Research

EDFacts — K-12 outcomes: assessment proficiency, ACGR graduation rates, ESSA accountability at school/district level (2009-2020). Within-state trends and subgroup gaps. Complements CCD with outcome data. Cannot compare across states — use NAEP.

CRDC — OCR civil rights collection for U.S. public schools; Portal families have topic-specific coverage from 2011 through 2022. Discipline, course access, harassment, restraint/seclusion by race/sex/disability/EL. Use for civil rights and equity analysis. Official evidence identifies 2013-14 as a universe collection; 2020-21 is COVID-impacted.

CCD — federal universe of all U.S. public K-12 schools (~100K) and districts (~18K). Enrollment, staffing, finance, directory data (1986-present). Use for public school analysis by grade/race/sex. Public only; excludes private and postsecondary.

CSS — annual Clery Act crime/fire safety for Title IV institutions. Portal: hate crimes only (2005-2021); primary offenses, VAWA, arrests, fire safety need ope.ed.gov directly. Use for campus crime analysis. Identified by IPEDS unitid.

Downloads education datasets from configured mirror sources (parquet/CSV) with local Polars filtering, including versioned mirror vintages (revision-pinned for reproducibility). Use when writing fetch scripts, retrieving CCD, IPEDS, CRDC, SAIPE data, or pinning a fetch to a specific mirror vintage. Load after education-data-explorer — retrieval here, not discovery.

Mirror-first discovery for Urban Institute Education Data: maps a research question to the mirror dataset FILES that answer it — canonical path, entity grain, year coverage, key variables, and join keys — for CCD, IPEDS, CRDC, College Scorecard, SAIPE, EDFacts, FSA, MEPS, NHGIS, PSEO, NACUBO, NCCS, EADA, and Campus Safety. Discovery output is the mirror path (plus grain, years, variables, caveats), the currency planning and acquisition consume. A pure readable-reference skill for read-only di...

Interpretation guidance for Urban Institute Education Data Portal datasets. The Portal is a curation layer over federal data: lowercase variable names, integer-encoded categoricals, standardized missing codes (-1 missing, -2 not applicable, -3 suppressed). Covers year definitions, grade encoding (grade=-1 is Pre-K, not missing), suppression rates, ODC-By licensing, and cross-source join identifiers. Load before analyzing any Portal data. Routes to source-specific deep-dive skills for individu...

Operational framework for the DAAF orchestrator. Defines engagement modes, confirmation protocol, subagent dispatch, context budget, and reference-loading. Loaded exclusively by the orchestrator — not for subagents or user questions.

Guide for creating DAAF agent definition files. Covers 12-section template, hook registration, skills-in-frontmatter, integration checklist. Use when adding or revising agents. For SKILL.md files, use skill-authoring instead.

> [!info] What it does > Turn plugin-eval findings into a concrete rewrite brief for a Codex skill. Use when the user already evaluated a skill and now wants Codex to improve it, especially after asking what to fix first. **Source:** [skills/improve-skill/SKILL.md](../../../skills/improve-skill/SKILL.md) · **Domain:** [Vault, Skills & Workflow Meta](../../maps/vault-meta.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data ...

> [!info] What it does > Submit compact NCBI PMC Open Access requests for article/file availability metadata. Use when a user wants concise PMC Open Access summaries; save raw XML only on request. **Source:** [skills/ncbi-pmc-skill/SKILL.md](../../../skills/ncbi-pmc-skill/SKILL.md) · **Domain:** [Literature Search & Knowledge Discovery](../../maps/literature-discovery.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact bioRxiv and medRxiv API requests for details, publication-linkage, and DOI lookups. Use when a user wants concise preprint metadata summaries **Source:** [skills/biorxiv-skill/SKILL.md](../../../skills/biorxiv-skill/SKILL.md) · **Domain:** [Literature Search & Knowledge Discovery](../../maps/literature-discovery.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries **Source:** [skills/rhea-skill/SKILL.md](../../../skills/rhea-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request. **Source:** [skills/rcsb-pdb-skill/SKILL.md](../../../skills/rcsb-pdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries **Source:** [skills/pubchem-pug-skill/SKILL.md](../../../skills/pubchem-pug-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact PharmGKB API requests for genes, variants, clinical annotations, dosing guidelines, and search. Use when a user wants concise PharmGKB summaries **Source:** [skills/pharmgkb-skill/SKILL.md](../../../skills/pharmgkb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries **Source:** [skills/hmdb-skill/SKILL.md](../../../skills/hmdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries **Source:** [skills/chembl-skill/SKILL.md](../../../skills/chembl-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries **Source:** [skills/chebi-skill/SKILL.md](../../../skills/chebi-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request. **Source:** [skills/bindingdb-skill/SKILL.md](../../../skills/bindingdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index...

> [!info] What it does > Route broad or ambiguous life-sciences research requests to the right skills, normalize core entities, optionally parallelize independent evidence gathering with subagents when available, and synthesize a concise evidence-backed answer. Use when a user asks a general life-sciences question that could span multiple sources or analysis types. **Source:** [skills/research-router-skill/SKILL.md](../../../skills/research-router-skill/SKILL.md) · **Domain:** [Bio Database...

> [!info] What it does > Submit compact MetaboLights requests for study discovery and study-level metabolomics metadata. Use when a user wants concise MetaboLights summaries **Source:** [skills/metabolights-skill/SKILL.md](../../../skills/metabolights-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

Use Zotero Desktop from Codex to enable/probe the local API, search a local Zotero library, list items/collections/tags, export BibTeX, insert citation keys into LaTeX or Markdown drafts, read indexed full text when requested, and import BibTeX/RIS records into Zotero through the connector server. Use when the user mentions Zotero, citations, references.bib, BibTeX export, local Zotero API, localhost:23119, or adding citations from a Zotero library.