Charles Tapley Hoyt

- [x] Make sorting put terms before instances - [ ] tests

check ``` plana - Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology [plana] failed to parse treat-xrefs-as-genus-differentia: CARO part_of NCBITaxon:79327; CL part_of NCBITaxon:79327 2025-02-14 15:12:53 WARNING [plana] synonym typedef with...

The goal here is to make it possible to use a Pydantic model to load a TSV file, while paying respect to columns that are CURIEs and labels for columns...

Convert mappings to SSSOM files

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This PR adds a script that converted the original mapping CSV files into standardized, self-contained SSSOM (Simple Standard for Sharing Ontological Mappings). There are still a few TODOs/questions to finish...

ORCID Collection

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@rjc955 @callahanr @pnavada @zweems-pnnl @hmhummel can you please share your ORCID identifiers with me?

This PR contains a draft manuscript describing $Y_0$ for submission to the [Journal of Open Source Software](https://joss.theoj.org). I'm planning to submit at latest on June 20th, 2025 (which is the...

Implements [Hierarchical Causal Models](https://arxiv.org/abs/2401.05330) (Weinstein and Blei, 2024)

Update pandoc docker image from 3.2 to 3.6.3

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This PR does the following: - [x] Updates the dockerfile from 3.2 (2024-05-11) to 3.6.3 (2025-02-10) - [x] Updates the LaTeX outputs with minor changes due to pandoc version bump,...

There appears to be a bug in the way that equations are labeled in the example paper in the following section: https://github.com/openjournals/inara/blob/92554be84ff1f1e8babd5958d8dfad9676f4c5e7/example/paper.md?plain=1#L432-L447 The latest 1.1.5 build of Inara produces the...