The Bioregistry aims to establish a comprehensive resource for the curation of biological identifiers. By efficiently identifying relevant resources, curators help expand the Bioregistry’s utility for the wider scientific community. This guide offers a structured approach for curators to assess and classify new information, ensuring that updates to the Bioregistry are both precise and thorough.

The Bioregistry uses a machine learning model to automatically identify PubMed papers that are potential candidates for curation. Each month, the model produces a ranked list of papers based on their relevance to the Bioregistry. These papers are relevant for expanding the Bioregistry in at least three ways:

  1. As a new prefix for a resource providing primary identifiers,
  2. As a new provider for resolving existing identifiers,
  3. As a new publication related to an existing prefix in the Bioregistry.

This guide provides a working table of relevancy_type tags, which are used to classify the relevance of each paper. Curators can use these tags to categorize papers during the review process. The tags are part of the following TSV file. These updates help retrain the model, improving its accuracy over time.

The ranked list of suggested papers can be found here. When reviewing a paper, curators should update the TSV file with the following information:

  • pmid: The PubMed ID of the paper being reviewed.
  • relevant: 1 for relevant, 0 for not relevant.
  • orcid: The ORCID of the curator reviewing the paper.
  • date_curated: The date the paper was reviewed.
  • relevancy_type: The type of relevance as defined in the table below.
  • pr_added: The pull request number associated with the curation.
  • notes: Any additional notes or comments regarding the paper’s relevance or findings.

Relevancy Type Table

This table of relevancy_type tags is continuously evolving as new papers are evaluated and is subject to change in the future.

Key Definition
new_prefix A resource for new primary identifiers
new_provider A resolver for existing identifiers
new_publication A new publication for an existing prefix
not_identifiers_resource A database, but not for identifier information
no_website Paper suggestive of a new database, but no link to website provided
existing An existing entry in the bioregistry
unclear Not clear how to curate in the bioregistry, follow up discussion required
irrelevant_other Completely unrelated information
not_notable Relevant for training purposes, but not curated in Bioregistry due to poor/unknown quality

Common Mistakes

New curators may encounter some common challenges when reviewing papers and curating data. Below are a few mistakes to be aware of, along with tips on how to avoid them:

1. Confusing Databases with Semantic Spaces

One common mistake is focusing on describing the database rather than the semantic space it organizes. A database provides structured data, such as identifiers, while a semantic space organizes entities and their relationships within a conceptual framework.

When curating a resource, the Bioregistry record should describe the semantic space, that is, the entities and relationships the resource represents rather than the database itself. Explore the resource to identify multiple potential semantic spaces and curate separate prefixes for each entity type if necessary. The goal is to capture how the resource organizes and relates concepts, not just the data it holds.

2. Mislabeling Existing Resources as New

Another common mistake is labeling an existing resource as a new_prefix or new_provider. Before curating a new_prefix or new_provider, first check if the resource is already listed in the Bioregistry. If the resource exists, consider whether the paper might be introducing a new_publication associated with that resource, rather than a completely new entry. This prevents duplicate entries for existing resources.

3. Misunderstanding the Scope of Irrelevant Information

Not every paper mentioning biological resources is relevant to the Bioregistry. Papers that discuss databases not focused on identifier information, for example, should be marked as not_identifiers_resource. Similarly, entirely unrelated papers should be tagged as irrelevant_other. Being clear on the scope of the Bioregistry’s focus can help avoid curating irrelevant materials.

Curation and Data Synchronization

When curators add rows to the curation TSV file, these entries should correspond to specific changes made in the Bioregistry data files. Each pull request should encompass both the updates to the TSV file and the relevant modifications to the data files in the Bioregistry repository.

Step-by-Step Example to Curating a New Prefix

The following step-by-step example is for the resource SCancerRNA based on the publication SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers.

1. Assess the Database for Identifier Creation

Begin by exploring the database to determine if it generates new identifiers for life sciences entities. This is an investigative process, and there isn’t a one-size-fits-all approach; however, most databases typically have a Browse or Search section, which serves as a good starting point. Take your time to navigate various categories to confirm that the resource creates relevant identifiers. Once verified, proceed to fill out the TSV file with the preliminary information you gathered.

pmid relevant orcid date_curated relevancy_type pr_added notes
39341795 1 0009-0009-5240-7463 2024-10-19 new_prefix 1215 identifiers of non-coding RNA biomarkers for cancers

2. Collect Essential Information

Gather easily accessible information for the resource, such as:

  • Name and Email for a point of contact (github and ORCID if possible as well)
  • Example identifier
  • Homepage URL
  • Name of the resource
  • Publication information (such as PubMed ID, DOI, title, year)
  • URI format to resolve identifiers

This data will be necessary for filling out the Bioregistry record.

