# Credits and data provenance

## Variant Toolkit sources

- fastVEP by Kuan-lin Huang and contributors: https://github.com/Huang-lab/fastVEP — Apache-2.0. Linked as an external full annotator; no fastVEP code or binary is bundled.
- Ensembl Plants Variant Effect Predictor: https://plants.ensembl.org/info/docs/tools/vep/index.html — linked as an external annotation service and workflow reference; no Ensembl VEP code or data is bundled.
- Sequence Ontology: https://www.sequenceontology.org/ — terminology reference for consequence concepts.
- Variant Toolkit parser and experimental teaching predictor: original browser-only code by Shoaib Munir. It uses the standard nuclear genetic code and is not an implementation or port of fastVEP or Ensembl VEP.

The public interface consolidates journal discovery, matching, OA/APC, timing and trust evidence in **Journal Hub**, and reference and identifier work in **Publishing Toolkit**. Original data, vendored libraries, provenance records and test fixtures remain at their documented paths so they are not duplicated and their audit trail is preserved.

This file records third-party software and public metadata services used by the research tools at smbajwa.com. Names are factual attribution and do not imply affiliation or endorsement.

## Logo

- Original artwork by the site owner; all rights reserved, © Dr. Shoaib Munir

## qrcode-generator

- Original author: Kazuhiko Arase
- Repository: https://github.com/kazuhikoarase/qrcode-generator
- Version: 1.4.4
- Package artifact and SHA-256 checksum: recorded in `tools/_shared/vendor/qrcode-generator/1.4.4/UPSTREAM.json`
- License: MIT (`tools/_shared/vendor/qrcode-generator/1.4.4/LICENSE`)
- Used by: the shared, browser-local share dialog to draw downloadable QR codes
- Vendored material: unmodified `qrcode.js`; no remote QR service is contacted
- Retrieved: 2026-10-07

## Emerging Journals Database 2026

- Implementation and English presentation: Shoaib Munir, smbajwa.com
- Local source: the translated emerging-journal title, ISSN, discipline and quartile list in `tools/emerging-journals-2026/data.js`
- Live enrichment: OpenAlex source metadata (CC0), requested only when a visitor explicitly selects “Refresh live OpenAlex”
- External reference: journal cards link by ISSN to SCImago; no SCImago or Scopus-derived values are bundled
- Requests: identify the site contact (Contact (at) smbajwa.com) through the documented `mailto` parameter; successful responses are cached locally for 30 days
- Excluded sources and fields: Clarivate, Scopus, CAS, Journal Impact Factor, blacklists and watchlists
- Limit: source-list quartiles are presented as supplied and are not an endorsement or quality verdict

## MiniSearch

- Original author: Luca Ongaro and contributors
- Repository: https://github.com/lucaong/minisearch
- Version/commit: 7.2.0 / `3d239d1c3ae7aef1bf5d8945dd7b5f0709f646f5`
- Package artifact: `minisearch@7.2.0` from the npm registry; integrity and SHA-256 checksums recorded in `tools/abstract-journal-matcher/third_party/minisearch/7.2.0/UPSTREAM.json`
- License: MIT (`tools/abstract-journal-matcher/third_party/minisearch/7.2.0/LICENSE.txt`)
- Used by: Abstract-to-Journal Matcher local lexical retrieval
- Vendored material: unmodified official UMD browser distribution `dist/umd/index.js`
- Retrieved: 2026-10-07

## Abstract-to-Journal Matcher data sources

- Compact journal profiles: original aggregate topic labels joined to smbajwa.com's curated journal identities; no abstracts or copied publisher scope prose
- DOAJ journal metadata: CC0, retrieved live by ISSN only after the user requests evidence
- OpenAlex source metadata: CC0, retrieved live by ISSN with the `mailto` parameter (Contact (at) smbajwa.com)
- Crossref: journal metadata retrieved live by ISSN; abstracts are not requested, stored, or exported
- Excluded sources: Clarivate, Scopus, CAS, and Journal Impact Factor values
- Cache: live evidence only, browser-local, 30-day expiry, user-clearable

## Fuse.js

- Original author: Kiro Risk and contributors
- Repository: https://github.com/krisk/Fuse
- Version/commit: 7.5.0 / `45bac9fe2e71fe8c680c861a35a8b226c4ae6d5a`
- Package artifact: `fuse.js@7.5.0` from the npm registry; package and file SHA-256 checksums recorded in `tools/journal-trust-profile/third_party/fuse/7.5.0/UPSTREAM.json`
- License: Apache-2.0 (`tools/journal-trust-profile/third_party/fuse/7.5.0/LICENSE`)
- Used by: Journal Trust Profile local typo-tolerant title/ISSN search
- Vendored material: unmodified `dist/fuse.min.mjs`
- Retrieved: 2026-10-07

The same verified, unmodified Fuse.js 7.5.0 browser artifact is also used by the OA & APC Explorer. Its complete Apache-2.0 license and checksums are repeated at `tools/oa-apc-explorer/third_party/fuse/7.5.0/` so that tool remains independently deployable.

