Sco-GEM 1.3.0 #122

edkerk · 2021-01-26T17:26:40Z

Main improvements in this PR:

fix:
- correct biocyc annotation ZCAROTDH2 (closes fix: ids and annotation bugs #33)
- UniProt ID, PFAM, Panther, GO term and refseq annotations as gathered from Uniprot (closes feat: additional annotations #44)
- correct invalid KEGG metabolite IDs identified in Sco4 paper (closes fix: Invalide KEGG ids #62)
- gene names are gathered from the Sanger genome annotation, strepDB, UniProt and additional literature (closes feat: Name cpk genes #64)
- directionality of ICDHyr (closes fix: direction of ICDhyr (isocitrate dehydrogenase) #87)
- remove reaction with incorrect co-factor (G6PDH1b) (closes feat: include cofactor information from Coze et al., 2013 #88)
- remove unnecessary anomers of carbohydrates, only keeping the generic forms (closes fix: alpha and beta variants of glucose-6-phosphate #89)
- directionality of ferredoxin-NAPD reductase (closes fix: direction of ferredoxin-NAPD reductase #90)
- remove incorrect in GPR for CAT reaction (closes Check if SCO2529 really is a catalase #100)
- curated duplicated reactions, involved GABTA, ABPYRATA, CA2abc1 and AMEt (closes Fix duplicated reactions #104)
- correct and deprecate multiple reaction and metabolite annotations (closes fix: clean-up annotations #105)
- remove reaction GND2, wrong co-factor (closes Block / Remove reaction R10221 #106)
- remove multiple annotations when only one is correct (KEGG, ec-code) (closes Invalid annotations? #111)
- acetyl-CoA rewiring from iKS1317 (closes fix: acetyl-CoA rewiring from iKS1317 #127)
- remove unused genes, not annotated to any reaction
- remove inconsistent and unnecessary <notes> entries, with information already covered elsewhere
- export.py recognizes sbo terms, adheres to standard-GEM, include subroutine to load previous releases of the model (export.get_earlier_model_unversioned)
- remove two unnecessary boundary metabolites (closes bug: two unnecessary boundary metabolites #136)
feat:
- protein sequence, length and mass are gathered from UniProt (closes feat: additional annotations #44)
- increaseVersion.py function that should be run on master branch to prepare a new version release (closes doc: update contributing guidelines and README.md #133)
- template curation script code/curation/vx_x_x.py
refactor:
- renamed folders and reformatted README.md to adhere to standard-GEM
- all model files (xml and yml for now) are located in the model/ folder (closes Unclear what the different model files represent #110)
- moved scripts, data and ec-models specific for Sulheim et al. (2020) to dedicated folders in /code and /data (closes Unclear what the different model files represent #110)
- separate requirements.txt for code/sulheim2020/, reducing the packages in /requirements.txt
- I/O by latest cobrapy (0.20) adds zero charge for metabolites whose charge was previously not specified (hence, metabolite charges should be curated, see feat: reaction mass balance and metabolite charge and formula #79)
doc:
- add Zenodo batch (closes chore: initiate Sco-GEM repo #15, closes docs: link repo to Zenodo #65)
- point to GitHub Discussions instead of Gitter (closes doc: delete gitter repo and update related docs #124)
- update contributing guidelines, move to .github folder (closes doc: update contributing guidelines and README.md #133)
chore:
- add model.id field (closes chore: add model id #128)

I hereby confirm that I have:

Tested my code with all requirements for running the model
Selected devel as a target branch (top left drop-down menu)

…o devel

- remove 3dmet, cas, kegg.drugs, kegg.orthology - correct metabetx to metanetx - correct a few CHEBI%3A to CHEBI:

- issue #62

- see issue #106, experimental prove

- see issue #104

- move /ComplementaryScripts to /scripts - move scripts specific for Sulheim et al. 2020 to /scripts/sulheim2020

- move /ComplementaryData to /data - move dataspecific for Sulheim et al. 2020 to /data/sulheim2020

- to follow standard-GEM, use /code

- rename /ModelFiles to /model to agree with standard-GEM - move ec-models to /data/sulheim2020/ecmodel/ecmodels as they are specific for Sulheim et al. 2020

- follow standard-GEM

refactor: modified file and folder structure

- not all reactions were properly sorted in previous model file - fix finding SBO terms - cobra 0.20 adds zero charge for metabolite without specified charge

chore: rerun model export

- update yaml

- solves #105 partially

- partial fixes #111

- fixes #111

- remove GO and PFAM gene annotation (#105) - replace pubchem.substance with pubchem.compound annotations (#105)

fix: annotations and minor reaction curations

- search for proteome:UP000001973 - edited file to separate genes with identical uniprot ID - gene name information supplemented from: - genome file: https://www.sanger.ac.uk/resources/downloads/bacteria/streptomyces-coelicolor.html - few manual searches in http://strepdb.streptomyces.org.uk/ - few references to papers

sulheim · 2021-01-27T19:55:43Z

I still think that it might make sense to have a model/archive folder. A pull reuqest from devel to master that cause a minor bup in version could archive the xml-version of that model. Thus, in the model folder you can always find the latest model version, but if you need the previous version for testing you can easily do that.

