renderg.host
A proof-of-concept set of scholarly lexicons for academic publishing - demonstrating how decentralised, content-addressed data structures could transform scholarly communication.
Initial commit: established file structure, added draft scholarly lexicons, and added foundational documentation
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.gitignore
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.gitignore
···
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# macOS
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.DS_Store
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.AppleDouble
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.LSOverride
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._*
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.DocumentRevisions-V100
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.fseventsd
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.Spotlight-V100
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.TemporaryItems
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.Trashes
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.VolumeIcon.icns
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.com.apple.timemachine.donotpresent
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.AppleDB
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.AppleDesktop
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Network Trash Folder
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Temporary Items
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.apdisk
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# Windows
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Thumbs.db
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Thumbs.db:encryptable
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ehthumbs.db
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ehthumbs_vista.db
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*.stackdump
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[Dd]esktop.ini
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$RECYCLE.BIN/
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*.cab
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*.msi
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*.msix
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*.msm
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*.msp
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*.lnk
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# Linux
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*~
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.directory
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.fuse_hidden*
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.Trash-*
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.nfs*
+674
LICENSE
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LICENSE
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GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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Preamble
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The GNU General Public License is a free, copyleft license for
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software and other kinds of works.
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The licenses for most software and other practical works are designed
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to take away your freedom to share and change the works. By contrast,
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the GNU General Public License is intended to guarantee your freedom to
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share and change all versions of a program--to make sure it remains free
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software for all its users. We, the Free Software Foundation, use the
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GNU General Public License for most of our software; it applies also to
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any other work released this way by its authors. You can apply it to
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your programs, too.
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When we speak of free software, we are referring to freedom, not
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price. Our General Public Licenses are designed to make sure that you
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have the freedom to distribute copies of free software (and charge for
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them if you wish), that you receive source code or can get it if you
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want it, that you can change the software or use pieces of it in new
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free programs, and that you know you can do these things.
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To protect your rights, we need to prevent others from denying you
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these rights or asking you to surrender the rights. Therefore, you have
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certain responsibilities if you distribute copies of the software, or if
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you modify it: responsibilities to respect the freedom of others.
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For example, if you distribute copies of such a program, whether
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gratis or for a fee, you must pass on to the recipients the same
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freedoms that you received. You must make sure that they, too, receive
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or can get the source code. And you must show them these terms so they
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know their rights.
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Developers that use the GNU GPL protect your rights with two steps:
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(1) assert copyright on the software, and (2) offer you this License
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giving you legal permission to copy, distribute and/or modify it.
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For the developers' and authors' protection, the GPL clearly explains
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that there is no warranty for this free software. For both users' and
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authors' sake, the GPL requires that modified versions be marked as
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changed, so that their problems will not be attributed erroneously to
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authors of previous versions.
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Some devices are designed to deny users access to install or run
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modified versions of the software inside them, although the manufacturer
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can do so. This is fundamentally incompatible with the aim of
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protecting users' freedom to change the software. The systematic
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pattern of such abuse occurs in the area of products for individuals to
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use, which is precisely where it is most unacceptable. Therefore, we
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have designed this version of the GPL to prohibit the practice for those
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products. If such problems arise substantially in other domains, we
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stand ready to extend this provision to those domains in future versions
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of the GPL, as needed to protect the freedom of users.
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Finally, every program is threatened constantly by software patents.
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States should not allow patents to restrict development and use of
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software on general-purpose computers, but in those that do, we wish to
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avoid the special danger that patents applied to a free program could
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make it effectively proprietary. To prevent this, the GPL assures that
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patents cannot be used to render the program non-free.
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The precise terms and conditions for copying, distribution and
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modification follow.
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TERMS AND CONDITIONS
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0. Definitions.
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"This License" refers to version 3 of the GNU General Public License.
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"Copyright" also means copyright-like laws that apply to other kinds of
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works, such as semiconductor masks.
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"The Program" refers to any copyrightable work licensed under this
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License. Each licensee is addressed as "you". "Licensees" and
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"recipients" may be individuals or organizations.
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To "modify" a work means to copy from or adapt all or part of the work
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in a fashion requiring copyright permission, other than the making of an
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exact copy. The resulting work is called a "modified version" of the
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earlier work or a work "based on" the earlier work.
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A "covered work" means either the unmodified Program or a work based
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on the Program.
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To "propagate" a work means to do anything with it that, without
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permission, would make you directly or secondarily liable for
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infringement under applicable copyright law, except executing it on a
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computer or modifying a private copy. Propagation includes copying,
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distribution (with or without modification), making available to the
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public, and in some countries other activities as well.
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To "convey" a work means any kind of propagation that enables other
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parties to make or receive copies. Mere interaction with a user through
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a computer network, with no transfer of a copy, is not conveying.
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An interactive user interface displays "Appropriate Legal Notices"
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to the extent that it includes a convenient and prominently visible
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feature that (1) displays an appropriate copyright notice, and (2)
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tells the user that there is no warranty for the work (except to the
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extent that warranties are provided), that licensees may convey the
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work under this License, and how to view a copy of this License. If
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the interface presents a list of user commands or options, such as a
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menu, a prominent item in the list meets this criterion.
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1. Source Code.
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The "source code" for a work means the preferred form of the work
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for making modifications to it. "Object code" means any non-source
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form of a work.
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A "Standard Interface" means an interface that either is an official
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standard defined by a recognized standards body, or, in the case of
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interfaces specified for a particular programming language, one that
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is widely used among developers working in that language.
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The "System Libraries" of an executable work include anything, other
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than the work as a whole, that (a) is included in the normal form of
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packaging a Major Component, but which is not part of that Major
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Component, and (b) serves only to enable use of the work with that
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Major Component, or to implement a Standard Interface for which an
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implementation is available to the public in source code form. A
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"Major Component", in this context, means a major essential component
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(kernel, window system, and so on) of the specific operating system
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(if any) on which the executable work runs, or a compiler used to
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produce the work, or an object code interpreter used to run it.
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The "Corresponding Source" for a work in object code form means all
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the source code needed to generate, install, and (for an executable
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work) run the object code and to modify the work, including scripts to
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control those activities. However, it does not include the work's
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System Libraries, or general-purpose tools or generally available free
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+
programs which are used unmodified in performing those activities but
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which are not part of the work. For example, Corresponding Source
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includes interface definition files associated with source files for
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the work, and the source code for shared libraries and dynamically
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linked subprograms that the work is specifically designed to require,
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such as by intimate data communication or control flow between those
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subprograms and other parts of the work.
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The Corresponding Source need not include anything that users
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can regenerate automatically from other parts of the Corresponding
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Source.
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The Corresponding Source for a work in source code form is that
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same work.
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2. Basic Permissions.
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All rights granted under this License are granted for the term of
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copyright on the Program, and are irrevocable provided the stated
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+
conditions are met. This License explicitly affirms your unlimited
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+
permission to run the unmodified Program. The output from running a
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covered work is covered by this License only if the output, given its
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+
content, constitutes a covered work. This License acknowledges your
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+
rights of fair use or other equivalent, as provided by copyright law.
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+
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+
You may make, run and propagate covered works that you do not
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convey, without conditions so long as your license otherwise remains
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in force. You may convey covered works to others for the sole purpose
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of having them make modifications exclusively for you, or provide you
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with facilities for running those works, provided that you comply with
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the terms of this License in conveying all material for which you do
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not control copyright. Those thus making or running the covered works
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for you must do so exclusively on your behalf, under your direction
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and control, on terms that prohibit them from making any copies of
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your copyrighted material outside their relationship with you.
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Conveying under any other circumstances is permitted solely under
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the conditions stated below. Sublicensing is not allowed; section 10
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+
makes it unnecessary.
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3. Protecting Users' Legal Rights From Anti-Circumvention Law.
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No covered work shall be deemed part of an effective technological
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measure under any applicable law fulfilling obligations under article
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11 of the WIPO copyright treaty adopted on 20 December 1996, or
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similar laws prohibiting or restricting circumvention of such
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measures.
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When you convey a covered work, you waive any legal power to forbid
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circumvention of technological measures to the extent such circumvention
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is effected by exercising rights under this License with respect to
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the covered work, and you disclaim any intention to limit operation or
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modification of the work as a means of enforcing, against the work's
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users, your or third parties' legal rights to forbid circumvention of
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technological measures.
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4. Conveying Verbatim Copies.
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You may convey verbatim copies of the Program's source code as you
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receive it, in any medium, provided that you conspicuously and
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appropriately publish on each copy an appropriate copyright notice;
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keep intact all notices stating that this License and any
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non-permissive terms added in accord with section 7 apply to the code;
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keep intact all notices of the absence of any warranty; and give all
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recipients a copy of this License along with the Program.
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You may charge any price or no price for each copy that you convey,
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and you may offer support or warranty protection for a fee.
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5. Conveying Modified Source Versions.
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You may convey a work based on the Program, or the modifications to
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produce it from the Program, in the form of source code under the
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+
terms of section 4, provided that you also meet all of these conditions:
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a) The work must carry prominent notices stating that you modified
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it, and giving a relevant date.
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b) The work must carry prominent notices stating that it is
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released under this License and any conditions added under section
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7. This requirement modifies the requirement in section 4 to
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"keep intact all notices".
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c) You must license the entire work, as a whole, under this
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License to anyone who comes into possession of a copy. This
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+
License will therefore apply, along with any applicable section 7
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+
additional terms, to the whole of the work, and all its parts,
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+
regardless of how they are packaged. This License gives no
227
+
permission to license the work in any other way, but it does not
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+
invalidate such permission if you have separately received it.
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d) If the work has interactive user interfaces, each must display
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Appropriate Legal Notices; however, if the Program has interactive
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+
interfaces that do not display Appropriate Legal Notices, your
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+
work need not make them do so.
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+
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+
A compilation of a covered work with other separate and independent
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+
works, which are not by their nature extensions of the covered work,
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and which are not combined with it such as to form a larger program,
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+
in or on a volume of a storage or distribution medium, is called an
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+
"aggregate" if the compilation and its resulting copyright are not
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+
used to limit the access or legal rights of the compilation's users
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+
beyond what the individual works permit. Inclusion of a covered work
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+
in an aggregate does not cause this License to apply to the other
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+
parts of the aggregate.
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+
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+
6. Conveying Non-Source Forms.
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+
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+
You may convey a covered work in object code form under the terms
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+
of sections 4 and 5, provided that you also convey the
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+
machine-readable Corresponding Source under the terms of this License,
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+
in one of these ways:
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+
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a) Convey the object code in, or embodied in, a physical product
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+
(including a physical distribution medium), accompanied by the
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Corresponding Source fixed on a durable physical medium
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+
customarily used for software interchange.
