ShareYourCloning_LinkML
A LinkML data model for ShareYourCloning
URI: https://w3id.org/genestorian/ShareYourCloning_LinkML
Name: ShareYourCloning_LinkML
Classes
| Class | Description |
|---|---|
| AssemblyJoin | Represents a joint between two fragments in an assembly |
| AssemblyJoinComponent | Represents a component of a join between two fragments in an assembly |
| CloningStrategy | Represents a cloning strategy |
| NamedThing | None |
| Sequence | Represents a sequence |
| Primer | An oligonucleotide or primer |
| TextFileSequence | A sequence (may have features) defined by the content of a text file |
| Source | Represents the source of a sequence |
| AssemblySource | Represents the source of a sequence that is an assembly of other sequences |
| GibsonAssemblySource | Represents the source of a sequence that is generated by Gibson assembly |
| HomologousRecombinationSource | Represents the source of a sequence that is generated by homologous recombination |
| CRISPRSource | Represents the source of a sequence that is generated by CRISPR |
| LigationSource | Represents the source of a sequence that is generated by ligation with sticky or blunt ends. |
| PCRSource | Represents the source of a sequence that is generated by PCR |
| RestrictionAndLigationSource | Represents the source of a sequence that is generated by restriction and ligation |
| GenomeCoordinatesSource | Represents the source of a sequence that is identified by genome coordinates, requested from NCBI |
| ManuallyTypedSource | Represents the source of a sequence that is manually typed by the user |
| OligoHybridizationSource | Represents the source of a sequence that is generated by oligo hybridization |
| PolymeraseExtensionSource | Represents the source of a sequence that is generated by polymerase extension |
| RepositoryIdSource | Represents the source of a sequence that is identified by a repository id |
| AddGeneIdSource | Represents the source of a sequence that is identified by an AddGene id |
| SequenceCutSource | Represents the source of a sequence that is a subfragment of another sequence, generated by sequence cutting. |
| RestrictionEnzymeDigestionSource | Represents the source of a sequence that is a subfragment of another sequence, generated by sequence cutting using restriction enzymes. |
| UploadedFileSource | Represents the source of a sequence that is uploaded as a file |
| SequenceCut | Represents a cut in a DNA sequence |
| RestrictionSequenceCut | Represents a cut in a DNA sequence that is made by a restriction enzyme |
| SimpleSequenceLocation | Represents a location within a sequence, for now support for ranges only |
Slots
| Slot | Description |
|---|---|
| addgene_sequence_type | |
| assembly | The joins between the fragments in the assembly |
| assembly_accession | The accession of the assembly |
| circular | Whether the sequence is circular or not |
| cut_watson | The position of the cut in the watson strand |
| description | A description of the cloning strategy |
| end | The ending coordinate (1-based) of the sequence in the sequence accession |
| file_content | |
| file_name | The name of the file |
| forward_oligo | The forward oligo used in the hybridization |
| forward_primer | The forward primer used in the PCR |
| gene_id | The gene id of the sequence |
| guides | The guide RNAs used in the CRISPR |
| id | A unique identifier for a thing |
| index_in_file | The index of the sequence in the file |
| input | The sequences that are an input to this source |
| left | |
| left_edge | |
| location | Location of the overlap in the fragment |
| locus_tag | The locus tag of the sequence |
| name | A human-readable name for a thing |
| output | Identifier of the sequence that is the output of this source |
| overhang | The length of the overhang that is left after the cut |
| overhang_crick_3prime | Taken from pydna's dseq::ovhgAn integer describing the length of the crick ... |
| overhang_watson_3prime | The equivalent of overhang_crick_3prime but for the watson strand |
| primers | The primers that are used in the cloning strategy |
| repository_id | The id of the sequence in the repository |
| repository_name | |
| restriction_enzyme | |
| restriction_enzymes | |
| reverse_complemented | Whether the sequence is reverse complemented in the join |
| reverse_oligo | The reverse oligo used in the hybridization |
| reverse_primer | The reverse primer used in the PCR |
| right | |
| right_edge | |
| sequence | |
| sequence_accession | The accession of the sequence |
| sequence_file_format | The format of a sequence file |
| sequence_file_url | The URL of a sequence file |
| sequences | The sequences that are used in the cloning strategy |
| sources | The sources of the sequences that are used in the cloning strategy |
| start | The starting coordinate (1-based) of the sequence in the sequence accession |
| strand | The strand of the sequence in the sequence accession, should be 1 or -1 |
| type | The type of the source |
| user_input |
Enumerations
| Enumeration | Description |
|---|---|
| AddGeneSequenceType | |
| RepositoryName | |
| SequenceFileFormat |
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|