Resource identification refers to the unambiguous reporting of research resources such as genes, organisms, tools, and reagents. These resources should be reported within publications with enough information that reviewers and subsequent researchers can identify the exact strain or reagent used. Preferably, authors should provide the full, descriptive name of the resource, its source and a unique identifier. Doing so allows for:
Many reporting standards will include guidance on how to identify such resources. This page provides further information and sources for unambiguous identifiers.
Use RRIDs when available! Research Resource Identifiers (RRIDs) are persistent and unique identifiers for organisms, cell lines, antibodies, and software tools available through The Resource Identification Initiative. They can be found through the portal below.
Alternatively, RRIDs are available for some species.
Again, RRIDs are available for many antibodies and cell lines and should be used when available.
Genes discussed in the literature often have multiple names, symbols, and IDs associated with them. This can cause confusion when reporting on genes or sequences and also when searching for them. Gene nomenclature committees and molecular sequence databases provide standardized names and identifiers as well as known synonyms.
Approved gene symbol: There are species-specific rules about naming genes. Nomenclature committees that assign gene names and symbols exist for a variety of organisms (see below). If you are publishing a report on a gene that does not have an assigned symbol, you can contact these committees to request that they assign one prior to publication. Some journals will require this step.
Accession IDs: Molecular sequence databases assign unique accession numbers to sequences. The International Nucleotide Sequence Database Collaboration (DDBJ/EMBL-EBI/NCBI) assigns accessions in a specific format. In NCBI, for example, you may find a record with an accession like: EF212037.2. While the "EF212037" is the Genbank (direct submission) accession number. The ".2" is the version number and indicates this is the second version of this record. It is, therefore, important to include the dot and version number when reporting accession IDs from these sources.
Reporting variants: HGVS is the standard for reporting human gene variants. Model organism nomenclature committees include species-specific rules for unambiguously naming variants.
The Human Genome Variation Society (HGVS) provides detailed recommendations for the unambiguous naming of sequence variants. HGVS notation includes a reference sequence, type of reference sequence (DNA, RNA, protein...), nucleotide/residue number, and type of variation (substitution, deletion, duplication...). The same variant can be named in various ways depending on the reference sequence selected. For example, allele 17, the "ultra-rapid metabolizer," of the CYP2C19 gene may be named:
You may also see the allele name used, CYP2C19*17, or the rs number from dbSNP, rs12248560.
For more information on how to report research resources unambiguously - particularly when no unique identifier is available, the following articles and sites provide guidance and some examples.