What is ceir-publication-sync?

A publication-sync workflow for a Charité research team. It fetches publication records from the Charité research database, PubMed, and ORCID, removes duplicates, filters by team affiliation, and syncs missing records into a Zotero group library.

Use it to fetch team publications, enrich records with PubMed data, verify identifiers, exclude papers from before an affiliation, and add missing items to Zotero collections.

It reduces the manual work of collecting publications, filling in missing metadata, checking existing Zotero entries, and organizing items by year.

How BIH-CEI/zotero-comfort configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to BIH-CEI/zotero-comfort. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/BIH-CEI/zotero-comfort/main/.claude/skills/ceir-publication-sync/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/BIH-CEI/zotero-comfort

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/bih-cei/zotero-comfort/ceir-publication-sync/github.svg)](https://agentmods.dev/skills/bih-cei/zotero-comfort/ceir-publication-sync)

Your own site

<a href="https://agentmods.dev/skills/bih-cei/zotero-comfort/ceir-publication-sync"><img src="https://agentmods.dev/badge/skills/bih-cei/zotero-comfort/ceir-publication-sync/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/bih-cei/zotero-comfort/ceir-publication-sync"><img src="https://agentmods.dev/badge/skills/bih-cei/zotero-comfort/ceir-publication-sync.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 134 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 772 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00134	$0.00772
Opus 5.5	$0.00054	$0.00309
Sonnet 5.5	$0.00027	$0.00154
Haiku 4.5	$0.00013	$0.00077

Measured 2mo ago against content hash 98d14736cbfb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

ceir-publication-sync scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/ceir-publication-sync/SKILL.md · 59 lines

How it starts

The opening of the file, as written. The whole thing — 59 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CEIR Publication Sync

Sync Workflow

Fetch publications from Charité API for all team members with tokens
Enrich with PubMed metadata where DOI/abstract missing
Deduplicate by DOI (primary) then normalized title (fallback)
Filter out pre-affiliation papers (see filtering rules in references)
Compare against existing Zotero items (match DOI or title)
Create missing items in Zotero, assign to year collections

Charité Forschungsdatenbank API

Primary source. No browser needed — call REST endpoints directly.

BASE = https://forschungsdatenbank.charite.de/experts/expert

GET /publications/pub_per_exp/{token}/FPS   → publications
GET /exp/co_per_exp/{token}/FPS             → co-authors
GET /exp/info_per_exp/{token}               → profile info

Use 0.3s delay between requests. Returns: title, authors, year, DOI, journal, volume/issue/pages, abstract, PubMed/PMC links, open access status, internal co-authors with tokens.

Implementation: src/zotero_comfort/external/charite.py — ChariteClient class, CEIR_TEAM roster.

Other Sources

PubMed (src/zotero_comfort/external/pubmed.py): Enrich metadata, verify DOIs, get PMIDs
ORCID (not yet implemented): 5 members have ORCID only — see references/roster.md
arXiv (src/zotero_comfort/external/arxiv.py): Low priority, most team output is journals/conferences
BIH website: Just links to Forschungsdatenbank profiles, no publications inline. Skip.

Deduplication

Publications appear under multiple members. Deduplicate with:

DOI (case-insensitive, stripped) — strongest
Normalized title (lowercase, non-alnum removed, first 50 chars) — fallback

First occurrence wins. See ChariteClient._deduplicate().

Zotero Sync Target

Library: CEI_Publications (ID 5767153), key at ~/.secret/ceir-os-zotero-token (format: library_id:api_key)
Collections: Year-based (2018–2026)
Item mapping: See workflows_external.py → _paper_to_zotero_item()
Blocker (2026-02-04): API key is read-only. Need write access.

Read the full file on GitHub · 59 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 59 lines · 134 tokens per session scan A 98d14736cbfb

Subscribe to this mod's changes

ceir-publication-sync is a skill published in the GitHub repository BIH-CEI/zotero-comfort (1 stars, last pushed 5mo ago), licensed MIT. It adds 134 tokens to every session and 772 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Research Scientific

ceir-publication-sync next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
ceir-publication-syncBIH-CEI/zotero-comfort	Skill	1	5mo ago	MIT	A	134	Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	2d ago	Apache-2.0	A	123	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	83	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	44	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	yesterday	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	yesterday	Apache-2.0	A	205	Claude Code

zotero-comfort: Skill for Claude Code