Linking metadata in non-Pubmed Commons indexed journal articles to records housed by NCBI
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8 weeks ago
LauferVA 4.2k

Suppose one is interested in a manuscript, and the RNA-Seq data it provides. So, she/he goes to BioProject, and picks up all the samples and metadata from SRA.

Suppose in addition, one downloads the sample metadata as a part of (example) Supplemental Table S4 from the manuscript itself, then compares that to metadata housed in the correspondent Entrez DB records for those samples, with a view to making one merged metadata table that now lists the study metadata from both the Supplmental Table and the NCBI databases together in one merged record.

My question is, do you know how, or have you every heard of attempts to, do this on a large scale? Some of the pubs will be on PMC. Others may be in journals to which one has a subscription through her/his org.

Do you know of attempts to automate or substantially automate the supplmentation of NCBI records using journal tables / metadata, or PMC info, or another way I am not thinking about?

Perhaps string matching of some kind could work?

Any all ideas would be useful... thank you!

NCBI Entrez SRA Journal Metadata • 388 views
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Ingenuity Pathway Analysis (Qiagen) has probably done this already with datasets they curate in the tool called "Analysis Match". Not a free option but in case you already have access to IPA then this should cover a large portion of human data (which I assume your primary interest will be).

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thanks - i would need to obtain all of it, which i dont think they would sell me. i located some promising angles in the mean time, including a GPT that will mine PDFs as well as links and attachments.

i wont tackle this in earnest for a couple weeks or months, but i will update or post as tutorial when i do.

VAL

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8 weeks ago

I have tried to do this for my course, and every single time I found that matching metadata to SRR numbers was incredibly convoluted,

lacked any kind of support for automated processing, sometimes you guess from file decoding weird acronyms,

to see all the metadata, and the mindboggling redundancy and lack of modeling that is out there do a

pip install bio

then

bio search SRR14575325 --all

then watch and weep as you see the enormous number of useful and useless fields, non of which are properly filled in

