The example below shows a subset of the record for 3D Metabolites (3dmet) that highlights the publications list. Note that each entry is a dictionary with several parts:

  1. title (required) - the title of the paper
  2. year (highly recommended) - the year of publication of the paper
  3. pubmed, doi, and pmc (one or more required) - identifiers for the paper
"3dmet": {
    "name": "3D Metabolites",
    "publications": [
      {
        "doi": "10.2142/biophysico.15.0_87",
        "pmc": "PMC5992871",
        "pubmed": "29892514",
        "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database",
        "year": 2018
      },
      {
        "doi": "10.1021/ci300309k",
        "pubmed": "23293959",
        "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures",
        "year": 2013
      }
    ]
  },

Similarly, there are URL references that are not publications that are worth curating. These can be stored in the references list. For example, the Registry of Toxic Effects of Chemical Substances (rtecs) entry appears in the Bioregistry because of its usage, but it is hard to find information on the internet about it. Therefore, the references list is perfect for storing references to PDFs and webpages that describe the resource.

"rtecs": {
   "name": "Registry of Toxic Effects of Chemical Substances",
   "publications": [
   {
      "doi": "10.1016/s1074-9098%2899%2900058-1",
      "title": "An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards",
      "year": 1999
   }
   ],
   "references": [
      "https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf",
      "https://www.cdc.gov/niosh/npg/npgdrtec.html"
   ]
}

What else is good to keep track of in the references list:

  1. Bioregistry issue or pull requests about the resource
  2. Links to webpages describing the identifier resource
  3. Links to discussions on Slack or other platforms (keeping in mind links might not last forever)
  4. Any other context that’s useful for a Bioregistry reader

Publications for Databases

A single database can correspond to several Bioregistry prefixes, such as in the case of KEGG, ChEMBL, and even smaller resources like HGNC, which has both a gene vocabulary (hgnc and gene group vocabulary (hgnc.genegroup).

Publications are often made on the database level, so, therefore, if you want to curate a publication for the database, it usually makes sense to duplicate the publication into each prefix.

However, it’s also possible that a long-standing database might have more generic publications describing the whole database, and specific publications describing a certain aspect. If one of the specific publications only corresponds to a single prefix, then use your best judgement to not duplicate it unnecessarily.

Why Should I Curate Publications and References?

  1. They give additional context for Bioregistry readers who want to know more about the paper
  2. They make it easier to attribute usage of identifiers from a given resource to its authors

  3. They enable global landscape analysis of when and where identifier resources are being made. The following image is automatically regenerated with each Bioregistry update:

  4. They support the training of a machine learning for semi-automated curation of additional literature. See this talk from the 2022 Workshop on Prefixes, CURIEs, and IRIs.