Re: [Chebi-ontology] glycan requirements

[Matthew B. <br...@oh...>]

Hi all. Apologies that the google doc was locked. It should be open now!

Best, Matt

From: Matthew Brush
Sent: Monday, March 02, 2015 6:10 PM
To: 'che...@li...'
Cc: Chris Mungall (cjm...@lb...); Melissa Haendel
Subject: glycan requirements


Hello ChEBI developers,



As part of a collaboration between the Monarch Initiative<http://monarchinitiative.org/> and Undiagnosed Disease Program (UDP)<http://www.genome.gov/27544402>, we are developing a molecular glyco-phenotype ontology (mgpo) describing abnormalities involving glycans and related molecular entities and processes. Logical descriptions of these phenotypes will require terms representing affected and effector chemical entities (e.g. glycans, glycoconjugates, metabolic enzymes, etc). Many of these are in scope of ChEBI, and we hope to implement much of the modeling of glycans and related chemical entities here.



We have drafted an initial hierarchy of glycans and related entities here<https://docs.google.com/document/d/1ddHNYuYn5P6az_PzBflsr2gNoQp9dJFxZL-vITiadpE/edit?pli=1#heading=h.6u2zkr1zccv2>, which accommodates  our requirements for defining molecular glyco-phenotypes. From our initial evaluation of glycan representation in ChEBI (also documented here<https://docs.google.com/document/d/1ddHNYuYn5P6az_PzBflsr2gNoQp9dJFxZL-vITiadpE/edit?pli=1>), we think that most of our needs are easily accommodated by extensions or simple refinements of what exists in ChEBI.  But some of the organizational classes we propose may not fit with ChEBI's classification - so the proposed hierarchy may only be fully implemented on our side, built from MIREOTed ChEBI content and a handful of locally implemented grouping classes.



What is best route to proceed with updating glycan representation in ChEBI in support of our requirements?  We would like this to be a near term goal to meet contract deadlines, and look forward to working with you.  Thanks!

Matthew Brush and Melissa Haendel

----------------------
Matthew H. Brush
Research Associate
OHSU Ontology Development Group
Portland, OR, USA
br...@oh...<mailto:br...@oh...>