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+
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b) Convey the object code in, or embodied in, a physical product
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+
(including a physical distribution medium), accompanied by a
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+
written offer, valid for at least three years and valid for as
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+
long as you offer spare parts or customer support for that product
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+
model, to give anyone who possesses the object code either (1) a
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+
copy of the Corresponding Source for all the software in the
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+
product that is covered by this License, on a durable physical
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+
medium customarily used for software interchange, for a price no
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+
more than your reasonable cost of physically performing this
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conveying of source, or (2) access to copy the
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Corresponding Source from a network server at no charge.
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+
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c) Convey individual copies of the object code with a copy of the
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written offer to provide the Corresponding Source. This
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+
alternative is allowed only occasionally and noncommercially, and
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+
only if you received the object code with such an offer, in accord
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+
with subsection 6b.
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+
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d) Convey the object code by offering access from a designated
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+
place (gratis or for a charge), and offer equivalent access to the
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Corresponding Source in the same way through the same place at no
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+
further charge. You need not require recipients to copy the
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Corresponding Source along with the object code. If the place to
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copy the object code is a network server, the Corresponding Source
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may be on a different server (operated by you or a third party)
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that supports equivalent copying facilities, provided you maintain
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+
clear directions next to the object code saying where to find the
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Corresponding Source. Regardless of what server hosts the
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Corresponding Source, you remain obligated to ensure that it is
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+
available for as long as needed to satisfy these requirements.
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+
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e) Convey the object code using peer-to-peer transmission, provided
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you inform other peers where the object code and Corresponding
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+
Source of the work are being offered to the general public at no
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+
charge under subsection 6d.
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+
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A separable portion of the object code, whose source code is excluded
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+
from the Corresponding Source as a System Library, need not be
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+
included in conveying the object code work.
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+
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+
A "User Product" is either (1) a "consumer product", which means any
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+
tangible personal property which is normally used for personal, family,
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+
or household purposes, or (2) anything designed or sold for incorporation
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+
into a dwelling. In determining whether a product is a consumer product,
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+
doubtful cases shall be resolved in favor of coverage. For a particular
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+
product received by a particular user, "normally used" refers to a
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+
typical or common use of that class of product, regardless of the status
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+
of the particular user or of the way in which the particular user
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+
actually uses, or expects or is expected to use, the product. A product
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+
is a consumer product regardless of whether the product has substantial
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+
commercial, industrial or non-consumer uses, unless such uses represent
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+
the only significant mode of use of the product.
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+
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"Installation Information" for a User Product means any methods,
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+
procedures, authorization keys, or other information required to install
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and execute modified versions of a covered work in that User Product from
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a modified version of its Corresponding Source. The information must
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+
suffice to ensure that the continued functioning of the modified object
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+
code is in no case prevented or interfered with solely because
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+
modification has been made.
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+
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+
If you convey an object code work under this section in, or with, or
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+
specifically for use in, a User Product, and the conveying occurs as
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+
part of a transaction in which the right of possession and use of the
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+
User Product is transferred to the recipient in perpetuity or for a
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+
fixed term (regardless of how the transaction is characterized), the
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+
Corresponding Source conveyed under this section must be accompanied
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+
by the Installation Information. But this requirement does not apply
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+
if neither you nor any third party retains the ability to install
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+
modified object code on the User Product (for example, the work has
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+
been installed in ROM).
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+
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+
The requirement to provide Installation Information does not include a
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+
requirement to continue to provide support service, warranty, or updates
331
+
for a work that has been modified or installed by the recipient, or for
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+
the User Product in which it has been modified or installed. Access to a
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+
network may be denied when the modification itself materially and
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+
adversely affects the operation of the network or violates the rules and
335
+
protocols for communication across the network.
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+
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+
Corresponding Source conveyed, and Installation Information provided,
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+
in accord with this section must be in a format that is publicly
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+
documented (and with an implementation available to the public in
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+
source code form), and must require no special password or key for
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+
unpacking, reading or copying.
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+
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+
7. Additional Terms.
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+
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+
"Additional permissions" are terms that supplement the terms of this
346
+
License by making exceptions from one or more of its conditions.
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+
Additional permissions that are applicable to the entire Program shall
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+
be treated as though they were included in this License, to the extent
349
+
that they are valid under applicable law. If additional permissions
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+
apply only to part of the Program, that part may be used separately
351
+
under those permissions, but the entire Program remains governed by
352
+
this License without regard to the additional permissions.
353
+
354
+
When you convey a copy of a covered work, you may at your option
355
+
remove any additional permissions from that copy, or from any part of
356
+
it. (Additional permissions may be written to require their own
357
+
removal in certain cases when you modify the work.) You may place
358
+
additional permissions on material, added by you to a covered work,
359
+
for which you have or can give appropriate copyright permission.
360
+
361
+
Notwithstanding any other provision of this License, for material you
362
+
add to a covered work, you may (if authorized by the copyright holders of
363
+
that material) supplement the terms of this License with terms:
364
+
365
+
a) Disclaiming warranty or limiting liability differently from the
366
+
terms of sections 15 and 16 of this License; or
367
+
368
+
b) Requiring preservation of specified reasonable legal notices or
369
+
author attributions in that material or in the Appropriate Legal
370
+
Notices displayed by works containing it; or
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+
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+
c) Prohibiting misrepresentation of the origin of that material, or
373
+
requiring that modified versions of such material be marked in
374
+
reasonable ways as different from the original version; or
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+
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+
d) Limiting the use for publicity purposes of names of licensors or
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+
authors of the material; or
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+
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+
e) Declining to grant rights under trademark law for use of some
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+
trade names, trademarks, or service marks; or
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+
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+
f) Requiring indemnification of licensors and authors of that
383
+
material by anyone who conveys the material (or modified versions of
384
+
it) with contractual assumptions of liability to the recipient, for
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+
any liability that these contractual assumptions directly impose on
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+
those licensors and authors.
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+
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+
All other non-permissive additional terms are considered "further
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+
restrictions" within the meaning of section 10. If the Program as you
390
+
received it, or any part of it, contains a notice stating that it is
391
+
governed by this License along with a term that is a further
392
+
restriction, you may remove that term. If a license document contains
393
+
a further restriction but permits relicensing or conveying under this
394
+
License, you may add to a covered work material governed by the terms
395
+
of that license document, provided that the further restriction does
396
+
not survive such relicensing or conveying.
397
+
398
+
If you add terms to a covered work in accord with this section, you
399
+
must place, in the relevant source files, a statement of the
400
+
additional terms that apply to those files, or a notice indicating
401
+
where to find the applicable terms.
402
+
403
+
Additional terms, permissive or non-permissive, may be stated in the
404
+
form of a separately written license, or stated as exceptions;
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+
the above requirements apply either way.
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+
407
+
8. Termination.
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+
409
+
You may not propagate or modify a covered work except as expressly
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+
provided under this License. Any attempt otherwise to propagate or
411
+
modify it is void, and will automatically terminate your rights under
412
+
this License (including any patent licenses granted under the third
413
+
paragraph of section 11).
414
+
415
+
However, if you cease all violation of this License, then your
416
+
license from a particular copyright holder is reinstated (a)
417
+
provisionally, unless and until the copyright holder explicitly and
418
+
finally terminates your license, and (b) permanently, if the copyright
419
+
holder fails to notify you of the violation by some reasonable means
420
+
prior to 60 days after the cessation.
421
+
422
+
Moreover, your license from a particular copyright holder is
423
+
reinstated permanently if the copyright holder notifies you of the
424
+
violation by some reasonable means, this is the first time you have
425
+
received notice of violation of this License (for any work) from that
426
+
copyright holder, and you cure the violation prior to 30 days after
427
+
your receipt of the notice.
428
+
429
+
Termination of your rights under this section does not terminate the
430
+
licenses of parties who have received copies or rights from you under
431
+
this License. If your rights have been terminated and not permanently
432
+
reinstated, you do not qualify to receive new licenses for the same
433
+
material under section 10.
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+
435
+
9. Acceptance Not Required for Having Copies.
436
+
437
+
You are not required to accept this License in order to receive or
438
+
run a copy of the Program. Ancillary propagation of a covered work
439
+
occurring solely as a consequence of using peer-to-peer transmission
440
+
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441
+
nothing other than this License grants you permission to propagate or
442
+
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443
+
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444
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445
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446
+
10. Automatic Licensing of Downstream Recipients.
447
+
448
+
Each time you convey a covered work, the recipient automatically
449
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450
+
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451
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452
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453
+
An "entity transaction" is a transaction transferring control of an
454
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455
+
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456
+
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457
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458
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459
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460
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461
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462
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463
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You may not impose any further restrictions on the exercise of the
464
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465
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466
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467
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468
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any patent claim is infringed by making, using, selling, offering for
469
+
sale, or importing the Program or any portion of it.
470
+
471
+
11. Patents.
472
+
473
+
A "contributor" is a copyright holder who authorizes use under this
474
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475
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476
+
477
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A contributor's "essential patent claims" are all patent claims
478
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479
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480
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481
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482
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483
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484
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485
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486
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487
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488
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489
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490
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491
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492
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493
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494
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496
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497
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498
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499
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500
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502
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503
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504
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508
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509
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510
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512
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513
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520
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521
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522
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523
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524
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528
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535
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536
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Nothing in this License shall be construed as excluding or limiting
537
+
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538
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539
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540
+
12. No Surrender of Others' Freedom.
541
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542
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If conditions are imposed on you (whether by court order, agreement or
543
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544
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545
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548
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549
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the Program, the only way you could satisfy both those terms and this
550
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551
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552
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13. Use with the GNU Affero General Public License.
553
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554
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555
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556
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557
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559
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560
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561
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562
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563
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14. Revised Versions of this License.
564
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565
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The Free Software Foundation may publish revised and/or new versions of
566
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567
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568
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address new problems or concerns.
569
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570
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Each version is given a distinguishing version number. If the
571
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572
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573
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574
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575
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576
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577
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578
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579
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If the Program specifies that a proxy can decide which future
580
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581
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582
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583
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584
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Later license versions may give you additional or different
585
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586
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587
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588
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589
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15. Disclaimer of Warranty.
590
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591
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592
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APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593
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594
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595
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597
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598
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ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599
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600
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16. Limitation of Liability.