Chore: Add model ID

fix: acetyl-CoA rewiring from iKS1317

* fix: remove remaining glucose anomer reactions * doc: increase readability Added som space, comments, and rearranged some lines to increase readability of code resolving issue #89 * feat: subroutine to load latest master model version * chore: all model changes tracked in code * feat: increaseVersion function - should be run on `master` branch to prepare for a new release * fix: bug in #129 * chore: model I/O Co-authored-by: Snorre Sulheim <[email protected]>

fix: remove remaining glucose anomers

- these pseudorxns are included to be able to activate reactions with unknown redox co-factor (donor or acceptor), but also has the risk to introduce unrealistic loops and unnaturally links NADPH and NADH pools. Reactions will remain in the model to allow enabling the reactions with unknown redox co-factor, while blocking it by default.

* feat: separate requirements.txt for sulheim2020 * doc: update folder-specific README.md

* doc: updated README.md - updated instructions on model usage and contribution * doc: new contributing guidelines - also, template for new curations, as referred to in contributing guidelines. * refactor: v1_3_0.py adjusted to template * fix: incorrect syntax export function * doc: text review Very minor textual changes. Co-authored-by: Snorre Sulheim <[email protected]>

* feat: subroutine to load latest master model version * chore: all model changes tracked in code * feat: increaseVersion function - should be run on `master` branch to prepare for a new release * chore: remove history.rst from devel branch - will be replaced with history.md in master branch only * fix: bug in #129 * chore: model I/O * feat: use dotenv to indicate root of repository * feat: load previous model from version tag e.g. `export.get_earlier_model_unversioned('v1.2.1')` * fix: remove unused gene SCO2529 Co-authored-by: Snorre Sulheim <[email protected]>

# Conflicts: # README.md

edkerk · 2021-03-04T20:48:42Z

Rerun the memote tests (including the custom growth / knockout phenotypes test) and assure that the accuracy is the same

Update memote report

Custom tests:
- Knockouts from transposon data: one less TP, as the unused gene SCO3946 was present in the previous model version and thereby a "false true positive". This gene is now not in the model and therefore not tested for essentiality.
- Knockouts from literature data: one more TP, but also one additional FN: SCO2726 at different carbon sources. Accuracy therefore unchanged.
Memote (run locally):
- Stoichiometric Consistency test has changed (Memote version 0.12.0 vs. 0.9.12). Overall score dropped from 77% to 72%.
- When running Memote 0.12.0 on the previous release, overall score increased from 71% to 72%.

Will include code that runs Memote locally with each release.

* fix: remove invalid refseq ids - starting with WP not valid according to identifiers.org * fix: legacy support get_earlier_model_unversioned - older versions of the model were stored with different folder structure * chore: update travis and memote scripts * chore: gitattributes text=auto for line-endings * refactor: basic_test and growth_test * feat: increaseVersion includes memote score * fix: remove boundary metabolites solves #136 * chore: travis bump python to 3.8

Following https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received

Must be merged with `devel` before Travis is using the changes..

should be mentioned in travis.yml, not travis_deploy.sh

refactor: travis prevent time-out

- travis_wait prevents showing memote output in realtime when running on Travis, making it more difficult to see what is happening. - just skip the test that is taking so long (other tests run in <3 mins, test_inconsistent_min_stoichiometry takes >1.5 h), it failed anyway

fix: revert travis time-out, skip memote test

and print memote output to log, handling of failed Memote run

sulheim

Great work! A very nice minor version bump 👍 Nice to get so many of those issues resolved.

sulheim and others added 30 commits November 15, 2020 20:39

Merge branch 'devel' of https://github.com/SysBioChalmers/Sco-GEM int…

c518535

…o devel

Merge branch 'devel' of https://github.com/SysBioChalmers/Sco-GEM int…

3c323a6

…o devel

Add reference and pubmed link (#113)

