Ported from https://github.com/egonw/compact-ids-in-reports (originally planned for FAIR CookBook)

Author: egonw

_posts/2026-03-29-using-compact-identifiers-in-project-reports.markdown

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+---
+layout: post
+title:  "Using compact identifiers in project reports"
+date:   2026-03-29
+doi: 10.59350/re9j2-hk972
+tags: identifier semweb cito cito:usesMethodIn,includesQuotationFrom:10.1038/sdata.2018.29
+  cito:obtainsBackgroundFrom:10.1007/s12021-015-9284-3 cito:usesMethodIn:10.1093/bioinformatics/btaa864
+  cito:usesMethodIn:10.1038/s41597-022-01807-3 cito:obtainsBackgroundFrom:10.1038/sdata.2016.18
+  cito:includesQuotationFrom:10.1186/s13321-022-00614-7 cito:includesQuotationFrom:10.1186/s13321-020-00448-1
+grants:
+  - grant:
+    title: "FAIR4ChemNL: Accelerating the adoption of universal data standards in chemistry"
+    acronym: "FAIR4ChemNL"
+    id: doi:10.61686/XVYQV45374
+    funder:
+      name: "Dutch Research Council"
+      ror: 04jsz6e67
+#comments:
+#  host: social.edu.nl
+#  username: egonw
+#  id: ...
+---
+
+This document describes how you can improve the FAIR-ness of your project report by using
+compact identifiers. Of course, it can be applied to any other document too, and has been used
+in, for example, journal articles and online documentation already.
+
+Compact identifiers find a balance between compactness in writing and being a persistent, unique,
+and global identifier. It "is a string constructed by concatenating a namespace prefix, a separating colon,
+and a locally unique identifier (LUI)" (doi:[10.1038/sdata.2018.29](https://doi.org/10.1038/sdata.2018.29)).
+For example, for proteins it can represent the PDB structure [2gc4](https://bioregistry.io/pdb:2gc4) as
+*pdb:2gc4*. There is a clear similarity with the SciCrunch [Research Resource Identifiers](https://rrid.site/)
+(RRIDs) as used by several journals, like
+[eLife](https://elifesciences.org/inside-elife/ff683ecc/rrids-how-did-we-get-here-and-where-are-we-going)
+(doi:[10.1007/s12021-015-9284-3](https://doi.org/10.1007/s12021-015-9284-3)).
+
+When the prefixes are defined by community standards, then a compact identifier can be resolved.
+There currently are multiple providers of prefix files (doi:[10.1038/sdata.2018.29](https://doi.org/10.1038/sdata.2018.29)),
+including Identifiers.org (doi:[10.1093/bioinformatics/btaa864](https://doi.org/10.1093/bioinformatics/btaa864))
+and Bioregistry (doi:[10.1038/s41597-022-01807-3](https://doi.org/10.1038/s41597-022-01807-3)).
+The Bioregistry has an overview of more than twenty registries of prefixes and their metadata
+(doi:[10.1038/s41597-022-01807-3](https://doi.org/10.1038/s41597-022-01807-3)). The metadata commonly
+includes information on the URL pattern for each identifier. Often this is more than one pattern, as
+there may more several databases with information for the same identifier.
+
+It is the URL pattern in the database that allows services to *resolve* the compact identifier
+into a link to a database. The above registries correspond to three existing *resolvers* that will take a compact
+identifier as part of a resolver URL and redirect to the database with the record matching
+that identifier:
+
+* Name-to-Thing (N2T): [https://n2t.net/](https://n2t.net/)
+* Identifiers.org: [https://identifiers.org/](https://identifiers.org/)
+* The Bioregistry: [https://bioregistry.io/](https://bioregistry.io/)
+
+Each of these URLs can be extended with a compact identifier. For example, a taxon record
+from the NCBI databases or the PDB entry mentioned earlier:
+
+* [https://bioregistry.io/pdb:2gc4](https://bioregistry.io/pdb:2gc4)
+* [https://identifiers.org/col:6MB3T](https://identifiers.org/col:6MB3T) (`col` is the prefix for the Catalogue of Life)
