Omics Day4 (9 17)

Day 4 (9/17)

AtMet metabolomics

PIERO Reaction Ontology

• http://aber-owl.net/ontology/PIERO Many thanks, Robert :)

More (partially known) reactions into PIERO

• There are still so many partially known reactions that are not in databases :(

Compound table

• PIERO compound ID [required]
• Name [required]
• Namae (Japanese name)[required]
• Molfile [required]
• DB links (KEGG COMPOUND, KEGG DRUG, KNApSAcK, Nikkaji, PubChem, ChEBI, ChEMBL, and others)[optional]
• Organism (positive/negative)[optional]

Reactant pair table

• PIERO pair ID [required]
• PIERO compound ID 1 [required]
• PIERO compound ID 2 [required]
• Reference [required]
• Organism (positive/negative)[optional]

Glycomics

• Perl parser made to convert monosaccharideDB XML into SMILES (Bolton)

• Discussions with GlyTouCan and MonosaccharideDB on what is a glycan

• Carbohydrates defined by ChEBI and all of ChEBI downloaded from PubChem for purposes to validate glycan detection algorithms

• Bugfixes in MonosaccharideDB WURCS parser - the 100 most frequent monosaccharides in GlyTouCan can be parsed now, further residues to be tested

• https://docs.google.com/document/d/1sj8tFa-lRCsxGaQ6r2InQ31IQVUkErWOp1EII7WDazo/edit#heading=h.em4vdc4piwyr

Proteomics

• Continuing development of jPOST metadata RDF schema and ontology