diff --git a/27/BH2022_ISAJSON_ENA_mapping.tsv b/27/BH2022_ISAJSON_ENA_mapping.tsv deleted file mode 100644 index 694481e..0000000 --- a/27/BH2022_ISAJSON_ENA_mapping.tsv +++ /dev/null @@ -1,72 +0,0 @@ -ISA path ENA fields ENA XML OBJECT core or optional comments -studies/assays/dataFiles/name -studies/assays/dataFiles/type Raw Data File run bold = hard coded by ISA -studies/assays/dataFiles/comments Title run core greyed-out = TBD -studies/assays/dataFiles/comments filetype run core -studies/assays/dataFiles/comments checksum_method run core -studies/assays/dataFiles/comments checksum run core -studies/assays/dataFiles/comments submission tool run core -studies/assays/dataFiles/comments run attribute (tag, value) run optional -studies/assays/dataFiles/comments run attribute (tag, value) run optional -studies/assays/dataFiles/comments status run from ENA -studies/assays/dataFiles/comments accession run from ENA -studies/protocols/name nucleic acid sequencig -studies/protocols/protocolType nucleic acid sequencig -studies/protocols/parameters/parameterName Instrument model run/experiment -studies/protocols/parameters/parameterName Submission tool run/experiment - -studies/assays/materials/otherMaterials/name -studies/assays/materials/otherMaterials/type library name -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Title experiment -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Study ref (refname (= alias in STUDY)) experiment -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Design description experiment -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Sample descriptor (accession) experiment -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Instrument model experiment -studies/assays/materials/otherMaterials/characteristics/value/annotationValue Submission tool experiment optional -studies/assays/materials/otherMaterials/characteristics/value/annotationValue submission date experiment from ENA -studies/assays/materials/otherMaterials/characteristics/value/annotationValue status experiment from ENA -studies/assays/materials/otherMaterials/characteristics/value/annotationValue accession experiment from ENA -studies/protocols/name library construction -studies/protocols/protocolType library construction -studies/protocols/parameters/parameterName/annotationValue library_construction_protocol experiment -studies/protocols/parameters/parameterName/annotationValue design_description experiment -studies/protocols/parameters/parameterName/annotationValue Library source experiment -studies/protocols/parameters/parameterName/annotationValue Library strategy experiment -studies/protocols/parameters/parameterName/annotationValue Library selection experiment -studies/protocols/parameters/parameterName/annotationValue Library Layout experiment -studies/protocols/parameters/parameterName/annotationValue insert size experiment -studies/protocols/parameters/parameterName/annotationValue library platform experiment - -studies/assays/materials/otherMaterials/type extract name na -studies/protocols/name extraction na -studies/protocols/protocolType extraction na -studies/protocols/parameters/@id na -studies/protocols/parameters/parameterName/annotationValue na - -studies/materials/samples/name sample name -studies/materials/samples/characteristics/value biosamples checklists? sub-sample -studies/protocols/name sample collection -studies/protocols/protocolType sample collection -studies/protocols/parameters/parameterName/annotationValue - -studies/materials/sources/name source name sample -studies/materials/sources/characteristics/value/annotationValue sample checklists sample - -studies/identifier from ENA -studies/title Title study -studies/description Description/Abstract study -studies/submissionDate study -studies/publicReleaseDate release date study -studies/studyDesignDescriptors/annotationValue Study type - CV study optional - other decide if these attributes should be annotationValue or comments -studies/studyDesignDescriptors/comments Study (center name, alias) study from ENA -studies/studyDesignDescriptors/comments Center project name study from ENA -studies/studyDesignDescriptors/comments