Agent Skills
› brycewang-stanford/Awesome-Journal-Skills
› est-reporting-and-reproducibility
est-reporting-and-reproducibility
GitHub用于ES&T稿件的SI组装、数据可用性声明撰写及公共数据/代码归档。指导按数据类型选择合规仓库，确保方法可复现并符合期刊要求。
触发场景
编写数据可用性声明
整理支持信息(SI)
向公共数据库提交数据或代码
安装
npx skills add brycewang-stanford/Awesome-Journal-Skills --skill est-reporting-and-reproducibility -g -y
SKILL.md
Frontmatter
{
"name": "est-reporting-and-reproducibility",
"description": "Use when assembling the Supporting Information (SI), data-availability statement, and public-data\/code deposit for an Environmental Science & Technology (ES&T) manuscript. ES&T expects materials, data, and protocols to be deposited in public databases and a data-availability statement, with SI submitted alongside the manuscript. It guides reporting and deposit; it does not generate the underlying data."
}
Reporting & Reproducibility (est-reporting-and-reproducibility)
ES&T strongly encourages public data and expects authors to make materials, data, and protocols available through public databases, with a data-availability statement and a Supporting Information file submitted alongside the manuscript and reviewed with it. Build these as you go, not the night before submission.
When to trigger
- Assembling the Supporting Information (SI) PDF/files
- Writing the data-availability statement and choosing repositories
- Depositing data, spectra, sequences, code, and protocols
- Making sure every figure/table can be regenerated from deposited data
What ES&T expects
- Supporting Information. Submitted simultaneously as separate file(s); describe contents and file type in the SI paragraph (e.g., "Additional analytical methods, calibration data, and NMR spectra (PDF)"). Available to reviewers; free to readers on publication.
- Data-availability statement. State where the data live and how to access them; cite accession codes / DOIs.
- Public deposition by data type (see
resources/external_tools.md):- Sequences → GenBank / ENA / DDBJ; omics/microarray → GEO / ArrayExpress; proteomics → PRIDE / ProteomeXchange; mass spectra → MassIVE / MetaboLights / MassBank.
- General data/code → Dryad, figshare, Zenodo, OSF.
- Methods reproducibility. Report instrument settings, reagents/standards, QA/QC, and analysis steps in enough detail to reproduce; deposit analysis code with seeds and pinned versions.
- Restricted data. If data cannot be fully shared (privacy/legal), explain why and give README instructions on how to obtain it; provide what can be shared.
SI assembly checklist
- Extended methods, reagents/standards, instrument parameters
- Calibration curves, QA/QC tables (blanks, recoveries, CRMs, LOD/LOQ)
- Supplementary figures/tables/spectra referenced in order (Figure S1, Table S1…)
- Data-availability statement with accession/DOI
- Code/scripts deposited; figures regenerate from deposited data
- Page/word limits and file formats per ACS SI guidance (待核实 on specifics)
Deposition routing: data type → repository
ES&T expects deposition in the community-standard repository for each data type, not a generic catch-all. Reviewers in a sub-field know the canonical home and notice when data are not there (confirm any volatile mandate against the journal's current author guidelines — 待核实):
| Data type | Expected repository | Reviewer's note if missing |
|---|---|---|
| DNA/RNA sequences | GenBank / ENA / DDBJ | not independently checkable |
| Omics / microarray | GEO / ArrayExpress | non-standard, hard to reuse |
| Proteomics | PRIDE / ProteomeXchange | unverifiable identifications |
| Mass spectra / metabolomics | MassIVE / MetaboLights / MassBank | spectra not reusable |
| General data / code | Dryad, figshare, Zenodo, OSF | "available on request" red flag |
Worked micro-example (illustrative — SI for a PFAS fate study)
For the river-PFAS study, a reviewer-ready Associated Content package (illustrative) contains:
- SI PDF: extended LC-MS/MS methods, transition list and collision energies, the QA/QC table (field blanks, 92% recovery, per-analyte LOQ), calibration curves (R² > 0.99, illustrative), and the ROS censoring detail — each item S-numbered and referenced in order from the main text.
- Deposited: raw and processed concentration tables plus the analysis code (with the random seed for the bootstrap CI and pinned package versions) on Zenodo with a DOI; the mass spectra on MassIVE.
- Data-availability statement: "Concentration data and analysis code are available at Zenodo (DOI: 10.xxxx/illustrative); raw mass spectra are deposited at MassIVE (accession: illustrative)."
The test that catches drift: re-run the deposited master script on a clean machine — every figure and the 2.4 ng/L headline number must regenerate exactly. If they do not, the SI and manuscript have diverged.
Referee-pushback patterns and the venue-specific fix
- "Data available on request is not sufficient." → Deposit in the type-appropriate repository and cite the accession/DOI in the statement.
- "Methods not reproducible." → Move instrument settings, standards, and QA/QC into the SI in enough detail to repeat the work; deposit code with seeds and versions.
- "SI contents not described." → Write the SI paragraph naming each file and its type.
Anti-patterns
- "Data available on request" with no statement, repository, or accession
- An SI that is a dumping ground with no described contents or ordering
- Spectra/sequences/omics not deposited in the expected community database
- Code that does not run, or that cannot regenerate the manuscript's exhibits
- Leaving SI + deposition to submission day, so numbers drift from the manuscript
Output format
【SI contents】described + ordered (S-numbered)? [Y/N]
【Data-availability statement】present with accession/DOI? [Y/N]
【Deposition】data type → repository (GenBank/GEO/PRIDE/MassIVE/Dryad/Zenodo/OSF)
【Code】deposited, seeds + pinned versions, regenerates exhibits? [Y/N]
【Restricted data】justified + README to obtain? [N/A or Y/N]
【Next】est-writing-style
Supplementary resources
../../resources/external_tools.md— repositories by data type; reproducibility tooling../../resources/official-source-map.md— data-availability and SI policy
版本历史
- 1839142 当前 2026-07-05 13:12
