Initial commit: established file structure, added draft scholarly lexicons, and added foundational documentation

.gitignore

···
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+._*
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# Windows
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+*.stackdump
+[Dd]esktop.ini
+$RECYCLE.BIN/
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+*.lnk
+
+# Linux
+*~
+.directory
+.fuse_hidden*
+.Trash-*
+.nfs*

LICENSE

···
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+
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+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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+
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+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
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+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
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+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
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+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
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+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
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+if any, to sign a "copyright disclaimer" for the program, if necessary.
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+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

···
+# at-scholarly-lexicons
+
+## What is this?
+
+A **proof-of-concept** set of AT Protocol lexicons for academic publishing - demonstrating how decentralised, content-addressed data structures could transform scholarly communication.
+
+> [!TIP] What is a Lexicon?
+> A **lexicon** in the AT Protocol is a schema definition that describes the structure of data records, similar to how a database schema defines tables and fields. Lexicons specify what fields exist, their data types, validation rules, and relationships between different record types. They enable interoperability by ensuring that different applications can read, write, and understand the same data structures in a standardised way.
+
+[Read the official documentation on atproto.com →](https://atproto.com/specs/lexicon)
+
+## Why does this exist?
+
+This project explores what a decentralised academic publishing system might look like, built on the [AT Protocol](https://atproto.com). It defines multiple interconnected lexicons covering the entire scholarly lifecycle: journals, manuscripts, peer review, editorial decisions, and researcher profiles.
+
+Think of it as a blueprint that any project could adopt, adapt, or fork to build modern scholarly publishing infrastructure.
+
+Academic publishing is ripe for disruption. This project imagines:
+- **Portable identities** (DIDs) that researchers own, not journals
+- **Immutable provenance** (content addressing) for submissions and peer reviews
+- **Transparent workflows** that respect blind peer review
+- **Interoperable standards** that any platform can implement
+
+## Getting Started
+
+Each lexicon directory contains:
+- `{name}.json` - The AT Protocol lexicon specification (self-documenting)
+- `README.md` - Practical implementation guide
+
+> [!IMPORTANT]
+> For detailed documentation about the lexicons themselves, see **[lexicons/README.md](./lexicons/README.md)**.
+
+## Contributors
+
+B. Prendergast - [@render.ghost](https://bsky.app/profile/renderg.host)
+
+## Contributing
+
+Feedback and improvements are welcome through community discussion.
+
+- **Fork & adapt** - Use these lexicons as a starting point for your own project
+- **Suggest improvements** - Open issues or discussions about the data model
+- **Build implementations** - Create tools, platforms, or services using these lexicons
+- **Propose additions** - New lexicons or fields that would be useful

lexicons/README.md

···
+# Scholarly Lexicons
+
+A broad set of *hypothetical* lexicons for academic publishing built on the [AT Protocol](https://atproto.com) specification. These lexicons propose data structures for journals, manuscripts, peer reviews, and scholarly profiles using decentralized identifiers and content-addressed storage.
+
+## Contexts
+
+> [!NOTE] Shared Definitions
+> **Definition** - Standard terms, categories, and reference patterns used consistently across the publishing system to ensure clarity and compatibility.
+
+### 📚 Publishing Context
+- **Publisher** - An organization that collects, reviews, and shares scholarly work, responsible for ensuring quality and integrity across the research it distributes.
+- **Portfolio** - A collection of related publications grouped together, often sharing similar editorial standards and subject areas.
+- **Publication** - A venue where scholarly work appears, such as a journal, preprint repository, or conference proceedings.
+- **Issue** - A numbered or themed collection of articles within a publication, helping organize content and provide stable reference points.
+- **Event** - A meeting or gathering—in person or online—where scholars share and discuss research, which may produce formal publications or proceedings.
+
+> [!IMPORTANT] Assumed Publishing Hierarchy
+> `Publisher` → `Portfolio` → `Publication` → `Issue` forms a publication context. A `Portfolio` can be optional.
+
+> [!IMPORTANT] Assumed Peer Review Workflow
+> 1. `Manuscript` submitted to `Publication`.
+> 2. `Version` created (v1, v2, etc.)
+> 3. `Review` references specific `Version`
+> 4. `Decision` references `Manuscript` and `Review`
+> 5. Process repeats across revisions
+
+### 📄 Submission Context
+- **Manuscript** - A piece of scholarly work that author(s) submits for feedback, revision, and eventual publication.
+- **Supplement** - Extra materials like data, code, or media that support and strengthen the claims in a manuscript.
+- **Version** - A specific snapshot of a manuscript at a particular time, allowing people to track changes and refer to exact iterations during review.
+- **Review** - Feedback from independent topical experts  who evaluate a manuscript's quality, methods, and contribution to the field.
+- **Decision** - The editorial verdict on a manuscript (can include accept, revise, reject, transfer, etc. ) that determines what happens next.
+- **Consent** - Formal agreements and approvals needed to publish work, covering ethics, copyright, and how works can be used.
+
+### 👥 User Context
+- **Author** - One who writes and submits scholarly work for publication.
+- **Reviewer** - A topical expert who reads and evaluates manuscripts, helping ensure the quality and credibility of published work.
+- **Editor** - One who manages the publication process, coordinates reviews, makes publication decisions, and maintains publication standards.
+
+## AT Protocol Principles
+
+### Namespacing
+All lexicons use `at.scholarly.*` - a *hypothetical* namespace for demonstration.
+
+### References
+- **`at-uri`** - Stable references to entities (publications, manuscripts)
+- **`strongRef`** - Versioned references with content hash (CID) for immutable linking
+- **`DID`** - Decentralized identifiers for users (authors, reviewers, editors)
+
+### Data Model
+- **Separate records** - Each entity is a distinct record (not embedded)
+- **Versioned linking** - Reviews and decisions reference specific manuscript versions
+- **Content addressing** - Immutable PDFs and data files with cryptographic hashes
+
+### Entity Relationships
+
+> [!IMPORTANT]
+> Mermaid diagrams may not display in all Markdown viewers. To view this diagram, paste it into https://mermaid.live/edit.
+
+```mermaid
+---
+config:
+  layout: elk
+---
+flowchart TB
+ subgraph Publishing["Publication Context"]
+        publisher["Publisher"]
+        portfolio["Portfolio"]
+        publication["Publication"]
+        issue["Issue"]
+        event["Event"]
+  end
+ subgraph Submission["Submission Context"]
+        manuscript["Manuscript"]
+        supplement["Supplement"]
+        version["Version"]
+        review["Review"]
+        decision["Decision"]
+        consent["Consent"]
+  end
+ subgraph Actor["Actor Context"]
+        author["Author"]
+        reviewer["Reviewer"]
+        editor["Editor"]
+  end
+    event --- publication
+    portfolio --- publisher
+    issue --- publication
+    publication --- portfolio & publisher
+    manuscript --- publication & issue & event & supplement & version & review & decision & consent & author
+    review --- version & reviewer
+    decision --- review & editor
+    editor --- publication
+    reviewer --- publication
+     publisher:::pubStyle
+     portfolio:::pubStyle
+     publication:::pubStyle
+     issue:::pubStyle
+     event:::pubStyle
+     manuscript:::subStyle
+     supplement:::subStyle
+     version:::subStyle
+     review:::subStyle
+     decision:::subStyle
+     consent:::subStyle
+     author:::userStyle
+     reviewer:::userStyle
+     editor:::userStyle
+    classDef pubStyle fill:#e1f5ff,stroke:#0288d1,stroke-width:1px,color:#000000;
+    classDef subStyle fill:#fff3e0,stroke:#f57c00,stroke-width:1px,color:#000000;
+    classDef userStyle fill:#f3e5f5,stroke:#7b1fa2,stroke-width:1px,color:#000000;
+
+```
+
+## Usage Examples
+
+### Publishing a Journal Article
+
+```json
+{
+  "$type": "at.scholarly.manuscript",
+  "title": "CRISPR-Cas9 Gene Editing in Human Embryos",
+  "abstract": "We demonstrate...",
+  "authors": [
+    {
+      "name": "Dr. Jane Smith",
+      "orcid": "0000-0002-1825-0097",
+      "affiliation": "Stanford University"
+    }
+  ],
+  "publication": "at://did:plc:abc123/at.scholarly.publication/nature",
+  "doi": "10.1038/nature12373",
+  "submittedDate": "2024-01-15T00:00:00Z",
+  "status": "published",
+  "manuscriptFile": { /* blob reference */ }
+}
+```
+
+### Submitting a Preprint
+
+```json
+{
+  "$type": "at.scholarly.manuscript",
+  "title": "Novel Machine Learning Architecture",
+  "abstract": "We propose...",
+  "authors": [{ /* personRef */ }],
+  "publication": "at://did:plc:xyz789/at.scholarly.publication/arxiv",
+  "submittedDate": "2024-02-01T00:00:00Z",
+  "status": "submitted",
+  "manuscriptFile": { /* blob reference */ }
+}
+```
+
+### Peer Review Workflow
+
+```json
+// 1. Review submitted
+{
+  "$type": "at.scholarly.review",
+  "manuscript": {
+    "uri": "at://did:plc:author123/at.scholarly.manuscript/abc",
+    "cid": "bafyreigh2akiscail..."
+  },
+  "version": {
+    "uri": "at://did:plc:author123/at.scholarly.version/v1",
+    "cid": "bafyreidvmu5qccl..."
+  },
+  "reviewer": "did:plc:reviewer456",
+  "submittedDate": "2024-03-01T00:00:00Z",
+  "recommendation": "minor-revision",
+  "confidentiality": "double-blind",
+  "comments": "The manuscript presents novel findings..."
+}
+
+// 2. Editorial decision
+{
+  "$type": "at.scholarly.decision",
+  "manuscript": {
+    "uri": "at://did:plc:author123/at.scholarly.manuscript/abc",
+    "cid": "bafyreigh2akiscail..."
+  },
+  "editor": "did:plc:editor789",
+  "decisionType": "major-revisions-required",
+  "decisionDate": "2024-03-15T00:00:00Z",
+  "reviews": [
+    {
+      "uri": "at://did:plc:reviewer456/at.scholarly.review/rev1",
+      "cid": "bafyreieakfcpe..."
+    }
+  ],
+  "commentsToAuthors": "Please address the reviewer's concerns...",
+  "dueDate": "2024-05-15T00:00:00Z"
+}
+```
+
+### Conference Paper Submission
+
+```json
+{
+  "$type": "at.scholarly.manuscript",
+  "title": "Neural Architecture Search at Scale",
+  "authors": [{ /* personRef */ }],
+  "publication": "at://did:plc:pub/at.scholarly.publication/neurips-proceedings",
+  "event": "at://did:plc:org/at.scholarly.event/neurips-2024",
+  "submittedDate": "2024-05-15T00:00:00Z",
+  "status": "under-review"
+}
+```
+
+## Resources
+
+- **AT Protocol Documentation**: https://atproto.com
+- **Lexicon Specification**: https://atproto.com/specs/lexicon
+- **AT Protocol GitHub**: https://github.com/bluesky-social/atproto
+- **Lexicon Guidance**: https://www.pfrazee.com/blog/lexicon-guidance

