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authorPjotr Prins2020-04-12 12:46:34 -0500
committerPjotr Prins2020-04-12 12:46:34 -0500
commit4bd502172e7b064ef802b191339e170874d2e5e2 (patch)
treed7e4b572b48d063f8d794a399000b250e847fd35
parentfc872f15da426926414fb7629bf6660d9880ed1e (diff)
parent31686ba2e1b2edec29229ab5adb28b366893f17b (diff)
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Merge branch 'master' of github.com:arvados/bh20-seq-resource
-rw-r--r--bh20sequploader/bh20seq-schema.yml45
-rw-r--r--bh20sequploader/rdf-mappings.ttl0
-rw-r--r--example/metadata.yaml5
-rw-r--r--example/minimal_example.yaml6
4 files changed, 45 insertions, 11 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 8a22db1..81a7f22 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -13,41 +13,52 @@ $graph:
type: record
fields:
host_species:
+ ## autocomplete # NCBITAXON
+ doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens)
type: string
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000532
host_id:
+ doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
host_common_name:
+ doc: Text label for the host species (e.g. homo sapiens)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NOMEN_0000037
host_sex:
+ doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998))
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
host_age:
+ doc: Age of the host as number (e.g. 50)
type: int?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000011
host_age_unit:
+ doc: Unit of host age.... this field is unstable as of now (might be removed)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/UO_0000036
host_health_status:
+ doc: A condition or state at a particular time
type: string?
jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
host_treatment:
+ doc: Process in which the act is intended to modify or alter
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
host_vaccination:
+ doc: Field is unstable
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000001
additional_host_information:
+ doc: Field for additional host information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
@@ -56,38 +67,47 @@ $graph:
type: record
fields:
collector_name:
+ doc: Name of the person that took the sample
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001895
collecting_institution:
+ doc: Institute that was responsible of sampeling
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
specimen_source:
+ 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?
jsonldPredicate:
_id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
collection_location:
+ doc: Geographical location where the sample was collected as Gazetteer (https://www.ebi.ac.uk/ols/ontologies/gaz) reference, e.g. http://purl.obolibrary.org/obo/GAZ_00002845 (China)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/GAZ_00000448
sample_storage_conditions:
+ doc: Information aboout storage of a specified type, e.g. frozen specimen, paraffin, fresh ....
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001472
additional_collection_information:
+ doc: Add additional comment about the circumstances that a sample was taken
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
sample_id:
+ doc: Id of the sample as defined by the submitter
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
source_database_accession:
+ doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here
type: string?
jsonldPredicate:
_id: http://edamontology.org/data_2091
@@ -96,10 +116,12 @@ $graph:
type: record
fields:
virus_species:
+ doc: The name of a taxon from the NCBI taxonomy database
type: string?
jsonldPredicate:
_id: http://edamontology.org/data_1875
virus_strain:
+ doc: Name of the virus strain
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_010055
@@ -108,14 +130,17 @@ $graph:
type: record
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
sequence_assembly_method:
+ doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
type: string?
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: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
@@ -124,22 +149,22 @@ $graph:
type: record
fields:
submitter_name:
+ doc: Name of the submitter
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000116
- submitter_date:
- type: string
- jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/NCIT_C94162
submitter_address:
+ doc: Address of the submitter
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000172
originating_lab:
+ doc: Name of the laboratory that took the sample
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37984
lab_address:
+ doc: Address of the laboratory where the sample was taken
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0600047
@@ -152,10 +177,17 @@ $graph:
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0001741
authors:
+ doc: Name of the author(s)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42781
- submitter_id:
+ publication:
+ doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C19026
+ submitter_orchid:
+ doc: ORCHID of the submitter
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
@@ -171,7 +203,8 @@ $graph:
submitter: submitterSchema
id:
doc: The subject (eg the fasta/fastq file) that the metadata describes
- type: string?
+ type: string
jsonldPredicate:
_id: "@id"
_type: "@id"
+ noLinkCheck: true
diff --git a/bh20sequploader/rdf-mappings.ttl b/bh20sequploader/rdf-mappings.ttl
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/bh20sequploader/rdf-mappings.ttl
diff --git a/example/metadata.yaml b/example/metadata.yaml
index c780921..d9e8e92 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -1,3 +1,5 @@
+id: placeholder
+
host:
host_id: XX1
host_species: string
@@ -36,5 +38,4 @@ submitter:
provider_sample_id: string
submitter_sample_id: string
authors: testAuthor
- submitter_id: X12
- submitter_date: Subdate
+ submitter_orchid: X12
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
index f312ab7..160d1d4 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_example.yaml
@@ -1,8 +1,9 @@
-submission: publicSequenceResource
+id: placeholder
host:
host_id: XX
host_species: string
+ host_sex: string
sample:
sample_id: XXX
@@ -14,5 +15,4 @@ technology:
submitter:
submitter_name: tester
- originating_lab: testLab
- submitter_date: Subdate \ No newline at end of file
+ originating_lab: testLab \ No newline at end of file