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Make more publication metadata available via `datasets download virus genome taxon 186538`

Open corneliusroemer opened this issue 3 months ago • 1 comments

Unfortunately some of the valuable metadata contained in genbank files is lost on the way to datasets. In particular crucial author/submitter metadata is lost. Things like: TITLE, JOURNAL, PUBMED and DOI are unfortunately lost entirely.

It would be great if these could be included in the submitter part of the jsonl report.

Compare what's available for the .gb file:

REFERENCE   1  (bases 1 to 2408)
  AUTHORS   Sanchez,A., Trappier,S.G., Mahy,B.W., Peters,C.J. and Nichol,S.T.
  TITLE     The virion glycoproteins of Ebola viruses are encoded in two
            reading frames and are expressed through transcriptional editing
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 93 (8), 3602-3607 (1996)
   PUBMED   [8622982](https://www.ncbi.nlm.nih.gov/pubmed/8622982)
REFERENCE   2  (bases 1 to 2408)
  AUTHORS   Sanchez,A., Trappier,S., Conaty,A.L., Brammer,L., Mahy,B.J.W.,
            Peters,C.J. and Nichol,S.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-1995) Anthony Sanchez, Special Pathogens Branch,
            Division of Viral and Rickettsial Diseases, Centers for Disease
            Control and Prevention, 1600 Clifton Road, Bldg. 15, Room SB611,
            Mail Stop G14, Atlanta, GA 30333, USA

with what's available via datasets download virus genome:

  "submitter": {
    "affiliation": "Anthony Sanchez, Special Pathogens Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Bldg. 15, Room SB611, Mail Stop G14, Atlanta, GA 30333",
    "country": "USA",
    "names": [
      "Sanchez,A.",
      "Trappier,S.G.",
      "Mahy,B.W.",
      "Peters,C.J.",
      "Nichol,S.T.",
      "Trappier,S.",
      "Conaty,A.L.",
      "Brammer,L.",
      "Mahy,B.J.W."
    ]
  }

corneliusroemer avatar Mar 21 '24 19:03 corneliusroemer