lexicons/author/README.md

···
+# at.scholarly.author
+
+Author profile for researchers who write and publish academic manuscripts.
+
+## Use Cases
+- Providing proper attribution and credit for research contributions
+- Disambiguating between researchers with same names using ORCID
+- Building publication portfolios showing all works by an author
+- Enabling co-author discovery and networking
+- Tracking institutional affiliations and career moves
+
+## Challenges
+- **Privacy concerns**: Email and contact information may be publicly exposed
+- **Maintenance burden**: Affiliations change frequently requiring updates
+- **Name changes**: Life events (marriage, transition) complicate identity continuity
+- **Multiple identities**: Some researchers use different names in different contexts/languages
+
+## Notes
+- Always include ORCID when available for reliable disambiguation (0000-0001-2345-6789)
+- Use `manuscripts` array to automatically build publication list for the author
+- Keep `affiliation` up-to-date as researchers move institutions frequently
+- Support name changes by updating `name` field whilst ORCID provides continuity
+- `expertise` array helps with manuscript-reviewer matching and discovery
+- Key is `literal:self` - one author profile per DID (user account)

lexicons/author/author.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.author",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an author profile - a user account for researchers who write and publish academic manuscripts. Authors are the primary creators of scholarly content. This profile stores their identity, institutional affiliation, research areas, and links to their published work. Authors use this profile when submitting manuscripts, responding to peer review, and managing their publication portfolio. Referenced by: at.scholarly.manuscript (via personRef in authors array). Key 'literal:self' means one profile per user (DID).",
+      "key": "literal:self",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "affiliation"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Full name of the author as it should appear in publications and citations. Format: usually 'FirstName MiddleName(s) LastName' but respect cultural naming conventions. Examples: 'Marie Curie', 'Francis H.C. Crick', 'Tu Youyou', 'Ada Lovelace'. This is the canonical name for all publications. Maximum 500 characters. Required field."
+          },
+          "orcid": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#orcid",
+            "description": "ORCID identifier - a unique persistent digital identifier for researchers. Format: 0000-0001-2345-6789 (16 digits in groups of 4). ORCID helps distinguish you from other researchers with similar names and links all your work together across name changes, institutions, and publishers. Highly recommended by most journals and funders. Free to obtain from orcid.org. See at.scholarly.definition#orcid for pattern. Optional but strongly recommended."
+          },
+          "email": {
+            "type": "string",
+            "format": "email",
+            "description": "Contact email address for professional correspondence about publications. Used by journals, co-authors, and readers to reach you. Format: [e-mail]. Should be a stable institutional or professional email rather than personal one (if possible). Privacy consideration: this may be public depending on profile settings. Optional field."
+          },
+          "affiliation": {
+            "type": "string",
+            "maxLength": 1000,
+            "description": "Current institutional affiliation - where you work or study. Include department and institution. Examples: 'Department of Physics, University of Cambridge, UK', 'Howard Hughes Medical Institute, USA', 'Independent Researcher', 'Google DeepMind, London, UK'. For multiple affiliations, separate with semicolons. This appears in publications and helps establish credibility. Maximum 1000 characters. Required field."
+          },
+          "bio": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Professional biography or research summary. Describe your research interests, career stage, major achievements, and current focus. Examples: 'PhD candidate studying machine learning applications in climate science', 'Professor of Biology specialising in evolutionary genomics. Author of 100+ papers on speciation'. Keep professional and up-to-date. Maximum 5000 characters. Optional field."
+          },
+          "website": {
+            "type": "string",
+            "format": "uri",
+            "description": "Personal or professional website URL - your academic homepage, research group page, or professional portfolio. Full URL format: https://www.example.edu/~researcher, https://researchgroup.org. Can be institutional page, personal domain, Google Scholar, or ResearchGate profile. Helps people learn more about your work. Optional field."
+          },
+          "expertise": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "maxLength": 200
+            },
+            "description": "List of research areas, fields, or topics you have expertise in. Use specific, meaningful terms. Examples: ['machine learning', 'climate modelling', 'carbon cycle'], ['CRISPR gene editing', 'developmental biology', 'zebrafish'], ['quantum computing', 'error correction']. Helps with manuscript assignment to appropriate reviewers and for discovery. Each expertise up to 200 characters. Optional field."
+          },
+          "manuscripts": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "format": "at-uri"
+            },
+            "description": "Array of AT Protocol URI references to manuscripts you've authored. Points to at.scholarly.manuscript records. Format: at://did:plc:abc123/at.scholarly.manuscript/xyz789. This creates your publication list - all papers you've written or contributed to. Automatically populated when you're listed as an author on a manuscript. Used to build your research portfolio and track your contributions. Optional field - populated over time."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this author profile was created in the system. ISO 8601 format. Indicates when you joined the platform. For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/consent/README.md

···
+# at.scholarly.consent
+
+Legal consents, approvals, and disclosures required for ethical and compliant publication.
+
+## Use Cases
+- Recording ethics committee/IRB approval for research involving human/animal subjects
+- Documenting informed consent from research participants
+- Tracking copyright transfer agreements with publishers
+- Declaring competing interests and conflicts of interest
+- Recording funding disclosures and grant information
+- Managing data sharing permissions and licences
+
+## Challenges
+- **Jurisdictional variation**: Different countries/institutions have different ethics requirements
+- **Documentation burden**: Requires scanning and uploading approval letters, signed forms
+- **Sensitive information**: May contain confidential institutional details
+- **Retroactive compliance**: Historical papers may lack proper consent documentation
+
+## Notes
+- Create separate consent record for each type (ethics, copyright, data-sharing, competing-interests, funding)
+- Set `consentType` appropriately to categorise the consent
+- Use `dateObtained` to record when approval was granted - important for compliance audits
+- Upload supporting documents (approval letters, signed forms) via `document` field when available
+- Include `referenceNumber` (e.g., IRB protocol number) for verification and lookup
+- For ethics approvals, ensure date precedes data collection start date

lexicons/consent/consent.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.consent",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a legal consent, approval, or disclosure required for ethical and compliant publication of research. Modern academic publishing requires various forms of consent and approval: ethics committee approval for research involving humans/animals, informed consent from study participants, copyright transfer agreements, competing interests declarations, data sharing permissions, and funding disclosures. This lexicon tracks these compliance requirements. Multiple consent records may be attached to a single manuscript. References: at.scholarly.manuscript (via strongRef).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "manuscript",
+          "consentType",
+          "description",
+          "dateObtained"
+        ],
+        "properties": {
+          "manuscript": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the manuscript this consent applies to. Uses strongRef (URI + CID hash) to create an immutable link between the consent and the specific manuscript version. Points to an at.scholarly.manuscript record. This ensures the consent record is permanently tied to the work it authorises. Required field for compliance audit trails. See at.scholarly.definition#strongRef."
+          },
+          "consentType": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#consentType",
+            "description": "Type of consent or approval this record represents. Values from at.scholarly.definition#consentType: 'ethics-approval' (IRB/ethics committee approval for human/animal research), 'informed-consent' (participants agreed to participate), 'data-sharing' (permission to share data publicly), 'copyright-transfer' (authors transfer rights to publisher), 'competing-interests' (disclosure of financial conflicts), 'funding-disclosure' (funding sources). Required field to categorise the consent."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Human-readable description of this consent/approval. Explain what was approved, by whom, and any relevant details or conditions. Examples: 'IRB approval granted by Stanford University Ethics Committee for human subjects research protocol #2024-001', 'All participants provided written informed consent', 'Authors have no competing financial interests to declare', 'Funded by Wellcome Trust grant 123456'. Maximum 5000 characters. Required field."
+          },
+          "dateObtained": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date when this consent or approval was obtained. ISO 8601 format: 2024-01-15T00:00:00Z. For ethics approval, this is when the committee approved the protocol. For copyright transfer, when the form was signed. Important for compliance - ethics approval must typically predate data collection. Required field for audit trails."
+          },
+          "document": {
+            "type": "blob",
+            "maxSize": 10000000,
+            "description": "Optional supporting document proving the consent/approval - scanned approval letter, signed consent form, copyright transfer agreement, etc. Useful for verification and compliance audits. Any file format but typically PDF. Maximum size 10MB (10,000,000 bytes). Content-addressed via CID hash for immutability. Optional field - not all consents require documentation."
+          },
+          "institution": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Name of the institution or organisation that granted the approval or with whom the agreement was made. Examples: 'Stanford University Institutional Review Board', 'UK Health Research Authority', 'Nature Publishing Group', 'European Research Council'. Provides context about who authorised what. Maximum 500 characters. Optional field."
+          },
+          "referenceNumber": {
+            "type": "string",
+            "maxLength": 200,
+            "description": "Reference or identification number assigned by the approving body. Examples: ethics protocol number 'IRB-2024-001', grant reference 'WT123456', copyright agreement 'CA-2024-567'. Allows verification and lookup in external systems. Often required to be included in published papers. Maximum 200 characters. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this consent record was created in the system. ISO 8601 format. Not the same as dateObtained (when the actual approval was granted). This is for system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/decision/README.md

···
+# at.scholarly.decision
+
+An editorial decision on a manuscript - the official outcome of peer review.
+
+## Use Cases
+- Recording accept/reject decisions with justification and next steps
+- Requesting major or minor revisions with specific guidance for authors
+- Tracking decision history across multiple revision rounds
+- Providing transparency in the editorial process
+- Documenting which reviews informed each decision
+
+## Challenges
+- **Sensitivity**: Decision letters may contain harsh criticism that affects author morale
+- **Finality concerns**: Decisions may be appealed or overturned, requiring decision history tracking
+- **Editor privacy**: Some journals protect editor identity until decision is made
+- **Liability**: Documented decisions create audit trail that may be scrutinised in disputes
+
+## Notes
+- Set `decisionType` to one of: accept, accept-with-minor-revisions, major-revisions-required, reject-with-resubmission, reject
+- Link all reviews that informed the decision via `reviews` array using `strongRef`
+- Provide clear guidance in `commentsToAuthors` - summarise reviews and give specific revision instructions
+- For revision decisions, set `dueDate` (typically 2-3 months for major revisions, 2-4 weeks for minor)
+- Create new decision record for each round - a manuscript may have multiple decisions (revisions required → accept)
+- Use `strongRef` for manuscript to create immutable decision record tied to specific version