[
    {
        "age": "",
        "aligned": "",
        "altitude": "",
        "assembly_quality": "",
        "assembly_software": "",
        "bam_aspera": "",
        "bam_bytes": "",
        "bam_ftp": "",
        "bam_galaxy": "",
        "bam_md5": "",
        "base_count": "971964750",
        "binning_software": "",
        "bio_material": "",
        "bisulfite_protocol": "",
        "broad_scale_environmental_context": "",
        "broker_name": "",
        "cage_protocol": "",
        "cell_line": "",
        "cell_type": "",
        "center_name": "GEO",
        "checklist": "",
        "chip_ab_provider": "",
        "chip_protocol": "",
        "chip_target": "",
        "collected_by": "",
        "collection_date": "",
        "collection_date_end": "",
        "collection_date_start": "",
        "completeness_score": "",
        "contamination_score": "",
        "control_experiment": "",
        "country": "",
        "cultivar": "",
        "culture_collection": "",
        "datahub": "",
        "depth": "",
        "description": "Illumina HiSeq 2000 sequencing: GSM5320434: TG3_1 Homo sapiens miRNA-Seq",
        "dev_stage": "",
        "disease": "",
        "dnase_protocol": "",
        "ecotype": "",
        "elevation": "",
        "environment_biome": "",
        "environment_feature": "",
        "environment_material": "",
        "environmental_medium": "",
        "environmental_sample": "",
        "experiment_accession": "SRX10918471",
        "experiment_alias": "GSM5320434",
        "experiment_target": "",
        "experiment_title": "Illumina HiSeq 2000 sequencing: GSM5320434: TG3_1 Homo sapiens miRNA-Seq",
        "experimental_factor": "",
        "experimental_protocol": "",
        "extraction_protocol": "",
        "faang_library_selection": "",
        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR145/025/SRR14575325/SRR14575325.fastq.gz",
        "fastq_bytes": "612817621",
        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR145/025/SRR14575325/SRR14575325.fastq.gz",
        "fastq_md5": "4a6120e81b28ef2552dbeb7027f932fb",
        "file_location": "",
        "first_created": "2021-05-20",
        "first_public": "2021-05-20",
        "germline": "",
        "hi_c_protocol": "",
        "host": "",
        "host_body_site": "",
        "host_genotype": "",
        "host_gravidity": "",
        "host_growth_conditions": "",
        "host_phenotype": "",
        "host_scientific_name": "",
        "host_sex": "",
        "host_status": "",
        "host_tax_id": "",
        "identified_by": "",
        "instrument_model": "Illumina HiSeq 2000",
        "instrument_platform": "ILLUMINA",
        "investigation_type": "",
        "isolate": "",
        "isolation_source": "",
        "last_updated": "2021-05-20",
        "lat": "",
        "library_construction_protocol": "Liver tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols",
        "library_gen_protocol": "",
        "library_layout": "SINGLE",
        "library_max_fragment_size": "",
        "library_min_fragment_size": "",
        "library_name": "",
        "library_pcr_isolation_protocol": "",
        "library_prep_date": "",
        "library_prep_date_format": "",
        "library_prep_latitude": "",
        "library_prep_location": "",
        "library_prep_longitude": "",
        "library_selection": "size fractionation",
        "library_source": "TRANSCRIPTOMIC",
        "library_strategy": "miRNA-Seq",
        "local_environmental_context": "",
        "location": "",
        "location_end": "",
        "location_start": "",
        "lon": "",
        "marine_region": "",
        "mating_type": "",
        "ncbi_reporting_standard": "Generic",
        "nominal_length": "",
        "nominal_sdev": "",
        "pcr_isolation_protocol": "",
        "ph": "",
        "project_name": "Identification of 5'isomiR in HCC patients.",
        "protocol_label": "",
        "read_count": "19439295",
        "read_strand": "",
        "restriction_enzyme": "",
        "restriction_enzyme_target_sequence": "",
        "restriction_site": "",
        "rna_integrity_num": "",
        "rna_prep_3_protocol": "",
        "rna_prep_5_protocol": "",
        "rna_purity_230_ratio": "",
        "rna_purity_280_ratio": "",
        "rt_prep_protocol": "",
        "run_accession": "SRR14575325",
        "run_alias": "GSM5320434_r1",
        "run_date": "",
        "salinity": "",
        "sample_accession": "SAMN19241174",
        "sample_alias": "GSM5320434",
        "sample_capture_status": "",
        "sample_collection": "",
        "sample_description": "TG3_1",
        "sample_material": "",
        "sample_prep_interval": "",
        "sample_prep_interval_units": "",
        "sample_storage": "",
        "sample_storage_processing": "",
        "sample_title": "TG3_1",
        "sampling_campaign": "",
        "sampling_platform": "",
        "sampling_site": "",
        "scientific_name": "Homo sapiens",
        "secondary_project": "",
        "secondary_sample_accession": "SRS9008346",
        "secondary_study_accession": "SRP320296",
        "sequencing_date": "",
        "sequencing_date_format": "",
        "sequencing_location": "",
        "sequencing_longitude": "",
        "sequencing_method": "",
        "sequencing_primer_catalog": "",
        "sequencing_primer_lot": "",
        "sequencing_primer_provider": "",
        "serotype": "",
        "serovar": "",
        "sex": "",
        "specimen_voucher": "",
        "sra_aspera": "fasp.sra.ebi.ac.uk:/vol1/srr/SRR145/025/SRR14575325",
        "sra_bytes": "604854335",
        "sra_ftp": "ftp.sra.ebi.ac.uk/vol1/srr/SRR145/025/SRR14575325",
        "sra_galaxy": "ftp.sra.ebi.ac.uk/vol1/srr/SRR145/025/SRR14575325",
        "sra_md5": "137a7ea70991c3b85f4e5e1aa3d3ac91",
        "status": "public",
        "strain": "",
        "study_accession": "PRJNA730731",
        "study_alias": "GSE174608",
        "study_title": "Identification of 5'isomiR in HCC patients.",
        "sub_species": "",
        "sub_strain": "",
        "submission_accession": "SRA1233621",
        "submission_tool": "",
        "submitted_aspera": "",
        "submitted_bytes": "",
        "submitted_format": "",
        "submitted_ftp": "",
        "submitted_galaxy": "",
        "submitted_host_sex": "",
        "submitted_md5": "",
        "submitted_read_type": "",
        "tag": "",
        "target_gene": "",
        "tax_id": "9606",
        "taxonomic_classification": "",
        "taxonomic_identity_marker": "",
        "temperature": "",
        "tissue_lib": "",
        "tissue_type": "",
        "transposase_protocol": "",
        "variety": "",
        "fastq_url": [
            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR145/025/SRR14575325/SRR14575325.fastq.gz"
        ],
        "info": "613 MB files; 19.4 million reads; 972.0 million sequenced bases"
    }
]
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Entering edit mode

hi istvan - i realized my posts' title was pretty misleading about what I actually want so i changed it - sorry your answer makes a ton of sense in that context.

but, what i am looking for is pretty different. I have the part you describe done. i can invite you to the git repo if you want. it works but its v0.1 right now. doesnt yet implement parallelization or error checking for the API calls yet, for instance.

VAL

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Entering edit mode

What i mean is, i have all the intra-Entrez metadata for bioprojects, biosamples, and SRA done. the script would work for any Entrez database with little or no modification though.

What i dont have is the functionality to compare this to what is in the published literature, in particular when that article is not on pubmed commons.

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