601
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602
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603
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604
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605
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608
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PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609
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EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610
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SUCH DAMAGES.
611
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612
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17. Interpretation of Sections 15 and 16.
613
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614
+
If the disclaimer of warranty and limitation of liability provided
615
+
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616
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reviewing courts shall apply local law that most closely approximates
617
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an absolute waiver of all civil liability in connection with the
618
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Program, unless a warranty or assumption of liability accompanies a
619
+
copy of the Program in return for a fee.
620
+
621
+
END OF TERMS AND CONDITIONS
622
+
623
+
How to Apply These Terms to Your New Programs
624
+
625
+
If you develop a new program, and you want it to be of the greatest
626
+
possible use to the public, the best way to achieve this is to make it
627
+
free software which everyone can redistribute and change under these terms.
628
+
629
+
To do so, attach the following notices to the program. It is safest
630
+
to attach them to the start of each source file to most effectively
631
+
state the exclusion of warranty; and each file should have at least
632
+
the "copyright" line and a pointer to where the full notice is found.
633
+
634
+
<one line to give the program's name and a brief idea of what it does.>
635
+
Copyright (C) <year> <name of author>
636
+
637
+
This program is free software: you can redistribute it and/or modify
638
+
it under the terms of the GNU General Public License as published by
639
+
the Free Software Foundation, either version 3 of the License, or
640
+
(at your option) any later version.
641
+
642
+
This program is distributed in the hope that it will be useful,
643
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but WITHOUT ANY WARRANTY; without even the implied warranty of
644
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
645
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GNU General Public License for more details.
646
+
647
+
You should have received a copy of the GNU General Public License
648
+
along with this program. If not, see <https://www.gnu.org/licenses/>.
649
+
650
+
Also add information on how to contact you by electronic and paper mail.
651
+
652
+
If the program does terminal interaction, make it output a short
653
+
notice like this when it starts in an interactive mode:
654
+
655
+
<program> Copyright (C) <year> <name of author>
656
+
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657
+
This is free software, and you are welcome to redistribute it
658
+
under certain conditions; type `show c' for details.
659
+
660
+
The hypothetical commands `show w' and `show c' should show the appropriate
661
+
parts of the General Public License. Of course, your program's commands
662
+
might be different; for a GUI interface, you would use an "about box".
663
+
664
+
You should also get your employer (if you work as a programmer) or school,
665
+
if any, to sign a "copyright disclaimer" for the program, if necessary.
666
+
For more information on this, and how to apply and follow the GNU GPL, see
667
+
<https://www.gnu.org/licenses/>.
668
+
669
+
The GNU General Public License does not permit incorporating your program
670
+
into proprietary programs. If your program is a subroutine library, you
671
+
may consider it more useful to permit linking proprietary applications with
672
+
the library. If this is what you want to do, use the GNU Lesser General
673
+
Public License instead of this License. But first, please read
674
+
<https://www.gnu.org/licenses/why-not-lgpl.html>.
+44
README.md
+44
README.md
···
1
+
# at-scholarly-lexicons
2
+
3
+
## What is this?
4
+
5
+
A **proof-of-concept** set of AT Protocol lexicons for academic publishing - demonstrating how decentralised, content-addressed data structures could transform scholarly communication.
6
+
7
+
> [!TIP] What is a Lexicon?
8
+
> 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.
9
+
10
+
[Read the official documentation on atproto.com →](https://atproto.com/specs/lexicon)
11
+
12
+
## Why does this exist?
13
+
14
+
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.
15
+
16
+
Think of it as a blueprint that any project could adopt, adapt, or fork to build modern scholarly publishing infrastructure.
17
+
18
+
Academic publishing is ripe for disruption. This project imagines:
19
+
- **Portable identities** (DIDs) that researchers own, not journals
20
+
- **Immutable provenance** (content addressing) for submissions and peer reviews
21
+
- **Transparent workflows** that respect blind peer review
22
+
- **Interoperable standards** that any platform can implement
23
+
24
+
## Getting Started
25
+
26
+
Each lexicon directory contains:
27
+
- `{name}.json` - The AT Protocol lexicon specification (self-documenting)
28
+
- `README.md` - Practical implementation guide
29
+
30
+
> [!IMPORTANT]
31
+
> For detailed documentation about the lexicons themselves, see **[lexicons/README.md](./lexicons/README.md)**.
32
+
33
+
## Contributors
34
+
35
+
B. Prendergast - [@render.ghost](https://bsky.app/profile/renderg.host)
36
+
37
+
## Contributing
38
+
39
+
Feedback and improvements are welcome through community discussion.
40
+
41
+
- **Fork & adapt** - Use these lexicons as a starting point for your own project
42
+
- **Suggest improvements** - Open issues or discussions about the data model
43
+
- **Build implementations** - Create tools, platforms, or services using these lexicons
44
+
- **Propose additions** - New lexicons or fields that would be useful
+215
lexicons/README.md
+215
lexicons/README.md
···
1
+
# Scholarly Lexicons
2
+
3
+
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.
4
+
5
+
## Contexts
6
+
7
+
> [!NOTE] Shared Definitions
8
+
> **Definition** - Standard terms, categories, and reference patterns used consistently across the publishing system to ensure clarity and compatibility.
9
+
10
+
### 📚 Publishing Context
11
+
- **Publisher** - An organization that collects, reviews, and shares scholarly work, responsible for ensuring quality and integrity across the research it distributes.
12
+
- **Portfolio** - A collection of related publications grouped together, often sharing similar editorial standards and subject areas.
13
+
- **Publication** - A venue where scholarly work appears, such as a journal, preprint repository, or conference proceedings.
14
+
- **Issue** - A numbered or themed collection of articles within a publication, helping organize content and provide stable reference points.
15
+
- **Event** - A meeting or gathering—in person or online—where scholars share and discuss research, which may produce formal publications or proceedings.
16
+
17
+
> [!IMPORTANT] Assumed Publishing Hierarchy
18
+
> `Publisher` → `Portfolio` → `Publication` → `Issue` forms a publication context. A `Portfolio` can be optional.
19
+
20
+
> [!IMPORTANT] Assumed Peer Review Workflow
21
+
> 1. `Manuscript` submitted to `Publication`.
22
+
> 2. `Version` created (v1, v2, etc.)
23
+
> 3. `Review` references specific `Version`
24
+
> 4. `Decision` references `Manuscript` and `Review`
25
+
> 5. Process repeats across revisions
26
+
27
+
### 📄 Submission Context
28
+
- **Manuscript** - A piece of scholarly work that author(s) submits for feedback, revision, and eventual publication.
29
+
- **Supplement** - Extra materials like data, code, or media that support and strengthen the claims in a manuscript.
30
+
- **Version** - A specific snapshot of a manuscript at a particular time, allowing people to track changes and refer to exact iterations during review.
31
+
- **Review** - Feedback from independent topical experts who evaluate a manuscript's quality, methods, and contribution to the field.
32
+
- **Decision** - The editorial verdict on a manuscript (can include accept, revise, reject, transfer, etc. ) that determines what happens next.
33
+
- **Consent** - Formal agreements and approvals needed to publish work, covering ethics, copyright, and how works can be used.
34
+
35
+
### 👥 User Context
36
+
- **Author** - One who writes and submits scholarly work for publication.
37
+
- **Reviewer** - A topical expert who reads and evaluates manuscripts, helping ensure the quality and credibility of published work.
38
+
- **Editor** - One who manages the publication process, coordinates reviews, makes publication decisions, and maintains publication standards.
39
+
40
+
## AT Protocol Principles
41
+
42
+
### Namespacing
43
+
All lexicons use `at.scholarly.*` - a *hypothetical* namespace for demonstration.
44
+
45
+
### References
46
+
- **`at-uri`** - Stable references to entities (publications, manuscripts)
47
+
- **`strongRef`** - Versioned references with content hash (CID) for immutable linking
48
+
- **`DID`** - Decentralized identifiers for users (authors, reviewers, editors)
49
+
50
+
### Data Model
51
+
- **Separate records** - Each entity is a distinct record (not embedded)
52
+
- **Versioned linking** - Reviews and decisions reference specific manuscript versions
53
+
- **Content addressing** - Immutable PDFs and data files with cryptographic hashes
54
+
55
+
### Entity Relationships
56
+
57
+
> [!IMPORTANT]
58
+
> Mermaid diagrams may not display in all Markdown viewers. To view this diagram, paste it into https://mermaid.live/edit.
59
+
60
+
```mermaid
61
+
---
62
+
config:
63
+
layout: elk
64
+
---
65
+
flowchart TB
66
+
subgraph Publishing["Publication Context"]
67
+
publisher["Publisher"]
68
+
portfolio["Portfolio"]
69
+
publication["Publication"]
70
+
issue["Issue"]
71
+
event["Event"]
72
+
end
73
+
subgraph Submission["Submission Context"]
74
+
manuscript["Manuscript"]
75
+
supplement["Supplement"]
76
+
version["Version"]
77
+
review["Review"]
78
+
decision["Decision"]
79
+
consent["Consent"]
80
+
end
81
+
subgraph Actor["Actor Context"]
82
+
author["Author"]
83
+
reviewer["Reviewer"]
84
+
editor["Editor"]
85
+
end
86
+
event --- publication
87
+
portfolio --- publisher
88
+
issue --- publication
89
+
publication --- portfolio & publisher
90
+
manuscript --- publication & issue & event & supplement & version & review & decision & consent & author
91
+
review --- version & reviewer
92
+
decision --- review & editor
93
+
editor --- publication
94
+
reviewer --- publication
95
+
publisher:::pubStyle
96
+
portfolio:::pubStyle
97
+
publication:::pubStyle
98
+
issue:::pubStyle
99
+
event:::pubStyle
100
+
manuscript:::subStyle
101
+
supplement:::subStyle
102
+
version:::subStyle
103
+
review:::subStyle
104
+
decision:::subStyle
105
+
consent:::subStyle
106
+
author:::userStyle
107
+
reviewer:::userStyle
108
+
editor:::userStyle
109
+
classDef pubStyle fill:#e1f5ff,stroke:#0288d1,stroke-width:1px,color:#000000;
110
+
classDef subStyle fill:#fff3e0,stroke:#f57c00,stroke-width:1px,color:#000000;
111
+
classDef userStyle fill:#f3e5f5,stroke:#7b1fa2,stroke-width:1px,color:#000000;
112
+
113
+
```
114
+
115
+
## Usage Examples
116
+
117
+
### Publishing a Journal Article
118
+
119
+
```json
120
+
{
121
+
"$type": "at.scholarly.manuscript",
122
+
"title": "CRISPR-Cas9 Gene Editing in Human Embryos",
123
+
"abstract": "We demonstrate...",
124
+
"authors": [
125
+
{
126
+
"name": "Dr. Jane Smith",
127
+
"orcid": "0000-0002-1825-0097",
128
+
"affiliation": "Stanford University"
129
+
}
130
+
],
131
+
"publication": "at://did:plc:abc123/at.scholarly.publication/nature",
132
+
"doi": "10.1038/nature12373",
133
+
"submittedDate": "2024-01-15T00:00:00Z",
134
+
"status": "published",
135
+
"manuscriptFile": { /* blob reference */ }
136
+
}
137
+
```
138
+
139
+
### Submitting a Preprint
140
+
141
+
```json
142
+
{
143
+
"$type": "at.scholarly.manuscript",
144
+
"title": "Novel Machine Learning Architecture",
145
+
"abstract": "We propose...",
146
+
"authors": [{ /* personRef */ }],
147
+
"publication": "at://did:plc:xyz789/at.scholarly.publication/arxiv",
148
+
"submittedDate": "2024-02-01T00:00:00Z",
149
+
"status": "submitted",
150
+
"manuscriptFile": { /* blob reference */ }
151
+
}
152
+
```
153
+
154
+
### Peer Review Workflow
155
+
156
+
```json
157
+
// 1. Review submitted
158
+
{
159
+
"$type": "at.scholarly.review",
160
+
"manuscript": {
161
+
"uri": "at://did:plc:author123/at.scholarly.manuscript/abc",
162
+
"cid": "bafyreigh2akiscail..."
