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. 2006 Aug 9:7:372.
doi: 10.1186/1471-2105-7-372.

Gene and protein nomenclature in public databases

Katrin Fundel  1 , Ralf Zimmer
Affiliations

Gene and protein nomenclature in public databases

Katrin Fundel et al. BMC Bioinformatics. .

Abstract

Background: Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap.

Results: We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism.

Conclusion: In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity. The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application.

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Figures

Figure 1
Figure 1
Size of gene name dictionaries. Number of objects (left plot) and synonyms (right plot) for gene name dictionaries compiled from different data sources (organism-specific database: Yeast: Saccharomyces Genome Database, Fly: FlyBase, Mouse: Mouse Genome Informatics, Rat: Rat Genome Database, Human: HUGO; 'combined' is the merged dictionary from the organism-specific database, Swiss-Prot and Entrez Gene; 'curated' is additionally expanded and pruned). In the right plot, the three marks for each dictionary correspond to the three definitions of equivalence: exact, mixed, and normalized, respectively, from left to right. For details see section 'Compilation of gene name dictionaries'.
Figure 2
Figure 2
Ambiguity within gene name dictionaries. The ambiguity within gene name dictionaries derived from different data sources and for different organisms varies significantly. Combined dictionaries generally show relatively high ambiguity, curation reduces ambiguity. For notation see Figure 1, for details see section 'Intra-species Ambiguity'.
Figure 3
Figure 3
Overlap between different data sources. The overlap between gene name dictionaries compiled from different data sources varies for different organisms and pairs of databases. Organism-specific databases and Entrez Gene show highest overlap for all organisms. For notation see Figure 1, for details see section 'Overlap between different data sources'.
Figure 4
Figure 4
Ambiguity between gene name dictionaries and general English terms and domain-related terms. Ambiguity between gene name dictionaries and general English terms (left plot) and domain-related non-gene and non-protein terms (right plot). Fly shows highest ambiguity with general English terms. All dictionaries show higher ambiguity for normalized gene names than for exact gene names. For notation see Figure 1, for details see section 'Ambiguity with English lexicon and domain-related terms'.
See this image and copyright information in PMC

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