lexicons/decision/decision.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.decision",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an editorial decision on a manuscript - the official outcome of the peer review process. After receiving peer reviews, the editor (or editorial board) makes a decision: accept for publication, reject, or request revisions. This is a critical milestone in the publication journey. A manuscript may receive multiple decisions if it goes through revision cycles (e.g., 'revisions required' followed by 'accept' after revision). References: at.scholarly.manuscript (via strongRef), at.scholarly.review (array of strongRefs), at.scholarly.editor (via DID).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "manuscript",
+          "editor",
+          "decisionType",
+          "decisionDate"
+        ],
+        "properties": {
+          "manuscript": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the manuscript this decision concerns. Uses strongRef (URI + CID hash) to lock the decision to a specific immutable version of the manuscript. Points to an at.scholarly.manuscript record. This creates an immutable audit trail - the decision is permanently tied to exactly what the editor evaluated. If authors revise and resubmit, a new decision record is created for the new version. Required field. See at.scholarly.definition#strongRef."
+          },
+          "editor": {
+            "type": "string",
+            "format": "did",
+            "description": "Decentralised Identifier (DID) of the editor who made this decision. Points to their at.scholarly.editor profile. Format: did:plc:abc123xyz. This identifies who is responsible for the decision - could be the editor-in-chief, associate editor, or section editor depending on journal structure. Provides accountability and allows tracking editor decisions. Required field."
+          },
+          "decisionType": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#decisionType",
+            "description": "The editor's decision outcome. Values from at.scholarly.definition#decisionType: 'accept' (approved for publication as-is), 'accept-with-minor-revisions' (approved but needs small fixes), 'major-revisions-required' (promising but needs substantial changes and re-review), 'reject-with-resubmission' (not acceptable now but authors can try again after major work), 'reject' (will not publish, do not resubmit). Note: 'major-revisions-required' is common and not a rejection. Required field."
+          },
+          "decisionDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when the editor made this decision. ISO 8601 format: 2024-04-10T10:30:00Z. This is when the decision was finalised, after considering all reviews. Used to track editorial speed and time-to-decision metrics. The date communicated to authors in the decision letter. Required field."
+          },
+          "reviews": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#strongRef"
+            },
+            "description": "Array of strongRef references to the peer reviews that informed this decision. Points to at.scholarly.review records. Typically 2-4 reviews per manuscript. The editor bases their decision on these reviews (though editor may override reviewers). Uses strongRef to create immutable links showing exactly which reviews the editor considered. Provides transparency and accountability in the decision-making process. Optional field."
+          },
+          "commentsToAuthors": {
+            "type": "string",
+            "maxLength": 50000,
+            "description": "The editor's comments to the authors explaining the decision - the 'decision letter'. Summarises the reviews, explains the reasoning, and provides guidance if revisions are needed. May say things like: 'Both reviewers found your work interesting but raised concerns about...', 'Please address the following points in your revision...'. For rejections, may suggest alternative venues. Can be quite lengthy. Maximum 50,000 characters (~8,000 words). Optional but highly recommended for transparency."
+          },
+          "dueDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Deadline for authors to submit revisions if the decision requires revisions ('major-revisions-required' or 'accept-with-minor-revisions'). ISO 8601 format. Typically 2-3 months for major revisions, 2-4 weeks for minor revisions. If authors miss this deadline, they may need to resubmit as a new submission. Only applicable when revisions are requested. Optional field - not relevant for accept/reject decisions."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this decision record was created in the system. ISO 8601 format. Not the same as decisionDate (when editor made the decision). This is for system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/definition/README.md

···
+# at.scholarly.definition
+
+Shared type definitions and enumerations used across all scholarly lexicons.
+
+## Use Cases
+- Ensuring consistent identifier formats (DOI, ORCID, ISSN) across all records
+- Providing immutable references between entities via `strongRef`
+- Standardising person information (`personRef`) for authors, reviewers, editors
+- Defining controlled vocabularies for statuses, types, and classifications
+
+## Challenges
+- **Breaking changes**: Modifying shared types impacts all lexicons using them
+- **Tight coupling**: Changes require coordinated updates across multiple lexicons
+- **Validation complexity**: Pattern matching for identifiers (DOI, ORCID, ISSN) must be precise
+- **Enum rigidity**: Adding new values to enums requires schema updates
+
+## Notes
+- Use `strongRef` (URI + CID) whenever you need immutable, content-addressed references between entities
+- Always validate identifier patterns (DOI, ORCID, ISSN) at write time to prevent invalid data
+- `personRef` is the standard way to represent people - use it consistently across author/reviewer/editor contexts
+- Enumerations like `reviewStatus`, `decisionType`, `confidentialityLevel` define the allowed workflow states
+- **Versioning strategy**: If breaking changes are needed, create a new version (e.g., `at.scholarly.definition.v2`)
+- **Optional by default**: When adding new fields to existing objects, make them optional to avoid breaking changes
+at.scholarly.definitionat.scholarly.definitionat.scholarly.definitionat.scholarly.definition

lexicons/definition/definition.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.definition",
+  "description": "Shared type definitions and enumerations used across all scholarly lexicons. This lexicon provides reusable components (like strongRef for versioned references, personRef for people, and standard identifier patterns for DOI/ORCID/ISSN) to ensure consistency and prevent duplication. Use these definitions by referencing them with 'ref': 'at.scholarly.definition#definitionName' in other lexicons.",
+  "definition": {
+    "strongRef": {
+      "type": "object",
+      "description": "A strongly-typed reference to a specific version of a record, combining an AT Protocol URI with a content hash (CID). This ensures immutability - you're referencing not just 'a manuscript' but 'manuscript version X with hash Y'. Used in reviews, decisions, and anywhere you need to reference a specific immutable version rather than 'the latest version'. Example: A review should reference the exact manuscript version that was reviewed, not just the manuscript in general.",
+      "required": [
+        "uri",
+        "cid"
+      ],
+      "properties": {
+        "uri": {
+          "type": "string",
+          "format": "at-uri",
+          "description": "AT Protocol URI pointing to the record. Format: at://did:plc:abc123/at.scholarly.manuscript/xyz789. This identifies WHICH record you're referencing."
+        },
+        "cid": {
+          "type": "string",
+          "format": "cid",
+          "description": "Content Identifier (CID) - a cryptographic hash of the record's content. This locks the reference to a specific version. If the record changes, the CID changes. Format: bafyreigh2akiscail... This ensures WHICH VERSION of the record you're referencing."
+        }
+      }
+    },
+    "personRef": {
+      "type": "object",
+      "description": "Reference to a person (author, reviewer, or editor) with their identifying information. This is used inline when listing manuscript authors or in places where you need to cite someone without requiring them to have a full profile record. Only name is required, but ORCID is strongly recommended to disambiguate people with common names. Used in: at.scholarly.manuscript (authors list), at.scholarly.version (authors list).",
+      "required": [
+        "name"
+      ],
+      "properties": {
+        "did": {
+          "type": "string",
+          "format": "did",
+          "description": "Optional Decentralized Identifier (DID) if this person has an AT Protocol account. Format: did:plc:abc123xyz. If provided, this links to their full author/reviewer/editor profile record. If not provided, this is just citation information."
+        },
+        "name": {
+          "type": "string",
+          "maxLength": 500,
+          "description": "Full name of the person as it should appear in citations and bylines. Required field. Examples: 'Jane Smith', 'Dr. John Doe', 'María García López'."
+        },
+        "orcid": {
+          "type": "string",
+          "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$",
+          "description": "ORCID identifier - a unique persistent identifier for researchers. Format: 0000-0002-1825-0097 (four groups of four digits, last digit can be X). Strongly recommended to disambiguate authors with common names. See orcid.org to get one."
+        },
+        "affiliation": {
+          "type": "string",
+          "maxLength": 1000,
+          "description": "Current institutional affiliation of the person at time of contribution. Examples: 'Stanford University', 'Max Planck Institute for Evolutionary Anthropology', 'Independent Researcher'. Can include department: 'Department of Computer Science, MIT'."
+        },
+        "email": {
+          "type": "string",
+          "format": "email",
+          "description": "Email address for correspondence. Optional but recommended especially for corresponding authors. Will be displayed publicly if this is used in author lists."
+        }
+      }
+    },
+    "doi": {
+      "type": "string",
+      "pattern": "^10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$",
+      "description": "Digital Object Identifier (DOI) - a persistent identifier for published works. Format: Always starts with '10.' followed by a publisher prefix and a suffix. Example: 10.1038/nature12373 or 10.1371/journal.pone.0123456. DOIs are the standard way to cite scholarly works and ensure links don't break even if the publisher changes their website. Assigned by publishers when an article is published."
+    },
+    "orcid": {
+      "type": "string",
+      "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$",
+      "description": "ORCID identifier (e.g., 0000-0002-1825-0097)."
+    },
+    "issn": {
+      "type": "string",
+      "pattern": "^\\d{4}-\\d{3}[0-9X]$",
+      "description": "International Standard Serial Number (e.g., 0028-0836)."
+    },
+    "dateRange": {
+      "type": "object",
+      "description": "Date range with start and optional end date.",
+      "required": [
+        "start"
+      ],
+      "properties": {
+        "start": {
+          "type": "string",
+          "format": "datetime",
+          "description": "Start date and time."
+        },
+        "end": {
+          "type": "string",
+          "format": "datetime",
+          "description": "End date and time (optional for ongoing events)."
+        }
+      }
+    },
+    "license": {
+      "type": "object",
+      "description": "License information for a work.",
+      "required": [
+        "type"
+      ],
+      "properties": {
+        "type": {
+          "type": "string",
+          "description": "License type (e.g., CC-BY-4.0, MIT, proprietary)."
+        },
+        "url": {
+          "type": "string",
+          "format": "uri",
+          "description": "URL to the full license text."
+        },
+        "text": {
+          "type": "string",
+          "maxLength": 5000,
+          "description": "Brief license description or full text."
+        }
+      }
+    },
+    "contributorRole": {
+      "type": "string",
+      "enum": [
+        "author",
+        "corresponding-author",
+        "equal-contributor",
+        "supervisor",
+        "principal-investigator"
+      ],
+      "description": "Role of a contributor to a manuscript."
+    },
+    "reviewStatus": {
+      "type": "string",
+      "enum": [
+        "draft",
+        "submitted",
+        "under-review",
+        "revision-requested",
+        "revision-submitted",
+        "accepted",
+        "rejected",
+        "published",
+        "retracted"
+      ],
+      "description": "Current status of a manuscript in the publication lifecycle. Values: 'draft' (being written, not submitted), 'submitted' (sent to journal/conference), 'under-review' (being peer-reviewed), 'revision-requested' (needs changes), 'revision-submitted' (revised version sent back), 'accepted' (approved for publication), 'rejected' (not accepted), 'published' (publicly available), 'retracted' (published but later withdrawn due to errors/misconduct). Used in at.scholarly.manuscript to track where a work is in the process."
+    },
+    "confidentialityLevel": {
+      "type": "string",
+      "enum": [
+        "open",
+        "single-blind",
+        "double-blind",
+        "triple-blind",
+        "confidential"
+      ],
+      "description": "Confidentiality model for peer review process. Values: 'open' (authors and reviewers know each other's identities, review is public), 'single-blind' (reviewers know who authors are, but authors don't know reviewers), 'double-blind' (neither authors nor reviewers know each other's identities), 'triple-blind' (authors, reviewers, AND editors don't know identities), 'confidential' (review contents are private even if identities are known). Most journals use double-blind. Used in at.scholarly.review."
+    },
+    "decisionType": {
+      "type": "string",
+      "enum": [
+        "accept",
+        "accept-with-minor-revisions",
+        "major-revisions-required",
+        "reject-with-resubmission",
+        "reject"
+      ],
+      "description": "Editorial decision made after peer review. Values: 'accept' (approved for publication as-is), 'accept-with-minor-revisions' (approved but needs small fixes like typos), 'major-revisions-required' (good work but needs substantial changes, will be re-reviewed), 'reject-with-resubmission' (not acceptable now but could resubmit after major work), 'reject' (will not be published, do not resubmit). Used in at.scholarly.decision. Getting 'major-revisions-required' is common and not a rejection!"
+    },
+    "publicationType": {
+      "type": "string",
+      "enum": [
+        "journal",
+        "preprint",
+        "conference",
+        "book",
+        "proceedings"
+      ],
+      "description": "Type of publication venue. Values: 'journal' (peer-reviewed periodical like Nature or PLOS ONE), 'preprint' (non-peer-reviewed early version on arXiv/bioRxiv), 'conference' (peer-reviewed conference presentation), 'book' (scholarly monograph or edited volume), 'proceedings' (collection of conference papers). Used in at.scholarly.publication to categorize the venue type."
+    },
+    "eventType": {
+      "type": "string",
+      "enum": [
+        "conference",
+        "workshop",
+        "symposium",
+        "seminar",
+        "colloquium"
+      ],
+      "description": "Type of academic event."
+    },
+    "supplementType": {
+      "type": "string",
+      "enum": [
+        "data",
+        "code",
+        "video",
+        "audio",
+        "image",
+        "appendix",
+        "other"
+      ],
+      "description": "Type of supplementary material."
+    },
+    "consentType": {
+      "type": "string",
+      "enum": [
+        "ethics-approval",
+        "informed-consent",
+        "data-sharing",
+        "copyright-transfer",
+        "competing-interests",
+        "funding-disclosure"
+      ],
+      "description": "Type of legal consent, approval, or disclosure required for ethical/legal publication. Values: 'ethics-approval' (IRB/ethics committee approval for human/animal research), 'informed-consent' (subjects agreed to participate), 'data-sharing' (permission to share research data publicly), 'copyright-transfer' (authors transfer rights to publisher), 'competing-interests' (disclosure of financial conflicts), 'funding-disclosure' (funding sources declaration). Used in at.scholarly.consent to track compliance with ethical and legal requirements."
+    }
+  }
+}

