From 6032a373003affa641ca1e70a44c29a232b5b3ed Mon Sep 17 00:00:00 2001
From: lltommy
Date: Tue, 28 Apr 2020 20:31:42 +0200
Subject: Changes to the structure - we use lists now instead of strings where
it makes sense. This allows us to have multiple values where in makes sense
---
bh20sequploader/bh20seq-options.yml | 30 ---------------------
bh20sequploader/bh20seq-schema.yml | 52 ++++++++++---------------------------
bh20sequploader/bh20seq-shex.rdf | 11 ++++----
3 files changed, 20 insertions(+), 73 deletions(-)
(limited to 'bh20sequploader')
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:
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:
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 ?;
}
--
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