163
+
},
164
+
"version": {
165
+
"uri": "at://did:plc:author123/at.scholarly.version/v1",
166
+
"cid": "bafyreidvmu5qccl..."
167
+
},
168
+
"reviewer": "did:plc:reviewer456",
169
+
"submittedDate": "2024-03-01T00:00:00Z",
170
+
"recommendation": "minor-revision",
171
+
"confidentiality": "double-blind",
172
+
"comments": "The manuscript presents novel findings..."
173
+
}
174
+
175
+
// 2. Editorial decision
176
+
{
177
+
"$type": "at.scholarly.decision",
178
+
"manuscript": {
179
+
"uri": "at://did:plc:author123/at.scholarly.manuscript/abc",
180
+
"cid": "bafyreigh2akiscail..."
181
+
},
182
+
"editor": "did:plc:editor789",
183
+
"decisionType": "major-revisions-required",
184
+
"decisionDate": "2024-03-15T00:00:00Z",
185
+
"reviews": [
186
+
{
187
+
"uri": "at://did:plc:reviewer456/at.scholarly.review/rev1",
188
+
"cid": "bafyreieakfcpe..."
189
+
}
190
+
],
191
+
"commentsToAuthors": "Please address the reviewer's concerns...",
192
+
"dueDate": "2024-05-15T00:00:00Z"
193
+
}
194
+
```
195
+
196
+
### Conference Paper Submission
197
+
198
+
```json
199
+
{
200
+
"$type": "at.scholarly.manuscript",
201
+
"title": "Neural Architecture Search at Scale",
202
+
"authors": [{ /* personRef */ }],
203
+
"publication": "at://did:plc:pub/at.scholarly.publication/neurips-proceedings",
204
+
"event": "at://did:plc:org/at.scholarly.event/neurips-2024",
205
+
"submittedDate": "2024-05-15T00:00:00Z",
206
+
"status": "under-review"
207
+
}
208
+
```
209
+
210
+
## Resources
211
+
212
+
- **AT Protocol Documentation**: https://atproto.com
213
+
- **Lexicon Specification**: https://atproto.com/specs/lexicon
214
+
- **AT Protocol GitHub**: https://github.com/bluesky-social/atproto
215
+
- **Lexicon Guidance**: https://www.pfrazee.com/blog/lexicon-guidance
+25
lexicons/consent/README.md
+25
lexicons/consent/README.md
···
1
+
# at.scholarly.consent
2
+
3
+
Legal consents, approvals, and disclosures required for ethical and compliant publication.
4
+
5
+
## Use Cases
6
+
- Recording ethics committee/IRB approval for research involving human/animal subjects
7
+
- Documenting informed consent from research participants
8
+
- Tracking copyright transfer agreements with publishers
9
+
- Declaring competing interests and conflicts of interest
10
+
- Recording funding disclosures and grant information
11
+
- Managing data sharing permissions and licences
12
+
13
+
## Challenges
14
+
- **Jurisdictional variation**: Different countries/institutions have different ethics requirements
15
+
- **Documentation burden**: Requires scanning and uploading approval letters, signed forms
16
+
- **Sensitive information**: May contain confidential institutional details
17
+
- **Retroactive compliance**: Historical papers may lack proper consent documentation
18
+
19
+
## Notes
20
+
- Create separate consent record for each type (ethics, copyright, data-sharing, competing-interests, funding)
21
+
- Set `consentType` appropriately to categorise the consent
22
+
- Use `dateObtained` to record when approval was granted - important for compliance audits
23
+
- Upload supporting documents (approval letters, signed forms) via `document` field when available
24
+
- Include `referenceNumber` (e.g., IRB protocol number) for verification and lookup
25
+
- For ethics approvals, ensure date precedes data collection start date
+62
lexicons/consent/consent.json
+62
lexicons/consent/consent.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.consent",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"manuscript",
13
+
"consentType",
14
+
"description",
15
+
"dateObtained"
16
+
],
17
+
"properties": {
18
+
"manuscript": {
19
+
"type": "ref",
20
+
"ref": "at.scholarly.definition#strongRef",
21
+
"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."
22
+
},
23
+
"consentType": {
24
+
"type": "ref",
25
+
"ref": "at.scholarly.definition#consentType",
26
+
"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."
27
+
},
28
+
"description": {
29
+
"type": "string",
30
+
"maxLength": 5000,
31
+
"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."
32
+
},
33
+
"dateObtained": {
34
+
"type": "string",
35
+
"format": "datetime",
36
+
"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."
37
+
},
38
+
"document": {
39
+
"type": "blob",
40
+
"maxSize": 10000000,
41
+
"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."
42
+
},
43
+
"institution": {
44
+
"type": "string",
45
+
"maxLength": 500,
46
+
"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."
47
+
},
48
+
"referenceNumber": {
49
+
"type": "string",
50
+
"maxLength": 200,
51
+
"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."
52
+
},
53
+
"createdAt": {
54
+
"type": "string",
55
+
"format": "datetime",
56
+
"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."
57
+
}
58
+
}
59
+
}
60
+
}
61
+
}
62
+
}
+24
lexicons/decision/README.md
+24
lexicons/decision/README.md
···
1
+
# at.scholarly.decision
2
+
3
+
An editorial decision on a manuscript - the official outcome of peer review.
4
+
5
+
## Use Cases
6
+
- Recording accept/reject decisions with justification and next steps
7
+
- Requesting major or minor revisions with specific guidance for authors
8
+
- Tracking decision history across multiple revision rounds
9
+
- Providing transparency in the editorial process
10
+
- Documenting which reviews informed each decision
11
+
12
+
## Challenges
13
+
- **Sensitivity**: Decision letters may contain harsh criticism that affects author morale
14
+
- **Finality concerns**: Decisions may be appealed or overturned, requiring decision history tracking
15
+
- **Editor privacy**: Some journals protect editor identity until decision is made
16
+
- **Liability**: Documented decisions create audit trail that may be scrutinised in disputes
17
+
18
+
## Notes
19
+
- Set `decisionType` to one of: accept, accept-with-minor-revisions, major-revisions-required, reject-with-resubmission, reject
20
+
- Link all reviews that informed the decision via `reviews` array using `strongRef`
21
+
- Provide clear guidance in `commentsToAuthors` - summarise reviews and give specific revision instructions
22
+
- For revision decisions, set `dueDate` (typically 2-3 months for major revisions, 2-4 weeks for minor)
23
+
- Create new decision record for each round - a manuscript may have multiple decisions (revisions required → accept)
24
+
- Use `strongRef` for manuscript to create immutable decision record tied to specific version
+65
lexicons/decision/decision.json
+65
lexicons/decision/decision.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.decision",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"manuscript",
13
+
"editor",
14
+
"decisionType",
15
+
"decisionDate"
16
+
],
17
+
"properties": {
18
+
"manuscript": {
19
+
"type": "ref",
20
+
"ref": "at.scholarly.definition#strongRef",
21
+
"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."
22
+
},
23
+
"editor": {
24
+
"type": "string",
25
+
"format": "did",
26
+
"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."
27
+
},
28
+
"decisionType": {
29
+
"type": "ref",
30
+
"ref": "at.scholarly.definition#decisionType",
31
+
"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."
32
+
},
33
+
"decisionDate": {
34
+
"type": "string",
35
+
"format": "datetime",
36
+
"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."
37
+
},
38
+
"reviews": {
39
+
"type": "array",
40
+
"items": {
41
+
"type": "ref",
42
+
"ref": "at.scholarly.definition#strongRef"
43
+
},
44
+
"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."
45
+
},
46
+
"commentsToAuthors": {
47
+
"type": "string",
48
+
"maxLength": 50000,
49
+
"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."
50
+
},
51
+
"dueDate": {
52
+
"type": "string",
53
+
"format": "datetime",
54
+
"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."
55
+
},
56
+
"createdAt": {
57
+
"type": "string",
58
+
"format": "datetime",
59
+
"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."
60
+
}
61
+
}
62
+
}
63
+
}
64
+
}
65
+
}
+24
lexicons/definition/README.md
+24
lexicons/definition/README.md
···
1
+
# at.scholarly.definition
2
+
3
+
Shared type definitions and enumerations used across all scholarly lexicons.
