OpenCloning_LinkML
A LinkML data model for OpenCloning
URI: https://opencloning.github.io/OpenCloning_LinkML
Name: OpenCloning_LinkML
Classes
| Class | Description |
|---|---|
| AnnotationReport | Represents a report of an annotation step |
| PlannotateAnnotationReport | Represents a report of an annotation step using Plannotate |
| AssemblyFragment | Represents a fragment in an assembly |
| AssociatedFile | Represents a file associated with a sequence |
| SequencingFile | Represents a sequencing file and its alignment to a sequence |
| CloningStrategy | Represents a cloning strategy |
| CollectionOption | Represents an option in a collection |
| CollectionOptionInfo | Additional information about a collection option |
| NamedThing | |
| Sequence | Represents a sequence |
| Primer | An oligonucleotide or primer |
| TemplateSequence | Represents a sequence that is part of a template, where the actual sequence c... |
| TextFileSequence | A sequence (may have features) defined by the content of a text file |
| Source | Represents the source of a sequence |
| AnnotationSource | Represents a computational step in which sequence features are annotated in a... |
| AssemblySource | Represents the source of a sequence that is an assembly of other sequences |
| CreLoxRecombinationSource | Represents the source of a sequence that is generated by Cre - Lox recombinat... |
| GatewaySource | Represents the source of a sequence that is generated by Gateway cloning |
| 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 recombina... |
| CRISPRSource | Represents the source of a sequence that is generated by CRISPR |
| InFusionSource | Represents the source of a sequence that is generated by In-Fusion cloning by... |
| InVivoAssemblySource | Represents the source of a sequence that is generated by in vivo assembly |
| LigationSource | Represents the source of a sequence that is generated by ligation with sticky... |
| OverlapExtensionPCRLigationSource | Represents the source of a sequence that is generated by ligation of PCR prod... |
| 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 liga... |
| CollectionSource | Represents a collection of possible sources in a template |
| DatabaseSource | Represents the source of a sequence that is identified by a database id |
| GenomeCoordinatesSource | Represents the source of a sequence that is identified by genome coordinates,... |
| 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 |
| BenchlingUrlSource | Represents the source of a sequence that is identified by a Benchling URL |
| EuroscarfSource | Represents the source of a sequence from the Euroscarf plasmid library |
| IGEMSource | Represents the source of a sequence from an iGEM collection |
| SEVASource | Represents the source of a sequence that is identified by a SEVA id |
| SnapGenePlasmidSource | Represents the source of a sequence from the SnapGene plasmid library identif... |
| WekWikGeneIdSource | Represents the source of a sequence that is identified by a WekWikGene id |
| ReverseComplementSource | Represents the in-silico transformation of a sequence into its reverse comple... |
| SequenceCutSource | Represents the source of a sequence that is a subfragment of another sequence... |
| RestrictionEnzymeDigestionSource | Represents the source of a sequence that is a subfragment of another sequence... |
| 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 |
Slots
| Slot | Description |
|---|---|
| add_primer_features | Whether to add primer features to the PCR product |
| addgene_sequence_type | |
| alignment | The alignment of the sequencing read to the sequence |
| annotation_report | |
| annotation_tool | |
| annotation_tool_version | The version of the annotation tool |
| assembly | A list of the fragments that are assembled, in order |
| assembly_accession | The accession of the assembly |
| backend_version | The version of the backend that was used to generate this cloning strategy |
| category_id | The identifier of the category of the part in the template |
| circular | Whether the sequence is circular or linear |
| circularize | Whether the sequence should be circularized (FASTA only) |
| coordinates | If provided, coordinates within the sequence of the file to extract a subsequ... |
| cut_watson | The position of the cut in the watson strand |
| database | |
| database_id | The id of an entity in a database |
| description | A description of the category |
| Description | |
| end | The ending coordinate (1-based) of the sequence in the sequence accession |
| end_location | |
| Feature | |
| file_content | |
| file_name | The name of the file |
| file_type | The type of file |
| files | Files associated with this cloning strategy |
| forward_oligo | The forward oligo used in the hybridization |
| fragment | |
| frontend_version | The version of the frontend that was used to generate this cloning strategy |
| full_length_of_feature_in_db | |
| gene_id | The gene id of the sequence |
| greedy | Whether to use a greedy consensus sequence for att sites (see https://github |
| guides | The guide RNAs used in the CRISPR |
| id | A unique identifier for a thing |
| image | URL and size of the image representing this category |
| index_in_file | The index of the sequence in the file |
| info | Additional information about this option |
| input | The sequences that are an input to this source |
| left_edge | |
| left_location | |
| length_of_found_feature | |
| locus_tag | The locus tag of the sequence |
| name | A human-readable name for a thing |
| options | The options available in this category |
| output | Identifier of the sequence that is the output of this source |
| output_name | Used to specify the name of the output sequence |
| 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 |
| percent_identity | |
| percent_match_length | |
| primer_design | Can be used to indicate the intended primer design for this sequence in the t... |
| primers | The primers that are used in the cloning strategy |
| reaction_type | |
| repository_id | The id of the sequence in the repository |
| repository_name | |
| resistance | The antibiotic resistance of the plasmid |
| restriction_enzyme | |
| restriction_enzymes | |
| reverse_complemented | Whether the sequence is reverse complemented in the assembly |
| reverse_oligo | The reverse oligo used in the hybridization |
| right_edge | |
| right_location | |
| schema_version | The version of the schema that was used to generate this cloning strategy |
| 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 |
| sequence_id | The sequence this file is associated with |
| sequences | The sequences that are used in the cloning strategy |
| source | The source of the sequence for this option |
| sources | The sources of the sequences that are used in the cloning strategy |
| sseqid | |
| start | The starting coordinate (1-based) of the sequence in the sequence accession |
| start_location | |
| strand | The strand of the sequence in the sequence accession, should be 1 or -1 |
| title | The title of the category |
| type | Designates the class |
| Type | |
| user_input | |
| well | The well position in the kit plate |
Enumerations
| Enumeration | Description |
|---|---|
| AddgeneSequenceType | |
| AnnotationTool | |
| AssociatedFileType | |
| Collection | |
| CollectionOptionType | |
| GatewayReactionType | |
| 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 |
| SequenceRange | A sequence range defined using genbank syntax (e |
| 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 |
| VersionNumber | A version number |
Subsets
| Subset | Description |
|---|---|