Download - A marriage of chemistry and biology
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A marriage of chemistry and biology
Aligning the Gene Ontology with CHEBI
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ontologies: what are they really for, and why do I care?
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systems of categorization, useful for handling large amounts of data
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Gene Ontology arose from a need to classify functional data about genes and proteins in various
databases
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Parallel efforts grew up elsewhere
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GO has always contained a chemical hierarchy
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Roncaglia
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Roncaglia
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Roncaglia
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biologists are not great chemists
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Use CHEBI to make chemical hierarchy in GO
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The story begins in 2009 when we decided to get started. We figured it would take a few months.
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GO terms were ‘decomposed’ and text-matched to ChEBI terms
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A few technical issues needed to be sorted out with the relationships in CHEBI first
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Once that was done, we generated a list of mismatches between GO and
CHEBI
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One of the first things we realized was that we weren’t even consistent with our chemical
classification with ourselves
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Generated the implicit chemical ontology of GO - GOChe
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Four of us sat in a room for a weekend with a large pot of coffee and edited GOChe
(March 2010)
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One of the things we consistently noticed was that ChEBI classified nucleotides as carbohydrates
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Called another meeting with ChEBI. Who confirmed that nucleotides are indeed carbohydrates.
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plurals e.g. pyridines v/s pyridine
“pyridine-containing compound”
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Acids and bases • Acids and bases
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Biologists are much more wooly and conflate these terms
acids and bases often interconvert during biological
processes
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Union terms of acids and bases in GO:
carboxylic acid OR carboxylic acid anion
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Where are we now?• Pretty much there• Bridging files between GO and CHEBI
ready• Single update – use reasoner to ‘fix’
GO• Editing will involve loading both GO
+ CHEBI and reasoning• Paper ready for submission
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What does this buy us?• Consistency and accuracy• Time savings• Potential for cool queries and
analysis that combine biology and chemistry
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People• David Hill• Jane Lomax• Harold Drabkin• Chris Mungall• Midori Harris• Tanya Berardini• Rebecca Foulger• Paola Roncaglia
• Marcus Ennis• Paula de Matos• Janna Hastings• Nico Adams• Mike Bada• Colin Bachelor