journal-abbrev

Journal Abbreviation Lookup

Look up journal/magazine name abbreviations using a multi-source cascade: JabRef database (~25K journals) → AbbrevISO API (ISO 4) → NLM Catalog (MEDLINE).

Critical rule: Always use jabbrv.py for lookups. Never guess abbreviations — even common journals have non-obvious abbreviations.

Quick Reference

User wants...	Tier	Command
Abbreviate a journal name	read	python3 jabbrv.py abbrev "Nature Medicine"
Expand an abbreviation	read	python3 jabbrv.py expand "Nat. Med."
Auto-detect direction	read	python3 jabbrv.py lookup "J. Am. Chem. Soc."
Fuzzy search (paginated)	read	python3 jabbrv.py search "biolog chem" --limit 10 --offset 0
Process a .bib file	write	python3 jabbrv.py bib refs.bib
Preview .bib changes (no write)	read	python3 jabbrv.py bib refs.bib --dry-run
Explicit .bib output path	write	python3 jabbrv.py bib refs.bib --output out.bib
Expand .bib abbreviations	write	python3 jabbrv.py bib refs.bib --expand
Replay-safe .bib (retry returns cached envelope)	write	python3 jabbrv.py bib refs.bib --idempotency-key run-001
Batch text list	read	python3 jabbrv.py batch journals.txt
Batch as NDJSON stream	read	python3 jabbrv.py batch journals.txt --stream
Inspect cache state	read	python3 jabbrv.py cache status
Download missing cache files	write	python3 jabbrv.py cache update
Preview what update would fetch	read	python3 jabbrv.py cache update --dry-run
Atomic rebuild	⚠️ destructive	python3 jabbrv.py cache rebuild --yes
Preview rebuild (no delete)	read	python3 jabbrv.py cache rebuild --dry-run
Suppress stderr progress	read	python3 jabbrv.py --quiet cache update
Machine-readable CLI contract	read	python3 jabbrv.py schema
Schema for one subcommand	read	python3 jabbrv.py schema lookup

Output format

Stdout is a stable JSON envelope when the CLI is not attached to a terminal (piped or captured by an agent), and a human table/indented view when run on a TTY. To force a format: --format json|table|human|auto. --json remains as a back-compat alias for --format json. Flags may appear before or after the subcommand.

Envelope shape (always the same fields for every subcommand):

• Success: { "ok": true, "data": ..., "meta": { "schema_version", "cli_version", "cache", "latency_ms" } }
• Partial success (batch): { "ok": "partial", "data": { "succeeded": [...], "failed": [...] }, "meta": {...} }
• Error: { "ok": false, "error": { "code", "message", "retryable", ... }, "meta": {...} }

Exit codes

Code	Meaning
0	success (including partial success)
1	runtime / upstream error
2	validation / bad input (missing file, bad flag)
3	not found (the looked-up journal does not exist)

Error codes (inside error.code)

Code	Retryable	Exit	Meaning
not_found	no	3	Lookup completed but no source matched
upstream_unavailable	yes	1	One or more upstream APIs failed transiently; the lookup could not be concluded. Carries error.sources[] listing each failure. Retry later.
file_not_found	no	2	Input file path does not exist
validation_error	no	2	Bad argument or flag combination
runtime_error	yes	1	Unexpected internal error

Branch on error.code + error.retryable rather than exit code alone — exit 1 covers both upstream_unavailable and runtime_error. Full machine-readable listing: python3 jabbrv.py schema → data.error_codes.

Environment variables (set by host, not by agent argv)

Variable	Effect
JABBRV_CACHE_DIR	Override the cache directory (default: <install>/cache). Useful in sandboxes where the install tree is read-only.
JABBRV_OFFLINE	Truthy (1/true/yes/on) skips AbbrevISO and NLM; only the local JabRef cache is consulted. Misses become definitive not_found (not retryable) since the host has declared upstream off-limits. meta.offline: true appears in every envelope so callers can see the policy.
NO_COLOR	https://no-color.org convention. Any non-empty value disables color. No ANSI is emitted today; meta.no_color: true appears when set so callers can see the policy.

