Biology Tier 3 — Family Indexes
Tier 3 catalogs enumerate the named entities a working life scientist uses every day: model organisms with their strain backgrounds, cell lines with their provenance, sequencing platforms with their read length and price, protein families with their fold and inhibitor scaffolds, pathway databases with their identifier conventions. Tier 1 = topic primer (see _index). Tier 2 = walkthrough or case study. Tier 3 = the lookup tables Tier 1 and Tier 2 reference but don’t duplicate.
Scope
A Biology Tier 3 family index should let an agent answer “which model organism is right for studying X” or “what’s the going price-per-genome on the dominant short-read platform 2024” without leaving the vault. The cost-per-genome trajectory (HGP 1990-2003 200) is the kind of fact that must live in a catalog, not a tutorial.
Status of Tier 3 catalogs
| Catalog | Status | Note |
|---|---|---|
| Model organisms and sequencing technology | DONE | model-organisms-and-sequencing-tech — prokaryote / yeast / invertebrate / plant / fish / amphibian / mammal model organism table; Sanger and NGS and long-read platform table; single-cell and spatial techs; CRISPR editing tool families |
| Protein families catalog | DONE | protein-families-and-drug-targets — GPCR (Class A/B/C/F), kinase (tyrosine vs ser-thr; Manning 518 kinome), nuclear receptor, ion channel (voltage-gated, ligand-gated), protease (serine, cysteine, metallo, aspartyl, threonine) |
| Drug target families catalog | DONE | protein-families-and-drug-targets — druggable proteome (Santos 2017 / 667 targets), FDA-approved drugs by target class, on-target / off-target |
| Cell-line catalog | DONE | cell-lines-and-antibody-catalog — production lines (CHO, HEK293, NS0/Sp2/0, PER.C6), research lines, ATCC / DSMZ / ECACC provenance and STR authentication |
| Antibody catalog | DONE | cell-lines-and-antibody-catalog — primary antibody vendors (Abcam, Cell Signaling, Sigma, Thermo, BioLegend, Invitrogen, BD, R&D); validation tiers; therapeutic mAbs by target |
| Pathway database mapping | DONE | pathway-database-and-bioinformatics-resources — sequence → structure → pathway (KEGG / Reactome / WikiPathways / BioCyc) → ontology (GO, MeSH, HPO, OMIM) → variant/disease → drug/chemistry → ML/pipeline tools; INSDC mirrors, gene-symbol harmonization (HGNC, MGI, RGD) |
Convention
- Year discovered / sequenced / released cited where it pins history (HGP, GRCh38, T2T-CHM13 2022).
- Costs in USD with year (cost-per-genome benchmarks).
- Read lengths in bp; throughput in Gb / Tb per run.
- Real product / instrument model numbers (NovaSeq X Plus, Revio, PromethION 48, Chromium iX, Visium HD, MERSCOPE).
- Strain backgrounds spelled out (C57BL/6J vs BALB/c not “mouse”).
- Vendor names retained (Illumina, PacBio, Oxford Nanopore, Thermo Fisher, BGI, Element Biosciences, Singular Genomics, Ultima, Roche-SBX, 10x Genomics, Bruker NanoString CosMx, Vizgen MERSCOPE).
Adjacent
- Tier 1: _index, genetics-and-genomics, cell-molecular-biology, microbiology-foundations, developmental-biology
- Tier 2: walkthroughs in (e.g., CRISPR screen design, scRNA-seq pipeline, organoid protocol)
- Adjacent reference vaults: _index (where chemistry enables biology — click chemistry probes, peptide synthesis, mAb conjugation), _index (bioinformatics tools, alignment, single-cell software)
- Tooling: agents-learning-protocol — canonical tag for Biology T3 saves is
biology-reference