Add SCOPe dataset to our pipeline

[sfluegel05]

Our goal is to reproduce the ontology pretraining on a protein-related task. For this, we have already implemented a GO dataset (see #36). The next step would be to add a pretraining task to that. This would give us the following alignment:

stage	chemistry	proteins
unsupervised pretraining	mask pretraining (ELECTRA)	mask pretraining (ESM2, optional)
ontology pretraining	ChEBI	SCOPe
finetuning task	Toxicity, Solubility, ...	GO (MF, BP, CC branches)

SCOPe is a good fit since it is mostly structure-based (unlike GO, which has more complex functional classes). It also has a manageable size (~140,000 entries, similar to ChEBI).

Goal

Add a SCOPe dataset to our pipeline. The data should be processed so that it can be used in the same way as, e.g., the GO data (just with different labels).

Links

• SCOPe website: https://scop.berkeley.edu/ (documentation for files: https://scop.berkeley.edu/help/ver=2.08#parseablefiles-2.08)
• Latest publication: https://academic.oup.com/nar/article/47/D1/D475/5219094?login=true
• Initial publication: https://scop.berkeley.edu/references/murzin-1995-jmb.pdf
• PDB (source of their proteins): https://www.rcsb.org/