Comments (14)
do you agree?
We don't subdivide the process of purine catabolism, seeing it as an interconnected single process, so the obsoletion looks fine to me, but also ask David @ukemi - he's the local expert.
from go-ontology.
It seems to be used for Aah1/Dea2, Hpt1/HPRT1 which have hypoxanthine as input/output
from go-ontology.
I suspect it is there because of clinical significance. eg. PMID:3818951
from go-ontology.
Is that a reason to include it as a term? The activities will be there and the overall process.
We could add "hypoxanthine salvage" as a related synonym for "IMP salvage" and any other end points?
from go-ontology.
@pgaudet do you agree with this change?
from go-ontology.
I dont know, you write that it's an unnecessary grouping term, but I dont see any children.
from go-ontology.
I mean it's an unecessary intermediate, I don't know what we call that. It's an intermediate in IMP salvage (and possibly othernucleotide salvage pathways)
from go-ontology.
Is it? Here it seems to be an 'input' :
2023 review:
https://www.sciencedirect.com/science/article/pii/S0028390822004294
from go-ontology.
Granted, it's quite underannotated. What we need to think about how to clearly define this pathway with a start and end. In this case hypoxanthine may be the start of some purine salvage pathway.
from go-ontology.
The pathway begins with adenine
It is an input.
So, we have
dea2 an adenine deaminase annotated to IMP salvage and hypoxanthine salvage
Then the next step
hpt1 hypoxanthine phosphoribosyltransferase activity
creates IMP from hypoxanthine
the hypoxanthine salvage seems unnecessary if it isn't an endpoint.
from go-ontology.
There may be other starting points but hypoxanthine isn't the end point?
from go-ontology.
this case hypoxanthine may be the start of some purine salvage pathway.
For what it's worth, here is our view of the purine salvage and catabolism processes in humans. We treat hypoxanthine as one of the start points for catabolism and it is one of the molecules generated by salvage so it could be an end point there.
from go-ontology.
I'm happy to close this one.
A couple of weeks ago, instead of opening tickets, I began a list of process terms that seemed superfluous to the GO-CAM models (i.e. because they seemed like an intermediate step rather than a start point or end point)
When I began opening tickets I didn't think there would be so many.
It will probably be better to review these at the end in case we missed something or if there are organism-specific differences.
I will continue to open tickets if there is a clear-cut case, but this one seems more cpmplicated
@deustp01 I tried to look at
https://reactome.org/PathwayBrowser/#/R-HSA-74217 but I could not get it to load. Is that just me?
from go-ontology.
I could not get it to load.
It worked for me when I was composing the message, and also just now. We have been having intermittent loading problems, though, so try again and if the problem persists send a message to [email protected]. Thanks
from go-ontology.
Related Issues (20)
- Catalytic activity terms with no cross references - terms in scope for GO
- Add check for database definition cross references to also be a general cross reference HOT 2
- Catalytic activity (MF) terms with multiple MetaCyc mappings
- Pathway (BP) terms with multiple MetaCyc mappings
- carbonyl reductase (NADPH) activity (GO:0004090)
- alcohol dehydrogenase/aldo-keto reductase hierarchy HOT 1
- EC mapping GO:0103045 | methione N-acyltransferase activity | IEA with 2.3.1.1 | GO_REF:0000003 HOT 2
- typo in term nameGO:0103045 | methione N-acyltransferase activity
- Obsoletion request: GO:0035629 N-terminal protein amino acid N-linked glycosylation; GO:0042543 protein N-linked glycosylation via arginine
- Obsoletion request: GO:0071170 | site-specific DNA replication termination GO:0071946 | cis-acting DNA replication termination
- Missing parent: polyphosphate import into vacuole HOT 1
- Obsoletion request: GO:0030242 autophagy of peroxisome HOT 3
- Obsoletion request: GO:0102028 cystathionine gamma-synthase activity (acts on O-phosphohomoserine) HOT 1
- True path violations under NON proteinogenic amino acid metabolic process HOT 6
- Obsoletion request: Wnt signaling pathway involved in x
- Query RNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase
- Missing parent: GO:0000162 tryptophan biosynthetic process HOT 5
- remove enzyme xrefs from obsolete terms
- broad/narrow xref qualifiers are not exported in OBO JSON format
- Obsoletion request: actin filament-based process
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from go-ontology.