diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 22 | ||||
| -rw-r--r-- | bh20sequploader/supporting_webuploader.yml | 28 |
2 files changed, 49 insertions, 1 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index d8641a6..7ffc15b 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -84,6 +84,11 @@ $graph: type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 + specimen_source2: + doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001479 collection_date: doc: Date when the sample was taken type: string? @@ -139,6 +144,11 @@ $graph: type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 + 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 sequence_assembly_method: doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome type: string? @@ -146,9 +156,19 @@ $graph: _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: int? + type: float? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/FLU_0000848 + sequencing_coverage2: + doc: If a second sequence technology was use you can submit its coverage here + type: float? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 + additional_technology_information: + doc: Field for additional technology information + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 - name: submitterSchema type: record diff --git a/bh20sequploader/supporting_webuploader.yml b/bh20sequploader/supporting_webuploader.yml index 6b8946f..3650526 100644 --- a/bh20sequploader/supporting_webuploader.yml +++ b/bh20sequploader/supporting_webuploader.yml @@ -10,6 +10,34 @@ host_sex: Female: http://purl.obolibrary.org/obo/NCIT_C27993 unknown: http://purl.obolibrary.org/obo/NCIT_C17998 +sample_sequencing_technology: + Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 + Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 + Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 + IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 + 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 + Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 + Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 + IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 + 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 + host_species: OLS-ontology: ncbitaxon |