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GOAL.md

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+# Active Goal: UniProt FoT/ToricGT Data Campaign
+
+Build a durable biological graph-reasoning data workspace for ToricGT on branch
+`toricblm-data`, centered at `/home/iska/Documents/amelie/bio/ToricGT/data`.
+The source evidence is the local bio-scale Parquet mirror at
+`/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale`, especially
+UniProt function text and UniRef50 sequence/annotation records, but also RFAM,
+RNAcentral, DNA coding-region, and PubChem SELFIES shards. Preserve provenance,
+avoid unnecessary duplication on the nearly full filesystem, and make every
+derived artifact inspectable, hashable, schema-valid, and suitable for Parquet
+publication.
+
+First, graphify the raw datasets into training rows that match the ToricGT
+papers' graph-first contract: stable graph JSON, node and edge token streams,
+directed source-field dependencies, clustered splits, content hashes, and rich
+metadata for TokenGT/TropicalGT/ToricGT loaders. For each biological row, keep
+the original sequence and source annotations together. UniProt-style rows should
+join sequence, protein/function text, GO labels, EC labels, taxonomy, UniRef
+cluster fields, representative accessions, sequence hashes, and AFDB/PDB-style
+lookup hooks whenever present or safely derivable. DNA rows should expose
+accession, organism, exons, introns, proteins, and sequence. RNA rows should
+expose UPI/id, type/family/clan, description, and sequence. PubChem SELFIES rows
+should be treated as medicinal-chemistry molecular strings that can later be
+lifted into atom/bond graphs if RDKit/selfies tooling is added.
+
+Second, add Forest-of-Thought structure without pretending that deterministic
+source conversion is authored reasoning. Each graphified row should carry a
+forest sidecar whose trees correspond to sequence evidence, annotation evidence,
+structure lookup evidence, and future design-condition evidence. Include sparse
+activation fields, consensus node sets, trajectory-balance metadata,
+continuous/hybrid latent coordinate proxies, GraphCG axis hints, tropical active
+support nodes, tropical margin proxies, toric phase-basis tags, and ConvexTok
+byte-packing notes. These sidecars should guide hidden-space FoT/GFlowNet
+training and test-time scaling without copying or fabricating reasoning traces.
+
+Third, create the next authored reasoning layer in reviewed batches. Each
+accepted authored record should be a rigorous FoT/ToT technical artifact
+grounded in UniProt-style evidence: difficult biochemistry, biomedicine,
+biophysics, cell biology, pathway reasoning, gene regulatory and adaptive
+systems, RNA medicine design, medicinal chemistry, molecular dynamics,
+neurobiology, morphology/phenotype/perturbation reasoning, expression and
+abundance reasoning, scientific coding, boolean circuit and graph grammar
+problems in biological settings, and advanced mathematics useful for the model.
+The forest should have multiple trees, genuine branch/evaluate/compare/merge
+logic, occasional rejected branches, safety-aware biomedical framing, and clear
+final targets. Scripts may validate, count, hash, shard, convert to Parquet, and
+publish accepted records; scripts must not mass-invent accepted reasoning text.
+
+Fourth, prepare Hugging Face publication for `AmelieSchreiber/uniprot_fot`.
+Publication should be Parquet-first, include dataset cards/manifests/split
+reports, preserve source provenance, and avoid uploading raw mixed-license data
+unless licensing has been reviewed. Push periodically after each 1K accepted
+authored entries or after meaningful graphified-data milestones. Any key usage
+must remain secret; never print tokens or commit secrets. Prefer existing
+authenticated HF tooling in the `iska-net-2` or `tokengt` conda environment.
+
+Completion requires evidence, not intention: raw source organization under
+ToricGT/data, graphified JSONL and Parquet outputs, successful validation of
+JSON parseability and directed edge integrity, manifests proving source shard
+counts and row counts, stable split clusters, records containing GFlowNet,
+FoT, continuous embedding, TokenGT, TropicalGT, and ToricGT fields, authored
+reasoning batches accepted in logs, and verified Parquet publication steps for
+the HF dataset repository.