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We are using new interactor types in IntAct that are not working with the viewer:
https://intact-portal.github.io/intact-portal-view/details/interaction/EBI-25816865
has double-stranded RNA -> i…
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This is a follow-up to discussions we had on the 2020-11-30 ontology editors call.
Molecular functions can have different 'parts' or sub-functions, but it seems that sometimes these parts are is_a …
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Before we start updating DRAO, we need to update the member ontologies and ensure there are no resulting conflicts. This ticket covers that update.
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'GO:0000976 transcription regulatory region sequence-specific DNA binding' should be reformulated as
'transcription cis-regulatory region binding'
(The other rationale is that GO:0000987 cis-regul…
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Biological interactions are often described using "higher-order" language, in which an interaction modulates another interaction. Here, we propose to allow this in SBOL by allowing Participation objec…
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Hi @mlacencio
Mouse Ybx3 is annotated to dbTF activity, but it isn't. Please review or remove the following annotations:
NTNU | Q9JKB3 | Ybx3 | | GO:0000977 | RNA polymerase II transcripti…
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This test in https://github.com/compSPI/ioSPI/blob/master/tests/test_iotools/test_atomic_models.py does not work, so I removed it to pass the CI tests.
```
def test_write_gemmi_model_cif(sel…
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When I run `funannotate update -i GCA_000091205.1_ASM9120v1_genomic.gbff -l 1.1.fastq -r 1.2.fastq --out /home/user/fun1 --stranded RF --memory 20G --cpus 4`
I encounter the following issue:
```
…
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A molecular species in contact with a DNA backbone is often used to show binding into a complex in a diagram. This SEP proposes a modification to support such diagrams.
Read the full SEP at: https…
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We use freeSASA in our ML data engineering stack and we are currently moving our stack from the pdb file format to the new format (mmCIF/CIF). I am wondering if the freeSASA library developers plan on…