lexicons/editor/README.md

···
+# at.scholarly.editor
+
+Editor profile for managing peer review and making publication decisions.
+
+## Use Cases
+- Establishing authority to make editorial decisions (accept/reject)
+- Tracking which editor handled which manuscripts for accountability
+- Organising editorial boards with different roles (editor-in-chief, associate, section)
+- Routing manuscripts to appropriate editors based on expertise
+- Maintaining editorial history and decision patterns
+
+## Challenges
+- **Role complexity**: Different journals have different editorial hierarchies and structures
+- **Privacy concerns**: Some journals protect editor identity until decision is made
+- **Accountability pressure**: Documented decisions create audit trail that may be scrutinised
+- **Workload visibility**: Public editor profiles may increase manuscript submissions
+
+## Notes
+- Set `editorRole` to define authority level: editor-in-chief > associate-editor > section-editor > guest-editor
+- Use `publications` array to specify which journals/conferences this editor manages
+- `expertise` array helps route manuscripts to editors with relevant subject knowledge
+- Email is required (unlike author/reviewer) as editors must be reachable for submissions
+- Link editor DID to decision records for transparency and accountability
+- Key is `literal:self` - one editor profile per DID (user account)

lexicons/editor/editor.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.editor",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an editor profile - a user account for researchers or professional editors who manage the peer review process and make publication decisions. Editors are gatekeepers of academic quality, coordinating peer review, interpreting reviewer feedback, and deciding which manuscripts to publish. This profile stores their identity, institutional affiliation, editorial role (editor-in-chief, associate, section), and the publications they manage. Different from authors and reviewers - editors have decision-making authority. Referenced by: at.scholarly.decision (via DID). Key 'literal:self' means one profile per user (DID).",
+      "key": "literal:self",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "email",
+          "affiliation"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Full name of the editor as it appears in editorial mastheads and decision letters. Format: usually 'FirstName MiddleName(s) LastName' or with title 'Dr./Prof. FirstName LastName' if customary. Examples: 'Barbara McClintock', 'Prof. Venki Ramakrishnan', 'Dr. Jennifer Doudna'. This name appears in decision letters to authors and on journal websites. Maximum 500 characters. Required field."
+          },
+          "orcid": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#orcid",
+            "description": "ORCID identifier - a unique persistent digital identifier for researchers. Format: 0000-0001-2345-6789 (16 digits in groups of 4). ORCID helps verify editor identity and link their editorial work to their research profile. Increasingly expected by publishers. Many journals list editor ORCIDs on their websites. See at.scholarly.definition#orcid for pattern. Optional but recommended."
+          },
+          "email": {
+            "type": "string",
+            "format": "email",
+            "description": "Contact email address for editorial correspondence and manuscript submissions. Format: [e-mail] or [e-mail]. This is where authors contact you with queries, where the system sends editorial notifications, and how reviewers can reach you. Must be reliable and regularly checked. Often listed publicly on journal websites. Required field."
+          },
+          "affiliation": {
+            "type": "string",
+            "maxLength": 1000,
+            "description": "Current institutional affiliation - where you work. Include department and institution. Examples: 'Department of Molecular Biology, Cold Spring Harbor Laboratory, USA', 'Medical Research Council, UK', 'Independent Science Editor'. Often listed on journal mastheads alongside your editorial role. Provides credibility and helps identify potential conflicts of interest. Maximum 1000 characters. Required field."
+          },
+          "bio": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Professional biography highlighting editorial experience and research background. What's your scientific expertise? Editorial philosophy? Notable achievements? Examples: 'Editor-in-Chief with 15 years experience in molecular biology publishing. Former researcher in epigenetics with 80+ publications. Committed to open access and rigorous peer review', 'Associate Editor focusing on computational methods in neuroscience'. Maximum 5000 characters. Optional field."
+          },
+          "editorRole": {
+            "type": "string",
+            "enum": [
+              "editor-in-chief",
+              "associate-editor",
+              "section-editor",
+              "guest-editor"
+            ],
+            "description": "Editorial role defining responsibility level and authority. Values: 'editor-in-chief' (top leadership, final decisions, journal strategy), 'associate-editor' (handles submissions in specific areas, makes accept/reject decisions), 'section-editor' (oversees particular journal section or topic), 'guest-editor' (temporary role for special issues). Hierarchy: Editor-in-Chief > Associate Editors > Section Editors. Role determines decision-making authority. Optional field."
+          },
+          "publications": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "format": "at-uri"
+            },
+            "description": "Array of AT Protocol URI references to publications (journals/conferences) this editor manages. Points to at.scholarly.publication records. Format: at://did:plc:abc123/at.scholarly.publication/xyz789. Examples: editor-in-chief of one journal, associate editor for multiple sections. This defines where you have editorial authority to make decisions. Used to route manuscripts to appropriate editors. Optional field."
+          },
+          "expertise": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "maxLength": 200
+            },
+            "description": "List of research areas and topics within your editorial expertise - subjects you can effectively evaluate and find reviewers for. Be specific. Examples: ['structural biology', 'X-ray crystallography', 'protein folding'], ['machine learning', 'natural language processing'], ['immunology', 'vaccine development', 'T cell biology']. Used to assign manuscripts to appropriate editors. Each expertise up to 200 characters. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this editor profile was created in the system. ISO 8601 format. Indicates when you joined the editorial team. For system record-keeping, tracking editor tenure, and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/event/README.md

···
+# at.scholarly.event
+
+An academic event - conference, workshop, symposium, or seminar where research is presented.
+
+## Use Cases
+- Providing context for conference papers (e.g., "Presented at NeurIPS 2024")
+- Linking manuscripts to the event where they were presented
+- Tracking presentations separately from publications
+- Managing event metadata (dates, location, organisers)
+- Connecting event to published proceedings
+
+## Challenges
+- **Recurring series**: Same conference name repeats annually requiring year-specific records (e.g., NeurIPS 2024, 2025, 2026)
+- **Hybrid complexity**: Post-pandemic mix of physical/virtual/hybrid formats
+- **Multi-day/location**: Events may span multiple days or even simultaneous locations
+- **Presentation vs. publication**: Paper may be presented at event but published elsewhere
+
+## Notes
+- Include year in event `name` for recurring conferences ("NeurIPS 2024" not just "NeurIPS")
+- Use `dates` with start and end to capture event duration (single day: same start/end, week-long: different)
+- Set `eventType` (conference, workshop, symposium, seminar, colloquium) to categorise event scale and format
+- Use `location` to specify city/country for physical events, or "Virtual" / "Hybrid" for online/mixed formats
+- Link to published proceedings via `publication` field if papers from event are published together
+- Record `organizer` (institution, society, foundation) for attribution and context

lexicons/event/event.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.event",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an academic event - a conference, workshop, symposium, seminar, or colloquium where researchers present and discuss their work. Events are important for knowledge dissemination, networking, and community building. Many conferences publish proceedings containing peer-reviewed papers. Examples: NeurIPS (major AI conference), Gordon Research Conferences (invitation-only symposia), departmental seminar series. Some events are annual (recurring), others one-off. Referenced by: at.scholarly.manuscript (conference papers). May reference: at.scholarly.publication (for proceedings).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "dates"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Official name of the event including year if part of a recurring series. Examples: 'NeurIPS 2024', 'Gordon Research Conference on X-Ray Science 2024', 'ICML 2025', 'Oxford Biology Departmental Seminar Series Spring 2024'. For recurring events, include the year to distinguish instances. Maximum 500 characters. Required field."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Description of the event's focus, scope, and purpose. What topics are covered? Who is the target audience? What makes this event significant? Examples: 'Annual conference on neural information processing systems bringing together researchers in machine learning, neuroscience, and artificial intelligence', 'Invitation-only symposium on cutting-edge X-ray techniques with 150 participants'. Maximum 5000 characters. Optional field."
+          },
+          "eventType": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#eventType",
+            "description": "Type of academic event. Values from at.scholarly.definition#eventType: 'conference' (large gathering with presentations, typically 100+ attendees), 'workshop' (focused working meeting, often 20-100 attendees), 'symposium' (thematic meeting with invited speakers), 'seminar' (single or series of talks, usually local), 'colloquium' (academic lecture series). Helps categorise and filter events. Optional field."
+          },
+          "dates": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#dateRange",
+            "description": "Start and end dates of the event. Uses dateRange from at.scholarly.definition with start (required) and end (optional) fields. ISO 8601 format. Examples: single-day seminar has same start/end, week-long conference spans multiple days. Format: {start: '2024-12-10T00:00:00Z', end: '2024-12-15T23:59:59Z'}. Critical for scheduling and historical records. Required field."
+          },
+          "location": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Location where the event takes place - city and country for physical events, platform for virtual ones. Examples: 'Vancouver, BC, Canada', 'Oxford, UK', 'Virtual (Zoom)', 'Hybrid: Singapore + Online'. Post-pandemic, many events are hybrid. Include venue name if significant: 'MIT, Cambridge, MA, USA'. Maximum 500 characters. Optional field."
+          },
+          "website": {
+            "type": "string",
+            "format": "uri",
+            "description": "Event's official website URL with programme, registration, and logistics information. Full URL format: https://neurips.cc/Conferences/2024, https://www.grc.org/x-ray-science-conference/2024. Often includes submission deadlines, accepted papers, speaker lists. Primary source of event information. Optional field."
+          },
+          "organizer": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Name of the organising institution, society, or committee responsible for the event. Examples: 'NeurIPS Foundation', 'Gordon Research Conferences', 'Association for Computing Machinery (ACM)', 'Department of Biology, University of Oxford'. May be a professional society, university department, or dedicated foundation. Maximum 500 characters. Optional field."
+          },
+          "publication": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "Optional AT Protocol URI reference to the proceedings publication if papers from this event are published in a collection. Points to an at.scholarly.publication record. Format: at://did:plc:abc123/at.scholarly.publication/xyz789. Example: NeurIPS 2024 papers published in 'NeurIPS 2024 Proceedings'. Not all events publish proceedings. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this event record was created in the system. ISO 8601 format. Not when the event actually took place (that's in 'dates'), but when this digital record was created. For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/issue/README.md