email adress study -studies/studyDesignDescriptors/comments submission tool study optional -studies/studyDesignDescriptors/comments alias study from ENA - -investigation/title title project core -investigation/description description project core -investigation/submissionDate project -investigation/publicReleaseDate project - alias project from ENA - submission_project project from ENA \ No newline at end of file diff --git a/27/ISASRAProject27/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java b/27/ISASRAProject27/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java index a5f1c5a..ed758f8 100644 --- a/27/ISASRAProject27/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java +++ b/27/ISASRAProject27/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java @@ -27,24 +27,20 @@ public Map createBioSamples(final List studies, final Str try { final Sample sourceBioSample = this.createSourceBioSample(studies, webinToken); - final Optional sourceBioSampleOrganism = - sourceBioSample.getAttributes().stream() - .map( - attribute -> { - if (attribute.getType().equalsIgnoreCase("organism")) { - return attribute; - } - - return null; - }) - .findFirst(); + Attribute sourceBioSampleOrganismAttribute = null; + for (final Attribute attribute : sourceBioSample.getAttributes()) { + if (attribute.getType().equalsIgnoreCase("organism")) { + sourceBioSampleOrganismAttribute = attribute; + } + } typeToBioSamplesAccessionMap.put("SOURCE", sourceBioSample.getAccession()); - if (sourceBioSampleOrganism.isPresent()) { + if (sourceBioSampleOrganismAttribute != null) { final AtomicInteger counter = new AtomicInteger(0); + final Attribute finalSourceBioSampleOrganismAttribute = sourceBioSampleOrganismAttribute; - studies.forEach( + studies.forEach( study -> { study .getAssays() @@ -59,7 +55,7 @@ public Map createBioSamples(final List studies, final Str this.createAndUpdateChildSampleWithRelationship( sample, sourceBioSample.getAccession(), - sourceBioSampleOrganism.get().getValue(), + finalSourceBioSampleOrganismAttribute.getValue(), webinToken); if (persistedChildSample != null) { @@ -172,7 +168,7 @@ private Sample updateSampleWithRelationshipsToBioSamples( biosamplesResponse = restTemplate.exchange( - "http://wwwdev.ebi.ac.uk/biosamples/samples/" + sampleWithRelationship.getAccession(), + "https://wwwdev.ebi.ac.uk/biosamples/samples/" + sampleWithRelationship.getAccession(), HttpMethod.PUT, entity, new ParameterizedTypeReference<>() {}); @@ -193,7 +189,7 @@ private EntityModel createSampleInBioSamples( biosamplesResponse = restTemplate.exchange( - "http://wwwdev.ebi.ac.uk/biosamples/samples/", + "https://wwwdev.ebi.ac.uk/biosamples/samples/", HttpMethod.POST, entity, new ParameterizedTypeReference<>() {}); diff --git a/27/README.md b/27/README.md deleted file mode 100644 index 72b0e3e..0000000 --- a/27/README.md +++ /dev/null @@ -1,58 +0,0 @@ -# Project 27: Streamlining data brokering from RDM platforms to ELIXIR Repositories - -## Working Document - -Please ensure you read the working document [here](https://github.com/elixir-europe/biohackathon-projects-2022/blob/main/27/working_doc.md) where you can find helpful links to additional material, information on test data files and the Biohackathon project agenda. - -## Abstract - -Mobilizing data from data infrastructures to data deposition databases is an integral service that research data management (RDM) platforms could offer. However, brokering the heterogeneous mixture of scientific data requires systems that are compatible with the diverse (meta)data models of the different RDM platforms, and diverse submission routes of different target repositories. - -The metadata management platform DataHub, an instance of the FAIRDOM-SEEK software, uses the well-established (Investigation Study Assay) framework to describe metadata. - -This BioHackathon project will specifically focus on designing and implementing data brokering systems from DataHub, to ELIXIR Deposition Databases, starting with the European Nucleotide Archive (ENA). During this project we will establish which existing tools can be reused, which need to be adapted or whether new tools need to be