diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 10 | ||||
| -rw-r--r-- | example/metadata.yaml | 43 | ||||
| -rw-r--r-- | example/minimal_example.yaml | 15 |
3 files changed, 35 insertions, 33 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index fc80080..c48ebce 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -13,7 +13,7 @@ $graph: type: record fields: host_species: - doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens) + 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 @@ -45,7 +45,7 @@ $graph: type: string? jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 host_treatment: - doc: Process in which the act is intended to modify or alter + doc: Process in which the act is intended to modify or alter host status type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000727 @@ -74,12 +74,12 @@ $graph: 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 + 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 specimen_source2: - doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ + doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155835 (=throat swabb) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 @@ -89,7 +89,7 @@ $graph: 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) + doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/GAZ_00000448 diff --git a/example/metadata.yaml b/example/metadata.yaml index bbd3e36..5e1be0a 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -6,35 +6,38 @@ host: host_sex: http://purl.obolibrary.org/obo/NCIT_C27993 host_age: 20 host_age_unit: http://purl.obolibrary.org/obo/UO_0000036 - host_health_status: string - host_treatment: string - additional_host_information: string + host_health_status: A condition or state at a particular time + host_treatment: Process in which the act is intended to modify or alter host status + host_vaccination: List of vaccines given to the host + additional_host_information: Field for additional host information sample: - sample_id: XXX - collector_name: XXX - collecting_institution: XXX - specimen_source: XXX - collection_date: 2020-01 - collection_location: http://purl.obolibrary.org/obo/GAZ_00002459 + sample_id: Id of the sample as defined by the submitter + collector_name: Name of the person that took the sample + collecting_institution: Institute that was responsible of sampeling + specimen_source: Method how specimen was derived + specimen_source2: Method how specimen was derived if two methods were used + collection_date: Date when the sample was taken + collection_location: http://www.wikidata.org/entity/Q148 sample_storage_conditions: XXX additional_collection_information: XXX virus: virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 - virus_strain: XX + virus_strain: SARS-CoV-2/human/CHN/HS_8/2020 technology: - sample_sequencing_technology: XX - sequence_assembly_method: XX + sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0009173 + sample_sequencing_technology2: http://www.ebi.ac.uk/efo/EFO_0009173 + sequence_assembly_method: Protocol used for assembly sequencing_coverage: 70 submitter: - submitter_name: tester - submitter_address: testerAdd - originating_lab: testLab - lab_address: labAdd - provider_sample_id: string - submitter_sample_id: string - authors: testAuthor - submitter_orcid: https://orcid.org/0000-0002-1825-0097 + submitter_name: John Doe + submitter_address: John Doe's adress + originating_lab: John Doe kitchen + lab_address: John Doe's adress + provider_sample_id: HmX + submitter_sample_id: xXx + authors: John Doe et all + submitter_orcid: https://orcid.org/0000-0000-0000-0000 diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index 0080c6d..f4118d1 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -1,21 +1,20 @@ id: placeholder host: - host_id: XX + host_id: XX1 host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 - host_sex: http://purl.obolibrary.org/obo/NCIT_C20197 sample: - sample_id: XXX - collector_name: XXX - collecting_institution: XXX + sample_id: XX + collector_name: John Doe + collecting_institution: Doe university virus: virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 technology: - sample_sequencing_technology: XX + sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632 submitter: - submitter_name: tester - originating_lab: testLab \ No newline at end of file + submitter_name: John Doe + originating_lab: John Doe's kitchen \ No newline at end of file |