Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix/duplicated components #213

Merged
merged 25 commits into from
Dec 17, 2020
Merged

Fix/duplicated components #213

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
25 commits
Select commit Hold shift + click to select a range
44437e7
Merge branch 'feat/newAnnotFormat_issue203' into fix/duplicatedCompon…
JonathanRob Oct 27, 2020
798cda0
feat: merge duplicated 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one
JonathanRob Oct 27, 2020
0f3143c
feat: merge duplicated 21-hydroxypregnenolone metabolite
JonathanRob Oct 27, 2020
bb12c21
feat: merge duplicated 5beta-cholestane-3alpha,7alpha,27-triol metab.
JonathanRob Oct 27, 2020
e597969
feat: merge duplicated D-alanyl-D-alanine metabolite
JonathanRob Oct 27, 2020
a9caff1
feat: merge duplicated homocarnosine metabolite
JonathanRob Oct 27, 2020
c656dd0
feat: merge duplicated indole-5,6-quinone metabolite
JonathanRob Oct 27, 2020
7052a65
feat: merge duplicated iso-A2E(11-cis) metabolite
JonathanRob Oct 27, 2020
22b258b
feat: merge duplicated iso-A2E(9-cis) metabolite
JonathanRob Oct 27, 2020
f5163dd
feat: merge duplicated maltoheptaose metabolite
JonathanRob Oct 27, 2020
0f0413a
feat: merge duplicated maltohexaose metabolite
JonathanRob Oct 27, 2020
03ac39b
feat: merge duplicated maltopentaose metabolite
JonathanRob Oct 27, 2020
6864d52
feat: merge duplicated maltotetraose metabolite
JonathanRob Oct 27, 2020
6f73b70
feat: merge duplicated nifedipine metabolite
JonathanRob Oct 27, 2020
e762f03
feat: merge duplicated phenylacetylglycine metabolite
JonathanRob Oct 27, 2020
a46ad67
feat: merge duplicated phytosphingosine metabolite
JonathanRob Oct 27, 2020
ad18b9b
feat: merge duplicated thromboxane B2 metabolite
JonathanRob Oct 27, 2020
a5d3871
feat: update annotation of 2,3-diketo-5-methylthiopentyl-1-phosphate
JonathanRob Oct 27, 2020
c72b148
feat: remove "others" reaction and metabolites occurring only therein
JonathanRob Oct 28, 2020
2339e1f
Merge branch 'devel' into fix/duplicatedComponents
JonathanRob Dec 1, 2020
1efadbb
chore: move Human-GEM annotation files to model/ directory
JonathanRob Dec 1, 2020
0a82bbc
doc: update README to reflect movement of annotation files
JonathanRob Dec 1, 2020
b556a7d
chore: update functions to reflect movement of annotation files
JonathanRob Dec 1, 2020
ec06a87
fix: metabolites.tsv remove compartment abbreviations from Recon3D IDs
JonathanRob Dec 1, 2020
c1f64c5
feat: update rxnConfidenceScores for reactions with curated PMIDs
haowang-bioinfo Dec 17, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions data/annotation/metabolites.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -451,7 +451,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"m00242s" "m00242" "" "C11088" "" "" "" "" "" "" "M00242" "MNXM6026" "m00242s"
"m00243c" "m00243" "" "C06205" "" "CHEBI:28516" "" "" "" "" "M00243" "MNXM114239" "m00243c"
"m00244c" "m00244" "" "C14784" "" "CHEBI:34048" "" "" "" "" "M00244" "MNXM9529" "m00244c"
"m00245c" "m00245" "" "C15606" "" "CHEBI:49252" "" "" "" "" "M00245" "MNXM494" "m00245c"
"m00245c" "m00245" "dhmtp" "C15606" "" "CHEBI:49252" "" "" "" "" "M00245;dhmtp_c" "MNXM494" "m00245c"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I couldn't find metabolite dhmtp_c in Recon3D.

