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authorlltommy2020-04-18 19:11:57 +0200
committerlltommy2020-04-18 19:11:57 +0200
commitbbca5ac9b2538e410efe3e09651f87e5573145de (patch)
tree0f120edbc392a72c0d6a3797f0a1c0dd7370293a
parent7cf44a7aed6dd190e16ac94958aefcf7bffed6a0 (diff)
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Extending yaml schema a bit and adding additional information for the UI
-rw-r--r--bh20sequploader/bh20seq-schema.yml22
-rw-r--r--bh20sequploader/supporting_webuploader.yml28
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