diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-options.yml | 30 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 52 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 11 |
3 files changed, 20 insertions, 73 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index 104ed6c..c553f41 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -35,38 +35,8 @@ sample_sequencing_technology: Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 -sample_sequencing_technology2: - Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 - Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566 - Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567 - Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 - Illumina: http://purl.obolibrary.org/obo/OBI_0000759 - IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 - Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894 - Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 - Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 - Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 - -sample_sequencing_technology3: - Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 - Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566 - Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567 - Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 - Illumina: http://purl.obolibrary.org/obo/OBI_0000759 - IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 - Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894 - Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 - Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 - Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 - specimen_source: nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 sputum: http://purl.obolibrary.org/obo/NCIT_C13278 bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 - -specimen_source2: - nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 - oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 - sputum: http://purl.obolibrary.org/obo/NCIT_C13278 - bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index ea813a0..f36a6e6 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -48,6 +48,7 @@ $graph: type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C25688 + _type: "@id" host_treatment: doc: Process in which the act is intended to modify or alter host status type: string? @@ -55,7 +56,7 @@ $graph: _id: http://www.ebi.ac.uk/efo/EFO_0000727 host_vaccination: doc: List of vaccines given to the host - type: string? + type: string[]? jsonldPredicate: _id: http://purl.obolibrary.org/obo/VO_0000002 additional_host_information: @@ -96,14 +97,7 @@ $graph: _id: http://purl.obolibrary.org/obo/NCIT_C41206 specimen_source: doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab) - type: string? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/OBI_0001479 - _type: "@id" - noLinkCheck: true - specimen_source2: - doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155835 (=throat swabb) - type: string? + type: string[]? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 _type: "@id" @@ -119,10 +113,11 @@ $graph: jsonldPredicate: _id: http://semanticscience.org/resource/SIO_001167 source_database_accession: - doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here - type: string? + doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here. Please use a resolveable URL (e.g. http://identifiers.org/insdc/LC522350.1#sequence) + type: string[]? jsonldPredicate: _id: http://edamontology.org/data_2091 + _type: "@id" - name: virusSchema type: record @@ -145,21 +140,7 @@ $graph: fields: sample_sequencing_technology: doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) - type: string? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/OBI_0600047 - _type: "@id" - noLinkCheck: true - sample_sequencing_technology2: - doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) - type: string? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/OBI_0600047 - _type: "@id" - noLinkCheck: true - sample_sequencing_technology3: - doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) - type: string? + type: string[]? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 _type: "@id" @@ -170,13 +151,8 @@ $graph: jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0002699 sequencing_coverage: - doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x) - type: float? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/FLU_0000848 - sequencing_coverage2: - doc: If a second sequence technology was used you can submit its coverage here - type: float? + doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20] + type: int[]? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 additional_technology_information: @@ -189,13 +165,13 @@ $graph: type: record fields: authors: - doc: Name of the author(s) - type: string + doc: Name(s) of the author(s) + type: string[] jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C42781 submitter_name: - doc: Name of the submitter - type: string? + doc: Name of the submitter(s) + type: string[]? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000116 submitter_address: @@ -228,7 +204,7 @@ $graph: _id: http://purl.obolibrary.org/obo/NCIT_C19026 submitter_orcid: doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097 - type: string? + type: string[]? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 _type: "@id" diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index c3b0ae1..4ec957d 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -25,7 +25,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> obo:NCIT_C42574 [ obo:UO_~ ] ?; obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ; efo:EFO_0000727 xsd:string ?; - obo:VO_0000002 xsd:string ?; + obo:VO_0000002 xsd:string {0,10}; sio:SIO_001167 xsd:string ?; } @@ -38,25 +38,26 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> obo:OBI_0001479 IRI {0,2}; obo:OBI_0001472 xsd:string ?; sio:SIO_001167 xsd:string ?; + edam:data_2091 IRI {0,3}; } :submitterShape { - obo:NCIT_C42781 xsd:string ; - sio:SIO_000116 xsd:string ?; + obo:NCIT_C42781 xsd:string * ; + sio:SIO_000116 xsd:string *; sio:SIO_000172 xsd:string ?; obo:NCIT_C37984 xsd:string ?; obo:OBI_0600047 xsd:string ?; obo:NCIT_C37900 xsd:string ?; efo:EFO_0001741 xsd:string ?; obo:NCIT_C19026 xsd:string ?; - sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?; + sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10}; sio:SIO_001167 xsd:string ?; } :technologyShape { obo:OBI_0600047 IRI {0,3} ; efo:EFO_0002699 xsd:string ?; - obo:FLU_0000848 xsd:double {0,2}; + obo:FLU_0000848 xsd:integer {0,2}; sio:SIO_001167 xsd:string ?; } |