···
+# at.scholarly.issue
+
+A specific issue of a journal - organising articles into volumes and issue numbers.
+
+## Use Cases
+- Providing citation information (e.g., "Nature Vol. 625, Issue 7994")
+- Organising journal articles chronologically by volume/issue
+- Managing special issues with guest editors and thematic focus
+- Displaying journal cover images for visual browsing
+- Grouping articles published together at a specific time
+
+## Challenges
+- **Not universal**: Preprint servers and many online-only journals don't use issues
+- **Numbering complexity**: Different publications use different schemes (continuous vs. annual volume numbering)
+- **Optional relevance**: May not be necessary for all publication types
+- **Metadata overhead**: Adds another organisational layer that may not provide value for all workflows
+
+## Notes
+- Only create issue records for publications that actually organise content into issues (traditional journals)
+- Leave `volume` and `number` optional as some journals use only one or the other
+- Use `year` for temporal filtering even if volume/issue numbering isn't clear
+- Set `specialIssue` to true and provide `specialIssueTitle` for themed collections with guest editors
+- Store `coverImage` (PNG/JPEG, max 2MB) for visual representation and browsing
+- Link to parent `publication` to establish which journal this issue belongs to

lexicons/issue/issue.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.issue",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a specific issue of a journal or conference proceedings - a collection of articles published together. Journals traditionally organise articles into volumes and issues (e.g., Nature Vol. 625, Issue 7994). Each issue contains multiple articles published on the same date. Not all publications use issues - preprint servers and some online-only journals publish articles individually without grouping them. Special issues focus on particular themes with guest editors. References: at.scholarly.publication. Referenced by: at.scholarly.manuscript.",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "publication"
+        ],
+        "properties": {
+          "publication": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "AT Protocol URI reference to the publication this issue belongs to. Points to an at.scholarly.publication record. Format: at://did:plc:abc123/at.scholarly.publication/xyz789. Every issue belongs to exactly one publication. This establishes the relationship: Publication > Issue > Articles. Required field."
+          },
+          "volume": {
+            "type": "integer",
+            "minimum": 1,
+            "description": "Volume number - typically one volume per year for traditional journals. Example: Volume 625 for Nature in 2024. Some journals use continuous numbering since inception, others restart each year. Minimum value 1. Used in citations as 'Vol. 625' or '625'. Optional field - some publications don't use volume numbering."
+          },
+          "number": {
+            "type": "integer",
+            "minimum": 1,
+            "description": "Issue number within the volume - typically multiple issues per volume. Example: Issue 7994 within Volume 625. Weekly journals might have 52 issues per volume, monthly ones have 12. Minimum value 1. Used in citations as 'No. 7994' or '(7994)'. Optional field - some publications only use volume or neither."
+          },
+          "year": {
+            "type": "integer",
+            "minimum": 1000,
+            "maximum": 9999,
+            "description": "Year this issue was published. Four-digit year: 2024, 1999, etc. Useful for chronological organisation and filtering even when volume/issue numbers aren't sequential or clear. Important for citation and discovery. Range 1000-9999 (supports historical journals). Optional field."
+          },
+          "publishedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Specific date when this issue was published and made available. ISO 8601 format: 2024-01-11T00:00:00Z. For print journals, this is the cover date. For online-first journals, when articles in this issue went live. More precise than just the year. Used for embargo dates and access timing. Optional field."
+          },
+          "coverImage": {
+            "type": "blob",
+            "accept": [
+              "image/png",
+              "image/jpeg"
+            ],
+            "maxSize": 2000000,
+            "description": "Cover image or artwork for this issue - the visual that appears on the journal's cover page. Journals often feature striking images from articles in the issue. Formats: PNG or JPEG. Maximum size 2MB (2,000,000 bytes). Content-addressed via CID hash. Used for visual browsing and marketing. Optional field - not all issues have custom covers."
+          },
+          "specialIssue": {
+            "type": "boolean",
+            "description": "Whether this is a special issue (true) or regular issue (false). Special issues focus on specific themes, topics, or events, often with guest editors and invited papers. Examples: 'Special Issue on Climate Change', 'COVID-19 Research Collection'. Helps readers identify thematic collections. Optional field."
+          },
+          "specialIssueTitle": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Title or theme of the special issue if this is one. Examples: 'Machine Learning in Healthcare', 'Women in STEM', '50th Anniversary Collection', 'Proceedings of the XYZ Conference'. Appears on the cover and in listings. Maximum 500 characters. Only applicable when specialIssue is true. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this issue record was created in the system. ISO 8601 format. Not the same as publishedDate (when the issue was actually published). This is for system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/manuscript/README.md

···
+# at.scholarly.manuscript
+
+The core scholarly work - journal article, conference paper, or preprint.
+
+## Use Cases
+- Submitting a research paper to a journal with complete provenance tracking
+- Publishing preprints with public versioning and open peer review
+- Tracking manuscript lifecycle from draft → submission → review → revision → publication
+- Linking manuscripts to supplementary materials, reviews, and editorial decisions
+- Managing multi-author attributions with ORCID identifiers
+
+## Challenges
+- **Schema complexity**: Many fields and relationships to manage
+- **File storage**: PDF files can be 1-5MB each, multiplied by versions
+- **Privacy concerns**: Contains potentially sensitive author and reviewer information
+- **Relationship management**: Maintaining links to versions, reviews, decisions requires careful state management
+
+## Notes
+- Always create a v1 `version` record when first submitted - this establishes the baseline
+- Use `status` field to track workflow state (draft, submitted, under-review, accepted, published, retracted)
+- Update `status` as manuscript progresses through editorial process
+- Link to `publication` (required) to establish where the work is submitted/published
+- Create separate `supplement` records for large datasets, code, videos rather than embedding in manuscript
+- Use `strongRef` for versions, reviews, decisions to ensure immutable audit trail
+- Populate `doi` only after publication - not assigned for preprints or under-review manuscripts
+- Include all authors in `authors` array with ORCID when available for proper attribution

lexicons/manuscript/manuscript.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.manuscript",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an academic manuscript - the core scholarly work such as a journal article, conference paper, or preprint. This is the central lexicon in the scholarly publishing system, connecting authors, publications, peer reviews, and editorial decisions. A manuscript progresses through multiple states (draft, submitted, under review, published) and may have multiple versions as it's revised. Referenced by: at.scholarly.supplement, at.scholarly.version, at.scholarly.review, at.scholarly.decision, at.scholarly.consent.",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "title",
+          "abstract",
+          "authors",
+          "publication",
+          "submittedDate",
+          "manuscriptFile"
+        ],
+        "properties": {
+          "title": {
+            "type": "string",
+            "maxLength": 1000,
+            "description": "Title of the manuscript as it should appear in citations and when published. Keep concise yet descriptive. Examples: 'CRISPR-Cas9 Gene Editing in Human Embryos', 'Machine Learning Approaches to Climate Modelling', 'The Structure of DNA'. Avoid ALL CAPS. Can include subtitles separated by colon. Maximum 1000 characters but most journals prefer under 200. Required field."
+          },
+          "abstract": {
+            "type": "string",
+            "maxLength": 10000,
+            "description": "Abstract or summary of the work - typically 150-300 words summarising the research question, methods, key findings, and conclusions. Should be self-contained and understandable without reading the full paper. Used for discovery in databases and search engines. Some journals require structured abstracts with sections like Background, Methods, Results, Conclusions. Maximum 10000 characters (~1500 words) though most journals require much shorter. Required field."
+          },
+          "keywords": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "maxLength": 100
+            },
+            "maxLength": 20,
+            "description": "Keywords or key phrases for discoverability in search engines and databases. Choose specific, relevant terms that researchers would use when searching for this work. Examples: 'gene editing', 'machine learning', 'climate change', 'peer review'. Avoid generic terms like 'research' or 'study'. Use singular or plural consistently. Maximum 20 keywords, each up to 100 characters. Optional but highly recommended."
+          },
+          "authors": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#personRef"
+            },
+            "description": "List of authors who contributed to this work, in the order they should appear in citations. Each author is a personRef object with name, ORCID (recommended), affiliation, and optional email. First author is typically the primary researcher; last author often the senior supervisor. Some fields recognise equal contribution (both first authors). See at.scholarly.definition#personRef for details. Required field with at least one author."
+          },
+          "correspondingAuthor": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#personRef",
+            "description": "The corresponding author - the person who handles communication with the journal/publisher, receives reviewer comments, and is the main contact for readers after publication. Usually one of the authors from the authors list. Email is particularly important for this field. Often marked with an asterisk (*) in publications. Optional field."
+          },
+          "publication": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "AT Protocol URI reference to the publication venue where this manuscript is published or submitted. Points to an at.scholarly.publication record (journal like Nature, preprint server like arXiv, or conference proceedings). Format: at://did:plc:abc123/at.scholarly.publication/xyz789. This indicates WHERE the work is being published. Required field."
+          },
+          "issue": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "Optional AT Protocol URI reference to the specific journal issue this manuscript appears in. Points to an at.scholarly.issue record. Only applicable for journals that organise articles into issues (e.g., Nature Vol. 625, Issue 7994). Preprints and some online-only journals don't use issues. Format: at://did:plc:abc123/at.scholarly.issue/xyz789."
+          },
+          "event": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "Optional AT Protocol URI reference to the academic conference, workshop, or symposium where this paper was presented. Points to an at.scholarly.event record. Only applicable for conference papers or papers presented at events. Format: at://did:plc:abc123/at.scholarly.event/xyz789. Example: linking a NeurIPS 2024 paper to the NeurIPS 2024 event."
+          },
+          "doi": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#doi",
+            "description": "Digital Object Identifier (DOI) assigned by the publisher when the manuscript is published. Provides a permanent, citable link to the work. Format: 10.1038/nature12373. Not assigned for unpublished preprints or manuscripts under review. See at.scholarly.definition#doi for pattern details. Optional field - only present after publication."
+          },
+          "submittedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when the manuscript was first submitted to the publication venue. ISO 8601 format: 2024-03-15T14:30:00Z. This is the start of the publication process. For journals, this is when authors submit to the journal. For preprints, this is when posted online. Used to establish priority and track time-to-publication. Required field."
+          },
+          "acceptedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when the manuscript was accepted for publication after peer review. ISO 8601 format. Only applicable for peer-reviewed journals and conferences. Marks successful completion of the review process. Often listed in the published article as 'Accepted: [date]'. Used to calculate review duration. Optional - only set after editorial acceptance."
+          },
+          "publishedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when the manuscript was officially published and made publicly available. ISO 8601 format. For journals, this is when it appears in an issue or online. For preprints, this is the posting date. This is the date to use for citations. Listed as 'Published: [date]' in articles. Optional - only set after publication."
+          },
+          "license": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#license",
+            "description": "Licence under which the manuscript is published, determining how others can use, share, and adapt the work. Common licences: CC-BY-4.0 (open access, most permissive), CC-BY-NC (non-commercial only), traditional copyright (all rights reserved). See at.scholarly.definition#license for structure. Important for open science and reuse rights. Optional but recommended for published works."
+          },
+          "manuscriptFile": {
+            "type": "blob",
+            "accept": [
+              "application/pdf"
+            ],
+            "maxSize": 50000000,
+            "description": "The manuscript itself as a PDF file. This is the actual document containing the research - introduction, methods, results, discussion, references. Must be PDF format. Maximum size 50MB (50,000,000 bytes) though most manuscripts are 1-5MB. Content-addressed via CID hash ensuring immutability. Required field - without this, there's no manuscript!"
+          },
+          "supplements": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "format": "at-uri"
+            },
+            "description": "Array of AT Protocol URI references to supplementary materials that accompany this manuscript. Points to at.scholarly.supplement records containing datasets, source code, videos, additional figures, appendices, etc. Format: at://did:plc:abc123/at.scholarly.supplement/xyz789. Modern research often includes substantial supplementary materials for reproducibility. Optional - not all manuscripts have supplements."
+          },
+          "versions": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#strongRef"
+            },
+            "description": "Array of strongRef references to different versions of this manuscript as it's revised. Points to at.scholarly.version records. Each version (v1, v2, v3...) represents a revision - initial submission, revised after peer review, final accepted version, etc. Uses strongRef (URI + CID) to lock references to specific immutable versions. Optional - only populated after revisions are made."
+          },
+          "reviews": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#strongRef"
+            },
+            "description": "Array of strongRef references to peer reviews of this manuscript. Points to at.scholarly.review records containing reviewer comments, recommendations (accept/reject), and scores. Uses strongRef to lock reviews to specific manuscript versions. Supports open peer review where reviews are public, or can remain private. Optional - only populated after peer review process begins."
+          },
+          "decisions": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#strongRef"
+            },
+            "description": "Array of strongRef references to editorial decisions made on this manuscript. Points to at.scholarly.decision records containing editor's decision (accept, reject, revisions required), comments to authors, and references to the reviews that informed the decision. Multiple decisions may exist if manuscript goes through revision cycles. Uses strongRef for immutable audit trail. Optional - only populated after editorial review."
+          },
+          "consents": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#strongRef"
+            },
+            "description": "Array of strongRef references to legal consents and approvals required for publication. Points to at.scholarly.consent records for ethics approval (IRB/ethics committee), informed consent from participants, copyright transfer, competing interests declarations, data sharing permissions, funding disclosures. Required for research involving humans/animals or sensitive data. Uses strongRef for immutable compliance records. Optional - depends on research type."
+          },
+          "status": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#reviewStatus",
+            "description": "Current status of the manuscript in the publication lifecycle. Values from at.scholarly.definition#reviewStatus: draft, submitted, under-review, revision-requested, revision-submitted, accepted, rejected, published, retracted. This tracks the manuscript's journey from initial submission to final publication (or rejection). Updated as the manuscript progresses. Optional but highly recommended for tracking."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this manuscript record was created in the system. ISO 8601 format. Not the same as submittedDate (which is when submitted to journal) or publishedDate (when made public). This is purely for system record-keeping. Optional but recommended for audit trails."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/portfolio/README.md