4
+
5
+
## Use Cases
6
+
- Ensuring consistent identifier formats (DOI, ORCID, ISSN) across all records
7
+
- Providing immutable references between entities via `strongRef`
8
+
- Standardising person information (`personRef`) for authors, reviewers, editors
9
+
- Defining controlled vocabularies for statuses, types, and classifications
10
+
11
+
## Challenges
12
+
- **Breaking changes**: Modifying shared types impacts all lexicons using them
13
+
- **Tight coupling**: Changes require coordinated updates across multiple lexicons
14
+
- **Validation complexity**: Pattern matching for identifiers (DOI, ORCID, ISSN) must be precise
15
+
- **Enum rigidity**: Adding new values to enums requires schema updates
16
+
17
+
## Notes
18
+
- Use `strongRef` (URI + CID) whenever you need immutable, content-addressed references between entities
19
+
- Always validate identifier patterns (DOI, ORCID, ISSN) at write time to prevent invalid data
20
+
- `personRef` is the standard way to represent people - use it consistently across author/reviewer/editor contexts
21
+
- Enumerations like `reviewStatus`, `decisionType`, `confidentialityLevel` define the allowed workflow states
22
+
- **Versioning strategy**: If breaking changes are needed, create a new version (e.g., `at.scholarly.definition.v2`)
23
+
- **Optional by default**: When adding new fields to existing objects, make them optional to avoid breaking changes
24
+
at.scholarly.definitionat.scholarly.definitionat.scholarly.definitionat.scholarly.definition
+213
lexicons/definition/definition.json
+213
lexicons/definition/definition.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.definition",
4
+
"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.",
5
+
"definition": {
6
+
"strongRef": {
7
+
"type": "object",
8
+
"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.",
9
+
"required": [
10
+
"uri",
11
+
"cid"
12
+
],
13
+
"properties": {
14
+
"uri": {
15
+
"type": "string",
16
+
"format": "at-uri",
17
+
"description": "AT Protocol URI pointing to the record. Format: at://did:plc:abc123/at.scholarly.manuscript/xyz789. This identifies WHICH record you're referencing."
18
+
},
19
+
"cid": {
20
+
"type": "string",
21
+
"format": "cid",
22
+
"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."
23
+
}
24
+
}
25
+
},
26
+
"personRef": {
27
+
"type": "object",
28
+
"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).",
29
+
"required": [
30
+
"name"
31
+
],
32
+
"properties": {
33
+
"did": {
34
+
"type": "string",
35
+
"format": "did",
36
+
"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."
37
+
},
38
+
"name": {
39
+
"type": "string",
40
+
"maxLength": 500,
41
+
"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'."
42
+
},
43
+
"orcid": {
44
+
"type": "string",
45
+
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$",
46
+
"description": "ORCID identifier - a unique persistent identifier for researchers. Format: 0000-0002-1825-0097 (four groups of four digits, last digit can be X). Strongly recommended to disambiguate authors with common names. See orcid.org to get one."
47
+
},
48
+
"affiliation": {
49
+
"type": "string",
50
+
"maxLength": 1000,
51
+
"description": "Current institutional affiliation of the person at time of contribution. Examples: 'Stanford University', 'Max Planck Institute for Evolutionary Anthropology', 'Independent Researcher'. Can include department: 'Department of Computer Science, MIT'."
52
+
},
53
+
"email": {
54
+
"type": "string",
55
+
"format": "email",
56
+
"description": "Email address for correspondence. Optional but recommended especially for corresponding authors. Will be displayed publicly if this is used in author lists."
57
+
}
58
+
}
59
+
},
60
+
"doi": {
61
+
"type": "string",
62
+
"pattern": "^10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$",
63
+
"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."
64
+
},
65
+
"orcid": {
66
+
"type": "string",
67
+
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}[0-9X]$",
68
+
"description": "ORCID identifier (e.g., 0000-0002-1825-0097)."
69
+
},
70
+
"issn": {
71
+
"type": "string",
72
+
"pattern": "^\\d{4}-\\d{3}[0-9X]$",
73
+
"description": "International Standard Serial Number (e.g., 0028-0836)."
74
+
},
75
+
"dateRange": {
76
+
"type": "object",
77
+
"description": "Date range with start and optional end date.",
78
+
"required": [
79
+
"start"
80
+
],
81
+
"properties": {
82
+
"start": {
83
+
"type": "string",
84
+
"format": "datetime",
85
+
"description": "Start date and time."
86
+
},
87
+
"end": {
88
+
"type": "string",
89
+
"format": "datetime",
90
+
"description": "End date and time (optional for ongoing events)."
91
+
}
92
+
}
93
+
},
94
+
"license": {
95
+
"type": "object",
96
+
"description": "License information for a work.",
97
+
"required": [
98
+
"type"
99
+
],
100
+
"properties": {
101
+
"type": {
102
+
"type": "string",
103
+
"description": "License type (e.g., CC-BY-4.0, MIT, proprietary)."
104
+
},
105
+
"url": {
106
+
"type": "string",
107
+
"format": "uri",
108
+
"description": "URL to the full license text."
109
+
},
110
+
"text": {
111
+
"type": "string",
112
+
"maxLength": 5000,
113
+
"description": "Brief license description or full text."
114
+
}
115
+
}
116
+
},
117
+
"contributorRole": {
118
+
"type": "string",
119
+
"enum": [
120
+
"author",
121
+
"corresponding-author",
122
+
"equal-contributor",
123
+
"supervisor",
124
+
"principal-investigator"
125
+
],
126
+
"description": "Role of a contributor to a manuscript."
127
+
},
128
+
"reviewStatus": {
129
+
"type": "string",
130
+
"enum": [
131
+
"draft",
132
+
"submitted",
133
+
"under-review",
134
+
"revision-requested",
135
+
"revision-submitted",
136
+
"accepted",
137
+
"rejected",
138
+
"published",
139
+
"retracted"
140
+
],
141
+
"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."
142
+
},
143
+
"confidentialityLevel": {
144
+
"type": "string",
145
+
"enum": [
146
+
"open",
147
+
"single-blind",
148
+
"double-blind",
149
+
"triple-blind",
150
+
"confidential"
151
+
],
152
+
"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."
153
+
},
154
+
"decisionType": {
155
+
"type": "string",
156
+
"enum": [
157
+
"accept",
158
+
"accept-with-minor-revisions",
159
+
"major-revisions-required",
160
+
"reject-with-resubmission",
161
+
"reject"
162
+
],
163
+
"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!"
164
+
},
165
+
"publicationType": {
166
+
"type": "string",
167
+
"enum": [
168
+
"journal",
169
+
"preprint",
170
+
"conference",
171
+
"book",
172
+
"proceedings"
173
+
],
174
+
"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."
175
+
},
176
+
"eventType": {
177
+
"type": "string",
178
+
"enum": [
179
+
"conference",
180
+
"workshop",
181
+
"symposium",
182
+
"seminar",
183
+
"colloquium"
184
+
],
185
+
"description": "Type of academic event."
186
+
},
187
+
"supplementType": {
188
+
"type": "string",
189
+
"enum": [
190
+
"data",
191
+
"code",
192
+
"video",
193
+
"audio",
194
+
"image",
195
+
"appendix",
196
+
"other"
197
+
],
198
+
"description": "Type of supplementary material."
199
+
},
200
+
"consentType": {
201
+
"type": "string",
202
+
"enum": [
203
+
"ethics-approval",
204
+
"informed-consent",
205
+
"data-sharing",
206
+
"copyright-transfer",
207
+
"competing-interests",
208
+
"funding-disclosure"
209
+
],
210
+
"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."
211
+
}
212
+
}
213
+
}
+24
lexicons/editor/README.md
+24
lexicons/editor/README.md
···
1
+
# at.scholarly.editor
2
+
3
+
Editor profile for managing peer review and making publication decisions.
4
+
5
+
## Use Cases
6
+
- Establishing authority to make editorial decisions (accept/reject)
7
+
- Tracking which editor handled which manuscripts for accountability
8
+
- Organising editorial boards with different roles (editor-in-chief, associate, section)
9
+
- Routing manuscripts to appropriate editors based on expertise
10
+
- Maintaining editorial history and decision patterns
11
+
12
+
## Challenges
13
+
- **Role complexity**: Different journals have different editorial hierarchies and structures
14
+
- **Privacy concerns**: Some journals protect editor identity until decision is made
15
+
- **Accountability pressure**: Documented decisions create audit trail that may be scrutinised
16
+
- **Workload visibility**: Public editor profiles may increase manuscript submissions
17
+
18
+
## Notes
19
+
- Set `editorRole` to define authority level: editor-in-chief > associate-editor > section-editor > guest-editor
20
+
- Use `publications` array to specify which journals/conferences this editor manages
21
+
- `expertise` array helps route manuscripts to editors with relevant subject knowledge
22
+
- Email is required (unlike author/reviewer) as editors must be reachable for submissions
23
+
- Link editor DID to decision records for transparency and accountability
24
+
- Key is `literal:self` - one editor profile per DID (user account)
+77
lexicons/editor/editor.json
+77
lexicons/editor/editor.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.editor",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "literal:self",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name",
13
+
"email",
14
+
"affiliation"
15
+
],
16
+
"properties": {
17
+
"name": {
18
+
"type": "string",
19
+
"maxLength": 500,
20
+
"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."
21
+
},
22
+
"orcid": {
23
+
"type": "ref",
24
+
"ref": "at.scholarly.definition#orcid",
25
+
"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."
26
+
},
27
+
"email": {
28
+
"type": "string",
29
+
"format": "email",
30
+
"description": "Contact email address for editorial correspondence and manuscript submissions. Format: name@institution.edu or editorial@journal.org. 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."
31
+
},
32
+
"affiliation": {
33
+
"type": "string",
34
+
"maxLength": 1000,
35
+
"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."
36
+
},
37
+
"bio": {
38
+
"type": "string",
39
+
"maxLength": 5000,
40
+
"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."
41
+
},
42
+
"editorRole": {
43
+
"type": "string",
44
+
"enum": [
45
+
"editor-in-chief",
46
+
"associate-editor",
47
+
"section-editor",
48
+
"guest-editor"
49
+
],
50
+
"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."
51
+
},
52
+
"publications": {
53
+
"type": "array",
54
+
"items": {
55
+
"type": "string",
56
+
"format": "at-uri"
57
+
},
58
+
"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."
59
+
},
60
+
"expertise": {
61
+
"type": "array",
62
+
"items": {
63
+
"type": "string",
64
+
"maxLength": 200
65
+
},
66
+
"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."
67
+
},
68
+
"createdAt": {
69
+
"type": "string",
70
+
"format": "datetime",
71
+
"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."
72
+
}
73
+
}
74
+
}
75
+
}
76
+
}
77
+
}
+24
lexicons/event/README.md
+24
lexicons/event/README.md
···
1
+
# at.scholarly.event
2
+
3
+
An academic event - conference, workshop, symposium, or seminar where research is presented.
