Enum: FormatEnum
The serialization/format of a product.
URI: kgr:FormatEnum
Permissible Values
| Value | Meaning | Description |
|---|---|---|
| biopax | edam:3156 | The BioPAX format, an RDF/OWL-based standard language for representing biolog… |
| boolnet | https://cran.r-project.org/package=BoolNet | The Boolean Network (BoolNet) format, which is a format for representing Bool… |
| chebi_sdf | https://docs.google.com/document/d/11G6SmTtQRQYFT7l9h5K0faUHiAaekcLeOweMOOTIpME/edit?pli=1&tab=t.0#heading=h.7ocxce8u265h | A ChEBI-specific SDF format |
| csv | edam:3752 | The Comma-Separated Values (CSV) format |
| doc | None | The Microsoft Word Document (DOC) format, a binary file format used by Micros… |
| docx | None | The Microsoft Word Open XML Document (DOCX) format, a modern file format for … |
| dot | https://graphviz.org/doc/info/lang.html | The DOT format, a plain text graph description language used to define the st… |
| fasta | edam:1929 | The FASTA format, a text-based format for representing nucleotide or peptide … |
| gff | None | The General Feature Format (GFF), a standard file format for describing genes… |
| graphql | None | The GraphQL format, a query language for APIs and a runtime for executing tho… |
| hdf5 | edam:3590 | The Hierarchical Data Format version 5 (HDF5) format, a file format and set o… |
| http | None | The Hypertext Transfer Protocol (HTTP) format |
| java | None | The Java source code format, which is a text file containing Java code |
| javascript | None | The JavaScript file format, which is a text file containing JavaScript code |
| json | edam:3464 | The JavaScript Object Notation (JSON) format, a lightweight data-interchange … |
| jsonld | edam:3749 | The JSON for Linked Data (JSON-LD) format, which extends JSON with semantics … |
| kgx | https://github.com/biolink/kgx/blob/master/specification/kgx-format.md | The KGX standard, which is a graph exchange format for knowledge graphs |
| kgx-json | https://github.com/biolink/kgx/blob/master/specification/kgx-format.md | The KGX standard, which is a graph exchange format for knowledge graphs |
| kgx-jsonl | https://github.com/biolink/kgx/blob/master/specification/kgx-format.md | The KGX standard, which is a graph exchange format for knowledge graphs |
| kgx-rdf | https://github.com/biolink/kgx/blob/master/specification/kgx-format.md | The KGX standard, which is a graph exchange format for knowledge graphs |
| mixed | None | A product that contains multiple formats or serializations |
| mysql | None | The MySQL relational database management system |
| neo4j | None | The Neo4j graph database management system |
| nquads | edam:3956 | The N-Quads format, an extension of the N-Triples format that adds an optiona… |
| ntriples | edam:3256 | The N-Triples format, a line-based, plain text serialization format for RDF g… |
| obo | edam:2196 | The Open Biomedical Ontologies (OBO) format, a file format for representing o… |
| owl | edam:2197 | The Web Ontology Language (OWL) format, a semantic web language designed to r… |
| None | The Portable Document Format (PDF), a file format developed by Adobe for pres… | |
| png | None | The Portable Network Graphics (PNG) format, a raster graphics file format tha… |
| postgres | None | The PostgreSQL relational database management system |
| protobuf | None | The Protocol Buffers (Protobuf) format, a language-neutral, platform-neutral,… |
| psi_mi_mitab | https://psicquic.github.io/MITAB28Format.html | The PSI-MI MITAB format, which is a tab-delimited format for representing mol… |
| psi_mi_xml | https://www.psidev.info/psi-mi-xml-specification | The PSI-MI XML format, which is a standard for representing molecular interac… |
| python | None | The Python script format, which is a text file containing Python code |
| rdfxml | edam:3261 | The RDF/XML format, an XML syntax for expressing RDF graphs as an XML documen… |
| sbgnml | https://sbgn.github.io/sbgn/ | The Systems Biology Graphical Notation (SBGN) XML format, which is a standard… |
| sbml | https://sbml.org/ | The Systems Biology Markup Language (SBML) XML format, which is a computer-re… |
| sdf | https://www.fda.gov/media/151718/download | The Structure Data File (SDF) format |
| shacl | None | The Shapes Constraint Language (SHACL) format, a language for validating RDF … |
| shex | None | The Shape Expressions (ShEx) format, a language for validating and describing… |
