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-rw-r--r--bh20sequploader/bh20seq-schema.yml145
-rw-r--r--bh20sequploader/main.py2
2 files changed, 120 insertions, 27 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 5c962d1..cf9b015 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -3,6 +3,10 @@ $namespaces:
sch: https://schema.org/
efo: http://www.ebi.ac.uk/efo/
obo: http://purl.obolibrary.org/obo/
+ sio: http://semanticscience.org/resource/
+ edam: http://edamontology.org/
+ evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
+
$graph:
- name: hostSchema
@@ -12,37 +16,93 @@ $graph:
type: string
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000532
- host_id: string
- host_common_name: string?
- host_sex: string?
- host_age: int?
- host_age_unit: string?
- host_health_status: string?
+ host_id:
+ type: string
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000115
+ host_common_name:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NOMEN_0000037
+ host_sex:
+ type: string
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/PATO_0000047
+ host_age:
+ type: int?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/PATO_0000011
+ host_age_unit:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/UO_0000036
+ host_health_status:
+ type: string?
+ jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688
host_treatment:
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
- additional_host_information: string?
+ host_vaccination:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/VO_0000001
+ additional_host_information:
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001167
- name: sampleSchema
type: record
fields:
- collector_name: string
- collecting_institution: string
- specimen_source: string?
- collection_date: string?
+ collector_name:
+ type: string
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0001895
+ collecting_institution:
+ type: string
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001167
+ specimen_source:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0001479
+ collection_date:
+ type: string?
+ jsonldPredicate:
+ _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
collection_location:
type: string?
jsonldPredicate:
- _id: https://schema.org/fromLocation
- sample_storage_conditions: string?
- additional_collection_information: string?
+ _id: http://purl.obolibrary.org/obo/GAZ_00000448
+ sample_storage_conditions:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0001472
+ additional_collection_information:
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001167
+ sample_id:
+ type: string
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000115
+ source_database_accession:
+ type: string?
+ jsonldPredicate:
+ _id: http://edamontology.org/data_2091
- name: virusSchema
type: record
fields:
- virus_species: string?
- virus_strain: string?
+ virus_species:
+ type: string?
+ jsonldPredicate:
+ _id: http://edamontology.org/data_1875
+ virus_strain:
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_010055
- name: technologySchema
type: record
@@ -50,7 +110,7 @@ $graph:
sample_sequencing_technology:
type: string
jsonldPredicate:
- _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ _id: http://purl.obolibrary.org/obo/OBI_0600047
sequence_assembly_method:
type: string?
jsonldPredicate:
@@ -63,14 +123,42 @@ $graph:
- name: submitterSchema
type: record
fields:
- submitter_name: string
- submitter_address: string?
- originating_lab: string
- lab_address: string?
- provider_sample_id: string?
- submitter_sample_id: string?
- authors: string?
- submitter_id: string?
+ submitter_name:
+ 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:
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000172
+ originating_lab:
+ type: string
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C37984
+ lab_address:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0600047
+ provider_sample_id:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C37900
+ submitter_sample_id:
+ type: string?
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0001741
+ authors:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C42781
+ submitter_id:
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000115
- name: MainSchema
type: record
@@ -81,9 +169,14 @@ $graph:
virus: virusSchema?
technology: technologySchema
submitter: submitterSchema
+ submission:
+ type: string
+ jsonldPredicate:
+ _id: "@id"
+ #_type: "@id"
sequencefile:
doc: The subject (eg the fasta/fastq file) that this metadata describes
type: string?
jsonldPredicate:
_id: "@id"
- _type: "@id"
+ _type: "@id" \ No newline at end of file
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 1d5b9c3..bfb8c51 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -8,7 +8,7 @@ from pathlib import Path
import urllib.request
import socket
import getpass
-import qc_metadata
+from qc_metadata import qc_metadata
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'