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Add BiGG Metabolite #124

Merged
merged 19 commits into from
Dec 4, 2024
Merged

Add BiGG Metabolite #124

merged 19 commits into from
Dec 4, 2024

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samuelbunga
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@samuelbunga samuelbunga commented Nov 10, 2021 •
edited by cthoyt
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This PR adds the BiGG Metabolite database

cthoyt
cthoyt reviewed Nov 10, 2021
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cthoyt
cthoyt reviewed Nov 10, 2021
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cthoyt
cthoyt reviewed Nov 10, 2021
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@cthoyt cthoyt added the Nomenclature Data Nomenclature to convert to OBO label Nov 10, 2021
@samuelbunga
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Hi Charlie, I just added new changes. Please review them in your free time. Thanks!

cthoyt
cthoyt reviewed Nov 12, 2021
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src/pyobo/sources/bigg.py Outdated
version=version,
)

for v in bigg_df.values:
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v is a bad variable name. Better is to use tuple unpacking

Suggested change
for v in bigg_df.values:
for bigg_id, name in bigg_df.values:

cthoyt
cthoyt requested changes Nov 12, 2021
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src/pyobo/sources/bigg.py Outdated
skiprows=18,
header=None,
names=HEADER,
usecols=['bigg_id', 'name'],
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what about the other columns? database_links has lots of information worth parsing out, for example. old_bigg_ids can be put in the alternative identifier field in the pyobo.Term

src/pyobo/sources/bigg.py Outdated
)


def get_terms(force: bool = False, version: Optional[str] = None) -> Iterable[Term]:
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check CI - this needs a docstring

cthoyt
cthoyt reviewed Nov 12, 2021
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src/pyobo/sources/bigg.py Outdated
@@ -0,0 +1,63 @@
# -*- coding: utf-8 -*-

"""Converter for bigg."""
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fix stylization of BiGG

cthoyt
cthoyt requested changes Nov 12, 2021
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src/pyobo/sources/bigg.py Outdated


def get_obo(force: bool = False) -> Obo:
"""Get bigg as OBO."""
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stylization

src/pyobo/sources/bigg.py Outdated
def get_obo(force: bool = False) -> Obo:
"""Get bigg as OBO."""
version = bioversions.get_version("bigg")
# version = '1.2'
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remove dead code

src/pyobo/sources/bigg.py Outdated
# version = '1.2'
return Obo(
ontology=PREFIX,
name="bigg models metabolites database",
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title case + stylization

src/pyobo/sources/bigg.py Outdated
name="bigg models metabolites database",
iter_terms=get_terms,
iter_terms_kwargs=dict(force=force, version=version),
typedefs=[has_role],
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why is this included?

src/pyobo/sources/bigg.py Outdated
for v in bigg_df.values:
bigg_id = v[0]
name = v[1]
synonyms = []
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why include this blank list?

@cthoyt cthoyt changed the title New source: BiGG Models Metabolite Database Add BiGG Metabolite Dec 4, 2024
@cthoyt cthoyt merged commit 9d76878 into biopragmatics:main Dec 4, 2024
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cthoyt commented Dec 4, 2024

@samuelbunga thanks for the initial check in here, I finally got around to cleaning it up! Hope all is well.

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codecov bot commented Dec 4, 2024

Codecov Report

Attention: Patch coverage is 32.83582% with 45 lines in your changes missing coverage. Please review.

Please upload report for BASE (main@7d8b1ca). Learn more about missing BASE report.

Files with missing lines Patch % Lines
src/pyobo/sources/bigg_metabolite.py 31.81% 45 Missing ⚠️
Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #124   +/-   ##
=======================================
  Coverage        ?   41.51%           
=======================================
  Files           ?      142           
  Lines           ?     8703           
  Branches        ?     1308           
=======================================
  Hits            ?     3613           
  Misses          ?     4973           
  Partials        ?      117

☔ View full report in Codecov by Sentry.
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@samuelbunga @cthoyt