Serena Lotreck

`named_entities` in `output.txt` contains all entities from previous documents when run on a directory

1

Related to the change introduced in #304. For each new YAML output document appended to the `output.txt` file, the `extracted_object` item is correct (only contains information from the current input...

When running `python download_files.py`, I get the following error: ``` Traceback (most recent call last): File "/mnt/home/lotrecks/.local/lib/python3.7/site-packages/urllib3/connection.py", line 175, in _new_conn (self._dns_host, self.port), self.timeout, **extra_kw File "/mnt/home/lotrecks/.local/lib/python3.7/site-packages/urllib3/util/connection.py", line 95, in...

Getting ontology as LinkML schema?

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I'm trying to use [OntoGPT](https://github.com/monarch-initiative/ontogpt) for information extraction, which is a tool that requires a schema input in LinkML format. I'd love to use PO, but I've been unable to...

Color nodes by partition incorrectly assigns attribute values for items with empty values

1

## Expected Behavior If there are nodes in a network that don't have a value for an attribute in the Data Laboratory (i.e. an empty string fills the cell), they...