···
+# at.scholarly.portfolio
+
+Optional organisational grouping within a publisher - for branded collections or portfolio structures.
+
+## Use Cases
+- Organising publications into branded collections (e.g., Nature Publishing Group within Springer Nature)
+- Enabling portfolio-level queries and analytics
+- Supporting hierarchical publisher structures (Publisher → Portfolio → Publication)
+- Grouping related journals under a common brand
+
+## Challenges
+- **Not universal**: Some publishers don't use portfolio structures, making this optional layer unnecessary
+- **Inconsistent usage**: Different publishers have different portfolio strategies and hierarchies
+- **Maintenance overhead**: Portfolio structures can change due to acquisitions and reorganisations
+- **Ambiguity**: Distinction between publisher, portfolio, and publication may be unclear
+
+## Notes
+- Only create portfolio records for publishers that actually use portfolio structures
+- Link portfolio to parent `publisher` (required) via at-uri
+- Publications can optionally reference a portfolio via at-uri
+- Include `website` if the portfolio has its own distinct web presence
+- For simple publishers with no portfolio structure, publications can reference publishers directly

lexicons/portfolio/portfolio.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.portfolio",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an optional organisational grouping within a publisher - a branded collection or family of publications. Many large publishers organise their journals and publications into named portfolios for marketing, management, and thematic coherence. Examples: Nature Publishing Group (within Springer Nature), BMC Series (BioMed Central journals within Springer Nature), Cell Press (within Elsevier). Not all publishers use portfolios - this is optional organisational structure. References: at.scholarly.publisher. Referenced by: at.scholarly.publication.",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "publisher"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Name of the publishing portfolio or imprint. Use the official brand name as it appears on publications. Examples: 'Nature Publishing Group', 'BMC Series', 'Cell Press', 'Oxford Handbooks', 'Wiley-Blackwell'. The portfolio name often appears alongside the publisher name on journal websites and publications. Maximum 500 characters. Required field."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Description of the portfolio's focus, mission, and scope. Explain what ties these publications together - subject area, publication type, target audience, or brand positioning. Examples: 'Portfolio of high-impact scientific journals including Nature and Nature-branded titles', 'Open-access biomedical journals with article processing charges', 'Leading life sciences journals covering cell biology, molecular biology, and related fields'. Maximum 5000 characters. Optional field."
+          },
+          "publisher": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "AT Protocol URI reference to the parent publisher that owns or operates this portfolio. Points to an at.scholarly.publisher record. Format: at://did:plc:abc123/at.scholarly.publisher/xyz789. This establishes the hierarchical relationship: Publisher > Group > Publications. A portfolio always belongs to exactly one publisher. Required field."
+          },
+          "website": {
+            "type": "string",
+            "format": "uri",
+            "description": "Group's dedicated website URL if they have one. Some portfolios have their own web presence separate from the main publisher site. Full URL format: https://www.nature.com, https://www.biomedcentral.com. May be a section of the publisher's site or a standalone domain. Optional field - not all portfolios have separate websites."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this portfolio record was created in the system. ISO 8601 format. Not when the portfolio was established in the real world, but when this digital record was created. For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/publication/README.md

···
+# at.scholarly.publication
+
+A publication venue - journal, preprint server, or conference proceedings where manuscripts are published.
+
+## Use Cases
+- Establishing where a manuscript is published (e.g., Nature, arXiv, NeurIPS Proceedings)
+- Categorising publications by type (journal vs. preprint vs. conference)
+- Filtering by peer review status or open access availability
+- Searching publications by subject area or discipline
+- Tracking metadata like ISSN for bibliographic systems
+
+## Challenges
+- **Type diversity**: Journals, preprints, conferences have very different characteristics and workflows
+- **Publisher changes**: Publications can transfer between publishers requiring updates
+- **Name ambiguity**: Same name used by different publishers (e.g., "Science" as magazine vs. conference proceedings)
+- **Lifecycle changes**: Publications cease, merge, split, or go on hiatus
+
+## Notes
+- Link to parent `publisher` (required) - every publication belongs to exactly one publisher
+- Set `publicationType` (journal, preprint, conference, book, proceedings) to distinguish venue types
+- Use `peerReviewed` flag to indicate if submissions undergo peer review (true for journals, false for preprints)
+- Use `openAccess` flag to indicate free availability (true for PLOS, arXiv; false for traditional subscription journals)
+- Include `issn` (eISSN preferred) for journals - not applicable to preprints or some conference proceedings
+- Populate `subjects` array with discipline tags for discovery and filtering
+- Optional `portfolio` field for publications belonging to publishing portfolios within larger publishers

lexicons/publication/publication.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.publication",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a publication venue - a journal, preprint server, or conference proceedings where scholarly manuscripts are published. This is a key entity connecting publishers to manuscripts. Examples: peer-reviewed journals (Nature, PLOS ONE), preprint servers (arXiv, bioRxiv), conference proceedings (NeurIPS Proceedings, ACM Digital Library). Publications have specific editorial policies, scope, peer review processes, and impact. References: at.scholarly.publisher (required), at.scholarly.portfolio (optional). Referenced by: at.scholarly.manuscript, at.scholarly.issue.",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "publisher"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Official name of the publication as it appears on the journal website, articles, and citations. Examples: 'Nature', 'PLOS ONE', 'arXiv', 'Proceedings of the National Academy of Sciences', 'NeurIPS 2024 Proceedings'. For journals with subtitles, include them: 'Nature Communications'. Use the current name even if the publication has been renamed. Maximum 500 characters. Required field."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Description of the publication's scope, focus areas, and editorial mission. What topics does it cover? What types of articles does it publish? What makes it distinctive? Examples: 'Weekly international journal of science publishing peer-reviewed research across all scientific disciplines', 'Open-access journal covering all areas of science and medicine with rigorous peer review', 'Free distribution service for scholarly preprints in physics, mathematics, computer science'. Maximum 5000 characters. Optional field."
+          },
+          "publisher": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "AT Protocol URI reference to the publisher that publishes this venue. Points to an at.scholarly.publisher record. Format: at://did:plc:abc123/at.scholarly.publisher/xyz789. Every publication belongs to exactly one publisher. Examples: Nature belongs to Springer Nature, PLOS ONE to Public Library of Science. Required field."
+          },
+          "portfolio": {
+            "type": "string",
+            "format": "at-uri",
+            "description": "Optional AT Protocol URI reference to a publishing portfolio this publication belongs to. Points to an at.scholarly.portfolio record. Format: at://did:plc:abc123/at.scholarly.portfolio/xyz789. Only applicable if the publisher organises publications into portfolios. Example: Nature journal belongs to Nature Publishing Group within Springer Nature. Optional field - many publications don't belong to portfolios."
+          },
+          "issn": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#issn",
+            "description": "International Standard Serial Number (ISSN) - a unique identifier for serial publications. Format: 0028-0836 (eight digits with hyphen). Journals typically have two ISSNs: one for print, one for electronic. Use the electronic ISSN (eISSN) if available. Required for journals, not applicable to preprints or some conference proceedings. See at.scholarly.definition#issn for pattern. Optional field."
+          },
+          "publicationType": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#publicationType",
+            "description": "Type of publication venue. Values from at.scholarly.definition#publicationType: 'journal' (peer-reviewed periodical), 'preprint' (non-peer-reviewed early versions), 'conference' (conference proceedings), 'book' (scholarly monograph), 'proceedings' (collection of conference papers). Helps categorise and filter publications. Important for citation styles and discovery. Optional field."
+          },
+          "website": {
+            "type": "string",
+            "format": "uri",
+            "description": "Publication's primary website URL where readers can access articles, submission information, and editorial details. Full URL format: https://www.nature.com/nature, https://journals.plos.org/plosone, https://arxiv.org. This is where people go to read and submit papers. Optional field."
+          },
+          "peerReviewed": {
+            "type": "boolean",
+            "description": "Whether this publication uses peer review to evaluate submissions before publication. True for most journals and conferences (they send manuscripts to expert reviewers). False for preprint servers (arXiv, bioRxiv) which publish without peer review. Critical distinction for assessing publication quality and citation appropriateness. Optional field."
+          },
+          "openAccess": {
+            "type": "boolean",
+            "description": "Whether this publication provides free, unrestricted online access to articles (open access). True for publications like PLOS ONE, arXiv (all free). False for traditional subscription journals. Some journals are hybrid (some articles open, some paywalled) - use true if predominantly open. Important for accessibility and compliance with funding mandates. Optional field."
+          },
+          "subjects": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "maxLength": 200
+            },
+            "maxLength": 20,
+            "description": "Subject areas, disciplines, or field classifications this publication covers. Use broad categories for multidisciplinary journals, specific terms for specialised ones. Examples: ['Multidisciplinary Sciences'], ['Cell Biology', 'Molecular Biology'], ['Computer Science', 'Artificial Intelligence'], ['Medicine', 'Public Health']. Helps with discovery and categorisation. Maximum 20 subjects, each up to 200 characters. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this publication record was created in the system. ISO 8601 format. Not when the publication was first published (which could be centuries ago for old journals), but when this digital record was created. For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/publisher/README.md

