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Follow scanpy's plotting conventions more closely.
* What should a plotting function return?
* What parameters should it have? Do we really need all of `show`, `ax`, `return_fig`?
* If you'd des…
grst updated
5 months ago
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```
Required to define:
{{{
[Term]
id: GO:0097029
name: mature dendritic cell differentiation
namespace: biological_process
def: "The process in which antigen-activated dendritic cells acquire the
s…
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Musing about a few things we could do for the next manuscript update
- Extend analysis to full open access subset of PubMed + bioRxiv
- Include metrics about how label functions improve over time,…
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These use 'has input', which is wrong WRT GO-CAM modeling guidelines.
We need to use either 'has small molecule activator activity' for small molecules, such that the logical definition would be:…
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I'm trying to use the higher-order elements functionality but I'm getting all kind of strange errors (floating point errors, index out-of-range, etc.). There is no example for how to use this, can you…
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### Background
We've recently been facing the issue of not knowing what (annotation extension) relations to use between 'cell-cell adhesion' GO terms (and its descendants) and cell type CL ontology…
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This rule could be implemented in SPARQL; if there is an in-taxon then all PRO IDs should be at the species level (i.e uniprot) or below and should reference a PRO class that has a matching in-taxon.
…
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> irGSEA.score(
+ object = all_revised,
+ assay = "RNA",
+ slot = "data",
+ min.cells = 3,
+ min.feature = 0,
+ seeds = 123,
+ ncores = 10,
+ custom = F,
+ geneset = NULL,
…
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- [ ] Is the class an entity or a process? Is it an information entity about a material entity/process, or a pure information entity/process?
- [ ] Specify the ontology URI for class. Is there a hier…
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# This is an umbrella ticket for the alignment of EFO measurement/trait terms with OBA terms
The focus of this ticket is the table [oba-efo-unreviewed.dosdp.tsv](https://github.com/obophenotype/bio-a…