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diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index fb68251..d0d6c7f 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -7,10 +7,19 @@ #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> #+OPTIONS: ^:nil +* Introduction + +In this document we explain how to upload data into COVID-19 PubSeq. +This can happen through a web page, or through a command line +script. We'll also show how to parametrize uploads by using templates. +The procedure is much easier than with other repositories and can be +fully automated. Once uploaded you can use our export API to prepare +for other repositories. * Table of Contents :TOC:noexport: - - [[#uploading-data][Uploading Data]] + - [[#introduction][Introduction]] + - [[#uploading-data][Uploading data]] - [[#step-1-upload-sequence][Step 1: Upload sequence]] - [[#step-2-add-metadata][Step 2: Add metadata]] - [[#obligatory-fields][Obligatory fields]] @@ -23,7 +32,7 @@ - [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]] - [[#example-preparing-metadata][Example: preparing metadata]] -* Uploading Data +* Uploading data The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a public resource for global comparisons. A recompute of the pangenome @@ -165,55 +174,91 @@ file an associated metadata in [[https://github.com/arvados/bh20-seq-resource/bl the web form and gets validated from the same [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]] looks. The YAML that you need to create/generate for your samples looks like +A minimal example of metadata looks like + +#+begin_src json + id: placeholder + + license: + license_type: http://creativecommons.org/licenses/by/4.0/ + + host: + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + + sample: + sample_id: XX + collection_date: "2020-01-01" + 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] +#+end_src + +a more elaborate example (note most fields are optional) may look like + #+begin_src json -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] - ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010 - additional_host_information: Optional free text field for additional 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 additional 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: [70.0, 100.0] - additional_technology_information: Optional free text field for additional information - -submitter: - authors: [John Doe, Joe Boe, Jonny Oe] - submitter_name: [John Doe] - submitter_address: John Doe's address - originating_lab: John Doe kitchen - lab_address: John Doe's address - provider_sample_id: XXX1 - submitter_sample_id: XXX2 - publication: PMID00001113 - submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] - additional_submitter_information: Optional free text field for additional information + 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] + ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010 + additional_host_information: Optional free text field for additional 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 additional 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: [70.0, 100.0] + additional_technology_information: Optional free text field for additional information + + submitter: + authors: [John Doe, Joe Boe, Jonny Oe] + submitter_name: [John Doe] + submitter_address: John Doe's address + originating_lab: John Doe kitchen + lab_address: John Doe's address + provider_sample_id: XXX1 + submitter_sample_id: XXX2 + publication: PMID00001113 + submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] + additional_submitter_information: Optional free text field for additional information #+end_src +more metadata is yummy when stored in RDF. [[https://yummydata.org/][Yummydata]] is useful to a wider community. Note +that many of the terms in above example are URIs, such as +host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606. We use +web ontologies for these to make the data less ambiguous and more +FAIR. Check out the option fields as defined in the schema. If it is not listed, +check the [[https://github.com/arvados/bh20-seq-resource/blob/master/semantic_enrichment/labels.ttl][labels.ttl]] file. Also, +a little bit of web searching may be required or [[./contact][contact]] us. + ** Run the uploader (CLI) Installing with pip you should be @@ -221,7 +266,6 @@ able to run : bh20sequploader sequence.fasta metadata.yaml - Alternatively the script can be installed from [[https://github.com/arvados/bh20-seq-resource#installation][github]]. Run on the command line @@ -274,13 +318,23 @@ done ** Example: preparing metadata -Usually, metadata are available in tabular format, like spreadsheets. As an example, we provide a script -[[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to show you how to parse -your metadata in YAML files ready for the upload. To execute the script, go in the ~bh20-seq-resource/scripts/esr_samples -and execute +Usually, metadata are available in a tabular format, such as +spreadsheets. As an example, we provide a script [[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to +show you how to parse your metadata in YAML files ready for the +upload. To execute the script, go in the +~bh20-seq-resource/scripts/esr_samples and execute #+BEGIN_SRC sh python3 esr_samples.py #+END_SRC -You will find the YAML files in the `yaml` folder which will be created in the same directory. +You will find the YAML files in the `yaml` folder which will be +created in the same directory. + +In the example we use Python pandas to read the spreadsheet into a +tabular structure. Next we use a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/template.yaml][template.yaml]] file that gets filled +in by ~esr_samples.py~ so we get a metadata YAML file for each sample. + +Next run the earlier CLI uploader for each YAML and FASTA combination. +It can't be much easier than this. For ESR we uploaded a batch of 600 +sequences this way writing a few lines of Python [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/esr_samples.py][code]]. See [[http://covid19.genenetwork.org/resource/20VR0995][example]]. |