This document describes how you can improve the FAIR-ness of your project report by using\ncompact identifiers. Of course, it can be applied to any other document too, and has been used\nin, for example, journal articles and online documentation already.
\n\nCompact identifiers find a balance between compactness in writing and being a persistent, unique,\nand global identifier. It “is a string constructed by concatenating a namespace prefix, a separating colon,\nand a locally unique identifier (LUI)” (doi:10.1038/sdata.2018.29).\nFor example, for proteins it can represent the PDB structure 2gc4 as\npdb:2gc4. There is a clear similarity with the SciCrunch Research Resource Identifiers\n(RRIDs) as used by several journals, like\neLife\n(doi:10.1007/s12021-015-9284-3).
\n\nWhen the prefixes are defined by community standards, then a compact identifier can be resolved.\nThere currently are multiple providers of prefix files (doi:10.1038/sdata.2018.29),\nincluding Identifiers.org (doi:10.1093/bioinformatics/btaa864)\nand Bioregistry (doi:10.1038/s41597-022-01807-3).\nThe Bioregistry has an overview of more than twenty registries of prefixes and their metadata\n(doi:10.1038/s41597-022-01807-3). The metadata commonly\nincludes information on the URL pattern for each identifier. Often this is more than one pattern, as\nthere may more several databases with information for the same identifier.
\n\nEach of these URLs can be extended with a compact identifier. For example, a taxon record\nfrom the NCBI databases or the PDB entry mentioned earlier:
\n\nUsing persistent identifiers is generally accepted as a good practice that benefits science\nand has been part of the ideas of FAIR data (doi:10.1038/sdata.2016.18)\nand of Open Science. Compact\nidentifiers make it easy to be precise in reports about what things the reports talk about: they\nare relatively short but very precise at the same time. also, that has the benefit that they\nare much easier to reuse than labels of things and concepts that intrinsically have a certain\nlevel of uncertainty; a database entry has commonly a very specific meaning.
\n\nThe use of compact identifiers can be used in two ways. The simplest is to just put the\ncompact identifier as plain text in the document, possibly in parentheses\n(with the compact identifier highlighted here in bold):
\n\nAlternatively, you can add a hyperlink with one of the resolvers, for example, Identifiers.org:
\n\nThe European Registry of Materials proposes to use the compact identifier for their\nERM identifiers (doi:10.1186/s13321-022-00614-7):
\n\nThe compact identifier has also been used as the method to include citation intentions in journal\narticles (doi:10.1186/s13321-020-00448-1,\ncompact identifier here highlighted in bold):
\n\nNote that in this use, the square brackets and bold typeface are used to make them easier to\nbe recognized. Also, note that this document uses this approach to indicate the intention of\nwhy the cited articles are cited.
\n\nThis document described what the compact identifier is, how it helps linking to online\ndatabases, and how they can be used in written reports as plain text, optionally\nhyperlinked with one of the compact identifier resolvers.
\n\n\n
Bandrowski, A., Brush, M., Grethe, J. S., Haendel, M. A., Kennedy, D. N., Hill, S., Hof, P. R., Martone, M. E., Pols, M., Tan, S. S., Washington, N., Zudilova-Seinstra, E., & Vasilevsky, N. (2015). The Resource Identification Initiative: A Cultural Shift in Publishing.
Neuroinformatics,
14(2), 169–182. https://doi.org/10.1007/s12021-015-9284-3
[cito:obtainsBackgroundFrom] CrossRef Scholia\n
Bernal-Llinares, M., Ferrer-Gómez, J., Juty, N., Goble, C., Wimalaratne, S. M., & Hermjakob, H. (2020). Identifiers.org: Compact Identifier services in the cloud.
Bioinformatics,
37(12), 1781–1782. https://doi.org/10.1093/bioinformatics/btaa864
[cito:usesMethodIn] CrossRef Scholia\n
Hoyt, C. T., Balk, M., Callahan, T. J., Domingo-Fernández, D., Haendel, M. A., Hegde, H. B., Himmelstein, D. S., Karis, K., Kunze, J., Lubiana, T., Matentzoglu, N., McMurry, J., Moxon, S., Mungall, C. J., Rutz, A., Unni, D. R., Willighagen, E., Winston, D., & Gyori, B. M. (2022). Unifying the identification of biomedical entities with the Bioregistry.
Scientific Data,
9(1). https://doi.org/10.1038/s41597-022-01807-3
[cito:usesMethodIn] CrossRef Scholia\n
van Rijn, J., Afantitis, A., Culha, M., Dusinska, M., Exner, T. E., Jeliazkova, N., Longhin, E. M., Lynch, I., Melagraki, G., Nymark, P., Papadiamantis, A. G., Winkler, D. A., Yilmaz, H., & Willighagen, E. (2022). European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials.
Journal of Cheminformatics,
14(1). https://doi.org/10.1186/s13321-022-00614-7
[cito:includesQuotationFrom] CrossRef Scholia\n
Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship.
Scientific Data,
3(1). https://doi.org/10.1038/sdata.2016.18
[cito:obtainsBackgroundFrom] CrossRef Scholia\n
Willighagen, E. (2020). Adoption of the Citation Typing Ontology by the Journal of Cheminformatics.
Journal of Cheminformatics,
12(1). https://doi.org/10.1186/s13321-020-00448-1
[cito:includesQuotationFrom] CrossRef Scholia\n
Wimalaratne, S. M., Juty, N., Kunze, J., Janée, G., McMurry, J. A., Beard, N., Jimenez, R., Grethe, J. S., Hermjakob, H., Martone, M. E., & Clark, T. (2018). Uniform resolution of compact identifiers for biomedical data.
Scientific Data,
5(1). https://doi.org/10.1038/sdata.2018.29
[cito:usesMethodIn] [cito:includesQuotationFrom] CrossRef Scholia\n