The purpose of these references is to contextualize the Physics Derivation Graph.
Recommendations for reading (not everything listed here is worth reading).

In the 1998 book by Edward O. Wilson, he tackled "the synthesis of knowledge from different specialized fields of human endeavor."

Science offers the boldest metaphysics of the age. It is a thoroughly human construct, driven by the faith that if we dream, press to discover, explain, and dream again, thereby plunging repeatedly into new terrain, the world will somehow come clearer and we will grasp the true strangeness of the universe.
And the strangeness will all prove to be connected, and make sense.

Much influence after 1994 is likely based on the QEC manifesto, so that is useful to read.

"The QED Manifesto after Two Decades -- Version 2.0" by Weiss (2016) source
Describes "Mathropolis" and a "mathematical content markup language"
A non-CAS based metalanguage is attempted in "The QED Manifesto after Two Decades -- Version 2.0"
The paper discusses Mathropolis, which is intended to optimize for readability over formality.
The paper describes a "mathematical content markup language" and provides an example.
In email conversation with Weiss, he says,

"I started fleshing out some code but when I realised the extent of the project is huge and that it would consume my maths research I decided to stop."

He also said,

"I still think that the idea of MCML would be extremely helpful in academia and particularly in subjects such as mathematics and physics (and others)."

"Extracting mathematical semantics from LATEX documents" semanticscholar.org
J. Stuber and M. Brand (2003)

"Semantic Enrichment of Mathematics via tooltips"
Moore, 2015
https://tug.org/tug2015/preprints/moore-mathsem-cicm2015-v7.pdf
notes: "mathsem" source code not found online

"Graph Representations for Higher-Order Logic and Theorem Proving"
C. Szegedy et al, 2019
comment thread: https://news.ycombinator.com/item?id=24389058
notes: This paper is not related to the Physics Derivation Graph as far as I can tell.

"Making Meaning with Math in Physics: A semantic analysis"
https://arxiv.org/abs/1002.0472
E. F. Redish and A. Gupta (2009)