developed for data brokering from DataHub. - -We aim to make brokering tools more flexible, to support researchers and data stewards with metadata collection. We will also focus on increasing the sustainability and reducing the burden of maintenance of the tools, trying to limit dependencies on static reference files and hard coded variables. - -The design and the implementation of tools during this project aim to provide easy to maintain and flexible solutions for data brokering that can be further developed to be applied to other data repositories, and other national or institutional data management platforms. - -Finally, describing and implementing models for brokering data to ELIXIR Deposition Databases in this way, is one aim of ELIXIR-Converge (2020-2023), in Task 1.2. - -## Topics - -Data Platform -Interoperability Platform -Tools Platform - -**Project Number:** 27 - -### Lead(s) - -Flora D'Anna = flora.danna90@gmail.com, flora.danna@psb.vib-ugent.be -Zahra Waheed = zahra@ebi.ac.uk - -## Expected outcomes - -Expected outcomes for the week: - -Unblock content agnostic conversion of ISA-JSON to ISA-Tab. -Design and/or expand a tool to convert ISA-JSON to SRA xml schema with limited dependency on static configuration files and hard coded variables. -Design and/or implement a system for automatic update of configuration files needed to convert ISA-JSON to SRA xml schema, based on changes of the SRA schema. -Design and/or implement a method to submit metadata exported from DataHub (FAIRDOM-SEEK instance) in ISA-JSON format to ENA, including proof of concept for conversion of metadata exported from DataHub in ISA-JSON format to SRA xml schema. -Unblock ISA-Tab to SRA xml schema conversion using ISA tools or new solutions. - - -Long-term expected outcomes and timeframe in months: - -M3: Adoption into other tools exporting ISA-JSON/Tab. -M6: Adoption of the ISA/ENA converter into the toolchain used by different FAIRDOM SEEK instances. -M12: Extension to various other relevant target formats e.g. PRIDE-XML and PAGE-JSON -M18: Successful conversion of ISA-JSON/Tab to the appropriate ISA formatted files required by each repository (BioSamples, BioStudies, Metabolights, ArrayExpress and PRIDE). -M24: Successful end-to-end brokering from national and institutional data management platforms. - -## Expected audience - -Knowledge of: ISA model, ENA submission process, FAIRDOM-SEEK, coding skills- particularly Python, JSON and XML - -**Number of expected hacking days**: 4 - diff --git a/27/ena_xml/01_ena_WEBIN_XML.xml b/27/ena_xml/01_ena_WEBIN_XML.xml deleted file mode 100644 index a0f772a..0000000 --- a/27/ena_xml/01_ena_WEBIN_XML.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - - - - - - Test_Project - Test BioHackathon Project - Test BioHackathon Project - - - - - - - - - Test_Study - Test BioHackathon Study - Test BioHackathon Project - - - - - test_attribute - test_value - - - release_date - 2022-10-25 - - - - - - - Test_Run - - - - - - - - - test_attribute - test_value - - - - - - - Test_Experiment - - - Test - - - other - OTHER - RT-PCR - - - - - - - - MinION - - - - - test_attribute - test_value - - - - - diff --git a/27/ena_xml/02_ena_WEBIN_INVALID_FILE_TYPE_XML.xml b/27/ena_xml/02_ena_WEBIN_INVALID_FILE_TYPE_XML.xml deleted file mode 100644 index 3c00452..0000000 --- a/27/ena_xml/02_ena_WEBIN_INVALID_FILE_TYPE_XML.xml +++ /dev/null @@ -1,3347 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - biohackathon-projects-2022/02_ena_WEBIN_INVALID_FILE_TYPE_XML.xml at main · elixir-europe/biohackathon-projects-2022 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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<?xml version="1.0" encoding="UTF-8"?>
<WEBIN>
<SUBMISSION>
<ACTIONS>
<ACTION>
<ADD />
</ACTION>
</ACTIONS>
</SUBMISSION>
<PROJECT_SET>
<PROJECT center_name="EMBL-EBI" alias="project_1" accession="">
<NAME>Test_Project</NAME>
<TITLE>Test BioHackathon Project</TITLE>
<DESCRIPTION>Test BioHackathon Project</DESCRIPTION>
<SUBMISSION_PROJECT>
<SEQUENCING_PROJECT />
</SUBMISSION_PROJECT>
</PROJECT>
</PROJECT_SET>
<STUDY_SET>
<STUDY center_name="EMBL-EBI" alias="test-study-1">
<DESCRIPTOR>
