Recognizing SBO annotations using lowercase "sbo".

[jonovik]

memote/memote/support/sbo.py

Line 45 in e331663

elem.annotation is None or 'SBO' not in elem.annotation]

I propose to replace "SBO" with "sbo" in the code above.

My SBO annotations are not recognized because I use lowercase "sbo" as the key, not "SBO". Lowercase sbo is the identifiers.org (Juty et al. 2012) namespace for SBO, and I like to use identifiers.org whenever possible. In particular I like the immediate reference to the ontology used; for example, http://identifiers.org/sbo explains what ontology http://identifiers.org/sbo/SBO:0000249 is from.

I think identifiers.org namespaces are a better alternative than hardcoding "SBO" into sbo.py, and the metabolite and reaction annotation checks all use identifiers.org namespace-identifiers: pubchem.compound kegg.compound seed.compound inchikey chebi hmdb reactome metanetx.chemical bigg.metabolite biocyc rhea kegg.reaction metanetx.reaction bigg.reaction ec-code brenda

@ChristianLieven

[jonovik]

I also suggest similar changes in other files, replacing
["']SBO["']
with
'sbo'

The change would affect the following files:

$ ag ["']SBO["'] memote

memote/tests/test_for_support/test_for_helpers.py
224: rxn.annotation["SBO"] = "SBO:0000655"

memote/memote/support/helpers.py
165: 'SBO' in rxn.annotation and
166: rxn.annotation['SBO'] in TRANSPORT_RXN_SBO_TERMS])
306: 'SBO' in rxn.annotation and
307: rxn.annotation['SBO'] == 'SBO:0000629'])

memote/memote/support/sbo.py
45: elem.annotation is None or 'SBO' not in elem.annotation]
69: 'SBO' not in elem.annotation or
70: elem.annotation['SBO'] not in term]

memote/tests/test_for_support/test_for_helpers.py
390: rxn1.annotation = {'SBO': 'SBO:0000629'}

memote/tests/test_for_support/test_for_sbo.py
48: met.annotation = {'SBO': 'SBO:1', 'bigg.metabolite': 'dad_2'}

[ChristianLieven]

Cheers @jonovik that was an oversight on our part. We want to facilitate MIRIAM-compliant behavior wherever possible.

Will be fixed in the next release!

[ChristianLieven]

I should also point out that the current sbo.py will likely be reworked in the future:
#469

[ChristianLieven]

Fixed in #486. Please reopen this issue if there are any remaining problems.