| sif | https://www.cytoscape.org/sif.html | The Simple Interaction Format (SIF), a simple text format for representing in… |
| sqlite | None | The SQLite relational database management system |
| sssom | https://mapping-commons.github.io/sssom/ | The Simple Standard for Sharing Ontological Mappings (SSSOM) format, which a … |
| stockholm | edam:1961 | The Stockholm format, a multiple sequence alignment format used in bioinforma… |
| svg | edam:3604 | The Scalable Vector Graphics (SVG) format, an XML-based format for describing… |
| trapi-jsonl | https://raw.githubusercontent.com/NCATSTranslator/ReasonerAPI/refs/heads/master/TranslatorReasonerAPI.yaml | The Translator Reasoner API (TRAPI) format, which is a JSON Lines format for … |
| tsv | edam:3475 | The Tab-Separated Values (TSV) format |
| ttl | edam:3255 | The Turtle (TTL) format, a textual syntax for RDF that allows RDF graphs to b… |
| txt | None | The Plain Text (TXT) format, a simple text format for representing unformatte… |
| vcf | edam:3016 | The Variant Call Format (VCF), a text file format for storing gene sequence v… |
| xgmml | edam:3618 | The eXtensible Graph Markup Language (XGMML) format, an XML-based format for … |
| xml | edam:2332 | The Extensible Markup Language (XML) format |
| yaml | edam:3750 | The YAML Ain’t Markup Language (YAML) format, a human-readable data serializa… |
Slots
| Name | Description |
|---|---|
| format | The format or serialization of the product |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/knowledge-graph-hub/kg_registry_schema
LinkML Source
```yaml
name: FormatEnum
description: The serialization/format of a product.
from_schema: https://w3id.org/knowledge-graph-hub/kg_registry_schema
rank: 1000
permissible_values:
biopax:
text: biopax
description: The BioPAX format, an RDF/OWL-based standard language for representing
biological pathways at the molecular and cellular level.
meaning: edam:3156
boolnet:
text: boolnet
description: The Boolean Network (BoolNet) format, which is a format for representing
Boolean networks. Used with the BoolNet package in R for modeling and analyzing
biological networks.
meaning: https://cran.r-project.org/package=BoolNet
chebi_sdf:
text: chebi_sdf
description: A ChEBI-specific SDF format. Unlike the general SDF format, Each
data item may be longer than 80 characters and has no maximum limit. Each line
after the Data Header is a separate data item. For example, each new line in
the synonyms is a separate synonym.
meaning: https://docs.google.com/document/d/11G6SmTtQRQYFT7l9h5K0faUHiAaekcLeOweMOOTIpME/edit?pli=1&tab=t.0#heading=h.7ocxce8u265h
csv:
text: csv
description: The Comma-Separated Values (CSV) format. It has rows of data separated
by newlines, and columns separated by commas.
meaning: edam:3752
doc:
text: doc
description: The Microsoft Word Document (DOC) format, a binary file format used
by Microsoft Word. It is commonly used for word processing documents.
docx:
text: docx
description: The Microsoft Word Open XML Document (DOCX) format, a modern file
format for Microsoft Word documents. It is a zipped, XML-based file format that
allows for more efficient storage and better compatibility with other software,
as compared to the older DOC format.
dot:
text: dot
description: The DOT format, a plain text graph description language used to define
the structure of graphs. It is often used with Graphviz to visualize graphs.
meaning: https://graphviz.org/doc/info/lang.html
fasta:
text: fasta
description: The FASTA format, a text-based format for representing nucleotide
or peptide sequences. It consists of a single header line followed by one or
more lines of sequence data.
meaning: edam:1929
gff:
text: gff
description: The General Feature Format (GFF), a standard file format for describing
genes and other features of DNA, RNA, and protein sequences. It is commonly
used in bioinformatics for storing and sharing genomic annotations.
graphql:
text: graphql
description: The GraphQL format, a query language for APIs and a runtime for executing
those queries against your data. It allows clients to request exactly what they
need and makes it easier to evolve APIs over time.
hdf5:
text: hdf5
description: The Hierarchical Data Format version 5 (HDF5) format, a file format
and set of tools for managing complex data. It is designed to store and organize
large amounts of data in a hierarchical structure, allowing for efficient access
and manipulation.
