turns-00031.parquet:46815
4ebdffce5a12030989a4f7ed
turn 1/1gpt-4o-2024-08-06EnglishUnited States455 words
degenerate_repetitionAbsentFinal dense release
USER
the following content is metadata for a bacteria genome sequencing data in json format, you need to extract information below from it and output the result in the following format:
<output>
accession number: xxx->species name: xxxx->strain name: xxxx->isolate or collection date in yyyy-mm-dd: xxxx format->geographic information of islateion: xxxx->host name: xxxx->mlst type: xxxx->serotype: xxxx->vaccine: yes|no
<output/>
where xxxx is corresponding information in 2nd row. xxxx is corresponding information. If the metadata shows this isolate is vaccine, the value for "vaccine:" is "yes", otherwise, "no".
Don't add any comments or explaining to output. If the appropriate information is not available, use "N/A" substitution; if the date has month or day, just print available information; if geographic information of islateion not avaiable, you can try to guess from submitter
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{'accession': 'GCA_029074185.1', 'annotation_info': {'method': 'Best-placed reference protein set; GeneMarkS-2+', 'name': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'pipeline': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'provider': 'NCBI', 'release_date': '2023-02-10', 'software_version': '6.4', 'stats': {'gene_counts': {'non_coding': 64, 'protein_coding': 1729, 'pseudogene': 5, 'total': 1798}}}, 'assembly_info': {'assembly_level': 'Contig', 'assembly_method': 'SPAdes v. 3.11.1', 'assembly_name': 'ASM2907418v1', 'assembly_status': 'current', 'assembly_type': 'haploid', 'bioproject_accession': 'PRJNA909344', 'bioproject_lineage': [{'bioprojects': [{'accession': 'PRJNA909344', 'title': 'Population Structure and Genomic Characteristics of Australian Erysipelothrix rhusiopathiae'}]}], 'biosample': {'accession': 'SAMN32081879', 'attributes': [{'name': 'strain', 'value': 'EMAI_66'}, {'name': 'host', 'value': 'pig'}, {'name': 'collection_date', 'value': '1997-09-05'}, {'name': 'geo_loc_name', 'value': 'Australia'}, {'name': 'sample_type', 'value': 'Cell Culture'}, {'name': 'genotype', 'value': 'MLST:78'}], 'bioprojects': [{'accession': 'PRJNA909344'}], 'description': {'organism': {'organism_name': 'Erysipelothrix rhusiopathiae', 'tax_id': 1648}, 'title': 'Microbe sample from Erysipelothrix rhusiopathiae'}, 'last_updated': '2023-03-20T22:59:48.337', 'models': ['Microbe, viral or environmental'], 'owner': {'contacts': [{}], 'name': 'Deparment of Primary Industries NSW'}, 'package': 'Microbe.1.0', 'publication_date': '2023-03-09T12:39:58.440', 'sample_ids': [{'label': 'Sample name', 'value': 'erysip_66'}, {'db': 'SRA', 'value': 'SRS17098829'}], 'status': {'status': 'live', 'when': '2023-03-09T12:39:58.440'}, 'submission_date': '2022-12-06T20:42:04.697'}, 'comments': 'The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/', 'genome_notes': ['from large multi-isolate project'], 'paired_assembly': {'accession': 'GCF_029074185.1', 'annotation_name': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'status': 'suppressed'}, 'release_date': '2023-03-09', 'sequencing_tech': 'Illumina MiSeq', 'submitter': 'Deparment of Primary Industries NSW'}, 'assembly_stats': {'contig_l50': 7, 'contig_n50': 109138, 'gc_count': '660343', 'gc_percent': 36, 'genome_coverage': '30.5x', 'number_of_component_sequences': 58, 'number_of_contigs': 58, 'total_sequence_length': '1823029', 'total_ungapped_length': '1823029'}, 'average_nucleotide_identity': {'best_ani_match': {'ani': 98.96, 'assembly': 'GCA_000160815.2', 'assembly_coverage': 90.64, 'category': 'type', 'organism_name': 'Erysipelothrix rhusiopathiae', 'type_assembly_coverage': 94.61}, 'category': 'category_na', 'comment': 'na', 'match_status': 'species_match', 'submitted_ani_match': {'ani': 98.96, 'assembly': 'GCA_000160815.2', 'assembly_coverage': 90.64, 'category': 'type', 'organism_name': 'Erysipelothrix rhusiopathiae ATCC 19414', 'type_assembly_coverage': 94.61}, 'submitted_organism': 'Erysipelothrix rhusiopathiae', 'submitted_species': 'Erysipelothrix rhusiopathiae', 'taxonomy_check_status': 'OK'}, 'checkm_info': {'checkm_marker_set': 'Erysipelothrix', 'checkm_marker_set_rank': 'genus', 'checkm_species_tax_id': 1648, 'checkm_version': 'v1.2.2', 'completeness': 92.55, 'completeness_percentile': 28.054298, 'contamination': 1.9}, 'current_accession': 'GCA_029074185.1', 'organism': {'infraspecific_names': {'strain': 'EMAI_66'}, 'organism_name': 'Erysipelothrix rhusiopathiae', 'tax_id': 1648}, 'paired_accession': 'GCF_029074185.1', 'source_database': 'SOURCE_DATABASE_GENBANK', 'wgs_info': {'master_wgs_url': 'https://www.ncbi.nlm.nih.gov/nuccore/JAQTDH000000000.1', 'wgs_contigs_url': 'https://www.ncbi.nlm.nih.gov/Traces/wgs/JAQTDH01', 'wgs_project_accession': 'JAQTDH01'}}ASSISTANT
<output> accession number: GCA_029074185.1->species name: Erysipelothrix rhusiopathiae->strain name: EMAI_66->isolate or collection date in yyyy-mm-dd: 1997-09-05 format->geographic information of islateion: Australia->host name: pig->mlst type: 78->serotype: N/A->vaccine: no <output/>