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I have to annotate a gene to “development of yolk syncytial layer”, however this term does not exist.
Should I request a new term or make the annotation in Noctua?
If making the annotation in Noctua : which relation is correct?
anatomical structure development (GO term) : results_in_development_of (RO term) : Yolk Syncytial layer (ZFA term)
OR
anatomical structure development (GO term) : occurs_in (RO term) : Yolk Syncytial layer (ZFA term)
Thanks!
I have to annotate a gene to “development of yolk syncytial layer”, however this term does not exist.
Should I request a new term or make the annotation in Noctua?
If making the annotation in Noctua : which relation is correct?
anatomical structure development (GO term) : results_in_development_of (RO term) : Yolk Syncytial layer (ZFA term)
OR
anatomical structure development (GO term) : occurs_in (RO term) : Yolk Syncytial layer (ZFA term)
Thanks!
I would like to move towards having a single relation used for all development terms->uberon. There are some technical reasons why we can’t do that yet (maybe we can revisit this at the Geneva meeting?).
For now, you have to use the same design pattern as we use in the ontology, and use the same relation (results_in_development_of), IF you want to post-compose.
I think that given we have some many pre-composed development terms we should just go ahead and add this one too
I am trying to capture the ligand for "nuclear receptors" using a Noctua model. (geneontology/go-ontology#16540)
Which relationship should I use between "nulcear receptor activity" and the Chebi term?
"directly activates" gives an "inconcistency" error.
Thanks!
Which relationship should I use between "nulcear receptor activity" and the Chebi term?
"directly activates" gives an "inconcistency" error.
Thanks!
I am still having some inconcistency error...
I used "has input" Chebi# ...
Is a Chebi# not allowed for "has input" relationship?
Here is the model link: http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100001025
I used "has input" Chebi# ...
Is a Chebi# not allowed for "has input" relationship?
Here is the model link: http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100001025
androgen is a role
same with thyroid hormone
You can make an intermediate node of type something like ‘chemical entity'
and relate it to the ‘androgen’ node using ‘has role'
I would be curious if any GO editors have other suggestions
How do I make a “contributes to” annotation in Noctua? I have two different proteins required to enable an activity (transmembrane transporter activity). Related to geneontology/noctua#438 but there hasn’t been any response in a while
What relation would I use in Noctua to add a target of a process? In gomodel:5b91dbd100001972, a specific portion of Bre1 is needed to prevent Lge1 from degradation. I don’t have any reliable info that Lge1 directly binds Bre1, although that is the implication and extremely likely. I have the annotation to Bre1/neg reg of protein catabolic proc, is there a way to include Lge1 in the output?
Hi, I'm looking for a term to use for cellular response to RNA repeats. Transcription of genes that have over a certain number of repeats causes RNA metabolic processes to occur, often called "repeat RNA toxicity"". I'm looking at a paper that characterizes the genetic responses to a specific RNA repeat 35+ poly[GGGGCC] and can't find a GO term. @vanaukenk and @ValWood do you know where in the tree I should start looking?
Any process involved in sustaining the fidelity and copy number of rDNA repeats. PMID:14528010