···
+# at.scholarly.publisher
+
+An academic publisher organisation - the entity that publishes journals, books, and proceedings.
+
+## Use Cases
+- Organising publications by publisher (e.g., all Springer Nature journals)
+- Providing institutional context and branding for publications
+- Tracking publisher metadata (location, founding date, policies)
+- Enabling publisher-level queries and analytics (acceptance rates, publication volume)
+- Managing publisher logos and visual identity for display
+
+## Challenges
+- **Traditional model bias**: Assumes centralised publisher structure, may not fit independent/decentralised publishing
+- **Mergers and acquisitions**: Publishers frequently merge, rebrand, or change ownership requiring updates
+- **Complexity**: Adds an organisational layer to the data model
+- **Historical changes**: Difficult to represent publisher evolution over time
+
+## Notes
+- Use the current publisher name even if it has changed (e.g., "Springer Nature" not "Springer" or "Nature Publishing Group")
+- For merged entities, use the new combined entity and note history in `description`
+- Store publisher logo via `logo` field for use in UI/branding (PNG/JPEG/SVG, max 1MB)
+- Link to publisher website via `website` for additional information
+- Use `established` date for the current legal entity (not historical predecessor organisations)

lexicons/publisher/publisher.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.publisher",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing an academic publisher organisation - the entity that publishes scholarly content such as journals, books, and conference proceedings. Publishers are the root organisational entity in the academic publishing hierarchy, providing the infrastructure, editorial oversight, and branding for scholarly publications. Examples include major commercial publishers (Elsevier, Springer Nature), university presses (Oxford, Cambridge), non-profit publishers (PLOS), and preprint servers (arXiv). Referenced by: at.scholarly.publication, at.scholarly.portfolio.",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "name"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Official legal or brand name of the publisher. Use the name as it appears on publications and official materials. Examples: 'Elsevier', 'Springer Nature', 'Public Library of Science', 'arXiv', 'Cambridge University Press'. For consistency, use the current name even if the publisher has been renamed or merged. Maximum 500 characters. Required field."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Description of the publisher's mission, scope, and focus areas. Include information about what they publish (which subjects, types of content), their publishing model (commercial, open access, hybrid), and any distinguishing characteristics. Examples: 'Global information analytics business specialising in science and health', 'Non-profit open-access science publisher', 'Free distribution service for scholarly preprints in physics and mathematics'. Maximum 5000 characters. Optional field."
+          },
+          "website": {
+            "type": "string",
+            "format": "uri",
+            "description": "Publisher's primary website URL - their main online presence where you can find their publications, about information, and contact details. Full URL format: https://www.elsevier.com, https://plos.org, https://arxiv.org. Use the main domain, not a specific sub-page. Optional field."
+          },
+          "logo": {
+            "type": "blob",
+            "accept": [
+              "image/png",
+              "image/jpeg",
+              "image/svg+xml"
+            ],
+            "maxSize": 1000000,
+            "description": "Publisher's logo image for display and branding purposes. Accepted formats: PNG, JPEG, or SVG (vector preferred for scalability). Ideally square or horizontal orientation. Maximum file size 1MB (1,000,000 bytes). Content-addressed via CID hash. Used in publication listings, citation tools, and discovery interfaces. Optional field."
+          },
+          "location": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Primary location or headquarters of the publisher - city and country. Examples: 'Amsterdam, Netherlands', 'San Francisco, CA, USA', 'Oxford, UK', 'Ithaca, NY, USA'. Provides geographical context and legal jurisdiction information. For distributed organisations, use the main office location. Maximum 500 characters. Optional field."
+          },
+          "established": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date when the publisher was established or founded. ISO 8601 format, can be just year: 1880-01-01T00:00:00Z. Historical context is valuable - some publishers have centuries of history (e.g., Oxford University Press founded 1586), whilst others are recent (arXiv founded 1991). For merged entities, use the date of the current entity. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this publisher record was created in the system. ISO 8601 format. Not the same as 'established' (when the publisher was founded). This is for system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/review/README.md

···
+# at.scholarly.review
+
+A peer review of a manuscript - expert evaluation determining publication worthiness.
+
+## Use Cases
+- Recording peer review feedback with recommendations (accept/reject/revise)
+- Enabling open peer review where reviews are public and attributed
+- Maintaining blind review confidentiality (single, double, triple-blind)
+- Providing reviewer credit via ORCID linkage
+- Tracking review turnaround times and reviewer performance
+- Separating public comments (to authors) from confidential notes (to editor)
+
+## Challenges
+- **Confidentiality requirements**: Must protect reviewer identity in blind review systems
+- **Sensitive content**: Reviews may contain harsh criticism requiring careful access control
+- **Bias documentation**: Published reviews may inadvertently reveal reviewer biases
+- **Privacy trade-offs**: Open peer review improves transparency but may discourage honest feedback
+
+## Notes
+- Use `strongRef` for both `manuscript` and `version` to lock review to exact content that was reviewed
+- Set `confidentiality` level (open, single-blind, double-blind) to control visibility of reviewer DID
+- Separate public feedback (`comments`) from confidential notes (`commentsToEditor`)
+- Set `recommendation` to guide editor: accept, reject, major-revision, minor-revision
+- Optional `score` (1-10) provides quantitative assessment alongside qualitative comments
+- For open peer review, make `reviewer` DID public; for blind review, restrict access
+- Link reviewer DID to their `at.scholarly.reviewer` profile for credit/attribution

lexicons/review/review.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.review",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a peer review of a manuscript - the expert evaluation that determines publication worthiness. Peer review is the cornerstone of academic quality control, where domain experts assess the validity, originality, and significance of research. Reviews contain the reviewer's comments, recommendations (accept/reject/revise), and optional scoring. Can be open (public) or confidential (single/double-blind). Referenced by: at.scholarly.decision. References: at.scholarly.manuscript, at.scholarly.version (both via strongRef), at.scholarly.reviewer (via DID).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "manuscript",
+          "version",
+          "reviewer",
+          "submittedDate",
+          "comments"
+        ],
+        "properties": {
+          "manuscript": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the manuscript being reviewed. Uses strongRef (URI + CID hash) to lock this review to a specific immutable version of the manuscript, not just 'the latest'. Points to an at.scholarly.manuscript record. This ensures the review is permanently tied to exactly what the reviewer read. Required field. See at.scholarly.definition#strongRef for structure."
+          },
+          "version": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the specific version of the manuscript being reviewed (e.g., v1, v2). Points to an at.scholarly.version record. Manuscripts often go through multiple revision cycles - this precisely identifies WHICH version this review evaluated. Uses strongRef for immutability. If authors submit v2 after revisions, a new review of v2 would be created. Required field."
+          },
+          "reviewer": {
+            "type": "string",
+            "format": "did",
+            "description": "Decentralised Identifier (DID) of the reviewer who evaluated this manuscript. Points to their at.scholarly.reviewer profile. Format: did:plc:abc123xyz. In double-blind review, this may be kept private/redacted until review is complete. In open peer review, this is public. Allows tracking reviewer contributions and expertise. Required field."
+          },
+          "submittedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when the reviewer submitted this review to the editor. ISO 8601 format: 2024-03-20T16:45:00Z. Used to track review speed and ensure timely peer review process. Most journals give reviewers 2-4 weeks to complete reviews. Required field."
+          },
+          "recommendation": {
+            "type": "string",
+            "enum": [
+              "accept",
+              "reject",
+              "major-revision",
+              "minor-revision"
+            ],
+            "description": "Reviewer's recommendation to the editor about what should happen with this manuscript. Values: 'accept' (publish as-is), 'reject' (do not publish), 'major-revision' (substantial changes needed, will need re-review), 'minor-revision' (small fixes needed, no re-review). Editor makes final decision based on all reviews. Getting 'major-revision' is common and not a rejection - it means the work has merit but needs improvement. Optional field."
+          },
+          "confidentiality": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#confidentialityLevel",
+            "description": "Confidentiality level of this review - determines who can see what. Values from at.scholarly.definition#confidentialityLevel: 'open' (reviewer identity and comments are public), 'single-blind' (authors don't know reviewer, but reviewer knows authors), 'double-blind' (neither party knows the other), 'triple-blind' (editor also doesn't know), 'confidential' (review contents private). Most journals use double-blind. Affects whether reviewer DID is exposed. Optional field."
+          },
+          "comments": {
+            "type": "string",
+            "maxLength": 50000,
+            "description": "The reviewer's substantive feedback on the manuscript - critique, suggestions for improvement, questions, praise for strengths. This is shared with the authors. Should be constructive, specific, and actionable. Examples: 'The methodology in Section 3 needs clarification...', 'Figure 2 is unclear...', 'The conclusions are well-supported by the data.' Can be quite lengthy for thorough reviews. Maximum 50,000 characters (~8,000 words). Required field - the core of the review."
+          },
+          "commentsToEditor": {
+            "type": "string",
+            "maxLength": 50000,
+            "description": "Confidential comments from the reviewer to the editor only - NOT shared with authors. Used to explain reasoning behind recommendation, flag concerns about ethics/plagiarism, or discuss sensitive issues. Example: 'I recommend rejection because this duplicates work in [unpublished paper X] that I'm aware of'. Helps editor make informed decision. Maximum 50,000 characters. Optional field."
+          },
+          "score": {
+            "type": "integer",
+            "minimum": 1,
+            "maximum": 10,
+            "description": "Optional numerical score rating the manuscript's quality. Scale 1-10 where 1 = poor/reject, 10 = excellent/accept. Different journals use different scales (some 1-5, some 1-10). This provides a quick quantitative summary alongside the qualitative comments. Not all journals use scoring. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this review record was created in the system. ISO 8601 format. Not the same as submittedDate (when reviewer finished writing). This is for system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/reviewer/README.md

···
+# at.scholarly.reviewer
+
+Reviewer profile for researchers who evaluate manuscripts through peer review.
+
+## Use Cases
+- Matching manuscripts to appropriate reviewers based on expertise
+- Providing recognition and credit for peer review contributions
+- Tracking reviewer performance (turnaround time, review count)
+- Supporting open peer review with attributed reviews
+- Avoiding conflicts of interest via affiliation checking
+
+## Challenges
+- **Privacy requirements**: Identity must be protected in single/double-blind review systems
+- **Expertise constraints**: Declared expertise may limit review invitation opportunities
+- **Profile maintenance**: Another profile to keep current alongside author profile
+- **Reviewer fatigue**: Making profile visible may increase unsolicited review requests
+
+## Notes
+- `expertise` array is critical for manuscript-reviewer matching - be specific and comprehensive
+- Set `reviewCount` to track total completed reviews for experience indication
+- Use `publications` array to identify potential conflicts of interest (shouldn't review papers heavily citing own work)
+- ORCID enables credit for peer review contributions via services like Publons/Web of Science
+- In blind review, restrict access to reviewer DID; in open review, make it public
+- Key is `literal:self` - one reviewer profile per DID (user account)

