search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
223 stars 40 forks source link

MetaCyc transport reaction xrefs to add to GO-MF transporter terms. #26941

Closed sjm41 closed 9 months ago

sjm41 commented 9 months ago

I downloaded existing GO-RHEA associations for RHEA transport reactions (using the RHEA site). This revealed ~60 MetaCyc xrefs present on the RHEA terms that could be added to the corresponding GO terms. This exercise also found a few mis-mappings and obsolete MetaCyc xrefs to be corrected. All are listed below.

RHEA_ID GO_ID MetaCyc_xref_to_add Notes
RHEA:28967 GO:0005298 TRANS-RXN-118  
RHEA:28699 GO:0005384 RXN0-16  
RHEA:29351 GO:0005385 RXN0-12  
RHEA:18105 GO:0005388 TRANS-RXN-194  
RHEA:11484 GO:0008121 RXN-15816 Also remove existing: MetaCyc:1.10.2.2-RXN (SUBTYPE)
RHEA:28747 GO:0008519 RXN-9615  
RHEA:12132 GO:0008551 RXN-21035 Keep existing: MetaCyc:3.6.3.3-RXN (SAME TRANSPORT REACTION)
RHEA:16777 GO:0008556 TRANS-RXN-2  
RHEA:22044 GO:0008900 3.6.3.10-RXN  
RHEA:29671 GO:0015085 TRANS-RXN-144  
RHEA:28578 GO:0015087 TRANS-RXN-141A  
RHEA:28486 GO:0015093 TRANS-RXN-8  
RHEA:29827 GO:0015095 TRANS-RXN-141  
RHEA:29831 GO:0015099 TRANS-RXN-141B  
RHEA:32807 GO:0015117 TRANS-RXN-496  
RHEA:28458 GO:0015225 TRANS-RXN0-240  
RHEA:29667 GO:0015250 TRANS-RXN-145  
RHEA:29675 GO:0015254 TRANS-RXN-131  
RHEA:37047 GO:0015333 RXN-14653 Make RHEA and MetaCyc xrefs = narrow
RHEA:29251 GO:0015385 TRANS-RXN-129  
RHEA:29467 GO:0015386 TRANS-RXN-42  
RHEA:28490 GO:0015387 TRANS-RXN-3  
RHEA:14613 GO:0015411 ABC-64-RXN Also remove existing: MetaCyc:ABC-70-RXN (WRONG)
RHEA:24440 GO:0015415 ABC-27-RXN  
RHEA:18065 GO:0015416 3.6.3.28-RXN Also remove existing: MetaCyc:ABC-23-RXN (SUBTYPE)
RHEA:29999 GO:0015417 ABC-24-RXN Make MetaCyc:ABC-24-RXN & RHEA:29999 xrefs - narrow
RHEA:11036 GO:0015418 RXN-8638 Also remove existing: MetaCyc:RXN-8665 (WRONG)
RHEA:10192 GO:0015419 ABC-70-RXN Also remove existing: MetaCyc:3.6.3.25-RXN (OBSOLETE)
RHEA:17873 GO:0015420 3.6.3.33-RXN Also remove existing: MetaCyc:ABC-5-RXN (SUBTYPE)
RHEA:22132 GO:0015423 ABC-16-RXN Also remove existing: MetaCyc:3.6.3.19-RXN (OBSOLETE)
RHEA:19121 GO:0015431 TRANS-RXN-358  
RHEA:19261 GO:0015439 3.6.3.41-RXN Also remove existing:TRANS-RXN0-162 (WRONG)
RHEA:14429 GO:0015440 3.6.3.23-RXN existing RHEA xref is wrong - remove. Move existing MetaCyc:3.6.3.43-RXN to GO:0015433. Put 3.6.3.23-RXN on GO:0015421
RHEA:29679 GO:0015499 TRANS-RXN-1  
RHEA:29031 GO:0015501 TRANS-RXN-122  
RHEA:29023 GO:0015535 TRANS-RXN-20  
RHEA:28987 GO:0015538 TRANS-RXN-25  
RHEA:29995 GO:0015594 ABC-25-RXN  
RHEA:15181 GO:0015607 3.6.3.47-RXN  
RHEA:29899 GO:0015614 ABC-33-RXN  
RHEA:29795 GO:0015633 ABC-63-RXN  
RHEA:29943 GO:0015649 TRANS-RXN-113  
RHEA:29283 GO:0015655 TRANS-RXN-125  
RHEA:49296 GO:0022871 RXN-15172 Make RHEA xref = narrow. Add more general MetaCyc xref (RXN-15094) to GO.
RHEA:32783 GO:0031459 TRANS-RXN-283  
RHEA:32779 GO:0032778 TRANS-RXN-459  
RHEA:32795 GO:0033230 RXN0-3  
RHEA:29779 GO:0033232 RXN0-4522 Wrong RHEA xref - change to RHEA:29767/TRANS-RXN0-202
RHEA:32747 GO:0034228 TRANS-RXN0-476  
RHEA:33163 GO:0034257 TRANS-RXN0-481  
RHEA:29427 GO:0044667 TRANS-RXN-100  
RHEA:29811 GO:0048502 ABC-32-RXN  
RHEA:32143 GO:0061459 RXN66-448  
RHEA:30011 GO:0102014 ABC-18-RXN  
RHEA:61716 GO:0103116 TRANS-RXN-333 Also remove existing: MetaCyc:TRANS-RXN0-491 (SUBTYPE)
RHEA:30403 GO:0140571 RXN-15598 Also remove existing MetaCyc:1.10.2.1-RXN (OBSOLETE)
RHEA:25792 GO:0140581 RXN-14455  
RHEA:66820 GO:0140613 RXN-20940  
RHEA:14633 GO:0140679 RXN-17739  
RHEA:35027 GO:1901238 TRANS-RXN-242B