<STUDY_TITLE>Test_Study</STUDY_TITLE>
<STUDY_DESCRIPTION>Test BioHackathon Study</STUDY_DESCRIPTION>
<STUDY_ABSTRACT>Test BioHackathon Project</STUDY_ABSTRACT>
<STUDY_TYPE existing_study_type="Other" />
</DESCRIPTOR>
<STUDY_ATTRIBUTES>
<STUDY_ATTRIBUTE>
<TAG>test_attribute</TAG>
<VALUE>test_value</VALUE>
</STUDY_ATTRIBUTE>
<STUDY_ATTRIBUTE>
<TAG>release_date</TAG>
<VALUE>2022-10-25</VALUE>
</STUDY_ATTRIBUTE>
</STUDY_ATTRIBUTES>
</STUDY>
</STUDY_SET>
<RUN_SET>
<RUN alias="run_experiment:1">
<TITLE>Test_Run</TITLE>
<EXPERIMENT_REF refname="run_experiment:1" />
<DATA_BLOCK>
<FILES>
<FILE filename="/complete_genomics" filetype="CompleteGenomics_native"/>
</FILES>
</DATA_BLOCK>
<RUN_ATTRIBUTES>
<RUN_ATTRIBUTE>
<TAG>test_attribute</TAG>
<VALUE>test_value</VALUE>
</RUN_ATTRIBUTE>
</RUN_ATTRIBUTES>
</RUN>
</RUN_SET>
<EXPERIMENT_SET>
<EXPERIMENT alias="run_experiment:1">
<TITLE>Test_Experiment</TITLE>
<STUDY_REF refname="test-study-1" />
<DESIGN>
<DESIGN_DESCRIPTION>Test</DESIGN_DESCRIPTION>
<SAMPLE_DESCRIPTOR accession="SAMEA9288569" />
<LIBRARY_DESCRIPTOR>
<LIBRARY_STRATEGY>other</LIBRARY_STRATEGY>
<LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
<LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
<LIBRARY_LAYOUT>
<SINGLE />
</LIBRARY_LAYOUT>
</LIBRARY_DESCRIPTOR>
</DESIGN>
<PLATFORM>
<OXFORD_NANOPORE>
<INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
</OXFORD_NANOPORE>
</PLATFORM>
<EXPERIMENT_ATTRIBUTES>
<EXPERIMENT_ATTRIBUTE>
<TAG>test_attribute</TAG>
<VALUE>test_value</VALUE>
</EXPERIMENT_ATTRIBUTE>
</EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>
</WEBIN>
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- biohackathon-projects-2022/27/03_ena_WEBIN_VALID_SIMPLE_TRANSCRIPTOME_STUDY_XML.xml -

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<?xml version="1.0" encoding="UTF-8"?>
<WEBIN>
<SUBMISSION>
<ACTIONS>
<ACTION>
<ADD />
</ACTION>
</ACTIONS>
</SUBMISSION>
<STUDY_SET>
<STUDY center_name="" alias="Test study 1" accession="">
<DESCRIPTOR>
<STUDY_TITLE>Whole transcriptome sequencing of human U937 cell line</STUDY_TITLE>
<STUDY_TYPE existing_study_type="Transcriptome Sequencing" />
<STUDY_ABSTRACT>RNA editing signature during myeloid leukemia cell differentiation.</STUDY_ABSTRACT>
<CENTER_PROJECT_NAME>Homo sapiens</CENTER_PROJECT_NAME>
</DESCRIPTOR>
</STUDY>
</STUDY_SET>
</WEBIN>
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- biohackathon-projects-2022/27/04_ena_WEBIN_ANALYSIS_XML.xml -

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<WEBIN>
<SUBMISSION>
<ACTIONS>
<ACTION>
<ADD/>
</ACTION>
</ACTIONS>
</SUBMISSION>
<STUDY_SET>
<STUDY center_name="" alias="Test study">
<DESCRIPTOR>
<STUDY_TITLE>Study title</STUDY_TITLE>
<STUDY_TYPE existing_study_type="Whole Genome Sequencing"/>
<STUDY_ABSTRACT></STUDY_ABSTRACT>
</DESCRIPTOR>
</STUDY>
</STUDY_SET>
<ANALYSIS_SET>
<ANALYSIS alias="graph_X_PGGB">
<TITLE>Pangenome assembly graph X - generated using PGGB pipeline</TITLE>
<DESCRIPTION>Pangenome assembly graph X was generated …. Etc. …</DESCRIPTION>
<STUDY_REF accession="ERP000004"/>
<SAMPLE_REF accession="ERS4591836"/>
<SAMPLE_REF accession="ERS4591837"/>
<SAMPLE_REF accession="ERS4591838"/>
<ANALYSIS_TYPE>
<ASSEMBLY_GRAPH>
<ASSEMBLY>
<STANDARD accession="GCA_012345.1"/>
</ASSEMBLY>
<ASSEMBLY>
<STANDARD accession="GCA_012346.1"/>
</ASSEMBLY>
<ASSEMBLY>
<STANDARD accession="GCA_012347.1"/>
</ASSEMBLY>
</ASSEMBLY_GRAPH>
</ANALYSIS_TYPE>
<FILES>
<FILE filename="assembly_graph.gfa.gz" filetype="gfa" checksum_method="MD5"
checksum="9f2976d079c10b111669b32590d1eb3e"/>
</FILES>
<ANALYSIS_ATTRIBUTES>
<ANALYSIS_ATTRIBUTE>
<TAG>pangenome name</TAG>
<VALUE>hprc-v1.0-mc-chm13-maxdel.10mb</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>file format version</TAG>
<VALUE>GFAv1.1</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>pipeline</TAG>
<VALUE>PGGB</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>resolution</TAG>
<VALUE>base level</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>number of nodes</TAG>
<VALUE>424643</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>number of components</TAG>
<VALUE>25</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>number of edges</TAG>