lexicons/reviewer/reviewer.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.reviewer",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a peer reviewer profile - a user account for researchers who evaluate and provide expert feedback on manuscripts submitted for publication. Reviewers are critical to maintaining quality in academic publishing through peer review. This profile stores their identity, institutional affiliation, areas of expertise (crucial for manuscript matching), and review history. Editors use these profiles to find appropriate reviewers for manuscripts. Referenced by: at.scholarly.review (via DID). Key 'literal:self' means one profile per user (DID).",
+      "key": "literal:self",
+      "record": {
+        "type": "object",
+        "required": [
+          "name",
+          "affiliation",
+          "expertise"
+        ],
+        "properties": {
+          "name": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Full name of the reviewer as it should appear in open peer review contexts. Format: usually 'FirstName MiddleName(s) LastName' but respect cultural naming conventions. Examples: 'Jane Smith', 'Dr. Ahmed Al-Rahman', 'Prof. Li Wei'. In double-blind review, this is kept private from authors. In open review, appears alongside the review. Maximum 500 characters. Required field."
+          },
+          "orcid": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#orcid",
+            "description": "ORCID identifier - a unique persistent digital identifier for researchers. Format: 0000-0001-2345-6789 (16 digits in groups of 4). ORCID helps link reviews to reviewer identity (in open peer review systems), disambiguate common names, and track peer review contributions. Some journals now give credit for peer review via ORCID. See at.scholarly.definition#orcid for pattern. Optional but increasingly expected."
+          },
+          "email": {
+            "type": "string",
+            "format": "email",
+            "description": "Contact email address for review invitations and communication with editors. Format: [e-mail]. Editors use this to send review requests, deadlines, and thank-you notes. Should be a reliable, regularly checked address. Privacy: typically kept private, not shared with authors. Optional field."
+          },
+          "affiliation": {
+            "type": "string",
+            "maxLength": 1000,
+            "description": "Current institutional affiliation - where you work. Include department and institution. Examples: 'Department of Chemistry, MIT, USA', 'Francis Crick Institute, London, UK', 'Independent Researcher'. Helps editors assess expertise and avoid conflicts of interest (reviewers shouldn't review work from their own institution). Maximum 1000 characters. Required field."
+          },
+          "bio": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Professional biography focusing on research background and reviewing experience. What makes you qualified to review in your fields? Career stage? Notable expertise? Examples: 'Assistant Professor with expertise in computational neuroscience. Published 20+ papers and completed 40+ peer reviews', 'Senior researcher specialising in organic synthesis and catalysis'. Maximum 5000 characters. Optional field."
+          },
+          "expertise": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "maxLength": 200
+            },
+            "description": "List of research areas and topics you can competently review. Be specific - this is critical for manuscript-reviewer matching. Examples: ['RNA splicing', 'CRISPR gene editing', 'developmental genetics'], ['machine learning', 'computer vision', 'medical image analysis'], ['climate modelling', 'atmospheric chemistry']. Editors use this to find appropriate reviewers. Each expertise up to 200 characters. Required field - at least one area needed."
+          },
+          "reviewCount": {
+            "type": "integer",
+            "minimum": 0,
+            "description": "Total number of peer reviews you have completed in this system. Starts at 0 for new reviewers, increments with each completed review. Editors may consider this when inviting reviewers - high count indicates experience and reliability. Also used for reviewer recognition and incentive schemes. Minimum 0. Optional - automatically tracked by system."
+          },
+          "publications": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "format": "at-uri"
+            },
+            "description": "Array of AT Protocol URI references to publications this reviewer has authored or co-authored. Points to at.scholarly.publication records. Format: at://did:plc:abc123/at.scholarly.publication/xyz789. Shows the journals/conferences the reviewer publishes in, helping editors assess suitability and avoid conflicts of interest (reviewers shouldn't review papers citing their own work heavily). Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this reviewer profile was created in the system. ISO 8601 format. Indicates when you became available for peer review. For system record-keeping and to track reviewer tenure/experience. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/supplement/README.md

···
+# at.scholarly.supplement
+
+Supplementary materials accompanying a manuscript - datasets, source code, videos, figures, appendices.
+
+## Use Cases
+- Providing raw datasets for reproducibility (CSV, Excel, HDF5 files)
+- Sharing source code and analysis scripts (Python, R, MATLAB)
+- Including video demonstrations of experiments or techniques
+- Publishing high-resolution images or additional figures
+- Attaching detailed methodological appendices
+
+## Challenges
+- **Storage limitations**: 100MB maximum file size may not accommodate very large datasets
+- **File format diversity**: Must support wide variety of formats with different viewers
+- **Version coupling**: Strongly tied to specific manuscript version, not easily reusable
+- **Discoverability**: Supplements may be overlooked compared to main manuscript
+
+## Notes
+- Use `strongRef` to lock supplement to specific manuscript version - ensures supplements match the paper they support
+- Set `supplementType` (data, code, video, image, appendix, etc.) to help with categorisation and appropriate rendering
+- For datasets > 100MB, consider external repositories (Zenodo, Dryad) and link in the `description` field
+- Include detailed `description` explaining file format, software requirements, and how to use the supplement
+- Assign separate DOI if the supplement is independently citable (e.g., major dataset)

lexicons/supplement/supplement.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.supplement",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing supplementary materials that accompany a manuscript - additional data, code, videos, figures, appendices, or other content too large or detailed for the main paper. Modern research increasingly includes substantial supplementary materials to support reproducibility and provide complete methodological details. Examples: raw datasets, source code repositories, additional statistical analyses, video demonstrations, high-resolution images. Often published alongside the paper with their own DOI. References: at.scholarly.manuscript (via strongRef).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "manuscript",
+          "title",
+          "file"
+        ],
+        "properties": {
+          "manuscript": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the manuscript this supplement accompanies. Uses strongRef (URI + CID hash) to lock this supplement to a specific immutable version of the manuscript. Points to an at.scholarly.manuscript record. Ensures supplements are permanently tied to the exact manuscript version they support, even if the manuscript is later revised. Required field."
+          },
+          "title": {
+            "type": "string",
+            "maxLength": 500,
+            "description": "Descriptive title of this supplementary material. Examples: 'Supplementary Data 1: Raw RNA-seq datasets', 'Supplementary Code: Source code for statistical analyses', 'Supplementary Video 1: Cell division timelapse', 'Supplementary Table S1: Complete gene expression data'. Should be specific enough to distinguish from other supplements. Maximum 500 characters. Required field."
+          },
+          "description": {
+            "type": "string",
+            "maxLength": 5000,
+            "description": "Detailed description of what this supplement contains and how to use it. Explain file formats, software requirements, data structure, or viewing instructions. Examples: 'CSV file containing normalised gene expression values for 20,000 genes across 100 samples. Column headers indicate sample IDs, row names are gene symbols', 'Python scripts for reproducing Figure 3 analyses. Requires pandas, numpy, matplotlib. Run main.py after installing dependencies'. Maximum 5000 characters. Optional but highly recommended."
+          },
+          "supplementType": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#supplementType",
+            "description": "Type of supplementary material. Values from at.scholarly.definition#supplementType: 'data' (datasets, raw data files), 'code' (source code, scripts, software), 'video' (movies, animations, timelapse), 'audio' (recordings, sounds), 'image' (high-resolution figures, photos), 'appendix' (additional text, methods), 'other' (anything else). Helps with categorisation and appropriate viewing/processing tools. Optional field."
+          },
+          "file": {
+            "type": "blob",
+            "maxSize": 100000000,
+            "description": "The actual supplementary file - dataset, code archive, video, etc. Any file format supported. Maximum size 100MB (100,000,000 bytes) which accommodates most supplementary materials. For larger datasets, consider providing download links in the description. Content-addressed via CID hash ensuring immutability and integrity. Required field - this is the actual supplement content."
+          },
+          "doi": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#doi",
+            "description": "Optional DOI assigned to this supplement if it has its own persistent identifier. Some publishers assign separate DOIs to major supplements (especially datasets) for independent citation. Format: 10.1038/nature12373.s1. Not all supplements get DOIs. See at.scholarly.definition#doi for pattern. Optional field."
+          },
+          "license": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#license",
+            "description": "Licence governing use of this supplement, which may differ from the main manuscript licence. Examples: code might be MIT licence whilst paper is traditional copyright, datasets might be CC0 (public domain). Important for reuse rights, especially for data and code. See at.scholarly.definition#license for structure. Optional field."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this supplement record was created in the system. ISO 8601 format. For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}

lexicons/version/README.md

···
+# at.scholarly.version
+
+A specific version of a manuscript during its revision process (v1 initial, v2 revised, v3 final).
+
+## Use Cases
+- Tracking manuscript evolution from initial submission through multiple revision rounds
+- Providing transparent revision history showing how peer review improved the work
+- Allowing citations to reference exact version that was used or reviewed
+- Enabling comparison of changes between versions (diff tools)
+
+## Challenges
+- **Storage overhead**: Each version stores a complete PDF file (can be 1-5MB each)
+- **Version number management**: Must maintain sequential versioning without gaps
+- **Authorship changes**: Authors may be added/removed between versions requiring version-specific author lists
+- **Review coupling**: Reviews are tied to specific versions, complicating cross-version analysis
+
+## Notes
+- Always create v1 when manuscript is first submitted - this is the baseline
+- Increment `versionNumber` sequentially for each revision (v1, v2, v3...)
+- Use `changeLog` to document what changed - helps reviewers and readers understand revisions
+- Store complete PDF for each version via `versionFile` - ensures exact reproducibility
+- Link version to parent manuscript using `strongRef` for immutable provenance
+- If authorship changes, populate the `authors` field; otherwise inherit from parent manuscript

lexicons/version/version.json

···
+{
+  "lexicon": 1,
+  "id": "at.scholarly.version",
+  "definition": {
+    "main": {
+      "type": "record",
+      "description": "Record representing a specific version of a manuscript during its revision process. Academic manuscripts typically go through multiple versions as authors respond to peer review: initial submission (v1), revised version (v2), final accepted version (v3), etc. Each version is a complete document with potentially different content, author lists, or methodology. Tracking versions provides transparency, reproducibility, and audit trails for the publication process. References: at.scholarly.manuscript (via strongRef). Referenced by: at.scholarly.review (reviews reference specific versions).",
+      "key": "tid",
+      "record": {
+        "type": "object",
+        "required": [
+          "manuscript",
+          "versionNumber",
+          "submittedDate",
+          "versionFile"
+        ],
+        "properties": {
+          "manuscript": {
+            "type": "ref",
+            "ref": "at.scholarly.definition#strongRef",
+            "description": "StrongRef reference to the parent manuscript this is a version of. Uses strongRef (URI + CID hash) to create an immutable link to the manuscript record. Points to an at.scholarly.manuscript record. This establishes the relationship: Manuscript > Versions (v1, v2, v3...). Required field."
+          },
+          "versionNumber": {
+            "type": "integer",
+            "minimum": 1,
+            "description": "Sequential version number starting from 1. Example: v1 (initial submission), v2 (first revision), v3 (second revision), v4 (final accepted version). Minimum value 1. Used in citations and to track manuscript evolution. Some systems use semantic versioning (1.0, 1.1) but integers are more common in academic publishing. Required field."
+          },
+          "submittedDate": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Date and time when this version was submitted to the journal or made available. ISO 8601 format: 2024-04-15T10:30:00Z. For v1, this matches the original manuscript submission date. For revisions, this is when the revised version was resubmitted. Used to track revision timing and process duration. Required field."
+          },
+          "versionFile": {
+            "type": "blob",
+            "accept": [
+              "application/pdf"
+            ],
+            "maxSize": 50000000,
+            "description": "The actual manuscript file for this version as a PDF. This is the complete document that was submitted/reviewed. Must be PDF format. Maximum size 50MB (50,000,000 bytes). Content-addressed via CID hash ensuring each version is immutably stored. Allows exact reproduction of what reviewers saw. Required field - this is the version content."
+          },
+          "changeLog": {
+            "type": "string",
+            "maxLength": 10000,
+            "description": "Summary of changes made in this version compared to the previous version. What was added, removed, or modified? Examples: 'Addressed reviewer comments about statistical methods. Added new control experiment (Figure 4). Fixed typos in abstract and discussion', 'Major revision incorporating all reviewer suggestions. Restructured paper with new introduction'. Maximum 10,000 characters. Optional but valuable for transparency."
+          },
+          "authors": {
+            "type": "array",
+            "items": {
+              "type": "ref",
+              "ref": "at.scholarly.definition#personRef"
+            },
+            "description": "List of authors for this specific version, if different from the main manuscript author list. Sometimes authors are added or removed during revision (new collaborators join, others leave). If not specified, assumes same authors as parent manuscript. Uses personRef for each author with name, ORCID, affiliation. Optional field - only needed if authorship changed."
+          },
+          "createdAt": {
+            "type": "string",
+            "format": "datetime",
+            "description": "Timestamp when this version record was created in the system. ISO 8601 format. Not the same as submittedDate (when this version was actually submitted). For system record-keeping and audit trails. Optional field."
+          }
+        }
+      }
+    }
+  }
+}