cmungall commented 9 months ago

This is great Steven

My question for the rest of the group is why aren’t we doing this automatically

On Fri, Feb 2, 2024 at 9:56 AM Steven Marygold @.***> wrote:

I downloaded existing GO-RHEA associations for RHEA transport reactions (using the RHEA site). This revealed ~60 MetaCyc xrefs present on the RHEA terms that could be added to the corresponding GO terms. This exercise also found a few mis-mappings and obsolete MetaCyc xrefs to be corrected. All are listed below. RHEA_ID GO_ID MetaCyc_xref_to_add Notes RHEA:28967 GO:0005298 TRANS-RXN-118 RHEA:28699 GO:0005384 RXN0-16 RHEA:29351 GO:0005385 RXN0-12 RHEA:18105 GO:0005388 TRANS-RXN-194 RHEA:11484 GO:0008121 RXN-15816 Also remove existing: MetaCyc:1.10.2.2-RXN (SUBTYPE) RHEA:28747 GO:0008519 RXN-9615 RHEA:12132 GO:0008551 RXN-21035 Keep existing: MetaCyc:3.6.3.3-RXN (SAME TRANSPORT REACTION) RHEA:16777 GO:0008556 TRANS-RXN-2 RHEA:22044 GO:0008900 3.6.3.10-RXN RHEA:29671 GO:0015085 TRANS-RXN-144 RHEA:28578 GO:0015087 TRANS-RXN-141A RHEA:28486 GO:0015093 TRANS-RXN-8 RHEA:29827 GO:0015095 TRANS-RXN-141 RHEA:29831 GO:0015099 TRANS-RXN-141B RHEA:32807 GO:0015117 TRANS-RXN-496 RHEA:28458 GO:0015225 TRANS-RXN0-240 RHEA:29667 GO:0015250 TRANS-RXN-145 RHEA:29675 GO:0015254 TRANS-RXN-131 RHEA:37047 GO:0015333 RXN-14653 Make RHEA and MetaCyc xrefs = narrow RHEA:29251 GO:0015385 TRANS-RXN-129 RHEA:29467 GO:0015386 TRANS-RXN-42 RHEA:28490 GO:0015387 TRANS-RXN-3 RHEA:14613 GO:0015411 ABC-64-RXN Also remove existing: MetaCyc:ABC-70-RXN (WRONG) RHEA:24440 GO:0015415 ABC-27-RXN RHEA:18065 GO:0015416 3.6.3.28-RXN Also remove existing: MetaCyc:ABC-23-RXN (SUBTYPE) RHEA:29999 GO:0015417 ABC-24-RXN Make MetaCyc:ABC-24-RXN & RHEA:29999 xrefs - narrow RHEA:11036 GO:0015418 RXN-8638 Also remove existing: MetaCyc:RXN-8665 (WRONG) RHEA:10192 GO:0015419 ABC-70-RXN Also remove existing: MetaCyc:3.6.3.25-RXN (OBSOLETE) RHEA:17873 GO:0015420 3.6.3.33-RXN Also remove existing: MetaCyc:ABC-5-RXN (SUBTYPE) RHEA:22132 GO:0015423 ABC-16-RXN Also remove existing: MetaCyc:3.6.3.19-RXN (OBSOLETE) RHEA:19121 GO:0015431 TRANS-RXN-358 RHEA:19261 GO:0015439 3.6.3.41-RXN Also remove existing:TRANS-RXN0-162 (WRONG) RHEA:14429 GO:0015440 3.6.3.23-RXN RHEA/EC xref are wrong - remove. Move existing MetaCyc:3.6.3.43-RXN to GO:0015433 RHEA:29679 GO:0015499 TRANS-RXN-1 RHEA:29031 GO:0015501 TRANS-RXN-122 RHEA:29023 GO:0015535 TRANS-RXN-20 RHEA:28987 GO:0015538 TRANS-RXN-25 RHEA:29995 GO:0015594 ABC-25-RXN RHEA:15181 GO:0015607 3.6.3.47-RXN RHEA:29899 GO:0015614 ABC-33-RXN RHEA:29795 GO:0015633 ABC-63-RXN RHEA:29943 GO:0015649 TRANS-RXN-113 RHEA:29283 GO:0015655 TRANS-RXN-125 RHEA:49296 GO:0022871 RXN-15172 Make RHEA xref = narrow. Add more general MetaCyc xref (RXN-15094) to GO. RHEA:32783 GO:0031459 TRANS-RXN-283 RHEA:32779 GO:0032778 TRANS-RXN-459 RHEA:32795 GO:0033230 RXN0-3 RHEA:29779 GO:0033232 RXN0-4522 Wrong RHEA xref - change to RHEA:29767/TRANS-RXN0-202 RHEA:32747 GO:0034228 TRANS-RXN0-476 RHEA:33163 GO:0034257 TRANS-RXN0-481 RHEA:29427 GO:0044667 TRANS-RXN-100 RHEA:29811 GO:0048502 ABC-32-RXN RHEA:32143 GO:0061459 RXN66-448 RHEA:30011 GO:0102014 ABC-18-RXN RHEA:61716 GO:0103116 TRANS-RXN-333 Also remove existing: MetaCyc:TRANS-RXN0-491 (SUBTYPE) RHEA:30403 GO:0140571 RXN-15598 Also remove existing MetaCyc:1.10.2.1-RXN (OBSOLETE) RHEA:25792 GO:0140581 RXN-14455 RHEA:66820 GO:0140613 RXN-20940 RHEA:14633 GO:0140679 RXN-17739 RHEA:35027 GO:1901238 TRANS-RXN-242B

— Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/26941, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOPAN36HQMYH6Q4RYCDYRUSD5AVCNFSM6AAAAABCXCIPJOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTKNBXHE2TSNY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

deustp01 commented 9 months ago

My question for the rest of the group is why aren’t we doing this automatically

Truly slow Monday morning question - what exactly did Steven do, and how would I apply that to my favorite groups of reactions? (Manually to start, then automatically later as a check on newly annotated material.)

cmungall commented 9 months ago

skos:exactMatch is transitive so we can assert inferences from this. GO:x exactMatch RHEA:y exactMatch MetaCyc:z ==> GO:x exactMatch MetaCyc:z

On Mon, Feb 5, 2024 at 7:58 AM deustp01 @.***> wrote:

My question for the rest of the group is why aren’t we doing this automatically

Truly slow Monday morning question - what exactly did Steven do, and how would I apply that to my favorite groups of reactions? (Manually to start, then automatically later as a check on newly annotated material.)

— Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/26941#issuecomment-1927321226, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOKMKQEBR23DHHS5EIDYSD6S5AVCNFSM6AAAAABCXCIPJOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRXGMZDCMRSGY . You are receiving this because you commented.Message ID: @.***>

sjm41 commented 9 months ago

My question for the rest of the group is why aren’t we doing this automatically

Right. @pgaudet and I discussed this recently and also thought that grabbing other DB xrefs (for catalytic and transporter MF terms) c/should be done automatically and regularly, using RHEA as our 'source of truth'. Would be good if a curator/editor looked over a report of such automated updates to sanity-check the changes - as noted above, 16/60 cases needed a bit of manual investigation (including a couple of tickets to RHEA).

The bigger issue here is how to accurately and efficiently associate GO transporter terms that have no current RHEA xref with their matching RHEA (and thereby other xrefs). That would be a separate ticket, unless this exercise is already underway somewhere?