<VALUE>637628</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>length (bp)</TAG>
<VALUE>3239764787</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>total path length (bp)</TAG>
<VALUE>3239764787</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>reference assembly</TAG>
<VALUE>GRCh38</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>reference assembly</TAG>
<VALUE>ABCD123</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>reference assembly</TAG>
<VALUE>ABCD234</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>reference based</TAG>
<VALUE>true</VALUE>
</ANALYSIS_ATTRIBUTE>
</ANALYSIS_ATTRIBUTES>
</ANALYSIS>
</ANALYSIS_SET>
</WEBIN>
-
- - - -
- -
- - - - -
- - -
- - -
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- -
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-
- -
- - - - - - - - - - - - - - - - - - - - - - diff --git a/27/images/brokering_strategy.jpg b/27/images/brokering_strategy.jpg deleted file mode 100644 index f52a377..0000000 Binary files a/27/images/brokering_strategy.jpg and /dev/null differ diff --git a/27/images/coversion_tool.jpg b/27/images/coversion_tool.jpg deleted file mode 100644 index 87affb5..0000000 Binary files a/27/images/coversion_tool.jpg and /dev/null differ diff --git a/27/images/images_collection.md b/27/images/images_collection.md deleted file mode 100644 index 7741316..0000000 --- a/27/images/images_collection.md +++ /dev/null @@ -1 +0,0 @@ -Here we collect all images and pictures generated during BH2022. diff --git a/27/images/mapping_1.jpg b/27/images/mapping_1.jpg deleted file mode 100644 index b04efc7..0000000 Binary files a/27/images/mapping_1.jpg and /dev/null differ diff --git a/27/images/mapping_2.jpg b/27/images/mapping_2.jpg deleted file mode 100644 index 894ad7a..0000000 Binary files a/27/images/mapping_2.jpg and /dev/null differ diff --git a/27/images/pseudocode_1.jpg b/27/images/pseudocode_1.jpg deleted file mode 100644 index 456a6b2..0000000 Binary files a/27/images/pseudocode_1.jpg and /dev/null differ diff --git a/27/images/pseudocode_2.jpg b/27/images/pseudocode_2.jpg deleted file mode 100644 index cad949c..0000000 Binary files a/27/images/pseudocode_2.jpg and /dev/null differ diff --git a/27/images/pubsub.png b/27/images/pubsub.png deleted file mode 100644 index 877af31..0000000 Binary files a/27/images/pubsub.png and /dev/null differ diff --git a/27/seek_isajson/isa_seek-investigation20_p14.json b/27/seek_isajson/isa_seek-investigation20_p14.json deleted file mode 100644 index 8d845ae..0000000 --- a/27/seek_isajson/isa_seek-investigation20_p14.json +++ /dev/null @@ -1 +0,0 @@ -{"investigation":{"identifier":"","title":"Test_BioHackathon_Investigation","description":"A investigation used as a test in the biohackathon","submissionDate":"","publicReleaseDate":"","ontologySourceReferences":[],"filename":"Test_BioHackathon_Investigation.txt","comments":[{"name":"ISAjson export time","value":"2022-11-07T08:10:24Z"},{"name":"SEEK Project name","value":"ISA ENA export"},{"name":"SEEK Project ID","value":"http://localhost:3000/single_pages/14"},{"name":"SEEK Investigation ID","value":"20"}],"publications":[],"people":[{"@id":"#people/4","lastName":"Alice","firstName":"Alice","midInitials":"","email":"alice@testing.com","phone":"","fax":"","address":"","affiliation":"","roles":[{"termAccession":"","termSource":"","annotationValue":""}],"comments":[{"@id":"","value":"","name":""}]}],"studies":[{"identifier":"","title":"Test_study","description":"Test BioHackathon Study","submissionDate":"","publicReleaseDate":"","filename":"Test_study.txt","comments":[{"name":"SEEK Study ID","value":"11"},{"name":"SEEK creation