Building a Glycan Hypothesis from glySpace

Building a Glycan Hypothesis from glySpace¶

Warning

GlyCosmos has changed the graph structure such that these queries can no longer function. This documentation is preserved for the future if they can be made to work.

The glycoinformatics community has developed a federation of databases called glySpace, which composes the “namespace of all glycan structures”. It uses semantic web technologies to describe and relate these entities, and gateways into glySpace such as [GlyTouCan] provide query-able access to this data.

You can build a glycan composition hypothesis from the set of annotated glycan structures in glySpace for N-glycans and O-glycans, with or without taxonomic filters.

glycresoft build-hypothesis glycan-glyspace¶

glycresoft build-hypothesis glycan-glyspace [OPTIONS] DATABASE_CONNECTION

Options

-r, --reduction <string>¶: Reducing end modification

-d, --derivatization <string>¶: Chemical derivatization to apply

-n, --name <string>¶: The name for the hypothesis to be created

-m, --motif-class <choice>¶: Specify a glycan structure family to search for

Choices: [

n-linked; o-linked]

-t, --target-taxon <string>¶: Only select structures annotated with this taxonomy

-i, --include-children¶: Include child taxa of –target-taxon. No effect otherwise. [default: False]

-s, --detatch-substituent <substituent>¶: Substituent type to detatch from all monosaccharides (May specify more than once)

Arguments

DATABASE_CONNECTION¶: Required argument <string> A connection URI for a database, or a path on the file system

For more information on reductions and derivatizations, please see Glycan Modifications

Usage Example¶

# Get all human N-glycans
$ glycresoft build-hypothesis glycan-glyspace -m n-linked -t 9606 glyspace-glycans.db -n "Human N-Linked Glycans"
Building Glycan Hypothesis Human N-Linked Glycans (2)
14:35:34 - glycresoft:log:175 - INFO - Begin N Glycan Glyspace Hypothesis Serializer
{'composition_cache': None,
 'derivatization': None,
 'engine': Engine(sqlite:///glyspace-glycans.db),
 'filter_functions': [TaxonomyFilter({'9606'})],
 'loader': None,
 'reduction': None,
 'seen': {},
 'simplify': True,
 'start_time': datetime.datetime(2017, 8, 31, 14, 35, 34, 164000),
 'status': 'started',
 'transformer': None,
 'uuid': '471041e33f23485c9a570a5b4ea6e0d2'}
14:35:34 - glycresoft:log:175 - INFO - Querying GlySpace
14:35:54 - glycresoft:log:175 - INFO - Translating Response
14:36:19 - glycresoft:log:175 - INFO - Stored 976 glycan structures and 195 glycan compositions
14:38:24 - glycresoft:log:175 - INFO - Hypothesis Completed
14:38:24 - glycresoft:log:175 - INFO - End N Glycan Glyspace Hypothesis Serializer
14:38:24 - glycresoft:log:175 - INFO - Started at 2017-08-31 14:35:34.164000.
Ended at 2017-08-31 14:38:24.535000.
Total time elapsed: 0:02:50.371000
NGlycanGlyspaceHypothesisSerializer completed successfully.

# Get all human O-glycans
$ glycresoft build-hypothesis glyspace-glycan -m o-linked -t 9606 glyspace-glycans.db -n "Human O-Linked Glycans"
Building Glycan Hypothesis Human O-Linked Glycans
15:33:49 - glycresoft:log:175 - INFO - Begin O Glycan Glyspace Hypothesis Serializer
{'composition_cache': None,
 'derivatization': None,
 'engine': Engine(sqlite:///glyspace-glycans.db),
 'filter_functions': [TaxonomyFilter({'9606'})],
 'loader': None,
 'reduction': None,
 'seen': {},
 'simplify': True,
 'start_time': datetime.datetime(2017, 8, 31, 15, 33, 49, 601000),
 'status': 'started',
 'transformer': None,
 'uuid': '714d52c2525c499286f673e294672b9e'}
15:33:49 - glycresoft:log:175 - INFO - Querying GlySpace
15:33:55 - glycresoft:log:175 - INFO - Translating Response
15:34:01 - glycresoft:log:175 - INFO - Stored 315 glycan structures and 95 glycan compositions
15:34:01 - glycresoft:log:175 - INFO - Hypothesis Completed
15:34:01 - glycresoft:log:175 - INFO - End O Glycan Glyspace Hypothesis Serializer
15:34:01 - glycresoft:log:175 - INFO - Started at 2017-08-31 15:33:49.601000.
Ended at 2017-08-31 15:34:01.737000.
Total time elapsed: 0:00:12.136000
OGlycanGlyspaceHypothesisSerializer completed successfully.

Bibliography¶

[GlyTouCan]

Aoki-Kinoshita, K., Agravat, S., Aoki, N. P., Arpinar, S., Cummings, R. D., Fujita, A., … Narimatsu, H. (2015). GlyTouCan 1.0 – The international glycan structure repository. Nucleic Acids Research, gkv1041. https://doi.org/10.1093/nar/gkv1041

glycresoft documentation