ncbi / ncbi/datasets

Add publication info to assembly or BioProject fields.

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Description

Is your feature request related to a problem? Please describe.
I would like to be able to quickly determine what research article I should reference simply from looking at the output of datasets for a particular genome assembly or BioProject. This publication information is often on the NCBI website, but when I programmatically access the same accession/BioProject, there is no reference to the publication.

For example, on the BioProject page for the common carp, there is a paper to cite: Chang YS et al., "The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome.", J Mol Evol, 1994 Feb;38(2):138-55

However, when I query the same BioProject on the command line there is no publication information: datasets summary genome accession PRJNA682709

{"reports": [{"accession":"GCF_018340385.1","annotation_info":{"busco":{"busco_lineage":"actinopterygii_odb10","busco_ver":"4.1.4","complete":0.98571426,"duplicated":0.62445056,"fragmented":0.0054945056,"missing":0.008791209,"single_copy":0.36126372,"total_count":"3640"},"method":"Best-placed RefSeq; Gnomon","name":"NCBI Cyprinus carpio Annotation Release 101","pipeline":"NCBI eukaryotic genome annotation pipeline","provider":"NCBI RefSeq","release_date":"2021-07-20","report_url":"https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Cyprinus_carpio/101","software_version":"9.0","stats":{"gene_counts":{"non_coding":9553,"other":301,"protein_coding":43531,"pseudogene":6174,"total":59559}},"status":"Full annotation"},"assembly_info":{"assembly_level":"Chromosome","assembly_method":"wtdbg v. 2; quickmerge v. 1","assembly_name":"ASM1834038v1","assembly_status":"current","assembly_type":"haploid","bioproject_accession":"PRJNA682709","bioproject_lineage":[{"bioprojects":[{"accession":"PRJNA682709","title":"Cyprinus carpio isolate:SPL01 Genome sequencing and assembly"}]}],"biosample":{"accession":"SAMN17005855","attributes":[{"name":"isolate","value":"SPL01"},{"name":"dev_stage","value":"adult"},{"name":"sex","value":"not collected"},{"name":"tissue","value":"muscle"}],"bioprojects":[{"accession":"PRJNA682709"}],"description":{"organism":{"organism_name":"Cyprinus carpio","tax_id":7962},"title":"Model organism or animal sample from Cyprinus carpio"},"last_updated":"2021-05-13T06:39:37.300","models":["Model organism or animal"],"owner":{"contacts":[{}],"name":"Chinese Academy of Fishery Sciences"},"package":"Model.organism.animal.1.0","publication_date":"2021-05-13T06:39:37.300","sample_ids":[{"label":"Sample name","value":"Common_carp"}],"status":{"status":"live","when":"2021-05-13T06:39:37.300"},"submission_date":"2020-12-05T07:09:04.477"},"blast_url":"https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch\u0026PROG_DEF=blastn\u0026BLAST_SPEC=GDH_GCF_018340385.1","paired_assembly":{"accession":"GCA_018340385.1","only_genbank":"7 unlocalized scaffolds on chromosome MT","only_refseq":"chromosome MT","status":"current"},"refseq_category":"representative genome","release_date":"2021-05-12","sequencing_tech":"PacBio; Oxford Nanopore; Illumina HiSeq","submitter":"Chinese Academy of Fishery Sciences"},"assembly_stats":{"contig_l50":229,"contig_n50":1558716,"gc_count":"620441384","gc_percent":37,"genome_coverage":"184.8x","number_of_component_sequences":6700,"number_of_contigs":19837,"number_of_organelles":1,"number_of_scaffolds":6700,"scaffold_l50":24,"scaffold_n50":29545497,"total_number_of_chromosomes":50,"total_sequence_length":"1680118328","total_ungapped_length":"1672146419"},"current_accession":"GCF_018340385.1","organelle_info":[{"description":"Mitochondrion","submitter":"Chinese Academy of Fishery Sciences","total_seq_length":"16575"}],"organism":{"common_name":"common