date","value":"2022-11-06T08:20:40Z"}],"publications":[],"people":[{"@id":"#people/4","lastName":"Alice","firstName":"Alice","midInitials":"","email":"alice@testing.com","phone":"","fax":"","address":"","affiliation":"","roles":[{"termAccession":"","termSource":"","annotationValue":""}],"comments":[{"@id":"","value":"","name":""}]}],"studyDesignDescriptors":[],"characteristicCategories":[{"@id":"#characteristic_category/Title_371","characteristicType":{"annotationValue":"Title","termAccession":"","termSource":""}},{"@id":"#characteristic_category/Description_372","characteristicType":{"annotationValue":"Description","termAccession":"","termSource":""}},{"@id":"#characteristic_category/tax_id_373","characteristicType":{"annotationValue":"tax_id","termAccession":"","termSource":""}},{"@id":"#characteristic_category/organism_374","characteristicType":{"annotationValue":"organism","termAccession":"","termSource":""}},{"@id":"#characteristic_category/collection_date_375","characteristicType":{"annotationValue":"collection_date","termAccession":"","termSource":""}},{"@id":"#characteristic_category/collected_by_376","characteristicType":{"annotationValue":"collected_by","termAccession":"","termSource":""}},{"@id":"#characteristic_category/geographic_location_(country_and/or_sea)_377","characteristicType":{"annotationValue":"geographic location (country and/or sea)","termAccession":"","termSource":""}},{"@id":"#characteristic_category/geographic_location_(region_and_locality)_378","characteristicType":{"annotationValue":"geographic location (region and locality)","termAccession":"","termSource":""}},{"@id":"#characteristic_category/sex_379","characteristicType":{"annotationValue":"sex","termAccession":"","termSource":""}},{"@id":"#characteristic_category/host_scientific_name_380","characteristicType":{"annotationValue":"host scientific name","termAccession":"","termSource":""}},{"@id":"#characteristic_category/isolate_381","characteristicType":{"annotationValue":"isolate","termAccession":"","termSource":""}},{"@id":"#characteristic_category/cell_line_382","characteristicType":{"annotationValue":"cell_line","termAccession":"","termSource":""}},{"@id":"#characteristic_category/serovar_383","characteristicType":{"annotationValue":"serovar","termAccession":"","termSource":""}},{"@id":"#characteristic_category/submission_date_384","characteristicType":{"annotationValue":"submission date","termAccession":"","termSource":""}},{"@id":"#characteristic_category/status_385","characteristicType":{"annotationValue":"status","termAccession":"","termSource":""}},{"@id":"#characteristic_category/accession_386","characteristicType":{"annotationValue":"accession","termAccession":"","termSource":""}}],"materials":{"sources":[{"@id":"#source/335","name":"COG-UK/LSPA-3F5B2AE","characteristics":[{"category":{"@id":"#characteristic_category/Title_371"},"value":{"annotationValue":"COG-UK/LSPA-3F5B2AE","termSource":"","termAccession":""},"unit":{"termSource":"","termAccession":"","comments":[]}},{"category":{"@id":"#characteristic_category/Description_372"},"value":{"annotationValue":"Samples prepared at Rosalind Franklin Laboratory by Donald Fraser, Suki Lee, Rob Howes, The Rosalind Franklin Laboratory and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team","termSource":"","termAccession":""},"unit":{"termSource":"","termAccession":"","comments":[]}},{"category":{"@id":"#characteristic_category/tax_id_373"},"value":{"annotationValue":"2697049","termSource":"","termAccession":""},"unit":{"termSource":"","termAccession":"","comments":[]}},{"category":{"@id":"#characteristic_category/organism_374"},"value":{"annotationValue":"Severe acute respiratory syndrome coronavirus 2","termSource":"","termAccession":""},"unit":{"termSource":"","termAccession":"","comments":[]}},{"category":{"@id":"#characteristic_category/collection_date_375"},"value":{"annotationValue":"2022-08-10","termSource":"","termAccession":""},"unit":{"termSource":"","termAccession":"","comments":[]}},{"category":{"@id":"#characteristic_category/collected_by_376"},"value":{"annotationValue":"Rosalind Franklin 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project. - -Please, follow the link and read carefully the material to acquire the necessary knowledge before the starting of the project. If you cannot access the document, do not hesitate to ask for access. - -## Graphical abstract - -![GA](https://user-images.githubusercontent.com/51486716/197958551-0da43bec-5980-45bb-a1b6-f41d2a62ef3e.png) - - - -## Introduction to the project - -![intro](https://user-images.githubusercontent.com/51486716/198538978-429d3640-10ad-4230-a769-f1b5ddf5dff1.png)