3. Write a Brief Description

Create a concise description that explains what kind of entities the resource makes identifiers for and its general purpose.

4. Write a Regex Pattern

Examine the format of the identifiers used by the resource and write a regex pattern to validate this format. It’s better to create a pattern that is somewhat flexible to accommodate potential future identifier additions.

5. Update bioregistry.json

"scancerna": {
    "contact": {
      "email": "zty2009@hit.edu.cn",
      "name": "Tianyi Zhao",
      "orcid": "0000-0001-7352-2959"
    },
    "contributor": {
      "email": "m.naguthana@hotmail.com",
      "github": "nagutm",
      "name": "Mufaddal Naguthanawala",
      "orcid": "0009-0009-5240-7463"
    },
    "description": "SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer.",
    "example": "9530",
    "github_request_issue": 1215,
    "homepage": "http://www.scancerrna.com/",
    "name": "SCancerRNA",
    "pattern": "^\\d+$",
    "publications": [
      {
        "doi": "10.1093/gpbjnl/qzae023",
        "pubmed": "39341795",
        "title": "SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers",
        "year": 2024
      }
    ],
    "uri_format": "http://www.scancerrna.com/toDetail?id=$1"
  },

6. Submit a Pull Request

Submit a pull request with the changes you made to both the TSV file and the bioregistry.json file. Make sure the PR includes all necessary updates.

Example Prefix Curation with Multiple Semantic Spaces

In this example, two prefixes have been curated from the Asteraceae Genome Database (AGD), based on the publication Asteraceae Genome Database: A Comprehensive Platform for Asteraceae Genomics.

The dot notation is used to indicate that both asteraceaegd.genome and asteraceaegd.plant are part of the same overarching resource (AGD), but each prefix represents a distinct semantic space:

  • asteraceaegd.genome focuses on the genomic information for Asteraceae species.
  • asteraceaegd.plant focuses on the broader phenotypic and genetic data about Asteraceae plants.

By curating separate prefixes for each semantic space, the Bioregistry ensures clear and precise representation of the different types of data provided by the AGD. This approach allows users to distinguish between the different kinds of identifiers and the types of biological information they refer to within the same database.

"asteraceaegd.genome": {
    "contact": {
      "email": "greatchen@cdutcm.edu.cn",
      "name": "Wei Chen"
    },
    "contributor": {
      "email": "m.naguthana@hotmail.com",
      "github": "nagutm",
      "name": "Mufaddal Naguthanawala",
      "orcid": "0009-0009-5240-7463"
    },
    "description": "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species.",
    "example": "0002",
    "github_request_issue": 1214,
    "homepage": "https://cbcb.cdutcm.edu.cn/AGD/",
    "name": "Asteraceae Genome Database",
    "pattern": "^\\d{4}$",
    "publications": [
      {
        "doi": "10.3389/fpls.2024.1445365",
        "pmc": "PMC11366637",
        "pubmed": "39224843",
        "title": "Asteraceae genome database: a comprehensive platform for Asteraceae genomics",
        "year": 2024
      }
    ],
    "uri_format": "https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id=$1"
  },
"asteraceaegd.plant": {
    "contact": {
      "email": "greatchen@cdutcm.edu.cn",
      "name": "Wei Chen"
    },
    "contributor": {
      "email": "m.naguthana@hotmail.com",
      "github": "nagutm",
      "name": "Mufaddal Naguthanawala",
      "orcid": "0009-0009-5240-7463"
    },
    "description": "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants.",
    "example": "0016",
    "github_request_issue": 1214,
    "homepage": "https://cbcb.cdutcm.edu.cn/AGD/",
    "name": "Asteraceae Genome Database",
    "pattern": "^\\d{4}$",
    "publications": [
      {
        "doi": "10.3389/fpls.2024.1445365",
        "pmc": "PMC11366637",
        "pubmed": "39224843",
        "title": "Asteraceae genome database: a comprehensive platform for Asteraceae genomics",
        "year": 2024
      }
    ],
    "uri_format": "https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id=$1"
  },