4
+
5
+
## Use Cases
6
+
- Providing context for conference papers (e.g., "Presented at NeurIPS 2024")
7
+
- Linking manuscripts to the event where they were presented
8
+
- Tracking presentations separately from publications
9
+
- Managing event metadata (dates, location, organisers)
10
+
- Connecting event to published proceedings
11
+
12
+
## Challenges
13
+
- **Recurring series**: Same conference name repeats annually requiring year-specific records (e.g., NeurIPS 2024, 2025, 2026)
14
+
- **Hybrid complexity**: Post-pandemic mix of physical/virtual/hybrid formats
15
+
- **Multi-day/location**: Events may span multiple days or even simultaneous locations
16
+
- **Presentation vs. publication**: Paper may be presented at event but published elsewhere
17
+
18
+
## Notes
19
+
- Include year in event `name` for recurring conferences ("NeurIPS 2024" not just "NeurIPS")
20
+
- Use `dates` with start and end to capture event duration (single day: same start/end, week-long: different)
21
+
- Set `eventType` (conference, workshop, symposium, seminar, colloquium) to categorise event scale and format
22
+
- Use `location` to specify city/country for physical events, or "Virtual" / "Hybrid" for online/mixed formats
23
+
- Link to published proceedings via `publication` field if papers from event are published together
24
+
- Record `organizer` (institution, society, foundation) for attribution and context
+65
lexicons/event/event.json
+65
lexicons/event/event.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.event",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name",
13
+
"dates"
14
+
],
15
+
"properties": {
16
+
"name": {
17
+
"type": "string",
18
+
"maxLength": 500,
19
+
"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."
20
+
},
21
+
"description": {
22
+
"type": "string",
23
+
"maxLength": 5000,
24
+
"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."
25
+
},
26
+
"eventType": {
27
+
"type": "ref",
28
+
"ref": "at.scholarly.definition#eventType",
29
+
"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."
30
+
},
31
+
"dates": {
32
+
"type": "ref",
33
+
"ref": "at.scholarly.definition#dateRange",
34
+
"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."
35
+
},
36
+
"location": {
37
+
"type": "string",
38
+
"maxLength": 500,
39
+
"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."
40
+
},
41
+
"website": {
42
+
"type": "string",
43
+
"format": "uri",
44
+
"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."
45
+
},
46
+
"organizer": {
47
+
"type": "string",
48
+
"maxLength": 500,
49
+
"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."
50
+
},
51
+
"publication": {
52
+
"type": "string",
53
+
"format": "at-uri",
54
+
"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."
55
+
},
56
+
"createdAt": {
57
+
"type": "string",
58
+
"format": "datetime",
59
+
"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."
60
+
}
61
+
}
62
+
}
63
+
}
64
+
}
65
+
}
+24
lexicons/issue/README.md
+24
lexicons/issue/README.md
···
1
+
# at.scholarly.issue
2
+
3
+
A specific issue of a journal - organising articles into volumes and issue numbers.
4
+
5
+
## Use Cases
6
+
- Providing citation information (e.g., "Nature Vol. 625, Issue 7994")
7
+
- Organising journal articles chronologically by volume/issue
8
+
- Managing special issues with guest editors and thematic focus
9
+
- Displaying journal cover images for visual browsing
10
+
- Grouping articles published together at a specific time
11
+
12
+
## Challenges
13
+
- **Not universal**: Preprint servers and many online-only journals don't use issues
14
+
- **Numbering complexity**: Different publications use different schemes (continuous vs. annual volume numbering)
15
+
- **Optional relevance**: May not be necessary for all publication types
16
+
- **Metadata overhead**: Adds another organisational layer that may not provide value for all workflows
17
+
18
+
## Notes
19
+
- Only create issue records for publications that actually organise content into issues (traditional journals)
20
+
- Leave `volume` and `number` optional as some journals use only one or the other
21
+
- Use `year` for temporal filtering even if volume/issue numbering isn't clear
22
+
- Set `specialIssue` to true and provide `specialIssueTitle` for themed collections with guest editors
23
+
- Store `coverImage` (PNG/JPEG, max 2MB) for visual representation and browsing
24
+
- Link to parent `publication` to establish which journal this issue belongs to
+68
lexicons/issue/issue.json
+68
lexicons/issue/issue.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.issue",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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.",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"publication"
13
+
],
14
+
"properties": {
15
+
"publication": {
16
+
"type": "string",
17
+
"format": "at-uri",
18
+
"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."
19
+
},
20
+
"volume": {
21
+
"type": "integer",
22
+
"minimum": 1,
23
+
"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."
24
+
},
25
+
"number": {
26
+
"type": "integer",
27
+
"minimum": 1,
28
+
"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."
29
+
},
30
+
"year": {
31
+
"type": "integer",
32
+
"minimum": 1000,
33
+
"maximum": 9999,
34
+
"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."
35
+
},
36
+
"publishedDate": {
37
+
"type": "string",
38
+
"format": "datetime",
39
+
"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."
40
+
},
41
+
"coverImage": {
42
+
"type": "blob",
43
+
"accept": [
44
+
"image/png",
45
+
"image/jpeg"
46
+
],
47
+
"maxSize": 2000000,
48
+
"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."
49
+
},
50
+
"specialIssue": {
51
+
"type": "boolean",
52
+
"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."
53
+
},
54
+
"specialIssueTitle": {
55
+
"type": "string",
56
+
"maxLength": 500,
57
+
"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."
58
+
},
59
+
"createdAt": {
60
+
"type": "string",
61
+
"format": "datetime",
62
+
"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."
63
+
}
64
+
}
65
+
}
66
+
}
67
+
}
68
+
}
+26
lexicons/manuscript/README.md
+26
lexicons/manuscript/README.md
···
1
+
# at.scholarly.manuscript
2
+
3
+
The core scholarly work - journal article, conference paper, or preprint.
4
+
5
+
## Use Cases
6
+
- Submitting a research paper to a journal with complete provenance tracking
7
+
- Publishing preprints with public versioning and open peer review
8
+
- Tracking manuscript lifecycle from draft → submission → review → revision → publication
9
+
- Linking manuscripts to supplementary materials, reviews, and editorial decisions
10
+
- Managing multi-author attributions with ORCID identifiers
11
+
12
+
## Challenges
13
+
- **Schema complexity**: Many fields and relationships to manage
14
+
- **File storage**: PDF files can be 1-5MB each, multiplied by versions
15
+
- **Privacy concerns**: Contains potentially sensitive author and reviewer information
16
+
- **Relationship management**: Maintaining links to versions, reviews, decisions requires careful state management
17
+
18
+
## Notes
19
+
- Always create a v1 `version` record when first submitted - this establishes the baseline
20
+
- Use `status` field to track workflow state (draft, submitted, under-review, accepted, published, retracted)
21
+
- Update `status` as manuscript progresses through editorial process
22
+
- Link to `publication` (required) to establish where the work is submitted/published
23
+
- Create separate `supplement` records for large datasets, code, videos rather than embedding in manuscript
24
+
- Use `strongRef` for versions, reviews, decisions to ensure immutable audit trail
25
+
- Populate `doi` only after publication - not assigned for preprints or under-review manuscripts
26
+
- Include all authors in `authors` array with ORCID when available for proper attribution
+154
lexicons/manuscript/manuscript.json
+154
lexicons/manuscript/manuscript.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.manuscript",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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.",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"title",
13
+
"abstract",
14
+
"authors",
15
+
"publication",
16
+
"submittedDate",
17
+
"manuscriptFile"
18
+
],
19
+
"properties": {
20
+
"title": {
21
+
"type": "string",
22
+
"maxLength": 1000,
23
+
"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."
24
+
},
25
+
"abstract": {
26
+
"type": "string",
27
+
"maxLength": 10000,
28
+
"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."
29
+
},
30
+
"keywords": {
31
+
"type": "array",
32
+
"items": {
33
+
"type": "string",
34
+
"maxLength": 100
35
+
},
36
+
"maxLength": 20,
37
+
"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."
38
+
},
39
+
"authors": {
40
+
"type": "array",
41
+
"items": {
42
+
"type": "ref",
43
+
"ref": "at.scholarly.definition#personRef"
44
+
},
45
+
"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."
46
+
},
47
+
"correspondingAuthor": {
48
+
"type": "ref",
49
+
"ref": "at.scholarly.definition#personRef",
50
+
"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."
51
+
},
52
+
"publication": {
53
+
"type": "string",
54
+
"format": "at-uri",
55
+
"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."
56
+
},
57
+
"issue": {
58
+
"type": "string",
59
+
"format": "at-uri",
60
+
"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."
61
+
},
62
+
"event": {
63
+
"type": "string",
64
+
"format": "at-uri",
65
+
"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."
66
+
},
67
+
"doi": {
68
+
"type": "ref",
69
+
"ref": "at.scholarly.definition#doi",
70
+
"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."
71
+
},
72
+
"submittedDate": {
73
+
"type": "string",
74
+
"format": "datetime",
75
+
"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."
76
+
},
77
+
"acceptedDate": {
78
+
"type": "string",
79
+
"format": "datetime",
80
+
"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."
81
+
},
82
+
"publishedDate": {
83
+
"type": "string",
84
+
"format": "datetime",
85
+
"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."
86
+
},
87
+
"license": {
88
+
"type": "ref",
89
+
"ref": "at.scholarly.definition#license",
90
+
"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."
91
+
},
92
+
"manuscriptFile": {
93
+
"type": "blob",
94
+
"accept": [
95
+
"application/pdf"
96
+
],
97
+
"maxSize": 50000000,
98
+
"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!"
99
+
},
100
+
"supplements": {
101
+
"type": "array",
102
+
"items": {
103
+
"type": "string",
104
+
"format": "at-uri"
105
+
},
106
+
"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."
107
+
},
108
+
"versions": {
109
+
"type": "array",
110
+
"items": {
111
+
"type": "ref",
112
+
"ref": "at.scholarly.definition#strongRef"
113
+
},
114
+
"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."
115
+
},
116
+
"reviews": {
117
+
"type": "array",
118
+
"items": {
119
+
"type": "ref",
120
+
"ref": "at.scholarly.definition#strongRef"
121
+
},
122
+
"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."
123
+
},
124
+
"decisions": {
125
+
"type": "array",
126
+
"items": {
127
+
"type": "ref",
128
+
"ref": "at.scholarly.definition#strongRef"
129
+
},
130
+
"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."
131
+
},
132
+
"consents": {
133
+
"type": "array",
134
+
"items": {
135
+
"type": "ref",
136
+
"ref": "at.scholarly.definition#strongRef"
137
+
},
138
+
"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."
139
+
},
140
+
"status": {
141
+
"type": "ref",
142
+
"ref": "at.scholarly.definition#reviewStatus",
143
+
"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."