## OA & APC Explorer data sources

- DOAJ journal metadata: CC0, retrieved live from https://doaj.org/api/ only after the user submits a search
- OpenAlex source metadata: CC0, retrieved live from https://api.openalex.org/ by exact ISSN with the `mailto` parameter (Contact (at) smbajwa.com)
- Local journal snapshot: intentionally empty; `tools/oa-apc-explorer/data/data-manifest.json` records the source and exclusion boundaries
- Cache: browser-local, 30-day expiry, user-clearable
- OpenAPC: linked as an independent historical-cost resource only; no OpenAPC ODbL/DbCL data are included, queried, cached, or merged
- Excluded sources: Clarivate, Scopus, CAS, and Journal Impact Factor data
- Used by: OA & APC Explorer

## Journal Trust Profile data sources

- DOAJ journal metadata: CC0, retrieved live from https://doaj.org/api/ after user confirmation
- OpenAlex source/work metadata: CC0, retrieved live from https://api.openalex.org/ with the `mailto` parameter (Contact (at) smbajwa.com)
- Crossref bibliographic facts: retrieved live from https://api.crossref.org/ after user confirmation; abstracts are neither requested nor stored
- Local journal search seed: derived on 2026-10-07 from `tools/emerging-journals-2026/data.js`, explicitly labeled as an smbajwa.com source
- Used by: Journal Trust Profile; cached in the browser for 30 days with a visible clear control

## Citation.js

- Original author: Lars Willighagen and contributors
- Repository: https://github.com/citation-js/citation-js
- Version/commit: 0.9.0 / `51a37ce28fd3508e5cc2957b7d17794cdbad8ed0`
- Package artifact: `citation-js@0.9.0` from the npm registry; integrity recorded in `UPSTREAM.json`
- License: MIT (`tools/_shared/vendor/citation-js/0.9.0/LICENSE.md`)
- Used by: Identifier & Citation Toolkit; Reference Integrity Checker
- Vendored material: unmodified browser bundle `build/citation.min.js`
- Local changes: upstream bundle unmodified; a separate local loader exposes its documented `require('citation-js')` module as `window.Cite`
- Retrieved: 2026-10-07

## Journal Timing data sources

- DOAJ journal CSV: CC0; self-reported average weeks from submission to publication, joined by print ISSN or e-ISSN
- Crossref REST API: publisher-deposited assertions and publication dates sampled for recent journal articles; aggregate medians only are committed
- Used by: Journal Timing; build retrieval only, with no live API calls from the page
- Method, validation, suppression, and coverage: `tools/journal-timing/METHODS.md` and `tools/journal-timing/data/coverage.json`

## Crossref

- Service: Crossref REST API, https://api.crossref.org/
- Documentation: https://www.crossref.org/documentation/retrieve-metadata/rest-api/
- Used by: Identifier & Citation Toolkit DOI and journal lookup; Reference Integrity Checker metadata and update lookup
- Data handling: bibliographic fields are retrieved live after user confirmation; abstracts are discarded and not exported
- Cache: browser-local, 30-day expiry, user-clearable
- Accessed: on demand; no repository snapshot

## OpenAlex

- Service and data: OpenAlex API, https://api.openalex.org/
- Data license: CC0, https://docs.openalex.org/download-all-data/openalex-snapshot
- Used by: optional Identifier & Citation Toolkit DOI/ISSN cross-check; optional Reference Integrity Checker secondary cross-check
- Requests: identify the site contact (Contact (at) smbajwa.com) through the documented `mailto` parameter
- Cache: browser-local, 30-day expiry, user-clearable
- Accessed: on demand; no repository snapshot

## DOAJ

- Service: DOAJ API, https://doaj.org/api/v3/docs
- Journal/article metadata: CC0, https://doaj.org/terms/
- Used by: optional Identifier & Citation Toolkit ISSN lookup
- Cache: browser-local, 30-day expiry, user-clearable
- Accessed: on demand; no repository snapshot

## ORCID

- Public record site: https://orcid.org/
- Used by: local ISO 7064 checksum validation and public-record links only
- No ORCID API credentials, client secrets, source code or public-data files are included
- ORCID is a trademark of ORCID, Inc.; this site is not affiliated with or endorsed by ORCID

## Retraction Watch via Crossref

- Data source: Retraction Watch database integrated into Crossref, https://www.crossref.org/blog/retraction-watch-data-now-part-of-crossref/
- Data license: CC0
- Used by: Reference Integrity Checker update classification through Crossref `update-to` metadata
- Data handling: records are retrieved live after user confirmation; no repository snapshot is included
- Cache: browser-local IndexedDB, 30-day expiry, user-clearable
- Attribution: Retraction Watch is named as requested; no affiliation or endorsement is implied

## Plant Lab Toolkit formula sources

- Implementation: independently written by Shoaib Munir for smbajwa.com; no third-party runtime or calculation code
- Used by: Plant Lab Toolkit dilution, molarity, qPCR, sequence and primer-Tm workflows
- Formula references: Livak & Schmittgen (2001), Pfaffl (2001), MIQE (2009), Wallace et al. (1979), and SantaLucia (1998)
- Full citations and DOI links: `tools/plant-lab-calculators/METHODS.md`
- Primer3 boundary: no Primer3 code, parameter files, interface, or bundled executable is included
- Local changes: not applicable; the source is original to this repository

## Browser-only calculation and preparation tools

- Implementation: original JavaScript in this repository; no third-party runtime or calculation library
- Used by: Plant Lab Toolkit, Descriptive Statistics, and Journal Figure Resizer
- Formula and transformation notes: each active tool's `METHODS.md`
- Published qPCR sources: Livak & Schmittgen (2001) and Pfaffl (2001), cited in `tools/plant-lab-calculators/METHODS.md`