Trust boundary: these are read from the process environment, not from arguments. The host or sandbox sets them; the agent cannot override them via argv. Schema introspection: python3 jabbrv.py schema → data.global_env.

Retries, idempotency, and destructive intent

• Branch on error.code + error.retryable, not exit code alone. Exit 1 covers both upstream_unavailable (retry) and runtime_error (retry once, then escalate).
• bib --idempotency-key <token> persists the success envelope next to the output file as <output>.<token>.envelope.json. A retry with the same key returns that envelope with meta.idempotent_replay: true instead of rerunning the rewrite. Token must match [A-Za-z0-9._-]{1,64}.
• cache rebuild is atomic — downloads stage into a sibling directory and the swap only happens if every file succeeded. If any fails, the existing cache is preserved and the response is upstream_unavailable (retryable). Add --yes to record meta.confirmed: true for audit policies; the CLI itself never prompts, so --yes is not a gate.

Workflow

Step 1: Detect Intent

Intent	Action
Single journal name/abbreviation	Use lookup (auto-detect) or abbrev/expand (explicit direction)
"What's the abbreviation for X?"	Use abbrev
"What journal is X?"	Use expand
Partial or uncertain name	Use search for fuzzy matching
Fix journal names in .bib file	Use bib
List of journals to process	Use batch

Step 2: Execute

Run the appropriate jabbrv.py command. The script handles:

1. Local cache lookup (instant, ~25K journals from JabRef)
2. AbbrevISO API fallback (algorithmic ISO 4 abbreviation, forward only)
3. NLM Catalog fallback (biomedical journals, bidirectional)

First run downloads JabRef CSV cache files automatically (~2-5 MB).

Step 3: Present Results

• Show the full name, abbreviation, and source
• Note the standard (ISO 4 vs MEDLINE) when relevant
• For .bib processing: show the change summary before confirming

ISO 4 vs MEDLINE

Two common abbreviation standards exist:

Standard	Periods	Example	Used by
ISO 4	Yes	Nat. Med.	Most publishers, BibTeX
MEDLINE	No	Nat Med	PubMed, NLM databases

JabRef provides ISO 4 style. NLM Catalog provides MEDLINE style. AbbrevISO computes ISO 4 algorithmically from LTWA (List of Title Word Abbreviations).

Common Abbreviation Patterns

Word	Abbreviation	Word	Abbreviation
Journal	J.	International	Int.
American	Am.	European	Eur.
Science/Sciences	Sci.	Medicine/Medical	Med.
Biology/Biological	Biol.	Chemistry/Chemical	Chem.
Physics/Physical	Phys.	Engineering	Eng.
Research	Res.	Review/Reviews	Rev.
Society	Soc.	National	Natl.
Proceedings	Proc.	Transactions	Trans.
Letters	Lett.	Communications	Commun.
Applied	Appl.	Computational	Comput.

Note: Single-word titles (e.g., "Nature", "Science", "Cell") are NOT abbreviated per ISO 4 rules.

Integration Examples

With Zotero

# Export BibTeX from Zotero, then standardize journal names
zot export COLLECTION_KEY --format bibtex > refs.bib
python3 jabbrv.py bib refs.bib

With LaTeX

# Before compiling, ensure all journal names are abbreviated
python3 jabbrv.py bib references.bib
# Use the output file (references_abbrev.bib) in your LaTeX document

Batch Processing

Create a text file with one journal name per line:

Nature Medicine
Journal of Biological Chemistry
Proceedings of the National Academy of Sciences

Then run:

python3 jabbrv.py batch journals.txt

Troubleshooting

Issue	Solution
"No result found"	Try search with partial name for fuzzy matching
Cache download fails	Check network connection, retry with cache update (or cache rebuild to force)
Wrong abbreviation style	JabRef = ISO 4 (with dots), NLM = MEDLINE (no dots)
BibTeX field not detected	Ensure format is journal = {Name} (curly braces)