144
+
},
145
+
"createdAt": {
146
+
"type": "string",
147
+
"format": "datetime",
148
+
"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."
149
+
}
150
+
}
151
+
}
152
+
}
153
+
}
154
+
}
+22
lexicons/portfolio/README.md
+22
lexicons/portfolio/README.md
···
1
+
# at.scholarly.portfolio
2
+
3
+
Optional organisational grouping within a publisher - for branded collections or portfolio structures.
4
+
5
+
## Use Cases
6
+
- Organising publications into branded collections (e.g., Nature Publishing Group within Springer Nature)
7
+
- Enabling portfolio-level queries and analytics
8
+
- Supporting hierarchical publisher structures (Publisher → Portfolio → Publication)
9
+
- Grouping related journals under a common brand
10
+
11
+
## Challenges
12
+
- **Not universal**: Some publishers don't use portfolio structures, making this optional layer unnecessary
13
+
- **Inconsistent usage**: Different publishers have different portfolio strategies and hierarchies
14
+
- **Maintenance overhead**: Portfolio structures can change due to acquisitions and reorganisations
15
+
- **Ambiguity**: Distinction between publisher, portfolio, and publication may be unclear
16
+
17
+
## Notes
18
+
- Only create portfolio records for publishers that actually use portfolio structures
19
+
- Link portfolio to parent `publisher` (required) via at-uri
20
+
- Publications can optionally reference a portfolio via at-uri
21
+
- Include `website` if the portfolio has its own distinct web presence
22
+
- For simple publishers with no portfolio structure, publications can reference publishers directly
+45
lexicons/portfolio/portfolio.json
+45
lexicons/portfolio/portfolio.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.portfolio",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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.",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name",
13
+
"publisher"
14
+
],
15
+
"properties": {
16
+
"name": {
17
+
"type": "string",
18
+
"maxLength": 500,
19
+
"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."
20
+
},
21
+
"description": {
22
+
"type": "string",
23
+
"maxLength": 5000,
24
+
"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."
25
+
},
26
+
"publisher": {
27
+
"type": "string",
28
+
"format": "at-uri",
29
+
"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."
30
+
},
31
+
"website": {
32
+
"type": "string",
33
+
"format": "uri",
34
+
"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."
35
+
},
36
+
"createdAt": {
37
+
"type": "string",
38
+
"format": "datetime",
39
+
"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."
40
+
}
41
+
}
42
+
}
43
+
}
44
+
}
45
+
}
+25
lexicons/publication/README.md
+25
lexicons/publication/README.md
···
1
+
# at.scholarly.publication
2
+
3
+
A publication venue - journal, preprint server, or conference proceedings where manuscripts are published.
4
+
5
+
## Use Cases
6
+
- Establishing where a manuscript is published (e.g., Nature, arXiv, NeurIPS Proceedings)
7
+
- Categorising publications by type (journal vs. preprint vs. conference)
8
+
- Filtering by peer review status or open access availability
9
+
- Searching publications by subject area or discipline
10
+
- Tracking metadata like ISSN for bibliographic systems
11
+
12
+
## Challenges
13
+
- **Type diversity**: Journals, preprints, conferences have very different characteristics and workflows
14
+
- **Publisher changes**: Publications can transfer between publishers requiring updates
15
+
- **Name ambiguity**: Same name used by different publishers (e.g., "Science" as magazine vs. conference proceedings)
16
+
- **Lifecycle changes**: Publications cease, merge, split, or go on hiatus
17
+
18
+
## Notes
19
+
- Link to parent `publisher` (required) - every publication belongs to exactly one publisher
20
+
- Set `publicationType` (journal, preprint, conference, book, proceedings) to distinguish venue types
21
+
- Use `peerReviewed` flag to indicate if submissions undergo peer review (true for journals, false for preprints)
22
+
- Use `openAccess` flag to indicate free availability (true for PLOS, arXiv; false for traditional subscription journals)
23
+
- Include `issn` (eISSN preferred) for journals - not applicable to preprints or some conference proceedings
24
+
- Populate `subjects` array with discipline tags for discovery and filtering
25
+
- Optional `portfolio` field for publications belonging to publishing portfolios within larger publishers
+77
lexicons/publication/publication.json
+77
lexicons/publication/publication.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.publication",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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.",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name",
13
+
"publisher"
14
+
],
15
+
"properties": {
16
+
"name": {
17
+
"type": "string",
18
+
"maxLength": 500,
19
+
"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."
20
+
},
21
+
"description": {
22
+
"type": "string",
23
+
"maxLength": 5000,
24
+
"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."
25
+
},
26
+
"publisher": {
27
+
"type": "string",
28
+
"format": "at-uri",
29
+
"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."
30
+
},
31
+
"portfolio": {
32
+
"type": "string",
33
+
"format": "at-uri",
34
+
"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."
35
+
},
36
+
"issn": {
37
+
"type": "ref",
38
+
"ref": "at.scholarly.definition#issn",
39
+
"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."
40
+
},
41
+
"publicationType": {
42
+
"type": "ref",
43
+
"ref": "at.scholarly.definition#publicationType",
44
+
"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."
45
+
},
46
+
"website": {
47
+
"type": "string",
48
+
"format": "uri",
49
+
"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."
50
+
},
51
+
"peerReviewed": {
52
+
"type": "boolean",
53
+
"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."
54
+
},
55
+
"openAccess": {
56
+
"type": "boolean",
57
+
"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."
58
+
},
59
+
"subjects": {
60
+
"type": "array",
61
+
"items": {
62
+
"type": "string",
63
+
"maxLength": 200
64
+
},
65
+
"maxLength": 20,
66
+
"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."
67
+
},
68
+
"createdAt": {
69
+
"type": "string",
70
+
"format": "datetime",
71
+
"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."
72
+
}
73
+
}
74
+
}
75
+
}
76
+
}
77
+
}
+23
lexicons/publisher/README.md
+23
lexicons/publisher/README.md
···
1
+
# at.scholarly.publisher
2
+
3
+
An academic publisher organisation - the entity that publishes journals, books, and proceedings.
4
+
5
+
## Use Cases
6
+
- Organising publications by publisher (e.g., all Springer Nature journals)
7
+
- Providing institutional context and branding for publications
8
+
- Tracking publisher metadata (location, founding date, policies)
9
+
- Enabling publisher-level queries and analytics (acceptance rates, publication volume)
10
+
- Managing publisher logos and visual identity for display
11
+
12
+
## Challenges
13
+
- **Traditional model bias**: Assumes centralised publisher structure, may not fit independent/decentralised publishing
14
+
- **Mergers and acquisitions**: Publishers frequently merge, rebrand, or change ownership requiring updates
15
+
- **Complexity**: Adds an organisational layer to the data model
16
+
- **Historical changes**: Difficult to represent publisher evolution over time
17
+
18
+
## Notes
19
+
- Use the current publisher name even if it has changed (e.g., "Springer Nature" not "Springer" or "Nature Publishing Group")
20
+
- For merged entities, use the new combined entity and note history in `description`
21
+
- Store publisher logo via `logo` field for use in UI/branding (PNG/JPEG/SVG, max 1MB)
22
+
- Link to publisher website via `website` for additional information
23
+
- Use `established` date for the current legal entity (not historical predecessor organisations)
+59
lexicons/publisher/publisher.json
+59
lexicons/publisher/publisher.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.publisher",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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.",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name"
13
+
],
14
+
"properties": {
15
+
"name": {
16
+
"type": "string",
17
+
"maxLength": 500,
18
+
"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."
19
+
},
20
+
"description": {
21
+
"type": "string",
22
+
"maxLength": 5000,
23
+
"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."
24
+
},
25
+
"website": {
26
+
"type": "string",
27
+
"format": "uri",
28
+
"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."
29
+
},
30
+
"logo": {
31
+
"type": "blob",
32
+
"accept": [
33
+
"image/png",
34
+
"image/jpeg",
35
+
"image/svg+xml"
36
+
],
37
+
"maxSize": 1000000,
38
+
"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."
39
+
},
40
+
"location": {
41
+
"type": "string",
42
+
"maxLength": 500,
43
+
"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."
44
+
},
45
+
"established": {
46
+
"type": "string",
47
+
"format": "datetime",
48
+
"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."
49
+
},
50
+
"createdAt": {
51
+
"type": "string",
52
+
"format": "datetime",
53
+
"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."
54
+
}
55
+
}
56
+
}
57
+
}
58
+
}
59
+
}
+26
lexicons/review/README.md
+26
lexicons/review/README.md
···
1
+
# at.scholarly.review
2
+
3
+
A peer review of a manuscript - expert evaluation determining publication worthiness.
4
+
5
+
## Use Cases
6
+
- Recording peer review feedback with recommendations (accept/reject/revise)
7
+
- Enabling open peer review where reviews are public and attributed
8
+
- Maintaining blind review confidentiality (single, double, triple-blind)
9
+
- Providing reviewer credit via ORCID linkage
10
+
- Tracking review turnaround times and reviewer performance
11
+
- Separating public comments (to authors) from confidential notes (to editor)
12
+
13
+
## Challenges
14
+
- **Confidentiality requirements**: Must protect reviewer identity in blind review systems
15
+
- **Sensitive content**: Reviews may contain harsh criticism requiring careful access control
16
+
- **Bias documentation**: Published reviews may inadvertently reveal reviewer biases
17
+
- **Privacy trade-offs**: Open peer review improves transparency but may discourage honest feedback
18
+
19
+
## Notes
20
+
- Use `strongRef` for both `manuscript` and `version` to lock review to exact content that was reviewed
21
+
- Set `confidentiality` level (open, single-blind, double-blind) to control visibility of reviewer DID
22
+
- Separate public feedback (`comments`) from confidential notes (`commentsToEditor`)
23
+
- Set `recommendation` to guide editor: accept, reject, major-revision, minor-revision
24
+
- Optional `score` (1-10) provides quantitative assessment alongside qualitative comments
25
+
- For open peer review, make `reviewer` DID public; for blind review, restrict access
26
+
- Link reviewer DID to their `at.scholarly.reviewer` profile for credit/attribution
+79
lexicons/review/review.json
+79
lexicons/review/review.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.review",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"manuscript",
13
+
"version",
14
+
"reviewer",
15
+
"submittedDate",
16
+
"comments"
17
+
],
18
+
"properties": {
19
+
"manuscript": {
20
+
"type": "ref",
21
+
"ref": "at.scholarly.definition#strongRef",
22
+
"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."