+
+## Why use in reports?
+
+Using persistent identifiers is generally accepted as a good practice that benefits science
+and has been part of the ideas of FAIR data (doi:[10.1038/sdata.2016.18](https://doi.org/10.1038/sdata.2016.18))
+and of Open Science. Compact
+identifiers make it easy to be precise in reports about what things the reports talk about: they
+are relatively short but very precise at the same time. also, that has the benefit that they
+are much easier to reuse than labels of things and concepts that intrinsically have a certain
+level of uncertainty; a database entry has commonly a very specific meaning.
+
+## Examples uses
+
+The use of compact identifiers can be used in two ways. The simplest is to just put the
+compact identifier as plain text in the document, possibly in parentheses
+(with the compact identifier highlighted here in bold):
+
+<ul>
+  <i>This report is only about the experimental data of the human (<b>NCBITaxon:9606</b>) cell lines.</i>
+</ul>
+
+Or:
+
+<ul>
+  <i>We found that BRCA1 (<b>ensembl:ENSG00000012048</b>) played an important role.</i>
+</ul>
+
+Alternatively, you can add a hyperlink with one of the resolvers, for example, Identifiers.org:
+
+<ul>
+  <i>We found that BRCA1 (<b><a href="https://identifiers.org/ensembl:ENSG00000012048">ensembl:ENSG00000012048</a></b>) played an important role.</i>
+</ul>
+
+### Compact identifiers for material identifiers
+
+The European Registry of Materials proposes to use the compact identifier for their
+ERM identifiers (doi:[10.1186/s13321-022-00614-7](https://doi.org/10.1186/s13321-022-00614-7)):
+
+<ul>
+  <i>
+    For example, the NanoSolveIT project registered a material with the ERM00000001 identifier.
+    The full Uniform Resource Identifier (URI) for this compound is
+    https://nanocommons.github.io/identifiers/registry#ERM00000001 which is too long to be used
+    in documentation. The corresponding compact identifier <b>erm:ERM00000001</b> is easy to use in written
+    material, analogous to the use of Protein Data Bank (PDB) identifiers for proteins in journals.
+  </i>
+</ul>
+
+### Compact identifiers for citation intent annotations
+
+The compact identifier has also been used as the method to include citation intentions in journal
+articles (doi:[10.1186/s13321-020-00448-1](https://doi.org/10.1186/s13321-020-00448-1),
+compact identifier here highlighted in bold):
+
+<ul>
+  <i>
+    We take advantage here of the ability to add notes to full form [..] references in bibliographies.
+    These are referred to as bibnotes. The content of the note will be strictly formatted: it will use
+    the syntax [<b>cito:usesMethodIn</b>] and formatted in bold. That is, the bibnote starts with the
+    [ character, followed by one of the CiTO types, and ends with the ] character. If you wish to
+    provide more than one annotation, you can repeat this syntax, separated by one or more spaces,
+    for example: [<b>cito:usesMethodIn</b>] [<b>cito:citeAsAuthority</b>].
+  </i>
+</ul>
+
+Note that in this use, the square brackets and bold typeface are used to make them easier to
+be recognized. Also, note that this document uses this approach to indicate the intention of
+why the cited articles are cited.
+
+## Conclusion
+
+This document described what the compact identifier is, how it helps linking to online
+databases, and how they can be used in written reports as plain text, optionally
+hyperlinked with one of the compact identifier resolvers.
+
+### Acknowledgments
+
+I thank [github:tabbassidaloii](https://n2t.net/github:tabbassidaloii),
+[github:cthoyt](https://n2t.net/github:cthoyt), and
+[github:larsgw](https://n2t.net/github:larsgw) for their comment on
+[this GitHub repo](https://github.com/egonw/compact-ids-in-reports).