Building Gold Corpus

What it does

When your agent uses it

• The user wants to create eval fixtures
• Set up annotation
• Define a label set
• Write guidelines

Example prompts

• “gold corpus”
• “annotation project”
• “label schema”
• “/building-gold-corpus”

Requirements

• Python 3

Workflow steps

7 steps, taken from the first numbered list in SKILL.md.

1. 1Define the label schema. Reuse OpenMed canonical labels (PERSON, DATE,
2. 2Write annotation guidelines. The manual is the contract: span boundaries,
3. 3Generate synthetic source text. Compose realistic clinical narratives
4. 4Configure the tool. BRAT uses annotation.conf (entity types) producing
5. 5Double-annotate and measure agreement. Have ≥2 annotators on an overlap
6. 6Split with discipline. Partition by document/patient, not by sentence,
7. 7Validate and commit. Run load_fixtures; confirm spans align and ids are

What it can do on your machine

Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  No scripts in the folder and no shell commands in SKILL.md (its code samples are json and python).

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • brat.nlplab.org
  • labelstud.io
  • i2b2.org
  • n2c2.dbmi.hms.harvard.edu
  • aclanthology.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Building Gold Corpus loads about 1.7k tokens when it runs. Until then it costs about 176 tokens; SKILL.md has 596 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~176

When it runs · the whole SKILL.md, loaded when a task matches

~1.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 596 words, ~1,689 tokens.

name

building-gold-corpus

description

Scaffold a synthetic gold-standard annotation project for evaluating OpenMed NER and de-identification models — label schema, annotation guidelines, BRAT or Label Studio config, and disjoint train/dev/test splits. Use when the user wants to create eval fixtures, set up annotation, define a label set, write guidelines, configure an annotation tool, or build a held-out gold set for the OpenMed eval harness. Trigger on "gold corpus", "annotation project", "label schema", "annotation guidelines", "BRAT", "Label Studio", "train dev test split", or "build eval fixtures" for OpenMed. Committed gold must be synthetic; licensed (i2b2/n2c2/MIMIC) data is eval-only and never committed.

license

Apache-2.0

metadata.project

OpenMed

metadata.category

evaluation-quality

metadata.pairs

adjacent

metadata.version

1.0

{
  "fixtures": [
    {
      "id": "synthetic-0001",
      "language": "en",
      "text": "Ms. Jane Roe (MRN 0000000) seen 2099-01-02 for type 2 diabetes.",
      "gold_spans": [
        {"start": 4,  "end": 12, "label": "PERSON"},
        {"start": 18, "end": 25, "label": "ID_NUM"},
        {"start": 32, "end": 42, "label": "DATE"},
        {"start": 47, "end": 62, "label": "DISEASE"}
      ]
    }
  ]
}

eval/
  gold/
    guidelines.md            # annotation manual + edge-case decisions
    label_schema.json        # canonical labels + definitions + examples
    synthetic/               # COMMITTED synthetic fixtures (CI-gateable)
      train.json
      dev.json
      test.json
  external/                  # GITIGNORED: licensed DUA corpora, eval-only
    .gitignore               # *  (never commit i2b2/n2c2/MIMIC)

from openmed.eval.harness import load_fixtures

fixtures = load_fixtures("eval/gold/synthetic/test.json")
print(len(fixtures), "fixtures;", sum(len(f.gold_spans) for f in fixtures), "spans")
# load_fixtures normalizes spans against source text and rejects duplicate ids.

© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/building-gold-corpus of maziyarpanahi/openmed.

Open the folder on GitHubat commit 34d7b8c