Provide links to epitopes for other databases
• Got GlycoCT structures for a third of the glycoepitopes in the database and will provide RDF data including the structures and corresponding links by end of July
• Still need to work on ontology - time frame: beginning of August with Okuda, Kawasaki, Sawaki and Kinoshita

GlycoCT to MOL

• Kato and Matthew
• Will be done by Friday
• Open source; Kiyoko will provide web tool/web service on RINGS

Other format conversion

CSDB to WURCS

• Phyl and Issaku

XXX to GlycoCT

• Rene and Kiyoko

Glyco-ontology

• Generate RDF samples for all data by mid-August
• TODO: NMR experiments by Yamada, Shinmachi and Matsubara
• TODO: HPLC by Matthew by end of July

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Next steps

GlycoRDF

• Registration in BioPortal (Rene)
• Word/HTML documentation (Rene) by mid-July
• Review description, class names, predicate names (all by end of July)

RDF generation using Glyco-ontology

• By mid-August by all databases

Paper

• Technical paper
• Glycobiology letters: ACGG-DB5, GlycoHackathon ASAP
• Start as soon as RDF data is available, around mid-August

Triplestores

• JCGGDB
• CCRC
• UniCarbKB
• RINGS

WURCS Working Group

• Yamada, Kotera, Kinoshita, Ranzinger, Campbell, Luetteke, Toukach, Sawaki, Kato

Glycan structure repository - user interfaces

• Build a prototype and get comments later

Accession number assignment

• Metadata: user, date registered

Web services for data access

Search functionality

• By composition
• By mass
• By (sub)structure
• By date (range) registered

Drawing tool (GlycanBuilder)