meaning: edam:3590
http:
text: http
description: The Hypertext Transfer Protocol (HTTP) format. This is a protocol
for transferring data over the web. If a product is in this format, it is likely
an web site or API.
java:
text: java
description: The Java source code format, which is a text file containing Java
code. It is used for writing scripts and programs in the Java language.
javascript:
text: javascript
description: The JavaScript file format, which is a text file containing JavaScript
code. It is used for writing scripts and programs in the JavaScript language.
json:
text: json
description: The JavaScript Object Notation (JSON) format, a lightweight data-interchange
format that's easy for humans to read and write and easy for machines to parse
and generate.
meaning: edam:3464
jsonld:
text: jsonld
description: The JSON for Linked Data (JSON-LD) format, which extends JSON with
semantics for linked data by providing a method of encoding linked data using
JSON. It enables data in JSON to be interpreted as RDF and allows JSON data
to be interoperable at Web-scale.
meaning: edam:3749
kgx:
text: kgx
description: The KGX standard, which is a graph exchange format for knowledge
graphs. By default, this assumes KGX as TSV with separate node and edge files,
usually named nodes.tsv and edges.tsv.
meaning: https://github.com/biolink/kgx/blob/master/specification/kgx-format.md
kgx-json:
text: kgx-json
description: The KGX standard, which is a graph exchange format for knowledge
graphs. This is the JSON format, with nodes and edges in a single file.
meaning: https://github.com/biolink/kgx/blob/master/specification/kgx-format.md
kgx-jsonl:
text: kgx-jsonl
description: The KGX standard, which is a graph exchange format for knowledge
graphs. This is the JSON Lines format, with separate node and edge files, usually
named nodes.jsonl and edges.jsonl.
meaning: https://github.com/biolink/kgx/blob/master/specification/kgx-format.md
kgx-rdf:
text: kgx-rdf
description: The KGX standard, which is a graph exchange format for knowledge
graphs. This is the RDF Turtle (TTL) format, with nodes and edges in a single
file.
meaning: https://github.com/biolink/kgx/blob/master/specification/kgx-format.md
mixed:
text: mixed
description: A product that contains multiple formats or serializations. This
is used when a product is not easily categorized into a single format, such
as a codebase that includes multiple file types (e.g., Python scripts, JSON
files, etc.).
mysql:
text: mysql
description: The MySQL relational database management system. If a product is
in this format, it is likely a MySQL database dump.
neo4j:
text: neo4j
description: The Neo4j graph database management system. If a product is in this
format, it is likely a Neo4j database dump. The file usually ends in .db, .dump,
or .db.dump.
nquads:
text: nquads
description: The N-Quads format, an extension of the N-Triples format that adds
an optional fourth element to represent the graph name or context. This allows
for representing multiple RDF graphs in a single document while maintaining
their separation.
meaning: edam:3956
ntriples:
text: ntriples
description: The N-Triples format, a line-based, plain text serialization format
for RDF graphs. Each line contains a single RDF triple consisting of subject,
predicate, and object, separated by whitespace and terminated by a period.
meaning: edam:3256
obo:
text: obo
description: The Open Biomedical Ontologies (OBO) format, a file format for representing
ontologies in the biomedical domain. It's designed to be simple and human-readable
while supporting the necessary expressivity for representing biological concepts.
meaning: edam:2196
owl:
text: owl
description: The Web Ontology Language (OWL) format, a semantic web language designed
to represent rich and complex knowledge about things and their relationships.
OWL builds on RDF and adds more vocabulary for describing properties and classes.
meaning: edam:2197
pdf:
text: pdf
description: The Portable Document Format (PDF), a file format developed by Adobe
for presenting documents in a manner independent of application software, hardware,
and operating systems. PDF files can contain text, images, and vector graphics.
png:
text: png
description: The Portable Network Graphics (PNG) format, a raster graphics file
format that supports lossless data compression. It is commonly used for web
images and supports transparency.
postgres:
text: postgres
description: The PostgreSQL relational database management system. If a product
is in this format, it is likely a PostgreSQL database dump.
protobuf:
text: protobuf
description: The Protocol Buffers (Protobuf) format, a language-neutral, platform-neutral,
extensible mechanism for serializing structured data. It's smaller, faster,
and simpler than XML, designed for high-performance data interchange.