"m00246c" "m00246" "" "C14783" "" "" "" "" "" "" "M00246" "MNXM9534" "m00246c"
"m00247c" "m00247" "13dpg" "C00236" "" "CHEBI:16001" "439191" "" "" "HC00214" "13dpg" "MNXM261" "m00247c"
"m00248c" "m00248" "13dampp" "C00986" "HMDB00002" "CHEBI:15725" "428" "" "" "" "13dampp" "MNXM146468;MNXM350" "m00248c"
Expand Down Expand Up @@ -7424,7 +7424,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"m02543s" "m02543" "acnam" "C19910" "HMDB00230" "CHEBI:45744" "445063" "" "" "HC00244" "acnam" "MNXM227" ""
"band_c" "band" "band" "" "" "" "" "" "" "" "band_c" "MNXM148099" ""
"bandmt_c" "bandmt" "bandmt" "" "" "" "" "" "" "" "bandmt_c" "MNXM148098" ""
"dhmtp_c" "dhmtp" "dhmtp" "C15606" "" "CHEBI:49252" "" "" "" "" "dhmtp_c" "MNXM494" ""
"m02525s" "m02525" "acgal" "C01074" "" "CHEBI:28800" "35717" "" "" "" "acgal" "MNXM395" ""
"m01609s" "m01609" "core4" "C04917" "" "CHEBI:16478" "" "" "" "" "core4" "MNXM4704" ""
"galam_s" "galam" "galam" "C06377" "" "CHEBI:18232" "" "" "" "" "galam_e" "MNXM147460" ""
Expand Down
6 changes: 2 additions & 4 deletions data/annotation/reactions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -997,9 +997,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"HMR_5381" "R02021" "" "RE3009C" "" "" "RE3009C" "MNXR102376" "HMR_5381" "RCR10548" "" 0 "MA_05381"
"HMR_5385" "R04420" "" "" "" "" "MTRI" "MNXR101759" "HMR_5385" "RCR14401" "" 0 "MA_05385"
"HMR_5386" "R07392" "" "" "" "" "MDRPD" "MNXR101445" "HMR_5386" "RCR11491" "" 0 "MA_05386"
"HMR_5387" "R07395" "" "" "" "" "HMR_5387" "MNXR94815" "HMR_5387" "RCR11492" "" 0 "MA_05387"
"HMR_5387" "R07395" "DKMPPD3" "" "" "" "HMR_5387;DKMPPD3" "MNXR126089" "HMR_5387" "RCR11492" "" 0 "MA_05387"
"HMR_5388" "R07363" "" "" "" "" "HMR_5388" "MNXR95228" "HMR_5388" "RCR11493" "" 0 "MA_05388"
"HMR_5389" "R07364" "" "" "" "" "HMR_5389" "MNXR95227" "HMR_5389" "RCR11494" "" 0 "MA_05389"
"HMR_5389" "R07364" "DKMPPD2" "" "" "" "HMR_5389;DKMPPD2" "MNXR95227" "HMR_5389" "RCR11494" "" 0 "MA_05389"
"HMR_5390" "R00648" "" "" "" "" "HMR_5390" "MNXR101478" "HMR_5390" "RCR10334" "" 0 "MA_05390"
"HMR_5391" "R07396" "" "" "" "" "UNK3r" "MNXR95923" "HMR_5391" "RCR10335" "" 0 "MA_05391"
"HMR_5418" "" "" "RE2030M" "" "" "RE2030M" "MNXR103591" "HMR_5418" "RCR14402" "" 0 "MA_05418"
Expand Down Expand Up @@ -11210,8 +11210,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"BANDMT" "" "BANDMT" "" "" "" "BANDMT" "MNXR96213" "" "" "" 0 ""
"C181CPT2rbc" "" "C181CPT2rbc" "" "" "" "C181CPT2rbc" "MNXR96396" "" "" "" 0 ""
"CA2t" "" "CA2t" "" "" "" "CA2t" "MNXR96436" "" "" "" 0 ""
"DKMPPD2" "" "DKMPPD2" "" "" "" "DKMPPD2" "MNXR97498" "" "" "" 0 ""
"DKMPPD3" "" "DKMPPD3" "" "" "" "DKMPPD3" "MNXR97500" "" "" "" 0 ""
"GTHOXti2" "" "GTHOXti2" "" "" "" "GTHOXti2" "MNXR100444" "" "" "" 0 ""
"HCYSte" "" "HCYSte" "" "" "" "HCYSte" "MNXR100580" "" "" "" 0 ""
"NORMETEVESSte" "" "NORMETEVESSte" "" "" "" "NORMETEVESSte" "MNXR102002" "" "" "" 0 ""
Expand Down
54 changes: 5 additions & 49 deletions model/Human-GEM.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2020-07-13"
date: "2020-10-27"
authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
email: "jonrob@chalmers.se"
organization: "Chalmers University of Technology"
Expand Down Expand Up @@ -59412,14 +59412,6 @@
- charge: 0
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "dhmtp_c"
- name: "1,2-Dihydroxy-5-(Methylthio)Pent-1-En-3-One"
- compartment: "c"
- formula: "C6H9O3S"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "m02525s"
- name: "N-acetylgalactosamine"
Expand Down Expand Up @@ -84887,7 +84879,7 @@
- confidence_score: 0
- !!omap
- id: "HMR_5387"
- name: ""
- name: "Acireductone Synthase"
- metabolites: !!omap
- m00245c: 1
- m00572c: -1
Expand All @@ -84898,7 +84890,7 @@
- gene_reaction_rule: "ENSG00000145293"
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.77"
- references: ""
- references: "PMID:21749716"
- subsystem:
- "Cysteine and methionine metabolism"
- confidence_score: 0
Expand All @@ -84923,7 +84915,7 @@
- confidence_score: 0
- !!omap
- id: "HMR_5389"
- name: ""
- name: "Acireductone Dixoygenase 1"
- metabolites: !!omap
- m00245c: -1
- m01016c: 1
Expand All @@ -84935,7 +84927,7 @@
- gene_reaction_rule: "ENSG00000182551"
- rxnFrom: "HMRdatabase"
- eccodes: "1.13.11.54"
- references: ""
- references: "PMID:21749716"
- subsystem:
- "Cysteine and methionine metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -262196,42 +262188,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "DKMPPD2"
- name: "Acireductone Dixoygenase 1 (Homo Sapiens)"
- metabolites: !!omap
- dhmtp_c: -1
- m01016c: 1
- m01833c: 1
- m02039c: 1
- m02630c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID: 21749716."
- subsystem:
- "Cysteine and methionine metabolism"
- confidence_score: 0
- !!omap
- id: "DKMPPD3"
- name: "Acireductone Synthase (Homo Sapiens)"
- metabolites: !!omap
- dhmtp_c: 1
- m00572c: -1
- m02039c: 1
- m02040c: -1
- m02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID: 21749716."
- subsystem:
- "Cysteine and methionine metabolism"
- confidence_score: 0
- !!omap
- id: "GTHOXti2"
- name: "Oxidized Glutathione Irreversible Active Transport (Rbc)"
Expand Down