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Omics Type(s): metagenomes, metatranscriptomes, proteomics, NOM
Steps:
- [x] Add missing omics and biosample records - must be done before running **update-study**
[20240129.spruce_mt_fixes.jso…
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Once the latest big [push on sssom-py](https://github.com/mapping-commons/sssom-py/pull/172) is completed, we should review the RDF and JSONLD serialisations with @graybeal and other people in the FAI…
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All the JSON-LD produced by LinkML is JSON-LD 1.1
In fact, rdflib assumes 1.0 by default, which is partly the cause of issues we have been experiencing, reported here:
https://github.com/RDFLib/…
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- [x] Is the class an entity or a process? Is it an information entity about a material entity/process, or a pure information entity/process?
Entity
- [x] Specify the ontology URI for class. Is …
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I installed oak with `pip install -e .[tests]` but it appears that linkml is a requirement for tests and is not installed. The solution is to add an optional dependency for `linkml` in the `tests` gro…
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```yaml
id: https://w3id.org/linkml/examples/personinfo
name: personinfo
imports:
- linkml:types
prefixes:
linkml: https://w3id.org/linkml/
classes:
Person:
attributes:
nam…
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Sample Operations need standard slot descriptions according to existing nmdc schema slots
defining terms could be done by ourselves or leveraging NIST approved definitions (https://www.nist.gov/biosci…
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Following https://linkml.io/linkml/contributing/contributing.html but taking 1 step further and limiting to a single test results in not informative enough
```shell
───────────────────────────────…
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**Bug report**
The `dataclass` copy constructor doesn't recognize the default_factory.
```python
@dataclass
class Orig2:
a: int
b: int = 1
c: List[int] = field(default_factory…
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Here is an example log of a bunch of command I ran within a few seconds:
(`git st` is actually an alias to `datalad next-status -r mono`)
```
❯ git st
modified: src/linkml/ontology/datasets.y…