carp","infraspecific_names":{"isolate":"SPL01"},"organism_name":"Cyprinus carpio","tax_id":7962},"paired_accession":"GCA_018340385.1","source_database":"SOURCE_DATABASE_REFSEQ","wgs_info":{"master_wgs_url":"https://www.ncbi.nlm.nih.gov/nuccore/JAEOAB000000000.1","wgs_contigs_url":"https://www.ncbi.nlm.nih.gov/Traces/wgs/JAEOAB01","wgs_project_accession":"JAEOAB01"}},{"accession":"GCA_018340385.1","assembly_info":{"assembly_level":"Chromosome","assembly_method":"wtdbg v. 2; quickmerge v. 1","assembly_name":"ASM1834038v1","assembly_status":"current","assembly_type":"haploid","bioproject_accession":"PRJNA682709","bioproject_lineage":[{"bioprojects":[{"accession":"PRJNA682709","title":"Cyprinus carpio isolate:SPL01 Genome sequencing and assembly"}]}],"biosample":{"accession":"SAMN17005855","attributes":[{"name":"isolate","value":"SPL01"},{"name":"dev_stage","value":"adult"},{"name":"sex","value":"not collected"},{"name":"tissue","value":"muscle"}],"bioprojects":[{"accession":"PRJNA682709"}],"description":{"organism":{"organism_name":"Cyprinus carpio","tax_id":7962},"title":"Model organism or animal sample from Cyprinus carpio"},"last_updated":"2021-05-13T06:39:37.300","models":["Model organism or animal"],"owner":{"contacts":[{}],"name":"Chinese Academy of Fishery Sciences"},"package":"Model.organism.animal.1.0","publication_date":"2021-05-13T06:39:37.300","sample_ids":[{"label":"Sample name","value":"Common_carp"}],"status":{"status":"live","when":"2021-05-13T06:39:37.300"},"submission_date":"2020-12-05T07:09:04.477"},"blast_url":"https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch\u0026PROG_DEF=blastn\u0026BLAST_SPEC=GDH_GCA_018340385.1","paired_assembly":{"accession":"GCF_018340385.1","annotation_name":"NCBI Cyprinus carpio Annotation Release 101","only_genbank":"7 unlocalized scaffolds on chromosome MT","only_refseq":"chromosome MT","status":"current"},"release_date":"2021-05-12","sequencing_tech":"PacBio; Oxford Nanopore; Illumina HiSeq","submitter":"Chinese Academy of Fishery Sciences"},"assembly_stats":{"contig_l50":229,"contig_n50":1558716,"gc_count":"620441384","gc_percent":37,"genome_coverage":"184.8x","number_of_component_sequences":6700,"number_of_contigs":19837,"number_of_organelles":1,"number_of_scaffolds":6700,"scaffold_l50":24,"scaffold_n50":29545497,"total_number_of_chromosomes":50,"total_sequence_length":"1680118328","total_ungapped_length":"1672146419"},"current_accession":"GCA_018340385.1","organelle_info":[{"description":"Mitochondrion","submitter":"Chinese Academy of Fishery Sciences"}],"organism":{"common_name":"common carp","infraspecific_names":{"isolate":"SPL01"},"organism_name":"Cyprinus carpio","tax_id":7962},"paired_accession":"GCF_018340385.1","source_database":"SOURCE_DATABASE_GENBANK","wgs_info":{"master_wgs_url":"https://www.ncbi.nlm.nih.gov/nuccore/JAEOAB000000000.1","wgs_contigs_url":"https://www.ncbi.nlm.nih.gov/Traces/wgs/JAEOAB01","wgs_project_accession":"JAEOAB01"}}],"total_count": 2}

Describe the solution you'd like
It would be nice if there were a meaningful "publication" field that was the publication that should be cited when that data source is used!

Thank you-

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Open the contributing guide

First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by running datasets summary genome accession PRJNA682709 and compare its assembly and BioProject metadata with the linked NCBI BioProject page. Determine where publication references can be represented and exposed in the summary output; done means the command includes a meaningful publication field for applicable data sources.

Written by the indexing model from the issue text.

Assessment

Domain
cli, data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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