23
+
},
24
+
"version": {
25
+
"type": "ref",
26
+
"ref": "at.scholarly.definition#strongRef",
27
+
"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."
28
+
},
29
+
"reviewer": {
30
+
"type": "string",
31
+
"format": "did",
32
+
"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."
33
+
},
34
+
"submittedDate": {
35
+
"type": "string",
36
+
"format": "datetime",
37
+
"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."
38
+
},
39
+
"recommendation": {
40
+
"type": "string",
41
+
"enum": [
42
+
"accept",
43
+
"reject",
44
+
"major-revision",
45
+
"minor-revision"
46
+
],
47
+
"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."
48
+
},
49
+
"confidentiality": {
50
+
"type": "ref",
51
+
"ref": "at.scholarly.definition#confidentialityLevel",
52
+
"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."
53
+
},
54
+
"comments": {
55
+
"type": "string",
56
+
"maxLength": 50000,
57
+
"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."
58
+
},
59
+
"commentsToEditor": {
60
+
"type": "string",
61
+
"maxLength": 50000,
62
+
"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."
63
+
},
64
+
"score": {
65
+
"type": "integer",
66
+
"minimum": 1,
67
+
"maximum": 10,
68
+
"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."
69
+
},
70
+
"createdAt": {
71
+
"type": "string",
72
+
"format": "datetime",
73
+
"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."
74
+
}
75
+
}
76
+
}
77
+
}
78
+
}
79
+
}
+24
lexicons/reviewer/README.md
+24
lexicons/reviewer/README.md
···
1
+
# at.scholarly.reviewer
2
+
3
+
Reviewer profile for researchers who evaluate manuscripts through peer review.
4
+
5
+
## Use Cases
6
+
- Matching manuscripts to appropriate reviewers based on expertise
7
+
- Providing recognition and credit for peer review contributions
8
+
- Tracking reviewer performance (turnaround time, review count)
9
+
- Supporting open peer review with attributed reviews
10
+
- Avoiding conflicts of interest via affiliation checking
11
+
12
+
## Challenges
13
+
- **Privacy requirements**: Identity must be protected in single/double-blind review systems
14
+
- **Expertise constraints**: Declared expertise may limit review invitation opportunities
15
+
- **Profile maintenance**: Another profile to keep current alongside author profile
16
+
- **Reviewer fatigue**: Making profile visible may increase unsolicited review requests
17
+
18
+
## Notes
19
+
- `expertise` array is critical for manuscript-reviewer matching - be specific and comprehensive
20
+
- Set `reviewCount` to track total completed reviews for experience indication
21
+
- Use `publications` array to identify potential conflicts of interest (shouldn't review papers heavily citing own work)
22
+
- ORCID enables credit for peer review contributions via services like Publons/Web of Science
23
+
- In blind review, restrict access to reviewer DID; in open review, make it public
24
+
- Key is `literal:self` - one reviewer profile per DID (user account)
+72
lexicons/reviewer/reviewer.json
+72
lexicons/reviewer/reviewer.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.reviewer",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "literal:self",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"name",
13
+
"affiliation",
14
+
"expertise"
15
+
],
16
+
"properties": {
17
+
"name": {
18
+
"type": "string",
19
+
"maxLength": 500,
20
+
"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."
21
+
},
22
+
"orcid": {
23
+
"type": "ref",
24
+
"ref": "at.scholarly.definition#orcid",
25
+
"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."
26
+
},
27
+
"email": {
28
+
"type": "string",
29
+
"format": "email",
30
+
"description": "Contact email address for review invitations and communication with editors. Format: name@institution.edu. 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."
31
+
},
32
+
"affiliation": {
33
+
"type": "string",
34
+
"maxLength": 1000,
35
+
"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."
36
+
},
37
+
"bio": {
38
+
"type": "string",
39
+
"maxLength": 5000,
40
+
"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."
41
+
},
42
+
"expertise": {
43
+
"type": "array",
44
+
"items": {
45
+
"type": "string",
46
+
"maxLength": 200
47
+
},
48
+
"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."
49
+
},
50
+
"reviewCount": {
51
+
"type": "integer",
52
+
"minimum": 0,
53
+
"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."
54
+
},
55
+
"publications": {
56
+
"type": "array",
57
+
"items": {
58
+
"type": "string",
59
+
"format": "at-uri"
60
+
},
61
+
"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."
62
+
},
63
+
"createdAt": {
64
+
"type": "string",
65
+
"format": "datetime",
66
+
"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."
67
+
}
68
+
}
69
+
}
70
+
}
71
+
}
72
+
}
+23
lexicons/supplement/README.md
+23
lexicons/supplement/README.md
···
1
+
# at.scholarly.supplement
2
+
3
+
Supplementary materials accompanying a manuscript - datasets, source code, videos, figures, appendices.
4
+
5
+
## Use Cases
6
+
- Providing raw datasets for reproducibility (CSV, Excel, HDF5 files)
7
+
- Sharing source code and analysis scripts (Python, R, MATLAB)
8
+
- Including video demonstrations of experiments or techniques
9
+
- Publishing high-resolution images or additional figures
10
+
- Attaching detailed methodological appendices
11
+
12
+
## Challenges
13
+
- **Storage limitations**: 100MB maximum file size may not accommodate very large datasets
14
+
- **File format diversity**: Must support wide variety of formats with different viewers
15
+
- **Version coupling**: Strongly tied to specific manuscript version, not easily reusable
16
+
- **Discoverability**: Supplements may be overlooked compared to main manuscript
17
+
18
+
## Notes
19
+
- Use `strongRef` to lock supplement to specific manuscript version - ensures supplements match the paper they support
20
+
- Set `supplementType` (data, code, video, image, appendix, etc.) to help with categorisation and appropriate rendering
21
+
- For datasets > 100MB, consider external repositories (Zenodo, Dryad) and link in the `description` field
22
+
- Include detailed `description` explaining file format, software requirements, and how to use the supplement
23
+
- Assign separate DOI if the supplement is independently citable (e.g., major dataset)
+61
lexicons/supplement/supplement.json
+61
lexicons/supplement/supplement.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.supplement",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"manuscript",
13
+
"title",
14
+
"file"
15
+
],
16
+
"properties": {
17
+
"manuscript": {
18
+
"type": "ref",
19
+
"ref": "at.scholarly.definition#strongRef",
20
+
"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."
21
+
},
22
+
"title": {
23
+
"type": "string",
24
+
"maxLength": 500,
25
+
"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."
26
+
},
27
+
"description": {
28
+
"type": "string",
29
+
"maxLength": 5000,
30
+
"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."
31
+
},
32
+
"supplementType": {
33
+
"type": "ref",
34
+
"ref": "at.scholarly.definition#supplementType",
35
+
"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."
36
+
},
37
+
"file": {
38
+
"type": "blob",
39
+
"maxSize": 100000000,
40
+
"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."
41
+
},
42
+
"doi": {
43
+
"type": "ref",
44
+
"ref": "at.scholarly.definition#doi",
45
+
"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."
46
+
},
47
+
"license": {
48
+
"type": "ref",
49
+
"ref": "at.scholarly.definition#license",
50
+
"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."
51
+
},
52
+
"createdAt": {
53
+
"type": "string",
54
+
"format": "datetime",
55
+
"description": "Timestamp when this supplement record was created in the system. ISO 8601 format. For system record-keeping and audit trails. Optional field."
56
+
}
57
+
}
58
+
}
59
+
}
60
+
}
61
+
}
+23
lexicons/version/README.md
+23
lexicons/version/README.md
···
1
+
# at.scholarly.version
2
+
3
+
A specific version of a manuscript during its revision process (v1 initial, v2 revised, v3 final).
4
+
5
+
## Use Cases
6
+
- Tracking manuscript evolution from initial submission through multiple revision rounds
7
+
- Providing transparent revision history showing how peer review improved the work
8
+
- Allowing citations to reference exact version that was used or reviewed
9
+
- Enabling comparison of changes between versions (diff tools)
10
+
11
+
## Challenges
12
+
- **Storage overhead**: Each version stores a complete PDF file (can be 1-5MB each)
13
+
- **Version number management**: Must maintain sequential versioning without gaps
14
+
- **Authorship changes**: Authors may be added/removed between versions requiring version-specific author lists
15
+
- **Review coupling**: Reviews are tied to specific versions, complicating cross-version analysis
16
+
17
+
## Notes
18
+
- Always create v1 when manuscript is first submitted - this is the baseline
19
+
- Increment `versionNumber` sequentially for each revision (v1, v2, v3...)
20
+
- Use `changeLog` to document what changed - helps reviewers and readers understand revisions
21
+
- Store complete PDF for each version via `versionFile` - ensures exact reproducibility
22
+
- Link version to parent manuscript using `strongRef` for immutable provenance
23
+
- If authorship changes, populate the `authors` field; otherwise inherit from parent manuscript
+63
lexicons/version/version.json
+63
lexicons/version/version.json
···
1
+
{
2
+
"lexicon": 1,
3
+
"id": "at.scholarly.version",
4
+
"definition": {
5
+
"main": {
6
+
"type": "record",
7
+
"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).",
8
+
"key": "tid",
9
+
"record": {
10
+
"type": "object",
11
+
"required": [
12
+
"manuscript",
13
+
"versionNumber",
14
+
"submittedDate",
15
+
"versionFile"
16
+
],
17
+
"properties": {
18
+
"manuscript": {
19
+
"type": "ref",
20
+
"ref": "at.scholarly.definition#strongRef",
21
+
"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."
22
+
},
23
+
"versionNumber": {
24
+
"type": "integer",
25
+
"minimum": 1,
26
+
"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."
27
+
},
28
+
"submittedDate": {
29
+
"type": "string",
30
+
"format": "datetime",
31
+
"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."
32
+
},
33
+
"versionFile": {
34
+
"type": "blob",
35
+
"accept": [
36
+
"application/pdf"
37
+
],
38
+
"maxSize": 50000000,
39
+
"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."
40
+
},
41
+
"changeLog": {
42
+
"type": "string",
43
+
"maxLength": 10000,
44
+
"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."
45
+
},
46
+
"authors": {
47
+
"type": "array",
48
+
"items": {
49
+
"type": "ref",
50
+
"ref": "at.scholarly.definition#personRef"
51
+
},
52
+
"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."
53
+
},
54
+
"createdAt": {
55
+
"type": "string",
56
+
"format": "datetime",
57
+
"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."
58
+
}
59
+
}
60
+
}
61
+
}
62
+
}
63
+
}