psi_mi_mitab:
text: psi_mi_mitab
description: The PSI-MI MITAB format, which is a tab-delimited format for representing
molecular interaction data. It is used to exchange information about molecular
interactions between different databases.
meaning: https://psicquic.github.io/MITAB28Format.html
psi_mi_xml:
text: psi_mi_xml
description: The PSI-MI XML format, which is a standard for representing molecular
interaction data in XML. It is used to exchange information about molecular
interactions between different databases.
meaning: https://www.psidev.info/psi-mi-xml-specification
python:
text: python
description: The Python script format, which is a text file containing Python
code. It is used for writing scripts and programs in the Python language.
rdfxml:
text: rdfxml
description: The RDF/XML format, an XML syntax for expressing RDF graphs as an
XML document. It was the first standardized syntax for RDF and is widely used
for interchange and archiving.
meaning: edam:3261
sbgnml:
text: sbgnml
description: The Systems Biology Graphical Notation (SBGN) XML format, which is
a standard for representing biological pathways and processes in a graphical
form.
meaning: https://sbgn.github.io/sbgn/
sbml:
text: sbml
description: The Systems Biology Markup Language (SBML) XML format, which is a
computer-readable format for representing models of biological processes.
meaning: https://sbml.org/
sdf:
text: sdf
description: The Structure Data File (SDF) format.
meaning: https://www.fda.gov/media/151718/download
shacl:
text: shacl
description: The Shapes Constraint Language (SHACL) format, a language for validating
RDF graphs against a set of conditions. SHACL allows for defining constraints
on RDF graphs, including the structure, values, and other features of data.
shex:
text: shex
description: The Shape Expressions (ShEx) format, a language for validating and
describing RDF data. ShEx provides a concise, human-readable syntax for expressing
constraints on RDF graphs, including cardinality constraints and datatype restrictions.
sif:
text: sif
description: The Simple Interaction Format (SIF), a simple text format for representing
interactions between biological entities. It is often used to represent networks
of interactions.
meaning: https://www.cytoscape.org/sif.html
sqlite:
text: sqlite
description: The SQLite relational database management system. If a product is
in this format, it is likely a SQLite database dump.
sssom:
text: sssom
description: The Simple Standard for Sharing Ontological Mappings (SSSOM) format,
which a format for mapping between different ontologies and other identifier
systems.
meaning: https://mapping-commons.github.io/sssom/
stockholm:
text: stockholm
description: The Stockholm format, a multiple sequence alignment format used in
bioinformatics. It is commonly used for representing alignments of protein or
nucleotide sequences.
meaning: edam:1961
svg:
text: svg
description: The Scalable Vector Graphics (SVG) format, an XML-based format for
describing two-dimensional vector graphics.
meaning: edam:3604
trapi-jsonl:
text: trapi-jsonl
description: The Translator Reasoner API (TRAPI) format, which is a JSON Lines
format for TRAPI responses.
meaning: https://raw.githubusercontent.com/NCATSTranslator/ReasonerAPI/refs/heads/master/TranslatorReasonerAPI.yaml
tsv:
text: tsv
description: The Tab-Separated Values (TSV) format. It has rows of data separated
by newlines, and columns separated by tabs.
meaning: edam:3475
ttl:
text: ttl
description: The Turtle (TTL) format, a textual syntax for RDF that allows RDF
graphs to be written in a compact and natural text form. Turtle provides prefixes
and keywords that make RDF data more readable compared to XML or N-Triples formats.
meaning: edam:3255
txt:
text: txt
description: The Plain Text (TXT) format, a simple text format for representing
unformatted text data.
vcf:
text: vcf
description: The Variant Call Format (VCF), a text file format for storing gene
sequence variations. It is commonly used in bioinformatics to store gene sequence
variations, such as single nucleotide polymorphisms (SNPs).
meaning: edam:3016
xgmml:
text: xgmml
description: The eXtensible Graph Markup Language (XGMML) format, an XML-based
format for representing graphs and networks.
meaning: edam:3618
xml:
text: xml
description: The Extensible Markup Language (XML) format. It is a markup language
that defines a set of rules for encoding documents in a format that is both
human-readable and machine-readable.
meaning: edam:2332
yaml:
text: yaml
description: The YAML Ain't Markup Language (YAML) format, a human-readable data
serialization format. It is often used for configuration files and data exchange
between languages with different data structures.
meaning: edam:3750
```