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synbio-schema

A schema for synthetic biology, inspired by IARPA FELIX

URI: https://example.com/synbio Name: synbio-schema

Classes

Class Description
Database A collection of instances from other classes
Modification A sequence that is different from some reference sequence
Organism A cellular life form or virus
Part Something that can serve as the input into or output from a genetic or genomi...
PartsSequence Data representing the nucleic acid composition of a Modification
Person
Placeholder
Plasmid A Part consisting of a single nucleic acid molecule that can be replicated wi...
Strain An population of organisms whose characteristics vary from the base organism ...

Slots

Slot Description
aa_change
abbreviation
associated_part found in this Modification
bio_safety_level
biosample_accessions An entry from NCBI's BioSample database
category
comment
creator
curated_enzyme_name corresponds to this enzyme, as determined by expert review
curated_gene_symbols corresponds to these genes, as determined by expert review
curated_protein_name corresponds to this protein, as determined by expert review
curated_uniprot_accession corresponds to this Uniprot entry, as determined by expert review
date_added date when this record was added to the Database
date_joined
descriptor
el_name_long
el_name_short
element
element_id
element_name
element_organism
email
examples
external_urls
first_name
funding_source
generation_date
genome_accessions An entry from NCBI's Genome database
genotype_phenotype
go_term_ids may be described by these annotations, as determined by a sequence similarity...
go_term_labels may be described by these annotations, as determined by a sequence similarity...
has_parts contains these genetic/genomic modifications
host_organism
id
intellectual_property
is_staff
is_superuser
keywords
last_name
license
match_ec_numbers corresponds to this enzyme, as determined by a sequence similarity search
match_gene_symbols_etc corresponds to this genes, as determined by a sequence similarity search
match_names similar to this sequence, as determined by a sequence similarity search
metamodel_version
modification_genes
modification_set Zero or more Modification instances
modification_taxon
modification_type
modifications_genes
name
notes
nt_sequence the nucleotide sequence of this entity
organism_basis
organism_set Zero or more Organism instances
other_accessions Especially fpbase identifiers
part_ofs appears in these genetic/genomic strains
permissible_values
person_set Zero or more Person instances
position
principal_investigator
references
scientific_names may originate in this organism, as determined by a sequence similarity search
selection_markers A genetic feature that encodes a trait used for artificial selection of a sub...
seq_name a name assigned to this entity by a person involved in teh modification proce...
seq_type
sequence_set Zero or more PartsSequence instances
size_bp
source_file
source_file_date
source_file_size
species_name
status
strain_agnostic_taxid
strain_set Zero or more Strain instances
strain_value
subcategory_size
summary
taxon_ids may originate in this organism, as determined by a sequence similarity search
uniprot_accessions similar to this sequence, as determined by a sequence similarity search
username

Enumerations

Enumeration Description
BioSafetyLevelEnum
CategoryEnum
DescriptorEnum
FundingSourceEnum
IntellectualPropertyEnum
ModificationTypeEnum
SeqTypeEnum
StatusEnum

Types

Type Description
xsd:boolean A binary (true or false) value
xsd:date a date (year, month and day) in an idealized calendar
linkml:DateOrDatetime Either a date or a datetime
xsd:dateTime The combination of a date and time
xsd:decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
xsd:double A real number that conforms to the xsd:double specification
xsd:float A real number that conforms to the xsd:float specification
xsd:integer An integer
xsd:string Prefix part of CURIE
shex:nonLiteral A URI, CURIE or BNODE that represents a node in a model
shex:iri A URI or CURIE that represents an object in the model
xsd:string A character string
xsd:dateTime A time object represents a (local) time of day, independent of any particular...
xsd:anyURI a complete URI
xsd:anyURI a URI or a CURIE

Subsets

Subset Description