Building a Glycan Hypothesis from glySpace¶
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
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-r,--reduction<string>¶ Reducing end modification
-
-d,--derivatization<string>¶ Chemical derivatization to apply
-
-n,--name<string>¶ The name for the hypothesis to be created
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-m,--motif-class<choice>¶ Specify a glycan structure family to search for
Choices: [n-linked; o-linked]
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-t,--target-taxon<string>¶ Only select structures annotated with this taxonomy
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-i,--include-children¶ Include child taxa of –target-taxon. No effect otherwise. [default: False]
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-s,--detatch-substituent<substituent>¶ Substituent type to detatch from all monosaccharides (May specify more than once)
Arguments
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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 |