Formats
JATS
Journal Article Tag Suite
Introduction
The JATS (Journal Article Tag Suite) is an XML format that can be used to tag and describe scientific articles. It was developed by the NIH and has been adopted by several journals as a de facto standard for describing journal articles.
Usage
Use the .jats.xml file extension, or the --to jats or --from jats options, when converting to/from JATS e.g.
stencila convert doc.smd doc.jats.xmlBy default, the encoded JATS is un-indented. Use the --pretty option for indented XML but note that this may affect whitespace.
Implementation
Stencila supports bi-direction conversion between Stencila document and JATS. Parsing of JATS built on top of the quick-xml Rust crate.
Support
Stencila supports these operations for JATS:
- decoding from a file
- decoding from a string
- encoding to a file
- encoding to a string
Support and degree of loss by node type:
| Node type | Encoding | Decoding | Notes |
|---|---|---|---|
| Works | |||
| Article | 🔷 Low loss | 🔷 Low loss | Encoded as <article> using special function |
| AudioObject | 🔷 Low loss | 🔷 Low loss | Encoded as <inline-media> using special function |
| AuthorRole | |||
| Chat | |||
| ChatMessage | |||
| ChatMessageGroup | |||
| Claim | 🔷 Low loss | Encoded as <statement> |
|
| Collection | |||
| Comment | |||
| CreativeWork | |||
| Directory | |||
| Figure | 🔷 Low loss | Encoded as <fig> |
|
| File | |||
| ImageObject | 🔷 Low loss | 🔷 Low loss | Encoded as <inline-graphic> using special function |
| MediaObject | Encoded as <inline-media> using special function |
||
| Periodical | |||
| Prompt | |||
| PublicationIssue | |||
| PublicationVolume | |||
| Review | |||
| SoftwareApplication | |||
| SoftwareSourceCode | |||
| Table | Encoded using special function | ||
| TableCell | Encoded using special function | ||
| TableRow | Encoded using special function | ||
| VideoObject | 🔷 Low loss | 🔷 Low loss | Encoded as <inline-media> using special function |
| Prose | |||
| Admonition | 🟢 No loss | 🟢 No loss | Encoded as <boxed-text> |
| Annotation | Encoded as <annotation> |
||
| Cite | Encoded using special function | ||
| CiteGroup | |||
| DefinedTerm | |||
| Emphasis | 🟢 No loss | 🟢 No loss | Encoded as <italic> |
| Heading | 🟢 No loss | 🟢 No loss | Encoded as <title> using special function |
| Link | 🔷 Low loss | 🔷 Low loss | Encoded as <ext-link> |
| List | 🔷 Low loss | Encoded as <list> |
|
| ListItem | 🔷 Low loss | Encoded as <list-item> |
|
| Note | 🟢 No loss | 🟢 No loss | Encoded as <fn> |
| Paragraph | 🟢 No loss | 🟢 No loss | Encoded as <p> |
| QuoteBlock | 🟢 No loss | 🟢 No loss | Encoded as <disp-quote> |
| QuoteInline | 🟢 No loss | 🟢 No loss | Encoded as <inline-quote> |
| Section | 🟢 No loss | 🟢 No loss | Encoded as <sec> |
| Strikeout | 🟢 No loss | 🟢 No loss | Encoded as <strike> |
| Strong | 🟢 No loss | 🟢 No loss | Encoded as <bold> |
| Subscript | 🟢 No loss | 🟢 No loss | Encoded as <sub> |
| Superscript | 🟢 No loss | 🟢 No loss | Encoded as <sup> |
| Text | 🟢 No loss | 🟢 No loss | Encoded using special function |
| ThematicBreak | 🟢 No loss | 🟢 No loss | Encoded as <hr> |
| Underline | 🟢 No loss | 🟢 No loss | Encoded as <underline> |
| Math | |||
| MathBlock | 🟢 No loss | 🔷 Low loss | Encoded as <disp-formula> using special function |
| MathInline | 🟢 No loss | 🔷 Low loss | Encoded as <inline-formula> using special function |
| Code | |||
| CodeBlock | 🟢 No loss | Encoded as <code> |
|
| CodeChunk | 🔷 Low loss | Encoded as <code> |
|
| CodeExpression | 🔷 Low loss | 🔷 Low loss | Encoded as <code> |
| CodeInline | 🟢 No loss | 🟢 No loss | Encoded as <code> |
| CompilationMessage | |||
| ExecutionMessage | |||
| Data | |||
| Array | |||
| ArrayHint | |||
| ArrayValidator | |||
| Boolean | 🔷 Low loss | ||
| BooleanValidator | |||
| ConstantValidator | |||
| Cord | 🟢 No loss | 🟢 No loss | |
| Datatable | |||
| DatatableColumn | |||
| DatatableColumnHint | |||
| DatatableHint | |||
| Date | 🟢 No loss | 🟢 No loss | Encoded as <date> using special function |
| DateTime | 🟢 No loss | 🟢 No loss | Encoded as <date-time> using special function |
| DateTimeValidator | |||
| DateValidator | |||
| Duration | 🟢 No loss | 🟢 No loss | Encoded as <duration> using special function |
| DurationValidator | |||
| EnumValidator | |||
| Integer | 🔷 Low loss | ||
| IntegerValidator | |||
| Null | 🔷 Low loss | ||
| Number | 🔷 Low loss | ||
| NumberValidator | |||
| Object | |||
| ObjectHint | |||
| String | 🟢 No loss | 🟢 No loss | |
| StringHint | |||
| StringValidator | |||
| Time | 🟢 No loss | 🟢 No loss | Encoded as <time> using special function |
| TimeValidator | |||
| Timestamp | 🟢 No loss | 🟢 No loss | Encoded as <timestamp> using special function |
| TimestampValidator | |||
| TupleValidator | |||
| Unknown | |||
| UnsignedInteger | 🔷 Low loss | ||
| Flow | |||
| Button | |||
| CallArgument | |||
| CallBlock | |||
| CodeLocation | |||
| CompilationDigest | |||
| ExecutionDependant | |||
| ExecutionDependency | |||
| ExecutionTag | |||
| ForBlock | |||
| Form | |||
| Function | |||
| IfBlock | |||
| IfBlockClause | |||
| IncludeBlock | |||
| Parameter | Encoded as <parameter> |
||
| Variable | |||
| Walkthrough | |||
| WalkthroughStep | |||
| Style | |||
| StyledBlock | |||
| StyledInline | 🟢 No loss | 🟢 No loss | Encoded as <styled-content> |
| Edits | |||
| InstructionBlock | |||
| InstructionInline | |||
| InstructionMessage | |||
| PromptBlock | |||
| SuggestionBlock | |||
| SuggestionInline | |||
| Config | |||
| Config | |||
| Other | |||
| Brand | |||
| ContactPoint | |||
| Enumeration | |||
| Grant | |||
| ModelParameters | |||
| MonetaryGrant | |||
| Organization | 🔷 Low loss | Encoded as <institution> |
|
| Person | |||
| PostalAddress | 🔷 Low loss | Encoded as <address> |
|
| Product | 🔷 Low loss | Encoded as <product> |
|
| PropertyValue | |||
| ProvenanceCount | |||
| RawBlock | |||
| Thing |
See the Rust crate codec-jats for more details.