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 --- example/maximum_metadata_example.yaml | 44 +++++++++++++++++++++++++++++++++++ example/metadata.yaml | 43 ---------------------------------- example/minimal_example.yaml | 18 -------------- example/minimal_metadata_example.yaml | 0 4 files changed, 44 insertions(+), 61 deletions(-) create mode 100644 example/maximum_metadata_example.yaml delete mode 100644 example/metadata.yaml delete mode 100644 example/minimal_example.yaml create mode 100644 example/minimal_metadata_example.yaml (limited to 'example') diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml new file mode 100644 index 0000000..0a6d910 --- /dev/null +++ b/example/maximum_metadata_example.yaml @@ -0,0 +1,44 @@ +id: placeholder + +host: + host_id: XX1 + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + host_sex: http://purl.obolibrary.org/obo/PATO_0000384 + host_age: 20 + host_age_unit: http://purl.obolibrary.org/obo/UO_0000036 + host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269 + host_treatment: Process in which the act is intended to modify or alter host status (Compounds) + host_vaccination: [vaccines1,vaccine2] + additional_host_information: Optional free text field for addtional information + +sample: + 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 sampling + specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835] + collection_date: "2020-01-01" + collection_location: http://www.wikidata.org/entity/Q148 + sample_storage_conditions: frozen specimen + source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence] + additional_collection_information: Optional free text field for addtional information + +virus: + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 + virus_strain: SARS-CoV-2/human/CHN/HS_8/2020 + +technology: + sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173] + sequence_assembly_method: Protocol used for assembly + sequencing_coverage: [70, 100] + additional_technology_information: Optional free text field for addtional information + +submitter: + submitter_name: [John Doe] + submitter_address: John Doe's adress + originating_lab: John Doe kitchen + lab_address: John Doe's address + provider_sample_id: XXX1 + submitter_sample_id: XXX2 + authors: [John Doe, Joe Boe, Jonny Oe] + submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] + additional_submitter_information: Optional free text field for addtional information \ No newline at end of file diff --git a/example/metadata.yaml b/example/metadata.yaml deleted file mode 100644 index a76616c..0000000 --- a/example/metadata.yaml +++ /dev/null @@ -1,43 +0,0 @@ -id: placeholder - -host: - host_id: XX1 - host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 - 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: http://purl.obolibrary.org/obo/NCIT_C25269 - host_treatment: Process in which the act is intended to modify or alter host status (Compounds) - host_vaccination: List of vaccines given to the host (RRIDs?) - additional_host_information: Field for additional host information - -sample: - 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 sampling - specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831 - specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835 - collection_date: "2020-01-01" - 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: SARS-CoV-2/human/CHN/HS_8/2020 - -technology: - 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: John Doe - submitter_address: John Doe's adress - originating_lab: John Doe kitchen - lab_address: John Doe's address - provider_sample_id: HmX - submitter_sample_id: xXx - authors: John Doe et all - submitter_orcid: https://orcid.org/0000-0000-0000-0000 \ No newline at end of file diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml deleted file mode 100644 index 0e36a25..0000000 --- a/example/minimal_example.yaml +++ /dev/null @@ -1,18 +0,0 @@ -id: placeholder - -host: - host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 - -sample: - sample_id: XX - collection_date: 2020-01 - collection_location: http://www.wikidata.org/entity/Q148 - -virus: - virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 - -technology: - sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632 - -submitter: - authors: John Doe \ No newline at end of file diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml new file mode 100644 index 0000000..e69de29 -- cgit v1.2.3