5033ffa

fix: annotations

540f36c

- remove 3dmet, cas, kegg.drugs, kegg.orthology - correct metabetx to metanetx - correct a few CHEBI%3A to CHEBI:

fix: correct KEGG compound IDs

693523c

- issue #62

fix: remove reaction GND2

edcaf13

- see issue #106, experimental prove

fix: duplicate reactions

834563e

- see issue #104

refactor: reorganize scripts

91c893e

- move /ComplementaryScripts to /scripts - move scripts specific for Sulheim et al. 2020 to /scripts/sulheim2020

refactor: reorganize data

bfd3c86

- move /ComplementaryData to /data - move dataspecific for Sulheim et al. 2020 to /data/sulheim2020

fix: /code instead of /script

e770c7d

- to follow standard-GEM, use /code

refactor: reorganize model files

3eb9462

- rename /ModelFiles to /model to agree with standard-GEM - move ec-models to /data/sulheim2020/ecmodel/ecmodels as they are specific for Sulheim et al. 2020

refactor: README.md

c7b116a

- follow standard-GEM

style: README.md headings

7a6edd2

doc: README.md link to releases

ca06d38

style: README.md fix

b52c712

chore: git and memote settings

cf43108

doc: zenodo batch

07baa87

Merge pull request #115 from SysBioChalmers/refactor/standardGEM

02aead3

refactor: modified file and folder structure

Merge remote-tracking branch 'origin/devel' into fix/misc

ceaf865

chore: rerun export.py

70296dc

- not all reactions were properly sorted in previous model file - fix finding SBO terms - cobra 0.20 adds zero charge for metabolite without specified charge

Merge pull request #116 from SysBioChalmers/chore/rerunExport

3379bfa

chore: rerun model export

Merge remote-tracking branch 'origin/devel' into fix/misc

926f17e

fix: closes #33 #87 #90

5096b32

- update yaml

fix: correct biocyc IDs, append META: prefix

ebe2ad8

- solves #105 partially

fix: correct pubmed ID annotations

f323ff0

- partial fixes #111

fix: remove multiple annotations when not suitable

fe36d32

- fixes #111

fix: remove incomplete and correct faulty annotation

c1f60e6

- remove GO and PFAM gene annotation (#105) - replace pubchem.substance with pubchem.compound annotations (#105)

Merge pull request #117 from SysBioChalmers/fix/misc

1b698f4

fix: annotations and minor reaction curations

fix: remove unused genes

5a35e26

sulheim mentioned this pull request Jan 27, 2021

Documentation of model development MetabolicAtlas/standard-GEM#20

Open

edkerk and others added 9 commits January 28, 2021 00:50

Merge pull request #130 from SysBioChalmers/chore/model_id

78fee57

Chore: Add model ID

Merge pull request #129 from SysBioChalmers/fix/acetyl_coa_rewiring

5097394

fix: acetyl-CoA rewiring from iKS1317

Merge branch 'devel' into fix/anomers

f2bbbeb

Merge pull request #126 from SysBioChalmers/fix/anomers

821a958

fix: remove remaining glucose anomers

refactor: separate requirements.txt for sulheim2020 (#134)

603087c

* feat: separate requirements.txt for sulheim2020 * doc: update folder-specific README.md

edkerk marked this pull request as ready for review February 1, 2021 20:09

Merge remote-tracking branch 'origin/master' into devel

de7382a

# Conflicts: # README.md

edkerk marked this pull request as draft February 1, 2021 20:43

edkerk added 9 commits March 5, 2021 18:20

fix: travis.yml prevent timeout

c150715

Following https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received

trav

19c42ba

fix: use travis_wait and remove unnecessary memote run

6661a22

Merge pull request #138 from SysBioChalmers/fix/travisTimeout

026a3ce

Must be merged with `devel` before Travis is using the changes..

refactor: travis prevent time-out

1da470d

should be mentioned in travis.yml, not travis_deploy.sh

Merge pull request #139 from SysBioChalmers/fix/travisTimeout

386e7a7

refactor: travis prevent time-out

Merge pull request #140 from SysBioChalmers/fix/travisTimeout

bea50ee

fix: revert travis time-out, skip memote test

edkerk marked this pull request as ready for review March 6, 2021 00:32

edkerk requested a review from sulheim March 6, 2021 00:32

refactor: increaseVersion.py --skipMemote flag

b39f6b2

and print memote output to log, handling of failed Memote run

sulheim approved these changes Mar 7, 2021

View reviewed changes

sulheim merged commit b5fe7fc into master Mar 7, 2021

edkerk mentioned this pull request Apr 4, 2021

Sco-GEM 1.3.1 #146

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Sco-GEM 1.3.0 #122

Sco-GEM 1.3.0 #122

edkerk commented Jan 26, 2021 •

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sulheim commented Jan 27, 2021

edkerk commented Mar 4, 2021 •

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Sco-GEM 1.3.0 #122

Sco-GEM 1.3.0 #122

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edkerk commented Jan 26, 2021 • edited Loading

Main improvements in this PR:

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edkerk commented Jan 26, 2021 •

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